ENGINEERED BACTERIA AND METHODS OF PRODUCING TRIACYLGLYCERIDES

SEQUENCE LISTING

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TECHNICAL FIELD

The technology described herein relates to engineered bacteria and methods of producing triacylglycerides.

BACKGROUND

A sustainable future relies, in part, on minimizing the usage of petrochemicals and reducing greenhouse gas (GHG) emissions. One way to accomplish this goal is through increasing the usage of sustainable bioproducts from engineered microorganisms, i.e., microbial bioproduction. Traditional microbial bioproduction utilizes carbohydrate-based feedstocks, but some of the cheapest and most sustainable feedstocks are gases (e.g., CO, CO₂, H₂, CH₄) from various point sources (e.g., steel mills, ethanol production plants, steam reforming plants, biogas). Compared to traditional bioproduction, gas fermentation represents a more cost-effective method that uses land more efficiently and has a smaller carbon footprint.

C. necator H16 (formerly known as Ralstonia eutropha H16) is an attractive species for industrial gas fermentation. It is a facultative chemolithotrophic bacterium that derives its energy from H₂and carbon from CO₂, is genetically tractable, can be cultured with inexpensive minimal media components, is non-pathogenic, has a high-flux carbon storage pathway, and fixes the majority of fed CO₂into biomass. However, many previous C. necator bioproduction methods have relied upon carbohydrate-based feedstocks (see e.g., U.S. Pat. No. 7,622,277; EP Patent 2,935,599; Green et al. Biomacromolecules. 2002 January-February, 3(1):208-13; Brigham et al. Deletion of Glyoxylate Shunt Pathway Genes Results in a 3-Hydroxybutyrate Overproducing Strain of Ralstonia eutropha. 2015 Synthetic Biology: Engineering, Evolution & Design. Poster Abstract 17: p. 32; the content of each of which is incorporated by reference in its entirety). There is a need to expand from this work by engineering C. necator to produce a large diversity of products using gas fermentation in order to promote the sustainable development of industrial bioproduction.

The area of animal-free replacements for lipids remains largely untapped. Milk fats are largely responsible for texture, flavor, energy content, and the solubility of some vitamins in dairy products. The possibility of biomanufacturing such animal-free milk fats to provide an alternative option for milk, butter, cheese, creams, ice cream, and meat represents a critical part of the solution for utilizing synthetic biology to lessen the environmental impacts of addressing humanity's increasing food production demands. Worldwide, cattle farming produces 11% of all greenhouse gas emissions and the dairy industry emits 3% annually. Current dairy alternatives are currently limited by the ability of plant fats to confer the same properties as dairy fats. Milk lipids are in a large part responsible for the taste and texture of dairy products, especially in the case of cheese and butter. Currently, there are no commercially available animal-free replacements for these fats, and plant-based options lack the physical properties for many applications as well as introduce unwanted flavors. There is thus a great need for engineered non-plant organisms that can produce such milk fats, such as triacylglycerides (TAGs), which are the major class of fats in dairy.

SUMMARY

The technology described herein is directed to engineered chemoautotrophic bacteria and methods of using them to produce triacylglycerides (TAGs). Herein, C. necator is shown to bridge the gap between cheap feedstocks and versatile bioproduction. The methods and compositions described herein permit the production of tailored polymers using C. necator, something not achieved by prior applications. The engineered bacteria and methods described herein can reduce greenhouse gas (GHG) emissions, e.g., when industrially scaled.

Accordingly, in one aspect described herein is an engineered Cupriavidus necator bacterium, comprising: (a) at least one exogenous copy of at least one functional acyltransferase gene; and/or (b) at least one exogenous copy of at least one functional phosphatidic acid (PA) phosphatase gene.

In one aspect, described herein is an engineered Cupriavidus necator bacterium, comprising: (a) at least one exogenous copy of at least one functional acyltransferase gene encoding an acyltransferase enzyme that catalyzes transesterification of the sn3 OH group of a diacylglycerol with a fatty acid; and/or (b) at least one exogenous copy of at least one functional phosphatidic acid (PA) phosphatase gene.

In some embodiments of any of the aspects, the acyltransferase gene encodes for an acyltransferase enzyme that catalyzes transesterification of the sn3 OH group, the sn2 OH group, or the sn1 OH group of a triacylglycerol (TAG) precursor with a fatty acid

In some embodiments of any of the aspects, the acyltransferase gene encodes an acyltransferase enzyme that catalyzes transesterification of the sn3 OH group of a diacylglycerol with a fatty acid.

In some embodiments of any of the aspects, the acyltransferase gene is a functional diglyceride acyltransferase (DGAT) gene, a functional wax synthase (WS) gene, or a hybrid thereof.

In some embodiments of any of the aspects, the functional DGAT gene is heterologous.

In some embodiments of any of the aspects, the acyltransferase gene encodes an acyltransferase enzyme that catalyzes transesterification of the sn2 OH group of a lysophosphatidic acid with a fatty acid.

In some embodiments of any of the aspects, the acyltransferase gene is a functional lysophosphatidic acid acyltransferase (LPAT) gene.

In some embodiments of any of the aspects, the functional LPAT gene is heterologous.

In some embodiments of any of the aspects, the functional heterologous LPAT gene comprises a Theobroma cacao LPAT gene.

In some embodiments of any of the aspects, the acyltransferase gene encodes an acyltransferase enzyme that catalyzes transesterification of the sn1 OH group of a glyceraldehyde-3-phosphate with a fatty acid.

In some embodiments of any of the aspects, the acyltransferase gene is a functional glycerol-3-phosphate acyltransferase (GPAT) gene.

In some embodiments of any of the aspects, the functional GPAT gene is heterologous.

In some embodiments of any of the aspects, the fatty acid is esterified with acyl carrier protein (ACP) or with acetyl-CoA.

In some embodiments of any of the aspects, the functional phosphatidic acid (PA) phosphatase gene encodes a phosphatidic acid (PA) phosphatase enzyme that catalyzes dephosphorylation at the sn3 position of phosphatidic acid (PA).

In some embodiments of any of the aspects, the phosphatidic acid (PA) phosphatase gene is a functional phosphatidate phosphatase (PAP) gene.

In some embodiments of any of the aspects, the functional PAP gene is heterologous.

In some embodiments of any of the aspects, the functional heterologous PAP gene comprises a Rhodococcus opacus PAP gene, or a Rhodococcus jostii PAP gene.

In some embodiments of any of the aspects, the engineered bacteria further comprises: at least one exogenous copy of at least one functional thioesterase (TE) gene.

In some embodiments of any of the aspects, the functional thioesterase gene is heterologous.

In some embodiments of any of the aspects, the functional heterologous thioesterase gene is selected from the group consisting of: a Marvinbryantia formatexigens TE gene, a Cuphea palustris FatB1 gene, a Cuphea palustris FatB2 gene, a Cuphea palustris FatB2-FatB1 hybrid gene, a Arachis hypogaea FatB2-1 gene, a Mangifera indica FatA gene, a Morella rubra FatA gene, a Pistacia vera FatA gene, a Theobroma cacao FatA gene, a Theobroma cacao FatB gene (e.g., FatB1, FatB2, FatB3, BatB4, FatB5, or FatB6), or a Limosilactobacillus reuteri TE gene.

In some embodiments of any of the aspects, the engineered bacteria further comprises: (i) at least one endogenous polyhydroxyalkanoate (PHA) synthase gene comprising at least one engineered inactivating modification; or (ii) at least one exogenous inhibitor of an endogenous polyhydroxyalkanoate (PHA) synthase gene or gene product.

In some embodiments of any of the aspects, the engineered inactivating modification of the endogenous PHA synthase comprises one or more of i) deletion of the entire coding sequence, ii) deletion of the promoter of the gene, iii) a frameshift mutation, iv) a nonsense mutation (i.e., a premature termination codon), v) a point mutation, vi) a deletion, vii) or an insertion.

In some embodiments of any of the aspects, the endogenous PHA synthase comprises phaC.

In some embodiments of any of the aspects, the engineered bacteria further comprises: (i) at least one endogenous diacylglycerol kinase gene comprising at least one engineered inactivating modification; or (ii) at least one exogenous inhibitor of an endogenous diacylglycerol kinase gene or gene product.

In some embodiments of any of the aspects, the engineered inactivating modification of the endogenous diacylglycerol kinase comprises one or more of i) deletion of the entire coding sequence, ii) deletion of the promoter of the gene, iii) a frameshift mutation, iv) a nonsense mutation (i.e., a premature termination codon), v) a point mutation, vi) a deletion, vii) or an insertion.

In some embodiments of any of the aspects, the endogenous diacylglycerol kinase comprises dgkA.

In some embodiments of any of the aspects, the engineered bacteria further comprises: (i) at least one endogenous beta-oxidation gene comprising at least one engineered inactivating modification; or (ii) at least one exogenous inhibitor of an endogenous beta-oxidation gene or gene product.

In some embodiments of any of the aspects, the engineered inactivating modification of the endogenous beta-oxidation gene comprises one or more of i) deletion of the entire coding sequence, ii) deletion of the promoter of the gene, iii) a frameshift mutation, iv) a nonsense mutation (i.e., a premature termination codon), v) a point mutation, vi) a deletion, vii) or an insertion.

In some embodiments of any of the aspects, the endogenous beta-oxidation gene comprises FadE or FadB.

In some embodiments of any of the aspects, said engineered bacteria is a chemoautotroph.

In some embodiments of any of the aspects, said engineered bacteria uses CO₂as its sole carbon source, and/or said engineered bacteria uses H₂as its sole energy source.

In some embodiments of any of the aspects, said engineered bacteria uses fructose as its sole carbon source.

In some embodiments of any of the aspects, said engineered bacteria uses glycerol as its sole carbon source.

In some embodiments of any of the aspects, said engineered bacteria produces triacylglycerides.

In some embodiments of any of the aspects, said engineered bacteria produces animal triacylglycerides.

In some embodiments of any of the aspects, said engineered bacteria produces milk fats.

In one aspect, described herein is a method of producing triacylglycerides (TAGs), comprising: (a) culturing an engineered bacterium as described herein in a culture medium comprising CO₂and/or H₂; and (b) isolating, collecting, or concentrating TAGs from said engineered bacterium or from the culture medium of said engineered bacterium.

In some embodiments of any of the aspects, the culture medium comprises CO₂as the sole carbon source, and/or the culture medium comprises H₂as the sole energy source.

In some embodiments of any of the aspects, the total TAG isolated comprises at least 50% TAGs comprising C4-C18 R-group fatty acids.

In some embodiments of any of the aspects, the total TAG isolated comprises at least 50% TAGs comprising C4-C8 R-group fatty acids.

In some embodiments of any of the aspects, the total TAG isolated comprises at least 50% TAGs comprising C16 R-group fatty acids.

In one aspect, described herein is a method of producing triacylglycerides (TAGs), comprising: (a) culturing an engineered bacterium as described herein in a culture medium comprising fructose and/or H₂; and (b) isolating, collecting, or concentrating TAGs from said engineered bacterium or from the culture medium of said engineered bacterium.

In some embodiments of any of the aspects, the culture medium comprises fructose as the sole carbon source, and/or the culture medium comprises H₂as the sole energy source.

In some embodiments of any of the aspects, the total TAG isolated comprises at least 50% TAGs comprising C4-C18 R-group fatty acids.

In some embodiments of any of the aspects, the total TAG isolated comprises at least 50% TAGs comprising C4-C8 R-group fatty acids.

In some embodiments of any of the aspects, the total TAG isolated comprises at least 50% TAGs comprising C16 R-group fatty acids.

In one aspect, described herein is a method of producing triacylglycerides (TAGs), comprising: (a) culturing an engineered bacterium as described herein in a culture medium comprising glycerol and/or H₂; and (b) isolating, collecting, or concentrating TAGs from said engineered bacterium or from the culture medium of said engineered bacterium.

In some embodiments of any of the aspects, the culture medium comprises glycerol as the sole carbon source, and/or the culture medium comprises H₂as the sole energy source.

In some embodiments of any of the aspects, the total TAG isolated comprises at least 50% TAGs comprising C4-C18 R-group fatty acids.

In some embodiments of any of the aspects, the total TAG isolated comprises at least 50% TAGs comprising C4-C8 R-group fatty acids.

In some embodiments of any of the aspects, the total TAG isolated comprises at least 50% TAGs comprising C16 R-group fatty acids.

In some embodiments of any of the aspects, the system further comprises a pair of electrodes in contact with the solution that split water to form the hydrogen.

In some embodiments of any of the aspects, the carbon source is carbon dioxide (CO₂), fructose, and/or glycerol.

In some embodiments of any of the aspects, the system further comprises an isolated gas volume above a surface of the solution within a head space of a reactor chamber.

In some embodiments of any of the aspects, the isolated gas volume comprises primarily carbon dioxide.

In some embodiments of any of the aspects, the system further comprises a power source comprising a renewable source of energy.

In some embodiments of any of the aspects, the renewable source of energy comprises a solar cell, wind turbine, generator, battery, or grid power.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A-1B is a series of schematics showing the composition of milk and biosynthesis of triacylglycerides. FIG. 1A is a schematic showing an exemplary composition of milk. TAGs form the majority (e.g., ˜98%) of total fats. The insert shows a general reaction formula for the production of TAGs from glycerol and fatty acids. FIG. 1B is a schematic showing biosynthesis of TAGs. The metabolic pathways were tuned by engineering key biosynthesis enzymes: e.g., thioesterases (TE), diglyceride acyltransferases (DGAT), and phosphatidate phosphatase (PAP).

FIG. 2A-2B is a series of schematics showing C. necator strains expressing engineered TAG biosynthesis pathways. FIG. 2A is a bar graph showing a normalized Nile Red fluorescence assay. FIG. 2B is a bar graph showing raw fluorescence and optical density from the Nile Red assay in FIG. 2A. Abbreviations: R. opacus PAP and A. baylyi DGAT (RoAb; “Strain 1”); R. jostii PAP and A. baylyi DGAT (RjAb; “Strain 2”); R. opacus PAP and T. curvata DGAT (RoTc; “Strain 3”); R. jostii PAP and T. curvata DGAT (RjTc; “Strain 4”); R. opacus PAP, T. curvata DGAT and Chimera 4 TE (Ch4RoTc; “Strain 5”); and R. opacus PAP, T. curvata (DGAT), and M. formatexigens (TE) (MfRoTc; “Strain 6”); all strains are on the ΔphaC C. necator background.

FIG. 3 is a bar graph showing the fatty acid profile in lipids of ΔphaC C. necator or strain 1 (R. opacus PAP and A. baylyi DGAT (RoAb) in ΔphaC C. necator) in 4 L or 10 L conditions. “C14” indicates acids that are 14 carbons long (e.g., myristic acid). “C16” indicates fatty acids that are 16 carbons long (e.g., palmitic acid). “C16:1” indicates fatty acids that are 16 carbons long with 1 unsaturated double bond (e.g., palmitoleic acid). RoAb has a higher fatty acid content and an altered distribution compared to ΔphaC. An overall increase in fatty acids and a change in fatty acid composition indicates TAG production.

FIG. 4A is a schematic representation of a reactor. FIG. 4B is a schematic representation of the production of one or more products within the reactor of FIG. 4A (indicated by dashed circle in FIG. 4A). Adapted from US 2018/0265898 A1.

FIG. 5 is a schematic of a triglyceride molecule showing the Sn positions and the numerical and alphabetical nomenclatures of fatty acids.

FIG. 6 is a schematic showing an exemplary TAG engineering strategy.

FIG. 7A-7B is a series of images showing PCR verification of engineered bacteria. “phaC” denotes Cupriavidus necator H16 ΔphaC1. “H16” denotes wild-type Cupriavidus necator H16. The strain designations for 873, 875, 878, 881, 884, and 887 are shown in Table 6. All PCRs were done using cells. FIG. 7A used a primer set that amplifies constructs on the plasmid (e.g., pBadT), showing inclusion of the plasmid (and associated added enzymes) in the engineered strains. FIG. 7B used a primer set that amplifies the genomic phaC1 region, showing phaC1 knockout in the engineered strains (lower bands).

FIG. 8 is an image showing thin layer chromatography (TLC) for TAG visualization. Note that the engineered 873 strain with induction (e.g., arabinose) shows produced of TAG tri-14, while no detectable TAGs were produced in the engineered 873 strain without induction.

FIG. 9 is an image showing high performance liquid chromatography data (HPLC). See e.g., Table 6 for strain designations of 873 and 881.

FIG. 10 is an image showing high performance gas chromatography-mass spectroscopy data (GC-MS) from strain 873.

DETAILED DESCRIPTION

Embodiments of the technology described herein are directed to engineered bacteria and methods of producing triacylglycerides (TAG). The methods and compositions described herein permit the production of triacylglycerides using C. necator. In one aspect, described herein are engineered bacteria and corresponding methods, compositions, and systems for the production of tailored animal triacylglycerides. Formula I below shows the general formula for a triacylglyceride (see e.g., FIG. 1A). TAGs can also be referred to interchangeably as triglyceride (TG) or triacylglycerol (TAG).

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As shown herein, coupling recent advancements in genetic engineering of microbes and gas-driven fermentation provides a path towards sustainable commodity chemical production. C. necator H16 is a suitable species primarily because it effectively utilizes H₂and CO₂and is genetically tractable. Demonstrated herein is the versatility of this organism in lithotrophic (e.g., using C02 as a carbon source) or heterotrophic conditions (e.g., using glycerol as a carbon source), for example the production of triacylglycerides.

Described herein are engineered bacteria that can be used to sustainably produce triacylglycerides. In some embodiments of any of the aspects, the engineered bacterium is a chemoautotroph. In some embodiments of any of the aspects, the engineered bacterium can grow under chemoautotrophic (i.e., lithotrophic) conditions. As used herein, the term “chemoautotroph” refers to an organism that uses inorganic energy sources to synthesize organic compounds from carbon dioxide. The term “chemolithotroph” can be used interchangeably with chemoautotroph. Chemoautotrophs stand in contrast to heterotrophs. As used herein, the term “heterotroph” refers to an organism that derives its nutritional requirements from complex organic substances (e.g., sugars).

In some embodiments of any of the aspects, the engineered bacterium is a chemolithotroph. As used herein, the term “chemolithotroph” refers to an organism that is able to use inorganic reduced compounds (e.g., hydrogen, nitrite, iron, sulfur) as a source of energy (e.g., as electron donors). The chemolithotrophy process is accomplished through oxidation of inorganic compounds and ATP synthesis. The majority of chemolithotrophs are able to fix carbon dioxide (CO₂) through the Calvin cycle, a metabolic pathway in which carbon enters as CO₂and leaves as glucose (see e.g., Kuenen, G. (2009). “Oxidation of Inorganic Compounds by Chemolithotrophs”. In Lengeler, J.; Drews, G.; Schlegel, H. (eds.). Biology of the Prokaryotes. John Wiley & Sons. p. 242. ISBN 9781444313307). The chemolithotroph group of organisms includes sulfur oxidizers, nitrifying bacteria, iron oxidizers, and hydrogen oxidizers. The term “chemolithotrophy” refers to a cell's acquisition of energy from the oxidation of inorganic compounds, also known as electron donors. This form of metabolism is known to occur only in prokaryotes. See e.g., Table 1 for non-limiting examples of chemolithotrophic bacteria and archaea.

TABLE 1

Chemolithotrophic bacteria and archaea

Non-Limiting
Source of
Respiration

Examples of
energy and
electron

Bacteria
Chemolithotrophs
electrons
acceptor

Iron

Acidithiobacillus

Fe²⁺ (ferrous iron) →
O₂(oxygen) →

bacteria

ferrooxidans

Fe³⁺ (ferric iron) +
H₂O (water)

e⁻

Nitrosifying

Nitrosomonas

NH₃(ammonia) →
O₂(oxygen) →

bacteria

NO₂⁻ (nitrite) +
H₂O (water)

e⁻

Nitrifying

Nitrobacter

NO₂⁻ (nitrite) →
O₂(oxygen) →

bacteria

NO₃⁻ (nitrate) +
H₂O (water)

e⁻

Chemotrophic
Halothiobacillaceae
S²⁻ (sulfide) →
O₂(oxygen) →

purple sulfur

S⁰(sulfur) + e⁻
H₂O (water)

bacteria

Sulfur-oxidizing
Chemotrophic Rhodobacteraceae
S⁰(sulfur) →
O₂(oxygen) →

bacteria
and Thiotrichaceae
SO₄²⁻ (sulfate) +
H₂O (water)

e⁻

Aerobic hydrogen

Cupriavidus necator;
H₂(hydrogen) → H₂O
O₂(oxygen) →

bacteria

Cupriavidus metallidurans

(water) + e⁻
H₂O (water

Anammox
Planctomycetes
NH₄⁺ (ammonium) →
N₂(nitrogen) +

bacteria

NO₂⁻ (nitrite)
H₂O (water)

Thiobacillus

Thiobacillus

S⁰(sulfur) →
NO₃⁻ (nitrate)

denitrificans

denitrificans

SO₄²⁻ (sulfate) +

e⁻

Sulfate-reducing

Desulfovibrio

H₂(hydrogen) → H₂O
Sulfate

bacteria: Hydrogen

paquesii

(water) + e⁻
(SO₄²⁻)

bacteria

Sulfate-reducing

Desulfotignum

PO₃³⁻ (phosphite) →
Sulfate

bacteria: Phosphite

phosphitoxidans

PO₄³⁻ (phosphate) +
(SO₄²⁻)

bacteria

e⁻

Methanogens
Archaea
H₂(hydrogen) → H₂O
CO₂(carbon

(water) + e⁻
dioxide)

Carboxydotrophic

Carboxydothermus

carbon monoxide
H₂O (water) →

bacteria

hydrogenoformans

(CO) → carbon dioxide
H₂(hydrogen)

(CO₂) + e⁻

In some embodiments of any of the aspects, the engineered bacteria is a chemolithotroph belonging to a classification selected from the group consisting of Acidithiobacillus, Alcaligenes, Carboxydothermus, Cupriavidus, Desulfotignum, Desulfovibrio, Halothiobacillaceae, Hydrogenomonas, Nitrobacter, Nitrosomonas, Planctomycetes, Ralstonia, Rhodobacteraceae, Thiobacillus, Thiotrichaceae, and Wautersia. In some embodiments of any of the aspects, the engineered organism is a methanogenic archaea (e.g., belonging to the genera Methanosarcina or Methanothrix). In some embodiments of any of the aspects, the engineered bacteria is selected from the group consisting of Acidithiobacillus ferrooxidans, Carboxydothermus hydrogenoformans, Cupriavidus metallidurans, Cupriavidus necator, Desulfotignum phosphitoxidans, Desulfovibrio paquesii, and Thiobacillus denitrificans. In some embodiments of any of the aspects, the engineered bacteria is further engineered to be chemolithotrophic. In some embodiments of any of the aspects, the engineered bacterium is aerobic and uses O₂as its respiration electron acceptor. In some embodiments of any of the aspects, the engineered bacteria can be a heterotroph or a chemolithotroph, e.g., depending on environmental conditions.

In some embodiments of any of the aspects, the engineered bacteria uses CO₂as its sole carbon source or H₂as its sole energy source. In some embodiments of any of the aspects, the engineered bacteria uses CO₂as its sole carbon source and H₂as its sole energy source. In some embodiments of any of the aspects, the engineered bacteria uses H₂as its sole energy source. In some embodiments of any of the aspects, the engineered bacteria uses CO₂as its sole carbon source.

In some embodiments of any of the aspects, the engineered bacteria is engineered from a bacteria that uses CO₂as its sole carbon source or H₂as its sole energy source. In some embodiments of any of the aspects, the engineered bacteria is engineered from a bacteria that uses CO₂as its sole carbon source and H₂as its sole energy source. In some embodiments of any of the aspects, the engineered bacteria is engineered from a bacteria that uses H₂as its sole energy source. In some embodiments of any of the aspects, the engineered bacteria is engineered from a bacteria that uses CO₂as its sole carbon source.

In some embodiments of any of the aspects, the engineered bacteria obtains at least 90%, at least 95%, at least 98%, at least 99% or more of its carbon from CO₂. In some embodiments of any of the aspects, the engineered bacteria obtains at least 90%, at least 95%, at least 98%, at least 99% or more of its energy from H₂. In some embodiments of any of the aspects, the engineered bacteria obtains at least 90%, at least 95%, at least 98%, at least 99% or more of its carbon from CO₂and at least 90%, at least 95%, at least 98%, at least 99% or more of its energy from H₂.

As used herein, the term “carbon source” refers to the molecules used by an organism as the source of carbon for building its biomass; a carbon source can be an organic compound or an inorganic compound. “Source” denotes an environmental source. In some embodiments of any of the aspects, the engineered bacteria fixes carbon dioxide (CO₂) through the Calvin cycle, a metabolic pathway in which carbon enters as CO₂and leaves as glucose. As used herein, the term “sole carbon source” denotes that the engineered bacteria uses only the indicated carbon source (e.g., CO₂) and no other carbon sources. For example, “sole carbon source” is intended to mean where the suitable conditions comprise a culture media containing a carbon source such that, as a fraction of the total carbon atoms in the media, the specific carbon source (e.g., CO₂), respectively, represent about 100% of the total carbon atoms in the media. In some embodiments, the sole carbon source of the engineered bacteria is inorganic carbon, including but not limited to carbon dioxide (CO₂) and bicarbonate (HCO₃⁻). In some embodiments of any of the aspects, the sole carbon source is atmospheric CO₂.

In some embodiments of any of the aspects, the engineered bacteria uses CO₂as its major carbon source, meaning at least 50% of its carbon atoms are obtained from CO₂. As a non-limiting example, the engineered bacteria obtains at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 99% of its carbon atoms from CO₂.

In some embodiments of any of the aspects, the engineered bacteria does not use organic carbon as a carbon source. Non-limiting example of organic carbon sources include fatty acids, gluconate, acetate, fructose, decanoate; see e.g., Jiang et al. Int J Mol Sci. 2016 July; 17(7): 1157).

In some embodiments of any of the aspects, the engineered bacteria uses a simple organic carbon source as its sole carbon source. Non-limiting examples of simple organic carbon sources include: glucose, glycerol, gluconate, acetate, fructose, or decanoate. In some embodiments of any of the aspects, the engineered bacteria uses fructose as its sole carbon source. In some embodiments of any of the aspects, the engineered bacteria uses fructose and CO₂as its carbon sources. In some embodiments of any of the aspects, the engineered bacteria is engineered from a bacteria that uses fructose as its sole carbon source. In some embodiments of any of the aspects, the engineered bacteria obtains at least 90%, at least 95%, at least 98%, at least 99% or more of its carbon from fructose. In some embodiments of any of the aspects, the engineered bacteria uses fructose as its major carbon source, meaning at least 50% of its carbon atoms are obtained from fructose. As a non-limiting example, the engineered bacteria obtains at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 99% of its carbon atoms from fructose.

In some embodiments of any of the aspects, the engineered bacteria uses glycerol as its sole carbon source. In some embodiments of any of the aspects, the engineered bacteria uses glycerol and CO₂as its carbon sources. In some embodiments of any of the aspects, the engineered bacteria is engineered from a bacteria that uses glycerol as its sole carbon source. In some embodiments of any of the aspects, the engineered bacteria obtains at least 90%, at least 95%, at least 98%, at least 99% or more of its carbon from glycerol. In some embodiments of any of the aspects, the engineered bacteria uses glycerol as its major carbon source, meaning at least 50% of its carbon atoms are obtained from glycerol. As a non-limiting example, the engineered bacteria obtains at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 99% of its carbon atoms from glycerol.

In some embodiments of any of the aspects, the engineered bacteria uses H₂as its sole energy source. As used herein, the term “energy source” refers to molecules that contribute electrons and contribute to the process of ATP synthesis. As described here, the engineered bacterium can be a chemolithotroph, i.e., an organism that is able to use inorganic reduced compounds (e.g., hydrogen, nitrite, iron, sulfur) as a source of energy (e.g., as electron donors). As used herein, the term “sole energy source” denotes that the engineered bacteria uses only the indicated energy source (e.g., H₂) and no other energy sources. In some embodiments of any of the aspects, the sole energy source is atmospheric H₂.

In some embodiments of any of the aspects, the engineered bacteria uses H₂as its major energy source, meaning at least 50% of its donated electrons (e.g., used for ATP synthesis) are obtained from H₂. As a non-limiting example, the engineered bacteria obtains at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 99% of its donated electrons from H₂.

Bacteria used in the systems and methods disclosed herein may be selected so that the bacteria both oxidize hydrogen as well as consume carbon dioxide. Accordingly, in some embodiments, the bacteria may include an enzyme capable of metabolizing hydrogen as an energy source such as with hydrogenase enzymes. Additionally, the bacteria may include one or more enzymes capable of performing carbon fixation such as Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). One possible class of bacteria that may be used in the systems and methods described herein to produce a product include, but are not limited to, chemolithoautotrophs. Additionally, appropriate chemolithoautotrophs may include any one or more of Ralstonia eutropha (R. eutropha) as well as Alcaligenes paradoxs I 360 bacteria, Alcaligenes paradoxs 12/X bacteria, Nocardia opaca bacteria, Nocardia autotrophica bacteria, Paracoccus denitrificans bacteria, Pseudomonas facilis bacteria, Arthrobacter species 1IX bacteria, Xanthobacter autotrophicus bacteria, Azospirillum lipferum bacteria, Derxia gummosa bacteria, Rhizobium japonicum bacteria, Microcyclus aquaticus bacteria, Microcyclus ebruneus bacteria, Renobacter vacuolatum bacteria, and any other appropriate bacteria.

In some embodiments of any of the aspects, the engineered bacteria belongs to the Cupriavidus genus. The Cupriavidus genus of bacteria includes the former genus Wautersia. Cupriavidus bacteria are characterized as Gram-negative, motile, rod-shaped organisms with oxidative metabolism. Cupriavidus bacteria possess peritrichous flagella, are obligate aerobic organisms, and are chemoorganotrophic or chemolithotrophic. In some embodiments of any of the aspects, the engineered bacteria is selected from the group consisting of Cupriavidus alkaliphilus, Cupriavidus basilensis, Cupriavidus campinensis, Cupriavidus gilardii, Cupriavidus laharis, Cupriavidus metallidurans, Cupriavidus necator, Cupriavidus nantongensis, Cupriavidus numazuensis, Cupriavidus oxalaticus, Cupriavidus pampae, Cupriavidus pauculus, Cupriavidus pinatubonensis, Cupriavidus plantarum, Cupriavidus respiraculi, Cupriavidus taiwanensis, and Cupriavidus yeoncheonensis.

In some embodiments of any of the aspects, the engineered bacterium is Cupriavidus necator. Cupriavidus necator can also be referred to as Ralstonia eutropha, Hydrogenomonas eutrophus, Alcaligenes eutropha, or Wautersia eutropha. In some embodiments of any of the aspects, the engineered bacterium is Cupriavidus necator strain H16. In some embodiments of any of the aspects, the engineered bacterium is Cupriavidus necator strain N-1.

Members of the species and genera described herein can be identified genetically and/or phenotypically. By way of non-limiting example, the engineered bacterium as described herein comprises a 16S rDNA sequence at least 97% identical to a 16S rDNA sequence present in a reference strain operational taxonomic unit for Cupriavidus necator. In some embodiments of any of the aspects, the engineered bacterium as described herein comprises a 16S rDNA that comprises SEQ ID NO: 1 or SEQ ID NO: 2 or a sequences that is at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the sequence of SEQ ID NO: 1 or SEQ ID NO: 2. In some embodiments of any of the aspects, the bacterium as described herein is engineered from Cupriavidus necator (e.g., strain H16 or strain N-1).

Cupriavidus necator strain N-1 16S ribosomal RNA,

partial sequence, NCBI Reference Sequence:

NR_028766.1 1356 nucleotides (nt)

SEQ ID NO: 1

TTAGATTGAACGCTGGCGGCATGCCTTACACATGCAAGTCGAACGGCAGC

ACGGGCTTCGGCCTGGTGGCGAGTGGCGAACGGGTGAGTAATACATCGGA

ACGTGCCCTGTAGTGGGGGATAACTAGTCGAAAGATTAGCTAATACCGCA

TACGACCTGAGGGTGAAAGCGGGGGACCGCAAGGCCTCGCGCTACAGGAG

CGGCCGATGTCTGATTAGCTAGTTGGTGGGGTAAAAGCCTACCAAGGCGA

CGATCAGTAGCTGGTCTGAGAGGACGATCAGCCACACTGGGACTGAGACA

CGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGG

GCAACCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGT

AAAGCACTTTTGTCCGGAAAGAAATGGCTCTGGTTAATACCCGGGGTCGA

TGACGGTACCGGAAGAATAAGCACCGGCTAACTACGTGCCAGCAGCCGCG

GTAATACGTAGGGTGCGAGCGTTAATCGGAATTACTGGGCGTAAAGCGTG

CGCAGGCGGTTTTGTAAGACAGGCGTGAAATCCCCGAGCTCAACTTGGGA

ATGGCGCTTGTGACTGCAAGGCTAGAGTATGTCAGAGGGGGGTAGAATTC

CACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAA

GGCAGCCCCCTGGGACGTCACTGACGCTCATGCACGAAAGCGTGGGGAGC

AAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCAACTAG

TTGTTGGGGATTCATTTCTTCAGTAACGTAGCTAACGCGTGAAGTTGACC

GCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGAC

CCGCACAAGCGGTGGATGATGTGGATTAATTCGATGCAACGCGAAAAACC

TTACCTACCCTTGACATGCCACTAACGAAGCAGAGATGCATTAGGTGCCC

GAAAGGGAAAGTGGACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCG

TGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTCTAGTTG

CTACGAAAGGGCACTCTAGAGAGACTGCCGGTGACAAACCGGAGGAAGGT

GGGGATGACGTCAAGTCCTCATGGCCCTTATGGGTAGGGCTTCACACGTC

ATACAATGGTGCGTACAGAGGGTTGCCAACCCGCGAGGGGGAGCTAATCC

CAGAAAACGCATCGTAGTCCGGATCGTAGTCTGCAACTCGACTACGTGAA

GCTGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATACGTTCC

CGGTCT,

Cupriavidus necator strain H16 16S ribosomal RNA,

1537 nt

SEQ ID NO: 2

AGATTGAACTGAAGAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCAT

GCCTTACACATGCAAGTCGAACGGCAGCACGGGCTTCGGCCTGGTGGCGA

GTGGCGAACGGGTGAGTAATACATCGGAACGTGCCCTGTAGTGGGGGATA

ACTAGTCGAAAGATTAGCTAATACCGCATACGACCTGAGGGTGAAAGCGG

GGGACCGCAAGGCCTCGCGCTACAGGAGCGGCCGATGTCTGATTAGCTAG

TTGGTGGGGTAAAAGCCTACCAAGGCGACGATCAGTAGCTGGTCTGAGAG

GACGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGG

CAGCAGTGGGGAATTTTGGACAATGGGGGCAACCCTGATCCAGCAATGCC

GCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTTGTCCGGAAAGA

AATGGCTCTGGTTAATACCCGGGGTCGATGACGGTACCGGAAGAATAAGC

ACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGT

TAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTTTGTAAGACAG

GCGTGAAATCCCCGAGCTCAACTTGGGAATGGCGCTTGTGACTGCAAGGC

TAGAGTATGTCAGAGGGGGAAGAATTCCACGTGTAGCAGTGAAATGCGTA

GAGATGTGGAGGAATACCGATGGCGAAGGCAGCCCCCTGGGACGTCACTG

ACGCTCATGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTA

GTCCACGCCCTAAACGATGTCAACTAGTTGTTGGGGATTCATTTCTTCAG

TAACGTAGCTAACGCGTGAAGTTGACCGCCTGGGGAGTACGGTCGCAAGA

TTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGATGATGTG

GATTAATTCGATGCAACGCGAAAAACCTTACCTACCCTTGACATGCCACT

AACGAAGCAGAGATGCATTAGGTGCCCGAAAGGGAAAGTGGACACAGGTG

CTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGC

AACGAGCGCAACCCTTGTCTCTAGTTGCTACGAAAGGGCACTCTAGAGAG

ACTGCCGGTGACAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATG

GCCCTTATGGGTAGGGCTTCACACGTCATACAATGGTGCGTACAGAGGGT

TGCCAACCCGCGAGGGGGAGCTAATCCCAGAAAACGCATCGTAGTCCGGA

TCGTAGTCTGCAACTCGACTACGTGAAGCTGGAATCGCTAGTAATCGCGG

ATCAGCATGCCGCGGTGAATACGTTCCCGGGTCTTGTACACACCGCCCGT

CACACCATGGGAGTGGGTTTTGCCAGAAGTAGTTAGCCTAACCGCAAGGA

GGGCGATTACCACGGCAGGGTTCATGACTGGGGTGAAGTCGTAACAAGGT

AGCCGTATCGGAAGGTGCGGCTGGATCACCTCCTTTC.

In some embodiments of any of the aspects, the engineered bacterium comprises at least one engineered inactivating modification of at least one endogenous gene. In some embodiments of any of the aspects, an engineered inactivating modification of an endogenous gene comprises one or more of: i) deletion of the entire coding sequence, ii) deletion of the promoter of the gene, iii) a frameshift mutation, iv) a nonsense mutation (i.e., a premature termination codon), v) a point mutation, vi) a deletion, vii) or an insertion. Non-limiting examples of inactivating modifications include a mutation that decreases gene or polypeptide expression, a mutation that decreases gene or polypeptide transport, a mutation that decreases gene or polypeptide activity, a mutation in the active site of an enzyme that decreases enzymatic activity, or a mutation that decreases the stability of a nucleic acid or polypeptide. Examples of loss-of-function mutations for each gene can be clear to a person of ordinary skill (e.g., a premature stop codon, a frameshift mutation); they can be measurable by an assay of nucleic acid or protein function, activity, expression, transport, and/or stability; or they can be known in the art.

In some embodiments of any of the aspects, an inactivating modification of an endogenous gene can be engineered in a bacterium using an integration vector (e.g., pT18mobsacB). In some embodiments of any of the aspects, the engineering of an inactivating modification of an endogenous gene in a bacterium further comprises conjugation methods and/or counterselection methods. In some embodiments of any of the aspects, the introduction of an integration vector comprising an endogenous gene comprising an inactivating modification causes the endogenous gene to be replaced with the endogenous gene comprising an inactivating modification.

In some embodiments of any of the aspects, the engineered bacterium comprises at least one overexpressed gene. In some embodiments of any of the aspects, the overexpressed gene is endogenous. In some embodiments of any of the aspects, the overexpressed gene is exogenous. In some embodiments of any of the aspects, the overexpressed gene is heterologous. In some embodiments of any of the aspects, a gene can be overexpressed using an expression vector (e.g., pBAD, pCR2.1).

In some embodiments of any of the aspects, the engineered bacterium comprises at least one exogenous copy of a functional gene. As a non-limiting example, the engineered bacterium can comprise 1, 2, 3, 4, or at least 5 exogenous copies of a functional gene. As used herein, the term “functional” refers to a form of a molecule which possesses either the native biological activity of the naturally existing molecule of its type, or any specific desired activity, for example as judged by its ability to bind to ligand molecules. In some embodiments of any of the aspects, a functional molecule can comprise at least 50%, at least 60%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or at least 99% of the activity of the wild-type molecule, e.g., in its native organism.

In some embodiments of any of the aspects, a functional gene as described herein is exogenous. In some embodiments of any of the aspects, a functional gene as described herein is ectopic. In some embodiments of any of the aspects, a functional gene as described herein is not endogenous.

The term “exogenous” refers to a substance present in a cell other than its native source. The term “exogenous” when used herein can refer to a nucleic acid (e.g. a nucleic acid encoding a polypeptide) or a polypeptide that has been introduced by a process involving the hand of man into a biological system such as a cell or organism, in which it is not normally found and one wishes to introduce the nucleic acid or polypeptide into such a cell or organism. Alternatively, “exogenous” can refer to a nucleic acid or a polypeptide that has been introduced by a process involving the hand of man into a biological system such as a cell or organism in which it is found in relatively low amounts and one wishes to increase the amount of the nucleic acid or polypeptide in the cell or organism, e.g., to create ectopic expression or levels. In contrast, the term “endogenous” refers to a substance that is native to the biological system or cell. As used herein, “ectopic” refers to a substance that is found in an unusual location and/or amount. An ectopic substance can be one that is normally found in a given cell, but at a much lower amount and/or at a different time. Ectopic also includes substance, such as a polypeptide or nucleic acid that is not naturally found or expressed in a given cell in its natural environment.

In some embodiments of any of the aspects, the engineered bacterium comprises at least one functional heterologous gene. As used herein, the term “heterologous” refers to that which is not endogenous to, or naturally occurring in, a referenced sequence, molecule (including e.g., a protein), virus, cell, tissue, or organism. For example, a heterologous sequence of the present disclosure can be derived from a different species, or from the same species but substantially modified from an original form. Also for example, a nucleic acid sequence that is not normally expressed in a virus or a cell is a heterologous nucleic acid sequence. The term “heterologous” can refer to DNA, RNA, or protein that does not occur naturally as part of the organism in which it is present or which is found in a location or locations in the genome that differ from that in which it occurs in nature. It is DNA, RNA, or protein that is not endogenous to the virus or cell and has been artificially introduced into the virus or cell.

In some embodiments of any of the aspects, at least one exogenous copy of a functional gene can be engineered into a bacterium using an expression vector (e.g., pBadT). In some embodiments of any of the aspects, the expression vector (e.g., pBadT) is translocated from a donor bacterium (e.g., MFDpir) into the engineered bacterium under conditions that promote conjugation.

In some embodiments of any of the aspects, at least one exogenous or heterologous gene as described herein can comprise a detectable label, including but not limited to c-Myc, HA, VSV-G, HSV, FLAG, V5, HIS, or biotin. Detectable labels can also include, but are not limited to, radioisotopes, bioluminescent compounds, chromophores, antibodies, chemiluminescent compounds, fluorescent compounds, metal chelates, and enzymes.

In some embodiments of any of the aspects, the engineered bacterium further comprises a selectable marker. Non-limiting examples of selectable markers include a positive selection marker; a negative selection marker; a positive and negative selection marker; resistance to at least one of ampicillin, kanamycin, triclosan, and/or chloramphenicol; or an auxotrophy marker. In some embodiments of any of the aspects, the selectable marker is selected from the group consisting of beta-lactamase, Neo gene (e.g., Kanamycin resistance cassette) from Tn5, mutant FabI gene, and an auxotrophic mutation.

Described herein are bacteria engineered for the production of TAGs (e.g., animal TAGs or milk fats). In one aspect, described herein is an engineered (e.g., Cupriavidus necator) bacterium, comprising at least one of the following: (a) at least one exogenous copy of at least one functional acyltransferase gene; and/or (b) at least one exogenous copy of at least one functional phosphatidic acid (PA) phosphatase gene. In some embodiments of any of the aspects, the acyltransferase gene encodes for an acyltransferase enzyme that catalyzes transesterification of the sn3 OH group, the sn2 OH group, or the sn1 OH group of a TAG precursor (e.g., diacylglycerol, lysophosphatidic acid, or glyceraldehyde-3-phosphate) with a fatty acid. In some embodiments of any of the aspects, the acyltransferase gene encodes an acyltransferase enzyme that catalyzes transesterification of the sn3 OH group of a diacylglycerol with a fatty acid. In some embodiments of any of the aspects, the acyltransferase gene is a functional diglyceride acyltransferase (DGAT) gene, a functional wax synthase (WS) gene, a hybrid of a DGAT and a WS, a functional lysophosphatidic acid acyltransferase (LPAT) gene, or a functional glycerol-3-phosphate acyltransferase (GPAT) gene. In one aspect, described herein is an engineered (e.g., Cupriavidus necator) bacterium, comprising at least one of the following: (a) at least one exogenous copy of at least one functional thioesterase (TE) gene; (b) at least one exogenous copy of at least one functional diglyceride acyltransferase (DGAT) gene; and/or (c) at least one exogenous copy of at least one phosphatidate phosphatases (PAP) gene. In some embodiments of any of the aspects, the engineered bacterium further comprises: (i) at least one endogenous polyhydroxyalkanoate (PHA) synthase gene comprising at least one engineered inactivating modification; or (ii) at least one exogenous inhibitor of an endogenous polyhydroxyalkanoate (PHA) synthase gene or gene product. In some embodiments of any of the aspects, the engineered bacterium is selected from Table 3.

TABLE 3

Exemplary engineered TAG bacteria (“X” indicates

inclusion in the engineered TAG bacteria)

Exogenous functionsl gene(s)
Inactivated or inhibited endogenous gene(s)

acyltransferase (e.g.,

beta-
diacylglycerol

DGAT, LPAT, and/or

oxidation
kinase (e.g.,

GPAT, see e.g., Table 7)
PAP
TE
PHA
(e.g., fadE)
dgkA)

X

X

X
X

X

X

X

X
X

X
X
X

X

X

X

X

X

X
X

X

X
X

X

X
X

X
X
X

X
X
X
X

X

X

X

X

X

X
X

X

X

X

X

X

X

X
X

X

X
X
X

X

X
X

X

X
X

X

X
X

X
X

X
X

X
X
X

X

X
X
X

X
X
X
X

X
X
X
X
X

X

X

X

X

X

X
X

X

X

X

X

X

X

X
X

X

X
X
X

X

X

X

X

X

X

X

X

X

X
X

X

X

X
X

X

X

X
X

X

X
X
X

X

X
X
X
X

X

X
X

X

X
X

X

X
X

X
X

X
X

X

X
X

X

X

X
X

X
X

X
X

X
X
X

X
X

X
X
X

X

X
X
X

X

X
X
X

X
X

X
X
X

X
X
X
X

X

X
X
X
X

X
X
X
X
X

X
X
X
X
X
X

In some embodiments of any of the aspects, the engineered bacterium is a chemoautotroph. In some embodiments of any of the aspects, the engineered bacterium uses CO₂as its sole carbon source, and/or said engineered bacteria uses H₂as its sole energy source. In some embodiments of any of the aspects, the engineered bacterium is Cupriavidus necator.

In some embodiments of any of the aspects, the engineered bacterium produces TAGs (e.g., C16 TAGs). In some embodiments of any of the aspects, the TAGs are produced and/or isolated using methods as described further herein.

In some embodiments of any of the aspects, the engineered bacterium comprises one or more of the following: (a)(i) at least one endogenous polyhydroxyalkanoate (PHA) synthase gene comprising at least one engineered inactivating modification or (a)(ii) at least one exogenous inhibitor of an endogenous polyhydroxyalkanoate (PHA) synthase gene or gene product (e.g., mRNA, protein). In some embodiments of any of the aspects, the engineered bacterium comprises (a)(i) at least one endogenous polyhydroxyalkanoate (PHA) synthase gene comprising at least one engineered inactivating modification. In some embodiments of any of the aspects, the engineered bacterium comprises (a)(ii) at least one exogenous inhibitor of an endogenous polyhydroxyalkanoate (PHA) synthase gene or gene product (e.g., mRNA, protein)

In some embodiments of any of the aspects, the engineered bacterium comprises an engineered inactivating modification of an endogenous polyhydroxyalkanoate (PHA) synthase gene. In some embodiments of any of the aspects, the endogenous PHA synthase comprises phaC. PhaC is a class I poly(R)-hydroxyalkanoic acid synthase, and is the key enzyme in the polymerization of polyhydroxyalkanoates (PHAs). PhaC catalyzes the polymerization of 3-R-hydroxyalkyl CoA thioester to form PHAs with concomitant release of CoA. In some embodiments of any of the aspects, the endogenous PHA synthase comprises Cupriavidus necator phaC.

In some embodiments of any of the aspects, the engineered bacterium comprises an engineered inactivating modification of the endogenous Cupriavidus necator phaC gene. In some embodiments of any of the aspects, the nucleic acid sequence of the endogenous Cupriavidus necator phaC gene comprises SEQ ID NO: 3 or a sequence that is at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the sequence of SEQ ID NO: 3 that maintains the same functions as SEQ ID NO: 3 (e.g., PHA synthase).

Cupriavidus necator N-1 chromosome 1, REGION:

1478083-1479852 GenBank: CP002877.1, 1770 bp DNA

SEQ ID NO: 3

ATGGCGACCGGCAAAGGCGCGGCAGCTTCCACTCAGGAAGGCAAGTCCCA

ACCATTCAAGTTCACGCCGGGGCCATTCGATCCAGCCACATGGCTGGAAT

GGTCCCGCCAGTGGCAGGGCACTGAAGGCAACGGCCACGCGGCCGCGTCC

GGCATTCCGGGCCTGGATGCGCTGGCAGGCGTCAAGATCGAGCCGGCGCA

GCTGGGTGATATCCAGCAGCGTTACATGAAGGACTTCTCAGCCCTGTGGC

AGGCCATGGCCGAGGGCAAGGCCGAGGCCACCGGGCCGCTGCACGACCGG

CGCTTCGCCGGCGACGCGTGGCGCACCAACCTGCCATACCGCTTCGCTGC

CGCGTTCTACCTGCTCAATGCGCGCGCCTTGACCGAGCTGGCCGATGCTG

TTGAGGCCGATGCCAAGACGCGCCAGCGCATCCGCTTTGCGATCTCGCAA

TGGGTCGATGCGATGTCGCCCGCCAACTTCCTCGCCACGAATCCCGAGGC

GCAGCGCCTGCTGATCGAGTCGGGCGGCGAATCGCTGCGTGCCGGCGTGC

GCAACATGATGGAAGACCTGACGCGCGGCAAGATCTCGCAGACCGACGAG

AGCGCGTTTGAGGTCGGCCGCAATGTCGCGGTGAGCGAAGGCGCCGTAGT

CTTCGAGAACGAATACTTCCAGCTGTTGCAGTACAAGCCGCTGACCGACA

AGGTGCATGCGCGCCCGCTGCTGATGGTGCCGCCGTGCATCAACAAGTAC

TACATCCTGGACCTGCAGCCGGAGAGCTCGCTGGTGCGTCATGTGGTGGA

GCAGGGGCATACGGTGTTCCTGGTGTCGTGGCGCAATCCGGACGCCAGCA

TGGCTGGCAGCACCTGGGACGACTACATCGAGCACGCGGCCATCCGCGCC

ATCGAAGTCGCGCGCGACATCAGCGGCCAGGACAAGATCAACGTGCTCGG

CTTCTGCGTGGGCGGCACCATTGTGTCGACTGCGCTGGCGGTGATGGCCG

CGCGCGGCCAGCACCCGGCTGCCAGCGTCACGCTGCTGACCACGCTGCTG

GACTTTGCCGACACCGGCATCCTCGACGTCTTTGTCGACGAGGGCCATGT

GCAGCTGCGCGAGGCCACGCTGGGCGGCGCCGCCGGCGCGCCGTGCGCGC

TGCTGCGCGGCCTTGAGCTGGCCAATACCTTCTCGTTCCTGCGCCCGAAC

GACCTGGTGTGGAACTACGTGGTCGACAACTACCTGAAGGGCAACACGCC

GGTGCCGTTCGACCTGCTGTTCTGGAACGGCGACGCCACCAACCTGCCGG

GGCCTTGGTACTGCTGGTACCTGCGCCACACCTACCTGCAGGACGAGCTC

AAGGTGCCGGGCAAGCTGACTGTGTGCGGCGTGCCCGTGGACCTGGCCAG

CATCGACGTGCCGACCTACATCTACGGCTCGCGCGAAGACCATATCGTGC

CATGGACCGCGGCCTATGCCTCGACCGCGCTGCTGGCGAACAAGCTGCGC

TTCGTGCTGGGTGCGTCGGGCCATATCGCCGGTGTGATCAACCCGCCGGC

CAAGAACAAGCGCAGCCACTGGACCAACGATGCGCTGCCGGAGTCGCCGC

AGCAATGGCTGGCTGGCGCCACCGAGCATCACGGCAGCTGGTGGCCGGAC

TGGACCGCATGGCTGGCAGGCCAGGCCGGCGCGAAACGTGCCGCGCCCGC

CAACTACGGCAATGCGCGCTATCCCGCGATCGAACCCGCGCCTGGGCGAT

ACGTCAAAGCCAAGGCATGA

In some embodiments of any of the aspects, the amino acid sequence encoded by the endogenous Cupriavidus necator phaC gene comprises SEQ ID NO: 4 or an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the sequence of SEQ ID NO: 4 that maintains the same functions as SEQ ID NO: 4 (e.g., PHA synthase).

class I poly(R)-hydroxyalkanoic acid synthase

[Cupriavidus necator], NCBI Reference Sequence:

WP_013956451.1, 589 aa

SEQ ID NO: 4

MATGKGAAASTQEGKSQPFKFTPGPFDPATWLEWSRQWQGTEGNGHAAAS

GIPGLDALAGVKIEPAQLGDIQQRYMKDFSALWQAMAEGKAEATGPLHDR

RFAGDAWRTNLPYRFAAAFYLLNARALTELADAVEADAKTRQRIRFAISQ

WVDAMSPANFLATNPEAQRLLIESGGESLRAGVRNMMEDLTRGKISQTDE

SAFEVGRNVAVSEGAVVFENEYFQLLQYKPLTDKVHARPLLMVPPCINKY

YILDLQPESSLVRHVVEQGHTVFLVSWRNPDASMAGSTWDDYIEHAAIRA

IEVARDISGQDKINVLGFCVGGTIVSTALAVMAARGQHPAASVTLLTTLL

DFADTGILDVFVDEGHVQLREATLGGAAGAPCALLRGLELANTFSFLRPN

DLVWNYVVDNYLKGNTPVPFDLLFWNGDATNLPGPWYCWYLRHTYLQDEL

KVPGKLTVCGVPVDLASIDVPTYIYGSREDHIVPWTAAYASTALLANKLR

FVLGASGHIAGVINPPAKNKRSHWTNDALPESPQQWLAGATEHHGSWWPD

WTAWLAGQAGAKRAAPANYGNARYPAIEPAPGRYVKAKA

In some embodiments of any of the aspects, the engineered inactivating modification of an endogenous polyhydroxyalkanoate (PHA) synthase gene comprises a point mutation. Non-limiting examples of inactivating point mutations of C. necator phaC (see e.g., SEQ ID NO: 4) include non-conservative substitutions of residues T323, C438, Y445, L446, or E267 (e.g., T323I, T323S, C438G, Y445F, L446K, or E267K). Additional non-limiting examples of point mutations of C. necator phaC (see e.g., SEQ ID NO: 4) include C319S, C459S, S260A, S260T, S5461, E267K, T323S, T323I, C438G, Y445F, L446K, W425A, D480N, H508Q, S35P, S80P, A154V, L231P, D306A, L358P, A391T, T393A, V470M, N519S, S546G, and A565E. In some embodiments of any of the aspects, the engineered inactivating modification of an endogenous polyhydroxyalkanoate (PHA) synthase gene comprises a deletion. Non-limiting examples include deletions of regions D281-D290, A372-C382, E578-A589 and/or V585-A589 of C. necator phaC (see e.g., SEQ ID NO: 4). See e.g., Rehm et al., Molecular characterization of the poly(3 hydroxybutyrate) (PHB) synthase from Ralstonia eutropha: in vitro evolution, site-specific mutagenesis and development of a PHB synthase protein model, Biochimica et Biophysica Acta 1594 (2002) 178-190, the content of which is incorporated herein by reference in its entirety. In some embodiments of any of the aspects, the engineered inactivating modification of an endogenous polyhydroxyalkanoate (PHA) synthase gene comprises a deletion of the entire coding sequence (e.g., a knockout of the endogenous phaC gene, denoted herein as ΔphaC).

In some embodiments of any of the aspects, the engineered bacterium comprises an engineered inactivating modification of an endogenous gene involved in the PHA synthesis pathway. In some embodiments of any of the aspects, the endogenous gene involved in the PHA synthesis pathway comprises phaA, phaB, and/or phaC (e.g., a Class I PHA synthase operon). In some embodiments of any of the aspects, the PHA synthesis pathway comprises Cupriavidus necator phaA, Cupriavidus necator phaB, and/or Cupriavidus necator phaC.

PhaA is an acetyl-CoA acetyltransferase that catalyzes the condensation of two acetyl-coA units to form acetoacetyl-CoA. PhaA is involved in the biosynthesis of PHAs (e.g., polyhydroxybutyrate (PHB)). PhaA also catalyzes the reverse reaction, i.e. the cleavage of acetoacetyl-CoA, and is therefore also involved in the reutilization of PHB.

In some embodiments of any of the aspects, the engineered bacterium comprises an engineered inactivating modification of the endogenous Cupriavidus necator phaA gene. In some embodiments of any of the aspects, the nucleic acid sequence of the endogenous Cupriavidus necator phaA gene comprises SEQ ID NO: 5 or a sequence that is at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the sequence of SEQ ID NO: 5 that maintains the same functions as SEQ ID NO: 5 (e.g., acetyl-CoA acetyltransferase).

Cupriavidus necator phaA acetyl-CoA acetyl-

transferase, Cupriavidus necator H16 chromosome

1, complete sequence, GenBank: CP039287.1, REGION:

1557857-1559035, 1179 bp

SEQ ID NO: 5

ATGACTGACGTTGTCATCGTATCCGCCGCCCGCACCGCGGTCGGCAAGTT

TGGCGGCTCGCTGGCCAAGATCCCGGCACCGGAACTGGGTGCCGTGGTCA

TCAAGGCCGCGCTGGAGCGCGCCGGCGTCAAGCCGGAGCAGGTGAGCGAA

GTCATCATGGGCCAGGTGCTGACCGCCGGTTCGGGCCAGAACCCCGCACG

CCAGGCCGCGATCAAGGCCGGCCTGCCGGCGATGGTGCCGGCCATGACCA

TCAACAAGGTGTGCGGCTCGGGCCTGAAGGCCGTGATGCTGGCCGCCAAC

GCGATCATGGCGGGCGACGCCGAGATCGTGGTGGCCGGCGGCCAGGAAAA

CATGAGCGCCGCCCCGCACGTGCTGCCGGGCTCGCGCGATGGTTTCCGCA

TGGGCGATGCCAAGCTGGTCGACACCATGATCGTCGACGGCCTGTGGGAC

GTGTACAACCAGTACCACATGGGCATCACCGCCGAGAACGTGGCCAAGGA

ATACGGCATCACACGCGAGGCGCAGGATGAGTTCGCCGTCGGCTCGCAGA

ACAAGGCCGAAGCCGCGCAGAAGGCCGGCAAGTTTGACGAAGAGATCGTC

CCGGTGCTGATCCCGCAGCGCAAGGGCGACCCGGTGGCCTTCAAGACCGA

CGAGTTCGTGCGCCAGGGCGCCACGCTGGACAGCATGTCCGGCCTCAAGC

CCGCCTTCGACAAGGCCGGCACGGTGACCGCGGCCAACGCCTCGGGCCTG

AACGACGGCGCCGCCGCGGTGGTGGTGATGTCGGCGGCCAAGGCCAAGGA

ACTGGGCCTGACCCCGCTGGCCACGATCAAGAGCTATGCCAACGCCGGTG

TCGATCCCAAGGTGATGGGCATGGGCCCGGTGCCGGCCTCCAAGCGCGCC

CTGTCGCGCGCCGAGTGGACCCCGCAAGACCTGGACCTGATGGAGATCAA

CGAGGCCTTTGCCGCGCAGGCGCTGGCGGTGCACCAGCAGATGGGCTGGG

ACACCTCCAAGGTCAATGTGAACGGCGGCGCCATCGCCATCGGCCACCCG

ATCGGCGCGTCGGGCTGCCGTATCCTGGTGACGCTGCTGCACGAGATGAA

GCGCCGTGACGCGAAGAAGGGCCTGGCCTCGCTGTGCATCGGCGGCGGCA

TGGGCGTGGCGCTGGCAGTCGAGCGCAAA

In some embodiments of any of the aspects, the amino acid sequence encoded by the endogenous Cupriavidus necator phaA gene comprises SEQ ID NO: 6 or an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the sequence of SEQ ID NO: 6 that maintains the same functions as SEQ ID NO: 6 (e.g., PHA synthase).

phaA, acetyl-CoA C-acetyltransferase

[Cupriavidus], NCBI Reference Sequence:

WP_010810132.1, 393 aa

SEQ ID NO: 6

MTDVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSE

VIMGQVLTAGSGQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAAN

AIMAGDAEIVVAGGQENMSAAPHVLPGSRDGFRMGDAKLVDTMIVDGLWD

VYNQYHMGITAENVAKEYGITREAQDEFAVGSQNKAEAAQKAGKFDEEIV

PVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKPAFDKAGTVTAANASGL

NDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGPVPASKRA

LSRAEWTPQDLDLMEINEAFAAQALAVHQQMGWDTSKVNVNGGAIAIGHP

IGASGCRILVTLLHEMKRRDAKKGLASLCIGGGMGVALAVERK,

In some embodiments of any of the aspects, the engineered inactivating modification of an endogenous gene involved in the PHA synthesis pathway comprises a deletion of the entire coding sequence (e.g., a knockout of the endogenous phaA gene, denoted herein as ΔphaA).

In some embodiments of any of the aspects, the engineered bacterium comprises an engineered inactivating modification of the endogenous Cupriavidus necator phaB gene. PhaB is an acetoacetyl-CoA reductase that catalyzes the chiral reduction of acetoacetyl-CoA to (R)-3-hydroxybutyryl-CoA. PhaB is involved in the biosynthesis of PHAs (e.g., polyhydroxybutyrate (PHB)). PhaB can also be referred to as phbB. In some embodiments of any of the aspects, the nucleic acid sequence of the endogenous Cupriavidus necator phaB gene comprises SEQ ID NO: 7 or a sequence that is at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the sequence of SEQ ID NO: 7 that maintains the same functions as SEQ ID NO: 7 (e.g., acetoacetyl-CoA reductase).

Cupriavidus necator strain A-04 acetoacetyl-CoA

reductase (phbB) gene, complete cds, GenBank:

FJ897462.1, 741 bp

SEQ ID NO: 7

ATGACTCAGCGCATTGCGTATGTGACCGGCGGCATGGGTGGTATCGGAAC

CGCCATTTGCCAGCGGCTGGCCAAGGATGGCTTTCGTGTGGTGGCCGGTT

GCGGCCCCAACTCGCCGCGCCGCGAAAAGTGGCTGGAGCAGCAGAAGGCC

CTGGGCTTCGATTTCATTGCCTCGGAAGGCAATGTGGCTGACTGGGACTC

GACCAAGACCGCATTCGACAAGGTCAAGTCCGAGGTCGGCGAGGTTGATG

TGCTGATCAACAACGCCGGTATCACCCGCGACGTGGTGTTCCGCAAGATG

ACCCGCGCCGACTGGGATGCGGTGATCGACACCAACCTGACCTCGCTGTT

CAACGTCACCAAGCAGGTGATCGACGGCATGGCCGACCGTGGCTGGGGCC

GCATCGTCAACATCTCGTCGGTGAACGGGCAGAAGGGCCAGTTCGGCCAG

ACCAACTACTCCACCGCCAAGGCCGGCCTGCATGGCTTCACCATGGCACT

GGCGCAGGAAGTGGCGACCAAGGGCGTGACCGTCAACACGGTCTCTCCGG

GCTATATCGCCACCGACATGGTCAAGGCGATCCGCCAGGACGTGCTCGAC

AAGATCGTCGCGACGATCCCGGTCAAGCGCCTGGGCCTGCCGGAAGAGAT

CGCCTCGATCTGCGCCTGGTTGTCGTCGGAGGAGTCCGGTTTCTCGACCG

GCGCCGACTTCTCGCTCAACGGCGGCCTGCATATGGGCTGA,

In some embodiments of any of the aspects, the amino acid sequence encoded by the endogenous Cupriavidus necator phaC gene comprises SEQ ID NO: 8 or an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the sequence of SEQ ID NO: 8 that maintains the same functions as SEQ ID NO: 8 (e.g., e.g., acetoacetyl-CoA reductase).

phaB 3-ketoacyl-ACP reductase [Cupriavidus], NCBI

Reference Sequence: WP_010810131.1, 246 aa

SEQ ID NO: 8

MTQRIAYVTGGMGGIGTAICQRLAKDGFRVVAGCGPNSPRREKWLEQQKA

LGFDFIASEGNVADWDSTKTAFDKVKSEVGEVDVLINNAGITRDVVFRKM

TRADWDAVIDTNLTSLFNVTKQVIDGMADRGWGRIVNISSVNGQKGQFGQ

TNYSTAKAGLHGFTMALAQEVATKGVTVNTVSPGYIATDMVKAIRQDVLD

KIVATIPVKRLGLPEEIASICAWLSSEESGFSTGADFSLNGGLHMG

In some embodiments of any of the aspects, the engineered bacterium comprises an engineered inactivating modification of an endogenous phaA (e.g., SEQ ID NOs: 5, 6), an engineered inactivating modification of an endogenous phaB (e.g., SEQ ID NOs: 7, 8), or an engineered inactivating modification of an endogenous phaC (e.g., SEQ ID NOs: 3, 4). In some embodiments of any of the aspects, the engineered bacterium comprises an engineered inactivating modification of an endogenous phaA (e.g., SEQ ID NOs: 5, 6). In some embodiments of any of the aspects, the engineered bacterium comprises an engineered inactivating modification of an endogenous phaB (e.g., SEQ ID NOs: 7, 8). In some embodiments of any of the aspects, the engineered bacterium comprises an engineered inactivating modification of an endogenous phaC (e.g., SEQ ID NOs: 3, 4).

In some embodiments of any of the aspects, the engineered bacterium comprises an engineered inactivating modification of an endogenous phaA (e.g., SEQ ID NOs: 5, 6), and an engineered inactivating modification of an endogenous phaB (e.g., SEQ ID NOs: 7, 8). In some embodiments of any of the aspects, the engineered bacterium comprises an engineered inactivating modification of an endogenous phaA (e.g., SEQ ID NOs: 5, 6) and an engineered inactivating modification of an endogenous phaC (e.g., SEQ ID NOs: 3, 4). In some embodiments of any of the aspects, the engineered bacterium comprises an engineered inactivating modification of an endogenous phaB (e.g., SEQ ID NOs: 7, 8) and an engineered inactivating modification of an endogenous phaC (e.g., SEQ ID NOs: 3, 4). In some embodiments of any of the aspects, the engineered bacterium comprises an engineered inactivating modification of an endogenous phaA (e.g., SEQ ID NOs: 5, 6), an engineered inactivating modification of an endogenous phaB (e.g., SEQ ID NOs: 7, 8), and an engineered inactivating modification of an endogenous phaC (e.g., SEQ ID NOs: 3, 4).

In some embodiments of any of the aspects, an organism can comprise alternative groups of genes involved in the PHA synthesis pathway. As an example, the Class II PHA synthase operon (e.g., in Pseudomonas oleovorans) comprises phaC1, phaZ, phaC2, and phaD. As another example, the Class III PHA synthase operon (e.g., in Allochromatium vinosum) comprises phaC, phaE, phaA, ORF4, phaP, and phaB. As such, an engineered bacterium can comprise an engineered inactivating modification and/or an inhibitor of at least one endogenous gene involved in the PHA synthesis pathway (e.g., phaC1, phaZ, phaC2, phaD, phaC, phaE, phaA, ORF4, phaP, and/or phaB).

In some embodiments of any of the aspects, the engineered bacterium comprises an inhibitor of an endogenous PHA synthase gene. Non-limiting examples of PHA synthase (e.g., PhaC, Enzyme Commission (E.C.) 2.3.1) inhibitors include carbadethia CoA analogs, sT-CH₂-CoA, sTet-CH₂-CoA, and sT-aldehyde. See e.g., Zhang et al., Chembiochem. 2015 Jan. 2; 16(1): 156-166, the contents of which are incorporated herein in be reference in their entireties. In some embodiments of any of the aspects, the engineered bacterium comprises an inhibitor of at least one endogenous gene involved in the PHA synthesis pathway. Non-limiting examples of such inhibitors include an inhibitory RNA (e.g., siRNA, miRNA) against a gene involved in PHA synthesis (e.g., a PHA synthase, PhaC, PhaB, PhaA), a small molecule inhibitor of a gene involved in PHA synthesis (e.g., a PHA synthase, PhaC, PhaB, PhaA), and the like.

In some embodiments of any of the aspects, the engineered bacterium comprises at least one exogenous copy of at least one functional thioesterase gene. In some embodiments of any of the aspects, the engineered bacterium does not comprise a functional endogenous thioesterase gene. Thioesterases are enzymes which belong to the esterase family. Esterases, in turn, are one type of the several hydrolases known. Thioesterases exhibit Esterase activity (e.g., splitting of an ester into acid and alcohol, in the presence of water) specifically at a thiol group. Thioesterases or thiolester hydrolases are identified as members of E.C.3.1.2.

Thioesterases (TEs) can determine the chain length of substrate fatty acids, for example in the synthesis of PHAs. As such, TEs can modulate polymer length and ratio or components of the PHA. In some embodiments of any of the aspects, the functional thioesterase gene preferentially produces or leads to the production of TAGs comprising a specific type of fatty acid R group (e.g., C16), as described herein. As such, the functional thioesterase gene can be selected from any thioesterase gene from any species that preferentially produces or leads to the production of TAGs comprising a specific type of fatty acid R group (e.g., C16). In some embodiments of any of the aspects, the functional thioesterase is an Acyl-Acyl Carrier Protein (acyl-ACP) Thioesterase. In some embodiments of any of the aspects, the functional thioesterase gene is heterologous. In some embodiments of any of the aspects, a thioesterase polypeptide as described herein is truncated to remove an organelle targeting sequence(s); in some embodiments, such a targeting sequence can contribute to poor expression of the thioesterase polypeptide, e.g., in the engineered bacteria described herein.

In some embodiments of any of the aspects, the functional heterologous thioesterase is from a plant species (e.g., Cuphea palustris, Arachis hypogaea, Mangifera indica, Morella rubra, Pistacia vera, or Theobroma cacao). In some embodiments of any of the aspects, the functional heterologous thioesterase gene comprises a Cuphea thioesterase. In some embodiments of any of the aspects, the functional heterologous thioesterase gene comprises a Arachis thioesterase. In some embodiments of any of the aspects, the functional heterologous thioesterase gene comprises a Mangifera thioesterase. In some embodiments of any of the aspects, the functional heterologous thioesterase gene comprises a Morella thioesterase. In some embodiments of any of the aspects, the functional heterologous thioesterase gene comprises a Pistacia thioesterase. In some embodiments of any of the aspects, the functional heterologous thioesterase gene comprises a Theobroma thioesterase. In some embodiments of any of the aspects, the functional heterologous thioesterase gene comprises a Cuphea palustris FatB1 gene (i.e., CpFatB1), a Cuphea palustris FatB2 gene (i.e., CpFatB2), a Cuphea palustris FatB2-FatB1 hybrid gene (i.e., CpFatB2-CpFatB1), a Arachis hypogaea FatB2-1 gene, a Mangifera indica FatA gene, a Morella rubra FatA gene, a Pistacia vera FatA gene, a Theobroma cacao FatA gene, a Theobroma cacao FatB gene (e.g., FatB1, FatB2, FatB3, BatB4, FatB5, or FatB6), or a Limosilactobacillus reuteri TE gene.

In some embodiments of any of the aspects, the engineered bacterium comprises at least one exogenous copy of at least one functional thioesterase gene comprising one of SEQ ID NOs: 9-11, SEQ ID NOs: 99-121 or a nucleic acid sequence that is at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the sequence of at least one of SEQ ID NOs: 9-11 or SEQ ID NOs: 99-121, that maintains the same functions as at least one of SEQ ID NOs: 9-11 or SEQ ID NOs: 99-121 (e.g., thioesterase).

Cuphea palustris FatB1, GenBank: U38188.1, 1236 bp, complete

CDS

SEQ ID NO: 9

ATGGTGGCTGCTGCAGCAAGTTCTGCATGCTTCCCTGTTCCATCCCCAGGAGCCTCCCCT

AAACCTGGGAAGTTAGGCAACTGGTCATCGAGTTTGAGCCCTTCCTTGAAGCCCAAGTCA

ATCCCCAATGGCGGATTTCAGGTTAAGGCAAATGCCAGTGCGCATCCTAAGGCTAACGG

TTCTGCAGTAACTCTAAAGTCTGGCAGCCTCAACACTCAGGAGGACACTTTGTCGTCGTC

CCCTCCTCCCCGGGCTTTTTTTAACCAGTTGCCTGATTGGAGTATGCTTCTGACTGCAATC

ACAACCGTCTTCGTGGCACCAGAGAAGCGGTGGACTATGTTTGATAGGAAATCTAAGAG

GCCTAACATGCTCATGGACTCGTTTGGGTTGGAGAGAGTTGTTCAGGATGGGCTCGTGTT

CAGACAGAGTTTTTCGATTAGGTCTTATGAAATATGCGCTGATCGAACAGCCTCTATAGA

GACGGTGATGAACCACGTCCAGGAAACATCACTCAATCAATGTAAGAGTATAGGTCTTC

TCGATGACGGCTTTGGTCGTAGTCCTGAGATGTGTAAAAGGGACCTCATTTGGGTGGTTA

CAAGAATGAAGATAATGGTGAATCGCTATCCAACTTGGGGCGATACTATCGAGGTCAGT

ACCTGGCTCTCTCAATCGGGGAAAATCGGTATGGGTCGCGATTGGCTAATAAGTGATTGC

AACACAGGAGAAATTCTTGTAAGAGCAACGAGTGTGTATGCCATGATGAATCAAAAGAC

GAGAAGATTCTCAAAACTCCCACACGAGGTTCGCCAGGAATTTGCGCCTCATTTTCTGGA

CTCTCCTCCTGCCATTGAAGACAACGACGGTAAATTGCAGAAGTTTGATGTGAAGACTGG

TGATTCCATTCGCAAGGGTCTAACTCCGGGGTGGTATGACTTGGATGTCAATCAGCACGT

AAGCAACGTGAAGTACATTGGGTGGATTCTCGAGAGTATGCCAACAGAAGTTTTGGAGA

CTCAGGAGCTATGTTCTCTCACCCTTGAATATAGGCGGGAATGCGGAAGGGACAGTGTG

CTGGAGTCCGTGACCTCTATGGATCCCTCAAAAGTTGGAGACCGGTTTCAGTACCGGCAC

CTTCTGCGGCTTGAGGATGGGGCTGATATCATGAAGGGAAGAACTGAGTGGCGGCCGAA

GAATGCAGGAACTAACGGGGCGATATCAACAGGAAAGACTTGA

Cuphea palustris FatB2, complete CDS, GenBank: U38189.1,

1408 bp

SEQ ID NO: 10

CCACGCGTCCGCTGAGTTTGCTGGTTACCATTTTCCCTGCGAACAAACATGGTGGCTGCC

GCAGCAAGTGCTGCATTCTTCTCCGTCGCAACCCCGCGAACAAACATTTCGCCATCGAGC

TTGAGCGTCCCCTTCAAGCCCAAATCAAACCACAATGGTGGCTTTCAGGTTAAGGCAAAC

GCCAGTGCCCATCCTAAGGCTAACGGTTCTGCAGTAAGTCTAAAGTCTGGCAGCCTCGAG

ACTCAGGAGGACAAAACTTCATCGTCGTCCCCTCCTCCTCGGACTTTCATTAACCAGTTG

CCCGTCTGGAGTATGCTTCTGTCTGCAGTCACGACTGTCTTCGGGGTGGCTGAGAAGCAG

TGGCCAATGCTTGACCGGAAATCTAAGAGGCCCGACATGCTTGTGGAACCGCTTGGGGTT

GACAGGATTGTTTATGATGGGGTTAGTTTCAGACAGAGTTTTTCGATTAGATCTTACGAA

ATAGGCGCTGATCGAACAGCCTCGATAGAGACCCTGATGAACATGTTCCAGGAAACATC

TCTTAATCATTGTAAGATTATCGGTCTTCTCAATGACGGCTTTGGTCGAACTCCTGAGATG

TGTAAGAGGGACCTCATTTGGGTGGTCACGAAAATGCAGATCGAGGTGAATCGCTATCC

TACTTGGGGTGATACTATAGAGGTCAATACTTGGGTCTCAGCGTCGGGGAAACACGGTAT

GGGTCGAGATTGGCTGATAAGTGATTGCCATACAGGAGAAATTCTTATAAGAGCAACGA

GCGTGTGGGCTATGATGAATCAAAAGACGAGAAGATTGTCGAAAATTCCATATGAGGTT

CGACAGGAGATAGAGCCTCAGTTTGTGGACTCTGCTCCTGTCATTGTAGACGATCGAAAA

TTTCACAAGCTTGATTTGAAGACCGGTGATTCCATTTGCAATGGTCTAACTCCAAGGTGG

ACTGACTTGGATGTCAATCAGCACGTTAACAATGTGAAATACATCGGGTGGATTCTCCAG

AGTGTTCCCACAGAAGTTTTCGAGACGCAGGAGCTATGTGGCCTCACCCTTGAGTATAGG

CGAGAATGCGGAAGGGACAGTGTGCTGGAGTCCGTGACCGCTATGGATCCATCAAAAGA

GGGAGACCGGTCTCTTTACCAGCACCTTCTCCGACTCGAGGACGGGGCTGATATCGTCAA

GGGGAGAACCGAGTGGCGGCCGAAGAATGCAGGAGCCAAGGGAGCAATATTAACCGGA

AAGACCTCAAATGGAAACTCTATATCTTAGAAGGAGGAAGGGACCTTTCCGAGTTGTGT

GTTTATTTGCTTTGCTTTGATTCACTCCATTGTATAATAATACTACGGTCAGCCGTCTTTGT

ATTTGCTAAGACAAATAGCACAGTCATTAAGTT

Engineered chimera of C. palustris FatB1 (aa 1-218) and FatB2

(aa 219-316) thioesterase—Chimera 4 (981 bp)

SEQ ID NO: 11

ATGCTGCTGACCGCCATCACGACCGTGTTCGTGGCCCCGGAGAAGCGCTGGACCATGTTC

GACCGCAAGTCGAAGCGCCCGAACATGCTGATGGACTCGTTCGGCCTGGAGCGCGTGGT

GCAGGACGGCCTGGTGTTCCGCCAGTCGTTCTCGATCCGCTCGTACGAGATCTGCGCCGA

CCGCACCGCCTCGATCGAGACCGTGATGAACCACGTGCAGGAGACCTCGCTGAACCAGT

GCAAGTCGATCGGCCTGCTGGACGACGGCTTCGGCCGTTCGCCGGAGATGTGCAAGCGC

GACCTGATCTGGGTGGTGACCCGCATGAAGATCATGGTGAACCGCTACCCGACCTGGGG

CGACACCATCGAGGTGAGCACCTGGCTGTCGCAGTCGGGCAAGATCGGCATGGGCCGCG

ATTGGCTGATCTCGGACTGCAACACCGGCGAGATCCTGGTGCGCGCCACCTCGGTGTACG

CCATGATGAACCAGAAGACCCGCCGCTTCTCGAAGCTGCCGCACGAGGTGCGCCAGGAG

TTCGCCCCGCACTTCCTGGATTCACCACCGGCCATCGAGGACAATGACGGCAAGCTGCAG

AAGTTCGACGTGAAGACCGGCGACTCGATCCGCAAGGGCCTGACCCCGGGCTGGTACGA

CCTGGACGTGAACCAGCACGTGAACAACGTGAAGTACATCGGCTGGATCCTGCAGTCGG

TGCCGACCGAGGTGTTCGAGACCCAGGAGCTGTGCGGCCTGACCCTGGAGTATCGCCGC

GAATGCGGCCGCGATTCGGTGCTGGAATCGGTGACCGCCATGGACCCGTCGAAGGAGGG

CGATCGCTCGCTGTACCAGCACCTGCTGCGCCTGGAAGATGGCGCCGACATCGTGAAGG

GCCGCACCGAATGGCGCCCGAAGAATGCAGGCGCAAAGGGCGCCATTCTGACCGGCAAG

ACCTCAGGCGGCCACCACCACCACCATCATTGA

Arachis hypogaea Acyl-[acyl-carrier-protein] hydrolase

(AhFatB2-1) codon-optimized, 1245 nt

SEQ ID NO: 99

ATGGTGGCCACCGCCGCCACCTCGTCGTTCTTCCCGGTGACCTCGCGCACCGGCGGCGAG

GGCGGCGGCGGCATCCCGGCCTCGCTGGGCGGCGGCCTGAAGCAGAACCACCGCTCGTC

GTCGGTGAAGGCCAACGCCCACGCCCCGTCGAAGATCAACGGCACCGCCACCAAGGTGC

CGAAGTCGATGGAGTCGATGAAGCTGGAGTCGTCGTCGACCACCGGCGCCAACGCCCCG

CGCACCTTCATCAACCAGATCCCGGACTGGTCGATGCTGCTGGCCGCCATCACCACCGCC

TTCCTGGCCGCCGAGAAGCAGTGGATGATGATCGACTGGAAGCCGAAGCGCTCGGACGT

GCTGTCGGACCCGTTCGGCATCGGCCGCATCGTGCAGGACGGCCTGGCCTTCCGCCAGAA

CTTCTCGATCCGCTCGTACGAGATCGGCGCCGACAAGACCGCCTCGATCGAGACCCTGAT

GAACCACCTGCAGGAGACCGCCCTGAACCACGTGAAGACCGCCGGCCTGCTGGGCGACG

GCTTCGGCTCGACCCCGGAGATGTGCAAGAAGAACCTGATCTGGGTGGTGACCCGCATG

CAGGTGGAGGTGGACCGCTACCCGACCTGGGGCGACGTGGTGCAGGTGGACACCTGGGT

GTCGGCCTCGGGCAAGAACGGCATGCGCCGCGACTGGATCATCCGCGACGCCAACACCG

GCGAGATCCTGACCCGCGCCTCGTCGATCTGGGTGATGATGAACAAGGTGACCCGCCGC

CTGTCGAAGATCCCGGAGGAGGTGCGCCAGGAGATCGCCTCGTACTTCGTGGACTCGCC

GCCGGTGGTGGAGGAGGACAACCGCAAGCTGTCGAAGCTGGACGACACCGCCGACCAC

ATCCGCCGCGGCCTGTCGCCGCGCTGGTCGGACCTGGACGTGAACCAGCACGTGAACAA

CGTGAAGTACATCGGCTGGCTGCTGGAGTCGGCCCCGCAGGCCATCCTGGAGTCGCACG

AGCTGCGCGCCATGACCCTGGAGTACCGCCGCGAGTGCGGCAAGGACTCGGTGCTGGAC

TCGCTGACCGACGTGTCGGGCGCCGACATCGGCAACCTGGCCGGCGGCGGCTCGCTGGA

GTGCAAGCACCTGCTGCGCCTGGAGGACGGCGGCGAGATCGTGCGCGGCCGCACCGAGT

GGCGCCCGAAGCCGGTGAACAACTTCGGCGCCATGAACCAGGTGTTCCCGGCCGAGAAC

TAA,

Arachis hypogaea palmitoyl-acyl carrier protein thioesterase,

chloroplastic (AhFatB2-1), NCBI Reference Sequence:

XM_025825221.1, 1245 nt

SEQ ID NO: 100

ATGGTTGCTACTGCTGCTACGTCGTCGTTTTTCCCTGTGACGTCACGAACCGGTGGAGAA

GGAGGAGGAGGAATCCCTGCCAGCCTCGGCGGAGGGCTCAAACAAAATCACAGGTCTTC

AAGTGTTAAGGCCAATGCGCATGCTCCTTCAAAGATCAACGGAACCGCCACAAAGGTTC

CAAAATCCATGGAGAGCATGAAGCTGGAATCCTCGTCGACGACGGGGGCTAATGCGCCG

AGGACTTTCATTAACCAGATTCCGGATTGGAGCATGCTGCTGGCCGCCATCACGACAGCC

TTCCTTGCGGCGGAGAAGCAGTGGATGATGATCGATTGGAAGCCGAAGCGATCCGATGT

GCTATCTGATCCATTTGGTATTGGGAGGATTGTGCAGGATGGGCTTGCTTTCAGGCAAAA

TTTCTCCATTCGATCTTACGAGATAGGCGCCGATAAGACCGCGTCTATAGAGACGCTAAT

GAATCATTTGCAGGAAACTGCACTTAATCATGTTAAGACTGCTGGGCTTCTTGGTGATGG

CTTTGGTTCGACGCCGGAAATGTGTAAGAAGAACCTGATATGGGTTGTGACTCGGATGCA

AGTTGAAGTTGATCGTTACCCAACATGGGGAGATGTAGTTCAAGTTGACACTTGGGTTTC

TGCATCAGGGAAAAATGGTATGCGTCGTGATTGGATCATACGTGATGCCAATACGGGTG

AAATCTTGACAAGAGCCTCCAGTATTTGGGTCATGATGAATAAAGTGACAAGGAGACTA

TCCAAAATTCCAGAAGAAGTCAGGCAAGAGATTGCGTCGTATTTTGTGGATTCTCCTCCA

GTTGTCGAAGAGGATAACAGAAAACTGTCTAAACTTGATGATACTGCAGATCATATTCGT

CGTGGTCTAAGTCCTAGATGGAGTGATCTAGATGTTAATCAGCATGTTAACAATGTGAAG

TACATTGGCTGGCTTCTGGAGAGTGCTCCACAGGCAATCTTGGAGAGTCATGAGCTGCGG

GCCATGACTCTGGAGTACAGGAGGGAATGTGGCAAGGACAGTGTGCTGGATTCCCTAAC

TGATGTCTCTGGTGCTGATATCGGGAACTTAGCTGGCGGCGGATCTCTCGAGTGCAAACA

CTTGCTTAGGCTTGAAGATGGTGGTGAGATTGTGAGGGGTAGGACTGAATGGAGGCCCA

AGCCTGTGAACAACTTTGGTGCTATGAATCAGGTTTTTCCAGCAGAAAACTGA,

Arachis hypogaea Acyl-[acyl-carrier-protein] hydrolase (AhFatB2-

1) truncated codon-optimized (corresponds to nt 187-1245 of

SEQ ID NO: 99), 1059 nt

SEQ ID NO: 101

ATGGAGTCGATGAAGCTGGAGTCGTCGTCGACCACCGGCGCCAACGCCCCGCGCACCTT

CATCAACCAGATCCCGGACTGGTCGATGCTGCTGGCCGCCATCACCACCGCCTTCCTGGC

CGCCGAGAAGCAGTGGATGATGATCGACTGGAAGCCGAAGCGCTCGGACGTGCTGTCGG

ACCCGTTCGGCATCGGCCGCATCGTGCAGGACGGCCTGGCCTTCCGCCAGAACTTCTCGA

TCCGCTCGTACGAGATCGGCGCCGACAAGACCGCCTCGATCGAGACCCTGATGAACCAC

CTGCAGGAGACCGCCCTGAACCACGTGAAGACCGCCGGCCTGCTGGGCGACGGCTTCGG

CTCGACCCCGGAGATGTGCAAGAAGAACCTGATCTGGGTGGTGACCCGCATGCAGGTGG

AGGTGGACCGCTACCCGACCTGGGGCGACGTGGTGCAGGTGGACACCTGGGTGTCGGCC

TCGGGCAAGAACGGCATGCGCCGCGACTGGATCATCCGCGACGCCAACACCGGCGAGAT

CCTGACCCGCGCCTCGTCGATCTGGGTGATGATGAACAAGGTGACCCGCCGCCTGTCGAA

GATCCCGGAGGAGGTGCGCCAGGAGATCGCCTCGTACTTCGTGGACTCGCCGCCGGTGG

TGGAGGAGGACAACCGCAAGCTGTCGAAGCTGGACGACACCGCCGACCACATCCGCCGC

GGCCTGTCGCCGCGCTGGTCGGACCTGGACGTGAACCAGCACGTGAACAACGTGAAGTA

CATCGGCTGGCTGCTGGAGTCGGCCCCGCAGGCCATCCTGGAGTCGCACGAGCTGCGCG

CCATGACCCTGGAGTACCGCCGCGAGTGCGGCAAGGACTCGGTGCTGGACTCGCTGACC

GACGTGTCGGGCGCCGACATCGGCAACCTGGCCGGCGGCGGCTCGCTGGAGTGCAAGCA

CCTGCTGCGCCTGGAGGACGGCGGCGAGATCGTGCGCGGCCGCACCGAGTGGCGCCCGA

AGCCGGTGAACAACTTCGGCGCCATGAACCAGGTGTTCCCGGCCGAGAACTAA,

Arachis hypogaea palmitoyl-acyl carrier protein thioesterase,

chloroplastic (AhFatB2-1) truncated (corresponds to nt 187-

1245 of SEQ ID NO: 100), 1059 nt

SEQ ID NO: 102

ATGGAGAGCATGAAGCTGGAATCCTCGTCGACGACGGGGGCTAATGCGCCGAGGACTTT

CATTAACCAGATTCCGGATTGGAGCATGCTGCTGGCCGCCATCACGACAGCCTTCCTTGC

GGCGGAGAAGCAGTGGATGATGATCGATTGGAAGCCGAAGCGATCCGATGTGCTATCTG

ATCCATTTGGTATTGGGAGGATTGTGCAGGATGGGCTTGCTTTCAGGCAAAATTTCTCCA

TTCGATCTTACGAGATAGGCGCCGATAAGACCGCGTCTATAGAGACGCTAATGAATCATT

TGCAGGAAACTGCACTTAATCATGTTAAGACTGCTGGGCTTCTTGGTGATGGCTTTGGTT

CGACGCCGGAAATGTGTAAGAAGAACCTGATATGGGTTGTGACTCGGATGCAAGTTGAA

GTTGATCGTTACCCAACATGGGGAGATGTAGTTCAAGTTGACACTTGGGTTTCTGCATCA

GGGAAAAATGGTATGCGTCGTGATTGGATCATACGTGATGCCAATACGGGTGAAATCTT

GACAAGAGCCTCCAGTATTTGGGTCATGATGAATAAAGTGACAAGGAGACTATCCAAAA

TTCCAGAAGAAGTCAGGCAAGAGATTGCGTCGTATTTTGTGGATTCTCCTCCAGTTGTCG

AAGAGGATAACAGAAAACTGTCTAAACTTGATGATACTGCAGATCATATTCGTCGTGGTC

TAAGTCCTAGATGGAGTGATCTAGATGTTAATCAGCATGTTAACAATGTGAAGTACATTG

GCTGGCTTCTGGAGAGTGCTCCACAGGCAATCTTGGAGAGTCATGAGCTGCGGGCCATG

ACTCTGGAGTACAGGAGGGAATGTGGCAAGGACAGTGTGCTGGATTCCCTAACTGATGT

CTCTGGTGCTGATATCGGGAACTTAGCTGGCGGCGGATCTCTCGAGTGCAAACACTTGCT

TAGGCTTGAAGATGGTGGTGAGATTGTGAGGGGTAGGACTGAATGGAGGCCCAAGCCTG

TGAACAACTTTGGTGCTATGAATCAGGTTTTTCCAGCAGAAAACTGA,

Mangifera indica palmitoyl-acyl carrier protein thioesterase,

chloroplastic-like (MiFatA), NCBI Reference Sequence:

XM_044638751.1 region 13-1161, 1149 nt

SEQ ID NO: 103

ATGACATCCGTGGCATGTAAGATCATCCTTTCCAGAGAATTATTCAAGGAAGAGAAGAA

GATTAAGCCCATGGCGACGGCCAAAGTGGGGCTTTGTTCATCAGGGAATTTGATAAGAC

GGAAACATGGAAGGCATTTGTTGATAGCAAGTGCCAGTAATCCAAATGGTCTAGACATG

ATGAAAGGAAAAAAGGTGAACGGAATTCACCATAACGAAGAGACTCATCATCAGCTGCT

ACTTAAACAAAGGGTTTCTAAGGCACCCCTTCATGCATGTTTGCTTGGAAGGTTTGTAGG

TGATAGGTTTATGTATAGACAAACCTTCATTATAAGATCATATGAAATTGGACCAGATAA

AACTGCCACTATGGAAACACTCTTGAATCTCCTTCAGGAGACTGCTCTGAATCATGTAAC

GGGCTCGGGACTAGCTGGGAACGGGTTTGGCGCTACCCGAGAGATGAGTCTTCGAAAAC

TCATCTGGGTCGTCACTCGCATCAACATTCAAGTGCAGAGATATAGCTGCTGGGGAGATG

TTGTGGAGATAGATACTTGGGTTGATTCTTCAGGAAAGAATGCCATGCGCAGGGACTGG

ATTATCCGAGATTATCATACCCAGGAAATAATAACAAGGGCAACAAGCACCTGGGTGAC

CATGAACAGAGAAACAAGGAGGTTATCAAAGATTCCTGAACAAGTAAAGCAAGAAGTG

TTTCCGTTTTACCTAGACAGAGTTGCAATTGCAAAAGAACAAAATGATGTTGGGAAAATT

GACAAGCTAACTGATGAAACTGCAGAGAGAATTCGATCTGGTTTAGCTCCAAGATGGAA

TGACATGGATGCCAATCAGCATGTAAACAATGTCAAATACATTGGATGGATTTTAGAGA

GTGTTCCAATACATGTATTAAAAGATTACAATATGACAAGCATGACCCTGGAGTATCGAC

GTGAGTGTCGCCAATCAAATTTGTTGGAGTCCTTGACAAGCTCAACAGCCAGCGTCACTG

GAGACCCCAACAATAATTCCAACAATCGCATTGCAGACTTGAAATACACACATCTACTTC

GAATGCAAGCTGATAAGGCTGAGATAGTCCGTGCCAGATCAGAATGGCAATCCAAACAA

ATAACACAAGTCATCACATAG,

Morella rubra Palmitoyl-acyl carrier protein thioesterase,

chloroplastic (MrFatA), GenBank: CM025852.1 region: complement

(27992667-27995211), CDS join (1-555, 852-985, 1369-1482,

1554-1731, 1875-1943, 2294-2545), 1302 nt

SEQ ID NO: 104

ATGTTGGAAACTTTTATTTTTTGTCTCCTCATCAGGCAACGTGAGTTCGAAGCTACATCGG

CCACCTTATATTTTCAAACCTATATTTTGCTCGGTTCTACAATTTCCCGCGGTATAGTATA

TCTCTCTGTTCAATCAGCGATGACAGTGATGGCTGCACTGAGTAACGCTCGACTGTATTT

TGGAGGGGATTTTTGCAGGGGAGATAAGAAGAATATGGCCATGGCGAGGTTGGGTTATT

ATCCTTCATTGAATTGTGCAATCAAGCCGAAGCAGCCAAGTTTATTAGTGATAGCAAGTG

CTAGTACTCCTCCGAGCATATATACCATCAACGGAAAGAAGGTGAATGGAATAAACTTC

GGGGAGGCTCCATTTAGGAGTAACAAGTATAGCGATTCAGCAAAAGAAAGCTGTGTTGA

TGCACCTCTTCATGCAGTTTTGCTTGGAAGGTTCGTGGAGGACCAGTTTGTTTATAGACA

GACATTCATTATCAGGTCTTACGAGATTGGACCAGACAAAACTGCTACCATGGAAACACT

GATGAATCTCCTTCAGGAGACAGCTCTCAATCATGTGACAAGCTCTGGCCTTGCTGGGAA

TGGCTTTGGTGCCACCCGCGAGATGAGCCTACGGAAACTTATTTGGGTTGTCACACGGGT

CCACATTCAAGTACAGAGATATAGCTGCTGGGGAGATGTTGTTGAGATTGATACTTGGGT

GGATGCCGAGGGGAAAAATGGGATGCGCAGGGACTGGATAATCCGGGATTACCACACA

CAAGAGATCATTACCAGGGCCACAAGTACTTGGGTTATCATGAATCAAGAAACACGACG

GTTGTCTAAGATCCCAGAACAAGTGAGAGAGGAAGTGGTACCGTTCTACCTGGACAGAC

TTGCAGTTTCCGCAGAAATGAATGATAGTGAAAAAATTGACAAGCTCACTGACGAAACC

GCAGAAAGAATTCGATCAGGATTAGCCCCAAGATGGAGCGACATGGATGCCAATCAGCA

CGTGAACAACGTGAAATATATTGGATGGATCCTGGAGAGCGTGCCCATAAACGTGCTTG

GAAATTATGATCTTACGAGCATGACTCTGGAGTACCGCCGTGAGTGCCGGCAATCAAATT

TGCTGGAGTCTTTGACAAGTTCAACAGCAAATGCAACTGAAGCCTCGTATAACTCCTTAC

ATCGATCTAAACCAGACTTGGAATTCACACACCTGCTTCGCATGCTAGCAGACAAGGCA

GAGATAGTACGGGCAAGAACACAGTGGCATTCCAAACAAAAACGAAACTGA,

Pistacia vera palmitoyl-acyl carrier protein thioesterase,

chloroplastic-like (PvFatA), NCBI Reference Sequence:

XM_031391868.1 region 92-1252, 1161 nt

SEQ ID NO: 105

ATGATATCCGTGGCACGAACAAGTTATGTAAGATTATCCTTTCCAGAGAATTTATTCAAG

GAAGAGAAGGAGATCGTACCCATGGCCATGGCCAAGGTCGGGTTTTGTTGCTCGTTGAA

TTTGATCCGACCAAAACATGGAAGGCTTTTGGTGATAGCAAGTGCTAGTAATGCGAAGA

GCCTGGACATCATGAATGGAAAAAAGGTGAATGGAATTCACGTTAATGAAGAGACTCGT

CATCAGCGGCTACTTAATCAAAGAGTTGCTGACGCACCCCTCCATGCATGTTTGCTTGGA

AAATTTGTAGAGGATAGGTTTTTGTATAGACAAACCTTCATTGTCAGGTCATATGAAATT

GGACCAGATAAAACTGCCACTATGGAAACACTCTTGAATCTCCTTCAGGAGACAGCTCTG

AATCATGTAACGAGCTCGGGACTTGCTGGGAACGGGTTTGGTGCTACCCGAGAGATGAG

TGTTAGAAAACTCATCTGGGTCGTCACTCGCATCAACATTCAAGTACAGAGATATAGCTG

CTGGGGAGATGTTGTTGAGATAGATACTTGGGTTGATGCAGCAGGAAAGAATGCGATGC

GCCGGGACTGGATTATCCGAGATTATCGTACCCAAGAGATAATAACAAGAGCAACAAGC

ACCTGGGTGATCATGAACAGAGAAACAAGAAGATTATCAAAGATTCCTGAACAAGTAAG

GCAAGAAGTGTTACCATTTTACCTAGGTAGAGTTGCAATTGCAAAAGAACAAAATGATG

TTGGGAAAATTGACAAGCTTACTGATGAAACTGCAGAGAGAATTCGGTCTGGTTTAGCTC

CAAGATGGAATGACATGGATGCCAATCAGCATGTAAATAATGTCAAATACATAGGATGG

ATTTTGGAGAGTGTGCCAATACACGTCTTAAAAGATTACAATCTGACAAGCATGACCCTG

GAGTATCGACGTGAATGTCGCCAATCAAATTTGCTAGAGTCCTTGACAAGTTCAACAGCC

AGTGTCACTGGAGACCCCAACAATAATTCCAATAATCGCATTGCAGACTTGGAATACAC

ACATCTACTTCGTATGCAAGCTGATAAAGCTGAGATAGTCCGAGCCAGATCAGAATGGC

AGTCCAAACAAATAACACAAGCCATCACTTGA,

Theobroma cacao oleoyl-acyl carrier protein thioesterase 1,

chloroplastic (TcFATA) codon-optimized, 1128 nt

SEQ ID NO: 106

ATGCTGAAGCTGTCGTCGTGCAACGTGACCGACCAGCGCCAGGCCCTGGCCCAGTGCCG

CTTCCTGGCCCCGCCGGCCCCGTTCTCGTTCCGCTGGCGCACCCCGGTGGTGGTGTCGTG

CTCGCCGTCGTCGCGCCCGAACCTGTCGCCGCTGCAGGTGGTGCTGTCGGGCCAGCAGCA

GGCCGGCATGGAGCTGGTGGAGTCGGGCTCGGGCTCGCTGGCCGACCGCCTGCGCCTGG

GCTCGCTGACCGAGGACGGCCTGTCGTACAAGGAGAAGTTCATCGTGCGCTGCTACGAG

GTGGGCATCAACAAGACCGCCACCGTGGAGACCATCGCCAACCTGCTGCAGGAGGTGGG

CTGCAACCACGCCCAGTCGGTGGGCTACTCGACCGACGGCTTCGCCACCACCCGCACCAT

GCGCAAGCTGCACCTGATCTGGGTGACCGCCCGCATGCACATCGAGATCTACAAGTACC

CGGCCTGGTCGGACGTGATCGAGATCGAGACCTGGTGCCAGTCGGAGGGCCGCATCGGC

ACCCGCCGCGACTGGATCCTGAAGGACTTCGGCACCGGCGAGGTGATCGGCCGCGCCAC

CTCGAAGTGGGTGATGATGAACCAGGACACCCGCCGCCTGCAGAAGGTGTCGGACGACG

TGCGCGAGGAGTACCTGGTGTTCTGCCCGCGCGAGCTGCGCCTGGCCTTCCCGGAGGAG

AACAACAACTCGCTGAAGAAGATCGCCAAGCTGGACGACTCGTTCCAGTACTCGCGCCT

GGGCCTGATGCCGCGCCGCGCCGACCTGGACATGAACCAGCACGTGAACAACGTGACCT

ACATCGGCTGGGTGCTGGAGTCGATGCCGCAGGAGATCATCGACACCCACGAGCTGCAG

ACCATCACCCTGGACTACCGCCGCGAGTGCCAGCAGGACGACGTGGTGGACTCGCTGAC

CTCGCCGGAGCAGGTGGAGGGCACCGAGAAGGTGTCGGCCATCCACGGCACCAACGGCT

CGGCCGCCGCCCGCGAGGACAAGCAGGACTGCCGCCAGTTCCTGCACCTGCTGCGCCTG

TCGTCGGACGGCCAGGAGATCAACCGCGGCCGCACCGAGTGGCGCAAGAAGCCGGCCCG

CTAA,

Theobroma cacao oleoyl-acyl carrier protein thioesterase 1,

chloroplastic (TcFATA), NCBI Reference Sequence: XM_007049650.2,

1128 nt

SEQ ID NO: 107

ATGTTGAAGCTTTCTTCCTGCAATGTGACGGACCAAAGACAGGCCTTGGCCCAATGCAGA

TTCCTCGCTCCGCCTGCTCCGTTCTCCTTTCGCTGGCGTACCCCAGTCGTCGTCTCCTGCTC

TCCTTCCAGCAGACCTAACCTGTCGCCTCTTCAAGTTGTCCTGTCTGGCCAGCAGCAAGC

TGGGATGGAGCTGGTCGAATCCGGGTCGGGGAGTTTGGCTGACCGGCTCCGGTTGGGTA

GCTTGACGGAAGATGGTTTGTCCTATAAGGAGAAGTTTATTGTGAGGTGTTATGAGGTGG

GAATTAACAAAACTGCCACTGTTGAAACCATTGCCAATCTCTTGCAGGAGGTTGGATGTA

ACCATGCTCAAAGTGTTGGATATTCCACAGATGGGTTTGCTACCACTCGCACCATGAGAA

AATTGCATCTCATTTGGGTAACTGCACGCATGCACATTGAAATATACAAATACCCTGCTT

GGAGTGATGTGATTGAAATAGAGACATGGTGCCAAAGTGAGGGAAGAATTGGAACCAG

AAGGGACTGGATTCTTAAGGACTTTGGAACTGGTGAAGTTATTGGAAGAGCTACTAGCA

AGTGGGTGATGATGAACCAGGACACTAGGCGGCTACAGAAAGTCAGTGATGATGTCAGG

GAAGAATATTTAGTCTTCTGTCCACGAGAACTCAGATTAGCATTTCCAGAGGAGAACAAT

AATAGTTTGAAGAAAATTGCCAAATTAGATGACTCTTTTCAGTATTCCAGGCTAGGGCTT

ATGCCAAGAAGAGCTGATCTGGACATGAACCAGCATGTCAATAATGTCACCTACATTGG

ATGGGTTCTGGAGAGCATGCCTCAAGAGATCATTGACACCCATGAACTGCAAACTATCA

CGTTAGATTACAGACGGGAATGCCAACAGGATGACGTGGTGGATTCACTTACCAGTCCA

GAACAAGTGGAGGGTACCGAAAAAGTTTCAGCGATTCACGGAACAAATGGGTCTGCAGC

TGCAAGAGAAGATAAGCAGGACTGCCGTCAGTTTTTGCATCTGTTGAGATTGTCTAGTGA

TGGACAGGAAATAAATCGAGGCCGTACTGAGTGGAGAAAGAAACCTGCGAGATGA,

Theobroma cacao oleoyl-acyl carrier protein thioesterase 1,

chloroplastic (TcFATA) truncated codon-optimized (corresponds

to nt 244-1128 of SEQ ID NO: 106), 888 nt

SEQ ID NO: 108

ATGCTGACCGAGGACGGCCTGTCGTACAAGGAGAAGTTCATCGTGCGCTGCTACGAGGT

GGGCATCAACAAGACCGCCACCGTGGAGACCATCGCCAACCTGCTGCAGGAGGTGGGCT

GCAACCACGCCCAGTCGGTGGGCTACTCGACCGACGGCTTCGCCACCACCCGCACCATG

CGCAAGCTGCACCTGATCTGGGTGACCGCCCGCATGCACATCGAGATCTACAAGTACCC

GGCCTGGTCGGACGTGATCGAGATCGAGACCTGGTGCCAGTCGGAGGGCCGCATCGGCA

CCCGCCGCGACTGGATCCTGAAGGACTTCGGCACCGGCGAGGTGATCGGCCGCGCCACC

TCGAAGTGGGTGATGATGAACCAGGACACCCGCCGCCTGCAGAAGGTGTCGGACGACGT

GCGCGAGGAGTACCTGGTGTTCTGCCCGCGCGAGCTGCGCCTGGCCTTCCCGGAGGAGA

ACAACAACTCGCTGAAGAAGATCGCCAAGCTGGACGACTCGTTCCAGTACTCGCGCCTG

GGCCTGATGCCGCGCCGCGCCGACCTGGACATGAACCAGCACGTGAACAACGTGACCTA

CATCGGCTGGGTGCTGGAGTCGATGCCGCAGGAGATCATCGACACCCACGAGCTGCAGA

CCATCACCCTGGACTACCGCCGCGAGTGCCAGCAGGACGACGTGGTGGACTCGCTGACC

TCGCCGGAGCAGGTGGAGGGCACCGAGAAGGTGTCGGCCATCCACGGCACCAACGGCTC

GGCCGCCGCCCGCGAGGACAAGCAGGACTGCCGCCAGTTCCTGCACCTGCTGCGCCTGT

CGTCGGACGGCCAGGAGATCAACCGCGGCCGCACCGAGTGGCGCAAGAAGCCGGCCCG

CTAA,

Theobroma cacao oleoyl-acyl carrier protein thioesterase 1,

chloroplastic (TcFATA) truncated (corresponds to nt 244-1128

of SEQ ID NO: 107), 888 nt

SEQ ID NO: 109

ATGTTGACGGAAGATGGTTTGTCCTATAAGGAGAAGTTTATTGTGAGGTGTTATGAGGTG

GGAATTAACAAAACTGCCACTGTTGAAACCATTGCCAATCTCTTGCAGGAGGTTGGATGT

AACCATGCTCAAAGTGTTGGATATTCCACAGATGGGTTTGCTACCACTCGCACCATGAGA

AAATTGCATCTCATTTGGGTAACTGCACGCATGCACATTGAAATATACAAATACCCTGCT

TGGAGTGATGTGATTGAAATAGAGACATGGTGCCAAAGTGAGGGAAGAATTGGAACCAG

AAGGGACTGGATTCTTAAGGACTTTGGAACTGGTGAAGTTATTGGAAGAGCTACTAGCA

AGTGGGTGATGATGAACCAGGACACTAGGCGGCTACAGAAAGTCAGTGATGATGTCAGG

GAAGAATATTTAGTCTTCTGTCCACGAGAACTCAGATTAGCATTTCCAGAGGAGAACAAT

AATAGTTTGAAGAAAATTGCCAAATTAGATGACTCTTTTCAGTATTCCAGGCTAGGGCTT

ATGCCAAGAAGAGCTGATCTGGACATGAACCAGCATGTCAATAATGTCACCTACATTGG

ATGGGTTCTGGAGAGCATGCCTCAAGAGATCATTGACACCCATGAACTGCAAACTATCA

CGTTAGATTACAGACGGGAATGCCAACAGGATGACGTGGTGGATTCACTTACCAGTCCA

GAACAAGTGGAGGGTACCGAAAAAGTTTCAGCGATTCACGGAACAAATGGGTCTGCAGC

TGCAAGAGAAGATAAGCAGGACTGCCGTCAGTTTTTGCATCTGTTGAGATTGTCTAGTGA

TGGACAGGAAATAAATCGAGGCCGTACTGAGTGGAGAAAGAAACCTGCGAGATGA,

Theobroma cacao palmitoyl-acyl carrier protein thioesterase,

chloroplastic (TcFatB1), NCBI Reference Sequence:

XM_007044056.2, 1188 nt

SEQ ID NO: 110

ATGGCTACTTTCTCTTGTCCAATCTCCTTCCCTTTCAGATGTTCTTTTAACGGTAATCATAA

CCATAACCACAGAGTCGATATCAAAATCAATGGAACTCATACAGGGCCCATTAAGCTCG

ACACATTGAATGAAATAGCTGCAGTTGTAAAAGCTGATTCCACTCCTCTTGCTAATGTCC

ACGAAAACGGGTACATATGCCAAGAGAAGATTCGGCAGAGGATTCCAACGCAGAAGCA

GCTGGTTGATCCTTACCGTCAAGGGCTTATCATTGAAAGGGGAGTTGGCTATAGACAGAC

TGTTGTCATCCGCTCCTATGAAGTTGGCCCTGATAAAACTGCTACCCTGGAGAGCCTCCT

TAATCTTTTCCAGGAAACAGCACTAAATCATGTCTGGATGTCTGGACTTCTGAGCAATGG

ATTTGGAGCCACACATGGAATGATGAGGAACAATCTCATATGGGTCGTCTCAAGAATGC

ACGTCCAAGTGCATCACTATCCCATATGGGGAGAGGTAGTGGAAATCGACACATGGGTT

GGAGCATCAGGGAAGAATGGGATGAGGCGAGACTGGCTAATTCGGAGTCAAGCCACCG

GCATCACCTACGCACGTGCAACCAGCACTTGGGTAATGATGAACGAGCAAACAAGGCGC

CTCTCAAAGATGCCGGAGGAAGTGAGGGGTGAAATCTCTCCTTGGTTTATTGAGAAGCA

AGCAATCAAAGAAGATGCTCCCGAGAAAATTGTCAAGTTGGACGACAAAGCAAAATATG

TGAACTCTGACTTGAAGCCAAAGAGGAGTGATTTGGACATGAACCACCATGTAAACAAT

GTCAAGTATGTACGATGGATGCTTGAGACAATTCCTGACAAATTTTTGGAGTCTCACCAG

CTATCTAGTATTGTACTAGAATATAGAAGGGAATGTGGGAGTTCGGATAAAGTTCAATCA

CTTTGCCAACCAGATGAAGATAGAATTTTAGCAAATGGACTGGAACAAAGTCTACTTGA

AAATATAGTTTTGGCATCGGGAATCATGCTAGGAAATGGACACCTAGGCTCCCTGGGTAT

GAAGACATATGGATTTACTCATCTCCTCCAAATCAAAGGGGACAGTCAAAATGACGAGA

TAGTCAGAGGGAGGACCAGATGGAAGAAAAAGCAATCTACCACGCCGTATTCCACTTAA,

Theobroma cacao palmitoyl-acyl carrier protein thioesterase,

chloroplastic (TcFatB1) truncated (corresponds to nt 280-1188

of SEQ ID NO: 110), 912 nt

SEQ ID NO: 111

ATGGGAGTTGGCTATAGACAGACTGTTGTCATCCGCTCCTATGAAGTTGGCCCTGATAAA

ACTGCTACCCTGGAGAGCCTCCTTAATCTTTTCCAGGAAACAGCACTAAATCATGTCTGG

ATGTCTGGACTTCTGAGCAATGGATTTGGAGCCACACATGGAATGATGAGGAACAATCT

CATATGGGTCGTCTCAAGAATGCACGTCCAAGTGCATCACTATCCCATATGGGGAGAGGT

AGTGGAAATCGACACATGGGTTGGAGCATCAGGGAAGAATGGGATGAGGCGAGACTGG

CTAATTCGGAGTCAAGCCACCGGCATCACCTACGCACGTGCAACCAGCACTTGGGTAAT

GATGAACGAGCAAACAAGGCGCCTCTCAAAGATGCCGGAGGAAGTGAGGGGTGAAATC

TCTCCTTGGTTTATTGAGAAGCAAGCAATCAAAGAAGATGCTCCCGAGAAAATTGTCAA

GTTGGACGACAAAGCAAAATATGTGAACTCTGACTTGAAGCCAAAGAGGAGTGATTTGG

ACATGAACCACCATGTAAACAATGTCAAGTATGTACGATGGATGCTTGAGACAATTCCTG

ACAAATTTTTGGAGTCTCACCAGCTATCTAGTATTGTACTAGAATATAGAAGGGAATGTG

GGAGTTCGGATAAAGTTCAATCACTTTGCCAACCAGATGAAGATAGAATTTTAGCAAAT

GGACTGGAACAAAGTCTACTTGAAAATATAGTTTTGGCATCGGGAATCATGCTAGGAAA

TGGACACCTAGGCTCCCTGGGTATGAAGACATATGGATTTACTCATCTCCTCCAAATCAA

AGGGGACAGTCAAAATGACGAGATAGTCAGAGGGAGGACCAGATGGAAGAAAAAGCAA

TCTACCACGCCGTATTCCACTTAA,

Theobroma cacao palmitoyl-acyl carrier protein thioesterase,

chloroplastic isoform X1 (TcFatB2), NCBI Reference Sequence:

XM_018116899.1, 1398 nt

SEQ ID NO: 112

ATGCACCAATGCCACTCGAATGCTCCCCTATTTGCGTGCAAGCTAACGACTGAGGTTTCT

CGATTTCTCCCCCACCCATTGGAAGTGGTTGAGCTGCAAATTGCATCTGCTCCTCTAGAT

GCTGGAGCTAGGGAGCTAGGGACTGCCATCTGTTTCTTTTTCCGAACTCGAAAGTTTGCT

AGCTTGGCTCTTTTTTTTTGTTCGCGGGTGAGCAAATGCGAGGCACTTACCATGGCATCA

ATGGCCAAAGCAAGCAATGTAACTTCATTATTTCTAGGGGGTGTATGCAAGGAAGAGAA

AACGAAGAATGTAGCCATGGCGAAGTTGGGTTTTTATTCTTCATGGAACTTGATCAAACC

GAAACGGAAAGGCCTTTTGCTAATTGCAAGTGCTAAAAATCCTCATAATCTGGACATGAT

CAACGGGAAAAAAGTAAATGGAATTTTTGTTGGTGAAGCTCCATATACGGGAAAGAAGA

GCACTGTGTTGATAAAAGAACACGTCCCTTATAAACAAGCCCACGCGGCGAGTTTGGTTG

GAAGGTTTGTGGAGGATAGGCATGTCTACAGGCAGACCTTCATCATCAGGTCTTATGAAA

CTGGACCGGACAAAACTGCCACCATGGAAACGGTTATGAATCTCCTTCAGGAAACAGCT

TTGAATCATGTAAGGAGCTCTGGTCTTGCTGGGAATGGCTTTGGGGCTACCCGTGAGATG

AGCCTTAGGAAACTCATATGGGTCGTCACCCGCATCCACGTTCAAGTGGAGAGATATAG

CTGCTGGGGAGATGTTGTGGAGATTGATACTTGGGTTGATGCAGCAGGAAAGAATGCAA

TGCGTAGGGACTGGATAATCAGAGACTACAATACACAGGAGATCATAACAAGAGCAACA

AGCACATGGGTGATTATGAACCACGAAACACGAAGATTAACCAAGATTCCTGAACAAGT

TAGGCAAGAAGTGATTCCATTCTACCTAAACAGGATTGCAATCGCTGAAGAGAAGAACG

ATATCGGAAAGATTGATAAGCTTACTGATGAAAACGCAGAAAGAATACGGTCTGGCTTA

GCTCCAAGATGGAGCGACATGGATGCCAATCAGCATGTAAACAATGTTAAATACATCGG

ATGGATTTTGGAGAGTGTGCCAATGGACGTCCTGGAAGAGTATCGTCTGACGAGCATGA

CCCTGGAGTATCGACGTGAATGCCGGAAATCCAATTTGCTAGAGTCCTTGACGAGTTCAA

CAGCAAATGTGACAGAAGATTCCAACAACAATTCTAATAATCGCAAGGCAGACTTGGAA

TACACACATCTGCTTCGCATGCAAGACGACGTGGCAGAGATAGTCCGAGCTAGATCAGA

ATGGCAATCCAAGGACAAACACAGCTGGTGA,

Theobroma cacao palmitoyl-acyl carrier protein thioesterase,

chloroplastic isoform X1 (TcFatB2) truncated (corresponds to

nt 547-1398 of SEQ ID NO: 112), 855 nt

SEQ ID NO: 113

ATGGTGGAGGATAGGCATGTCTACAGGCAGACCTTCATCATCAGGTCTTATGAAACTGG

ACCGGACAAAACTGCCACCATGGAAACGGTTATGAATCTCCTTCAGGAAACAGCTTTGA

ATCATGTAAGGAGCTCTGGTCTTGCTGGGAATGGCTTTGGGGCTACCCGTGAGATGAGCC

TTAGGAAACTCATATGGGTCGTCACCCGCATCCACGTTCAAGTGGAGAGATATAGCTGCT

GGGGAGATGTTGTGGAGATTGATACTTGGGTTGATGCAGCAGGAAAGAATGCAATGCGT

AGGGACTGGATAATCAGAGACTACAATACACAGGAGATCATAACAAGAGCAACAAGCA

CATGGGTGATTATGAACCACGAAACACGAAGATTAACCAAGATTCCTGAACAAGTTAGG

CAAGAAGTGATTCCATTCTACCTAAACAGGATTGCAATCGCTGAAGAGAAGAACGATAT

CGGAAAGATTGATAAGCTTACTGATGAAAACGCAGAAAGAATACGGTCTGGCTTAGCTC

CAAGATGGAGCGACATGGATGCCAATCAGCATGTAAACAATGTTAAATACATCGGATGG

ATTTTGGAGAGTGTGCCAATGGACGTCCTGGAAGAGTATCGTCTGACGAGCATGACCCTG

GAGTATCGACGTGAATGCCGGAAATCCAATTTGCTAGAGTCCTTGACGAGTTCAACAGC

AAATGTGACAGAAGATTCCAACAACAATTCTAATAATCGCAAGGCAGACTTGGAATACA

CACATCTGCTTCGCATGCAAGACGACGTGGCAGAGATAGTCCGAGCTAGATCAGAATGG

CAATCCAAGGACAAACACAGCTGGTGA,

Theobroma cacao palmitoyl-acyl carrier protein thioesterase,

chloroplastic isoform X2, (TcFatB3), NCBI Reference Sequence:

XM_018116900.1, 1167 nt

SEQ ID NO: 114

ATGGCATCAATGGCCAAAGCAAGCAATGTAACTTCATTATTTCTAGGGGGTGTATGCAAG

GAAGAGAAAACGAAGAATGTAGCCATGGCGAAGTTGGGTTTTTATTCTTCATGGAACTT

GATCAAACCGAAACGGAAAGGCCTTTTGCTAATTGCAAGTGCTAAAAATCCTCATAATCT

GGACATGATCAACGGGAAAAAAGTAAATGGAATTTTTGTTGGTGAAGCTCCATATACGG

GAAAGAAGAGCACTGTGTTGATAAAAGAACACGTCCCTTATAAACAAGCCCACGCGGCG

AGTTTGGTTGGAAGGTTTGTGGAGGATAGGCATGTCTACAGGCAGACCTTCATCATCAGG

TCTTATGAAACTGGACCGGACAAAACTGCCACCATGGAAACGGTTATGAATCTCCTTCAG

GAAACAGCTTTGAATCATGTAAGGAGCTCTGGTCTTGCTGGGAATGGCTTTGGGGCTACC

CGTGAGATGAGCCTTAGGAAACTCATATGGGTCGTCACCCGCATCCACGTTCAAGTGGA

GAGATATAGCTGCTGGGGAGATGTTGTGGAGATTGATACTTGGGTTGATGCAGCAGGAA

AGAATGCAATGCGTAGGGACTGGATAATCAGAGACTACAATACACAGGAGATCATAACA

AGAGCAACAAGCACATGGGTGATTATGAACCACGAAACACGAAGATTAACCAAGATTCC

TGAACAAGTTAGGCAAGAAGTGATTCCATTCTACCTAAACAGGATTGCAATCGCTGAAG

AGAAGAACGATATCGGAAAGATTGATAAGCTTACTGATGAAAACGCAGAAAGAATACG

GTCTGGCTTAGCTCCAAGATGGAGCGACATGGATGCCAATCAGCATGTAAACAATGTTA

AATACATCGGATGGATTTTGGAGAGTGTGCCAATGGACGTCCTGGAAGAGTATCGTCTG

ACGAGCATGACCCTGGAGTATCGACGTGAATGCCGGAAATCCAATTTGCTAGAGTCCTTG

ACGAGTTCAACAGCAAATGTGACAGAAGATTCCAACAACAATTCTAATAATCGCAAGGC

AGACTTGGAATACACACATCTGCTTCGCATGCAAGACGACGTGGCAGAGATAGTCCGAG

CTAGATCAGAATGGCAATCCAAGGACAAACACAGCTGGTGA,

Theobroma cacao palmitoyl-acyl carrier protein thioesterase,

chloroplastic isoform X2, (TcFatB3) truncated (corresponds to

nt 316-1167 of SEQ ID NO: 114), 855 nt

SEQ ID NO: 115

ATGGTGGAGGATAGGCATGTCTACAGGCAGACCTTCATCATCAGGTCTTATGAAACTGG

ACCGGACAAAACTGCCACCATGGAAACGGTTATGAATCTCCTTCAGGAAACAGCTTTGA

ATCATGTAAGGAGCTCTGGTCTTGCTGGGAATGGCTTTGGGGCTACCCGTGAGATGAGCC

TTAGGAAACTCATATGGGTCGTCACCCGCATCCACGTTCAAGTGGAGAGATATAGCTGCT

GGGGAGATGTTGTGGAGATTGATACTTGGGTTGATGCAGCAGGAAAGAATGCAATGCGT

AGGGACTGGATAATCAGAGACTACAATACACAGGAGATCATAACAAGAGCAACAAGCA

CATGGGTGATTATGAACCACGAAACACGAAGATTAACCAAGATTCCTGAACAAGTTAGG

CAAGAAGTGATTCCATTCTACCTAAACAGGATTGCAATCGCTGAAGAGAAGAACGATAT

CGGAAAGATTGATAAGCTTACTGATGAAAACGCAGAAAGAATACGGTCTGGCTTAGCTC

CAAGATGGAGCGACATGGATGCCAATCAGCATGTAAACAATGTTAAATACATCGGATGG

ATTTTGGAGAGTGTGCCAATGGACGTCCTGGAAGAGTATCGTCTGACGAGCATGACCCTG

GAGTATCGACGTGAATGCCGGAAATCCAATTTGCTAGAGTCCTTGACGAGTTCAACAGC

AAATGTGACAGAAGATTCCAACAACAATTCTAATAATCGCAAGGCAGACTTGGAATACA

CACATCTGCTTCGCATGCAAGACGACGTGGCAGAGATAGTCCGAGCTAGATCAGAATGG

CAATCCAAGGACAAACACAGCTGGTGA,

Theobroma cacao palmitoyl-acyl carrier protein thioesterase,

chloroplastic isoform X3 (TcFatB4), NCBI Reference Sequence:

XM_018116901.1, 1158 nt

SEQ ID NO: 116

ATGCACCAATGCCACTCGAATGCTCCCCTATTTGCGTGCAAGCTAACGACTGAGGTTTCT

CGATTTCTCCCCCACCCATTGGAAGTGGTTGAGCTGCAAATTGCATCTGCTCCTCTAGAT

GCTGGAGCTAGGGAGCTAGGGACTGCCATCTGTTTCTTTTTCCGAACTCGAAAGTTTGCT

AGCTTGGCTCTTTTTTTTTGTTCGCGGGTGAGCAAATGCGAGGCACTTACCATGGCATCA

ATGGCCAAAGCAAGCAATGTAACTTCATTATTTCTAGGGGGTGTATGCAAGGAAGAGAA

AACGAAGAATGTAGCCATGGCGAAGTTGGGTTTTTATTCTTCATGGAACTTGATCAAACC

GAAACGGAAAGGCCTTTTGCTAATTGCAAGTGCTAAAAATCCTCATAATCTGGACATGAT

CAACGGGAAAAAAGTAAATGGAATTTTTGTTGGTGAAGCTCCATATACGGGAAAGAAGA

GCACTGTGTTGATAAAAGAACACGTCCCTTATAAACAAGCCCACGCGGCGAGTTTGGTTG

GAAGGTTTGTGGAGGATAGGCATGTCTACAGGCAGACCTTCATCATCAGGTCTTATGAAA

CTGGACCGGACAAAACTGCCACCATGGAAACGGTTATGAATCTCCTTCAGGAAACAGCT

TTGAATCATGTAAGGAGCTCTGGTCTTGCTGGGAATGGCTTTGGGGCTACCCGTGAGATG

AGCCTTAGGAAACTCATATGGGTCGTCACCCGCATCCACGTTCAAGTGGAGAGATATAG

CTGCTGGGGAGATGTTGTGGAGATTGATACTTGGGTTGATGCAGCAGGAAAGAATGCAA

TGCGTAGGGACTGGATAATCAGAGACTACAATACACAGGAGATCATAACAAGAGCAACA

AGCACATGGGTGATTATGAACCACGAAACACGAAGATTAACCAAGATTCCTGAACAAGT

TAGGCAAGAAGTGATTCCATTCTACCTAAACAGGATTGCAATCGCTGAAGAGAAGAACG

ATATCGGAAAGATTGATAAGCTTACTGATGAAAACGCAGAAAGAATACGGTCTGGCTTA

GCTCCAAGATGGAGCGACATGGATGCCAATCAGCATGTAAACAATGTTAAATACATCGG

ATGGATTTTGGAGGCATTCACCAACTAA,

Theobroma cacao palmitoyl-acyl carrier protein thioesterase,

chloroplastic isoform X3 (TcFatB4) truncated (corresponds to nt

547-1158 of SEQ ID NO: 116), 615 nt

SEQ ID NO: 117

ATGGTGGAGGATAGGCATGTCTACAGGCAGACCTTCATCATCAGGTCTTATGAAACTGG

ACCGGACAAAACTGCCACCATGGAAACGGTTATGAATCTCCTTCAGGAAACAGCTTTGA

ATCATGTAAGGAGCTCTGGTCTTGCTGGGAATGGCTTTGGGGCTACCCGTGAGATGAGCC

TTAGGAAACTCATATGGGTCGTCACCCGCATCCACGTTCAAGTGGAGAGATATAGCTGCT

GGGGAGATGTTGTGGAGATTGATACTTGGGTTGATGCAGCAGGAAAGAATGCAATGCGT

AGGGACTGGATAATCAGAGACTACAATACACAGGAGATCATAACAAGAGCAACAAGCA

CATGGGTGATTATGAACCACGAAACACGAAGATTAACCAAGATTCCTGAACAAGTTAGG

CAAGAAGTGATTCCATTCTACCTAAACAGGATTGCAATCGCTGAAGAGAAGAACGATAT

CGGAAAGATTGATAAGCTTACTGATGAAAACGCAGAAAGAATACGGTCTGGCTTAGCTC

CAAGATGGAGCGACATGGATGCCAATCAGCATGTAAACAATGTTAAATACATCGGATGG

ATTTTGGAGGCATTCACCAACTAA,

Theobroma cacao palmitoyl-acyl carrier protein thioesterase,

chloroplastic, (TcFatB5), NCBI Reference Sequence:

XM_007023975.2, 1131 nt

SEQ ID NO: 118

ATGGCAGCATCTTCAAACATTATGACATCGAAGTTCTTCATGGCGACCTCTCCCTCATCCT

GGAATTCAACGAATAAATCAAAGATTTGCTTGCAACAAATCGATAGAAGTTCAAATACG

AATGGAAAGATGGTTAAGTTTACTCGAGACAGTAGTTTGAAGGTCAAATTGCAGGCTCA

AGCACTGCTTACTAATGACAGTAGAGCAACATCAATGATAGAAAGCCTGAAGGATGAGG

AAATGATGACTTCACCACCCGCAACAATGGAACACCTGACAACGGAAGGAAGATTGATA

AATGACGGACTGGTTTTCCAGCAGAATTTTTCCATTAGGTCATTCGAGATAGACTCTGAG

TACAAAGTTTCAGCAAGGGCTATAATGAATTATTTGCAGGAGTCATCACTTAACCATAGA

AAGAAGATGGGGATGTCAAGCGATTCCCTTGTAGGTGTAACGCCAGAGATGATTAAAAG

GGACTTGCTATGGATATTCCGTGGCATGTGTATTGAGGTGGATCGCTATCCTTCTTGGGCT

GATGTTGTCCAGATATACCACCGGATCTATACATCAGGAAGGACTGGTTTGCGTTTGGAA

TGGATTGTCAATGACAGCAAGACAGGCGAAACTCTAGTTCGAGCATCATGCTTAGCTGTG

ATGATGAATAAGAAAACAAGAAAAACATGCAAGTTTCCGGAGGAAGTCAAACAGGAGC

TAAAGCCTTATCTTACGACAGACGCTGAGCCTCTCTTCGAAGCTGACAAAATTTTATGTC

CCCAAGTTGGGAAAATGGATAACATCCGAACCGGATTGACTTCCTGTTGGCATGACCTGG

ATTTCAATTACCATGTAAACAATGCAAAGTATCTTGACTGGATTTTGGAGGGTACTCCTA

CCTCTCTTATACATAGCCATGAGCTTTCTAGAGTAAGTCTCCAGTACCGAAAGGAGTGCT

TGAAAGATGATGTGATTCAATCTTTATCCAGAGTTGTTACCAAGGAAACTGGTCTCTCAA

CGAACAATCAAGAAATTGAATTAGAACACGTCCTCCGTCTTGAGAGTGGACCGGAACTT

GCAGGGGCAAGGACCGCTTGGAGGCCAAAATCTATCTGCCGACAAACTATAAATTAA

Theobroma cacao palmitoyl-acyl carrier protein thioesterase,

chloroplastic, (TcFatB5) truncated (corresponds to nt 292-1131

of SEQ ID NO: 118), 843 nt

SEQ ID NO: 119

ATGTTGATAAATGACGGACTGGTTTTCCAGCAGAATTTTTCCATTAGGTCATTCGAGATA

GACTCTGAGTACAAAGTTTCAGCAAGGGCTATAATGAATTATTTGCAGGAGTCATCACTT

AACCATAGAAAGAAGATGGGGATGTCAAGCGATTCCCTTGTAGGTGTAACGCCAGAGAT

GATTAAAAGGGACTTGCTATGGATATTCCGTGGCATGTGTATTGAGGTGGATCGCTATCC

TTCTTGGGCTGATGTTGTCCAGATATACCACCGGATCTATACATCAGGAAGGACTGGTTT

GCGTTTGGAATGGATTGTCAATGACAGCAAGACAGGCGAAACTCTAGTTCGAGCATCAT

GCTTAGCTGTGATGATGAATAAGAAAACAAGAAAAACATGCAAGTTTCCGGAGGAAGTC

AAACAGGAGCTAAAGCCTTATCTTACGACAGACGCTGAGCCTCTCTTCGAAGCTGACAA

AATTTTATGTCCCCAAGTTGGGAAAATGGATAACATCCGAACCGGATTGACTTCCTGTTG

GCATGACCTGGATTTCAATTACCATGTAAACAATGCAAAGTATCTTGACTGGATTTTGGA

GGGTACTCCTACCTCTCTTATACATAGCCATGAGCTTTCTAGAGTAAGTCTCCAGTACCG

AAAGGAGTGCTTGAAAGATGATGTGATTCAATCTTTATCCAGAGTTGTTACCAAGGAAAC

TGGTCTCTCAACGAACAATCAAGAAATTGAATTAGAACACGTCCTCCGTCTTGAGAGTGG

ACCGGAACTTGCAGGGGCAAGGACCGCTTGGAGGCCAAAATCTATCTGCCGACAAACTA

TAAATTAA,

Theobroma cacao palmitoyl-acyl carrier protein thioesterase,

chloroplastic, (TcFatB6), NCBI Reference Sequence:

XM_007013216.2, 1263 nt

SEQ ID NO: 120

ATGGTTGCTACTGCTGCATCATCTGCATTCTTTCCGGTCACTTCATCCCCGGACTCCTCTG

ACTCAAAAAACAAGAAGCTTGGAAGTGGATCTACTAACCTTGGAGGTATCAAGTCGAAA

CCATCTACTCCTTCTGGAATTTTGCAAGTCAAGGCAAATGCTCAAGCTCCTCCAAAAATA

AATGGTACCACGGTCGTGACAACTCCAGTGGAAAGTTTCAAGAATGAGGACACTGCTAG

TTCCCCTCCTCCCAGGACATTTATAAACCAGTTACCTGATTGGAGCATGCTTCTTGCTGCT

ATCACGACAATTTTCTTGGCTGCTGAGAAGCAGTGGATGATGCTTGATTGGAAACCCAGG

CGGCCTGACATGCTCATTGATCCATTTGGTATAGGGAGGATTGTTCAGGATGGTCTTGTT

TTCCGCCAGAATTTCTCTATAAGGTCTTACGAGATAGGTGCTGATCGGACAGCATCCATA

GAGACGCTAATGAATCATTTACAGGAAACGGCTATTAATCATTGTAGAAGCGCTGGACT

GCTTGGAGAAGGTTTTGGTTCAACCCCTGAGATGTGCAAGAAAAACCTAATATGGGTAG

TCACTCGCATGCAAGTIGTGGTTGATCGCTATCCTACATGGGGTGATGTTGTTCAAGTAG

ACACTTGGGCCAGTGCATCGGGAAAGAATGGTATGCGACGGGATTGGCTTGTCAGTGAT

AGTAAAACTGGTGAAATTTTAACAAGAGCCTCAAGTGTATGGGTGATGATGAATAAGCT

TACTAGAAGGTTATCTAAAATTCCAGAAGAGGTCCGAGGAGAAATAGAACCTTATTTTAT

GAATTCTGATCCTGTTGTGGCTGAGGATAGTAGGAAATTAGTGAAACTTGATGACAGCAC

AGCAGATTATGTCCGTAAAGGTTTAACTCCCAGATGGGGTGATTTGGATGTCAACCAGCA

TGTCAATAATGTGAAGTACATTGGCTGGATCCTTGAGAGTGCTCCACTGCCAATCTTGGA

GACTCACGAGCTTTCTTCAATGACACTGGAATATAGGAGGGAGTGTGGGAGAGACGGTG

TGCTGCAGTCCCTAACTGCTGTCTCTGACTCTGGTGTGGGCAACTTGGTGAACTTTGGTG

AAATCGAGTGCCAGCACTTGCTCCGACTCGAGGATGGGTCTGAGATTGTGAGAGGGAGG

ACTGAGTGGAGGCCGAAGTATGCGAAAAGTTTTGGTAATGTGGGCCAACTTCCTGCTGA

AAGTGCATAG,

Theobroma cacao palmitoyl-acyl carrier protein thioesterase,

chloroplastic, (TcFatB6) truncated (corresponds to nt 400-1263

of SEQ ID NO: 120), 867 nt

SEQ ID NO: 121

ATGATTGTTCAGGATGGTCTTGTTTTCCGCCAGAATTTCTCTATAAGGTCTTACGAGATAG

GTGCTGATCGGACAGCATCCATAGAGACGCTAATGAATCATTTACAGGAAACGGCTATT

AATCATTGTAGAAGCGCTGGACTGCTTGGAGAAGGTTTTGGTTCAACCCCTGAGATGTGC

AAGAAAAACCTAATATGGGTAGTCACTCGCATGCAAGTTGTGGTTGATCGCTATCCTACA

TGGGGTGATGTTGTTCAAGTAGACACTTGGGCCAGTGCATCGGGAAAGAATGGTATGCG

ACGGGATTGGCTTGTCAGTGATAGTAAAACTGGTGAAATTTTAACAAGAGCCTCAAGTGT

ATGGGTGATGATGAATAAGCTTACTAGAAGGTTATCTAAAATTCCAGAAGAGGTCCGAG

GAGAAATAGAACCTTATTTTATGAATTCTGATCCTGTTGTGGCTGAGGATAGTAGGAAAT

TAGTGAAACTTGATGACAGCACAGCAGATTATGTCCGTAAAGGTTTAACTCCCAGATGG

GGTGATTTGGATGTCAACCAGCATGTCAATAATGTGAAGTACATTGGCTGGATCCTTGAG

AGTGCTCCACTGCCAATCTTGGAGACTCACGAGCTTTCTTCAATGACACTGGAATATAGG

AGGGAGTGTGGGAGAGACGGTGTGCTGCAGTCCCTAACTGCTGTCTCTGACTCTGGTGTG

GGCAACTTGGTGAACTTTGGTGAAATCGAGTGCCAGCACTTGCTCCGACTCGAGGATGG

GTCTGAGATTGTGAGAGGGAGGACTGAGTGGAGGCCGAAGTATGCGAAAAGTTTTGGTA

ATGTGGGCCAACTTCCTGCTGAAAGTGCATAG,

In some embodiments of any of the aspects, the amino acid sequence encoded by the functional thioesterase gene comprises one of SEQ ID NOs: 16-21, 68, 70, 123-139 or an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the sequence of at least one of SEQ ID NOs: 16-21, 68, 70, 123-139, that maintains the same functions as at least one of SEQ ID NOs: 16-21, 68, 70, 123-139 (e.g., thioesterase).

Engineered chimera of C. palustris FatB1(aa 1-218) and FatB2 (aa 219-

316) thioesterase-Chimera 4 (326 aa)

SEQ ID NO: 16

MLLTAITTVFVAPEKRWTMFDRKSKRPNMLMDSFGLERVVQDGLVFRQSFSIRSYEICADRT

ASIETVMNHVQETSLNQCKSIGLLDDGFGRSPEMCKRDLIWVVTRMKIMVNRYPTWGDTIEV

STWLSQSGKIGMGRDWLISDCNTGEILVRATSVYAMMNQKTRRFSKLPHEVRQEFAPHFLDS

PPAIEDNDGKLQKFDVKTGDSIRKGLTPGWYDLDVNQHVNNVKYIGWILQSVPTEVFETQEL

CGLTLEYRRECGRDSVLESVTAMDPSKEGDRSLYQHLLRLEDGADIVKGRTEWRPKNAGAK

GAILTGKTSGGHHHHHH,

Cuphea palustris FatB1, GenBank: AAC49179.1, 411 aa; bolded text

corresponds to SEQ ID NO: 18 (e.g., residues 96-411 of SEQ ID NO: 17)

SEQ ID NO: 17

MVAAAASSACFPVPSPGASPKPGKLGNWSSSLSPSLKPKSIPNGGFQVKANASAHPKANG

SAVTLKSGSLNTQEDTLSSSPPPRAFFNQLPDWSMLLTAITTVFVAPEKRWTMFDRKSKR

PNMLMDSFGLERVVQDGLVFRQSFSIRSYEICADRTASIETVMNHVQETSLNQCKSIGLL

DDGFGRSPEMCKRDLIWVVTRMKIMVNRYPTWGDTIEVSTWLSQSGKIGMGRDWLIS

DCNTGEILVRATSVYAMMNQKTRRFSKLPHEVRQEFAPHFLDSPPAIEDNDGKLQKFDV

KTGD

SIRKGLTPGWYDLDVNQHVSNVKYIGWILESMPTEVLETQELCSLTLEYRRECGRDSVL

E

SVTSMDPSKVGDRFQYRHLLRLEDGADIMKGRTEWRPKNAGTNGAISTGKT,

Cuphea palustris FatB1, fragment, 316 aa, corresponds to bolded text

of SEQ ID NO: 17 (e.g., residues 96-411 of SEQ ID NO: 17); italicized

text corresponds to portion in SEQ ID NO: 21 (e.g., residues

1-218 of SEQ ID NO: 18)

SEQ ID NO: 18

LLTAITTVFVAPEKRWTMFDRKSKRPNMLMDSFGLERVVQDGLVFRQSFSIRSYEICADRTASIETV

MNHVQETSLNQCKSIGLLDDGFGRSPEMCKRDLIWVVTRMKIMVNRYPTWGDTIEVSTWLSQSGK

IGMGRDWLISDCNTGEILVRATSVYAMMNQKTRRFSKLPHEVRQEFAPHFLDSPPAIEDNDGKLQ

KFDVKTGDSIRKGLTPGWYDLDVNQHVSNVKYIGWILESMPTEVLETQELCSLTLEYRRECGR

DSVLESVTSMDPSKVGDRFQYRHLLRLEDGADIMKGRTEWRPKNAGTNGAISTGKT,

Cuphea palustris FatB2, GenBank: AAC49180.1, 411 aa; bolded text

corresponds to SEQ ID NO: 20 (e.g., residues 90-404 of SEQ ID NO: 19)

SEQ ID NO: 19

MVAAAASAAFFSVATPRTNISPSSLSVPFKPKSNHNGGFQVKANASAHPKANGSAVSLKS

GSLETQEDKTSSSSPPPRTFINQLPVWSMLLSAVTTVFGVAEKQWPMLDRKSKRPDMLVE

PLGVDRIVYDGVSFRQSFSIRSYEIGADRTASIETLMNMFQETSLNHCKIIGLLNDGFGR

TPEMCKRDLIWVVTKMQIEVNRYPTWGDTIEVNTWVSASGKHGMGRDWLISDCHTGE

ILI

RATSVWAMMNQKTRRLSKIPYEVRQEIEPQFVDSAPVIVDDRKFHKLDLKTGDSICNGL

T

PRWTDLDVNQHVNNVKYIGWILQSVPTEVFETQELCGLTLEYRRECGRDSVLESVTAM

DP

SKEGDRSLYQHLLRLEDGADIVKGRTEWRPKNAGAKGAILTGKT SNGNSIS,

Cuphea palustris FatB2, fragment, 315 aa, corresponds to bolded text

of SEQ ID NO: 19 (e.g., residues 90-404 of SEQ ID NO: 19); italicized

text corresponds to portion in SEQ ID NO: 21 (e.g., residues

218-315 of SEQ ID NO: 20)

SEQ ID NO: 20

LLSAVTTVFGVAEKQWPMLDRKSKRPDMLVEPLGVDRIVYDGVSFRQSFSIRSYEIGADRTA

SIETLMNMFQETSLNHCKIIGLLNDGFGRTPEMCKRDLIWVVTKMQIEVNRYPTWGDTIEVN

TWVSASGKHGMGRDWLISDCHTGEILIRATSVWAMMNQKTRRLSKIPYEVRQEIEPQFVDSA

PVIVDDRKFHKLDLKTGDSICNGLTPRWTDLDVNQHVNNVKYIGWILQSVPTEVFETQELCGLT

LEYRRECGRDSVLESVTAMDPSKEGDRSLYQHLLRLEDGADIVKGRTEWRPKNAGAKGAILTGKT,

Cuphea palustris FatB2-FatB1 hybrid, 316 aa; bolded text corresponds

to italicized text of SEQ ID NO: 18 (e.g., residues 1-218 of SEQ ID

NO: 18); and plain text corresponds to italicized text of SEQ

ID NO: 20 (e.g., residues 218-315 of SEQ ID NO: 20)

SEQ ID NO: 21

LLTAITTVFVAPEKRWTMFDRKSKRPNMLMDSFGLERVVQDGLVFRQSFSIRSYEICAD

RTASIETVMNHVQETSLNQCKSIGLLDDGFGRSPEMCKRDLIWVVTRMKIMVNRYPTW

GDTIEVSTWLSQSGKIGMGRDWLISDCNTGEILVRATSVYAMMNQKTRRFSKLPHEVR

QEFAPHFLDSPPAIEDNDGKLQKFDVKTGDSIRKGLTPGWYDLDVNQHVNNVKYIGWIL

QSVPTEVFETQELCGLTLEYRRECGRDSVLESVTAMDPSKEGDRSLYQHLLRLEDGADIVKG

RTEWRPKNAGAKGAILTGKT,

Arachis hypogaea Acyl-[acyl-carrier-protein] hydrolase OS = Arachis

hypogaea OX = 3818 GN = FatB2-1 PE = 2 SV = 1 (AhFatB2-1) Ref. No.

tr|A0A444X7E1|A0A444X7E1_ARAHY (corresponds to SEQ ID NO: 99 or 100),

414 aa

SEQ ID NO: 123

MVATAATSSFFPVTSRTGGEGGGGIPASLGGGLKQNHRSSSVKANAHAPSKINGTATKVPKS

MESMKLESSSTTGANAPRTFINQIPDWSMLLAAITTAFLAAEKQWMMIDWKPKRSDVLSDPF

GIGRIVQDGLAFRQNFSIRSYEIGADKTASIETLMNHLQETALNHVKTAGLLGDGFGSTPEMC

KKNLIWVVTRMQVEVDRYPTWGDVVQVDTWVSASGKNGMRRDWIIRDANTGEILTRASSI

WVMMNKVTRRLSKIPEEVRQEIASYFVDSPPVVEEDNRKLSKLDDTADHIRRGLSPRWSDLD

VNQHVNNVKYIGWLLESAPQAILESHELRAMTLEYRRECGKDSVLDSLTDVSGADIGNLAG

GGSLECKHLLRLEDGGEIVRGRTEWRPKPVNNFGAMNQVFPAEN,

Arachis hypogaea Acyl-[acyl-carrier-protein] hydrolase (AhFatB2-1)

truncated (corresponds to SEQ ID NO: 101 or 102; corresponds to aa

63-414 of SEQ ID NO: 123), 352 aa

SEQ ID NO: 124

MESMKLESSSTTGANAPRTFINQIPDWSMLLAAITTAFLAAEKQWMMIDWKPKRSDVLSDPF

GIGRIVQDGLAFRQNFSIRSYEIGADKTASIETLMNHLQETALNHVKTAGLLGDGFGSTPEMC

KKNLIWVVTRMQVEVDRYPTWGDVVQVDTWVSASGKNGMRRDWIIRDANTGEILTRASSI

WVMMNKVTRRLSKIPEEVRQEIASYFVDSPPVVEEDNRKLSKLDDTADHIRRGLSPRWSDLD

VNQHVNNVKYIGWLLESAPQAILESHELRAMTLEYRRECGKDSVLDSLTDVSGADIGNLAG

GGSLECKHLLRLEDGGEIVRGRTEWRPKPVNNFGAMNQVFPAEN,

Mangifera indica palmitoyl-acyl carrier protein thioesterase,

chloroplastic-like (MiFatA) Ref. No. XP_044494686.1 (corresponds

to SEQ ID NO: 103), 382 aa

SEQ ID NO: 125

MTSVACKIILSRELFKEEKKIKPMATAKVGLCSSGNLIRRKHGRHLLIASASNPNGLDMMKG

KKVNGIHHNEETHHQLLLKQRVSKAPLHACLLGRFVGDRFMYRQTFIIRSYEIGPDKTATME

TLLNLLQETALNHVTGSGLAGNGFGATREMSLRKLIWVVTRINIQVQRYSCWGDVVEIDTW

VDSSGKNAMRRDWIIRDYHTQEIITRATSTWVTMNRETRRLSKIPEQVKQEVFPFYLDRVAIA

KEQNDVGKIDKLTDETAERIRSGLAPRWNDMDANQHVNNVKYIGWILESVPIHVLKDYNMT

SMTLEYRRECRQSNLLESLTSSTASVTGDPNNNSNNRIADLKYTHLLRMQADKAEIVRARSE

WQSKQITQVIT,

Morella rubra Palmitoyl-acyl carrier protein thioesterase,

chloroplastic (MrFatA) Ref. No. KAB1217487.1 (corresponds to SEQ

ID NO: 104), 433 aa

SEQ ID NO: 126

MLETFIFCLLIRQREFEATSATLYFQTYILLGSTISRGIVYLSVQSAMTVMAALSNARLYFGGD

FCRGDKKNMAMARLGYYPSLNCAIKPKQPSLLVIASASTPPSIYTINGKKVNGINFGEAPFRS

NKYSDSAKESCVDAPLHAVLLGRFVEDQFVYRQTFIIRSYEIGPDKTATMETLMNLLQETAL

NHVTSSGLAGNGFGATREMSLRKLIWVVTRVHIQVQRYSCWGDVVEIDTWVDAEGKNGMR

RDWIIRDYHTQEIITRATSTWVIMNQETRRLSKIPEQVREEVVPFYLDRLAVSAEMNDSEKID

KLTDETAERIRSGLAPRWSDMDANQHVNNVKYIGWILESVPINVLGNYDLTSMTLEYRRECR

QSNLLESLTSSTANATEASYNSLHRSKPDLEFTHLLRMLADKAEIVRARTQWHSKQKRN,

Pistacia vera palmitoyl-acyl carrier protein thioesterase,

chloroplastic-like (PvFatA) Ref. No. XP_031247728.1 (corresponds

to SEQ ID NO: 105) 386 aa

SEQ ID NO: 127

MISVARTSYVRLSFPENLFKEEKEIVPMAMAKVGFCCSLNLIRPKHGRLLVIASASNAKSLDI

MNGKKVNGIHVNEETRHQRLLNQRVADAPLHACLLGKFVEDRFLYRQTFIVRSYEIGPDKTA

TMETLLNLLQETALNHVTSSGLAGNGFGATREMSVRKLIWVVTRINIQVQRYSCWGDVVEID

TWVDAAGKNAMRRDWIIRDYRTQEIITRATSTWVIMNRETRRLSKIPEQVRQEVLPFYLGRV

AIAKEQNDVGKIDKLTDETAERIRSGLAPRWNDMDANQHVNNVKYIGWILESVPIHVLKDY

NLTSMTLEYRRECRQSNLLESLTSSTASVTGDPNNNSNNRIADLEYTHLLRMQADKAEIVRA

RSEWQSKQITQAIT,

Theobroma cacao oleoyl-acyl carrier protein thioesterase 1,

chloroplastic ID = Tc01v2_p018360.1|Name = Tc01v2_p018360.1|

organism = Theobroma cacao|type = polypeptide|length = 375 bp

(TcFATA) Ref. No. Tc01v2_p018360.1, NCBI Reference Sequence:

XP_007049712.2 (corresponds to SEQ ID NO: 106 or 107), 375 aa

SEQ ID NO: 128

MLKLSSCNVTDQRQALAQCRFLAPPAPFSFRWRTPVVVSCSPSSRPNLSPLQVVLSGQQQAG

MELVESGSGSLADRLRLGSLTEDGLSYKEKFIVRCYEVGINKTATVETIANLLQEVGCNHAQS

VGYSTDGFATTRTMRKLHLIWVTARMHIEIYKYPAWSDVIEIETWCQSEGRIGTRRDWILKD

FGTGEVIGRATSKWVMMNQDTRRLQKVSDDVREEYLVFCPRELRLAFPEENNNSLKKIAKL

DDSFQYSRLGLMPRRADLDMNQHVNNVTYIGWVLESMPQEIIDTHELQTITLDYRRECQQD

DVVDSLTSPEQVEGTEKVSAIHGTNGSAAAREDKQDCRQFLHLLRLSSDGQEINRGRTEWRK

KPAR,

Theobroma cacao oleoyl-acyl carrier protein thioesterase 1,

chloroplastic (TcFATA) truncated (corresponds to SEQ ID NO: 108

or 109; corresponds to aa 82-375 of SEQ ID NO: 128), 295 aa

SEQ ID NO: 129

MLTEDGLSYKEKFIVRCYEVGINKTATVETIANLLQEVGCNHAQSVGYSTDGFATTRTMRKL

HLIWVTARMHIEIYKYPAWSDVIEIETWCQSEGRIGTRRDWILKDFGTGEVIGRATSKWVMM

NQDTRRLQKVSDDVREEYLVFCPRELRLAFPEENNNSLKKIAKLDDSFQYSRLGLMPRRADL

DMNQHVNNVTYIGWVLESMPQEIIDTHELQTITLDYRRECQQDDVVDSLTSPEQVEGTEKVS

AIHGTNGSAAAREDKQDCRQFLHLLRLSSDGQEINRGRTEWRKKPAR,

Theobroma cacao palmitoyl-acyl carrier protein thioesterase,

chloroplastic ID = Tc02v2_p018460.1|Name = Tc02v2_p018460.1|

organism = Theobroma cacao|type = polypeptide|length = 395 bp

(TcFatB1) Ref. No. Tc02v2_p018460.1, NCBI Reference

Sequence: XP_007044118.2 (corresponds to SEQ ID NO: 110), 395 aa

SEQ ID NO: 130

MATFSCPISFPFRCSFNGNHNHNHRVDIKINGTHTGPIKLDTLNEIAAVVKADSTPLANVHEN

GYICQEKIRQRIPTQKQLVDPYRQGLIIERGVGYRQTVVIRSYEVGPDKTATLESLLNLFQETA

LNHVWMSGLLSNGFGATHGMMRNNLIWVVSRMHVQVHHYPIWGEVVEIDTWVGASGKNG

MRRDWLIRSQATGITYARATSTWVMMNEQTRRLSKMPEEVRGEISPWFIEKQAIKEDAPEKI

VKLDDKAKYVNSDLKPKRSDLDMNHHVNNVKYVRWMLETIPDKFLESHQLSSIVLEYRREC

GSSDKVQSLCQPDEDRILANGLEQSLLENIVLASGIMLGNGHLGSLGMKTYGFTHLLQIKGDS

QNDEIVRGRTRWKKKQSTTPYST,

Theobroma cacao palmitoyl-acyl carrier protein thioesterase,

chloroplastic (TcFatB1) truncated (corresponds to SEQ ID NO: 111;

corresponds to aa 94-395 of SEQ ID NO: 130), 303 aa

SEQ ID NO: 131

MGVGYRQTVVIRSYEVGPDKTATLESLLNLFQETALNHVWMSGLLSNGFGATHGMMRNNL

IWVVSRMHVQVHHYPIWGEVVEIDTWVGASGKNGMRRDWLIRSQATGITYARATSTWVM

MNEQTRRLSKMPEEVRGEISPWFIEKQAIKEDAPEKIVKLDDKAKYVNSDLKPKRSDLDMNH

HVNNVKYVRWMLETIPDKFLESHQLSSIVLEYRRECGSSDKVQSLCQPDEDRILANGLEQSLL

ENIVLASGIMLGNGHLGSLGMKTYGFTHLLQIKGDSQNDEIVRGRTRWKKKQSTTPYST,

Theobroma cacao palmitoyl-acyl carrier protein thioesterase,

chloroplastic isoform X1 ID = Tc03v2_p010930.1|Name = Tc03v2_p010930.1|

organism = Theobroma cacao|type = polypeptide|length = 465bp (TcFatB2)

Ref. No. Tc03v2_p010930.1, NCBI Reference

Sequence: XP_017972388.1 (corresponds to SEQ ID NO: 112), 465 aa

SEQ ID NO: 132

MHQCHSNAPLFACKLTTEVSRFLPHPLEVVELQIASAPLDAGARELGTAICFFFRTRKFASLAL

FFCSRVSKCEALTMASMAKASNVTSLFLGGVCKEEKTKNVAMAKLGFYSSWNLIKPKRKGL

LLIASAKNPHNLDMINGKKVNGIFVGEAPYTGKKSTVLIKEHVPYKQAHAASLVGRFVEDRH

VYRQTFIIRSYETGPDKTATMETVMNLLQETALNHVRSSGLAGNGFGATREMSLRKLIWVVT

RIHVQVERYSCWGDVVEIDTWVDAAGKNAMRRDWIIRDYNTQEIITRATSTWVIMNHETRR

LTKIPEQVRQEVIPFYLNRIAIAEEKNDIGKIDKLTDENAERIRSGLAPRWSDMDANQHVNNV

KYIGWILESVPMDVLEEYRLTSMTLEYRRECRKSNLLESLTSSTANVTEDSNNNSNNRKADL

EYTHLLRMQDDVAEIVRARSEWQSKDKHSW,

Theobroma cacao palmitoyl-acyl carrier protein thioesterase,

chloroplastic isoform X1 (TcFatB2) truncated (corresponds to SEQ

ID NO: 113; corresponds to aa 183-465 of SEQ ID NO: 132), 284 aa

SEQ ID NO: 133

MVEDRHVYRQTFIIRSYETGPDKTATMETVMNLLQETALNHVRSSGLAGNGFGATREMSLR

KLIWVVTRIHVQVERYSCWGDVVEIDTWVDAAGKNAMRRDWIIRDYNTQEIITRATSTWVI

MNHETRRLTKIPEQVRQEVIPFYLNRIAIAEEKNDIGKIDKLTDENAERIRSGLAPRWSDMDA

NQHVNNVKYIGWILESVPMDVLEEYRLTSMTLEYRRECRKSNLLESLTSSTANVTEDSNNNS

NNRKADLEYTHLLRMQDDVAEIVRARSEWQSKDKHSW,

Theobroma cacao palmitoyl-acyl carrier protein thioesterase,

chloroplastic isoform X2, ID = Tc03v2_p010930.2|Name = Tc03v2_p010930.2|

organism = Theobroma cacao|type = polypeptide|length = 388 bp (TcFatB3)

Ref. No. Tc03v2_p010930.2 (corresponds to SEQ ID NO: 114; corresponds

to aa 78-465 of SEQ ID NO: 132), NCBI Reference Sequence:

XP_017972389.1, 388 aa

SEQ ID NO: 134

MASMAKASNVTSLFLGGVCKEEKTKNVAMAKLGFYSSWNLIKPKRKGLLLIASAKNPHNLD

MINGKKVNGIFVGEAPYTGKKSTVLIKEHVPYKQAHAASLVGRFVEDRHVYRQTFIIRSYET

GPDKTATMETVMNLLQETALNHVRSSGLAGNGFGATREMSLRKLIWVVTRIHVQVERYSC

WGDVVEIDTWVDAAGKNAMRRDWIIRDYNTQEIITRATSTWVIMNHETRRLTKIPEQVRQE

VIPFYLNRIAIAEEKNDIGKIDKLTDENAERIRSGLAPRWSDMDANQHVNNVKYIGWILESVP

MDVLEEYRLTSMTLEYRRECRKSNLLESLTSSTANVTEDSNNNSNNRKADLEYTHLLRMQD

DVAEIVRARSEWQSKDKHSW,

Theobroma cacao palmitoyl-acyl carrier protein thioesterase,

chloroplastic isoform X2, (TcFatB3) truncated (corresponds to

SEQ ID NO: 115; corresponds to aa 106-388 of SEQ ID NO: 134), 284 aa

SEQ ID NO: 135

MVEDRHVYRQTFIIRSYETGPDKTATMETVMNLLQETALNHVRSSGLAGNGFGATREMSLR

KLIWVVTRIHVQVERYSCWGDVVEIDTWVDAAGKNAMRRDWIIRDYNTQEIITRATSTWVI

MNHETRRLTKIPEQVRQEVIPFYLNRIAIAEEKNDIGKIDKLTDENAERIRSGLAPRWSDMDA

NQHVNNVKYIGWILESVPMDVLEEYRLTSMTLEYRRECRKSNLLESLTSSTANVTEDSNNNS

NNRKADLEYTHLLRMQDDVAEIVRARSEWQSKDKHSW,

Theobroma cacao palmitoyl-acyl carrier protein thioesterase,

chloroplastic isoform X3 ID=Tc03v2_p010930.3|Name = Tc03v2_p010930.3|

organism = Theobroma cacao|type = polypeptide|length = 385 bp

(TcFatB4) Ref. No. Tc03v2_p010930.3, NCBI Reference

Sequence: XP_017972390.1 (corresponds to SEQ ID NO: 116) 385 aa

SEQ ID NO: 136

MHQCHSNAPLFACKLTTEVSRFLPHPLEVVELQIASAPLDAGARELGTAICFFFRTRKFASLAL

FFCSRVSKCEALTMASMAKASNVTSLFLGGVCKEEKTKNVAMAKLGFYSSWNLIKPKRKGL

LLIASAKNPHNLDMINGKKVNGIFVGEAPYTGKKSTVLIKEHVPYKQAHAASLVGRFVEDRH

VYRQTFIIRSYETGPDKTATMETVMNLLQETALNHVRSSGLAGNGFGATREMSLRKLIWVVT

RIHVQVERYSCWGDVVEIDTWVDAAGKNAMRRDWIIRDYNTQEIITRATSTWVIMNHETRR

LTKIPEQVRQEVIPFYLNRIAIAEEKNDIGKIDKLTDENAERIRSGLAPRWSDMDANQHVNNV

KYIGWILEAFTN,

Theobroma cacao palmitoyl-acyl carrier protein thioesterase,

chloroplastic isoform X3 (TcFatB4) truncated (corresponds to SEQ

ID NO: 117; corresponds to aa 183-385 of SEQ ID NO: 136), 204 aa

SEQ ID NO: 137

MVEDRHVYRQTFIIRSYETGPDKTATMETVMNLLQETALNHVRSSGLAGNGFGATREMSLR

KLIWVVTRIHVQVERYSCWGDVVEIDTWVDAAGKNAMRRDWIIRDYNTQEIITRATSTWVI

MNHETRRLTKIPEQVRQEVIPFYLNRIAIAEEKNDIGKIDKLTDENAERIRSGLAPRWSDMDA

NQHVNNVKYIGWILEAFTN,

Theobroma cacao palmitoyl-acyl carrier protein thioesterase,

chloroplastic, ID = Tc06v2_p006710.1|Name = Tc06v2_p006710.1|

organism = Theobroma cacao|type = polypeptide|length = 376 bp

(TcFatB5) Ref. No. Tc06v2_p006710.1, NCBI Reference Sequence:

XP_007024037.2 (corresponds to SEQ ID NO: 118), 376 aa

SEQ ID NO: 138

MAASSNIMTSKFFMATSPSSWNSTNKSKICLQQIDRSSNTNGKMVKFTRDSSLKVKLQAQAL

LTNDSRATSMIESLKDEEMMTSPPATMEHLTTEGRLINDGLVFQQNFSIRSFEIDSEYKVSARA

IMNYLQESSLNHRKKMGMSSDSLVGVTPEMIKRDLLWIFRGMCIEVDRYPSWADVVQIYHRI

YTSGRTGLRLEWIVNDSKTGETLVRASCLAVMMNKKTRKTCKFPEEVKQELKPYLTTDAEP

LFEADKILCPQVGKMDNIRTGLTSCWHDLDFNYHVNNAKYLDWILEGTPTSLIHSHELSRVS

LQYRKECLKDDVIQSLSRVVTKETGLSTNNQEIELEHVLRLESGPELAGARTAWRPKSICRQT

IN

Theobroma cacao palmitoyl-acyl carrier protein thioesterase,

chloroplastic, (TcFatB5) truncated (corresponds to SEQ ID NO: 119;

corresponds to aa 98-376 of SEQ ID NO: 138), 280 aa

SEQ ID NO: 139

MLINDGLVFQQNFSIRSFEIDSEYKVSARAIMNYLQESSLNHRKKMGMSSDSLVGVTPEMIKR

DLLWIFRGMCIEVDRYPSWADVVQIYHRIYTSGRTGLRLEWIVNDSKTGETLVRASCLAVM

MNKKTRKTCKFPEEVKQELKPYLTTDAEPLFEADKILCPQVGKMDNIRTGLTSCWHDLDFN

YHVNNAKYLDWILEGTPTSLIHSHELSRVSLQYRKECLKDDVIQSLSRVVTKETGLSTNNQEI

ELEHVLRLESGPELAGARTAWRPKSICRQTIN,

Theobroma cacao palmitoyl-acyl carrier protein thioesterase,

chloroplastic, ID = Tc09v2_p009980.1|Name = Tc09v2_p009980.1|organism =

Theobroma cacao|type = polypeptide|length = 420 bp (TcFatB6)

Ref. No. Tc09v2_p009980.1, NCBI Reference Sequence: XP_007013278.2

(corresponds to SEQ ID NO: 120), 420 aa

SEQ ID NO: 68

MVATAASSAFFPVTSSPDSSDSKNKKLGSGSTNLGGIKSKPSTPSGILQVKANAQAPPKINGTT

VVTTPVESFKNEDTASSPPPRTFINQLPDWSMLLAAITTIFLAAEKQWMMLDWKPRRPDMLI

DPFGIGRIVQDGLVFRQNFSIRSYEIGADRTASIETLMNHLQETAINHCRSAGLLGEGFGSTPE

MCKKNLIWVVTRMQVVVDRYPTWGDVVQVDTWASASGKNGMRRDWLVSDSKTGEILTR

ASSVWVMMNKLTRRLSKIPEEVRGEIEPYFMNSDPVVAEDSRKLVKLDDSTADYVRKGLTP

RWGDLDVNQHVNNVKYIGWILESAPLPILETHELSSMTLEYRRECGRDGVLQSLTAVSDSGV

GNLVNFGEIECQHLLRLEDGSEIVRGRTEWRPKYAKSFGNVGQLPAESA,

Theobroma cacao palmitoyl-acyl carrier protein thioesterase,

chloroplastic, (TcFatB6) truncated (corresponds to SEQ ID NO: 121;

corresponds to aa 134-420 of SEQ ID NO: 68), 288 aa

SEQ ID NO: 70

MIVQDGLVFRQNFSIRSYEIGADRTASIETLMNHLQETAINHCRSAGLLGEGFGSTPEMCKKN

LIWVVTRMQVVVDRYPTWGDVVQVDTWASASGKNGMRRDWLVSDSKTGEILTRASSVWV

MMNKLTRRLSKIPEEVRGEIEPYFMNSDPVVAEDSRKLVKLDDSTADYVRKGLTPRWGDLD

VNQHVNNVKYIGWILESAPLPILETHELSSMTLEYRRECGRDGVLQSLTAVSDSGVGNLVNF

GEIECQHLLRLEDGSEIVRGRTEWRPKYAKSFGNVGQLPAESA,

In some embodiments of any of the aspects, the functional heterologous thioesterase is from a bacterial species (e.g., Marvinbryantia formatexigens or Limosilactobacillus reuteri). In some embodiments of any of the aspects, the functional heterologous thioesterase gene comprises a Marvinbryantia thioesterase gene. In some embodiments of any of the aspects, the functional heterologous thioesterase gene comprises a Limosilactobacillus thioesterase gene. In some embodiments of any of the aspects, the functional heterologous thioesterase gene comprises a Marvinbryantia formatexigens thioesterase gene. In some embodiments of any of the aspects, the functional heterologous thioesterase gene comprises a Limosilactobacillus reuteri thioesterase gene. In some embodiments of any of the aspects, the engineered bacterium comprises at least one exogenous copy of at least one functional thioesterase gene comprising one of SEQ ID NOs: 22-23, SEQ ID NO: 98, or a nucleic acid sequence that is at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the sequence of one of SEQ ID NOs: 22-23 or SEQ ID NO: 98, that maintains the same functions as one of SEQ ID NO: 22-23 or SEQ ID NO: 98 (e.g., thioesterase).

In some embodiments of any of the aspects, the amino acid sequence encoded by the functional thioesterase gene comprises one of SEQ ID NO: 24, SEQ ID NO: 122, or an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the sequence of SEQ ID NO: 24 or SEQ ID NO: 122, that maintains the same functions as SEQ ID NO: 24 or SEQ ID NO: 122 (e.g., thioesterase).

Marvinbryantia formatexigens thioesterase (MfTE), Marvinbryantia

formatexigens DSM 14469 B_formatexigens-1.0.1_Cont6.1, whole genome

shotgun sequence, GenBank: ACCL02000007.1, REGION: 41936-42652, 717 bp

SEQ ID NO: 22

ATGATTTATATGGCATATCAATACCGCAGCCGCATCCGCTACAGCGAAATTGGCGAGGA

CAAAAAGCTTACGCTGCCCGGTCTGGTGAATTATTTCCAGGACTGCAGCACCTTCCAGTC

GGAGGCACTCGGCATAGGGCTGGACACGCTGGGAGCGCGCCAGCGGGCATGGCTTCTGG

CGTCCTGGAAAATTGTAATAGACAGGCTGCCGCGGCTTGGGGAGGAGGTTGTGACGGAG

ACCTGGCCATATGGCTTTAAGGGCTTCCAGGGAAACCGCAACTTCCGTATGCTGGACCAG

GAGGGACATACACTGGCTGCAGCGGCATCCGTCTGGATTTATTTAAATGTGGAAAGCGG

GCATCCGTGCCGGATTGACGGGGATGTTCTGGAGGCATATGAGCTGGAAGAGGAGCTGC

CGCTCGGTCCGTTTTCGCGCAAGATTCCGGTTCCGGAGGAAAGCACGGAGCGGGACAGC

TTTCTGGTGATGCGCAGTCACCTGGACACCAATCACCATGTCAACAACGGGCAGTATATA

CTGATGGCGGAGGAATATCTGCCGGAGGGCTTTAAAGTAAAGCAGATACGCGTGGAGTA

CCGCAAAGCCGCCGTTCTGCACGATACGATTGTGCCGTTTGTGTGCACAGAGCCGCAGCG

CTGCACGGTCAGCCTTTGCGGAAGTGATGAAAAGCCGTTTGCCGTCGTAGAATTTTCGGA

ATAA,

CnDNA_MfTE, codon-optimized, 714 bp

SEQ ID NO: 23

ATGATCTACATGGCCTACCAGTACCGCTCGCGCATCCGCTACTCGGAGATCGGCGAGGAC

AAGAAGCTGACCCTGCCGGGCCTGGTGAACTACTTCCAGGACTGCTCGACCTTCCAGTCG

GAGGCCCTGGGCATCGGCCTGGACACCCTGGGCGCCCGCCAGCGCGCCTGGCTGCTGGC

CTCGTGGAAGATCGTGATCGACCGCCTGCCGCGCCTGGGCGAGGAGGTGGTGACCGAGA

CCTGGCCGTACGGCTTCAAGGGCTTCCAGGGCAACCGCAACTTCCGCATGCTGGACCAG

GAGGGCCACACCCTGGCCGCCGCCGCCTCGGTGTGGATCTACCTGAACGTGGAGTCGGG

CCACCCGTGCCGCATCGACGGCGACGTGCTGGAGGCCTACGAGCTGGAGGAGGAGCTGC

CGCTGGGCCCGTTCTCGCGCAAGATCCCGGTGCCGGAGGAGTCGACCGAGCGCGACTCG

TTCCTGGTGATGCGCTCGCACCTGGACACCAACCACCACGTGAACAACGGCCAGTACATC

CTGATGGCCGAGGAGTACCTGCCGGAGGGCTTCAAGGTGAAGCAGATCCGCGTGGAGTA

CCGCAAGGCCGCCGTGCTGCACGACACCATCGTGCCGTTCGTGTGCACCGAGCCGCAGC

GCTGCACCGTGTCGCTGTGCGGCTCGGACGAGAAGCCGTTCGCCGTGGTGGAGTTCTCGG

AG,

Acyl-ACP thioesterase [Marvinbryantia formatexigens DSM 14469],

GenBank: EET61113.1, 238 aa (corresponds to SEQ ID NOs: 22-23)

SEQ ID NO: 24

MIYMAYQYRSRIRYSEIGEDKKLTLPGLVNYFQDCSTFQSEALGIGLDTLGARQRAWLLASW

KIVIDRLPRLGEEVVTETWPYGFKGFQGNRNFRMLDQEGHTLAAAASVWIYLNVESGHPCRI

DGDVLEAYELEEELPLGPFSRKIPVPEESTERDSFLVMRSHLDTNHHVNNGQYILMAEEYLPE

GFKVKQIRVEYRKAAVLHDTIVPFVCTEPQRCTVSLCGSDEKPFAVVEFSE,

Limosilactobacillus reuteri (also referred to as Lactobacillus reuteri)

Acyl-ACP thioesterase (LreuTE), NC_009513, region: 379328-380089, 762 nt

SEQ ID NO: 98

ATGGAGTTAAAGCAAGAAGCACAAACATTCGAAATGCCGCACTTACTAACATATTATGA

GTGTGATGAAACAAGTCATCCAAGCCTAAGCATGATATTAAGTATGATTTCCATGGTATC

CGATGAGCATAGTATGTCTTTAGGAATGGGCACCAAAGAAATACAATCTACTGGCGGTA

CATGGGTAGTAAGCGGCTATGAAGGACATCTTTCCGCAAAGCAACCTTCTTTTGGCGAAA

CAGTTATTTTAGGAACAAAAGCTGTTTCCTATAACCGCTTTTTTGCTGTTCGTGATTTTTG

GATAACGGGTAAAGAACACCAGATTGAATATGCACGAATTAGGTCGATTTTTGTGTTTAT

GAATCTAAAGACGCGGCGAATGCAATCAATTCCACCAGCTTTAATTGAACCGTTTAATGC

TCCCGTTGCGAAAAGAATTCCTCGTCTAAAGCGACCTCAAAAATTGGATGAAAATGCTTC

GGTAATAAAGAAGAATTATCAAGTTCGTTATTTTGACCTTGATGCTAATCACCATGTTAA

TAATGCTCGTTACTTTGATTGGCTTCTTGATCCTCTTGGCCGTGATTTTTTACGCGGAAAT

CAGATAAAGAGATTTAATTTGCAGTATCTTCAAGAGGTACGCAATGGAGAAATGGTAGA

AAGTAAAGTTAATAAGCTTCAAACAAATGATGAAAAGGTAACTTATCATCAGATTGGTG

TTGGTGAGCAAATTGATGCAATTGCTGAGATAGAATGGTATTAA,

Limosilactobacillus reuteri (also referred to as Lactobacillus reuteri)

Acyl-ACP thioesterase, OS = Lactobacillus reuteri (strain DSM 20016)

OX = 557436 GN = Lreu_0335 PE = 3 SV = 1 (LreuTE) Ref. No.

tr|A5VID1|A5VID1_LACRD, NCBI Reference Sequence: WP_003667392.1

(corresponds to SEQ ID NO: 98), 253 aa

SEQ ID NO: 122

MELKQEAQTFEMPHLLTYYECDETSHPSLSMILSMISMVSDEHSMSLGMGTKEIQSTGGTWV

VSGYEGHLSAKQPSFGETVILGTKAVSYNRFFAVRDFWITGKEHQIEYARIRSIFVFMNLKTR

RMQSIPPALIEPFNAPVAKRIPRLKRPQKLDENASVIKKNYQVRYFDLDANHHVNNARYFDW

LLDPLGRDFLRGNQIKRFNLQYLQEVRNGEMVESKVNKLQTNDEKVTYHQIGVGEQIDAIAE

IEWY,

In some embodiments of any of the aspects, the engineered bacterium comprises a Cuphea palustris FatB1 gene or polypeptide (e.g., SEQ ID NOs: 9, 17, 18), a Cuphea palustris FatB2 gene or polypeptide (e.g., SEQ ID NOs: 10, 19, 20), a Cuphea palustris FatB2-FatB1 hybrid gene or polypeptide (e.g., SEQ ID NOs: 11, 16, 21), a Marvinbryantia formatexigens thioesterase gene or polypeptide (e.g., SEQ ID NOs: 22-24), a Limosilactobacillus reuteri thioesterase gene or polypeptide (e.g., SEQ ID NOs: 98, 122), a Arachis hypogaea thioesterase gene or polypeptide (e.g., SEQ ID NOs: 99-102, 123-124), a Mangifera indica thioesterase gene or polypeptide (e.g., SEQ ID NOs: 103, 125), a Morella rubra thioesterase gene or polypeptide (e.g., SEQ ID NOs: 104, 126), a Pistacia vera thioesterase gene or polypeptide (e.g., SEQ ID NOs: 105, 127), or a Theobroma cacao thioesterase gene or polypeptide (e.g., SEQ ID NOs: 68, 70 106-121, 128-139).

In some embodiments of any of the aspects, the engineered bacterium comprises at least one exogenous copy of at least one functional acyltransferase gene. An acyltransferase is a type of transferase enzyme that acts upon acyl groups. In general, acyltransferases share the ability to transfer thioester-activated acyl substrates to a hydroxyl or amine acceptor to form an ester or amide bond. Non-limiting examples of acyltransferases that can be used for TAG synthesis in the engineered bacteria described herein include diglyceride acyltransferase (DGAT), wax synthase (WS), a hybrid of a DGAT and a WS, lysophosphatidic acid acyltransferase (LPAT), and glycerol-3-phosphate acyltransferase (GPAT) (see e.g., FIG. 6). In some embodiments of any of the aspects, the acyltransferase catalyzes transesterification of the sn3 OH group, the sn2 OH group, or the sn1 OH group of a TAG precursor (e.g., diacylglycerol, lysophosphatidic acid, or glyceraldehyde-3-phosphate) with a fatty acid. In some embodiments of any of the aspects, the fatty acid is esterified with acyl carrier protein (ACP) or with acetyl-CoA. In some embodiments of any of the aspects, the acetyltransferase is a bacterial acetyltransferase. In some embodiments of any of the aspects, the acetyltransferase is a plant acetyltransferase. In some embodiments of any of the aspects, an acyltransferase polypeptide as described herein (e.g., DGAT, WS, DGAT-WS hybrid, LPAT, or GPAT) is truncated to remove an organelle targeting sequence(s); in some embodiments, such a targeting sequence can contribute to poor expression of the acyltransferase polypeptide, e.g., in the engineered bacteria described herein. See e.g., Table 7 for exemplary combinations of exogenous acyltransferase(s) in the engineered bacteria.

TABLE 7

Exemplary combinations of exogenous acyltransferase

DGAT-WS

DGAT
LPAT
GPAT
WS
hybrid

X

X

X
X

X

X

X

X
X

X
X
X

X

X

X

X

X

X
X

X

X
X

X

X
X

X
X
X

X
X
X
X

X

X

X

X

X

X
X

X

X

X

X

X

X

X
X

X

X
X
X

X

X
X

X

X
X

X

X
X

X
X

X
X

X
X
X

X

X
X
X

X
X
X
X

X
X
X
X
X

In some embodiments of any of the aspects, the acyltransferase catalyzes transesterification of the sn3 OH group of diacylglycerol with a fatty acid. As a non-limiting example, such an acyltransferase is diglyceride acyltransferase (DGAT; E.C. 2.3.1.20; also referred to as O-acyltransferase or acyl-CoA:diacylglycerol acyltransferase). DGAT catalyzes the formation of triglycerides from diacylglycerol and Acyl-CoA. The reaction catalyzed by DGAT is considered the terminal and only committed step in triglyceride synthesis. In competition assays, DGATs can show preferences for fatty acyl-CoA substrates of specific chain length and desaturation. In some embodiments of any of the aspects, the functional DGAT gene preferentially produces or leads to the production of TAGs comprising a specific type of fatty acid R group (e.g., C16). As such, the functional DGAT gene can be selected from any DGAT gene from any species that preferentially produces or leads to the production of TAGs comprising a specific type of fatty acid R group (e.g., C16). In some embodiments of any of the aspects, the DGAT is a bacterial DGA T. In some embodiments of any of the aspects, the DGAT is a plant DGAT.

In some embodiments of any of the aspects, the acyltransferase is a wax synthase. In some embodiments of any of the aspects, the acyltransferase comprises a wax synthase. In some embodiments of any of the aspects, the DGAT comprises a wax synthase. In some embodiments of any of the aspects, the DGAT is a bifunctional Wax Ester Synthase/Diacylglycerol Acyltransferase (WS/DGAT), which can also be referred to as a DGAT-WS hybrid. A wax synthase can also be referred to herein as acyl-CoA:long-chain-alcohol O-acyltransferase, wax-ester synthase, or a long-chain-alcohol O-fatty-acyltransferase (EC 2.3.1.75). A wax synthase is an enzyme that catalyzes the chemical reaction acyl-CoA+a long-chain alcohol→CoA+a long-chain ester. Thus, the two substrates of this enzyme are acyl-CoA and long-chain alcohol, whereas its two products are CoA and long-chain ester. This enzyme belongs to the family of transferases, specifically those acyltransferases transferring groups other than aminoacyl groups. In general, wax synthases naturally accept acyl groups with carbon chain lengths of C16 or C18 and linear alcohols with carbon chain lengths ranging from C12 to C20.

In some embodiments of any of the aspects, the engineered bacterium comprises at least one exogenous copy of at least one functional DGAT gene. In some embodiments of any of the aspects, the engineered bacterium does not comprise a functional endogenous DGAT gene. In some embodiments of any of the aspects, the functional DGAT gene is heterologous. In some embodiments of any of the aspects, the functional heterologous DGAT gene comprises a Acinetobacter DGAT gene. In some embodiments of any of the aspects, the functional heterologous DGAT gene comprises a Thermomonospora DGAT gene. In some embodiments of any of the aspects, the functional heterologous DGAT gene comprises a Theobroma DGAT gene. In some embodiments of any of the aspects, the functional heterologous DGAT gene comprises a Rhodococcus DGAT gene.

In some embodiments of any of the aspects, the functional heterologous DGAT gene comprises a Acinetobacter baylyi DGAT gene, a Thermomonospora curvata DGAT gene, a Theobroma cacao DGAT gene, or a Rhodococcus opacus DGAT gene. In some embodiments of any of the aspects, the engineered bacterium comprises at least one exogenous copy of at least one functional DGAT gene comprising one of SEQ ID NOs: 25-28 or SEQ ID NOs: 37-45, or a nucleic acid sequence that is at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the sequence of at least one of SEQ ID NOs: 25-28 or SEQ ID NOs: 37-45, that maintains the same functions as at least one of SEQ ID NOs: 25-28 or SEQ ID NOs: 37-45 (e.g., diglyceride acyltransferase).

In some embodiments of any of the aspects, the amino acid sequence encoded by the functional DGAT gene comprises one of SEQ ID NOs: 29-30 or SEQ ID NOs: 46-51, or an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the sequence of at least one of SEQ ID NOs: 29-30 or SEQ ID NOs: 46-51, that maintains the same functions as at least one of SEQ ID NOs: 29-30 or SEQ ID NOs: 46-51 (e.g., diglyceride acyltransferase).

Acinetobacter baylyi dgaT (AbDGAT), bifunctional wax ester

synthase/diacylglycerol acyltransferase (Acinetobacter baylyi ADP1),

Gene ID: 45233297, NCBI Reference Sequence: NC_005966.1, REGION:

complement (819360-820736), 1377 bp

SEQ ID NO: 25

ATGCGCCCATTACATCCGATTGATTTTATATTCCTGTCACTAGAAAAAAGACAACAGCCT

ATGCATGTAGGTGGTTTATTTTTGTTTCAGATTCCTGATAACGCCCCAGACACCTTTATTC

AAGATCTGGTGAATGATATCCGGATATCAAAATCAATCCCTGTTCCACCATTCAACAATA

AACTGAATGGGCTTTTTTGGGATGAAGATGAAGAGTTTGATTTAGATCATCATTTTCGTC

ATATTGCACTGCCTCATCCTGGTCGTATTCGTGAATTGCTTATTTATATTTCACAAGAGCA

CAGTACGCTGCTAGATCGGGCAAAGCCCTTGTGGACCTGCAATATTATTGAAGGAATTGA

AGGCAATCGTTTTGCCATGTACTTCAAAATTCACCATGCGATGGTCGATGGCGTTGCTGG

TATGCGGTTAATTGAAAAATCACTCTCCCATGATGTAACAGAAAAAAGTATCGTGCCACC

TTGGTGTGTTGAGGGAAAACGTGCAAAGCGCTTAAGAGAACCTAAAACAGGTAAAATTA

AGAAAATCATGTCTGGTATTAAGAGTCAGCTTCAGGCGACACCCACAGTCATTCAAGAG

CTTTCTCAGACAGTATTTAAAGATATTGGACGTAATCCTGATCATGTTTCAAGCTTTCAGG

CGCCTTGTTCTATTTTGAATCAGCGTGTGAGCTCATCGCGACGTTTTGCAGCACAGTCTTT

TGACCTAGATCGTTTTCGTAATATTGCCAAATCGTTGAATGTGACCATTAATGATGTTGTA

CTAGCGGTATGTTCTGGTGCATTACGTGCGTATTTGATGAGTCATAATAGTTTGCCTTCAA

AACCATTAATTGCCATGGTTCCAGCCTCTATTCGCAATGACGATTCAGATGTCAGCAACC

GTATTACGATGATTCTGGCAAATTTGGCAACCCACAAAGATGATCCTTTACAACGTCTTG

AAATTATCCGCCGTAGTGTTCAAAACTCAAAGCAACGCTTCAAACGTATGACCAGCGATC

AGATTCTAAATTATAGTGCTGTCGTATATGGCCCTGCAGGACTCAACATAATTTCTGGCA

TGATGCCAAAACGCCAAGCCTTCAATCTGGTTATTTCCAATGTGCCTGGCCCAAGAGAGC

CACTTTACTGGAATGGTGCCAAACTTGATGCACTCTACCCAGCTTCAATTGTATTAGACG

GTCAAGCATTGAATATTACAATGACCAGTTATTTAGATAAACTTGAAGTTGGTTTGATTG

CATGCCGTAATGCATTGCCAAGAATGCAGAATTTACTGACACATTTAGAAGAAGAAATT

CAACTATTTGAAGGCGTAATTGCAAAGCAGGAAGATATTAAAACAGCCAATTAA,

CnDNA_AbDGAT, codon-optimized, 1374 bp

SEQ ID NO: 26

ATGCGCCCGCTGCACCCGATCGACTTCATCTTCCTGTCGCTGGAGAAGCGCCAGCAGCCG

ATGCACGTGGGCGGCCTGTTCCTGTTCCAGATCCCGGACAACGCCCCGGACACCTTCATC

CAGGACCTGGTGAACGACATCCGCATCTCGAAGTCGATCCCGGTGCCGCCGTTCAACAA

CAAGCTGAACGGCCTGTTCTGGGACGAGGACGAGGAGTTCGACCTGGACCACCACTTCC

GCCACATCGCCCTGCCGCACCCGGGCCGCATCCGCGAGCTGCTGATCTACATCTCGCAGG

AGCACTCGACCCTGCTGGACCGCGCCAAGCCGCTGTGGACCTGCAACATCATCGAGGGC

ATCGAGGGCAACCGCTTCGCCATGTACTTCAAGATCCACCACGCCATGGTGGACGGCGT

GGCCGGCATGCGCCTGATCGAGAAGTCGCTGTCGCACGACGTGACCGAGAAGTCGATCG

TGCCGCCGTGGTGCGTGGAGGGCAAGCGCGCCAAGCGCCTGCGCGAGCCGAAGACCGGC

AAGATCAAGAAGATCATGTCGGGCATCAAGTCGCAGCTGCAGGCCACCCCGACCGTGAT

CCAGGAGCTGTCGCAGACCGTGTTCAAGGACATCGGCCGCAACCCGGACCACGTGTCGT

CGTTCCAGGCCCCGTGCTCGATCCTGAACCAGCGCGTGTCGTCGTCGCGCCGCTTCGCCG

CCCAGTCGTTCGACCTGGACCGCTTCCGCAACATCGCCAAGTCGCTGAACGTGACCATCA

ACGACGTGGTGCTGGCCGTGTGCTCGGGCGCCCTGCGCGCCTACCTGATGTCGCACAACT

CGCTGCCGTCGAAGCCGCTGATCGCCATGGTGCCGGCCTCGATCCGCAACGACGACTCG

GACGTGTCGAACCGCATCACCATGATCCTGGCCAACCTGGCCACCCACAAGGACGACCC

GCTGCAGCGCCTGGAGATCATCCGCCGCTCGGTGCAGAACTCGAAGCAGCGCTTCAAGC

GCATGACCTCGGACCAGATCCTGAACTACTCGGCCGTGGTGTACGGCCCGGCCGGCCTG

AACATCATCTCGGGCATGATGCCGAAGCGCCAGGCCTTCAACCTGGTGATCTCGAACGTG

CCGGGCCCGCGCGAGCCGCTGTACTGGAACGGCGCCAAGCTGGACGCCCTGTACCCGGC

CTCGATCGTGCTGGACGGCCAGGCCCTGAACATCACCATGACCTCGTACCTGGACAAGCT

GGAGGTGGGCCTGATCGCCTGCCGCAACGCCCTGCCGCGCATGCAGAACCTGCTGACCC

ACCTGGAGGAGGAGATCCAGCTGTTCGAGGGCGTGATCGCCAAGCAGGAGGACATCAAG

ACCGCCAAC,

Thermomonospora curvata DGAT (TcDGAT), Thermomonospora

curvata DSM 43183, complete sequence, NC_013510 REGION complement

(4367068-4368516), 1449 bp

SEQ ID NO: 27

ATGCGCCAGCTGACGGCGGTGGACGCCAACTTCCTGAACGTCGAGACCGGCACCACGCA

CGCCCATATCGCCGGCCTGGGGATCCTCGACCCGGTCGCCTGCCCCGGCGGCCGGCTCAC

CGCCGAGGACCTCATCGAGGTGATCCGCGAACGCGCCCACCTGGCCCCCCGGCCGCTGC

GGATGCGGCTGGCCGCGGTGCCGCTGGGCATCGACCGGCCCTACTGGGAGGACGACCCG

GACTTCGACCCGGCCCGCCACGTCTTCGAGGTGGGGCTGCCGGCCCCGGGCAACGCCGC

CCAGCTCGCCGACGTCGTGGCGATGCTGCACGAACGGCCGCTGGACCGCGCCCGGCCGC

TGTGGGAGGCGGTGGTCATCCAGGGCCTGGAGGGCGGCCGCACCGCCGTCTACATCAAG

GTCCACCACGCCGCGGTGGACGGGGTCCTGGCCACCGAGACCCTGGCCGCCCTGCTGGA

CCTGTCCCCGCAGCCGCGCGAGCTGCCCCCCGACGACACCGTGCCGCAGCAGGCGCCGG

CCCTGGCCGAACGGGTGCGCACCGGGCTGCTGCGCGCGCTCGCCCACCCGGTGCGCGGC

GCCCGCATGCTGGCCCGCACCGCCCCCTACCTGGATGAGATCCCCGGCCTTGCGCAACTG

CCGGGAGTGCAGCCGCTGGCCCGGGCGATCCAGGGGGCGCTCGGCCGCGACGGCGTCGT

GCCGCTGCCCCGCACCGTCGCCCCGCCCACCCCGTTCAACGGGACGATCAGCGCCCGCCG

GGCGGTGGCCTTCGGCGAGCTGCCGCTGGCGGAGATCCGGCGCATCCGCCGGGAGCTGG

GCGGCAGCGTCAACGACGTGGTGATGGCGCTGGTGGCCACGGCGCTGCACCGCTGGCTG

GACAAGCGCGGCGAGCTGCCCGACCGGCCGCTGGTGGCGGCGGTGCCGGTGTCGCTGCG

CCGCGGCCGGGACGGCGATGCGGCGGGCGGCAACCGGATGTCGGCGATGGTGACGCCGC

TGGCCACCCATCTGGCCGACCCGGCCGAGCGCTTCGCCGCGATCCGCGGCGACCTGGCG

GCGGCCAAACGGCGCTTCGCCCGCTCCTCGGGCGCCTGGCTGGAGGGGCTGAGCGAACT

GGTGCCCGCCCCGCTGGCCGGCCCGCTGCTGCGGCTGGCCCTGCAGGCCCGGCCGGGCG

AGTACCTGCGCCCGGTCAATCTGCTGGTCTCCAACGTGCCCGGCCCGGACTTCCCGCTGT

ACCTGCGCGGCGCCCGGGTGCTCGGCTACTTCCCGATCTCGGTGGTCAGCGACCTGACCG

GCGGGCTGAACATCACCGTGCTGTCCTATGACGGCAAGCTCGACGTCGGCATCGTGACCT

GCCGCCAGATGATCCCCGACCCCTGGGAGATCATGGACCACCTCGACGACGCCCTGGGG

GAGCTGAGGGGCCTCATCGACGGCTGA,

CnDNA_TcDGAT, codon-optimized, 1446 bp

SEQ ID NO: 28

ATGCGCCAGCTGACCGCCGTGGACGCCAACTTCCTGAACGTGGAGACCGGCACCACCCA

CGCCCACATCGCCGGCCTGGGCATCCTGGACCCGGTGGCCTGCCCGGGCGGCCGCCTGA

CCGCCGAGGACCTGATCGAGGTGATCCGCGAGCGCGCCCACCTGGCCCCGCGCCCGCTG

CGCATGCGCCTGGCCGCCGTGCCGCTGGGCATCGACCGCCCGTACTGGGAGGACGACCC

GGACTTCGACCCGGCCCGCCACGTGTTCGAGGTGGGCCTGCCGGCCCCGGGCAACGCCG

CCCAGCTGGCCGACGTGGTGGCCATGCTGCACGAGCGCCCGCTGGACCGCGCCCGCCCG

CTGTGGGAGGCCGTGGTGATCCAGGGCCTGGAGGGCGGCCGCACCGCCGTGTACATCAA

GGTGCACCACGCCGCCGTGGACGGCGTGCTGGCCACCGAGACCCTGGCCGCCCTGCTGG

ACCTGTCGCCGCAGCCGCGCGAGCTGCCGCCGGACGACACCGTGCCGCAGCAGGCCCCG

GCCCTGGCCGAGCGCGTGCGCACCGGCCTGCTGCGCGCCCTGGCCCACCCGGTGCGCGG

CGCCCGCATGCTGGCCCGCACCGCCCCGTACCTGGACGAGATCCCGGGCCTGGCCCAGCT

GCCGGGCGTGCAGCCGCTGGCCCGCGCCATCCAGGGCGCCCTGGGCCGCGACGGCGTGG

TGCCGCTGCCGCGCACCGTGGCCCCGCCGACCCCGTTCAACGGCACCATCTCGGCCCGCC

GCGCCGTGGCCTTCGGCGAGCTGCCGCTGGCCGAGATCCGCCGCATCCGCCGCGAGCTG

GGCGGCTCGGTGAACGACGTGGTGATGGCCCTGGTGGCCACCGCCCTGCACCGCTGGCT

GGACAAGCGCGGCGAGCTGCCGGACCGCCCGCTGGTGGCCGCCGTGCCGGTGTCGCTGC

GCCGCGGCCGCGACGGCGACGCCGCCGGCGGCAACCGCATGTCGGCCATGGTGACCCCG

CTGGCCACCCACCTGGCCGACCCGGCCGAGCGCTTCGCCGCCATCCGCGGCGACCTGGCC

GCCGCCAAGCGCCGCTTCGCCCGCTCGTCGGGCGCCTGGCTGGAGGGCCTGTCGGAGCT

GGTGCCGGCCCCGCTGGCCGGCCCGCTGCTGCGCCTGGCCCTGCAGGCCCGCCCGGGCG

AGTACCTGCGCCCGGTGAACCTGCTGGTGTCGAACGTGCCGGGCCCGGACTTCCCGCTGT

ACCTGCGCGGCGCCCGCGTGCTGGGCTACTTCCCGATCTCGGTGGTGTCGGACCTGACCG

GCGGCCTGAACATCACCGTGCTGTCGTACGACGGCAAGCTGGACGTGGGCATCGTGACC

TGCCGCCAGATGATCCCGGACCCGTGGGAGATCATGGACCACCTGGACGACGCCCTGGG

CGAGCTGCGCGGCCTGATCGACGGC,

Theobroma cacao TcDGAT1, GenBank: KX982582.1, 1506 nt

SEQ ID NO: 37

ATGGCCATTTCTGATTCCCCAGAAATTTTGGGTTCTACTGCTACTGTTACCTCCTCTTCTC

ATTCCGATTCTGATTTGAACTTGTTGTCCATCAGAAGAAGAACTTCTACTACTGCTGCTGG

TAGAGCACCAGATAGAGATGATTCTGGTAATGGTGAAGCTGTTGATGATAGAGATCAAG

TTGAATCCGCTAACTTGATGTCTAACGTTGCTGAAAATGCTAACGAAATGCCAAACTCTT

CTGATACCAGATTCACTTACAGACCAAGAGTTCCAGCTCACAGAAGAATCAAAGAATCT

CCATTATCTTCCGGTGCCATCTTCAAACAATCTCATGCTGGTTTGTTCAACTTGTGCATCG

TTGTTTTGGTTGCCGTTAACTCCAGATTGATCATCGAAAACTTGATGAAGTACGGTTGGTT

GATCAGATCTGGTTTTTGGTTCTCTTCCAGATCTTTGTCTGATTGGCCATTATTCATGTGTT

GTTTGACCTTGCCAATTTTCCCATTGGCTGCTTTTGTTGTTGAAAAGTTGGTCCAAAGAAA

CTACATCTCCGAACCAGTTGTTGTTTTCTTGCATGCCATTATTTCTACAACCGCTGTCTTG

TATCCAGTCATCGTTAATTTGAGATGCGATTCCGCTTTTTTGTCTGGTGTTGCTTTGATGTT

GTTCGCTTGTATCGTTTGGTTGAAGTTGGTTTCTTACGCTCATACCAACAACGATATGAGA

GCTTTGGCTAAATCTGCTGAAAAGGGTGATGTTGATCCATCCTACGATGTTTCTTTTAAGT

CCTTGGCTTACTTCATGGTTGCTCCAACTTTGTGTTACCAACAATCTTATCCAAGAACCCC

AGCTGTTAGAAAATCTTGGGTTGTTAGACAATTCATTAAGTTGATCGTTTTCACCGGTTTG

ATGGGTTTCATCATCGAACAATATATCAACCCAATCGTCCAAAACTCCCAACATCCATTG

AAAGGTAATTTGTTGTACGCCATCGAAAGAGTCTTGAAGTTGTCTGTTCCAAACTTGTAT

GTCTGGTTGTGCATGTTCTACTGTTTCTTCCATTTGTGGTTGAACATCTTGGCCGAATTAT

TGAGATTCGGTGACAGAGAATTTTACAAGGATTGGTGGAATGCTAAGACCGTCGAAGAA

TATTGGAGAATGTGGAATATGCCAGTTCACAAGTGGATGGTTAGACATATCTACTTCCCA

TGTTTGAGAAACGGTATTCCAAAAGGTGTTGCTATCGTTATTGCCTTCTTGGTTTCTGCTG

TTTTCCACGAATTGTGTATTGCTGTTCCATGCCATATTTTCAAGTTGTGGGCTTTCATTGG

TATCATGTTCCAAGTTCCATTGGTCTTGATTACCAACTACTTGCAAGATAAGTTCAGATCC

TCTATGGTCGGTAACATGATTTTCTGGTTCATCTTCTCCATTTTGGGTCAACCTATGTGTG

TCTTGTTGTACTACCATGATTTGATGAACAGAAAGGGTAAGGCCGATTGA,

Theobroma cacao TcDGAT1, truncated (e.g., to remove organelle

targeting sequences), 1332 nt

SEQ ID NO: 38

ATGCAAGTTGAATCCGCTAACTTGATGTCTAACGTTGCTGAAAATGCTAACGAAATGCCA

AACTCTTCTGATACCAGATTCACTTACAGACCAAGAGTTCCAGCTCACAGAAGAATCAAA

GAATCTCCATTATCTTCCGGTGCCATCTTCAAACAATCTCATGCTGGTTTGTTCAACTTGT

GCATCGTTGTTTTGGTTGCCGTTAACTCCAGATTGATCATCGAAAACTTGATGAAGTACG

GTTGGTTGATCAGATCTGGTTTTTGGTTCTCTTCCAGATCTTTGTCTGATTGGCCATTATTC

ATGTGTTGTTTGACCTTGCCAATTTTCCCATTGGCTGCTTTTGTTGTTGAAAAGTTGGTCC

AAAGAAACTACATCTCCGAACCAGTTGTTGTTTTCTTGCATGCCATTATTTCTACAACCGC

TGTCTTGTATCCAGTCATCGTTAATTTGAGATGCGATTCCGCTTTTTTGTCTGGTGTTGCTT

TGATGTTGTTCGCTTGTATCGTTTGGTTGAAGTTGGTTTCTTACGCTCATACCAACAACGA

TATGAGAGCTTTGGCTAAATCTGCTGAAAAGGGTGATGTTGATCCATCCTACGATGTTTC

TTTTAAGTCCTTGGCTTACTTCATGGTTGCTCCAACTTTGTGTTACCAACAATCTTATCCA

AGAACCCCAGCTGTTAGAAAATCTTGGGTTGTTAGACAATTCATTAAGTTGATCGTTTTC

ACCGGTTTGATGGGTTTCATCATCGAACAATATATCAACCCAATCGTCCAAAACTCCCAA

CATCCATTGAAAGGTAATTTGTTGTACGCCATCGAAAGAGTCTTGAAGTTGTCTGTTCCA

AACTTGTATGTCTGGTTGTGCATGTTCTACTGTTTCTTCCATTTGTGGTTGAACATCTTGG

CCGAATTATTGAGATTCGGTGACAGAGAATTTTACAAGGATTGGTGGAATGCTAAGACC

GTCGAAGAATATTGGAGAATGTGGAATATGCCAGTTCACAAGTGGATGGTTAGACATAT

CTACTTCCCATGTTTGAGAAACGGTATTCCAAAAGGTGTTGCTATCGTTATTGCCTTCTTG

GTTTCTGCTGTTTTCCACGAATTGTGTATTGCTGTTCCATGCCATATTTTCAAGTIGTGGG

CTTTCATTGGTATCATGTTCCAAGTTCCATTGGTCTTGATTACCAACTACTTGCAAGATAA

GTTCAGATCCTCTATGGTCGGTAACATGATTTTCTGGTTCATCTTCTCCATTTTGGGTCAA

CCTATGTGTGTCTTGTTGTACTACCATGATTTGATGAACAGAAAGGGTAAGGCCGATTGA,

Theobroma cacao TcDGAT2, GenBank: KX982583.1, 984 nt

SEQ ID NO: 39

ATGATGGGTGAAGAAATGGAAGAAAGAAAAGCTACCGGTTACAGAGAATTTTCCGGTAG

ACATGAATTCCCATCTAACACTATGCATGCTTTGTTGGCTATGGGTATTTGGTTGGGTGCT

ATTCATTTTAACGCCTTGTTGTTGTTATTCTCCTTCTTGTTCTTGCCATTCTCCAAGTTCTT

GGTTGTTTTCGGTTTGTTGTTGTTGTTCATGATCTTGCCAATCGACCCATACTCTAAGTTT

GGTAGAAGATTGTCTAGATATATCTGCAAGCACGCTTGTTCCTACTTTCCAATTACATTGC

ACGTTGAAGATATCCATGCTTTCCATCCAGATAGAGCTTACGTTTTTGGTTTCGAACCAC

ATTCCGTTTTGCCAATTGGTGTTGTTGCTTTGGCTGATTTGACTGGTTTTATGCCATTGCC

AAAGATTAAGGTTTTGGCTTCTTCTGCTGTTTTCTACACTCCATTCTTGAGACATATTTGG

ACATGGTTGGGTTTGACTCCAGCTACTAAGAAGAATTTCTCCTCTTTGTTGGATGCTGGTT

ACTCCTGTATTTTGGTTCCAGGTGGTGTTCAAGAAACTTTTCATATGGAACCAGGTTCCG

AAATTGCTTTCTTGAGAGCTAGAAGAGGTTTCGTTAGAATTGCTATGGAAATGGGTTCTC

CTTTGGTTCCTGTTTTTTGTTTCGGTCAATCCCATGTTTACAAATGGTGGAAACCAGGTGG

TAAGTTCTACTTGCAATTTTCCAGAGCTATTAAGTTCACCCCAATCTTTTTCTGGGGTATT

TTTGGTTCTCCATTGCCATATCAACATCCAATGCATGTTGTTGTCGGTAAGCCAATTGATG

TCAAGAAAAATCCACAACCTATCGTCGAAGAAGTTATCGAAGTTCACGATAGATTTGTCG

AAGCCTTGCAAGATTTGTTCGAAAGACATAAGGCTCAAGTTGGTTTTGCCGATTTGCCAT

TGAAGATCTTGTGA,

Rhodococcus opacus PD630 diacylglycerol O-acyltransferase

(RoDGAT_atf1) codon-optimized, 1419 nt

SEQ ID NO: 40

ATGACCGACGTGTCGACCACCAACCAGCGCTACATGACCCAGACCGACTTCATGTCGTG

GCGCATGGAGGAGGACCCGATCCTGCGCTCGACCATCGTGGCCGTGGCCCTGCTGGACC

GCTCGCCGGACCAGTCGCGCTTCGTGGACATGATGCGCCGCGCCGTGGACCTGGTGCCGC

TGTTCCGCCGCACCGCCATCGAGGCCCCGATGGGCTTCGCCCCGCCGCGCTGGGCCGACG

ACCACGACTTCGACCTGTCGTGGCACCTGCGCCGCTACACCCTGCCGGAGCCGCGCACCT

GGGACGGCGTGCTGGACTTCGCCCGCACCGCCGAGATGACCGCCTTCGACAAGCGCCGC

CCGCTGTGGGAGTTCACCGTGCTGGACGGCCTGCACGACGGCCGCTCGGCCCTGGTGATG

AAGGTGCACCACTCGCTGACCGACGGCGTGTCGGGCATGCAGATCGCCCGCGAGATCGT

GGACTTCACCCGCGACGGCGGCCCGCGCCCGGACCGCACCGACCACCGCACCGCCGCCC

CGAACGGCGAGTCGCCGACCCCGCCGGGCCGCCTGTCGTGGTACCGCAACACCGCCACC

GACGTGGCCCGCCGCGCCTCGAACACCCTGGGCCGCAACTCGGTGCGCCTGGTGCGCAC

CCCGCGCGCCACCTGGCGCGACGCCGCCGCCCTGGCCGGCTCGACCCTGCGCCTGACCCG

CCCGGTGGTGTCGACCCTGTCGCCGGTGATGAAGAAGCGCTCGACCCGCCGCCACTGCG

CCGTGCTGGACGTGCCGGTGGAGGCCCTGGCCCAGGCCGCCGCCGCCGGCGCCGGCTCG

ATCAACGACGCCTTCCTGGCCGCCGTGCTGCTGGGCATGGCCAAGTACCACCGCCTGCAC

GGCGCCGAGATCTCGGAGCTGCGCATGACCCTGCCGATCTCGCTGCGCGCCGAGACCGA

CCCGGTGGGCGGCAACCGCATCACCCTGGCCCGCTTCGCCCTGCCGGCCGACATCGACG

ACCCGGCCGAGCTGATGCACCGCGTGCACGCCACCGTGGACGCCTGGCGCCACGAGCCG

GCCATCCCGCTGTCGCCGACCATCGCCGGCGCCCTGAACCTGCTGCCGGCCTCGACCCTG

GGCAACATGCTGAAGCACGTGGACTTCGTGGCCTCGAACGTGGTGGGCTCGCCGGTGCC

GCTGTTCATCGCCGGCTCGGAGGTGCTGCACTACTACGCCTTCTCGCCGACCCTGGGCTC

GGCCTTCAACGTGACCCTGATGTCGTACACCACCCGCTGCTGCGTGGGCATCAACGCCGA

CACCGACGCCATCCCGGACCTGGCCACCCTGACCGACTCGATCGCCGACGGCTTCCGCGC

CGTGCTGGGCCTGTGCACCAAGACCACCGACACCCGCGTGGTGGTGGCCTCG,

Rhodococcus opacus PD630 GenBank: CP080954.1 reverse

complement 4246604-4248022 (RODGAT_atfl), 1419 nt

SEQ ID NO: 41

TTGACCGACGTGAGCACGACGAATCAGCGCTACATGACCCAGACGGACTTCATGTCGTG

GCGGATGGAGGAGGACCCGATCCTCCGGTCGACCATCGTGGCGGTCGCACTGCTCGACC

GCAGTCCGGATCAGAGCCGATTCGTCGACATGATGCGCAGGGCGGTCGACCTGGTTCCC

CTCTTCCGGCGGACGGCGATCGAGGCTCCGATGGGCTTTGCGCCGCCGAGGTGGGCGGA

CGATCACGATTTCGATCTCAGCTGGCACCTGCGCCGCTACACCCTCCCCGAACCACGAAC

ATGGGACGGGGTTCTCGACTTCGCCCGGACCGCCGAGATGACCGCCTTCGACAAGCGCC

GTCCGCTCTGGGAGTTCACCGTTCTCGACGGACTCCACGACGGCAGGTCCGCCCTCGTGA

TGAAGGTGCATCACTCTCTCACCGACGGTGTCAGTGGAATGCAGATTGCCCGGGAGATC

GTGGATTTCACCCGCGATGGCGGGCCACGGCCGGACCGGACCGACCACCGCACGGCCGC

GCCGAACGGTGAATCGCCCACTCCGCCGGGCCGCCTCTCCTGGTACCGGAACACGGCCA

CCGACGTGGCCCGCCGGGCATCGAACACGCTGGGCCGCAACAGTGTTCGACTGGTTCGG

ACTCCGAGGGCCACCTGGCGCGACGCAGCCGCACTAGCCGGCTCCACACTGCGCCTCAC

GCGTCCCGTGGTCTCCACACTGTCCCCGGTCATGAAAAAACGCAGCACGCGGCGTCACTG

TGCGGTGCTCGACGTGCCGGTGGAGGCGCTCGCTCAGGCGGCCGCGGCGGGTGCCGGTT

CGATCAACGACGCGTTTCTCGCTGCTGTCCTGCTGGGAATGGCGAAGTACCACCGACTGC

ACGGCGCCGAGATCAGCGAACTGCGGATGACGCTGCCGATCAGCCTGCGTGCCGAGACG

GACCCGGTGGGAGGCAACCGCATCACCCTGGCACGTTTTGCACTACCCGCCGACATCGA

CGACCCCGCCGAGTTGATGCACCGGGTGCACGCCACGGTGGATGCCTGGCGCCACGAGC

CCGCGATTCCGCTGTCACCGACGATCGCCGGCGCCTTGAACCTGCTTCCGGCCTCGACAC

TCGGAAACATGCTCAAACACGTCGACTTCGTCGCCTCGAACGTCGTCGGATCTCCGGTAC

CACTGTTCATCGCCGGGTCGGAGGTTCTGCACTACTACGCGTTCAGCCCCACACTCGGAT

CGGCGTTCAACGTCACCTTGATGTCCTACACCACGCGATGCTGTGTCGGGATCAACGCCG

ACACGGACGCAATCCCGGACCTCGCAACCCTGACCGATTCGATAGCGGACGGGTTTCGC

GCCGTCCTCGGACTGTGCACGAAGACAACCGATACGAGGGTGGTCGTGGCCTCG,

Rhodococcus opacus PD630 wax ester synthase/diacylglycerol

acyltransferase (RoDGAT_atf2) codon-optimized, 1359 nt

SEQ ID NO: 42

ATGCCGGTGACCGACTCGATCTTCCTGCTGGGCGAGTCGCGCGAGCACCCGATGCACGTG

GGCTCGCTGGAGCTGTTCACCCCGCCGGAGGACGCCGGCCCGGACTACGTGAAGTCGAT

GCACGAGACCCTGCTGAAGCACACCGACGTGGACCCGACCTTCCGCAAGAAGCCGGCCG

GCCCGGTGGGCTCGCTGGGCAACCTGTGGTGGGCCGACGAGTCGGACGTGGACCTGGAG

TACCACGTGCGCCACTCGGCCCTGCCGGCCCCGTACCGCGTGCGCGAGCTGCTGACCCTG

ACCTCGCGCCTGCACGGCACCCTGCTGGACCGCCACCGCCCGCTGTGGGAGATGTACCTG

ATCGAGGGCCTGTCGGACGGCCGCTTCGCCATCTACACCAAGCTGCACCACTCGCTGATG

GACGGCGTGTCGGGCCTGCGCCTGCTGATGCGCACCCTGTCGACCGACCCGGACGTGCG

CGACGCCCCGCCGCCGTGGAACCTGCCGCGCCGCGCCTCGGCCAACGGCGCCGCCCCGG

CCCCGGACCTGTGGTCGGTGGTGAACGGCGTGCGCCGCACCGTGGGCGAGGTGGCCGGC

CTGGCCCCGGCCTCGCTGCGCATCGCCCGCACCGCCATGGGCCAGCACGACATGCGCTTC

CCGTACGAGGCCCCGCGCACCATGCTGAACGTGCCGATCGGCGGCGCCCGCCGCTTCGC

CGCCCAGTCGTGGCCGCTGGAGCGCGTGCACGCCGTGCGCAAGGCCGCCGGCGTGTCGG

TGAACGACGTGGTGATGGCCATGTGCGCCGGCGCCCTGCGCGGCTACCTGGAGGAGCAG

AAGGCCCTGCCGGACGAGCCGCTGATCGCCATGGTGCCGGTGTCGCTGCGCGACGAGCA

GAAGGCCGACGCCGGCGGCAACGCCGTGGGCGTGACCCTGTGCAACCTGGCCACCGACG

TGGACGACCCGGCCGAGCGCCTGACCGCCATCTCGGCCTCGATGTCGCAGGGCAAGGAG

CTGTTCGGCTCGCTGACCTCGATGCAGGCCCTGGCCTGGTCGGCCTTCAACATGTCGCCG

ATCGCCCTGACCCCGGTGCCGGGCTTCGTGCGCTTCACCCCGCCGCCGTTCAACGTGATC

ATCTCGAACGTGCCGGGCCCGCGCAAGACCATGTACTGGAACGGCTCGCGCCTGGACGG

CATCTACCCGACCTCGGTGGTGCTGGACGGCCAGGCCCTGAACATCACCCTGACCACCAA

CGGCGGCAACCTGGACTTCGGCGTGATCGGCTGCCGCCGCTCGGTGCCGTCGCTGCAGCG

CATCCTGTTCTACCTGGAGACCGCCCTGGGCGAGCTGGAGGCCGCCCTGCTG,

Rhodococcus opacus PD630 wax ester synthase/diacylglycerol

acyltransferase (RoDGAT_atf2), GenBank: JH377359.1 2198124-2199485,

1362 nt

SEQ ID NO: 43

ATGCCGGTTACCGATTCGATATTCCTTCTCGGCGAATCGCGAGAGCATCCGATGCACGTG

GGATCGCTCGAATTGTTCACACCGCCGGAGGATGCCGGCCCCGACTACGTGAAGTCGAT

GCACGAAACTCTGCTGAAGCACACGGACGTCGACCCCACTTTCCGCAAGAAGCCAGCGG

GCCCCGTGGGCAGTCTCGGGAATCTGTGGTGGGCCGACGAGTCGGACGTCGATCTCGAA

TACCACGTGCGTCATTCGGCCCTGCCGGCCCCGTACCGGGTCCGGGAACTGCTGACGCTG

ACGTCCCGGTTGCACGGCACGCTCCTGGACCGTCATCGCCCGCTGTGGGAGATGTATCTG

ATCGAGGGGCTCAGCGACGGCCGGTTCGCGATCTACACCAAGCTGCACCATTCGCTGAT

GGACGGGGTCTCCGGTTTGCGGCTGCTGATGCGGACGCTGTCGACCGACCCGGACGTGC

GCGACGCACCGCCGCCGTGGAACCTGCCGCGCAGGGCGTCGGCCAATGGTGCCGCCCCC

GCTCCCGACCTCTGGTCGGTGGTGAACGGGGTCCGTCGCACGGTCGGTGAGGTGGCCGG

TCTCGCGCCGGCGTCGCTGCGCATCGCCCGCACCGCGATGGGGCAGCACGACATGAGGT

TTCCGTACGAGGCGCCTCGCACCATGCTGAACGTCCCGATCGGGGGCGCGCGCCGGTTCG

CCGCGCAGTCCTGGCCGCTCGAACGCGTCCACGCCGTGCGGAAGGCAGCCGGGGTCAGT

GTCAACGACGTCGTGATGGCCATGTGCGCCGGGGCGTTGCGGGGTTACCTCGAGGAACA

GAAGGCGCTACCGGACGAGCCGCTGATCGCGATGGTTCCGGTGTCCCTGCGCGACGAGC

AGAAGGCCGACGCCGGCGGCAACGCGGTCGGGGTCACGTTGTGCAACCTGGCGACCGAC

GTCGACGACCCGGCCGAACGTCTGACGGCGATCTCCGCCTCCATGTCCCAGGGGAAGGA

ACTGTTCGGCAGCCTCACCTCGATGCAGGCGCTGGCGTGGTCCGCGTTCAACATGTCGCC

GATCGCCCTGACGCCCGTGCCCGGGTTCGTCCGCTTCACACCGCCGCCGTTCAACGTGAT

CATCTCCAACGTCCCGGGACCGCGGAAGACCATGTACTGGAACGGGTCCCGGCTGGACG

GCATCTACCCGACATCGGTGGTGCTGGACGGGCAGGCACTCAACATCACACTCACCACC

AACGGCGGCAACCTCGATTTCGGTGTCATCGGGTGCCGCCGCTCGGTGCCGAGCCTGCAA

CGCATCCTCTTCTATCTCGAGACGGCTCTGGGCGAACTCGAGGCGGCATTGCTCTGA,

Rhodococcus opacus PD630 acyltransferase 8

(RODGAT_atf8) codon-optimized, 1389 nt

SEQ ID NO: 44

ATGCCGCTGCCGATGTCGCCGCTGGACTCGATGTTCCTGCTGGGCGAGTCGCGCGAGCAC

CCGATGCACGTGGGCTGCGTGGAGATCTTCCAGCTGCCGGAGGGCGCCGACACCTACGA

CATGCGCGCCATGCTGGACCGCGCCCTGGCCGACGGCGACGGCATCGTGACCCCGCGCC

TGGCCAAGCGCGCCCACCGCTCGTTCTCGACCCTGGGCCAGTGGTCGTGGGAGACCGTG

GACGACATCGACCTGGGCCACCACATCCGCCACGACGCCCTGCCGGCCCCGGGCGGCGA

GGCCGAGCTGATGGCCCTGTGCTCGCGCCTGCACGGCTCGCTGCTGGACCGCTCGCGCCC

GCTGTGGGAGATGCACCTGATCGAGGGCCTGTCGGACGGCCGCTTCGCCGTGTACACCA

AGATCCACCACGCCGTGGCCGACGGCGTGACCGCCATGAAGATGCTGCGCAACGCCTTC

TCGGAGAACTCGGAGGACCGCGACGTGCCGGCCCCGTGGCAGCCGCGCGGCCCGCGCCG

CCAGCGCACCCCGTCGAAGGCCTTCTCGCTGTCGGGCCTGGCCGGCTCGACCTTCCGCGC

CGCCCGCGACACCGTGGGCGAGGTGGCCGGCCTGGTGCCGGCCCTGGCCGGCACCGTGT

CGCGCGCCTTCCGCGACCAGGGCGGCCCGCTGGCCCTGTCGGCCCCGAAGACCCCGTTCA

ACGTGCCGATCACCGGCGCCTGCCAGTTCGCCGCCCAGTCGTGGCCGCTGGAGCGCCTGC

GCCTGGTGGCCAAGCTGTCGGACACCGCCATCAACGACGTGGTGCTGGCCATGTCGTCG

GGCGCCCTGCGCTCGTACCTGGAGGACCAGAACGCCCTGCCGGCCGAGCCGCTGATCGC

CATGGTGCCGGTGTCGCTGAAGTCGCAGCGCGAGGCCTCGAACGGCAACAACATCGGCG

TGCTGATGTGCAACCTGGGCACCCACCTGCCGGACCTGGCCGACCGCCTGGACACCATCC

GCACCTCGATGCGCGAGGGCAAGGAGGCCTACGAGACCCTGTCGGCCACCCAGATCCTG

GCCATGTCGGCCCTGGGCGCCGCCCCGATCGGCGCCTCGATGCTGTTCGGCCACAACTCG

CGCGTGCGCCCGCCGTTCAACCTGATCATCTCGAACGTGCCGGGCCCGTCGTCGCCGCTG

TACTGGAACGGCGCCCGCCTGGACGCCATCTACCCGCTGTCGGTGCCGGTGGACGGCCA

GGGCCTGAACATCACCTGCACCTCGAACGACGACATCATCTCGTTCGGCGTGACCGGCTG

CCGCTCGGCCGTGCCGGACCTGAAGTCGATCCCGGCCCGCCTGGGCCACGAGCTGCGCG,

Rhodococcus opacus PD630 acyltransferase 8 (RODGAT_atf8),

GenBank: GU067777.1, 1392 nt

SEQ ID NO: 45

ATGCCGCTCCCCATGTCCCCTCTCGACTCGATGTTCCTTCTCGGAGAGTCCCGTGAGCACC

CGATGCATGTTGGCTGCGTAGAGATCTTCCAGCTCCCGGAAGGCGCCGACACCTACGAC

ATGCGCGCGATGCTCGACCGCGCGCTTGCCGACGGCGACGGGATCGTCACGCCCCGGCT

CGCCAAGCGAGCCCACCGGTCCTTCTCGACGCTCGGTCAGTGGAGCTGGGAGACCGTCG

ACGACATCGACCTCGGTCACCACATCCGGCACGATGCGCTGCCCGCCCCCGGGGGCGAG

GCCGAGCTGATGGCACTGTGCTCGCGGCTGCACGGATCGCTGCTCGACCGCAGCCGCCC

GCTGTGGGAGATGCACCTGATCGAGGGACTGAGCGACGGACGGTTCGCCGTCTACACCA

AGATCCACCACGCGGTCGCCGACGGCGTCACCGCGATGAAGATGCTGCGCAACGCGTTC

AGCGAGAACTCCGAGGACCGGGACGTGCCGGCCCCGTGGCAGCCGCGGGGACCGCGGC

GACAGCGGACGCCGTCGAAGGCGTTCAGCCTGTCGGGACTGGCCGGTTCCACGTTCCGC

GCCGCCCGCGACACCGTCGGTGAGGTCGCCGGGCTCGTGCCCGCGCTCGCTGGCACCGT

GTCCCGCGCCTTCCGCGACCAGGGCGGCCCGCTCGCCTTGTCCGCACCCAAGACCCCGTT

CAACGTGCCGATCACCGGTGCCTGCCAGTTCGCGGCGCAGTCGTGGCCGCTCGAACGTCT

CCGGCTCGTCGCCAAGCTGTCCGACACCGCCATCAACGACGTCGTGCTCGCGATGTCCTC

GGGAGCACTCCGCAGCTATCTCGAGGATCAGAACGCCCTGCCCGCCGAGCCGCTGATCG

CGATGGTGCCGGTGTCGCTGAAGAGTCAGCGCGAGGCGTCGAACGGCAACAACATCGGG

GTGCTCATGTGCAACCTCGGCACCCACCTCCCCGACCTGGCGGATCGCCTCGACACCATC

CGGACGTCGATGCGCGAGGGCAAGGAGGCGTACGAGACGCTGAGTGCGACGCAGATCCT

CGCGATGAGCGCTCTCGGCGCGGCACCGATCGGCGCGAGCATGCTGTTCGGGCACAACT

CGCGGGTGCGCCCGCCGTTCAACCTCATCATCTCCAATGTTCCGGGTCCCAGCTCGCCGC

TGTATTGGAACGGGGCACGGCTCGATGCCATCTACCCGCTGTCGGTGCCCGTCGACGGCC

AGGGCCTGAACATCACCTGCACCAGCAACGACGACATCATCTCGTTCGGGGTCACCGGC

TGCCGCAGCGCGGTGCCCGACCTGAAGTCGATCCCCGCCCGGCTGGGGCACGAACTGCG

CGCCCTCGAGCGCGCGGTCGGAATCTGA,

Acinetobacter baylyi DGAT (AbDGAT), e.g., strain ADP1,

bifunctional wax ester synthase/diacylglycerol acyltransferase,

AAO17391.1, NCBI Reference Sequence: WP_004922247.1, 458 aa

(corresponds to SEQ ID NOs: 25-26)

SEQ ID NO: 29

MRPLHPIDFIFLSLEKRQQPMHVGGLFLFQIPDNAPDTFIQDLVNDIRISKSIPVPPFNNKLNGLF

WDEDEEFDLDHHFRHIALPHPGRIRELLIYISQEHSTLLDRAKPLWTCNIIEGIEGNRFAMYFKI

HHAMVDGVAGMRLIEKSLSHDVTEKSIVPPWCVEGKRAKRLREPKTGKIKKIMSGIKSQLQA

TPTVIQELSQTVFKDIGRNPDHVSSFQAPCSILNQRVSSSRRFAAQSFDLDRFRNIAKSLNVTIN

DVVLAVCSGALRAYLMSHNSLPSKPLIAMVPASIRNDDSDVSNRITMILANLATHKDDPLQR

LEIIRRSVQNSKQRFKRMTSDQILNYSAVVYGPAGLNIISGMMPKRQAFNLVISNVPGPREPLY

WNGAKLDALYPASIVLDGQALNITMTSYLDKLEVGLIACRNALPRMQNLLTHLEEEIQLFEG

VIAKQEDIKTAN,

Thermomonospora curvata DGAT, wax ester/triacylglycerol synthase

family O-acyltransferase, NCBI Reference Sequence: WP_012854133.1,

482 aa (corresponds to SEQ ID NOs: 27-28)

SEQ ID NO: 30

MRQLTAVDANFLNVETGTTHAHIAGLGILDPVACPGGRLTAEDLIEVIRERAHLAPRPLRMRL

AAVPLGIDRPYWEDDPDFDPARHVFEVGLPAPGNAAQLADVVAMLHERPLDRARPLWEAV

VIQGLEGGRTAVYIKVHHAAVDGVLATETLAALLDLSPQPRELPPDDTVPQQAPALAERVRT

GLLRALAHPVRGARMLARTAPYLDEIPGLAQLPGVQPLARAIQGALGRDGVVPLPRTVAPPT

PFNGTISARRAVAFGELPLAEIRRIRRELGGSVNDVVMALVATALHRWLDKRGELPDRPLVA

AVPVSLRRGRDGDAAGGNRMSAMVTPLATHLADPAERFAAIRGDLAAAKRRFARSSGAWL

EGLSELVPAPLAGPLLRLALQARPGEYLRPVNLLVSNVPGPDFPLYLRGARVLGYFPISVVSD

LTGGLNITVLSYDGKLDVGIVTCRQMIPDPWEIMDHLDDALGELRGLIDG,

Theobroma cacao TcDGAT1, Ref No. XP_007012778.1, 501 aa

(corresponds to SEQ ID NO: 37)

SEQ ID NO: 46

MAISDSPEILGSTATVTSSSHSDSDLNLLSIRRRTSTTAAGRAPDRDDSGNGEAVDDRDQVES

ANLMSNVAENANEMPNSSDTRFTYRPRVPAHRRIKESPLSSGAIFKQSHAGLFNLCIVVLVAV

NSRLIIENLMKYGWLIRSGFWFSSRSLSDWPLFMCCLTLPIFPLAAFVVEKLVQRNYISEPVVV

FLHAIISTTAVLYPVIVNLRCDSAFLSGVALMLFACIVWLKLVSYAHTNNDMRALAKSAEKG

DVDPSYDVSFKSLAYFMVAPTLCYQQSYPRTPAVRKSWVVRQFIKLIVFTGLMGFIIEQYINPI

VQNSQHPLKGNLLYAIERVLKLSVPNLYVWLCMFYCFFHLWLNILAELLRFGDREFYKDWW

NAKTVEEYWRMWNMPVHKWMVRHIYFPCLRNGIPKGVAIVIAFLVSAVFHELCIAVPCHIFK

LWAFIGIMFQVPLVLITNYLQDKFRSSMVGNMIFWFIFSILGQPMCVLLYYHDLMNRKGKAD,

Theobroma cacao TcDGATI truncated, 443 aa (corresponds to SEQ ID

NO: 38; corresponds to aa 60-501 of SEQ ID NO: 46)

SEQ ID NO: 47

MQVESANLMSNVAENANEMPNSSDTRFTYRPRVPAHRRIKESPLSSGAIFKQSHAGLFNLCIV

VLVAVNSRLIIENLMKYGWLIRSGFWFSSRSLSDWPLFMCCLTLPIFPLAAFVVEKLVQRNYIS

EPVVVFLHAIISTTAVLYPVIVNLRCDSAFLSGVALMLFACIVWLKLVSYAHTNNDMRALAK

SAEKGDVDPSYDVSFKSLAYFMVAPTLCYQQSYPRTPAVRKSWVVRQFIKLIVFTGLMGFIIE

QYINPIVQNSQHPLKGNLLYAIERVLKLSVPNLYVWLCMFYCFFHLWLNILAELLRFGDREFY

KDWWNAKTVEEYWRMWNMPVHKWMVRHIYFPCLRNGIPKGVAIVIAFLVSAVFHELCIAV

PCHIFKLWAFIGIMFQVPLVLITNYLQDKFRSSMVGNMIFWFIFSILGQPMCVLLYYHDLMNR

KGKAD,

Theobroma cacao TcDGAT2, Ref No. XP_007046425.1, 327 aa

(corresponds to SEQ ID NO: 39)

SEQ ID NO: 48

MMGEEMEERKATGYREFSGRHEFPSNTMHALLAMGIWLGAIHFNALLLLFSFLFLPFSKFLV

VFGLLLLFMILPIDPYSKFGRRLSRYICKHACSYFPITLHVEDIHAFHPDRAYVFGFEPHSVLPI

GVVALADLTGFMPLPKIKVLASSAVFYTPFLRHIWTWLGLTPATKKNFSSLLDAGYSCILVPG

GVQETFHMEPGSEIAFLRARRGFVRIAMEMGSPLVPVFCFGQSHVYKWWKPGGKFYLQFSR

AIKFTPIFFWGIFGSPLPYQHPMHVVVGKPIDVKKNPQPIVEEVIEVHDRFVEALQDLFERHKA

QVGFADLPLKIL,

Rhodococcus opacus diacylglycerol O-acyltransferase RODGAT_atfl,

Ref No. EHI42943.1, 473 aa (corresponds to SEQ ID NO: 40 or

SEQ ID NO: 41)

SEQ ID NO: 49

MTDVSTTNQRYMTQTDFMSWRMEEDPILRSTIVAVALLDRSPDQSRFVDMMRRAVDLVPLF

RRTAIEAPMGFAPPRWADDHDFDLSWHLRRYTLPEPRTWDGVLDFARTAEMTAFDKRRPL

WEFTVLDGLHDGRSALVMKVHHSLTDGVSGMQIAREIVDFTRDGGPRPDRTDHRTAAPNGE

SPTPPGRLSWYRNTATDVARRASNTLGRNSVRLVRTPRATWRDAAALAGSTLRLTRPVVSTL

SPVMKKRSTRRHCAVLDVPVEALAQAAAAGAGSINDAFLAAVLLGMAKYHRLHGAEISELR

MTLPISLRAETDPVGGNRITLARFALPADIDDPAELMHRVHATVDAWRHEPAIPLSPTIAGAL

NLLPASTLGNMLKHVDFVASNVVGSPVPLFIAGSEVLHYYAFSPTLGSAFNVTLMSYTTRCC

VGINADTDAIPDLATLTDSIADGFRAVLGLCTKTTDTRVVVAS,

Rhodococcus opacus wax ester synthase/diacylglycerol acyltransferase

RODGAT atf2, Ref No. EHI41112.1, 453 aa (corresponds to SEQ ID NO: 42

or SEQ ID NO: 43)

SEQ ID NO: 50

MPVTDSIFLLGESREHPMHVGSLELFTPPEDAGPDYVKSMHETLLKHTDVDPTFRKKPAGPV

GSLGNLWWADESDVDLEYHVRHSALPAPYRVRELLTLTSRLHGTLLDRHRPLWEMYLIEGL

SDGRFAIYTKLHHSLMDGVSGLRLLMRTLSTDPDVRDAPPPWNLPRRASANGAAPAPDLWS

VVNGVRRTVGEVAGLAPASLRIARTAMGQHDMRFPYEAPRTMLNVPIGGARRFAAQSWPLE

RVHAVRKAAGVSVNDVVMAMCAGALRGYLEEQKALPDEPLIAMVPVSLRDEQKADAGGN

AVGVTLCNLATDVDDPAERLTAISASMSQGKELFGSLTSMQALAWSAFNMSPIALTPVPGFV

RFTPPPFNVIISNVPGPRKTMYWNGSRLDGIYPTSVVLDGQALNITLTINGGNLDFGVIGCRRS

VPSLQRILFYLETALGELEAALL,

Rhodococcus opacus acyltransferase 8, RODGAT_atf8, Ref No.

ACY38595.1, 463 aa (corresponds to SEQ ID NO: 44 or SEQ ID NO: 45)

SEQ ID NO: 51

MPLPMSPLDSMFLLGESREHPMHVGCVEIFQLPEGADTYDMRAMLDRALADGDGIVTPRLA

KRAHRSFSTLGQWSWETVDDIDLGHHIRHDALPAPGGEAELMALCSRLHGSLLDRSRPLWE

MHLIEGLSDGRFAVYTKIHHAVADGVTAMKMLRNAFSENSEDRDVPAPWQPRGPRRQRTPS

KAFSLSGLAGSTFRAARDTVGEVAGLVPALAGTVSRAFRDQGGPLALSAPKTPFNVPITGAC

QFAAQSWPLERLRLVAKLSDTAINDVVLAMSSGALRSYLEDQNALPAEPLIAMVPVSLKSQR

EASNGNNIGVLMCNLGTHLPDLADRLDTIRTSMREGKEAYETLSATQILAMSALGAAPIGAS

MLFGHNSRVRPPFNLIISNVPGPSSPLYWNGARLDAIYPLSVPVDGQGLNITCTSNDDIISFGVT

GCRSAVPDLKSIPARLGHELRALERAVGI,

In some embodiments of any of the aspects, the engineered bacterium comprises a Acinetobacter baylyi DGAT gene or polypeptide (e.g., SEQ ID NOs: 25, 26, or 29) or a Thermomonospora curvata DGAT gene or polypeptide (e.g., SEQ ID NOs: 27, 28, or 30).

In some embodiments of any of the aspects, the acyltransferase catalyzes transesterification of the sn2 OH group of a lysophosphatidic acid with a fatty acid. As a non-limiting example, such an acyltransferase is lysophosphatidic acid acyltransferase (LPAT or LPAAT; E.C. 2.3.1.51; also referred to as acyl-CoA: 1-acylglycerol-sn-3-phosphate acyltransferase (AGPAT) or 1-acyl-sn-glycerol-3-phosphate acyltransferase). LPAT catalyzes acylation of the sn-2 position on lysophosphatidic acid by an acyl CoA substrate to produce phosphatidic acid, which is a precursor of triacylglycerols (TAGs), as well as polar glycerolipids and. LPAT catalyzes an important step of the de novo phospholipid biosynthesis pathway and thus has a strong flux control in the biosynthesis of TAG or phospholipids. In competition assays, LPATs can show preferences for fatty acyl-CoA substrates of specific chain length and desaturation. In some embodiments of any of the aspects, the functional LPAT gene preferentially produces or leads to the production of TAGs comprising a specific type of fatty acid R group (e.g., C16). As such, the functional LPAT gene can be selected from any LPAT gene from any species that preferentially produces or leads to the production of TAGs comprising a specific type of fatty acid R group (e.g., C16). In some embodiments of any of the aspects, the LPAT is a bacterial LPAT. In some embodiments of any of the aspects, the LPAT is a plant LPAT.

In some embodiments of any of the aspects, the engineered bacterium comprises at least one exogenous copy of at least one functional LPAT gene. In some embodiments of any of the aspects, the engineered bacterium does not comprise a functional endogenous LPAT gene. In some embodiments of any of the aspects, the functional LPAT gene is heterologous. In some embodiments of any of the aspects, the functional heterologous LPAT gene comprises a Theobroma LPAT gene.

In some embodiments of any of the aspects, the functional heterologous LPAT gene comprises a Theobroma cacao LPAT gene. In some embodiments of any of the aspects, the engineered bacterium comprises at least one exogenous copy of at least one functional LPAT gene comprising one of SEQ ID NOs: 52-58, or a nucleic acid sequence that is at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the sequence of at least one of SEQ ID NOs: 52-58, that maintains the same functions as at least one of SEQ ID NOs: 52-58 (e.g., lysophosphatidic acid acyltransferase).

In some embodiments of any of the aspects, the amino acid sequence encoded by the functional LPAT gene comprises one of SEQ ID NOs: 59-63, or an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the sequence of at least one of SEQ ID NOs: 59-63, that maintains the same functions as at least one of SEQ ID NOs: 59-63 (e.g., lysophosphatidic acid acyltransferase).

Theobroma cacao 1-acyl-sn-glycerol-3-phosphate acyltransferase 1,

chloroplastic (TcLPAT1), XM_007011850.2 301-1380, 1080 nt

SEQ ID NO: 52

ATGGAGCTCTCTTCCCTCCCTTCCGTTTCTTCTTTCTCGCTATGTCACCCAAAGCCCAGGA

GTTCTGCTACGTTGCCTTTCTTGCCTTTTTCGAATCGTAAAGGAGCTTACTTTGGCTATTCT

CTGTGTAAACGGGCAACTTTGAGAAATTCATGTAACTCTGCTCAAAATAACTTTTTGCGT

ATTTCAAGGACGCATGATGGTGTATCTCGGTGTTATTTTAATCAAAAGGAAGGTTTAAAT

AGATCGTATTACAATAGTAAATTACATAACGAGAACAAATTGTCCAGATACATAGTTGC

GAGATCTGAATTTGCTGGGACTGGGACCCCTGATGCTGCCTATTCTTTATCAGAAATTAA

ACCGGGTTCAAAAGTTAGAGGAGTATGCTTTTATGCTGTTACAGCAATAGCAGCCATTTT

ACTTATTTGGTTTATGCTGGTTTTGCATCCCTTTGTGCTCTTGTTTGATCGCTACAGAAGA

AAAGCTCAGCATTTTATTGCCAAACTTTGGGCTATGGCAACAGTTGCTCCTTTTTTTAAAA

TTGAGTTTGAAGGATTGGAGAATCTGCCTCCACAGGATGTTCCTGCCGTATATGTTTCCA

ACCACCAGAGTTTTTTAGACATCTATACACTTCTAACTCTTGGAAGAAGCTTCAAGTTCA

TCAGCAAGACGGGGATATTTCTTTATCCCATTATTGGGTGGGCCATGTCTATGATGGGTC

TAATTCCATTAAAGCGCATGGACAGCAGAAGCCAGTTGGACTGTCTTAAGAGATGTATG

GATCTCATCAGGAACGGTGCCTCTGTCTTTTTCTTCCCAGAAGGCACACGGAGTAAGGAT

GGGAAGCTAGGTGCTTTCAAGAAAGGTGCATTTAGTGTTGCAGCAAAAACTGGAGTGCC

TGTCGTTCCTATGACCCTAATTGGCACAGGCAAAATCATGCCTTTAGGACTGGAGGGTGT

CATAAATTCAGGATCCGTAAAAGTTGTTATTCACAAGCCGATCAAAGGAAGTGATCCAG

AAATATTATGCAATGAAGCTAGAAACACAATAGCAGATACGCTTAAGCATCAATGCTGA,

Theobroma cacao 1-acyl-sn-glycerol-3-phosphateacyltransferase

(TcLPAT2), codon-optimized, 933 nt

SEQ ID NO: 53

ATGGAGTCGTCGGGCTCGGGCTCGTTCCTGCGCAACCGCCGCCTGGGCTCGTTCCTGGAC

ACCAACTCGGACCCGAACGTGCGCGAGACCCAGAAGGTGCTGTCGAAGGGCGGCGCCCG

CCAGCGCCCGAAGACCGACGACGCCTTCGTGGACGACGACGGCTGGATCTGCTCGCTGA

TCTCGTGCGTGCGCATCGTGGCCTGCTTCCTGACCATGATGGTGACCACCTTCATCTGGG

CCCTGATCATGCTGCTGCTGCTGCCGTGGCCGTCGCAGCGCATCCGCCAGGGCAACATCT

ACGGCCACGTGACCGGCCGCCTGCTGATGTGGATCCTGGGCAACCCGATCAAGATCGAG

GGCACCGAGTTCTCGAACGAGCGCGCCATCTACATCTGCAACCACGCCTCGCCGATCGAC

ATCTTCCTGATCATGTGGCTGACCCCGACCGGCACCGTGGGCATCGCCAAGAAGGAGAT

CATCTGGTACCCGCTGTTCGGCCAGCTGTACGTGCTGGCCAACCACCTGCGCATCGACCG

CTCGAACCCGTCGACCGCCATCCAGTCGATGAAGGAGGCCGTGCAGGCCGTGATCAAGC

ACAACCTGTCGCTGATCATCTTCCCGGAGGGCACCCGCTCGAAGAACGGCCGCCTGCTGC

CGTTCAAGAAGGGCTTCGTGCACCTGGCCCTGCAGTCGCACATCCCGATCGTGCCGATCG

TGCTGACCGGCACCCACCTGGCCTGGCGCAAGGGCTCGCTGCACGTGCGCCCGGCCCCG

ATCTCGGTGAAGTACCTGCCGCCGATCTCGACCGACTCGTGGAAGGACGACAAGATCGA

CGACTACATCAAGATGGTGCACGACATCTACGTGGAGAACCTGCCGGAGCCGCAGAAGC

CGATCGTGTCGGAGGACACCACCAACTCGTCGCGCTCGTAA,

Theobroma cacao 1-acyl-sn-glycerol-3-phosphate acyltransferase

(TcLPAT2), NCBI Reference Sequence: XM_007020795.2 141-1073, 933 nt

SEQ ID NO: 54

ATGGAGAGTTCTGGAAGTGGTTCTTTCTTGAGGAACAGAAGATTAGGGAGCTTCCTCGAT

ACAAATTCTGATCCAAATGTGAGAGAAACTCAGAAAGTTTTGAGCAAAGGAGGAGCAAG

ACAGAGGCCTAAGACTGATGATGCTTTTGTTGATGATGACGGATGGATTTGTTCATTGAT

ATCTTGTGTAAGGATTGTTGCATGTTTCCTGACAATGATGGTCACAACATTCATTTGGGC

ATTGATCATGCTCTTGCTCCTTCCTTGGCCTTCCCAGCGAATCAGGCAAGGAAATATTTAT

GGCCATGTGACTGGTAGATTGCTGATGTGGATCTTAGGAAATCCTATAAAGATTGAAGG

AACAGAGTTCTCCAATGAGAGAGCCATTTATATCTGCAATCATGCATCTCCCATAGACAT

TTTCCTCATTATGTGGTTGACTCCAACAGGGACTGTTGGCATTGCAAAGAAAGAGATCAT

TTGGTATCCCCTATTTGGACAACTATATGTTCTAGCGAATCATCTCCGCATTGATCGATCT

AACCCTAGTACAGCCATTCAGTCCATGAAAGAGGCAGTTCAGGCTGTGATAAAACACAA

CCTATCTTTGATTATTTTTCCTGAGGGCACAAGGTCAAAAAATGGACGATTGCTCCCCTTT

AAAAAGGGCTTTGTTCATTTGGCCTTGCAGTCACACATTCCAATAGTTCCAATAGTCTTG

ACAGGTACTCATCTAGCATGGAGGAAAGGTAGCTTGCATGTTCGACCGGCTCCTATATCT

GTAAAATATCTCCCTCCGATAAGTACCGATAGTTGGAAAGATGACAAGATTGATGACTA

CATAAAAATGGTGCATGACATATATGTCGAAAACCTCCCTGAGCCTCAAAAGCCTATTGT

ATCAGAAGACACCACTAACAGTTCAAGATCATAA,

Theobroma cacao (TcLPAT2) truncated, codon-optimized (corresponds

to nt 136-933 of SEQ ID NO: 53), 798 nt

SEQ ID NO: 55

GACGACGCCTTCGTGGACGACGACGGCTGGATCTGCTCGCTGATCTCGTGCGTGCGCATC

GTGGCCTGCTTCCTGACCATGATGGTGACCACCTTCATCTGGGCCCTGATCATGCTGCTG

CTGCTGCCGTGGCCGTCGCAGCGCATCCGCCAGGGCAACATCTACGGCCACGTGACCGG

CCGCCTGCTGATGTGGATCCTGGGCAACCCGATCAAGATCGAGGGCACCGAGTTCTCGA

ACGAGCGCGCCATCTACATCTGCAACCACGCCTCGCCGATCGACATCTTCCTGATCATGT

GGCTGACCCCGACCGGCACCGTGGGCATCGCCAAGAAGGAGATCATCTGGTACCCGCTG

TTCGGCCAGCTGTACGTGCTGGCCAACCACCTGCGCATCGACCGCTCGAACCCGTCGACC

GCCATCCAGTCGATGAAGGAGGCCGTGCAGGCCGTGATCAAGCACAACCTGTCGCTGAT

CATCTTCCCGGAGGGCACCCGCTCGAAGAACGGCCGCCTGCTGCCGTTCAAGAAGGGCT

TCGTGCACCTGGCCCTGCAGTCGCACATCCCGATCGTGCCGATCGTGCTGACCGGCACCC

ACCTGGCCTGGCGCAAGGGCTCGCTGCACGTGCGCCCGGCCCCGATCTCGGTGAAGTAC

CTGCCGCCGATCTCGACCGACTCGTGGAAGGACGACAAGATCGACGACTACATCAAGAT

GGTGCACGACATCTACGTGGAGAACCTGCCGGAGCCGCAGAAGCCGATCGTGTCGGAGG

ACACCACCAACTCGTCGCGCTCGTAA,

Theobroma cacao (TcLPAT2) truncated (e.g., to remove organelle

targeting sequences) (corresponds to nt 136-933 of SEQ ID NO: 54),

798 nt

SEQ ID NO: 56

GATGATGCTTTTGTTGATGATGACGGATGGATTTGTTCATTGATATCTTGTGTAAGGATTG

TTGCATGTTTCCTGACAATGATGGTCACAACATTCATTTGGGCATTGATCATGCTCTTGCT

CCTTCCTTGGCCTTCCCAGCGAATCAGGCAAGGAAATATTTATGGCCATGTGACTGGTAG

ATTGCTGATGTGGATCTTAGGAAATCCTATAAAGATTGAAGGAACAGAGTTCTCCAATGA

GAGAGCCATTTATATCTGCAATCATGCATCTCCCATAGACATTTTCCTCATTATGTGGTTG

ACTCCAACAGGGACTGTTGGCATTGCAAAGAAAGAGATCATTTGGTATCCCCTATTTGGA

CAACTATATGTTCTAGCGAATCATCTCCGCATTGATCGATCTAACCCTAGTACAGCCATT

CAGTCCATGAAAGAGGCAGTTCAGGCTGTGATAAAACACAACCTATCTTTGATTATTTTT

CCTGAGGGCACAAGGTCAAAAAATGGACGATTGCTCCCCTTTAAAAAGGGCTTTGTTCAT

TTGGCCTTGCAGTCACACATTCCAATAGTTCCAATAGTCTTGACAGGTACTCATCTAGCA

TGGAGGAAAGGTAGCTTGCATGTTCGACCGGCTCCTATATCTGTAAAATATCTCCCTCCG

ATAAGTACCGATAGTTGGAAAGATGACAAGATTGATGACTACATAAAAATGGTGCATGA

CATATATGTCGAAAACCTCCCTGAGCCTCAAAAGCCTATTGTATCAGAAGACACCACTAA

CAGTTCAAGATCATAA,

Theobroma cacao 1-acyl-sn-glycerol-3-phosphate acyltransferase

4 (TcLPAT3), XM_007017391.2 348-1493, 1146 nt

SEQ ID NO: 57

ATGGAAGTTTGCAGGCCCCTCAAACCTGATGATAAATTAAAGCACCGCCCTTTGACTCCT

TTTAGGTTTTTAAGGGGTCTGATATGTTTAGTGGTGTTTCTCTTGACTGCTTTTATGTTTCT

AGCGTATTTAGGACCTGGGGCTGTCCTATTGCGATTTTTCAGCCTACACTACTGTAGGAA

GGCAACATCCTTCTTCTTTGGCCTATGGCTAGCTTTGTGGCCCTTTCTTTTTGAAAAAATA

AACAGGACTAAAGTGGTTTTCTCTGGGGATAATGCTCCACAGAAGGAACGTGTTTTACTT

ATTGTCAATCACAGGACTGAAGTTGATTGGATGTACCTCTGGGATCTTGCAATGCGAAAG

GGCTGCCTGGGCTACATCAAATATATTCTTAAGAGCAGCCTGATGAAACTACCTGTCCTT

GGTTGGGGATTTCACATCTTGGAGTTCATTTCAGTAGATAGGAAGTGGGAAACTGATGAA

AATGTCCTGCGCCAAATGCTTTCAACCTTTAAGAATCCTCGAGATCCTTTATGGCTTGCTC

TTTTCCCTGAAGGAACCGATTTTACCGAAGAAAAATGCAGGAACAGTCAGAAGTTTGCA

GCTGAAGTTGGATTGCCTGTGTTGACAAATGTGCTGCTACCGAGAACAAGGGGGTTTTGC

CTTTGCTTAGAAACACTTAGGGACTCTTTGGATGCAGTTTACGATTTGAGTATTGCATATA

AGCACCAATGCCCCTTCTTTCTGGACAATGTTTTTGGTGTGGATCCATCAGAGGTTCACAT

TCATGTTCGACGTATCCCAGTTAAGGAGATCCCAACATCTAATGCAGAGGCTGCTGCTTG

GTTAATTGATACATTCAAGCTCAAGGACCAGTTGCTCTCAGATTTCAAATCTCAGGGACA

TTTTCCTAACCAAGGAACTCAACAAGAACTTTCTTCTTTGAAGTCCTTATTAAATCTAACA

GTGATAATATCCTTGACAGCCATATTCACTTATCTTACCTTTTCTTCCAATTTGTACATGA

TATATGTAAGCTTAGCTTGTCTATACCTTGCTTACATTACTCATTATAAAATTCGCCCAAT

GCCAGTTCTAAGCTCTGTAAAACCGCTGTCTTACCCAAAGGGCAAGAGAGATGAATAA,

Theobroma cacao Lysophosphatidyl acyltransferase 5 (TcLPAT4),

GenBank: CM001880.1 REGION: 6183094-6185435 with CDS: 1-563,

806-936, 1918-2342; 1119 nt

SEQ ID NO: 58

ATGGAAGTTCCTAGTGCAAATCATGAAATGAGGCATCGTTCATTGACCCCGCTAAGGGTG

TTTAGGGGTCTAATATGTTTGCTAGTGCTGTTTTCAACAGCTTTTATGATGATAGTGTATT

GTGGCTTTCTTACCACTGTTATATTCAGGCTTTTCAGCATACATTACAGTCGGAAAGCAA

CTTCTTTCTTCTTTAGTGCTTGGCTGTCTTTATGGCCCTTTTTATTTGAGAAAATAAACAA

AACAAAAGTCATTTTTTCTGGAGATGATGTTCCTCCAAGGGAACGCGTTTTGCTTATTTGC

AACCACAGAACCGAGGTTGACTGGATGTACTTGTGGGACTTTGCATTGCGGAAAGGTTG

CCTGGGATACATAAAGTATATCCTTAAGAGCAGCTTGATGAAATTACCTGTATTTGGTTG

GGCTTTCCATATTTTAGAGTTCATCCCTGTGGAAAGGAAGTGGGAGGTTGATGAATCTAA

CATGCGCAACATGCTTTCAACATTCAAAGATCCTCAAGATCCTCTCTGGCTTGTTCTCTTT

CCCGAAGGAACAGATTTCACTGAGCAAAAATGCTTAAGAAGTCAAAAATATGCAGCTGA

AAATGGCTTACCTATCCTAAAGAATTTGCTGCTTCCAAAATCAAAGGGTTTTTTCGCCTG

CTTGGAAGATTTGAGGAGCTCTTTGGATGCAGTTTATGATGTGACCATTGGATATAAGCA

TTGCTGCCCATCCTTCTTGGACAATGTCTTCGGGGTAGACCCTTCTGAAGTTCATATTCAC

ATCAGACGCATTACCCTGGATGACATTCCAATATCTGAAAGGGAGTTAACCGCTTGGTTA

ATGGATACATTTCAACATAAAGATCAATTGCTTTCTAATTTCAAGTCTGAAGGTTATTTCC

CTCGGCAAGGACCGGAAGTAAACCTCTCTGCAGTGAAGTGCATTGTAGACGTTGTGCTG

GTGCTTTTCTTGACTAGTGCATTCATATTTTTCACCTTTTTCTCATCCATTTGGTTTAAGAT

ATTTGTATCTTTATCTTGTGCCTATATGACTTCTGCAACTTATTTAAACACCCGTCCAGTA

CCAGTCTTCAGCCTTGTGAAAACTTGTGTCTAA,

Theobroma cacao 1-acyl-sn-glycerol-3-phosphate acyltransferase 1,

chloroplastic (TcLPAT1), Ref. No. XP_007011912.2, 359 aa (corresponds

to SEQ ID NO: 52)

SEQ ID NO: 59

MELSSLPSVSSFSLCHPKPRSSATLPFLPFSNRKGAYFGYSLCKRATLRNSCNSAQNNFLRISR

THDGVSRCYFNQKEGLNRSYYNSKLHNENKLSRYIVARSEFAGTGTPDAAYSLSEIKPGSKV

RGVCFYAVTAIAAILLIWFMLVLHPFVLLFDRYRRKAQHFIAKLWAMATVAPFFKIEFEGLEN

LPPQDVPAVYVSNHQSFLDIYTLLTLGRSFKFISKTGIFLYPIIGWAMSMMGLIPLKRMDSRSQ

LDCLKRCMDLIRNGASVFFFPEGTRSKDGKLGAFKKGAFSVAAKTGVPVVPMTLIGTGKIMP

LGLEGVINSGSVKVVIHKPIKGSDPEILCNEARNTIADTLKHQC,

Theobroma cacao 1-acyl-sn-glycerol-3-phosphate acyltransferase

(TcLPAT2), Ref. No. XP_007020857.2 (corresponds to SEQ ID NO: 53

or SEQ ID NO: 54), 310 aa

SEQ ID NO: 60

MESSGSGSFLRNRRLGSFLDTNSDPNVRETQKVLSKGGARQRPKTDDAFVDDDGWICSLISC

VRIVACFLTMMVTTFIWALIMLLLLPWPSQRIRQGNIYGHVTGRLLMWILGNPIKIEGTEFSNE

RAIYICNHASPIDIFLIMWLTPTGTVGIAKKEIIWYPLFGQLYVLANHLRIDRSNPSTAIQSMKE

AVQAVIKHNLSLIIFPEGTRSKNGRLLPFKKGFVHLALQSHIPIVPIVLTGTHLAWRKGSLHVR

PAPISVKYLPPISTDSWKDDKIDDYIKMVHDIYVENLPEPQKPIVSEDTTNSSRS,

Theobroma cacao TcLPAT2 truncated (corresponds to SEQ ID NO: 55

or SEQ ID NO: 56; corresponds to aa 46-310 of SEQ ID NO: 60), 266 aa

SEQ ID NO: 61

MDDAFVDDDGWICSLISCVRIVACFLTMMVTTFIWALIMLLLLPWPSQRIRQGNIYGHVTGR

LLMWILGNPIKIEGTEFSNERAIYICNHASPIDIFLIMWLTPTGTVGIAKKEIIWYPLFGQLYVLA

NHLRIDRSNPSTAIQSMKEAVQAVIKHNLSLIIFPEGTRSKNGRLLPFKKGFVHLALQSHIPIVPI

VLTGTHLAWRKGSLHVRPAPISVKYLPPISTDSWKDDKIDDYIKMVHDIYVENLPEPQKPIVS

EDTTNSSRS,

Theobroma cacao 1-acyl-sn-glycerol-3-phosphate acyltransferase 4

(TcLPAT3) Ref. No. XP_007017453.1 (corresponds to SEQ ID NO: 57),

381 aa

SEQ ID NO: 62

MEVCRPLKPDDKLKHRPLTPFRFLRGLICLVVFLLTAFMFLAYLGPGAVLLRFFSLHYCRKAT

SFFFGLWLALWPFLFEKINRTKVVFSGDNAPQKERVLLIVNHRTEVDWMYLWDLAMRKGCL

GYIKYILKSSLMKLPVLGWGFHILEFISVDRKWETDENVLRQMLSTFKNPRDPLWLALFPEGT

DFTEEKCRNSQKFAAEVGLPVLTNVLLPRTRGFCLCLETLRDSLDAVYDLSIAYKHQCPFFLD

NVFGVDPSEVHIHVRRIPVKEIPTSNAEAAAWLIDTFKLKDQLLSDFKSQGHFPNQGTQQELS

SLKSLLNLTVIISLTAIFTYLTFSSNLYMIYVSLACLYLAYITHYKIRPMPVLSSVKPLSYPKGK

RDE,

Theobroma cacao Lysophosphatidyl acyltransferase 5 (TcLPAT4) Ref.

No. EOX98557.1 (corresponds to SEQ ID NO: 58), 372 aa

SEQ ID NO: 63

MEVPSANHEMRHRSLTPLRVFRGLICLLVLFSTAFMMIVYCGFLTTVIFRLFSIHYSRKATSFF

FSAWLSLWPFLFEKINKTKVIFSGDDVPPRERVLLICNHRTEVDWMYLWDFALRKGCLGYIK

YILKSSLMKLPVFGWAFHILEFIPVERKWEVDESNMRNMLSTFKDPQDPLWLVLFPEGTDFTE

QKCLRSQKYAAENGLPILKNLLLPKSKGFFACLEDLRSSLDAVYDVTIGYKHCCPSFLDNVFG

VDPSEVHIHIRRITLDDIPISERELTAWLMDTFQHKDQLLSNFKSEGYFPRQGPEVNLSAVKCI

VDVVLVLFLTSAFIFFTFFSSIWFKIFVSLSCAYMTSATYLNTRPVPVFSLVKTCV,

In some embodiments of any of the aspects, the acyltransferase catalyzes transesterification of the sn1 OH group of a glyceraldehyde-3-phosphate with a fatty acid. As a non-limiting example, such an acyltransferase is glycerol-3-phosphate acyltransferase (GPAT; E.C. 2.3.1.15). GPAT transfers an acyl-group from acyl-ACP to the sn-1 position of glycerol-3-phosphate producing a lysophosphatidic acid (LPA), an essential step for the triacylglycerol (TAG) and glycerophospholipids. In competition assays, GPATs can show preferences for fatty acyl-CoA substrates of specific chain length and desaturation. In some embodiments of any of the aspects, the functional GPAT gene preferentially produces or leads to the production of TAGs comprising a specific type of fatty acid R group (e.g., C16). As such, the functional GPAT gene can be selected from any GPAT gene from any species that preferentially produces or leads to the production of TAGs comprising a specific type of fatty acid R group (e.g., C16). In some embodiments of any of the aspects, the GPAT is a bacterial GPAT. In some embodiments of any of the aspects, the GPAT is a plant GPAT.

In some embodiments of any of the aspects, the engineered bacterium comprises at least one exogenous copy of at least one functional GPAT gene. In some embodiments of any of the aspects, the engineered bacterium does not comprise a functional endogenous GPAT gene. In some embodiments of any of the aspects, the functional GPAT gene is heterologous. In some embodiments of any of the aspects, the functional heterologous GPAT gene comprises a Durio GPAT gene. In some embodiments of any of the aspects, the functional heterologous GPAT gene comprises a Gossypium GPAT gene. In some embodiments of any of the aspects, the functional heterologous GPAT gene comprises a Hibiscus GPAT gene. In some embodiments of any of the aspects, the functional heterologous GPAT gene comprises a Theobroma GPAT gene.

In some embodiments of any of the aspects, the functional heterologous GPAT gene comprises a Durio zibethinus GPAT gene, Gossypium arboreum GPAT gene, Hibiscus syriacus GPAT gene, or a Theobroma cacao GPAT gene. In some embodiments of any of the aspects, the engineered bacterium comprises at least one exogenous copy of at least one functional GPAT gene comprising one of SEQ ID NOs: 64-67, 69, 71-79, or a nucleic acid sequence that is at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the sequence of at least one of SEQ ID NOs: 64-67, 69, 71-79, that maintains the same functions as at least one of SEQ ID NOs: 64-67, 69, 71-79 (e.g., glycerol-3-phosphate acyltransferase).

In some embodiments of any of the aspects, the amino acid sequence encoded by the functional GPAT gene comprises one of SEQ ID NOs: 80-89, or an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the sequence of at least one of SEQ ID NOs: 80-89, that maintains the same functions as at least one of SEQ ID NOs: 80-89 (e.g., glycerol-3-phosphate acyltransferase).

Durio zibethinus glycerol-3-phosphate acyltransferase 8 isoform X1

(DzGPAT) XM_022914718.1 216-1718, 1503 nt

SEQ ID NO: 64

ATGGCTCCACTGAAAGCGGCGCAAAGCTTTCCATCGATAACGGAATGCGACGGTTCTAC

GTACGAATCGATCGCCGCTGATCTCGATGGCACGCTTTTAATCTCTCGAAGCTCTTTTCCT

TACTTCATGCTCGTCGCCGTGGAAGCGGGAAGCCTCTTTCGAGGTCTTATCCTTCTTCTCT

CTCTGCCTCTGATAATTATTTCTTATCTCTTCGTTTCCGAAGCTATTGGTATCCAAATCCTC

ATTTTTATCTCCTTCGCTGGACTCAAGATCCGCGACATCGAGCTCGTCTCCCGCGCTGTTC

TTCCCAGATTTTATGCTGCGAATGTGAGGAAGGAAAGTTTCGAAGTGTTTGACAGATGCA

AGAGGAAGGTGGTGGTGACGGCGAATCCGACATTCATGGTTGAGCCGTTTGTGAAGGAT

TTTCTAGGTGGAGATAAGGTTTTGGGCACGGAGATTGAAGTGAACCCTAAAACAAAGAA

GGCCACGGGGTTTGTCAAGAAGCCAGGGGTTTTAGTAGGAAAGTTGAAGAGATTGGCCA

TTTTCAAGGAGTTCGGTGATGAATCACCTGATCTTGGAATCGGAGACCGTGAATCTGATC

ACGATTTCATGTCAATTTGCAAGGAGGGTTACATGGTGCACCCTAGTAAGTCAGCAACAC

CGGTACAACTGGATCGTTTAAAAAGCCGCATCATCTTTCATGATGGTCGCTTTGTTCAGC

GCCCGGACCCACTCAATGCCTTAATCACTTATATTTGGCTGCCATTTGGCTTCATCCTATC

CATCATTCGAGTTTACTTCAATCTACCTTTACCAGAGCGTATTGTACGCTACACATACGA

AATGCTGGGTATCCACCTCGTGATCCGTGGGAAGAGACCTCCCCCACCATCTCCTGGGAC

TCCAGGTAACCTCTACGTCTGCAATCACCGTTCAGCTCTTGATCCAATTGTGATCGCCATC

GCACTCGGACGCAAAGTTTCGTGTGTTACATACAGCGTAAGCCGTCTCTCGAGGTTCCTT

TCCCCAATCCCAGCGATTGCTTTAACTCGTGATCGTGCGGCTGATGCTGCCCGAATTTCA

GAACTATTACAAAAAGGTGATTTAGTGGTGTGTCCAGAGGGGACCACGTGCCGCGAGCA

GTTCTTATTACGATTCAGTGCTTTGTTTGCAGAAATGAGCGATAGGATAGTGCCCGTGGC

GGTCAATTGCAGGCAAAACATGTTTTATGGGACGACCGTGAGAGGGGTCAAATTTTGGG

ACCCTTATTTTTTCTTCATGAATCCTAGGCCAACATACGAGGTCACTTTCCTTGATCGATT

GCCGGAGGAGATGACGGTGAAGGCCGGAGGGAAATCGGCTATTGAGGTGGCTAATCAC

GTGCAGAAGGTGCTGGGTGATGTCCTGGGGTTTGAGTGCACTGGATTGACAAGGAAGGA

TAAATATATGTTGCTTGGGGGAAATGATGGTAAGGTTGAATCGATTTACAATGCAAAGA

AATAA

Gossypium arboreum glycerol-3-phosphate acyltransferase 8-like

protein (GaGPAT), GenBank: KN449683 REGION: 14316-18632, CDS join (1-311, 432-744, 3439-

4317), 1503 nt

SEQ ID NO: 65

ATGGCTCCACCGAAAGCAGGGAAAACCTTTCCATCGATAACGGAATGCGATGGATTGAA

GTATGAATCGATCGCCGCCGATCTGGATGGCACGCTTTTAATCTCACGAAGCTCTTTCCC

CTACTTCATGCTTATTGCCGTCGAAGCGGGAAGCCTCCTTCGAGGTCTTATCCTTCTTCTT

TCTCTGCCTCTGGTCATCATATCTTATCTCTTCATTTCCGAAGCTATTGGTATTCAAATCCT

CATTTTCATCTCCTTCGCTGGACTCAAGATCCGCGACATCGAGCTGGTATCTCGCGCTGTT

CTTCCCAGATTCTATGCTGCAAATGTAAGGAAGGAAAGTTTCGAGGTATTTGACAGATGC

AAGAGGAAAGTAGTGGTAACGGCGAATCCGACGTTCATGGTGGAGCCGTTTGTGAAGGA

TTTTCTCGGCGGAGATAAAGTTTTAGGCACAGAGATTGAAGTGAACCCTAAAACAAAGA

AGGCGACGGGATTTGTGAAGAATCCCGGGGTTTTAGTAGGGAAGTTTAAGAGATTAGCC

ATTTTGAAGGAGTTTGGTGATGAATCGCCTGATCTTGGAATCGGAGACCGTGAATCTGAT

CATGATTTCATGTCAATTTGCAAGGAGGGGTACATGGTGCACCCTAGCAAATCAGCATCA

CCAGTACCGCTTGATCGCCTAAAGAGCCGCATTATCTTCCACGATGGTCGCTTTGTCCAA

CGTCCGGATCCACTCAATGCCTGGCTAACCTACCTTTGGCTGCCATTTGGCTTCATCCTCT

CCATTATTCGTGTCTACTTCAATCTACCTTTACCCGAGCGTATCGTACGCTACACTTACGA

GATGCTCGGCATTCACCTCGTGATCCGCGGAAAGCGACCACCCCCACCATCTGCGGGGA

CCCCAGGCAACCTCTACGTCTGCAATCACCGCACAGCTCTTGACCCGATTGTGATCGCCA

TCGCACTTGGACGCAAAGTCTCGTGTGTCACATACAGCGTAAGCCGTCTCTCGAGGTTCC

TATCTCCAATCCCAGCCATTGCTTTAACTCGTGATCGTGCGGCCGATGCTGCCCGAATTTC

AGAACTGTTGCAAAAAGGTGATCTAGTAGTTTGTCCGGAGGGGACCACGTGTCGTGAGC

AATTCTTGTTGAGGTTCAGTGCTTTGTTCGCAGAAATGAGCGATAGGATCGTCCCCGTTG

CCGTCAATTGCAAGCAGAGCATGTTCTACGGGACGACCGTGAGAGGGGTCAAATTCTGG

GACCCTTATTTCTTCTTCATGAATCCAAGGCCAACATACGAGGTCACGTTCCTTGATCGAT

TGCCGGAAGAGATGACAGTGAAGGCCGGAGGGAAATCGGCGATCGAGGTAGCGAATCA

CGTGCAGAAGGTGTTGGGTGATGTCCTGGGGTTTGAATGCACTGGATTGACTAGGAAAG

ATAAATACATGTTGCTTGGAGGAAACGATGGTAAGGTAGAATCGATGTACAATGGCAAG

AAATAA

Hibiscus syriacus glycerol-3-phosphate acyltransferase 8 (HsGPAT),

NCBI Reference Sequence: XM_039207737.1 52-1554, 1503 nt

SEQ ID NO: 66

ATGACTCCACTAAGAGCTGGGAGAAGGTTTCCTTCAATAACGGAATGCAACGGATCGAC

ATACGAATCGATCGCCGCCGATCTCGATGGCACGCTTTTAATCTCACGTAGCTCTTTTCCG

TATTTCATGCTCATTGCCGTCGAAGCGGGAAGCCTCCTTCGAGGTCTTATCCTTCTTCTTT

CACTGCCTCTTGTCATTGTATCTTATCTCTTCATTTCCGAAGCTATTGGTATACAAATCCT

CATTTTCATCTCCTTCGCTGGACTCAAGATCCGCGACATCGAGTTGGTCTCCCGCGCTATT

CTTCCCAGATTTTATGCTGCGAATGTGAGGAAGGAAAGTTTCGAAGTATTTGACAGATGC

AAGAGGAAAGTGGTAGTGACGGCGAATCCGACGTTCATGGTGGAGCCGTTTGTGAAGGA

TTTTCTTGGTGGAGATAAGGTTTTAGGCACAGAGATCGAAGTGAACCCTAAAACAAAGA

AGGCCACGGGATTTGTTAAGAAGCCAGGCGTTTTAGTAAGCGAATTGAAGAGATTGGCC

ATTCTGAAGGAGTTTGGTGACGATTCGCCCGATCTTGGAATCGGAGACCGTGAATCTGAT

CACGATTTCATGTCAATTTGCAAGGAGGGCTACATGGTGCACCCTAGCAAATCAGCATCA

CCGGTACCACTTGATCGCCTGAGAAGCCGCATCATCTTCCACGATGGTCGGTTTGTTCAA

CGCCCGGACCCACTCAATGCCTTGATCACCTACATTTGGCTGCCATTCGGCTTCATCTTGT

CCATCATTCGCGTCTACTTCAATCTACCTTTACCCGAGCGCATCGTACGCTACACATACG

AAATGTTGGGCATTCACCTCGTGATCCGCGGGAAGCGACCGTCGCCGCCGTCTCCGGGTA

CCCCAGGCAACCTCTACGTCTGTAATCACCGTTCAGCACTTGATCCAATCGTCATCGCCA

TCGCTCTCGGACGTAAAGTTTCGTGTGTCACATACAGTGTAAGCCGTCTCTCGAGGTTCC

TATCACCAATCCCAGCCATCGCTTTAACTCGTGATCGTGCGGCTGATGCCGCCCGAATTT

CAGAGCTATTACAAAAAGGTGATCTAGTAGTTTGTCCGGAGGGGACCACGTGTCGCGAG

CCATTCCTGTTGCGATTCAGTGCTTTGTTCGCAGAAATGAGCGATAGAATCGTCCCCGTC

GCCGTCAATTGCAAGCAGAGCATGTTCTACGGGACGACCGTGAGAGGGGTAAAATTCTG

GGACCCTTACTTTTTCTTCATGAACCCAAGGCCAACATACGAGGTCACGTTCCTCGACCG

GTTGCCGGAAGAGATGACGGTGAAGGCCGGAGGAAAATCGGCTATCGAGGTGGCGAAT

CACGTGCAGAAGGTGTTGGGCGATGTACTGGGCTTTGAATGCACGGGATTGACTAGGAA

AGACAAGTATATGTTGCTCGGTGGAAATGATGGTAAGGTCGAATCCATGTACAATGGCA

AGAAATAA

Theobroma cacao Glycerol-3-phosphate acyltransferase 8 (TcGPAT1),

GenBank: CM001879.1 region: complement (36085880-36088399), CDS join (1-311, 448-760, 1642-

2520), 1503 nt

SEQ ID NO: 67

ATGGCTCCAGCGAAATCGGGGCGAAGCTTTCCTTCGATAACGAAATGCGAAGGTTCGAC

GTACGAATCGATAGCCGCCGACCTCGACGGCACGCTTTTAATCTCTCGAAGCTCTTTTCC

TTACTTCATGCTTGTCGCCGTCGAAGCTGGAAGCCTCCTTCGAGGTCTTATCCTTCTTCTC

TCTCTGCCTCTGGTCATTGTTTCTTATCTCTTCATTTCCGAAGCTATTGGCATCCAAATCCT

CATATTTATCTCCTTCGCTGGACTCAAGATCCGCGACATCGAGCTCGTCTCCCGTGCTGTT

CTTCCCAGGTTTTATGCTGCGAATGTGAGGAAGGAAAGTTTCGAGGTGTTTGACAGATGT

AAGAGGAAAGTGGTGGTGACGGCGAATCCGACGTTCATGGTGGAGCCGTTTGTGAAGGA

TTTTCTAGGTGGAGACAAGGTTTTAGGCACAGAAATTGAAGTGAACCCCAAAACAAAGA

AGGCCACGGGGTTTGTCAAGAAGCCTGGGGTTTTAGTCTCGGAGTTGAAGAGACTGGCC

ATTTTGAAGGAGTTTGGAGAGGAATCACCTGATCTTGGAATCGGAGACCGTGAATCTGAT

CATGATTTCATGTCAATTTGCAAGGAGGGCTACATGGTGCACCCTAGCAAATCAGCAACA

CCAGTACCTCTTGATCGCCTAAAGAGCCGCATCATCTTCCATGATGGTCGCTTTGTCCAG

CGCCCGGACCCGCTCAATGCCTTGATCACCTATTTGTGGCTGCCATTTGGCTTCATCCTAT

CCATCGTTCGCGTTTACTTCAATCTGCCTTTACCAGAGCGTATCGTACGCTACACATACGA

AATGCTGGGCATCCACCTCGTGATCCGCGGGAAGCGTCCTCCCCCTCCATCCCCTGGGAC

CCCAGGCAACCTCTACGTCTGCAATCACCGTTCAGCTCTTGATCCAATCGTGATTGCCAT

CGCACTCGGTCGCAAAGTTTCGTGTGTCACGTACAGCGTAAGCCGCCTCTCGAGGTTCCT

GTCTCCAATCCCAGCCGTCGCTTTAACTCGTGATCGTGCGGCTGATGCTGCTAGAATTTC

AGAACTATTGCAAAAAGGTGATCTAGTTGTGTGCCCAGAGGGGACCACGTGCCGCGAGC

AGTTCCTGTTGCGATTCAGTGCTTTGTTCGCAGAGTTGAGCGATAGGATCGTGCCCGTGG

CGGTCAATTGCAGGCAGAACATGTTTTATGGTACGACCGTGAGAGGGGTCAAATTTTGG

GACCCTTATTTTTTCTTCATGAATCCTAGGCCAACGTACGAGGTCACTTTCCTTGATCGTT

TGCCGGAGGAGATGACGGTTAAGGCCGGAGGGAAATCGTCGATTGAGGTGGCCAATCAC

GTGCAGAAGGTGCTGGGCGATGTCCTGGGGTTTGAGTGCACTGGATTGACTAGGAAGGA

TAAATATCTGTTGCTTGGAGGAAACGACGGTAAGGTTGAATCAATGTACAATGCCAAGA

AATAA

Theobroma cacao Glycerol-3-phosphate acyltransferase 9 isoform 1

(TcGPAT2), GenBank: CM001880.1 region: complement (2403687-2408244) CDS join (1-242, 364-

421, 746-864, 1029-1128, 1370-1465, 1653-1749, 2474-2561, 2642-2738, 2834-2919, 3493-3612,

3752-3850, 4510-4558), 1251 nt

SEQ ID NO: 69

ATGAAGAAGGAAAAGCTGTTTGGTTTTATCAATATAAAGAAAAAAGAAAAAGAAGAAA

AAAAACCAAAACCAAACAAAAATCCCAACAGCCAAACCAAATCAGAAAGCGAAAGGGA

AGGCATGAGTAGCAGAGGAGGGAAGCTGAGCTCATCCAGCTCCGAATTGGACTTGGATG

GACCTAACATCGAAGATTATCTCCCGTCCGGATCCTCCATTAACGAACCTCGCGGGAAGC

TTCGCCTACGCGATTTGCTTGATATTTCTCCCACTTTAACTGAAGCTGCTGGTGCCATTGT

TGATGATTCATTCACACGATGTTTTAAGTCGAATCCCCCTGAACCATGGAACTGGAATGT

ATATTTGTTCCCACTGTGGTGTTTTGGTGTGGCAGTTCGGTACTTGATTTTATTCCCTGCG

AGGGTTGTGGTGTTGACAATAGGATGGATAATATTTCTTTCATCCTTCATTCCCGTACACT

TTCTACTCAAAGGGCATGATAAGTTGCGGAAAAAGATGGAGAGGGTTTTGGTGGAGCTA

ATGTGCAGCTTCTTTGTTGCATCGTGGACTGGAGTTGTGAAGTACCATGGACCACGGCCT

AGCATTCGGCCCAAGCAGGTGTTTGTGGCCAATCATACTTCTATGATCGATTTCATCATA

TTAGAACAGATGACTGCATTTGCTGTCATTATGCAGAAGCACCCTGGATGGGTTGGACTG

TTGCAGAGCACTATTTTAGAGAGTGTGGGGTGTATTTGGTTCAACCGTTCAGAGGCAAAA

GATCGGGAAATTGTAGCAAAGAAGTTAAGGGATCATGTTCAGGGGGTTGACAATAACCC

GCTTCTCATTTTTCCTGAAGGGACCTGCATAAACAATCAGTACAGTGTCATGTTTAAGAA

GGGTGCATTTGAACTCGGTTGCACAGTTTGTCCGATTGCAATCAAGTACAATAAAATTTT

TGTTGATGCGTTTTGGAATAGCCGGAAGCAGTCCTTCACGATGCATCTGTTGCAGCTTAT

GACATCCTGGGCTGTTGTTTGTGATGTGTGGTACCTAGAACCCCAAAATCTAAGGCCTGG

AGAAACACCAATTGAATTTGCAGAGAGGGTCAGAGACATAATATCTGTTCGAGCAGGTC

TTAAAAAGGTTCCATGGGATGGATATTTGAAGTACTCTCGCCCTAGCCCTAAGCATAGAG

AGCGAAAGCAACAAAGCTTTGCTGAGTCCGTGCTTCTGCGACTGGAGGAAAAGTGA

Theobroma cacao Glycerol-3-phosphate acyltransferase 9 isoform 1

(TcGPAT2) truncated (corresponds to nt 211-1251 of SEQ ID NO: 69), 1044 nt

SEQ ID NO: 71

ATGTCCATTAACGAACCTCGCGGGAAGCTTCGCCTACGCGATTTGCTTGATATTTCTCCC

ACTTTAACTGAAGCTGCTGGTGCCATTGTTGATGATTCATTCACACGATGTTTTAAGTCGA

ATCCCCCTGAACCATGGAACTGGAATGTATATTTGTTCCCACTGTGGTGTTTTGGTGTGGC

AGTTCGGTACTTGATTTTATTCCCTGCGAGGGTTGTGGTGTTGACAATAGGATGGATAAT

ATTTCTTTCATCCTTCATTCCCGTACACTTTCTACTCAAAGGGCATGATAAGTTGCGGAAA

AAGATGGAGAGGGTTTTGGTGGAGCTAATGTGCAGCTTCTTTGTTGCATCGTGGACTGGA

GTTGTGAAGTACCATGGACCACGGCCTAGCATTCGGCCCAAGCAGGTGTTTGTGGCCAAT

CATACTTCTATGATCGATTTCATCATATTAGAACAGATGACTGCATTTGCTGTCATTATGC

AGAAGCACCCTGGATGGGTTGGACTGTTGCAGAGCACTATTTTAGAGAGTGTGGGGTGT

ATTTGGTTCAACCGTTCAGAGGCAAAAGATCGGGAAATTGTAGCAAAGAAGTTAAGGGA

TCATGTTCAGGGGGTTGACAATAACCCGCTTCTCATTTTTCCTGAAGGGACCTGCATAAA

CAATCAGTACAGTGTCATGTTTAAGAAGGGTGCATTTGAACTCGGTTGCACAGTTTGTCC

GATTGCAATCAAGTACAATAAAATTTTTGTTGATGCGTTTTGGAATAGCCGGAAGCAGTC

CTTCACGATGCATCTGTTGCAGCTTATGACATCCTGGGCTGTTGTTTGTGATGTGTGGTAC

CTAGAACCCCAAAATCTAAGGCCTGGAGAAACACCAATTGAATTTGCAGAGAGGGTCAG

AGACATAATATCTGTTCGAGCAGGTCTTAAAAAGGTTCCATGGGATGGATATTTGAAGTA

CTCTCGCCCTAGCCCTAAGCATAGAGAGCGAAAGCAACAAAGCTTTGCTGAGTCCGTGCT

TCTGCGACTGGAGGAAAAGTGA

Theobroma cacao Glycerol-3-phosphate acyltransferase 1 (TcGPAT3)

codon-optimized, 1623 nt

SEQ ID NO: 72

ATGGTGTTCCCGGTGGTGTTCCTGAAGCTGGCCGACTGGGTGCTGTACCAGCTGCTGGCC

AACTCGTGCTACCGCGCCGCCCGCAAGATGCGCAACTACGGCTTCTTCCTGCGCAACCAG

ACCCTGCGCTCGCCGCCGCAGCAGCAGGCCGCCTCGCTGTTCCCGTCGGTGACCAAGTGC

GACGTGGGCAACTCGCGCCGCTTCGACACCCTGGTGTGCGACATCCACGGCGTGCTGCTG

GGCTCGGACACCTTCTTCCCGTACTTCATGCTGGTGGCCTTCGAGGGCGGCTCGATCGTG

CGCGCCTTCCTGCTGCTGCTGTCGTGCTCGTTCCTGTGGGTGCTGGACTCGGAGCTGAAG

CTGCGCATCATGATCTTCATCTCGTTCTGCGGCCTGCGCAAGAAGGACATCGAGTCGGTG

GGCCGCGCCGTGCTGCCGAAGTTCTACCTGGAGAACCTGAACCTGCAGGTGTACGAGGT

GTGGTCGAAGACCTCGTCGCGCGTGGTGTTCACCTCGATCCCGCGCGTGATGGTGGAGGG

CTTCCTGCACGAGTACATGTCGGCCTCGGGCGTGGTGGGCACCGAGCTGCACACCGTGG

GCAACCGCTTCACCGGCCTGCTGTCGTCGTCGGGCCTGCTGGTGAAGCACAACGCCCTGA

AGGAGCACTTCGGCGACAAGAAGCCGGACGTGGGCCTGGGCTCGTCGTCGCTGCACGAC

CAGTACTTCATCTCGCTGTGCAAGGAGGCCTACGTGGTGAACATGGAGGACGGCAAGTC

GAACCTGTCGTCGTTCATGCCGCGCGACAAGTACCCGAAGCCGCTGATCTTCCACGACGG

CCGCCTGGCCTTCCTGCCGACCCCGTTCGCCACCCTGTCGATGTTCCTGTGGCTGCCGTTC

GGCATCGTGCTGTCGATCCTGCGCATCTTCGTGGGCATCTGCCTGCCGTACAAGCTGGCC

GTGATCTGCGCCACCCTGTCGGGCGTGCAGCTGAAGTTCCAGGGCTGCTTCCCGTCGTCG

AACTCGCAGCACAAGAAGGGCGTGCTGTACGTGTGCACCCACCGCACCCTGCTGGACCC

GGTGTTCCTGTCGACCGCCCTGTGCAAGCCGCTGACCGCCGTGACCTACTCGCTGTCGAA

GATGTCGGAGCTGATCGCCCCGATCAAGACCGTGCGCCTGACCCGCGACCGCAAGCAGG

ACGGCGAGACCATGCAGAAGCTGCTGTCGGAGGGCGACCTGGTGGTGTGCCCGGAGGGC

ACCACCTGCCGCGAGCCGTACCTGCTGCGCTTCTCGTCGCTGTTCGCCGAGCTGGCCGAC

GAGATCGTGCCGGTGGCCATCAACGCCCACGTGTCGATGTTCTACGGCACCACCGCCTCG

GGCCTGAAGTGCCTGGACCCGATCTTCTTCCTGATGAACCCGCGCCCGTCGTACCACGTG

CAGATCCTGGGCAAGGTGCCGCAGGAGTTCACCTGCGCCGGCGGCCGCTCGTCGCTGGA

GGTGGCCAACTACATCCAGCGCAAGCTGGCCGACGCCCTGGGCTTCGAGTGCACCACCC

TGACCCGCCGCGACAAGTACCTGATGCTGGCCGGCAACGAGGGCGTGGTGCACGAGAAC

AAGCGCAACTAA

Theobroma cacao Glycerol-3-phosphate acyltransferase 1 (TcGPAT3),

GenBank: CM001879.1 region: 9957750-9959837, CDS join (1-741, 1207-2088), 1623 nt

SEQ ID NO: 73

ATGGTTTTCCCTGTGGTATTTCTGAAGCTAGCAGACTGGGTCTTGTACCAGCTGCTGGCC

AACTCATGTTATAGAGCTGCAAGGAAGATGAGAAACTACGGGTTCTTTCTAAGGAACCA

AACTCTTAGGTCACCACCACAGCAACAAGCTGCTTCTTTGTTCCCTAGTGTTACCAAGTG

TGATGTAGGCAATAGTAGAAGGTTTGATACATTGGTCTGTGATATCCATGGAGTCTTGTT

AGGATCAGACACATTTTTTCCTTACTTCATGCTAGTTGCTTTTGAAGGTGGTAGCATTGTG

AGAGCCTTTCTGTTGCTTTTATCATGCTCCTTTTTGTGGGTATTGGACTCAGAGCTCAAGT

TGAGGATTATGATTTTTATTTCCTTTTGTGGGCTTAGGAAGAAGGACATCGAGAGTGTTG

GCAGGGCTGTTTTGCCAAAGTTTTATCTCGAGAATCTAAATCTCCAAGTCTATGAAGTTT

GGTCTAAAACAAGTTCAAGGGTTGTCTTTACAAGTATACCTAGAGTAATGGTGGAAGGA

TTTCTCCACGAATACATGAGTGCTAGTGGTGTTGTAGGCACCGAATTGCACACTGTTGGG

AACCGATTCACAGGTTTGTTGTCCAGCTCCGGGTTGCTTGTAAAGCATAATGCTTTAAAG

GAACACTTCGGAGATAAAAAGCCTGATGTTGGCCTCGGAAGTTCAAGCCTCCATGACCA

ATACTTTATCTCCCTTTGCAAGGAAGCCTATGTGGTGAACATGGAAGATGGCAAAAGCA

ATCTAAGCAGTTTCATGCCAAGGGACAAGTACCCGAAGCCTCTTATATTTCATGATGGGA

GGCTAGCTTTCTTGCCAACTCCATTTGCAACTCTTTCAATGTTCCTGTGGCTTCCATTTGG

AATAGTTCTTTCCATTCTTAGGATTTTCGTTGGTATCTGCCTGCCTTACAAGCTAGCTGTT

ATCTGCGCTACTCTGAGTGGTGTACAGCTGAAATTCCAAGGGTGCTTCCCTTCATCAAAT

TCACAACATAAAAAAGGGGTTCTTTATGTTTGTACCCATAGAACTCTTCTGGACCCAGTT

TTCCTTAGCACAGCATTATGCAAGCCTTTGACTGCAGTTACTTATAGTCTAAGCAAAATG

TCTGAACTGATAGCTCCCATCAAAACAGTTAGGTTGACAAGGGACAGGAAACAAGATGG

AGAAACCATGCAAAAATTGCTCAGTGAAGGTGATTTGGTAGTGTGCCCGGAAGGAACCA

CATGCAGAGAGCCTTACTTGTTAAGGTTTAGCTCATTGTTTGCTGAGCTAGCCGATGAGA

TAGTCCCAGTGGCCATAAACGCACATGTAAGCATGTTTTACGGGACAACTGCAAGTGGG

TTAAAATGCTTGGATCCTATCTTCTTTCTGATGAACCCCAGACCTAGCTACCATGTTCAAA

TCCTTGGGAAGGTGCCTCAAGAGTTTACATGTGCAGGGGGCAGGTCTAGCCTTGAAGTG

GCAAATTATATTCAGAGAAAGCTGGCTGATGCTCTGGGATTTGAGTGCACTACCCTTACA

AGGAGAGACAAGTACTTGATGCTAGCAGGCAATGAAGGGGTTGTCCATGAAAATAAGAG

AAATTAA

Theobroma cacao Glycerol-3-phosphate acyltransferase 1 (TcGPAT3)

truncated codon-optimized (corresponds to nt 61-1623 of SEQ ID NO: 72), 1566 nt

SEQ ID NO: 74

ATGAACTCGTGCTACCGCGCCGCCCGCAAGATGCGCAACTACGGCTTCTTCCTGCGCAAC

CAGACCCTGCGCTCGCCGCCGCAGCAGCAGGCCGCCTCGCTGTTCCCGTCGGTGACCAAG

TGCGACGTGGGCAACTCGCGCCGCTTCGACACCCTGGTGTGCGACATCCACGGCGTGCTG

CTGGGCTCGGACACCTTCTTCCCGTACTTCATGCTGGTGGCCTTCGAGGGCGGCTCGATC

GTGCGCGCCTTCCTGCTGCTGCTGTCGTGCTCGTTCCTGTGGGTGCTGGACTCGGAGCTG

AAGCTGCGCATCATGATCTTCATCTCGTTCTGCGGCCTGCGCAAGAAGGACATCGAGTCG

GTGGGCCGCGCCGTGCTGCCGAAGTTCTACCTGGAGAACCTGAACCTGCAGGTGTACGA

GGTGTGGTCGAAGACCTCGTCGCGCGTGGTGTTCACCTCGATCCCGCGCGTGATGGTGGA

GGGCTTCCTGCACGAGTACATGTCGGCCTCGGGCGTGGTGGGCACCGAGCTGCACACCG

TGGGCAACCGCTTCACCGGCCTGCTGTCGTCGTCGGGCCTGCTGGTGAAGCACAACGCCC

TGAAGGAGCACTTCGGCGACAAGAAGCCGGACGTGGGCCTGGGCTCGTCGTCGCTGCAC

GACCAGTACTTCATCTCGCTGTGCAAGGAGGCCTACGTGGTGAACATGGAGGACGGCAA

GTCGAACCTGTCGTCGTTCATGCCGCGCGACAAGTACCCGAAGCCGCTGATCTTCCACGA

CGGCCGCCTGGCCTTCCTGCCGACCCCGTTCGCCACCCTGTCGATGTTCCTGTGGCTGCCG

TTCGGCATCGTGCTGTCGATCCTGCGCATCTTCGTGGGCATCTGCCTGCCGTACAAGCTG

GCCGTGATCTGCGCCACCCTGTCGGGCGTGCAGCTGAAGTTCCAGGGCTGCTTCCCGTCG

TCGAACTCGCAGCACAAGAAGGGCGTGCTGTACGTGTGCACCCACCGCACCCTGCTGGA

CCCGGTGTTCCTGTCGACCGCCCTGTGCAAGCCGCTGACCGCCGTGACCTACTCGCTGTC

GAAGATGTCGGAGCTGATCGCCCCGATCAAGACCGTGCGCCTGACCCGCGACCGCAAGC

AGGACGGCGAGACCATGCAGAAGCTGCTGTCGGAGGGCGACCTGGTGGTGTGCCCGGAG

GGCACCACCTGCCGCGAGCCGTACCTGCTGCGCTTCTCGTCGCTGTTCGCCGAGCTGGCC

GACGAGATCGTGCCGGTGGCCATCAACGCCCACGTGTCGATGTTCTACGGCACCACCGCC

TCGGGCCTGAAGTGCCTGGACCCGATCTTCTTCCTGATGAACCCGCGCCCGTCGTACCAC

GTGCAGATCCTGGGCAAGGTGCCGCAGGAGTTCACCTGCGCCGGCGGCCGCTCGTCGCT

GGAGGTGGCCAACTACATCCAGCGCAAGCTGGCCGACGCCCTGGGCTTCGAGTGCACCA

CCCTGACCCGCCGCGACAAGTACCTGATGCTGGCCGGCAACGAGGGCGTGGTGCACGAG

AACAAGCGCAACTAA

Theobroma cacao Glycerol-3-phosphate acyltransferase 1 (TcGPAT3)

truncated (corresponds to nt 61-1623 of SEQ ID NO: 73), 1566 nt

SEQ ID NO: 75

ATGAACTCATGTTATAGAGCTGCAAGGAAGATGAGAAACTACGGGTTCTTTCTAAGGAA

CCAAACTCTTAGGTCACCACCACAGCAACAAGCTGCTTCTTTGTTCCCTAGTGTTACCAA

GTGTGATGTAGGCAATAGTAGAAGGTTTGATACATTGGTCTGTGATATCCATGGAGTCTT

GTTAGGATCAGACACATTTTTTCCTTACTTCATGCTAGTTGCTTTTGAAGGTGGTAGCATT

GTGAGAGCCTTTCTGTTGCTTTTATCATGCTCCTTTTTGTGGGTATTGGACTCAGAGCTCA

AGTTGAGGATTATGATTTTTATTTCCTTTTGTGGGCTTAGGAAGAAGGACATCGAGAGTG

TTGGCAGGGCTGTTTTGCCAAAGTTTTATCTCGAGAATCTAAATCTCCAAGTCTATGAAG

TTTGGTCTAAAACAAGTTCAAGGGTTGTCTTTACAAGTATACCTAGAGTAATGGTGGAAG

GATTTCTCCACGAATACATGAGTGCTAGTGGTGTTGTAGGCACCGAATTGCACACTGTTG

GGAACCGATTCACAGGTTTGTTGTCCAGCTCCGGGTTGCTTGTAAAGCATAATGCTTTAA

AGGAACACTTCGGAGATAAAAAGCCTGATGTTGGCCTCGGAAGTTCAAGCCTCCATGAC

CAATACTTTATCTCCCTTTGCAAGGAAGCCTATGTGGTGAACATGGAAGATGGCAAAAGC

AATCTAAGCAGTTTCATGCCAAGGGACAAGTACCCGAAGCCTCTTATATTTCATGATGGG

AGGCTAGCTTTCTTGCCAACTCCATTTGCAACTCTTTCAATGTTCCTGTGGCTTCCATTTG

GAATAGTTCTTTCCATTCTTAGGATTTTCGTTGGTATCTGCCTGCCTTACAAGCTAGCTGT

TATCTGCGCTACTCTGAGTGGTGTACAGCTGAAATTCCAAGGGTGCTTCCCTTCATCAAA

TTCACAACATAAAAAAGGGGTTCTTTATGTTTGTACCCATAGAACTCTTCTGGACCCAGT

TTTCCTTAGCACAGCATTATGCAAGCCTTTGACTGCAGTTACTTATAGTCTAAGCAAAAT

GTCTGAACTGATAGCTCCCATCAAAACAGTTAGGTTGACAAGGGACAGGAAACAAGATG

GAGAAACCATGCAAAAATTGCTCAGTGAAGGTGATTTGGTAGTGTGCCCGGAAGGAACC

ACATGCAGAGAGCCTTACTTGTTAAGGTTTAGCTCATTGTTTGCTGAGCTAGCCGATGAG

ATAGTCCCAGTGGCCATAAACGCACATGTAAGCATGTTTTACGGGACAACTGCAAGTGG

GTTAAAATGCTTGGATCCTATCTTCTTTCTGATGAACCCCAGACCTAGCTACCATGTTCAA

ATCCTTGGGAAGGTGCCTCAAGAGTTTACATGTGCAGGGGGCAGGTCTAGCCTTGAAGT

GGCAAATTATATTCAGAGAAAGCTGGCTGATGCTCTGGGATTTGAGTGCACTACCCTTAC

AAGGAGAGACAAGTACTTGATGCTAGCAGGCAATGAAGGGGTTGTCCATGAAAATAAGA

GAAATTAA

Theobroma cacao Glycerol-3-phosphate acyltransferase 3 (TcGPAT4)

codon-optimized, 1614 nt

SEQ ID NO: 76

ATGGCCAAGCTGTCGATGGAGTTCTCGTTCTTCCAGACCCTGTTCTTCCTGTTCTGCCGCG

TGGTGTTCCGCCAGTCGAAGAACCACAAGTCGCTGCACCGCAACGTGTCGAACATCCAC

GCCAACGAGGGCAAGTACCACAAGTACCCGTCGTTCGTGCACCGCTCGAACCTGTCGAA

CCAGACCCTGGTGTTCTCGGTGGAGGAGGCCCTGCTGAAGTCGTCGTCGCTGTTCCCGTA

CTTCATGCTGGTGGCCTTCGAGGCCGGCGGCCTGCTGCGCGCCTTCATCCTGTTCGTGCTG

TACCCGATCCTGTGCCTGGTGTCGGAGGAGATGGGCCTGAAGATCATGGTGCTGGTGTGC

TTCTTCGGCATCAAGAAGAAGTCGTTCCGCGTGGGCTCGGCCGTGCTGCCGAAGTTCTTC

CTGGAGGACGTGGGCCTGGAGCCGTTCGAGATGCTGAAGAAGGGCGGCAAGAAGGTGG

CCGTGTCGAAGATCCCGCAGGTGATGATCGAGTCGTTCCTGAAGGACTACCTGGAGATC

GACTTCGTGGTGGGCCGCGAGCTGAAGGAGTTCTGCGGCTACTTCCTGGGCGTGATGGA

GGAGAAGAAGCGCTCGAAGGCCGCCCTGGACGAGATCATCGGCTCGGAGTCGATGGGCT

TCGACGTGATCGGCATCTCGGGCCTGAAGAAGTCGCTGGACTACCACTTCTTCTCGCACT

GCAAGGAGATCTACCAGGTGCGCAAGGCCGACAAGCGCAACTGGCGCCACGTGCCGCGC

CAGGAGTACTCGAAGCCGCTGATCTTCCACGACGGCCGCCTGGCCCTGCGCCCGACCCTG

GTGGCCTCGCTGACCATGTTCGTGTGGTTCCCGTTCGGCCTGGCCCTGTCGATCCTGCGCG

CCGTGGTGGGCCTGATGCTGCCGTACAAGATCTCGATCCCGCTGCTGGCCTACTCGGGCC

TGCACCTGTTCCTGTCGACCCCGGAGTCGTCGCTGCACCCGCTGTCGCTGCCGAACTCGA

AGAAGCAGAACCCGAAGGGCCGCCTGTACGTGTGCAACCACCGCACCCTGCTGGACCCG

GTGTACCTGTCGTTCGCCCTGCAGAAGGACCTGACCGCCGTGACCTACTCGCTGTCGCGC

ATCTCGGAGCTGCTGGCCCCGATCAAGACCGTGCGCCTGGCCCGCGACCGCGACCAGGA

CGGCAAGATGATGGAGAAGATGCTGAACCTGGGCGACCTGGTGGTGTGCCCGGAGGGCA

CCACCTGCCGCGAGCCGTACCTGCTGCGCTTCTCGCCGCTGTTCTCGGAGATGTCGGACG

ACATCGTGCCGGTGGCCATGGACTCGAACGTGTCGCTGTTCTACGGCACCACCGCCTCGG

GCCTGAAGTGCCTGGACCCGCTGTTCTTCCTGATGAACCCGCGCCCGATCTACACCGTGC

AGATCCTGGACGGCGTGTCGGGCCTGTACACCTGCCACGACGGCCAGCGCTCGCGCTTCA

AGGTGGCCAACCAGGTGCAGAACGAGATCGGCAAGGCCCTGGGCTTCGAGTGCACCAAG

CTGACCCGCCGCGACAAGTACCTGATCATGGCCGGCAACGAGGGCATCATCTCGCAGAC

CTAA

Theobroma cacao Glycerol-3-phosphate acyltransferase 3 (TcGPAT4),

GenBank: CM001879.1 region: 33774144-33776095, CDS join (1-720, 1059-1952), 1614 nt

SEQ ID NO: 77

ATGGCTAAACTTTCTATGGAGTTTTCCTTTTTCCAAACCCTTTTCTTCTTATTCTGTCGAGT

TGTCTTTAGACAGTCTAAGAATCACAAATCTCTCCACAGAAATGTCAGCAATATCCATGC

AAACGAGGGTAAATATCATAAGTATCCTTCTTTTGTTCATAGATCAAACCTGTCAAACCA

AACTCTGGTCTTCAGTGTAGAAGAGGCTTTGTTGAAATCCTCATCATTGTTTCCTTACTTC

ATGCTTGTAGCCTTTGAAGCTGGAGGGCTCTTGAGGGCCTTTATTCTTTTTGTTTTATACC

CAATTCTATGCTTAGTTAGCGAAGAGATGGGGTTGAAGATAATGGTCCTGGTTTGCTTCT

TTGGGATTAAGAAAAAGAGCTTCAGAGTTGGAAGTGCTGTTCTGCCGAAGTTCTTCTTGG

AGGATGTTGGCTTGGAACCATTTGAGATGTTGAAGAAAGGCGGGAAAAAGGTGGCTGTC

AGTAAAATTCCTCAAGTGATGATCGAGAGTTTCTTGAAGGATTACCTGGAAATTGATTTT

GTAGTTGGAAGAGAGCTGAAGGAGTTCTGTGGGTACTTTTTGGGAGTCATGGAAGAGAA

GAAGAGAAGTAAGGCTGCTTTGGACGAGATAATTGGAAGCGAAAGTATGGGCTTTGATG

TTATTGGCATCAGTGGCCTCAAGAAATCTCTTGACTATCATTTTTTTTCTCATTGCAAGGA

AATATACCAGGTGAGAAAAGCAGACAAAAGAAACTGGCGACACGTCCCAAGACAGGAG

TATTCCAAACCACTCATTTTCCATGACGGGAGACTAGCTCTCAGGCCAACTCTGGTGGCC

TCCCTGACCATGTTCGTGTGGTTCCCCTTCGGCTTGGCTCTTTCCATACTCAGAGCTGTTG

TCGGCTTAATGCTTCCGTACAAGATTTCCATCCCCTTATTAGCCTACAGCGGGTTGCACCT

GTTTCTTTCAACCCCGGAAAGCTCCCTGCATCCTCTTTCACTTCCGAACTCGAAGAAACA

AAACCCAAAAGGCCGCCTTTATGTTTGCAATCATAGAACACTGCTGGATCCCGTCTACCT

TTCTTTTGCATTACAGAAAGACCTCACTGCTGTTACTTACAGCTTAAGCAGGATATCAGA

GCTGTTAGCTCCAATCAAAACCGTTCGATTAGCAAGGGATCGTGATCAAGATGGTAAAA

TGATGGAAAAGATGCTAAATTTAGGGGACCTAGTCGTATGCCCGGAAGGGACTACGTGT

AGGGAGCCCTATCTCTTAAGGTTCAGCCCTTTATTTTCAGAGATGAGCGACGATATAGTC

CCTGTTGCGATGGACAGCAATGTGAGTTTGTTCTATGGGACAACAGCCAGTGGCCTGAAA

TGTCTGGACCCACTTTTCTTTCTCATGAACCCACGACCAATCTACACTGTCCAGATACTTG

ATGGTGTATCTGGCTTGTACACTTGTCATGATGGTCAAAGATCAAGGTTTAAAGTGGCTA

ATCAGGTTCAGAATGAGATTGGTAAGGCTCTGGGTTTTGAGTGCACCAAGCTTACGAGA

AGAGACAAGTACCTAATCATGGCTGGCAACGAAGGAATAATTAGCCAAACCTAA

Theobroma cacao Glycerol-3-phosphate acyltransferase 3 (TcGPAT4)

truncated codon-optimized (corresponds to nt 73-1614 of SEQ ID NO: 76), 1545 nt

SEQ ID NO: 78

ATGCAGTCGAAGAACCACAAGTCGCTGCACCGCAACGTGTCGAACATCCACGCCAACGA

GGGCAAGTACCACAAGTACCCGTCGTTCGTGCACCGCTCGAACCTGTCGAACCAGACCCT

GGTGTTCTCGGTGGAGGAGGCCCTGCTGAAGTCGTCGTCGCTGTTCCCGTACTTCATGCT

GGTGGCCTTCGAGGCCGGCGGCCTGCTGCGCGCCTTCATCCTGTTCGTGCTGTACCCGAT

CCTGTGCCTGGTGTCGGAGGAGATGGGCCTGAAGATCATGGTGCTGGTGTGCTTCTTCGG

CATCAAGAAGAAGTCGTTCCGCGTGGGCTCGGCCGTGCTGCCGAAGTTCTTCCTGGAGGA

CGTGGGCCTGGAGCCGTTCGAGATGCTGAAGAAGGGCGGCAAGAAGGTGGCCGTGTCGA

AGATCCCGCAGGTGATGATCGAGTCGTTCCTGAAGGACTACCTGGAGATCGACTTCGTGG

TGGGCCGCGAGCTGAAGGAGTTCTGCGGCTACTTCCTGGGCGTGATGGAGGAGAAGAAG

CGCTCGAAGGCCGCCCTGGACGAGATCATCGGCTCGGAGTCGATGGGCTTCGACGTGAT

CGGCATCTCGGGCCTGAAGAAGTCGCTGGACTACCACTTCTTCTCGCACTGCAAGGAGAT

CTACCAGGTGCGCAAGGCCGACAAGCGCAACTGGCGCCACGTGCCGCGCCAGGAGTACT

CGAAGCCGCTGATCTTCCACGACGGCCGCCTGGCCCTGCGCCCGACCCTGGTGGCCTCGC

TGACCATGTTCGTGTGGTTCCCGTTCGGCCTGGCCCTGTCGATCCTGCGCGCCGTGGTGG

GCCTGATGCTGCCGTACAAGATCTCGATCCCGCTGCTGGCCTACTCGGGCCTGCACCTGT

TCCTGTCGACCCCGGAGTCGTCGCTGCACCCGCTGTCGCTGCCGAACTCGAAGAAGCAGA

ACCCGAAGGGCCGCCTGTACGTGTGCAACCACCGCACCCTGCTGGACCCGGTGTACCTGT

CGTTCGCCCTGCAGAAGGACCTGACCGCCGTGACCTACTCGCTGTCGCGCATCTCGGAGC

TGCTGGCCCCGATCAAGACCGTGCGCCTGGCCCGCGACCGCGACCAGGACGGCAAGATG

ATGGAGAAGATGCTGAACCTGGGCGACCTGGTGGTGTGCCCGGAGGGCACCACCTGCCG

CGAGCCGTACCTGCTGCGCTTCTCGCCGCTGTTCTCGGAGATGTCGGACGACATCGTGCC

GGTGGCCATGGACTCGAACGTGTCGCTGTTCTACGGCACCACCGCCTCGGGCCTGAAGTG

CCTGGACCCGCTGTTCTTCCTGATGAACCCGCGCCCGATCTACACCGTGCAGATCCTGGA

CGGCGTGTCGGGCCTGTACACCTGCCACGACGGCCAGCGCTCGCGCTTCAAGGTGGCCA

ACCAGGTGCAGAACGAGATCGGCAAGGCCCTGGGCTTCGAGTGCACCAAGCTGACCCGC

CGCGACAAGTACCTGATCATGGCCGGCAACGAGGGCATCATCTCGCAGACCTAA

Theobroma cacao Glycerol-3-phosphate acyltransferase 3 (TcGPAT4)

truncated (corresponds to nt 73-1614 of SEQ ID NO: 77), 1545 nt

SEQ ID NO: 79

ATGCAGTCTAAGAATCACAAATCTCTCCACAGAAATGTCAGCAATATCCATGCAAACGA

GGGTAAATATCATAAGTATCCTTCTTTTGTTCATAGATCAAACCTGTCAAACCAAACTCT

GGTCTTCAGTGTAGAAGAGGCTTTGTTGAAATCCTCATCATTGTTTCCTTACTTCATGCTT

GTAGCCTTTGAAGCTGGAGGGCTCTTGAGGGCCTTTATTCTTTTTGTTTTATACCCAATTC

TATGCTTAGTTAGCGAAGAGATGGGGTTGAAGATAATGGTCCTGGTTTGCTTCTTTGGGA

TTAAGAAAAAGAGCTTCAGAGTTGGAAGTGCTGTTCTGCCGAAGTTCTTCTTGGAGGATG

TTGGCTTGGAACCATTTGAGATGTTGAAGAAAGGCGGGAAAAAGGTGGCTGTCAGTAAA

ATTCCTCAAGTGATGATCGAGAGTTTCTTGAAGGATTACCTGGAAATTGATTTTGTAGTT

GGAAGAGAGCTGAAGGAGTTCTGTGGGTACTTTTTGGGAGTCATGGAAGAGAAGAAGAG

AAGTAAGGCTGCTTTGGACGAGATAATTGGAAGCGAAAGTATGGGCTTTGATGTTATTG

GCATCAGTGGCCTCAAGAAATCTCTTGACTATCATTTTTTTTCTCATTGCAAGGAAATATA

CCAGGTGAGAAAAGCAGACAAAAGAAACTGGCGACACGTCCCAAGACAGGAGTATTCC

AAACCACTCATTTTCCATGACGGGAGACTAGCTCTCAGGCCAACTCTGGTGGCCTCCCTG

ACCATGTTCGTGTGGTTCCCCTTCGGCTTGGCTCTTTCCATACTCAGAGCTGTTGTCGGCT

TAATGCTTCCGTACAAGATTTCCATCCCCTTATTAGCCTACAGCGGGTTGCACCTGTTTCT

TTCAACCCCGGAAAGCTCCCTGCATCCTCTTTCACTTCCGAACTCGAAGAAACAAAACCC

AAAAGGCCGCCTTTATGTTTGCAATCATAGAACACTGCTGGATCCCGTCTACCTTTCTTTT

GCATTACAGAAAGACCTCACTGCTGTTACTTACAGCTTAAGCAGGATATCAGAGCTGTTA

GCTCCAATCAAAACCGTTCGATTAGCAAGGGATCGTGATCAAGATGGTAAAATGATGGA

AAAGATGCTAAATTTAGGGGACCTAGTCGTATGCCCGGAAGGGACTACGTGTAGGGAGC

CCTATCTCTTAAGGTTCAGCCCTTTATTTTCAGAGATGAGCGACGATATAGTCCCTGTTGC

GATGGACAGCAATGTGAGTTTGTTCTATGGGACAACAGCCAGTGGCCTGAAATGTCTGG

ACCCACTTTTCTTTCTCATGAACCCACGACCAATCTACACTGTCCAGATACTTGATGGTGT

ATCTGGCTTGTACACTTGTCATGATGGTCAAAGATCAAGGTTTAAAGTGGCTAATCAGGT

TCAGAATGAGATTGGTAAGGCTCTGGGTTTTGAGTGCACCAAGCTTACGAGAAGAGACA

AGTACCTAATCATGGCTGGCAACGAAGGAATAATTAGCCAAACCTAA

Durio zibethinus glycerol-3-phosphate acyltransferase 8 isoform X1

(DzGPAT), Ref. No. XP_022770453.1 (corresponds to SEQ ID NO: 64), 500 aa

SEQ ID NO: 80

MAPLKAAQSFPSITECDGSTYESIAADLDGTLLISRSSFPYFMLVAVEAGSLFRGLILLLSLPLIII

SYLFVSEAIGIQILIFISFAGLKIRDIELVSRAVLPRFYAANVRKESFEVFDRCKRKVVVTANPTF

MVEPFVKDFLGGDKVLGTEIEVNPKTKKATGFVKKPGVLVGKLKRLAIFKEFGDESPDLGIG

DRESDHDFMSICKEGYMVHPSKSATPVQLDRLKSRIIFHDGRFVQRPDPLNALITYIWLPFGFI

LSIIRVYFNLPLPERIVRYTYEMLGIHLVIRGKRPPPPSPGTPGNLYVCNHRSALDPIVIAIALGR

KVSCVTYSVSRLSRFLSPIPAIALTRDRAADAARISELLQKGDLVVCPEGTTCREQFLLRFSAL

FAEMSDRIVPVAVNCRQNMFYGTTVRGVKFWDPYFFFMNPRPTYEVTFLDRLPEEMTVKAG

GKSAIEVANHVQKVLGDVLGFECTGLTRKDKYMLLGGNDGKVESIYNAKK

Gossypium arboreum glycerol-3-phosphate acyltransferase 8-like

protein (GaGPAT) Ref. No. KHG29408.1 (corresponds to SEQ ID NO: 65), 500 aa

SEQ ID NO: 81

MAPPKAGKTFPSITECDGLKYESIAADLDGTLLISRSSFPYFMLIAVEAGSLLRGLILLLSLPLVI

ISYLFISEAIGIQILIFISFAGLKIRDIELVSRAVLPRFYAANVRKESFEVFDRCKRKVVVTANPTF

MVEPFVKDFLGGDKVLGTEIEVNPKTKKATGFVKNPGVLVGKFKRLAILKEFGDESPDLGIG

DRESDHDFMSICKEGYMVHPSKSASPVPLDRLKSRIIFHDGRFVQRPDPLNAWLTYLWLPFGF

ILSIIRVYFNLPLPERIVRYTYEMLGIHLVIRGKRPPPPSAGTPGNLYVCNHRTALDPIVIAIALG

RKVSCVTYSVSRLSRFLSPIPAIALTRDRAADAARISELLQKGDLVVCPEGTTCREQFLLRFSA

LFAEMSDRIVPVAVNCKQSMFYGTTVRGVKFWDPYFFFMNPRPTYEVTFLDRLPEEMTVKA

GGKSAIEVANHVQKVLGDVLGFECTGLTRKDKYMLLGGNDGKVESMYNGKK

Hibiscus syriacus glycerol-3-phosphate acyltransferase 8 (HsGPAT)

Ref. No. XP_039063668.1 (corresponds to SEQ ID NO: 66), 500 aa

SEQ ID NO: 82

MTPLRAGRRFPSITECNGSTYESIAADLDGTLLISRSSFPYFMLIAVEAGSLLRGLILLLSLPLVI

VSYLFISEAIGIQILIFISFAGLKIRDIELVSRAILPRFYAANVRKESFEVFDRCKRKVVVTANPTF

MVEPFVKDFLGGDKVLGTEIEVNPKTKKATGFVKKPGVLVSELKRLAILKEFGDDSPDLGIG

DRESDHDFMSICKEGYMVHPSKSASPVPLDRLRSRIIFHDGRFVQRPDPLNALITYIWLPFGFIL

SIIRVYFNLPLPERIVRYTYEMLGIHLVIRGKRPSPPSPGTPGNLYVCNHRSALDPIVIAIALGRK

VSCVTYSVSRLSRFLSPIPAIALTRDRAADAARISELLQKGDLVVCPEGTTCREPFLLRFSALFA

EMSDRIVPVAVNCKQSMFYGTTVRGVKFWDPYFFFMNPRPTYEVTFLDRLPEEMTVKAGGK

SAIEVANHVQKVLGDVLGFECTGLTRKDKYMLLGGNDGKVESMYNGKK

Theobroma cacao Glycerol-3-phosphate acyltransferase 8 (TcGPAT1)

Ref. No. XP_007051782.1 or EOX95939.1 (corresponds to SEQ ID NO: 67), 500 aa

SEQ ID NO: 83

MAPAKSGRSFPSITKCEGSTYESIAADLDGTLLISRSSFPYFMLVAVEAGSLLRGLILLLSLPLVI

VSYLFISEAIGIQILIFISFAGLKIRDIELVSRAVLPRFYAANVRKESFEVFDRCKRKVVVTANPT

FMVEPFVKDFLGGDKVLGTEIEVNPKTKKATGFVKKPGVLVSELKRLAILKEFGEESPDLGIG

DRESDHDFMSICKEGYMVHPSKSATPVPLDRLKSRIIFHDGRFVQRPDPLNALITYLWLPFGFI

LSIVRVYFNLPLPERIVRYTYEMLGIHLVIRGKRPPPPSPGTPGNLYVCNHRSALDPIVIAIALG

RKVSCVTYSVSRLSRFLSPIPAVALTRDRAADAARISELLQKGDLVVCPEGTTCREQFLLRFSA

LFAELSDRIVPVAVNCRQNMFYGTTVRGVKFWDPYFFFMNPRPTYEVTFLDRLPEEMTVKA

GGKSSIEVANHVQKVLGDVLGFECTGLTRKDKYLLLGGNDGKVESMYNAKK

Theobroma cacao Glycerol-3-phosphate acyltransferase 9 isoform 1

(TcGPAT2) Ref. No. XP_007041647.1 or EOX97478.1 (corresponds to SEQ ID NO: 69), 416 aa

SEQ ID NO: 84

MKKEKLFGFINIKKKEKEEKKPKPNKNPNSQTKSESEREGMSSRGGKLSSSSSELDLDGPNIE

DYLPSGSSINEPRGKLRLRDLLDISPTLTEAAGAIVDDSFTRCFKSNPPEPWNWNVYLFPLWCF

GVAVRYLILFPARVVVLTIGWIIFLSSFIPVHFLLKGHDKLRKKMERVLVELMCSFFVASWTG

VVKYHGPRPSIRPKQVFVANHTSMIDFIILEQMTAFAVIMQKHPGWVGLLQSTILESVGCIWF

NRSEAKDREIVAKKLRDHVQGVDNNPLLIFPEGTCINNQYSVMFKKGAFELGCTVCPIAIKYN

KIFVDAFWNSRKQSFTMHLLQLMTSWAVVCDVWYLEPQNLRPGETPIEFAERVRDIISVRAG

LKKVPWDGYLKYSRPSPKHRERKQQSFAESVLLRLEEK

Theobroma cacao Glycerol-3-phosphate acyltransferase 9 isoform 1 (TcGPAT2) truncated

(corresponds to SEQ ID NO: 71; corresponds to aa 71-416 of SEQ ID NO: 84), 347 aa

SEQ ID NO: 85

MSINEPRGKLRLRDLLDISPTLTEAAGAIVDDSFTRCFKSNPPEPWNWNVYLFPLWCFGVAVR

YLILFPARVVVLTIGWIIFLSSFIPVHFLLKGHDKLRKKMERVLVELMCSFFVASWTGVVKYH

GPRPSIRPKQVFVANHTSMIDFIILEQMTAFAVIMQKHPGWVGLLQSTILESVGCIWFNRSEAK

DREIVAKKLRDHVQGVDNNPLLIFPEGTCINNQYSVMFKKGAFELGCTVCPIAIKYNKIFVDA

FWNSRKQSFTMHLLQLMTSWAVVCDVWYLEPQNLRPGETPIEFAERVRDIISVRAGLKKVP

WDGYLKYSRPSPKHRERKQQSFAESVLLRLEEK

Theobroma cacao Glycerol-3-phosphate acyltransferase 1 (TcGPAT3)

Ref. No. EOX93017.1 (corresponds to SEQ ID NO: 72 or SEQ ID NO: 73), 540 aa

SEQ ID NO: 86

MVFPVVFLKLADWVLYQLLANSCYRAARKMRNYGFFLRNQTLRSPPQQQAASLFPSVTKCD

VGNSRRFDTLVCDIHGVLLGSDTFFPYFMLVAFEGGSIVRAFLLLLSCSFLWVLDSELKLRIMI

FISFCGLRKKDIESVGRAVLPKFYLENLNLQVYEVWSKTSSRVVFTSIPRVMVEGFLHEYMSA

SGVVGTELHTVGNRFTGLLSSSGLLVKHNALKEHFGDKKPDVGLGSSSLHDQYFISLCKEAY

VVNMEDGKSNLSSFMPRDKYPKPLIFHDGRLAFLPTPFATLSMFLWLPFGIVLSILRIFVGICLP

YKLAVICATLSGVQLKFQGCFPSSNSQHKKGVLYVCTHRTLLDPVFLSTALCKPLTAVTYSLS

KMSELIAPIKTVRLTRDRKQDGETMQKLLSEGDLVVCPEGTTCREPYLLRFSSLFAELADEIVP

VAINAHVSMFYGTTASGLKCLDPIFFLMNPRPSYHVQILGKVPQEFTCAGGRSSLEVANYIQR

KLADALGFECTTLTRRDKYLMLAGNEGVVHENKRN

Theobroma cacao Glycerol-3-phosphate acyltransferase 1 (TcGPAT3 )truncated (corresponds

to SEQ ID NO: 74 or SEQ ID NO: 75; corresponds to aa 21-540 of SEQ ID NO: 86), 521 aa

SEQ ID NO: 87

MNSCYRAARKMRNYGFFLRNQTLRSPPQQQAASLFPSVTKCDVGNSRRFDTLVCDIHGVLL

GSDTFFPYFMLVAFEGGSIVRAFLLLLSCSFLWVLDSELKLRIMIFISFCGLRKKDIESVGRAVL

PKFYLENLNLQVYEVWSKTSSRVVFTSIPRVMVEGFLHEYMSASGVVGTELHTVGNRFTGLL

SSSGLLVKHNALKEHFGDKKPDVGLGSSSLHDQYFISLCKEAYVVNMEDGKSNLSSFMPRDK

YPKPLIFHDGRLAFLPTPFATLSMFLWLPFGIVLSILRIFVGICLPYKLAVICATLSGVQLKFQG

CFPSSNSQHKKGVLYVCTHRTLLDPVFLSTALCKPLTAVTYSLSKMSELIAPIKTVRLTRDRK

QDGETMQKLLSEGDLVVCPEGTTCREPYLLRFSSLFAELADEIVPVAINAHVSMFYGTTASGL

KCLDPIFFLMNPRPSYHVQILGKVPQEFTCAGGRSSLEVANYIQRKLADALGFECTTLTRRDK

YLMLAGNEGVVHENKRN

Theobroma cacao Glycerol-3-phosphate acyltransferase 3 (TcGPAT4)

Ref. No. EOX95331.1 (corresponds to SEQ ID NO: 76 or SEQ ID NO: 77), 537 aa

SEQ ID NO: 88

MAKLSMEFSFFQTLFFLFCRVVFRQSKNHKSLHRNVSNIHANEGKYHKYPSFVHRSNLSNQT

LVFSVEEALLKSSSLFPYFMLVAFEAGGLLRAFILFVLYPILCLVSEEMGLKIMVLVCFFGIKK

KSFRVGSAVLPKFFLEDVGLEPFEMLKKGGKKVAVSKIPQVMIESFLKDYLEIDFVVGRELKE

FCGYFLGVMEEKKRSKAALDEIIGSESMGFDVIGISGLKKSLDYHFFSHCKEIYQVRKADKRN

WRHVPRQEYSKPLIFHDGRLALRPTLVASLTMFVWFPFGLALSILRAVVGLMLPYKISIPLLA

YSGLHLFLSTPESSLHPLSLPNSKKQNPKGRLYVCNHRTLLDPVYLSFALQKDLTAVTYSLSRI

SELLAPIKTVRLARDRDQDGKMMEKMLNLGDLVVCPEGTTCREPYLLRFSPLFSEMSDDIVP

VAMDSNVSLFYGTTASGLKCLDPLFFLMNPRPIYTVQILDGVSGLYTCHDGQRSRFKVANQV

QNEIGKALGFECTKLTRRDKYLIMAGNEGIISQT

Theobroma cacao Glycerol-3-phosphate acyltransferase 3 (TcGPAT4) truncated (corresponds

to SEQ ID NO: 78 or SEQ ID NO: 79; corresponds to aa 25-537 of SEQ ID NO: 88), 514 aa

SEQ ID NO: 89

MQSKNHKSLHRNVSNIHANEGKYHKYPSFVHRSNLSNQTLVFSVEEALLKSSSLFPYFMLVA

FEAGGLLRAFILFVLYPILCLVSEEMGLKIMVLVCFFGIKKKSFRVGSAVLPKFFLEDVGLEPF

EMLKKGGKKVAVSKIPQVMIESFLKDYLEIDFVVGRELKEFCGYFLGVMEEKKRSKAALDEII

GSESMGFDVIGISGLKKSLDYHFFSHCKEIYQVRKADKRNWRHVPRQEYSKPLIFHDGRLAL

RPTLVASLTMFVWFPFGLALSILRAVVGLMLPYKISIPLLAYSGLHLFLSTPESSLHPLSLPNSK

KQNPKGRLYVCNHRTLLDPVYLSFALQKDLTAVTYSLSRISELLAPIKTVRLARDRDQDGKM

MEKMLNLGDLVVCPEGTTCREPYLLRFSPLFSEMSDDIVPVAMDSNVSLFYGTTASGLKCLD

PLFFLMNPRPIYTVQILDGVSGLYTCHDGQRSRFKVANQVQNEIGKALGFECTKLTRRDKYLI

MAGNEGIISQT

In some embodiments of any of the aspects, the engineered bacterium comprises a Durio zibethinus GPAT gene or polypeptide (e.g., SEQ ID NOs: 64, 80). In some embodiments of any of the aspects, the engineered bacterium comprises a Gossypium arboreum GPAT gene or polypeptide (e.g., SEQ ID NOs: 65, 81). In some embodiments of any of the aspects, the engineered bacterium comprises a Hibiscus syriacus GPAT gene or polypeptide (e.g., SEQ ID NOs: 66, 82). In some embodiments of any of the aspects, the engineered bacterium comprises a Theobroma cacao GPAT gene or polypeptide (e.g., SEQ ID NOs: 67, 69, 71-79, 83-89).

In some embodiments of any of the aspects, the engineered bacterium comprises at least one exogenous copy of at least one functional phosphatidic acid (PA) phosphatase gene. Phosphatidic acid (PA) phosphatases catalyze dephosphorylation at the sn3 position of phosphatidic acid (PA). As a non-limiting example, such a phosphatase is phosphatidate phosphatase (PAP) (E.C. 3.1.3.4), which is a key regulatory enzyme in lipid metabolism, catalyzing the conversion of phosphatidate to diacylglycerol. PAP belongs to the family of enzymes known as hydrolases, and more specifically to the hydrolases that act on phosphoric monoester bonds. The two substrates of PAP are phosphatidate and H₂O, and its two products are diacylglycerol and phosphate. When PAP is active, diacylglycerols formed by PAP can go on to form any of several products, including phosphatidylethanolamine, phosphatidylcholine, phosphatidylserine, and triacylglycerol. The systematic name of the PAP enzyme class is diacylglycerol-3-phosphate phosphohydrolase. Other names in common use include: phosphatidic acid phosphatase (PAP), 3-sn-phosphatidate phosphohydrolase, acid phosphatidyl phosphatase, phosphatidic acid phosphohydrolase, phosphatidate phosphohydrolase, and lipid phosphate phosphohydrolase (LPP).

In some embodiments of any of the aspects, the functional PAP gene preferentially produces or leads to the production of TAGs comprising a specific type of fatty acid R group (e.g., C16). As such, the functional PAP gene can be selected from any PAP gene from any species that preferentially produces or leads to the production of TAGs comprising a specific type of fatty acid R group (e.g., C16). In some embodiments of any of the aspects, the engineered bacterium comprises at least one exogenous copy of at least one functional PAP gene. In some embodiments of any of the aspects, the engineered bacterium does not comprise a functional endogenous PAP gene. In some embodiments of any of the aspects, the functional PAP is heterologous. In some embodiments of any of the aspects, a PAP polypeptide as described herein is truncated to remove an organelle targeting sequence(s); in some embodiments, such a targeting sequence can contribute to poor expression of the PAP polypeptide, e.g., in the engineered bacteria described herein.

In some embodiments of any of the aspects, the functional heterologous PAP gene comprises a Rhodococcus PAP gene. In some embodiments of any of the aspects, the functional heterologous PAP gene comprises a Rhodococcus opacus PAP gene, or a Rhodococcus jostii PAP gene. In some embodiments of any of the aspects, the engineered bacterium comprises at least one exogenous copy of at least one functional PAP gene comprising one of SEQ ID NOs: 31-34, or a nucleic acid sequence that is at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the sequence of at least one of SEQ ID NOs: 31-34, that maintains the same functions as at least one of SEQ ID NOs: 31-34 (e.g., phosphatidate phosphatase).

In some embodiments of any of the aspects, the amino acid sequence encoded by the functional PAP gene comprises one of SEQ ID NOs: 35-36, or an amino acid sequence that is at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% identical to the sequence of at least one of SEQ ID NOs: 35-36, that maintains the same functions as at least one of SEQ ID NOs: 35-36 (e.g., phosphatidate phosphatase).

Rhodococcus opacus PAP (RoPAP), Rhodococcus opacus PD630,

complete genome, GenBank: CP003949.1, REGION: 4275960-4276643, 684 bp

SEQ ID NO: 31

ATGCCCCACACCTCTGCCGCTCACGCCGGGCTTCGTATGTCCGCCCTGACGCTGATATTG

GCCGTGCTCTGCGTGCAGGTCCACGACGGCGGCCCACTGACCGGTGCCGACGTGCCCGT

GACGTCGTGGGCCGTCGGAAACCGTTCCGCGGTCCTCGACCACGCGGCGCTCCTCGTCAC

CGACCTCGGCAGCCCCGTCGCCACCGTGGCCCTCGCCGTGATCTGCGGGCTCGCGCTCGC

GTGGCATCGGCGTTCCGCGATTCCCGCCGTCCTCGTCGTCGGAACGGTCGGGGCCGCCAC

CACGGCAAGCACGGCCCTGAAGCTGGTGGTCGGGCGCAGCCGGCCGGCCCTCGACCTGC

AGGAGGTCCTGGAGACGGACTACTCGTTCCCGTCCGGACATGTCACGGGTACGGTGGCTT

TGCTCGGCATCACGGCCGCGATCCTGCTCGGCCGCCGGCGCCGCCTCGTCCGGGTGTGTG

GCGGGGCCGTGGTCGGGTGCGGGGTGGTGATCGTTGCCGCGACCCGCGTGTACCTCGGT

GTCCACTGGCTCACCGATGTTGTCGCCGGCGCGATCCTGGGCGCGGTGTTCGTGACGGTG

GGGGCCGCCACGTACGAGCGTGTCCACCCGCCGGTCGGCACCCCCGCTCCGTCGAAACC

GCTCGCGGCCGTCGACCGAGTGGGAGGC

CnDNA_RoPAP, codon-optimized, 684 bp

SEQ ID NO: 32

ATGCCGCACACCTCGGCCGCCCACGCCGGCCTGCGCATGTCGGCCCTGACCCTGATCCTG

GCCGTGCTGTGCGTGCAGGTGCACGACGGCGGCCCGCTGACCGGCGCCGACGTGCCGGT

GACCTCGTGGGCCGTGGGCAACCGCTCGGCCGTGCTGGACCACGCCGCCCTGCTGGTGA

CCGACCTGGGCTCGCCGGTGGCCACCGTGGCCCTGGCCGTGATCTGCGGCCTGGCCCTGG

CCTGGCACCGCCGCTCGGCCATCCCGGCCGTGCTGGTGGTGGGCACCGTGGGCGCCGCC

ACCACCGCCTCGACCGCCCTGAAGCTGGTGGTGGGCCGCTCGCGCCCGGCCCTGGACCTG

CAGGAGGTGCTGGAGACCGACTACTCGTTCCCGTCGGGCCACGTGACCGGCACCGTGGC

CCTGCTGGGCATCACCGCCGCCATCCTGCTGGGCCGCCGCCGCCGCCTGGTGCGCGTGTG

CGGCGGCGCCGTGGTGGGCTGCGGCGTGGTGATCGTGGCCGCCACCCGCGTGTACCTGG

GCGTGCACTGGCTGACCGACGTGGTGGCCGGCGCCATCCTGGGCGCCGTGTTCGTGACCG

TGGGCGCCGCCACCTACGAGCGCGTGCACCCGCCGGTGGGCACCCCGGCCCCGTCGAAG

CCGCTGGCCGCCGTGGACCGCGTGGGCGGC

Rhodococcus jostii PAP (RjPAP), Rhodococcus jostii RHA1, complete

sequence, NCBI Reference Sequence: NC_008268.1, REGION: 83452-84138, 687 bp

SEQ ID NO: 33

ATGCCCCACACCTCCATCGCCACCGCCGGGCTTCGTGTGTCCGCGCTGACGCTGATCCTG

GCCGTGCTCTGTGTGCAGGTCCGCGACGGCGGCCCACTGACCGGTGCCGACGTGCCCGC

GACGTCGTGGGTCGTCGGTCACCGCTCCGCCACCCTTGACCATGTGGCTCTCCTCGTCAC

CGCCCTCGGCAGCCCCGTCGCCACCGTGGCCCTCGCCGTGATCTGCGGGCTCGCCCTCGC

CTGGCGCCGGCGTTCCGCGATCCCCGCCGCCGTCGTCGTCGGGACGGTCGGGGCCGCCAC

CGCGGCGAGCACGGCCCTGAAGCTGGTCGTCGAACGCAGCCGGCCGGCCGTCGACCTGC

AGGAGGTCCTGGAGACGGACTACTCGTTCCCGTCCGGGCACGTCACGGGCACCGCGGCC

CTGCTCGGGGTCACGGCGGCGATCCTGCTCGGCCGCCGGCATCTCCGCGTCCGGGTGTGC

GGCGCGGCGGTGGCCGGGTGCGGGGTGGTGATCGTTGCCGTGACCCGCGTCTACCTCGG

TGTCCACTGGATGTCCGACGTCGTCGCCGGCGCGATCCTCGGCGCGGTGTTCGTGACGGT

AGGCGCCGCCACGTACGAGCGTGTCCACCGTCCGCTCGTCGCCGTCGCTCCGTCGAAACC

GCTCGCGGTCCTCGACCGAGTGGGAGGCTGA

CnDNA_RjPAP, codon-optimized, 684 bp

SEQ ID NO: 34

ATGCCGCACACCTCGATCGCCACCGCCGGCCTGCGCGTGTCGGCCCTGACCCTGATCCTG

GCCGTGCTGTGCGTGCAGGTGCGCGACGGCGGCCCGCTGACCGGCGCCGACGTGCCGGC

CACCTCGTGGGTGGTGGGCCACCGCTCGGCCACCCTGGACCACGTGGCCCTGCTGGTGAC

CGCCCTGGGCTCGCCGGTGGCCACCGTGGCCCTGGCCGTGATCTGCGGCCTGGCCCTGGC

CTGGCGCCGCCGCTCGGCCATCCCGGCCGCCGTGGTGGTGGGCACCGTGGGCGCCGCCA

CCGCCGCCTCGACCGCCCTGAAGCTGGTGGTGGAGCGCTCGCGCCCGGCCGTGGACCTG

CAGGAGGTGCTGGAGACCGACTACTCGTTCCCGTCGGGCCACGTGACCGGCACCGCCGC

CCTGCTGGGCGTGACCGCCGCCATCCTGCTGGGCCGCCGCCACCTGCGCGTGCGCGTGTG

CGGCGCCGCCGTGGCCGGCTGCGGCGTGGTGATCGTGGCCGTGACCCGCGTGTACCTGG

GCGTGCACTGGATGTCGGACGTGGTGGCCGGCGCCATCCTGGGCGCCGTGTTCGTGACCG

TGGGCGCCGCCACCTACGAGCGCGTGCACCGCCCGCTGGTGGCCGTGGCCCCGTCGAAG

CCGCTGGCCGTGCTGGACCGCGTGGGCGGC

Rhodococcus opacus PAP, phosphatase PAP2 family protein, NCBI

Reference Sequence: WP_005246202.1, 228 aa (corresponds to SEQ ID NOs: 31-32)

SEQ ID NO: 35

MPHTSAAHAGLRMSALTLILAVLCVQVHDGGPLTGADVPVTSWAVGNRSAVLDHAALLVT

DLGSPVATVALAVICGLALAWHRRSAIPAVLVVGTVGAATTASTALKLVVGRSRPALDLQE

VLETDYSFPSGHVTGTVALLGITAAILLGRRRRLVRVCGGAVVGCGVVIVAATRVYLGVHW

LTDVVAGAILGAVFVTVGAATYERVHPPVGTPAPSKPLAAVDRVGG

Rhodococcus jostii PAP, RHA1_RS00400 phosphatase PAP2 family

protein (Rhodococcus jostii RHA1), NCBI Reference Sequence: WP_011593404.1,

tr|Q0SKM5|Q0SKM5_RHOJR, Phosphatidic acid phosphatase, type 2 OS = Rhodococcus jostii

(strainRHA1) OX = 101510 GN = RHA1_ro00075 PE = 4 SV = 1, 228 aa (corresponds to SEQ ID

NOs: 33-34)

SEQ ID NO: 36

MPHTSIATAGLRVSALTLILAVLCVQVRDGGPLTGADVPATSWVVGHRSATLDHVALLVTA

LGSPVATVALAVICGLALAWRRRSAIPAAVVVGTVGAATAASTALKLVVERSRPAVDLQEV

LETDYSFPSGHVTGTAALLGVTAAILLGRRHLRVRVCGAAVAGCGVVIVAVTRVYLGVHW

MSDVVAGAILGAVFVTVGAATYERVHRPLVAVAPSKPLAVLDRVGG

In some embodiments of any of the aspects, the engineered bacterium comprises a Rhodococcus opacus PAP gene or polypeptide (e.g., SEQ ID NOs: 31, 32, or 35) or a Rhodococcus jostii PAP gene or polypeptide (e.g., SEQ ID NOs: 33, 34, or 36).

In some embodiments of any of the aspects, the engineered bacterium comprises any combination of phaC inactivation, Marvinbryantia formatexigens thioesterase, Cuphea palustris thioesterase, Acinetobacter baylyi DGAT, Thermomonospora curvata DGAT, Rhodococcus opacus PAP, or Rhodococcus jostii PAP (see e.g., Table 4).

TABLE 4

Non-Limiting Exemplary Combinations, eg., in C. necator; “ΔphaC” indicates

inactivation (e.g., genetic or chemical) of phaC; “Mf TE” indicates Marvinbryantia

formatexigens thioesterase; “Cp TE” indicates Cuphea palustris thioesterase (e.g.,

CpFatB1, CpFatB2, and/or Cp FatB2-B1 hybrid); “Ab DG” indicates Acinetobacter

baylyi DGAT; “Tc DG” indicates Thermomonospora curvata DGAT; “Ro PAP”

indicates Rhodococcus opacus PAP; “Rj PAP” indicates Rhodococcus jostii PAP.

Mf
Cp
Ab
Tc
Ro
Rj

Mf
Cp
Ab
Tc
Ro
Rj

ΔphaC
TE
TE
DG
DG
PAP
PAP
ΔphaC
TE
TE
DG
DG
PAP
PAP

X

X

X

X

X

X

X

X
X

X
X

X

X

X

X

X

X

X

X

X

X
X

X
X

X

X
X
X

X
X
X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X
X

X

X
X

X

X

X
X

X
X

X

X

X
X

X

X
X

X

X
X
X

X
X
X

X

X
X
X
X

X
X
X
X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X
X

X

X
X

X

X

X

X

X

X

X

X

X

X

X

X

X

X

X
X

X

X
X

X

X

X
X
X

X

X
X
X

X

X

X
X

X
X

X

X

X
X

X

X
X

X

X

X
X

X

X
X

X

X
X

X
X

X
X

X
X

X

X
X
X

X
X
X

X

X

X
X
X

X

X
X
X

X

X
X
X
X

X
X
X
X

X

X
X
X
X
X

X
X
X
X
X

X

X

X
X

X

X

X

X
X

X

X

X

X
X

X
X

X

X
X

X
X

X

X

X

X
X

X

X

X

X

X

X
X

X
X

X

X
X

X
X

X
X
X

X

X
X
X

X
X

X

X

X

X
X

X

X

X

X

X

X
X

X

X

X

X

X

X
X

X
X

X

X

X
X

X

X
X

X
X

X

X
X

X
X

X

X
X

X

X

X
X

X
X

X
X
X

X

X
X
X

X
X

X
X
X
X

X

X
X
X
X

X
X

X
X

X
X
X

X

X
X

X

X
X
X

X

X
X

X

X
X
X

X
X

X
X

X
X

X
X
X

X

X
X

X

X
X
X

X

X

X
X

X

X

X
X
X

X
X

X
X

X
X

X
X
X

X
X
X

X
X

X
X
X

X
X
X

X
X
X

X
X
X
X

X

X
X
X

X

X
X
X
X

X

X
X
X

X

X
X
X
X

X
X

X
X
X

X
X

X
X
X
X

X
X
X
X

X
X
X
X
X

X

X
X
X
X

X

X
X
X
X
X

X
X
X
X
X

X
X
X
X
X
X

X
X
X
X
X
X

X
X
X
X
X
X
X

In some embodiments of any of the aspects, the engineered bacterium comprises (i) at least one endogenous diacylglycerol kinase gene (E.C. 2.7.1.174) comprising at least one engineered inactivating modification; and/or (ii) at least one exogenous inhibitor of an endogenous diacylglycerol kinase gene or gene product. In some embodiments of any of the aspects, the engineered bacterium comprises at least one endogenous diacylglycerol kinase gene comprising at least one engineered inactivating modification. In some embodiments of any of the aspects, the engineered bacterium comprises at least one exogenous inhibitor of at least one endogenous diacylglycerol kinase enzyme. In some embodiments of any of the aspects, the engineered bacterium comprises at least one endogenous diacylglycerol kinase gene comprising at least one engineered inactivating modification and an inhibitor of an endogenous diacylglycerol kinase enzyme. Diacylglycerol kinases perform the reverse reaction to phosphatidate phosphatase (PAP). By knocking out dgkA, the precursor pool for TAGs (e.g., DAGs) is increased and therefore TAG production is increased.

In some embodiments of any of the aspects, the endogenous diacylglycerol kinase comprises diacylglycerol kinase A (dgkA). Diacylglycerol kinase converts diacylglycerol/DAG into phosphatidic acid/phosphatidate/PA and regulates the respective levels of these two bioactive lipids.

In some embodiments of any of the aspects, the engineered bacterium comprises an engineered inactivating modification of the endogenous Cupriavidus necator dgkA gene. In some embodiments of any of the aspects, the nucleic acid sequence of the endogenous Cupriavidus necator dgkA gene comprises SEQ ID NO: 90 or a sequence that is at least 95% (e.g., at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the sequence of SEQ ID NO: 90 that maintains the same functions as SEQ ID NO: 90 (e.g., diacylglycerol kinase).

In some embodiments of any of the aspects, the amino acid sequence encoded by the endogenous Cupriavidus necator dgkA gene comprises SEQ ID NO: 91 or an amino acid sequence that is at least 95% (e.g., at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the sequence of SEQ ID NO: 91 that maintains the same functions as SEQ ID NO: 91 (e.g., diacylglycerol kinase).

Cupriavidus necator dgkA gene, GenBank: CP039287.1 region

1123858 to 1124343, 486 nt (see e.g., Kennedy pathway)

SEQ ID NO: 90

atgcccaaaccccatccggaactgccgtccgacccgcctctgcagaggccgccgcaggcagtccagagcgctgactattcgatcgagcagaac

ccccacaaggccaaccgcggcctgacgcgcgcctggcatgcggccatcaattcgctgtcggggctgcgctatgcggtgctcgaggaaagcgcg

ttccgccaggagctgacgctggtggcaatcctggcgccgtgggcattcctgctgccggtggacgtggtcgagcgcatcctgctgctgggcacgct

gctggtggtgctgatcgtcgagttgctcaattccagcgtcgaggcggcaatcgaccgcatttcgctggagcggcacagcctgtccaagcgtgcca

aggatttcggcagcgccgcggtaatgctggcgctggtgctgtgcggcggcacctgggtcgccatcgccgggccgcacgtggtgcgctgggtgc

ggacgctggcgggctga

Cupriavidus necator dgkA polypeptide, NCBI Reference Sequence:

WP_010809153.1, 161 aa

SEQ ID NO: 91

MPKPHPELPSDPPLQRPPQAVQSADYSIEQNPHKANRGLTRAWHAAINSLSGLRYAVLEESAF

RQELTLVAILAPWAFLLPVDVVERILLLGTLLVVLIVELLNSSVEAAIDRISLERHSLSKRAKDF

GSAAVMLALVLCGGTWVAIAGPHVVRWVRTLAG

In some embodiments of any of the aspects, the engineered inactivating modification of an endogenous diacylglycerol kinase gene comprises a deletion of the entire coding sequence (e.g., a knockout of an endogenous dgkA gene, denoted herein as ΔdgkA). In some embodiments of any of the aspects, the engineered inactivating modification of an endogenous diacylglycerol kinase gene comprises at least one exogenous inhibitor of an endogenous diacylglycerol kinase gene or gene product.

In some embodiments of any of the aspects, the engineered bacterium comprises (i) at least one endogenous beta-oxidation gene comprising at least one engineered inactivating modification; and/or (ii) at least one exogenous inhibitor of an endogenous beta-oxidation gene or gene product. In some embodiments of any of the aspects, the engineered bacterium comprises at least one endogenous beta-oxidation gene comprising at least one engineered inactivating modification. In some embodiments of any of the aspects, the engineered bacterium comprises at least one exogenous inhibitor of at least one endogenous beta-oxidation enzyme. In some embodiments of any of the aspects, the engineered bacterium comprises at least one endogenous beta-oxidation gene comprising at least one engineered inactivating modification and an inhibitor of an endogenous beta-oxidation enzyme.

Beta-oxidation is the catabolic process by which fatty acid molecules are broken down to generate acetyl-CoA. Beta-oxidation thus counteracts the formation of TAGs, and as such can be inhibited in order to increase TAG synthesis. Thus inhibition of beta oxidation increases the flux of fatty acids into TAG biosynthesis. Inhibition of beta-oxidation also prevents re-uptake of TAGs. Non-limiting examples of enzymes involved in beta oxidation include acyl-CoA ligase (or synthetase), acyl CoA dehydrogenase, enoyl CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase, and β-ketothiolase. In some embodiments of any of the aspects, an engineered bacterium comprises an engineered inactivating modification and/or an inhibitor of an endogenous acyl-CoA ligase (or synthetase), acyl CoA dehydrogenase, an enoyl CoA hydratase, a 3-hydroxyacyl-CoA dehydrogenase, and/or a β-ketothiolase.

In some embodiments of any of the aspects, the endogenous beta-oxidation gene is an acyl-coenzyme A dehydrogenase (also referred to as acyl-CoA dehydrogenase; EC:1.3.8.8; e.g., fadE or a gene with a FadE-like function, e.g., a FadE homolog). Acyl-coenzyme A dehydrogenase catalyzes the dehydrogenation of acyl-coenzymes A (acyl-CoAs) to 2-enoyl-CoAs, the first step of the beta-oxidation cycle of fatty acid degradation.

In some embodiments of any of the aspects, the endogenous beta-oxidation gene is a 3-hydroxyacyl-CoA dehydrogenase (EC:1.1.1.35; e.g., fadB or a gene with a FadB-like function, e.g., a FadB homolog). 3-hydroxyacyl-CoA dehydrogenase is involved in the aerobic and anaerobic degradation of long-chain fatty acids via beta-oxidation cycle. 3-hydroxyacyl-CoA dehydrogenase catalyzes the formation of 3-oxoacyl-CoA from enoyl-CoA via L-3-hydroxyacyl-CoA. FadB can also use D-3-hydroxyacyl-CoA and cis-3-enoyl-CoA as substrate.

In some embodiments of any of the aspects, the engineered bacterium comprises an engineered inactivating modification of the endogenous Cupriavidus necator 3-hydroxyacyl-CoA dehydrogenase gene. In some embodiments of any of the aspects, the nucleic acid sequence of the endogenous Cupriavidus necator 3-hydroxyacyl-CoA dehydrogenase gene comprises one of SEQ ID NO: 92-94 or a sequence that is at least 95% (e.g., at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the sequence of SEQ ID NO: 92-94 that maintains the same functions as SEQ ID NO: 92-94 (e.g., beta-oxidation, acyl-CoA dehydrogenase, or 3-hydroxyacyl-CoA dehydrogenase).

In some embodiments of any of the aspects, the amino acid sequence encoded by the endogenous Cupriavidus necator 3-hydroxyacyl-CoA dehydrogenase gene comprises SEQ ID NO: 95-97 or an amino acid sequence that is at least 95% (e.g., at least 95%, at least 96%, at least 97%, at least 98%, or at least 99%) identical to the sequence of SEQ ID NO: 95-97 that maintains the same functions as SEQ ID NO: 95-97 (e.g., beta-oxidation, acyl-CoA dehydrogenase, or 3-hydroxyacyl-CoA dehydrogenase).

Cupriavidus necator N-1, acyl-CoA dehydrogenase fadE: A0460,

GenBank: CP039287.1 region 483888 to 485675, 1788 nt

SEQ ID NO: 92

atgggccagtacaccgcaccgttgcgcgacatgcagttcgtgctccatgaactgctcggcgccgaagccgaactcaaggcgatgccgccgcacg

cggacatcgacgcggacaccatcaaccaggttatcgaggaagccggcaagttctgctcggacgtggtgttcccgctcaaccaggtgggcgaccg

cgaaggctgcacctacgtcggcgacggcgtggtcaaggctcccaccggcttcaaggaagcctaccagcagtatgtcgaggccggctggccggc

gctggcgtgcgatcccgagttcggcggccagggcctgccgatcgtgatcaacaatgtggtctacgagatgctgaactcggccggccaggcctgg

accatgtacccgggcctgtcgcacggcgcgtacgaggcgctgcacgcgcacggcacgccagaactgcagcagacctacctgcccaagctggtc

tccggcgtgtggaccggcaccatgtgcctgaccgagccgcactgcggcaccgacctcggcatcctgcgttccaaggcagagccgcaggccgac

ggttcctacctgatctcgggcaccaagatcttcatctcggccggcgagcacgacatggccgagaacatcatccacctggtgctggcacgcctgc

cggacgcgccgggcggcaccaagggcatctcgctgttcgtggtgcccaagttcatccccgatgccaacggcaacccgggcgagcgcaacggcat

caagtgcggctcgatcgagcacaagatgggcatccacggcaacgccacctgcgtgatgaacctggacggcgcgcgcggctggatggtgggcg

agcccaacaagggcctgaacgccatgttcgtgatgatgaacgccgcgcgcctgggcgtgggcgcgcagggcctggggctgaccgaagtggcg

taccagaactcgctggcctacgccaaggaccgcctgcagatgcgcgcgctgaccggcccgaaggcgccggacaagcccgccgacccgatcat

cgtgcacccggacgtgcgccgcatgctgctgacgcagaaggcctacgccgaaggcggccgcgccttcagctactggaccgcgctgcagatcga

ccgcgagttgtcgcaccctgacgaagccgtgcgcaagcaggccggcgacctggtcgcgctgctcacgccggtgatcaaggccttcctgaccga

caacgccttcacgtccaccaatgagggcatgcaggtgttcggcggccacggctatatcgccgagtggggcatggagcagtatgtgcgcgatgcg

cgcatcaacatgatctacgaaggcaccaacaccatccaggcgctggacctgctgggccgcaagatcctgggcgacatgggcgccaggatgaag

gccttcggcaagatcgtgcaggaattcgttgaagccgaaggcaccaacgaagccatgcaggagttcatcaacccgctcgccgacattggcgaca

aggtgcagaagctcaccatggaaatcggcatgaaggcgatgggcaatgccgacgaggtgggcgctgccgcggtgccgtacctgcgcgtggtg

ggccacctggtgttctcatacttctgggcccgcatggccaagatcgcgctggagaaggaagcgagcggcgacaagttctacaccgccaagctgg

ccacggcacgcttctactttgccaggctgctgccggaaaccgccgccgagatccgcaaggcgcgcgccggttcggccacgctgatggcgctgg

acgcagacctgttctga

Cupriavidus necator N-1, acyl-CoA dehydrogenase fadE: A1530,

GenBank: CP039287.1 region 1662438 to 1664300, 1863 nt

SEQ ID NO: 93

atgtcgatgatcctatcccgccgcgacctgaatttcgtgctgtacgaatggctcaaggtcgacgagctcacgcgcatcccgcgctatgccgacc

actcgcgcgagactttcgacgccgcgctggacacctgcgagaaaatcgccaccgacctgttcgcgccgcacaacaagaagaacgaccagcaaga

gccgcatttcgacggcgagaccgtcagcatcatccccgaggtcagcaccgcgctgaaggccttctgcgaggccggcttgatggccgccggccag

gactatgaactgggcggcatgcaactgccggtggtggtcgagaaggctggctttgcctacttcaagggtgccaacgtcggcaccagctcgtaccc

gttcctgaccatcggcaacgccaacctgctgctgacgcacggcacgccggcgcaggtcgagaccttcgtcaagccggagatggacggtcgcttc

ttcggcaccatgtgcctgtccgagccgcaggcgggctcgtcgctgtcggacatcaccacgcgcgccgagtacgagggcgaatcgccgctgggc

gcgcagtaccggctgcgcggcaacaagatgtggatctctgccggcgagcacgagctgtcggaaaatatcgtccacctggtgctggccaagatcc

ccggcccggacggcaagctgatcccgggcgtgaagggcatctcgctcttcatcgtgcccaagtacctggtcaatgaagacggctcgctgggcga

gcacaacgacgtggtgctggccggcctgaaccacaagatgggctaccgcggcaccaccaactgcctgctcaacttcggcgaaggcatgaagta

ccggccgggcggcaaggccggcgcgatcggctacctggtgggcgagccgcacaagggcctggcctgcatgttccacatgatgaacgaggcg

cgcatcggcgtgggcctgggcgcggtgatgctgggctataccggctacctgcacgcgctggactacgcgcgcaaccgcccgcaaggccgcgc

ggtcggccccggcggcaaggatgcggccagcccgcaggtgaagctggtcgagcacgccgatatccgccgcatgctgctggcgcagaagagct

atgtcgaaggcggcctggcgctgaacctctattgcgcgcgcctggtcgacgaggaagaggccgctgcggccgccggcgaccaagccgcgcat

gcgcgcctggcgctattgctcgatatcctgaccccgatcgccaagagctggccgtcgcaatggtgcctggaggccaacaacctggcgatccaggt

gcatggcggctacggctatacgcgcgagtacaacgtcgagcagttctaccgcgacaaccgcctcaacccgatccacgaaggcacgcacggcat

ccagggcctggacctgctgggccgcaaggtggtgatgaaggacggcgccgccttcaagctgctgggcgagcgcgtgcaggacaccatcaccc

gcgcgctcgccgccggcaatgccgagttgtcgcagcaggcaggcgccctcggcaccgccaccaagcgcctggccgaggtcacgcaggcgct

gtggagcgcgggcgaccccaacgtgacgctggccaatgcctcggtctacctggaggccttcgggcacgtggtggtggcgtggatctggctgga

acaggcactgctggcgcaagccgcgctgccgcgcgcgaacggcaaggaagacgaggacttctaccgcggcaagctggccgcggcggcctac

ttcttccgctgggagctgcccaaggtcggcccgcagctggcgctgctcgagtcgctcgaccgcaccacgctcgacatgcaggacgcgtggttctg

a

Cupriavidus necator N-1, 3-hydroxyacyl-CoA dehydrogenase (fadB),

NCBI Reference Sequence: NC_015727.1, REGION: complement (968973-971117), 2145 bp

SEQ ID NO: 94

1
atgcaagccc cgattcagta ccacaagacc gacgacggca tcgtcacgct gacgttcgat

61
gcgcctgagc aaagcgtcaa taccatgacc gatgagatgc ggcaatgtct ggcggacatg

121
gtgagccggc tggaagcgga gaaggaagcg gttagcggcg tcattcttac ctcggccaag

181
gagacgttct ttgcgggagg caatctcaat cgcctgtaca agctgcagcc ggcggatgcg

241
gctacgcagt tcgatgcctc ggagcgtgcc aagtctgcgc tgaggcggct cgaaacgctg

301
ggcaagccgg tggtggcggc gctcaatggc acggcgctgg gtggcggctt cgaaattgcg

361
ctggcctgcc accatcgcat tgcgctggac aagcccaaag tgcaattcgg cctgcccgaa

421
gcgacgctgg gcctgatgcc gggggcgggc ggcgtcgtgc gtctgaatcg gctgctgggg

481
cttgctgcga gccagcctta tttgcaggac agcaagctca tgtcgccggc agaggcgacc

541
aaggttgggc tggtgcatga gcttgcggac acacccgcgg cactgctgga gaaggcacga

601
gcatggatcg cggcccaccc ggaaagcaag cagccgtggg acaaggccgg ctacacgccg

661
ccgggaggct gggccgatgc gagtgaggcg cggcgctgga tctccacggc cgccgcgcag

721
gtgcgcgcca agaccaaagg ttgctaccct gcgccggaag ccatcttgtg cgcttcggtc

781
gaaggcatgc aggtggactt cgacaccgct agccgcattg agacgcgcta cttcgtgaag

841
cttgtgactg gccaggttgc gaagaacatc atcagcacct tctggttcca cgccaacggc

901
atcaagtcag gcgcgcagcg tcctgcaggg gtggccaagg gcaagatcaa gacggtgggc

961
gtgctgggcg cagggatgat gggcaagggg attgcgtatg tggcggcctc gcgtggtatc

102
gaggtgtggg tcaaggatgc cacccttgcg caggccgaag gggcacgtgc caatgcggac

108
caactgctgg ccaagcgtga ggagaagggg gaaattgatg ccgcgacccg ccgacagatt

1141
gtcgagcgca ttcacgcgac tgaccgctat gaggactttg cccatgtcga cctggtggtg

1201
gaagccatcc cagagaaccc tgcgcttaag gcggagatca cccggcaggc cgagcccgtg

1261
ctcggagatg gggcgatctg ggcctccaac acctcgacgc tgcccatcac cggcctggcc

1321
aaggcatcga gccggcccga gcgcttcgtc gggctgcact tcttctcgcc ggtgcaccgc

1381
atgcagttgg tggaagtgat taagggccag cagacctcgc cggagaccct ggcccatgcg

1441
ctggacttcg tgatgcagct tggcaagacg ccgatcgtcg tcaacgacaa ccgcggcttc

1501
tttaccagcc gggtattcag tactttcaca cgcgaagcag tggcgatgct gggtgagggg

1561
caggacccgg ccgccatcga ggcggcggcc atcctgtcag ggttccctgc cgggccgctg

1621
gcggtgctgg acgaggtcag cttgagcttg aactacaaca accggctcga gacgctcagg

1681
gcgcatgcgg aggagggtcg tccgctgccg ccacatccgg ccgacgcagt gatggagcgc

1741
atgctcaatg aattcggccg caaggggcgt gccgcgggtg gcggcttcta cgattatccg

1801
gccgacggca agaaggtgtt ctggagcggt ctggctaagc acttcctgcg cccggccgaa

1861
cagattccac agcgtgacaa acaggatcgg ttgttgttct gcatggccct ggagtcggtg

1921
cgtgtactgc aggatggcgt gctggacagc gcgggggacg gcaacattgg ctcggtactg

1981
gggattggct tcccgcgctg gagcggcggc gtgttccagt tcctgaacca gtatgggctg

2041
gaaaaggccg tggcacgtgc ggagtacctg gccgagcatt atggcgaacg gttcacgcca

2101
ccgcaattgc tacgggaaaa ggccaaacga gccgagccat tctga

Cupriavidus necator N-1, acyl-CoA dehydrogenase fadE: A0460,

NCBI Reference Sequence: WP_011615135.1, NCBI Reference Sequence: WP_010813929.1, 595 aa

SEQ ID NO: 95

MGQYTAPLRDMQFVLHELLGAEAELKAMPPHADIDADTINQVIEEAGKFCSDVVFPLNQVG

DREGCTYVGDGVVKAPTGFKEAYQQYVEAGWPALACDPEFGGQGLPIVINNVVYEMLNSA

GQAWTMYPGLSHGAYEALHAHGTPELQQTYLPKLVSGVWTGTMCLTEPHCGTDLGILRSK

AEPQADGSYLISGTKIFISAGEHDMAENIIHLVLARLPDAPGGTKGISLFVVPKFIPDANGNPGE

RNGIKCGSIEHKMGIHGNATCVMNLDGARGWMVGEPNKGLNAMFVMMNAARLGVGAQG

LGLTEVAYQNSLAYAKDRLQMRALTGPKAPDKPADPIIVHPDVRRMLLTQKAYAEGGRAFS

YWTALQIDRELSHPDEAVRKQAGDLVALLTPVIKAFLTDNAFTSTNEGMQVFGGHGYIAEW

GMEQYVRDARINMIYEGTNTIQALDLLGRKILGDMGARMKAFGKIVQEFVEAEGTNEAMQE

FINPLADIGDKVQKLTMEIGMKAMGNADEVGAAAVPYLRVVGHLVFSYFWARMAKIALEK

EASGDKFYTAKLATARFYFARLLPETAAEIRKARAGSATLMALDADLF

Cupriavidus necator N-1, acyl-CoA dehydrogenase fadE: A1530, 620 aa

SEQ ID NO: 96

MSMILSRRDLNFVLYEWLKVDELTRIPRYADHSRETFDAALDTCEKIATDLFAPHNKKNDQQ

EPHFDGETVSIIPEVSTALKAFCEAGLMAAGQDYELGGMQLPVVVEKAGFAYFKGANVGTSS

YPFLTIGNANLLLTHGTPAQVETFVKPEMDGRFFGTMCLSEPQAGSSLSDITTRAEYEGESPL

GAQYRLRGNKMWISAGEHELSENIVHLVLAKIPGPDGKLIPGVKGISLFIVPKYLVNEDGSLG

EHNDVVLAGLNHKMGYRGTTNCLLNFGEGMKYRPGGKAGAIGYLVGEPHKGLACMFHMM

NEARIGVGLGAVMLGYTGYLHALDYARNRPQGRAVGPGGKDAASPQVKLVEHADIRRMLL

AQKSYVEGGLALNLYCARLVDEEEAAAAAGDQAAHARLALLLDILTPIAKSWPSQWCLEAN

NLAIQVHGGYGYTREYNVEQFYRDNRLNPIHEGTHGIQGLDLLGRKVVMKDGAAFKLLGER

VQDTITRALAAGNAELSQQAGALGTATKRLAEVTQALWSAGDPNVTLANASVYLEAFGHV

VVAWIWLEQALLAQAALPRANGKEDEDFYRGKLAAAAYFFRWELPKVGPQLALLESLDRT

TLDMQDAWF

3-hydroxyacyl-CoA dehydrogenase (fadB) [Cupriavidus necator],

NCBI Reference Sequence: WP_013959369.1, 714 aa

SEQ ID NO: 97

1
mqapiqyhkt ddgivtltfd apeqsvntmt demrqcladm vsrleaekea vsgviltsak

61
etffaggnln rlyklqpada atqfdasera ksalrrletl gkpvvaalng talgggfeia

121
lachhriald kpkvqfglpe atlglmpgag gvvrlnrllg laasqpylqd sklmspaeat

181
kvglvhelad tpaallekar awiaahpesk qpwdkagytp pggwadasea rrwistaaaq

241
vraktkgcyp apeailcasv egmqvdfdta srietryfvk lvtgqvakni istfwfhang

301
iksgaqrpag vakgkiktvg vlgagmmgkg iayvaasrgi evwvkdatla qaegaranad

361
qllakreekg eidaatrrqi verihatdry edfahvdlvv eaipenpalk aeitrqaepv

421
lgdgaiwasn tstlpitgla kassrperfv glhffspvhr mqlvevikgq qtspetlaha

481
ldfvmqlgkt pivvndnrgf ftsrvfstft reavamlgeg qdpaaieaaa ilsgfpagpl

541
avldevslsl nynnrletlr ahaeegrplp phpadavmer mlnefgrkgr aagggfydyp

601
adgkkvfwsg lakhflrpae qipqrdkqdr llfcmalesv rvlqdgvlds agdgnigsvl

661
gigfprwsgg vfqflnqygl ekavaraeyl achygerftp pqllrekakr aepf

In some embodiments of any of the aspects, the engineered inactivating modification of an endogenous beta-oxidation gene comprises a deletion of the entire coding sequence (e.g., a knockout of an endogenous fadB gene, denoted herein as ΔfadB).

In some embodiments of any of the aspects, the engineered bacterium comprises an inhibitor of an endogenous beta-oxidation enzyme. In some embodiments of any of the aspects, the inhibitor of an endogenous beta-oxidation enzyme is acrylic acid. In some embodiments of any of the aspects, the inhibitor of an endogenous beta-oxidation enzyme comprises enzymes that catalyze the production of acrylic acid (e.g., malonyl-CoA reductase (MCR), malonate semialdehyde reductase (MSR), 3-hydroxypropionyl-CoA synthetase (3HPCS), and 3-hydroxypropionyl-CoA dehydratase (3HPCD) from Metallosphaera sedula; overexpressed succinyl-CoA synthetase (SCS) from E. coli). In some embodiments of any of the aspects, the engineered bacterium comprises at least one functional exogenous gene that catalyzes the production of acrylic acid (e.g., M sedula MCR, M sedula MSR, M sedula 3HPCS, M sedula 3HPCD, and/or E. coli SCS). See e.g., Liu and Liu, Production of acrylic acid and propionic acid by constructing a portion of the 3-hydroxypropionate/4-hydroxybutyrate cycle from Metallosphaera sedula in Escherichia coli; J Ind Microbiol Biotechnol. 2016 December, 43(12):1659-1670. Epub 2016 Oct. 8; the content of which is incorporated herein by reference in its entirety.

In some embodiments of any of the aspects, the inhibitor of an endogenous beta-oxidation enzyme is 2-bromooctanoic acid or 4-pentenoic acid; see e.g., Lee et al., Appl Environ Microbiol. 2001 November; 67(11):4963-74. Additional non-limiting examples of beta oxidation inhibitors include an inhibitory RNA (e.g., siRNA, miRNA) against a beta oxidation gene (e.g., FadB, a 3-hydroxyacyl-CoA dehydrogenase gene), a small molecule inhibitor of a beta oxidation gene (e.g., FadB, a 3-hydroxyacyl-CoA dehydrogenase gene), and the like.

Described herein are methods of sustainably producing TAGs, the general structure of which is shown in Formula I above or FIG. 1A. In one aspect, the method comprises: (a) culturing an engineered bacterium as described herein in a culture medium comprising CO₂and/or H₂; and (b) isolating, collecting, or concentrating TAGs from said engineered bacterium or from the culture medium of said engineered bacterium. In another aspect, described herein are methods of sustainably producing TAGs comprising: (a) culturing an engineered bacterium as described herein in a culture medium comprising a simple organic carbon source (e.g., glycerol) and/or H₂; and (b) isolating, collecting, or concentrating TAGs from said engineered bacterium or from the culture medium of said engineered bacterium. In some embodiments of any of the aspects, the culture medium comprises CO₂and glycerol.

TAGs can comprise any combination of fatty acid R groups. Varying the expression of different thioesterases (TE) can lead to the production of TAGs with specific chain-length or composition fatty acid R groups. In some embodiments, all three R group fatty acids of the TAG are the same fatty acids. In some embodiments, the engineered bacteria uses short-chain fatty acids (SCFAs), which are fatty acids with aliphatic tails of five or fewer carbons (e.g. butyric acid), to produce short-chain triglycerides. In some embodiments, the engineered bacteria uses medium-chain fatty acids (MCFA), which are fatty acids with aliphatic tails of 6 to 12 carbons, to form medium-chain triglycerides. In some embodiments, the engineered bacteria uses long-chain fatty acids (LCFA), which are fatty acids with aliphatic tails of 13 to 21 carbons, to produce long-chain triglycerides. In some embodiments, the engineered bacteria uses very long chain fatty acids (VLCFA), which are fatty acids with aliphatic tails of 22 or more carbons, to produce very-long-chain triglycerides.

In some embodiments, the fatty acids used to produce the TAG comprise C4-C18 fatty acids (e.g., C4, C5, C6, C7, C8, C9, C10, C11, C12, C13, C14, C15, C16, etc.). Naturally occurring fatty acids generally have an even number of carbons arranged in a straight chain (e.g., C4, C6, C8, C10, C12, C14, C16, etc.), but fatty acids can also comprise an odd number of carbon atoms in a straight chain (e.g., C5, C7, C9, C11, C13, C15, C17, etc.) In some embodiments, the three fatty acids used to produce the TAG can all comprise C4-C18 fatty acids, either saturated or non-saturated fatty acids. In some embodiments of any of the aspects, the TAG produced by the engineered bacterium comprises R group fatty acids which are 4 to 18 carbons long (C4-C18); such produced TAGs can be referred to herein as “C4-C18 TAGs.” In some embodiments of any of the aspects, the major product of the engineered bacterium is C4-C18 TAG. In some embodiments of any of the aspects, the isolated TAG comprises a majority of C4-C18 TAG. In some embodiments of any of the aspects, the total TAG isolated comprises at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or least 99% C4-C18 TAG.

In some embodiments, the fatty acids used to produce the TAG comprise C4-C8 fatty acids e.g., C4, C5, C6, C7, C8, etc.). Such short-medium chain-length fatty acids (e.g., C4-C8) predominate in animal fats, compared to longer chain-length fatty acids in plants. In particular, dairy fats, such as those produced by the engineered bacteria, can comprise TAGs with odd-number-length fatty acids and/or significant amounts of short-chain fatty acids. In some embodiments, the three fatty acids used to produce the TAG can all comprise C4-C8 fatty acids, either saturated or non-saturated fatty acids. In some embodiments of any of the aspects, the TAG produced by the engineered bacterium comprises R group fatty acids which are 4 to 8 carbons long (C4-C8); such produced TAGs can be referred to herein as “C4-C8 TAGs.” In some embodiments of any of the aspects, the major product of the engineered bacterium is C4-C8 TAG. In some embodiments of any of the aspects, the isolated TAG comprises a majority of C4-C8 TAG. In some embodiments of any of the aspects, the total TAG isolated comprises at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, or least 99% C4-C8 TAG.

In some embodiments, the fatty acids used to produce the TAG comprise C16 fatty acids. In some embodiments, the three fatty acids used to produce the TAG can all comprise C16 fatty acids, such as saturated C16 fatty acids (e.g., palmitic acid) or unsaturated C16 fatty acids. In some embodiments of any of the aspects, the TAG produced by the engineered bacterium comprises R group fatty acids which are 16 carbons long (C16); such produced TAGs can be referred to herein as “C16 TAGs.” In some embodiments of any of the aspects, the major product of the engineered bacterium is TAG. In some embodiments of any of the aspects, the major product of the engineered bacterium is C16 TAG. In some embodiments of any of the aspects, the isolated TAG comprises a majority of C16 TAG (see e.g., FIG. 3). In some embodiments of any of the aspects, the total TAG isolated comprises at least 50% C16 TAG, at least 55% C16 TAG, at least 60% C16 TAG, at least 65% C16 TAG, at least 70% C16 TAG, at least 75% C16 TAG, at least 80% C16 TAG, at least 85% C16 TAG, at least 90% C16 TAG, at least 95% C16 TAG, at least 96% C16 TAG, at least 97% C16 TAG, at least 98% C16 TAG, or least 99% C16 TAG.

In some embodiments of any of the aspects, the TAG produced by the engineered bacterium comprises specific fatty acids attached at a specific position of the glycerol backbone (see e.g., FIG. 5), e.g., the sn1 carbon, the sn2 carbon, or the sn3 carbon. In some embodiments of any of the aspects, the TAG produced by the engineered bacterium comprises C12-C16 fatty acids on positions sn1 and sn2. In some embodiments of any of the aspects, the TAG produced by the engineered bacterium comprises C4-C10 fatty acids on position sn3. In some embodiments of any of the aspects, the TAG produced by the engineered bacterium comprises C12-C16 fatty acids on positions sn1 and sn2, and C4-C10 fatty acids on position sn3.

In some embodiments of any of the aspects, the cells can be maintained in culture. As used herein, “maintaining” refers to continuing the viability of a cell or population of cells. A maintained population of cells will have at least a subpopulation of metabolically active cells.

As used herein, the term “sustainable” refers to a method of harvesting or using a resource so that the resource is not depleted or permanently damaged. In some embodiments of any of the aspects, the resource is a product that is produced by an engineered bacterium as described herein. In some embodiments of any of the aspects, the engineered bacterium sustainably produces TAGs using a minimal culture medium that comprises CO₂as the sole carbon source and H₂as the sole energy source.

As used herein the term “culture medium” refers to a solid, liquid or semi-solid designed to support the growth of microorganisms or cells. In some embodiments of any of the aspects, the culture medium is a liquid. In some embodiments of any of the aspects, the culture medium comprises both the liquid medium and the bacterial cells within it.

In some embodiments of any of the aspects, the culture medium is a minimal medium. As used herein, the term “minimal medium” refers to a cell culture medium in which only few and necessary nutrients are supplied, such as a carbon source, a nitrogen source, salts and trace metals dissolved in water with a buffer. Non-limiting examples of components in a minimal medium include Na₂HPO₄(e.g., 3.5 g/L), KH₂PO₄(e.g., 1.5 g/L), (NH₄)₂SO₄(e.g., 1.0 g/L), MgSO₄·7H₂O (e.g., 80 mg/L), CaSO₄·2H₂O (e.g., 1 mg/L), NiSO₄·7H₂O (e.g., 0.56 mg/L), ferric citrate (e.g., 0.4 mg/L), and NaHCO₃(200 mg/L). In some embodiments of any of the aspects, a minimal medium can be used to promote lithotrophic growth, e.g., of a chemolithotroph. In some embodiments, (NH₄)Cl (e.g., 1.0 g/L) is used in addition to or instead of (NH₄)₂SO₂. In some embodiments, the minimal media comprises at least one trace metal from Table 5.

TABLE 5

Exemplary trace metals in culture media; see e.g.,

Mozumder et al., Modeling pure culture heterotrophic

production of polyhydroxybutyrate (PHB), Bioresour

Technol. 2014 March; 155: 272-80.

exemplary

component
concentration

FeSO₄*7H₂O
10
g/L

ZnSO₄*7H₂O
2.25
g/L

CuSO₄*5H₂O
1
g/L

MnSO₄*5H₂O
0.5
g/L

35% HCl
10
mL/L

CaCl₂*2H₂O
2
g/L

Na₂B₄O₇*10H₂O
0.23
g/L

(NH₄)₆Mo₇O₂₄
0.1
g/L

In some embodiments of any of the aspects, the culture medium is a rich medium. As used herein, the term “rich medium” refers to a cell culture medium in which more than just a few and necessary nutrients are supplied, i.e., a non-minimal medium. In some embodiments of any of the aspects, rich culture medium can comprise nutrient broth (e.g., 17.5 g/L), yeast extract (7.5 g/L), and/or (NH₄)₂SO₄(e.g., 5 g/L). In some embodiments of any of the aspects, a rich medium comprises glycerol. In some embodiments of any of the aspects, a rich medium comprises a minimal media, as described herein or known in the art, and additional nutrients (e.g., nutrient broth, yeast extract, etc.). In some embodiments of any of the aspects, a rich medium does necessarily promote lithotrophic growth. In some embodiments of any of the aspects, a rich medium does not necessarily promote lithotrophic growth. In some embodiments of any of the aspects, a rich medium promotes heterotrophic growth.

In some embodiments of any of the aspects, the culture medium, culture vessel, or environment surrounding the culture medium or culture vessel (e.g., an incubator) comprises approximately 30% H₂and approximately 15% CO₂. In some embodiments of any of the aspects, the culture medium, culture vessel, or environment surrounding the culture medium or culture vessel (e.g., an incubator) comprises at most 10% H₂, at most 20% H₂, at most 30% H₂, at most 40% H₂, or at most 50% H₂. In some embodiments of any of the aspects, the culture medium, culture vessel, or environment surrounding the culture medium or culture vessel (e.g., an incubator) comprises at most 5% CO₂, at most 10% CO₂, at most 15% CO₂at most 20% CO₂, or at most 25% CO₂.

In some embodiments of any of the aspects, the culture medium comprises CO₂as the sole carbon source. In some embodiments of any of the aspects, CO₂is at least 90%, at least 95%, at least 98%, at least 99% or more of the carbon sources present in the culture medium. In some embodiments of any of the aspects, the culture medium comprises CO₂in the form of bicarbonate (e.g., HCO₃⁻, NaHCO₃) and/or dissolved CO₂(e.g., atmospheric CO₂; e.g., CO₂provided by a cell culture incubator). In some embodiments of any of the aspects, the culture medium does not comprise organic carbon as a carbon source. Non-limiting example of organic carbon sources include fatty acids, gluconate, acetate, fructose, decanoate; see e.g., Jiang et al. Int J Mol Sci. 2016 July; 17(7): 1157).

In some embodiments of any of the aspects, the culture medium comprises glycerol as the sole carbon source. In some embodiments of any of the aspects, glycerol is at least 90%, at least 95%, at least 98%, at least 99% or more of the carbon sources present in the culture medium. In some embodiments of any of the aspects, the culture medium comprises glycerol and CO₂as the sole carbon sources. In some embodiments of any of the aspects, the glycerol and CO₂is at least 90%, at least 95%, at least 98%, at least 99% or more of the carbon sources present in the culture medium.

In some embodiments of any of the aspects, the culture medium comprises H₂as the sole energy source. In some embodiments of any of the aspects, H₂is at least 90%, at least 95%, at least 98%, at least 99% or more of the energy sources present in the culture medium. In some embodiments of any of the aspects, H₂is supplied by water-splitting electrodes in the culture medium. Accordingly, in one aspect described herein is a system comprising a reactor chamber with a solution (e.g., culture medium) contained therein. The solution may include hydrogen (H₂), carbon dioxide (CO₂), bioavailable nitrogen (e.g., ammonia, (NH₄)₂SO₄, amino acids), and an engineered bacterium as described herein. Gasses such as one or more of hydrogen (H₂), carbon dioxide (CO₂), nitrogen (N₂), and oxygen (O₂) may also be located within a headspace of the reactor chamber, though embodiments in which a reactor does not include a headspace such as in a flow through reactor are also contemplated. The system may also include a pair of electrodes immersed in the solution (e.g., culture medium). The electrodes are configured to apply a voltage potential to, and pass a current through, the solution to split water contained within the culture medium to form at least hydrogen (H₂) and oxygen (O₂) gasses in the solution. These gases may then become dissolved in the solution. During use, a concentration of the bioavailable nitrogen in the solution may be maintained below a threshold nitrogen concentration that causes the bacteria to produce a desired product (e.g., TAGs). This product may either by excreted from the bacteria and/or stored within the bacteria as the disclosure is not so limited (see e.g., US Patent Publication 2018/0265898, the contents of which are incorporated herein by reference in their entirety).

In some embodiments of any of the aspects, the culture medium does not comprise oxygen (O₂) gasses in the solution, i.e., the culture is grown under anaerobic conditions. In some embodiments of any of the aspects, the culture medium comprises low levels of oxygen (O₂) gasses in the solution, i.e., the culture is grown under hypoxic conditions. As a non-limiting example, the culture medium can comprise at most 30%, at most 20%, at most 15%, at most 10%, at most 5%, at most 4%, at most 3%, at most 2%, or at most 1% O₂gasses in the solution.

In some embodiments of any of the aspects, the culture medium further comprises arabinose. In some embodiments of any of the aspects, arabinose acts as an inducer for genes in a pBAD vector. In some embodiments of any of the aspects, the culture medium further comprises at least 0.1% arabinose. As a non-limiting example, the culture medium further comprises at least 0.1% arabinose, at least 0.2% arabinose, at least 0.3% arabinose, at least 0.4% arabinose, at least 0.5% arabinose, 0.6% arabinose, at least 0.7% arabinose, at least 0.8% arabinose, at least 0.9% arabinose, or at least 1.0% arabinose.

In some embodiments of any of the aspects, methods described herein comprise isolating, collecting, or concentrating a product from an engineered bacterium or from the culture medium of an engineered bacterium. As used herein the terms “isolate,” “collect,” “concentrate”, “purify” and “extract” are used interchangeably and refer to a process whereby a target component (e.g., TAGs) is removed from a source, such as a fluid (e.g., culture medium). In some embodiments of any of the aspects, methods of isolation, collection, concentration, purification, and/or extraction comprise a reduction in the amount of at least one heterogeneous element (e.g., proteins, nucleic acids; i.e., a contaminant). In some embodiments of any of the aspects, methods of isolation, collection, concentration, purification, and/or extraction reduce by 1%, 2%, 3%, 4%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90% or 95%, or more, the amount of heterogeneous elements, for example biological macromolecules such as proteins or DNA, that may be present in a sample comprising a molecule of interest. The presence of heterogeneous proteins can be assayed by any appropriate method including High-performance Liquid Chromatography (HPLC), gel electrophoresis and staining and/or ELISA assay. The presence of DNA and other nucleic acids can be assayed by any appropriate method including gel electrophoresis and staining and/or assays employing polymerase chain reaction.

Described herein are systems comprising at least one of the engineered bacteria as described herein. In one aspect, the system comprises at least one of the engineered bacteria and a support. In some embodiments of any of the aspects, the bacteria is linked to the support using intrinsic mechanisms (e.g., pili, biofilm, etc.) and/or extrinsic mechanisms (e.g., chemical crosslinking, antibiotics, opsonin, etc.). In some embodiments of any of the aspects, the system further comprises a container and a solution, in which the bacteria linked to the support are submerged. In some embodiments of any of the aspects, the system further comprises a pair of electrodes that split water contained within the solution to form hydrogen. In some embodiments of any of the aspects, the solution (e.g., a culture medium) comprises hydrogen (H₂) and carbon dioxide (CO₂). In some embodiments of any of the aspects, the solution (e.g., a culture medium) comprises hydrogen (H₂) and glycerol. In some embodiments of any of the aspects, the solution (e.g., a culture medium) comprises hydrogen (H₂), glycerol, and carbon dioxide (CO₂).

In some embodiments of any of the aspects, the support comprises a solid substrate. Examples of solid substrate can include, but are not limited to, film, beads or particles (including nanoparticles, microparticles, polymer microbeads, magnetic microbeads, and the like), filters, fibers, screens, mesh, tubes, hollow fibers, scaffolds, plates, channels, gold particles, magnetic materials, medical apparatuses (e.g., needles or catheters) or implants, dipsticks or test strips, filtration devices or membranes, hollow fiber cartridges, microfluidic devices, mixing elements (e.g., spiral mixers), extracorporeal devices, and other substrates commonly utilized in assay formats, and any combinations thereof. In some embodiments of any of the aspects, the solid substrate can be a magnetic particle or bead.

In several aspects, the system comprises a reactor chamber and at least one of the engineered bacteria as described herein. Accordingly, in one aspect, described herein is a system comprising: (a) a reactor chamber with a solution contained therein, wherein the solution comprises hydrogen (H₂) and carbon dioxide (CO₂); and (b) at least one engineered bacterium as described herein in the solution. Also described herein is a system comprising: (a) a reactor chamber with a solution contained therein, wherein the solution comprises hydrogen (H₂) and glycerol; and (b) at least one engineered bacterium as described herein in the solution. In some embodiments of any of the aspects, the system further comprises a pair of electrodes in contact with the solution that split water to form the hydrogen. In one aspect, described herein is a system comprising: (a) a reactor chamber; and (b) at least one engineered bacterium. In some embodiments of any of the aspects, the system further comprises a pair of electrodes in contact with reactor chamber.

In one aspect, described herein is a system comprising: (a) a reactor chamber with a solution contained therein, wherein the solution comprises hydrogen (H₂) and a carbon source; and (b) an engineered bacterium as described herein. In some embodiments of any of the aspects, the carbon source is carbon dioxide (CO₂) and/or glycerol. In some embodiments of any of the aspects, the system further comprises a pair of electrodes in contact with the solution that split water to form the hydrogen. In some embodiments of any of the aspects, the system (e.g., a system comprising a reactor chamber, a system comprising a support) can comprise any combination of engineered bacteria as described herein.

In one aspect, described herein is a system comprising: (a) a reactor chamber with a solution contained therein, wherein the solution comprises hydrogen (H₂) and carbon dioxide (CO₂); (b) an engineered TAG bacterium as described herein in the solution; and (c) a pair of electrodes in contact with the solution that split water to form the hydrogen.

In one aspect, described herein is a system comprising: (a) a reactor chamber with a solution contained therein, wherein the solution comprises hydrogen (H₂) and glycerol; (b) an engineered TAG bacterium as described herein in the solution; and (c) a pair of electrodes in contact with the solution that split water to form the hydrogen.

In one aspect, described herein is a system comprising: (a) a reactor chamber with a solution contained therein, wherein the solution comprises hydrogen (H₂), glycerol, and carbon dioxide (CO₂); (b) an engineered TAG bacterium as described herein in the solution; and (c) a pair of electrodes in contact with the solution that split water to form the hydrogen.

In some embodiments of any of the aspects, the pair of electrodes comprise a cathode including a cobalt-phosphorus alloy and an anode including cobalt phosphate. In some embodiments of any of the aspects, a concentration of the bioavailable nitrogen in the solution is below a threshold nitrogen concentration to cause the engineered bacteria to produce a product. In some embodiments of any of the aspects, the solution is also referred to as a culture medium and can comprise a minimal medium as described further herein.

In one embodiment, a system includes a reactor chamber containing a solution. The solution may include hydrogen (H₂), carbon dioxide (CO₂), bioavailable nitrogen, and an engineered bacteria. Gasses such as one or more of hydrogen (H₂), carbon dioxide (CO₂), nitrogen (N₂), and oxygen (O₂) may also be located within a headspace of the reactor chamber, though embodiments in which a reactor does not include a headspace such as in a flow through reactor are also contemplated. The system may also include a pair of electrodes immersed in the solution. The electrodes are configured to apply a voltage potential to, and pass a current through, the solution to split water contained within the solution to form at least hydrogen (H₂) and oxygen (O₂) gasses in the solution. These gases may then become dissolved in the solution. During use, a concentration of the bioavailable nitrogen in the solution may be maintained below a threshold nitrogen concentration that causes the bacteria to produce a desired product. This product may either by excreted from the bacteria and/or stored within the bacteria as the disclosure is not so limited.

Concentrations of the above noted gases both dissolved within a solution, and/or within a headspace above the solution, may be controlled in any number of ways including bubbling gases through the solution, generating the dissolved gases within the solution as noted above (e.g. electrolysis/water splitting), periodically refreshing a composition of gases located within a headspace above the solution, or any other appropriate method of controlling the concentration of dissolved gas within the solution. Additionally, the various methods of controlling concentration may either be operated in a steady-state mode with constant operating parameters, and/or a concentration of one or more of the dissolved gases may be monitored to enable a feedback process to actively change the concentrations, generation rates, or other appropriate parameter to change the concentration of dissolved gases to be within the desired ranges noted herein. Monitoring of the gas concentrations may be done in any appropriate manner including pH monitoring, dissolved oxygen meters, gas chromatography, or any other appropriate method.

As noted above, in one embodiment, the composition of a volume of gas located in a headspace of a reactor may include one or more of carbon dioxide, oxygen, hydrogen, and nitrogen. A concentration of the carbon dioxide may be between 10 volume percent (vol %) and 100 vol %. However, carbon dioxide may also be greater than equal to 0.04 vol % and/or any other appropriate concentration. For example, carbon dioxide may be between or equal to 0.04 vol % and 100 vol %. A concentration of the oxygen may be between 1 vol % and 99 vol % and/or any other appropriate concentration. A concentration of the hydrogen may be greater than or equal to 0.05 vol % and 99%. A concentration of the nitrogen may be between 0 vol % and 99 vol %.

As also noted, in one embodiment, a solution within a reactor chamber may include water as well as one or more of carbon dioxide, oxygen, and hydrogen dissolved within the water. A concentration of the carbon dioxide in the solution may be between 0.04 vol % to saturation within the solution. A concentration of the oxygen in the solution may be between 1 vol % to saturation within the solution. A concentration of the hydrogen in the solution may be between 0.05 vol % to saturation within the solution provided that appropriate concentrations of carbon dioxide and/or oxygen are also present.

As noted previously, and as described further below, production of a desired end product by bacteria located within the solution may be controlled by limiting a concentration of bioavailable nitrogen, such as in the form of ammonia, amino acids, or any other appropriate source of nitrogen useable by the bacteria within the solution to below a threshold nitrogen concentration. However, and without wishing to be bound by theory, the concentration threshold may be different for different bacteria and/or for different concentrations of bacteria. For example, a solution containing enough ammonia to support a Ralstonia eutropha (i.e., Cupriavidus necator) population up to an optical density (OD) of 2.3 produces product at molar concentrations less than or equal to 0.03 M while a population with an OD of 0.7 produces product at molar concentrations less than or equal to 0.9 mM. Accordingly, higher optical densities may be correlated with producing product at higher nitrogen concentrations while lower optical densities may be correlated with producing product at lower nitrogen concentrations. Further, bacteria may be used to produce product by simply placing them in solutions containing no nitrogen. In view of the above, an optical density of bacteria within a solution may be between or equal to 0.1 and 12, 0.7 and 12, or any other appropriate concentration including concentrations both larger and smaller than those noted above. Additionally, a concentration of nitrogen within the solution may be between or equal to 0 and 0.2 molar, 0.0001 and 0.1 molar, 0.0001 and 0.05 molar, 0.0001 and 0.03 molar, or any other appropriate composition including compositions greater and less than the ranges noted above.

While particular gasses and compositions have been detailed above, it should be understood that the gasses located with a headspace of a reactor as well as a solution within the reactor may include compositions and/or concentrations as the disclosure is not limited in this fashion.

Bacteria used in the systems and methods disclosed herein may be selected so that the bacteria both oxidize hydrogen as well as consume carbon dioxide. Accordingly, in some embodiments, the bacteria may include an enzyme capable of metabolizing hydrogen as an energy source such as with hydrogenase enzymes. Additionally, the bacteria may include one or more enzymes capable of performing carbon fixation such as Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). One possible class of bacteria that may be used in the systems and methods described herein to produce a product include, but are not limited to, chemolithoautotrophs. Additionally, appropriate chemolithoautotrophs may include any one or more of Ralstonia eutropha (R. eutropha) as well as Alcaligenes paradoxs I 360 bacteria, Alcaligenes paradoxs 12/X bacteria, Nocardia opaca bacteria, Nocardia autotrophica bacteria, Paracoccus denitrificans bacteria, Pseudomonas facilis bacteria, Arthrobacter species 1IX bacteria, Xanthobacter autotrophicus bacteria, Azospirillum lipferum bacteria, Derxia Gummosa bacteria, Rhizobium japonicum bacteria, Microcyclus aquaticus bacteria, Microcyclus ebruneus bacteria, Renobacter vacuolatum bacteria, and any other appropriate bacteria.

A bacterium in the system or bioreactor can either naturally include a TAG production pathway, or may be appropriately engineered, to include a TAG production pathway when placed under the appropriate growth conditions.

FIG. 4A shows a schematic of one embodiment of a system including one or more reactor chambers. In the depicted embodiment, a single-chamber reactor 2 houses one or more pairs of electrodes including an anode 4a and a cathode 4b immersed in a water based solution 6. Bacteria 8 are also included in the solution. A headspace 10 corresponding to a volume of gas that is isolated from an exterior environment is located above the solution within the reactor chamber. The gas volume may correspond to any appropriate composition including, but not limited to, carbon dioxide, nitrogen, hydrogen, oxygen, and any other appropriate gases as the disclosure is not so limited. Additionally, as detailed further below, the various gases may be present in any appropriate concentration as detailed previously. However, it should be understood that embodiments in which a reactor chamber is exposed to an external atmosphere that may either be a controlled composition and/or a normal atmosphere are also contemplated. The system may also include one or more temperature regulation devices such as a water bath, temperature controlled ovens, or other appropriate configurations and/or devices to maintain a reactor chamber at any desirable temperature range for bacterial growth.

In embodiments where a reactor chamber interior is isolated from an exterior environment, the system may include one or more seals 12. In the depicted embodiment, the seal corresponds to a cork, stopper, a threaded cap, a latched lid, or any other appropriate structure that seals an outlet from an interior of the reactor chamber. In this particular embodiment, a power source 14 is electrically connected to the anode and cathode via two or more electrical leads 16 that pass through one or more pass throughs in the seal to apply a potential to and pass a current IDC to split water within the solution into hydrogen and oxygen through an oxygen evolution reaction (OER) at the anode and a hydrogen evolution reaction (HER) at the cathode. While the leads have been depicted as passing through the seal, it should be understood that embodiments in which the leads pass through a different portion of the system, such as a wall of the reactor chamber, are also contemplated as the disclosure is so limited.

Depending on the particular embodiment, the above-described power source may correspond to any appropriate source of electrical current that is applied to the electrodes. However, in at least one embodiment, the power source may correspond to a renewable source of energy such as a solar cell, wind turbine, or any other appropriate source of current though embodiments in which a non-renewable energy source, such as a generator, battery, grid power, or other power source is used are also contemplated. In either case, a current from the power source is passed through the electrodes and solution to evolve hydrogen and oxygen. The current may be controlled to produce hydrogen and/or oxygen at a desired rate of production as noted above. In some embodiments of any of the aspects, a system comprising a renewable source of energy (e.g., a solar cell) can also be referred to as a “bionic leaf”.

Accordingly, in one aspect, described herein is a system comprising: (a) a reactor chamber with a solution contained therein, wherein the solution comprises hydrogen (H₂) and carbon dioxide (CO₂); (b) an engineered bacteria as described herein; (c) a pair of electrodes in contact with the solution that split water to form the hydrogen; and (d) comprising a power source comprising a renewable source of energy.

In another aspect, described herein is a system comprising: (a) a reactor chamber with a solution contained therein, wherein the solution comprises hydrogen (H₂) and glycerol; (b) an engineered bacteria as described herein; (c) a pair of electrodes in contact with the solution that split water to form the hydrogen; and (d) comprising a power source comprising a renewable source of energy.

In one aspect, described herein is a system comprising: (a) a reactor chamber with a solution contained therein, wherein the solution comprises hydrogen (H₂), glycerol and carbon dioxide (CO₂); (b) an engineered bacteria as described herein; (c) a pair of electrodes in contact with the solution that split water to form the hydrogen; and (d) comprising a power source comprising a renewable source of energy.

In some embodiments, the electrodes may be coated with, or formed from, a water splitting catalyst to further facilitate water splitting and/or reduce the voltage applied to the solution. In some embodiments, the catalysts may be coated onto an electrode substrate including, for example, carbon fabrics, porous carbon foams, porous metal foams, metal fabrics, solid electrodes, and/or any other appropriate geometry or material as the disclosure is not so limited. In another embodiment, the electrodes may simply be made from a desired catalyst material. Several appropriate materials for use as catalysts include, but are not limited to, one or more of a cobalt-phosphorus (Co—P) alloy, cobalt phosphate (CoPi), cobalt oxide, cobalt hydroxide, cobalt oxyhydroxide, a NiMoZn alloy, or any other appropriate material. As noted further below, certain catalysts offer additional benefits as well. For example, in one specific embodiment, the electrodes may correspond to a cathode including a cobalt-phosphorus alloy and an anode including cobalt phosphate, which may help to reduce the presence of reactive oxygen species and/or metal ions within a solution. A composition of the CoPi coating and/or electrode may include phosphorous compositions between or equal to 0 weight percent (wt %) and 50 wt %. Additionally, the Co—P alloy may include between 80 wt % and 99 wt % Co as well as 1 wt % and 20 wt % P. However, embodiments in which different element concentrations are used and/or other types of catalysts and/or electrodes are used are also contemplated as the disclosure is not so limited. For example, stainless steel, platinum, and/or other types of electrodes may be used.

As also shown in FIG. 4A, in some embodiments, it may be desirable to either continuously, or periodically, bubble, i.e. sparge or flush, one or more gases through a solution 6 and/or to refresh a composition of gases located within a head space 10 of the reactor chamber 2 above a surface of the solution. In such an embodiment, a gas source 18 may be in fluid communication with one or more gas inlets 20 that pass through either a seal 12 and/or another portion of the reactor chamber 2 such as a side wall to place the gas source in fluid communication with an interior of the reactor chamber. Additionally, in some embodiments, one or more inlets discharge a flow of gas into the solution so that the gas will bubble through the solution. However, embodiments in which the one or more gas inlets discharge a flow of gas into the headspace of the reactor chamber instead are also contemplated as the disclosure is not so limited. Additionally, one or more corresponding gas outlets 22 may be formed in a seal and/or another portion of the reactor chamber to permit a flow of gas to flow from an interior to an exterior of the reactor chamber. It should be noted that gas inlets and outlets may correspond to any appropriate structure including, but not limited to, tubes, pipes, flow passages, ports in direct fluid communication with the reactor chamber interior, or any other appropriate structure.

Gas sources may correspond to any appropriate gas source capable of providing a pressurized flow of gas to the chamber through the inlet including, for example, one or more pressurized gas cylinders. While a gas source may include any appropriate composition of one or more gasses, in one embodiment, a gas source may provide one or more of hydrogen, nitrogen, carbon dioxide, and oxygen. The flow of gas provided by the gas source may have a composition equivalent to the range of gas compositions described above for the gas composition with a headspace of the reactor chamber. Further, in some embodiments, the gas source may simply be a source of carbon dioxide. Of course embodiments in which a different mix of gases, other including different gases and/or different concentrations than those noted above, is bubbled through a solution or otherwise input into a reactor chamber are also contemplated as the disclosure is not so limited. Additionally, the gas source may be used to help maintain operation of a reactor at, below, and/or above atmospheric pressure as the disclosure is not limited to any particular pressure range.

The above noted one or more gas inlets and outlets may also include one or more valves located along a flow path between the gas source and an exterior end of the one or more outlets. These valves may include for example, manually operated valves, pneumatically or hydraulically actuated valves, unidirectional valves (i.e. check valves) may also be incorporated in the one or more inlets and/or outlets to selectively prevent the flow of gases into or out of the reactor either entirely or in the upstream direction into the chamber and/or towards the gas source.

While the use of inlet and/or outlet gas passages have been described above, embodiments in which there are no inlet and/or outlets for gasses are present are also contemplated. For example, in one embodiment, a system including a sealable reactor may simply be flushed with appropriate gasses prior to being sealed. The system may then be flushed with an appropriate composition of gasses at periodic intervals to refresh the desired gas composition in the solution and/or headspace prior to resealing the reactor chamber. Alternatively, the head space may be sized to contain a gas volume sufficient for use during an entire production run.

In instances where electrodes are run at high enough rates and/or for sufficient durations, concentration may be formed within a solution in a reactor chamber. Accordingly, it may be desirable to either prevent and/or mitigate the presence of concentration gradients in the solution. Therefore, in some embodiments, a system may include a mixer such as a stir bar 24 illustrated in FIG. 4A. Alternatively, a shaker table, and/or any other way of inducing motion in the solution to reduce the presence of concentration gradients may also be used as the disclosure is not so limited.

While the above embodiment has been directed to an isolated reactor chamber, embodiments in which a flow-through reaction chamber with two or more corresponding electrodes immersed in a solution that is flowed through the reaction chamber and past the electrodes are also contemplated. For example, one possible embodiment, one or more corresponding electrodes may be suspended within a solution flowing through a chamber, tube, passage, or other structure. Similar to the above embodiment, the electrodes are electrically coupled with a corresponding power source to perform water splitting as the solution flows past the electrodes. Such a system may either be a single pass flow through system and/or the solution may be continuously flowed passed the electrodes in a continuous loop though other configurations are also contemplated as well.

Without wishing to be bound by theory, FIG. 4B illustrates one possible pathway for a system to produce one or more desired products. In the depicted embodiment, the hydrogen evolution reaction occurs at the cathode 4b. During the reaction at the cathode, two hydrogen ions (H⁺) are combined with two electrons to form hydrogen gas H₂that dissolves within the solution 6 along with carbon dioxide (CO₂), which dissolved in the solution as well. At the same time various toxicants such as reactive oxygen species (ROS) including, for example, hydrogen peroxide (H₂O₂), superoxides (O₂⁻), and/or hydroxyl radical (HO·) species as well as metallic ions may be generated at the cathode. For example, CO²⁺ ions may be dissolved into solution when a cobalt based cathode is used. As described further below, in some embodiments, the use of certain catalysts may help to reduce the production of ROS and the metallic ions leached into the solution may be deposited onto the anode using one or more elements located within the solution to form compounds such as a cobalt phosphate.

As also illustrated in FIG. 4B, once hydrogen and carbon dioxide are provided within a solution, bacteria 8 present within the solution may be used to transform these compounds into useful products (e.g., TAGs). For example, in one embodiment, the bacteria uses hydrogenase to metabolize the dissolved hydrogen gas and one or more appropriate enzymes, such as RuBisCO or other appropriate enzyme, to provide a carbon fixation pathway. This may include absorbing the carbon dioxide and forming Acetyl-CoA through the Calvin cycle. Further, depending on the concentration of nitrogen within the solution, the bacteria may either form biomass or one or more desired products. For instance, if a concentration of nitrogen within the solution is below a predetermined nitrogen concentration threshold, the bacteria may form one or more products such as TAGs, as depicted in the figure.

Depending on the embodiment, a solution placed in the chamber of a reactor may include water with one or more additional solvents, compounds, and/or additives. For example, the solution may include: inorganic salts such as phosphates including sodium phosphates and potassium phosphates; trace metal supplements such as iron, nickel, manganese, zinc, copper, and molybdenum; or any other appropriate component in addition to the dissolved gasses noted above. In one such embodiment, a phosphate may have a concentration between 9 and 90 mM, 9 and 72 mM, 9 and 50 mM, or any other appropriate concentration. In a particular embodiment, a water based solution may include one or more of the following in the listed concentrations: 12 mM to 123 mM of Na₂HPO₄, 11 mM to 33 mM of KH₂PO₄, 1.25 mM to 15 mM of (NH₄)₂SO₄, 0.16 mM to 0.64 mM of MgSO₄, 2.4 M to 5.8 μM of CaSO₄, 1 μM to 4 μM of NiSO₄, 0.81 μM to 3.25 μM molar concentration of Ferric Citrate, 60 mM to 240 mM molar concentration of NaHCO₃.

As noted above in regards to the discussion of FIG. 4B, reactive oxygen species (ROS) as well as metallic ions may be formed and/or dissolved into a solution during the hydrogen evolution reaction at the cathode. However, ROS and larger concentrations of the metallic ions within the solution may be detrimental to cell growth above certain concentrations. It is noted that the use of continuous hydrogen production within a reactor to form hydrogen for conversion into one or more desired products has been hampered by the production of these ROS and metallic ion concentrations because the bacteria used to form the desired products tend to be sensitive to these compounds and ions limiting the growth of, and above certain concentrations, killing the bacteria. Therefore, in some embodiments, it may be desirable to apply voltages, use electrodes that produce less ROS, remove and/or prevent the dissolution of metallic ions from the electrodes, and/or use bacteria that are resistant to the presence of these toxicants as detailed further below.

As noted above, it may be desirable to select one or more catalysts for use as the electrodes that produce fewer reactive oxygen species (ROS) during use. Specifically, a biocompatible catalyst system that is not toxic to the bacterium and lowers the overpotential for water splitting may be used in some embodiments. One such example of a catalyst includes a ROS-resistant cobalt-phosphorus (Co—P) alloy cathode. This cathode may be combined with a cobalt phosphate (CoPi) anode. This catalyst pair has the added benefit of the anode being self-healing. In other words, the catalyst pair helps to remove metallic Co²⁺ions present with a solution in a reactor. Without wishing to be bound by theory, the electrode pair works in concert to remove extracted metal ions from the cathode by depositing them onto the anode which may help to maintain extraneous cobalt ions at relatively low concentrations within solution and to deliver a low applied electrical potential to split water to generate H₂. Without wishing to be bound by theory, it is believed that during electrolysis of the water, phosphorus and/or cobalt is extracted from the electrodes. The reduction potential of leached cobalt is such that formation of cobalt phosphate using phosphate available in the solution is energetically favored. Cobalt phosphate formed in solution then deposits onto the anode at a rate linearly proportional to free Co²⁺, providing a self-healing process for the electrodes. In view of the above, the cobalt-phosphorus (Co—P) alloy and cobalt phosphate (CoPi) catalysts may be used to help mitigate the presence of both ROS and metal ions within the solution to help promote growth of bacteria within the reactor chamber.

It should be understood that any appropriate voltage may be applied to a pair of electrodes immersed in a solution to split water into hydrogen and oxygen. However, in some embodiments, the applied voltage may be limited to fall between upper and lower voltage thresholds. For example, the self-healing properties of a cobalt phosphate and cobalt phosphorous based alloy electrode pair may function at voltage potentials greater than about 1.42 V. Additionally, the thermodynamic minimum potential for splitting water is about 1.23 V. Therefore, depending on the particular embodiment, the voltage applied to the electrodes may be greater than or equal to about 1.23 V, 1.42 V, 1.5 V, 2 V, 2.2 V, 2.4 V, or any other appropriate voltage. Additionally, the applied voltage may be less than or equal to about 10 V, 5 V, 4 V, 3 V, 2.9 V, 2.8 V, 2.7 V, 2.6 V, 2.5 V, or any other appropriate voltage. Combinations of the above noted voltage ranges are contemplated including, for example, a voltage applied to a pair of electrodes may be between 1.23 V and 10 V, 1.42 V and 5 V, 2 V and 3 V, 2.3 V and 2.7 V as well as other appropriate ranges. Additionally, it should be understood that voltages both greater than and less than those noted above, as well as different combinations of the above ranges, are also contemplated as the disclosure is not so limited. In addition to the applied voltages, any appropriate current may be passed through the electrodes to perform water splitting which will depend on the desired rate of hydrogen generation for a given volume of a reactor being used. For example, in some embodiments, a current used to split water may be controlled to generate hydrogen at a rate substantially equal to a rate of hydrogen consumption by bacteria in the solution. However, embodiments in which hydrogen is produced at rates both greater than or less than consumption by the bacteria are also contemplated.

In addition to using catalysts, controlling the solution pH, and applying appropriate driving potentials, and/or controlling any other appropriate parameter to reduce the presence of reactive oxygen species (ROS) within the solution in a reaction chamber, it may also be desirable to use bacteria that are resistant to the presence of ROS and/or metallic ions present within the solution as noted previously. Specifically, a chemolithoautotrophic bacterium that is resistant to reactive oxygen species may be used. Further, in some embodiments a R. eutropha bacteria that is resistant to ROS as compared to a wild-type H16 R. eutropha may be used. US 2018/0265898 and Table 2 below detail several genetic polymorphisms found between the wild-type H16 R. eutropha and a ROS-tolerant BC4 strain that was purposefully evolved. Mutations of the BC4 strain relative to the wild type bacteria are detailed further below.

TABLE 2

Mutations in ROS-tolerant BC4 strain

Mutation
Position
Annotation
Gene
Description

G → T
611,894
R133R
acrC1
cation/multidrug

efflux system outer

membrane protein

Δ45 bp
611,905
344-388 of
acrC1
cation/multidrug

1494 nt

efflux system outer

membrane protein

G → A
2,563,281
intergenic,
Hfq and
uncharacterized host

(−1/+210)
H16_A2360
factor I protein/

GTP-binding protein

Δ15 bp
241,880
363-377 of
H16_B0214
transcriptional

957 nt

regulator,

LysR-Family

Two single nucleotide polymorphisms and two deletion events have been observed. Without wishing to be bound by theory, the large deletion from acrC1 may indicate a decrease in overall membrane permeability, possibly affecting superoxide entry to the cell resulting in the observed ROS resistance. The genome sequences are accessible at the NCBI SRA database under the accession number SRP073266 and specific mutations of the BC4 strain are listed below. The standard genome sequence for the wild-type H16 R. eutropha is also accessible at the RCSB Protein Data Bank under accession number AM260479 which the following mutations may also be referenced to.

In reference to the above table, an R. eutropha bacteria may include at least one to four mutations selected from the mutations noted above in Table 2 and may be selected in any combination. These specific mutations are listed below in more detail with mutations noted relative to the wild type R. eutropha bolded and underlined within the sequences given below.

The first noted mutation may correspond to the sequence listed below ranging from position 611790-611998 for Ralstonia eutropha H16 chromosome 1. The bolded, double underlined text indicates a mutation (e.g., nt 105 of SEQ ID NO: 12).

(209 nt)

SEQ ID NO: 12

GCCTCGCTGCTTTCCACCTGGCGCCGCACGCGGCCCCAGACGTCGA

TTTCCCAGGTTGCGCCCAGGGTCGCGCTCTGCCCGTTGAGCGTGCTGCCG CTGGCGCC G

CGCGCGCGCGAGGCGCCGGCCTGTGCGTCGACGGTCGGGAA

GAAGCCGGCGCGCGCGGCCTGCAGCGACGCCACCGCCTGGCGGTACTGCG

CCTCGGCGGCCTT

The second noted mutation may correspond to the sequence listed below ranging from

position 611905-613399 for Ralstonia eutropha H16 chromosome 1. The bolded, double

underlined text indicates a mutation (e.g., nt 345-390 of SEQ ID NO: 13).

(1495 nt)

SEQ ID NO: 13

AGGCGCCGGCCTGTGCGTCGACGGTCGGGAAGAAGCCGGCGCGCG

CGGCCTGCAGCGACGCCACCGCCTGGCGGTACTGCGCCTCGGCGGCCTTG

ATGTTCTGGTTCGAGATCTGCACCTCGGACATCAGCGCGTCGAGCTGCGC

ATCGCCGAACACGGTCCACCAGTCGGCGCGTGCCAGCGCATCCTGCGGCT

CGGCGGGCTTCCAGTCGCCGGTCCAGGCGGGGGTGGCGGCATCGGCTTCC

TTGAAGGATGCGGAAACCGGCGCGTCGGGGCGCTGGTAGTCGGGGCCGAC

GGCGCAGCCGGCCAGCAGCAGCGCGCAGGCCAGCGACACCGGCAGGGCA T

GGGTCAGGAGGCGGGAAAGAACTGTCATGTCGAGTCTTCGCAAAT
CTAGA

CGGCGGCCGGCTGGTCAGGCGTGCCGGCACCACGGCGGCGCTGGCGCCAG

GCCTTGACCTTCAGGCGCCAGCGGTCCAGCGTCAGGTAGACCACCGGCGT

GGTGTACAGCGTCAGCAGCTGGCTTACCACCAGTCCGCCGACAATGGAGA

TGCCCAGCGGCGCGCGCAGTTCGGCGCCGTCGCCGCGGCCGATTGCCAGC

GGCACCGCGCCCAGCAGCGCGGCCATGGTGGTCATCAGGATCGGGCGGAA

GCGCAGCAGGCAGGCGCGGTAGATCGCGTCGCGCGGCGACAGGCCATCGC

GCCGTTCGGCATCGATGGCGAAGTCGATCATCATGATCGCGTTCTTTTTC

ACGATGCCGATCAGCAGGATCACGCCGATCAGCGCGATGATGCTGAAGTC

GGTCTTCGATGCCAGCAGCGCCAGCAGCGCGCCCACGCCGGCGGAGGGCA

GCGTCGACAGGATCGTCAGCGGATGCACATAGCTTTCATACAGCACGCCC

AGCACGATGTAGATCGTGATCAGCGCCGCCAGGATCAGGATCGGCTGACT

CTTGAGCGAATCCTGGAACGCCTTGGCGCCGCCCTGGAAGTTGGCGCGCA

GCGTCTCCGGCACGCCGATGCGCGCCATCTCGCGCGTGATCGCGTCGGTC

GCCTGCGACAGCGAAGTGCCCTCGGCCAGGTTGAACGAGATCGTCGAGGC

CGCGAACTGGCCCTGGTGGTTCACGCCCAGCGGCGTGCTGGACGGGGTCA

CGCGCGCGAACGCCGCCAGCGGCACGCGGTTGCCGTTGCCGGTGACCACG

TAGATGTCCTTGAGCGCATCGGGCCCTTGCAGGTATTCCTGGCTCAGCTC

CATCACCACGCGGTACTGGTTCAGCGGATGGTAGATGGTGGACACCAGCC

GCTGGCCGAAGGCATCGTTGAGCACCGCATCCACCTGCTGCGCGGTCACG

CCCAGGCGCGAGGCCGCGTCGCGGTCGATGATCACCGAGGTCTGCAGGCC

CTTGTCGTTGGTATCGGTGTCGATATCCTCCAGCCCCTTCAGGTTCGACA

ACGCGGCGCGCACCTTGGGCTCCCACGCGCGCAGCACTTCCAGGTCGTCC

The third noted mutation may correspond to the sequence listed below ranging from

position 2563181-2563281 for Ralstonia eutropha H16 chromosome 1. The bolded, double

underlined text indicates a mutation (e.g., nt 101 of SEQ ID NO: 14).

(201 nt)

SEQ ID NO: 14

GCAGCTTGATGCCATTGACGAGGTAGATGGAAACCGGCACGTGCTC

TTTGCGCAGCGCGTTCAGGAACGGGCCTTGTAGCAGTTGCCCTTTGTTGC TCAT G

GCACACTCCAAATTTATAGGTTTAGTGGTGAATGATGGGGATGGA

AATCCCCGGTTCAAGTCAGGCGGCGCAAAAACGCGCCAGAAAAAAGATCA AAAAC

The fourth noted mutation may correspond to the sequence listed below ranging from

position 241880-242243 for Ralstonia eutropha H16 chromosome 1. The bolded, double

underlined text indicates a mutation (e.g., nt 364-379 of SEQ ID NO: 15).

(479 nt)

SEQ ID NO: 15

GAGGATGCCATGTCCGAAGCGCCTGTCCTTGCCCCCTCGACCTCAA

CCCAGCCGCCCGCCGCCGGCCAGCTCAACCTGATCCGCCCGCAGCCATAT

GCCGACTGGGCGCCGCAGGTCACGGCCGAAGAACGCGCCACGCTGCGCCG

CGAGCTGGAGCAGGGCGCCGTGCTGTACTTCCCGAACCTGAATTTCCGCT

TCCAGCCGGGCGAAGAGCGCTTCCTTGACAGCCGCTATTCCGACGGCAAG

TCCAAGAACATCAACCTGCGCGCCGACGACACCGCGGTGCGCGGCGCCCA

GGGCAGTCCGCAGGACCTGGCGGACCTGTACACGCTGATCCGCCGCTACG

CCGACAACAGCGAATTG CTGGTGCGCACGCTGT TCCCTGAATACATCCCG

CACATGACGCGCGCCGGCACCTCGCTGCGGCCCAGCGAGATCGCCGGGCG

CCCGGTCAGCTGGCGCAAGGACGACACCCGCCT

In the above sequences, it should be understood that a bacteria may include changes in one or more base pairs relative to the mutation sequences noted above that still produce the same functionality and/or amino acid within the bacteria. For example, a bacteria may include 95%, 96%, 97%, 98%, 99%, or any other appropriate percentage of the same mutation sequences listed above while still providing the noted enhanced ROS resistance.

As elaborated on in the examples, the systems described herein are capable of undergoing intermittent production. For example, when a driving potential is applied to the electrodes to generate hydrogen, the bacteria produce the desired product. Correspondingly, when the potential is removed and hydrogen is no longer generated, production of the product is ceased once the available hydrogen is consumed and a reduction in overall biomass is observed until the potential is once again applied to the electrodes to generate hydrogen. The system will then resume biomass and/or product formation. Thus, while a system may be run continuously to produce a desired product, in some modes of operation a driving potential may be intermittently applied to the electrodes to intermittently split water to form hydrogen and correspondingly intermittently produce a desired product. A frequency of the intermittently applied potential may be any frequency and may either be uniform or non-uniform as the disclosure is not so limited. This ability to intermittently produce a product may be desirable in applications such as when intermittent renewable energy sources are used to provide the power applied to the electrodes including, but not limited to, intermittent power sources such as solar and wind energy.

In some embodiments of any of the aspects, the systems or compositions described herein can be scaled up to meet bioproduction needs. As used herein, the term “scale up” refers to an increase in production capacity (e.g., of a system as described herein). In some embodiments of the aspects, a system (e.g., a bioreactor system) as described herein can be scaled up by at least 1-fold, at least 2-fold, at least 3-fold, at least 4-fold, at least 5-fold, at least 6-fold, at least 7-fold, at least 8-fold, at least 9-fold, at least 10-fold, at least 20-fold, at least 30-fold, at least 40-fold, at least 50-fold, at least 60-fold, at least 70-fold, at least 80-fold, at least 90-fold, or at least 100-fold. In some embodiments of the aspects, a bioreactor system as described herein can be scaled up to at least a 100 ml reactor, at least a 500 ml reactor, at least a 1000 mL reactor, at least a 2 L reactor, at least a 5 L reactor, at least a 10 L reactor, at least a 25 L reactor, at least a 50 L reactor, at least a 100 L reactor, at least a 500 L reactor, or at least a 1,000 L reactor.

In some embodiments, one or more of the genes described herein is expressed in a recombinant expression vector or plasmid. As used herein, the term “vector” refers to a polynucleotide sequence suitable for transferring transgenes into a host cell. The term “vector” includes plasmids, mini-chromosomes, phage, naked DNA and the like. See, for example, U.S. Pat. Nos. 4,980,285; 5,631,150; 5,707,828; 5,759,828; 5,888,783 and, 5,919,670, and, Sambrook et al, Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Press (1989). One type of vector is a “plasmid,” which refers to a circular double stranded DNA loop into which additional DNA segments are ligated. Another type of vector is a viral vector, wherein additional DNA segments are ligated into the viral genome. Certain vectors are capable of autonomous replication in a host cell into which they are introduced (e.g., bacterial vectors having a bacterial origin of replication and episomal mammalian vectors). Moreover, certain vectors are capable of directing the expression of genes to which they are operatively linked. Such vectors are referred to herein as “expression vectors”. In general, expression vectors of utility in recombinant DNA techniques are often in the form of plasmids. In the present specification, “plasmid” and “vector” is used interchangeably as the plasmid is the most commonly used form of vector. However, the invention is intended to include such other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, adenoviruses and adeno-associated viruses), which serve equivalent functions.

A cloning vector is one which is able to replicate autonomously or integrated in the genome in a host cell, and which is further characterized by one or more endonuclease restriction sites at which the vector may be cut in a determinable fashion and into which a desired DNA sequence can be ligated such that the new recombinant vector retains its ability to replicate in the host cell. In the case of plasmids, replication of the desired sequence can occur many times as the plasmid increases in copy number within the host cell such as a host bacterium or just a single time per host before the host reproduces by mitosis. In the case of phage, replication can occur actively during a lytic phase or passively during a lysogenic phase.

An expression vector is one into which a desired DNA sequence can be inserted by restriction and ligation such that it is operably joined to regulatory sequences and can be expressed as an RNA transcript. Vectors can further contain one or more marker sequences suitable for use in the identification of cells which have or have not been transformed or transformed or transfected with the vector. Markers include, for example, genes encoding proteins which increase or decrease either resistance or sensitivity to antibiotics or other compounds, genes which encode enzymes whose activities are detectable by standard assays known in the art (e.g., β-galactosidase, luciferase or alkaline phosphatase), and genes which visibly affect the phenotype of transformed or transfected cells, hosts, colonies or plaques (e.g., green fluorescent protein). In certain embodiments, the vectors used herein are capable of autonomous replication and expression of the structural gene products present in the DNA segments to which they are operably joined.

As used herein, a coding sequence and regulatory sequences are said to be “operably” joined when they are covalently linked in such a way as to place the expression or transcription of the coding sequence under the influence or control of the regulatory sequences. If it is desired that the coding sequences be translated into a functional protein, two DNA sequences are said to be operably joined if induction of a promoter in the 5′ regulatory sequences results in the transcription of the coding sequence and if the nature of the linkage between the two DNA sequences does not (1) result in the introduction of a frame-shift mutation, (2) interfere with the ability of the promoter region to direct the transcription of the coding sequences, or (3) interfere with the ability of the corresponding RNA transcript to be translated into a protein. Thus, a promoter region would be operably joined to a coding sequence if the promoter region were capable of effecting transcription of that DNA sequence such that the resulting transcript can be translated into the desired protein or polypeptide.

When the nucleic acid molecule that encodes any of the polypeptides described herein is expressed in a cell, a variety of transcription control sequences (e.g., promoter/enhancer sequences) can be used to direct its expression. The promoter can be a native promoter, i.e., the promoter of the gene in its endogenous context, which provides normal regulation of expression of the gene. In some embodiments the promoter can be constitutive, i.e., the promoter is unregulated allowing for continual transcription of its associated gene. A variety of conditional promoters also can be used, such as promoters controlled by the presence or absence of a molecule.

The precise nature of the regulatory sequences needed for gene expression can vary between species or cell types, but in general can include, as necessary, 5′ non-transcribed and 5′ non-translated sequences involved with the initiation of transcription and translation respectively, such as a TATA box, capping sequence, CAAT sequence, and the like. In particular, such 5′ non-transcribed regulatory sequences will include a promoter region which includes a promoter sequence for transcriptional control of the operably joined gene. Regulatory sequences can also include enhancer sequences or upstream activator sequences as desired. The vectors of the invention may optionally include 5′ leader or signal sequences. The choice and design of an appropriate vector is within the ability and discretion of one of ordinary skill in the art.

Expression vectors containing all the necessary elements for expression are commercially available and known to those skilled in the art. See, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual, Second Edition, Cold Spring Harbor Laboratory Press, 1989. Cells are genetically engineered by the introduction into the cells of heterologous DNA (RNA). That heterologous DNA (RNA) is placed under operable control of transcriptional elements to permit the expression of the heterologous DNA in the host cell.

In some embodiments, the vector is pBadT. In some embodiments of any of the aspects, pBadT is an expression vector for at least one functional, heterologous gene. In some embodiments, the vector is arabinose-responsive promoter (e.g., P_BADpromoter).

Without limitations, the genes described herein can be included in one vector or separate vectors. For example, the functional heterologous thioesterase gene (e.g., a Cuphea palustris FatB1 gene, a Cuphea palustris FatB2 gene, a Cuphea palustris FatB2-FatB1 hybrid gene, or a Marvinbryantia formatexigens TE gene); the functional heterologous DGAT gene (e.g., Acinetobacter baylyi DGAT gene, or a Thermomonospora curvata DGAT gene); and the functional heterologous PAP gene (e.g., Rhodococcus opacus PAP gene, or a Rhodococcus jostii PAP gene) can be included in the same vector.

In some embodiments, the functional heterologous thioesterase gene (e.g., a Cuphea palustris FatB1 gene, a Cuphea palustris FatB2 gene, a Cuphea palustris FatB2-FatB1 hybrid gene, or a Marvinbryantia formatexigens TE gene) can be included in a first vector; the functional heterologous DGAT gene (e.g., Acinetobacter baylyi DGAT gene, or a Thermomonospora curvata DGAT gene) can be included in a second vector; and the functional heterologous PAP gene (e.g., Rhodococcus opacus PAP gene, or a Rhodococcus jostii PAP gene) can be included in a third vector.

In some other embodiments, the vector is pT18mobsacB. In some embodiments of any of the aspects, pT18mobsacB is an integration vector that can be used to engineer at least one inactivating modification of at least one endogenous gene in a bacterium, such as an endogenous polyhydroxyalkanoate (PHA) synthase gene (e.g., phaC).

In some embodiments, one or more of the recombinantly expressed gene can be integrated into the genome of the cell.

A nucleic acid molecule that encodes the enzyme of the claimed invention can be introduced into a cell or cells using methods and techniques that are standard in the art. For example, nucleic acid molecules can be introduced by standard protocols such as conjugation or transformation including chemical transformation and electroporation, transduction, particle bombardment, etc. Expressing the nucleic acid molecule encoding the enzymes of the claimed invention also may be accomplished by integrating the nucleic acid molecule into the genome.

For convenience, the meaning of some terms and phrases used in the specification, examples, and appended claims, are provided below. Unless stated otherwise, or implicit from context, the following terms and phrases include the meanings provided below. The definitions are provided to aid in describing particular embodiments, and are not intended to limit the claimed invention, because the scope of the invention is limited only by the claims. Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. If there is an apparent discrepancy between the usage of a term in the art and its definition provided herein, the definition provided within the specification shall prevail.

For convenience, certain terms employed herein, in the specification, examples and appended claims are collected here.

In microbiology, “16S sequencing” or “16S rRNA” or “16S-rRNA” or “16S” refers to sequence derived by characterizing the nucleotides that comprise the 16S ribosomal RNA gene(s). The bacterial 16S rDNA is approximately 1500 nucleotides in length and is used in reconstructing the evolutionary relationships and sequence similarity of one bacterial isolate to a second isolate using phylogenetic approaches. 16S sequences are used for phylogenetic reconstruction as they are in general highly conserved, but contain specific hypervariable regions that harbor sufficient nucleotide diversity to differentiate genera and species of most bacteria, as well as fungi.

The “V1-V9 regions” of the 16S rRNA refers to the first through ninth hypervariable regions of the 16S rRNA gene that are used for genetic typing of bacterial samples. These regions in bacteria are defined by nucleotides 69-99, 137-242, 433-497, 576-682, 822-879, 986-1043, 1117-1173, 1243-1294 and 1435-1465 respectively using numbering based on the E. coli system of nomenclature. Brosius et al., Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia co/i, PNAS 75(10):4801-4805 (1978). In some embodiments, at least one of the V1, V2, V3, V4, V5, V6, V7, V8, and V9 regions are used to characterize an OTU. In one embodiment, the V1, V2, and V3 regions are used to characterize an OTU. In another embodiment, the V3, V4, and V5 regions are used to characterize an OTU. In another embodiment, the V4 region is used to characterize an OTU. A person of ordinary skill in the art can identify the specific hypervariable regions of a candidate 16S rRNA by comparing the candidate sequence in question to the reference sequence and identifying the hypervariable regions based on similarity to the reference hypervariable regions.

“Operational taxonomic unit (OTU, plural OTUs)” refers to a terminal leaf in a phylogenetic tree and is defined by a specific genetic sequence and all sequences that share a specified degree of sequence identity to this sequence at the level of species. A “type” or a plurality of “types” of bacteria includes an OTU or a plurality of different OTUs, and also encompasses a strain, species, genus, family or order of bacteria. The specific genetic sequence may be the 16S rRNA sequence or a portion of the 16S rRNA sequence, or it may be a functionally conserved housekeeping gene found broadly across the eubacterial kingdom. OTUs generally share at least 95%, 96%, 97%, 98%, or 99% sequence identity. OTUs are frequently defined by comparing sequences between organisms. Sequences with less than the specified sequence identity (e.g., less than 97%) are not considered to form part of the same OTU.

“Clade” refers to the set of OTUs or members of a phylogenetic tree downstream of a statistically valid node in a phylogenetic tree. The clade comprises a set of terminal leaves in the phylogenetic tree that is a distinct monophyletic evolutionary unit.

The terms “decrease”, “reduced”, “reduction”, or “inhibit” are all used herein to mean a decrease by a statistically significant amount. In some embodiments, “reduce,” “reduction” or “decrease” or “inhibit” typically means a decrease by at least 10% as compared to a reference level (e.g. the absence of a given treatment or agent) and can include, for example, a decrease by at least about 10%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 98%, at least about 99%, or more. As used herein, “reduction” or “inhibition” does not encompass a complete inhibition or reduction as compared to a reference level. “Complete inhibition” is a 100% inhibition as compared to a reference level. A decrease can be preferably down to a level accepted as within the range of normal for an individual without a given disorder.

The terms “increased”, “increase”, “enhance”, or “activate” are all used herein to mean an increase by a statically significant amount. In some embodiments, the terms “increased”, “increase”, “enhance”, or “activate” can mean an increase of at least 10% as compared to a reference level, for example an increase of at least about 20%, or at least about 30%, or at least about 40%, or at least about 50%, or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90% or up to and including a 100% increase or any increase between 10-100% as compared to a reference level, or at least about a 2-fold, or at least about a 3-fold, or at least about a 4-fold, or at least about a 5-fold or at least about a 10-fold increase, or any increase between 2-fold and 10-fold or greater as compared to a reference level. In the context of a marker or symptom, a “increase” is a statistically significant increase in such level.

As used herein, a “subject” means a human or animal. Usually the animal is a vertebrate such as a primate, rodent, domestic animal or game animal. Primates include chimpanzees, cynomolgus monkeys, spider monkeys, and macaques, e.g., Rhesus. Rodents include mice, rats, woodchucks, ferrets, rabbits and hamsters. Domestic and game animals include cows, horses, pigs, deer, bison, buffalo, feline species, e.g., domestic cat, canine species, e.g., dog, fox, wolf, avian species, e.g., chicken, emu, ostrich, and fish, e.g., trout, catfish and salmon. In some embodiments, the subject is a mammal, e.g., a primate, e.g., a human. The terms, “individual,” “patient” and “subject” are used interchangeably herein. Preferably, the subject is a mammal. The mammal can be a human, non-human primate, mouse, rat, dog, cat, horse, or cow, but is not limited to these examples. A subject can be male or female. In some embodiments, the subject is a plant. In some embodiments, the subject is a bacterium.

As used herein, the terms “protein” and “polypeptide” are used interchangeably herein to designate a series of amino acid residues, connected to each other by peptide bonds between the alpha-amino and carboxy groups of adjacent residues. The terms “protein”, and “polypeptide” refer to a polymer of amino acids, including modified amino acids (e.g., phosphorylated, glycated, glycosylated, etc.) and amino acid analogs, regardless of its size or function. “Protein” and “polypeptide” are often used in reference to relatively large polypeptides, whereas the term “peptide” is often used in reference to small polypeptides, but usage of these terms in the art overlaps. The terms “protein” and “polypeptide” are used interchangeably herein when referring to a gene product and fragments thereof. Thus, exemplary polypeptides or proteins include gene products, naturally occurring proteins, homologs, orthologs, paralogs, fragments and other equivalents, variants, fragments, and analogs of the foregoing.

In the various embodiments described herein, it is further contemplated that variants (naturally occurring or otherwise), alleles, homologs, conservatively modified variants, and/or conservative substitution variants of any of the particular polypeptides described are encompassed. As to amino acid sequences, one of skill will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters a single amino acid or a small percentage of amino acids in the encoded sequence is a “conservatively modified variant” where the alteration results in the substitution of an amino acid with a chemically similar amino acid and retains the desired activity of the polypeptide. Such conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homologs, and alleles consistent with the disclosure.

A given amino acid can be replaced by a residue having similar physiochemical characteristics, e.g., substituting one aliphatic residue for another (such as Ile, Val, Leu, or Ala for one another), or substitution of one polar residue for another (such as between Lys and Arg; Glu and Asp; or Gln and Asn). Other such conservative substitutions, e.g., substitutions of entire regions having similar hydrophobicity characteristics, are well known. Polypeptides comprising conservative amino acid substitutions can be tested in any one of the assays described herein to confirm that a desired activity, e.g. activity and specificity of a native or reference polypeptide is retained.

Amino acids can be grouped according to similarities in the properties of their side chains (in A. L. Lehninger, in Biochemistry, second ed., pp. 73-75, Worth Publishers, New York (1975)): (1) non-polar: Ala (A), Val (V), Leu (L), Ile (I), Pro (P), Phe (F), Trp (W), Met (M); (2) uncharged polar: Gly (G), Ser (S), Thr (T), Cys (C), Tyr (Y), Asn (N), Gln (Q); (3) acidic: Asp (D), Glu (E); (4) basic: Lys (K), Arg (R), His (H). Alternatively, naturally occurring residues can be divided into groups based on common side-chain properties: (1) hydrophobic: Norleucine, Met, Ala, Val, Leu, Ile; (2) neutral hydrophilic: Cys, Ser, Thr, Asn, Gln; (3) acidic: Asp, Glu; (4) basic: His, Lys, Arg; (5) residues that influence chain orientation: Gly, Pro; (6) aromatic: Trp, Tyr, Phe. Non-conservative substitutions will entail exchanging a member of one of these classes for another class. Particular conservative substitutions include, for example; Ala into Gly or into Ser; Arg into Lys; Asn into Gln or into His; Asp into Glu; Cys into Ser; Gln into Asn; Glu into Asp; Gly into Ala or into Pro; His into Asn or into Gln; Ile into Leu or into Val; Leu into Ile or into Val; Lys into Arg, into Gln or into Glu; Met into Leu, into Tyr or into Ile; Phe into Met, into Leu or into Tyr; Ser into Thr; Thr into Ser; Trp into Tyr; Tyr into Trp; and/or Phe into Val, into Ile or into Leu.

In some embodiments, the polypeptide described herein (or a nucleic acid encoding such a polypeptide) can be a functional fragment of one of the amino acid sequences described herein. As used herein, a “functional fragment” is a fragment or segment of a peptide which retains at least 50% of the wild-type reference polypeptide's activity according to the assays described below herein. A functional fragment can comprise conservative substitutions of the sequences disclosed herein. In some embodiments of any of the aspects, a polypeptide as described herein is truncated to remove an organelle targeting sequence(s); in some embodiments, such a targeting sequence can contribute to poor expression of the polypeptide, e.g., in the engineered bacteria described herein.

In some embodiments, the polypeptide described herein can be a variant of a sequence described herein. In some embodiments, the variant is a conservatively modified variant. Conservative substitution variants can be obtained by mutations of native nucleotide sequences, for example. A “variant,” as referred to herein, is a polypeptide substantially homologous to a native or reference polypeptide, but which has an amino acid sequence different from that of the native or reference polypeptide because of one or a plurality of deletions, insertions or substitutions. Variant polypeptide-encoding DNA sequences encompass sequences that comprise one or more additions, deletions, or substitutions of nucleotides when compared to a native or reference DNA sequence, but that encode a variant protein or fragment thereof that retains activity. A wide variety of PCR-based site-specific mutagenesis approaches are known in the art and can be applied by the ordinarily skilled artisan.

A variant amino acid or DNA sequence can beat least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or more, identical to a native or reference sequence. The degree of homology (percent identity) between a native and a mutant sequence can be determined, for example, by comparing the two sequences using freely available computer programs commonly employed for this purpose on the world wide web (e.g. BLASTp or BLASTn with default settings).

Alterations of the native amino acid sequence can be accomplished by any of a number of techniques known to one of skill in the art. Mutations can be introduced, for example, at particular loci by synthesizing oligonucleotides containing a mutant sequence, flanked by restriction sites enabling ligation to fragments of the native sequence. Following ligation, the resulting reconstructed sequence encodes an analog having the desired amino acid insertion, substitution, or deletion. Alternatively, oligonucleotide-directed site-specific mutagenesis procedures can be employed to provide an altered nucleotide sequence having particular codons altered according to the substitution, deletion, or insertion required. Techniques for making such alterations are very well established and include, for example, those disclosed by Walder et al. (Gene 42:133, 1986); Bauer et al. (Gene 37:73, 1985); Craik (BioTechniques, January 1985, 12-19); Smith et al. (Genetic Engineering: Principles and Methods, Plenum Press, 1981); and U.S. Pat. Nos. 4,518,584 and 4,737,462, which are herein incorporated by reference in their entireties. Any cysteine residue not involved in maintaining the proper conformation of the polypeptide also can be substituted, generally with serine, to improve the oxidative stability of the molecule and prevent aberrant crosslinking. Conversely, cysteine bond(s) can be added to the polypeptide to improve its stability or facilitate oligomerization.

As used herein, the term “nucleic acid” or “nucleic acid sequence” refers to any molecule, preferably a polymeric molecule, incorporating units of ribonucleic acid, deoxyribonucleic acid or an analog thereof. The nucleic acid can be either single-stranded or double-stranded. A single-stranded nucleic acid can be one nucleic acid strand of a denatured double-stranded DNA. Alternatively, it can be a single-stranded nucleic acid not derived from any double-stranded DNA. In one aspect, the nucleic acid can be DNA. In another aspect, the nucleic acid can be RNA. Suitable DNA can include, e.g., genomic DNA or cDNA. Suitable RNA can include, e.g., mRNA.

The term “expression” refers to the cellular processes involved in producing RNA and proteins and as appropriate, secreting proteins, including where applicable, but not limited to, for example, transcription, transcript processing, translation and protein folding, modification and processing. Expression can refer to the transcription and stable accumulation of sense (mRNA) or antisense RNA derived from a nucleic acid fragment or fragments of the invention and/or to the translation of mRNA into a polypeptide.

In some embodiments, the expression of a biomarker(s), target(s), or gene/polypeptide described herein is/are tissue-specific. In some embodiments, the expression of a biomarker(s), target(s), or gene/polypeptide described herein is/are global. In some embodiments, the expression of a biomarker(s), target(s), or gene/polypeptide described herein is systemic.

“Expression products” include RNA transcribed from a gene, and polypeptides obtained by translation of mRNA transcribed from a gene. The term “gene” means the nucleic acid sequence which is transcribed (DNA) to RNA in vitro or in vivo when operably linked to appropriate regulatory sequences. The gene may or may not include regions preceding and following the coding region, e.g. 5′ untranslated (5′UTR) or “leader” sequences and 3′ UTR or “trailer” sequences, as well as intervening sequences (introns) between individual coding segments (exons).

In some embodiments, the methods described herein relate to measuring, detecting, or determining the level of at least one marker. As used herein, the term “detecting” or “measuring” refers to observing a signal from, e.g. a probe, label, or target molecule to indicate the presence of an analyte in a sample. Any method known in the art for detecting a particular label moiety can be used for detection. Exemplary detection methods include, but are not limited to, spectroscopic, fluorescent, photochemical, biochemical, immunochemical, electrical, optical or chemical methods. In some embodiments of any of the aspects, measuring can be a quantitative observation.

In some embodiments of any of the aspects, a polypeptide, nucleic acid, or cell as described herein can be engineered. As used herein, “engineered” refers to the aspect of having been manipulated by the hand of man. For example, a polypeptide is considered to be “engineered” when at least one aspect of the polypeptide, e.g., its sequence, has been manipulated by the hand of man to differ from the aspect as it exists in nature. As is common practice and is understood by those in the art, progeny of an engineered cell are typically still referred to as “engineered” even though the actual manipulation was performed on a prior entity.

In some embodiments, a nucleic acid encoding a polypeptide as described herein (e.g. a TE polypeptide, a DGAT polypeptide, a LPAT polypeptide, a GPAT polypeptide, a PAP polypeptide) is comprised by a vector. In some of the aspects described herein, a nucleic acid sequence encoding a given polypeptide as described herein, or any module thereof, is operably linked to a vector. The term “vector”, as used herein, refers to a nucleic acid construct designed for delivery to a host cell or for transfer between different host cells. As used herein, a vector can be viral or non-viral. The term “vector” encompasses any genetic element that is capable of replication when associated with the proper control elements and that can transfer gene sequences to cells. A vector can include, but is not limited to, a cloning vector, an expression vector, a plasmid, phage, transposon, cosmid, chromosome, virus, virion, etc.

In some embodiments of any of the aspects, the vector is recombinant, e.g., it comprises sequences originating from at least two different sources. In some embodiments of any of the aspects, the vector comprises sequences originating from at least two different species. In some embodiments of any of the aspects, the vector comprises sequences originating from at least two different genes, e.g., it comprises a fusion protein or a nucleic acid encoding an expression product which is operably linked to at least one non-native (e.g., heterologous) genetic control element (e.g., a promoter, suppressor, activator, enhancer, response element, or the like).

In some embodiments of any of the aspects, the vector or nucleic acid described herein is codon-optimized, e.g., the native or wild-type sequence of the nucleic acid sequence has been altered or engineered to include alternative codons such that altered or engineered nucleic acid encodes the same polypeptide expression product as the native/wild-type sequence, but will be transcribed and/or translated at an improved efficiency in a desired expression system. In some embodiments of any of the aspects, the expression system is an organism other than the source of the native/wild-type sequence (or a cell obtained from such organism). In some embodiments of any of the aspects, the vector and/or nucleic acid sequence described herein is codon-optimized for expression in a mammal or mammalian cell, e.g., a mouse, a murine cell, or a human cell. In some embodiments of any of the aspects, the vector and/or nucleic acid sequence described herein is codon-optimized for expression in a human cell. In some embodiments of any of the aspects, the vector and/or nucleic acid sequence described herein is codon-optimized for expression in a yeast or yeast cell. In some embodiments of any of the aspects, the vector and/or nucleic acid sequence described herein is codon-optimized for expression in a bacterial cell. In some embodiments of any of the aspects, the vector and/or nucleic acid sequence described herein is codon-optimized for expression in an E. coli cell.

As used herein, the term “expression vector” refers to a vector that directs expression of an RNA or polypeptide from sequences linked to transcriptional regulatory sequences on the vector. The sequences expressed will often, but not necessarily, be heterologous to the cell. An expression vector may comprise additional elements, for example, the expression vector may have two replication systems, thus allowing it to be maintained in two organisms, for example in human cells for expression and in a prokaryotic host for cloning and amplification.

As used herein, the term “viral vector” refers to a nucleic acid vector construct that includes at least one element of viral origin and has the capacity to be packaged into a viral vector particle. The viral vector can contain the nucleic acid encoding a polypeptide as described herein in place of non-essential viral genes. The vector and/or particle may be utilized for the purpose of transferring any nucleic acids into cells either in vitro or in vivo. Numerous forms of viral vectors are known in the art.

It should be understood that the vectors described herein can, in some embodiments, be combined with other suitable compositions and therapies. In some embodiments, the vector is episomal. The use of a suitable episomal vector provides a means of maintaining the nucleotide of interest in the subject in high copy number extra chromosomal DNA thereby eliminating potential effects of chromosomal integration.

As used herein, the term “administering,” refers to the placement of a compound as disclosed herein into a subject by a method or route which results in at least partial delivery of the agent at a desired site. Pharmaceutical compositions comprising the compounds disclosed herein can be administered by any appropriate route which results in an effective treatment in the subject. In some embodiments, administration comprises physical human activity, e.g., an injection, act of ingestion, an act of application, and/or manipulation of a delivery device or machine. Such activity can be performed, e.g., by a medical professional and/or the subject being treated.

As used herein, “contacting” refers to any suitable means for delivering, or exposing, an agent to at least one cell. Exemplary delivery methods include, but are not limited to, direct delivery to cell culture medium, perfusion, injection, or other delivery method well known to one skilled in the art. In some embodiments, contacting comprises physical human activity, e.g., an injection; an act of dispensing, mixing, and/or decanting; and/or manipulation of a delivery device or machine.

The term “statistically significant” or “significantly” refers to statistical significance and generally means a two standard deviation (2SD) or greater difference.

Other than in the operating examples, or where otherwise indicated, all numbers expressing quantities of ingredients or reaction conditions used herein should be understood as modified in all instances by the term “about.” The term “about” when used in connection with percentages can mean ±1%.

As used herein, the term “comprising” means that other elements can also be present in addition to the defined elements presented. The use of “comprising” indicates inclusion rather than limitation.

The term “consisting of” refers to compositions, methods, and respective components thereof as described herein, which are exclusive of any element not recited in that description of the embodiment.

As used herein the term “consisting essentially of” refers to those elements required for a given embodiment. The term permits the presence of additional elements that do not materially affect the basic and novel or functional characteristic(s) of that embodiment of the invention.

As used herein, the term “corresponding to” refers to an amino acid or nucleotide at the enumerated position in a first polypeptide or nucleic acid, or an amino acid or nucleotide that is equivalent to an enumerated amino acid or nucleotide in a second polypeptide or nucleic acid. Equivalent enumerated amino acids or nucleotides can be determined by alignment of candidate sequences using degree of homology programs known in the art, e.g., BLAST.

The singular terms “a,” “an,” and “the” include plural referents unless context clearly indicates otherwise. Similarly, the word “or” is intended to include “and” unless the context clearly indicates otherwise. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of this disclosure, suitable methods and materials are described below. The abbreviation, “e.g.” is derived from the Latin exempli gratia, and is used herein to indicate a non-limiting example. Thus, the abbreviation “e.g.” is synonymous with the term “for example.”

Groupings of alternative elements or embodiments of the invention disclosed herein are not to be construed as limitations. Each group member can be referred to and claimed individually or in any combination with other members of the group or other elements found herein. One or more members of a group can be included in, or deleted from, a group for reasons of convenience and/or patentability. When any such inclusion or deletion occurs, the specification is herein deemed to contain the group as modified thus fulfilling the written description of all Markush groups used in the appended claims.

Unless otherwise defined herein, scientific and technical terms used in connection with the present application shall have the meanings that are commonly understood by those of ordinary skill in the art to which this disclosure belongs. It should be understood that this invention is not limited to the particular methodology, protocols, and reagents, etc., described herein and as such can vary. The terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention, which is defined solely by the claims. Definitions of common terms in immunology and molecular biology can be found in The Merck Manual of Diagnosis and Therapy, 20th Edition, published by Merck Sharp & Dohme Corp., 2018 (ISBN 0911910190, 978-0911910421); Robert S. Porter et al. (eds.), The Encyclopedia of Molecular Cell Biology and Molecular Medicine, published by Blackwell Science Ltd., 1999-2012 (ISBN 9783527600908); and Robert A. Meyers (ed.), Molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by VCH Publishers, Inc., 1995 (ISBN 1-56081-569-8); Immunology by Werner Luttmann, published by Elsevier, 2006; Janeway's Immunobiology, Kenneth Murphy, Allan Mowat, Casey Weaver (eds.), W. W. Norton & Company, 2016 (ISBN 0815345054, 978-0815345053); Lewin's Genes XI, published by Jones & Bartlett Publishers, 2014 (ISBN-1449659055); Michael Richard Green and Joseph Sambrook, Molecular Cloning: A Laboratory Manual, 4th ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., USA (2012) (ISBN 1936113414); Davis et al., Basic Methods in Molecular Biology, Elsevier Science Publishing, Inc., New York, USA (2012) (ISBN 044460149X); Laboratory Methods in Enzymology: DNA, Jon Lorsch (ed.) Elsevier, 2013 (ISBN 0124199542); Current Protocols in Molecular Biology (CPMB), Frederick M. Ausubel (ed.), John Wiley and Sons, 2014 (ISBN 047150338X, 9780471503385), Current Protocols in Protein Science (CPPS), John E. Coligan (ed.), John Wiley and Sons, Inc., 2005; and Current Protocols in Immunology (CPI) (John E. Coligan, ADA M Kruisbeek, David H Margulies, Ethan M Shevach, Warren Strobe, (eds.) John Wiley and Sons, Inc., 2003 (ISBN 0471142735, 9780471142737), the contents of which are all incorporated by reference herein in their entireties.

Other terms are defined herein within the description of the various aspects of the invention.

All patents and other publications; including literature references, issued patents, published patent applications, and co-pending patent applications; cited throughout this application are expressly incorporated herein by reference for the purpose of describing and disclosing, for example, the methodologies described in such publications that might be used in connection with the technology described herein. These publications are provided solely for their disclosure prior to the filing date of the present application. Nothing in this regard should be construed as an admission that the inventors are not entitled to antedate such disclosure by virtue of prior invention or for any other reason. All statements as to the date or representation as to the contents of these documents is based on the information available to the applicants and does not constitute any admission as to the correctness of the dates or contents of these documents.

The description of embodiments of the disclosure is not intended to be exhaustive or to limit the disclosure to the precise form disclosed. While specific embodiments of, and examples for, the disclosure are described herein for illustrative purposes, various equivalent modifications are possible within the scope of the disclosure, as those skilled in the relevant art will recognize. For example, while method steps or functions are presented in a given order, alternative embodiments may perform functions in a different order, or functions may be performed substantially concurrently. The teachings of the disclosure provided herein can be applied to other procedures or methods as appropriate. The various embodiments described herein can be combined to provide further embodiments. Aspects of the disclosure can be modified, if necessary, to employ the compositions, functions and concepts of the above references and application to provide yet further embodiments of the disclosure. Moreover, due to biological functional equivalency considerations, some changes can be made in protein structure without affecting the biological or chemical action in kind or amount. These and other changes can be made to the disclosure in light of the detailed description. All such modifications are intended to be included within the scope of the appended claims.

Specific elements of any of the foregoing embodiments can be combined or substituted for elements in other embodiments. Furthermore, while advantages associated with certain embodiments of the disclosure have been described in the context of these embodiments, other embodiments may also exhibit such advantages, and not all embodiments need necessarily exhibit such advantages to fall within the scope of the disclosure.

Some embodiments of the technology described herein can be defined according to any of the following numbered paragraphs:

1. An engineered Cupriavidus necator bacterium, comprising:

- a) at least one exogenous copy of at least one functional acyltransferase gene; and/or
- b) at least one exogenous copy of at least one functional phosphatidic acid (PA) phosphatase gene.

2. An engineered Cupriavidus necator bacterium, comprising:

- a) at least one exogenous copy of at least one functional acyltransferase gene encoding an acyltransferase enzyme that catalyzes transesterification of the sn3 OH group of a diacylglycerol with a fatty acid; and/or
- b) at least one exogenous copy of at least one functional phosphatidic acid (PA) phosphatase gene.

3. The engineered bacterium of paragraph 1, wherein the acyltransferase gene encodes for an acyltransferase enzyme that catalyzes transesterification of the sn3 OH group, the sn2 OH group, or the sn1 OH group of a triacylglycerol (TAG) precursor with a fatty acid

4. The engineered bacterium of paragraph 1, wherein the acyltransferase gene encodes an acyltransferase enzyme that catalyzes transesterification of the sn3 OH group of a diacylglycerol with a fatty acid.

5. The engineered bacterium of any one of paragraphs 1-4, wherein the acyltransferase gene is a functional diglyceride acyltransferase (DGAT) gene, a functional wax synthase (WS) gene, or a hybrid thereof.

6. The engineered bacterium of paragraph 5, wherein the functional DGAT gene is heterologous.

7. The engineered bacterium of paragraph 6, wherein the functional heterologous DGAT gene comprises a Acinetobacter baylyi DGAT gene, a Thermomonospora curvata DGAT gene, a Theobroma cacao DGAT gene, or a Rhodococcus opacus DGAT gene.

8. The engineered bacterium of paragraph 1, wherein the acyltransferase gene encodes an acyltransferase enzyme that catalyzes transesterification of the sn2 OH group of a lysophosphatidic acid with a fatty acid.

9. The engineered bacterium of paragraph 8, wherein the acyltransferase gene is a functional lysophosphatidic acid acyltransferase (LPAT) gene.

10. The engineered bacterium of paragraph 9, wherein the functional LPAT gene is heterologous.

11. The engineered bacterium of paragraph 10, wherein the functional heterologous LPAT gene comprises a Theobroma cacao LPAT gene.

12. The engineered bacterium of paragraph 1, wherein the acyltransferase gene encodes an acyltransferase enzyme that catalyzes transesterification of the sn1 OH group of a glyceraldehyde-3-phosphate with a fatty acid.

13. The engineered bacterium of paragraph 12, wherein the acyltransferase gene is a functional glycerol-3-phosphate acyltransferase (GPAT) gene.

14. The engineered bacterium of paragraph 13, wherein the functional GPAT gene is heterologous.

15. The engineered bacterium of paragraph 14, wherein the functional heterologous GPAT gene comprises a Durio zibethinus GPAT gene, Gossypium arboreum GPAT gene, Hibiscus syriacus GPAT gene, or a Theobroma cacao GPAT gene.

16. The engineered bacterium of any one of paragraphs 2-4, 8, or 12, wherein the fatty acid is esterified with acyl carrier protein (ACP) or with acetyl-CoA.

17. The engineered bacterium of paragraph 1, wherein the functional phosphatidic acid (PA) phosphatase gene encodes a phosphatidic acid (PA) phosphatase enzyme that catalyzes dephosphorylation at the sn3 position of phosphatidic acid (PA).

18. The engineered bacterium of paragraph 17, wherein the phosphatidic acid (PA) phosphatase gene is a functional phosphatidate phosphatase (PAP) gene.

19. The engineered bacterium of paragraph 18, wherein the functional PAP gene is heterologous.

20. The engineered bacterium of paragraph 19, wherein the functional heterologous PAP gene comprises a Rhodococcus opacus PAP gene, or a Rhodococcus jostii PAP gene.

21. The engineered bacterium of paragraph 1 or 2, further comprising: at least one exogenous copy of at least one functional thioesterase (TE) gene.

22. The engineered bacterium of paragraph 21, wherein the functional thioesterase gene is heterologous.

23. The engineered bacterium of paragraph 22, wherein the functional heterologous thioesterase gene is selected from the group consisting of: a Marvinbryantia formatexigens TE gene, a Cuphea palustris FatB1 gene, a Cuphea palustris FatB2 gene, a Cuphea palustris FatB2-FatB1 hybrid gene, a Arachis hypogaea FatB2-1 gene, a Mangifera indica FatA gene, a Morella rubra FatA gene, a Pistacia vera FatA gene, a Theobroma cacao FatA gene, a Theobroma cacao FatB gene (e.g., FatB1, FatB2, FatB3, BatB4, FatB5, or FatB6), or a Limosilactobacillus reuteri TE gene.

24. The engineered bacterium of paragraph 1 or 2, further comprising: (i) at least one endogenous polyhydroxyalkanoate (PHA) synthase gene comprising at least one engineered inactivating modification; or (ii) at least one exogenous inhibitor of an endogenous polyhydroxyalkanoate (PHA) synthase gene or gene product.

25. The engineered bacterium of paragraph 24, wherein the engineered inactivating modification of the endogenous PHA synthase comprises one or more of i) deletion of the entire coding sequence, ii) deletion of the promoter of the gene, iii) a frameshift mutation, iv) a nonsense mutation (i.e., a premature termination codon), v) a point mutation, vi) a deletion, vii) or an insertion.

26. The engineered bacterium of paragraph 24 or 25, wherein the endogenous PHA synthase comprises phaC.

27. The engineered bacterium of paragraph 1 or 2, further comprising: (i) at least one endogenous diacylglycerol kinase gene comprising at least one engineered inactivating modification; or (ii) at least one exogenous inhibitor of an endogenous diacylglycerol kinase gene or gene product.

28. The engineered bacterium of paragraph 27, wherein the engineered inactivating modification of the endogenous diacylglycerol kinase comprises one or more of i) deletion of the entire coding sequence, ii) deletion of the promoter of the gene, iii) a frameshift mutation, iv) a nonsense mutation (i.e., a premature termination codon), v) a point mutation, vi) a deletion, vii) or an insertion.

29. The engineered bacterium of paragraph 27 or 28, wherein the endogenous diacylglycerol kinase comprises dgkA.

30. The engineered bacterium of paragraph 1 or 2, further comprising: (i) at least one endogenous beta-oxidation gene comprising at least one engineered inactivating modification; or (ii) at least one exogenous inhibitor of an endogenous beta-oxidation gene or gene product.

31. The engineered bacterium of paragraph 30, wherein the engineered inactivating modification of the endogenous beta-oxidation gene comprises one or more of i) deletion of the entire coding sequence, ii) deletion of the promoter of the gene, iii) a frameshift mutation, iv) a nonsense mutation (i.e., a premature termination codon), v) a point mutation, vi) a deletion, vii) or an insertion.

32. The engineered bacterium of paragraph 30 or 31, wherein the endogenous beta-oxidation gene comprises FadE or FadB.

33. The engineered bacterium of any one of paragraphs 1-32, wherein said engineered bacteria is a chemoautotroph.

34. The engineered bacterium of any one of paragraphs 1-33, wherein said engineered bacteria uses CO₂as its sole carbon source, and/or said engineered bacteria uses H₂as its sole energy source.

35. The engineered bacterium of any one of paragraphs 1-34, wherein said engineered bacteria uses fructose as its sole carbon source.

36. The engineered bacterium of any one of paragraphs 1-35, wherein said engineered bacteria uses glycerol as its sole carbon source.

37. The engineered bacterium of any one of paragraphs 1-36, wherein said engineered bacteria produces triacylglycerides.

38. The engineered bacterium of any one of paragraphs 1-37, wherein said engineered bacteria produces animal triacylglycerides.

39. The engineered bacterium of any one of paragraphs 1-38, wherein said engineered bacteria produces milk fats.

40. A method of producing triacylglycerides (TAGs), comprising:

- a) culturing the engineered bacterium of any of paragraphs 1-39 in a culture medium comprising CO₂and/or H₂; and
- b) isolating, collecting, or concentrating TAGs from said engineered bacterium or from the culture medium of said engineered bacterium.

41. The method of paragraph 40, wherein the culture medium comprises CO₂as the sole carbon source, and/or the culture medium comprises H₂as the sole energy source.

42. The method of any one of paragraphs 40-41, wherein the total TAG isolated comprises at least 50% TAGs comprising C4-C18 R-group fatty acids.

43. The method of any one of paragraphs 40-42, wherein the total TAG isolated comprises at least 50% TAGs comprising C4-C8 R-group fatty acids.

44. The method of any one of paragraphs 40-43, wherein the total TAG isolated comprises at least 50% TAGs comprising C16 R-group fatty acids.

45. A method of producing triacylglycerides (TAGs), comprising:

- a) culturing the engineered bacterium of any of paragraphs 1-39 in a culture medium comprising fructose and/or H₂; and
- b) isolating, collecting, or concentrating TAGs from said engineered bacterium or from the culture medium of said engineered bacterium.

46. The method of paragraph 45, wherein the culture medium comprises fructose as the sole carbon source, and/or the culture medium comprises H₂as the sole energy source.

47. The method of any one of paragraphs 45-46, wherein the total TAG isolated comprises at least 50% TAGs comprising C4-C18 R-group fatty acids.

48. The method of any one of paragraphs 45-47, wherein the total TAG isolated comprises at least 50% TAGs comprising C4-C8 R-group fatty acids.

49. The method of any one of paragraphs 45-48, wherein the total TAG isolated comprises at least 50% TAGs comprising C16 R-group fatty acids.

50. A method of producing triacylglycerides (TAGs), comprising:

- a) culturing the engineered bacterium of any of paragraphs 1-39 in a culture medium comprising glycerol and/or H₂; and
- b) isolating, collecting, or concentrating TAGs from said engineered bacterium or from the culture medium of said engineered bacterium.

51. The method of paragraph 50, wherein the culture medium comprises glycerol as the sole carbon source, and/or the culture medium comprises H₂as the sole energy source.

52. The method of any one of paragraphs 50-51, wherein the total TAG isolated comprises at least 50% TAGs comprising C4-C18 R-group fatty acids.

53. The method of any one of paragraphs 50-52, wherein the total TAG isolated comprises at least 50% TAGs comprising C4-C8 R-group fatty acids.

54. The method of any one of paragraphs 50-53, wherein the total TAG isolated comprises at least 50% TAGs comprising C16 R-group fatty acids.

55. A system comprising:

- a) a reactor chamber with a solution contained therein, wherein the solution comprises hydrogen (H₂) and a carbon source; and
- b) the engineered bacterium of any of paragraphs 1-39 in the solution.

56. The system of paragraph 55, further comprising a pair of electrodes in contact with the solution that split water to form the hydrogen.

57. The system of any one of paragraphs 55-56, wherein the carbon source is carbon dioxide (CO₂), fructose, and/or glycerol.

58. The system of any one of paragraphs 55-57, further comprising an isolated gas volume above a surface of the solution within a head space of a reactor chamber.

59. The system of any one of paragraphs 55-58, wherein the isolated gas volume comprises primarily carbon dioxide.

60. The system of any one of paragraphs 55-59, further comprising a power source comprising a renewable source of energy.

61. The system of any one of paragraphs 55-60, wherein the renewable source of energy comprises a solar cell, wind turbine, generator, battery, or grid power.

Some embodiments of the technology described herein can be defined according to any of the following numbered paragraphs:

101. An engineered Cupriavidus necator bacterium, comprising:

- a) at least one exogenous copy of at least one functional thioesterase (TE) gene;
- b) at least one exogenous copy of at least one functional diglyceride acyltransferase (DGAT) gene; and/or
- c) at least one exogenous copy of at least one phosphatidate phosphatases (PAP) gene.

102. The engineered bacterium of paragraph 101, further comprising: (i) at least one endogenous polyhydroxyalkanoate (PHA) synthase gene comprising at least one engineered inactivating modification; or (ii) at least one exogenous inhibitor of an endogenous polyhydroxyalkanoate (PHA) synthase gene or gene product.

103. The engineered bacterium of any one of paragraphs 101-102, wherein said engineered bacteria is a chemoautotroph.

104. The engineered bacterium of any one of paragraphs 101-103, wherein said engineered bacteria uses CO₂as its sole carbon source, and/or said engineered bacteria uses H₂as its sole energy source.

105. The engineered bacterium of any one of paragraphs 101-104, wherein said engineered bacteria uses fructose as its sole carbon source.

106. The engineered bacterium of any one of paragraphs 101-105, wherein said engineered bacteria uses glycerol as its sole carbon source.

107. The engineered bacterium of any one of paragraphs 101-106, wherein the functional thioesterase gene is heterologous.

108. The engineered bacterium of paragraph 107, wherein the functional heterologous thioesterase gene comprises a Marvinbryantia formatexigens TE gene, a Cuphea palustris FatB1 gene, a Cuphea palustris FatB2 gene, or a Cuphea palustris FatB2-FatB1 hybrid gene.

109. The engineered bacterium of any one of paragraphs 101-108, wherein the functional DGAT gene is heterologous.

110. The engineered bacterium of paragraph 109, wherein the functional heterologous DGAT gene comprises a Acinetobacter baylyi DGAT gene, or a Thermomonospora curvata DGAT gene.

111. The engineered bacterium of any one of paragraphs 101-110, wherein the functional PAP gene is heterologous.

112. The engineered bacterium of paragraph 111, wherein the functional heterologous PAP gene comprises a Rhodococcus opacus PAP gene, or a Rhodococcus jostii PAP gene.

113. The engineered bacterium of any one of paragraphs 102-112, wherein the engineered inactivating modification of the endogenous PHA synthase comprises one or more of i) deletion of the entire coding sequence, ii) deletion of the promoter of the gene, iii) a frameshift mutation, iv) a nonsense mutation (i.e., a premature termination codon), v) a point mutation, vi) a deletion, vii) or an insertion.

114. The engineered bacterium of any one of paragraphs 102-113, wherein the endogenous PHA synthase comprises phaC.

115. The engineered bacterium of any one of paragraphs 101-114, wherein said engineered bacteria produces triacylglycerides.

116. The engineered bacterium of any one of paragraphs 101-115, wherein said engineered bacteria produces animal triacylglycerides.

117. The engineered bacterium of any one of paragraphs 101-116, wherein said engineered bacteria produces milk fats.

118. A method of producing triacylglycerides (TAGs), comprising:

- a) culturing the engineered bacterium of any of paragraphs 101-117 in a culture medium comprising CO₂and/or H₂; and
- b) isolating, collecting, or concentrating TAGs from said engineered bacterium or from the culture medium of said engineered bacterium.

119. The method of paragraph 18, wherein the culture medium comprises CO₂as the sole carbon source, and/or the culture medium comprises H₂as the sole energy source.

120. The method of any one of paragraphs 118-119, wherein the total TAG isolated comprises at least 50% TAGs comprising C4-C18 R-group fatty acids.

121. The method of any one of paragraphs 118-120, wherein the total TAG isolated comprises at least 50% TAGs comprising C4-C8 R-group fatty acids.

122. The method of any one of paragraphs 118-121, wherein the total TAG isolated comprises at least 50% TAGs comprising C16 R-group fatty acids.

123. A method of producing triacylglycerides (TAGs), comprising:

- a) culturing the engineered bacterium of any of paragraphs 101-117 in a culture medium comprising fructose and/or H₂; and
- b) isolating, collecting, or concentrating TAGs from said engineered bacterium or from the culture medium of said engineered bacterium.

124. The method of paragraph 123, wherein the culture medium comprises fructose as the sole carbon source, and/or the culture medium comprises H₂as the sole energy source.

125. The method of any one of paragraphs 123-124, wherein the total TAG isolated comprises at least 50% TAGs comprising C4-C18 R-group fatty acids.

126. The method of any one of paragraphs 123-125, wherein the total TAG isolated comprises at least 50% TAGs comprising C4-C8 R-group fatty acids.

127. The method of any one of paragraphs 123-126, wherein the total TAG isolated comprises at least 50% TAGs comprising C16 R-group fatty acids.

128. A method of producing triacylglycerides (TAGs), comprising:

- a) culturing the engineered bacterium of any of paragraphs 101-117 in a culture medium comprising glycerol and/or H₂; and
- b) isolating, collecting, or concentrating TAGs from said engineered bacterium or from the culture medium of said engineered bacterium.

129. The method of paragraph 128, wherein the culture medium comprises glycerol as the sole carbon source, and/or the culture medium comprises H₂as the sole energy source.

130. The method of any one of paragraphs 128-129, wherein the total TAG isolated comprises at least 50% TAGs comprising C4-C18 R-group fatty acids.

131. The method of any one of paragraphs 128-130, wherein the total TAG isolated comprises at least 50% TAGs comprising C4-C8 R-group fatty acids.

132. The method of any one of paragraphs 128-131, wherein the total TAG isolated comprises at least 50% TAGs comprising C16 R-group fatty acids.

133. A system comprising:

- a) a reactor chamber with a solution contained therein, wherein the solution comprises hydrogen (H₂) and a carbon source; and
- b) the engineered bacterium of any of paragraphs 101-117 in the solution.

134. The system of paragraph 133, further comprising a pair of electrodes in contact with the solution that split water to form the hydrogen.

135. The system of any one of paragraphs 133-134, wherein the carbon source is carbon dioxide (CO₂), fructose, and/or glycerol.

136. The system of any one of paragraphs 133-135, further comprising an isolated gas volume above a surface of the solution within a head space of a reactor chamber.

137. The system of any one of paragraphs 133-136, wherein the isolated gas volume comprises primarily carbon dioxide.

138. The system of any one of paragraphs 133-137, further comprising a power source comprising a renewable source of energy.

139. The system of any one of paragraphs 133-138, wherein the renewable source of energy comprises a solar cell, wind turbine, generator, battery, or grid power.

Some embodiments of the technology described herein can be defined according to any of the following numbered paragraphs:

201. An engineered Cupriavidus necator bacterium, comprising:

- a) at least one exogenous copy of at least one functional thioesterase (TE) gene;
- b) at least one exogenous copy of at least one functional diglyceride acyltransferase (DGAT) gene; and/or
- c) at least one exogenous copy of at least one phosphatidate phosphatases (PAP) gene.

202. The engineered bacterium of paragraph 201, further comprising: (i) at least one endogenous polyhydroxyalkanoate (PHA) synthase gene comprising at least one engineered inactivating modification; or (ii) at least one exogenous inhibitor of an endogenous polyhydroxyalkanoate (PHA) synthase gene or gene product.

203. The engineered bacterium of any one of paragraphs 201-202, wherein said engineered bacteria is a chemoautotroph.

204. The engineered bacterium of any one of paragraphs 201-203, wherein said engineered bacteria uses CO₂as its sole carbon source, and/or said engineered bacteria uses H₂as its sole energy source.

205. The engineered bacterium of any one of paragraphs 201-204, wherein said engineered bacteria uses glycerol as its sole carbon source.

206. The engineered bacterium of any one of paragraphs 201-205, wherein the functional thioesterase gene is heterologous.

207. The engineered bacterium of paragraph 206, wherein the functional heterologous thioesterase gene comprises a Marvinbryantia formatexigens TE gene, a Cuphea palustris FatB1 gene, a Cuphea palustris FatB2 gene, or a Cuphea palustris FatB2-FatB1 hybrid gene.

208. The engineered bacterium of any one of paragraphs 201-207, wherein the functional DGAT gene is heterologous.

209. The engineered bacterium of paragraph 208, wherein the functional heterologous DGAT gene comprises a Acinetobacter baylyi DGAT gene, or a Thermomonospora curvata DGAT gene.

210. The engineered bacterium of any one of paragraphs 201-209, wherein the functional PAP gene is heterologous.

211. The engineered bacterium of paragraph 2010, wherein the functional heterologous PAP gene comprises a Rhodococcus opacus PAP gene, or a Rhodococcus jostii PAP gene.

212. The engineered bacterium of any one of paragraphs 202-2011, wherein the engineered inactivating modification of the endogenous PHA synthase comprises one or more of i) deletion of the entire coding sequence, ii) deletion of the promoter of the gene, iii) a frameshift mutation, iv) a nonsense mutation (i.e., a premature termination codon), v) a point mutation, vi) a deletion, vii) or an insertion.

213. The engineered bacterium of any one of paragraphs 202-212, wherein the endogenous PHA synthase comprises phaC.

214. The engineered bacterium of any one of paragraphs 201-213, wherein said engineered bacteria produces triacylglycerides.

215. The engineered bacterium of any one of paragraphs 201-214, wherein said engineered bacteria produces animal triacylglycerides.

216. The engineered bacterium of any one of paragraphs 201-214, wherein said engineered bacteria produces milk fats.

217. A method of producing triacylglycerides (TAGs), comprising:

- a) culturing the engineered bacterium of any of paragraphs 201-216 in a culture medium comprising CO₂and/or H₂; and
- b) isolating, collecting, or concentrating TAGs from said engineered bacterium or from the culture medium of said engineered bacterium.

218. The method of paragraph 217, wherein the culture medium comprises CO₂as the sole carbon source, and/or the culture medium comprises H₂as the sole energy source.

219. The method of any one of paragraphs 217-218, wherein the total TAG isolated comprises at least 50% TAGs comprising C16 R-group fatty acids.

220. A method of producing triacylglycerides (TAGs), comprising:

- a) culturing the engineered bacterium of any of paragraphs 201-216 in a culture medium comprising glycerol and/or H₂; and
- b) isolating, collecting, or concentrating TAGs from said engineered bacterium or from the culture medium of said engineered bacterium.

221. The method of paragraph 220, wherein the culture medium comprises glycerol as the sole carbon source, and/or the culture medium comprises H₂as the sole energy source.

222. The method of any one of paragraphs 220-221, wherein the total TAG isolated comprises at least 50% TAGs comprising C16 R-group fatty acids.

223. A system comprising:

- a) a reactor chamber with a solution contained therein, wherein the solution comprises hydrogen (H₂) and a carbon source; and
- b) the engineered bacterium of any of paragraphs 201-216 in the solution.

224. The system of paragraph 223, further comprising a pair of electrodes in contact with the solution that split water to form the hydrogen.

225. The system of any one of paragraphs 223-224, wherein the carbon source is carbon dioxide (CO₂) and/or glycerol.

226. The system of any one of paragraphs 223-225, further comprising an isolated gas volume above a surface of the solution within a head space of a reactor chamber.

227. The system of any one of paragraphs 223-226, wherein the isolated gas volume comprises primarily carbon dioxide.

228. The system of any one of paragraphs 223-227, further comprising a power source comprising a renewable source of energy.

229. The system of any one of paragraphs 223-228, wherein the renewable source of energy comprises a solar cell, wind turbine, generator, battery, or grid power.

The technology described herein is further illustrated by the following examples which in no way should be construed as being further limiting.

EXAMPLES
Example 1: Production of Tailored Animal Triacylglycerides from C. necator

The area of animal-free replacements for lipids remains largely untapped. Milk fats are largely responsible for texture, flavor, energy content, and the solubility of some vitamins in dairy products. The possibility of biomanufacturing such animal-free milk fats to provide an alternative option for milk, butter, cheese, creams, ice cream, and meat represents a critical part of the solution for utilizing synthetic biology to lessen the environmental impacts of addressing humanity's increasing food production demands. Worldwide, cattle farming produces 11% of all greenhouse gas emissions and the dairy industry emits 3% annually. Current dairy alternatives are currently limited by the ability of plant fats to confer the same properties as dairy fats. Milk lipids are in a large part responsible for the taste and texture of dairy products, especially in the case of cheese and butter. Currently, there are no commercially available animal-free replacements for these fats, and plant-based options lack the physical properties for many applications as well as introduce unwanted flavors. By producing identical, or substantially similar, milk lipid replacements, the engineered bacteria and methods described herein permit a broader application of animal-free dairy. Without wishing to be bound by theory, the engineered bacteria and methods described herein are expected to have 120% lower GHG emissions, use 99% less land, and use half the amount of water needed in current dairy practices.

Described herein are engineered bacteria that produce triacylglycerides (TAGs), the major class of fats in dairy (see e.g., FIG. 1A). The composition of the TAGs can be tailored by changing specific enzymes in the biosynthetic pathway. Varying the expression of different thioesterases (TE) leads to the production of specific chain-length fatty acids. For those fatty acids to be added to the glycerol backbone, diglyceride acyltransferases (DGAT) can also be varied. Phosphatidate phosphatases (PAP) can be engineered to achieve specific TAGs (see e.g., FIG. 1B).

Using a chassis organism, C. necator, capable of both heterotrophic and autotrophic growth, provided herein is a proof-of-concept of this approach. Using a parent strain of a PHA synthesis deletion strain (ΔphaC), the following combinations were over-expressed: R. opacus PAP and A. baylyi DGAT (RoAb; “Strain 1”); R. jostii PAP and A. baylyi DGAT (RjAb; “Strain 2”); R. opacus PAP and T. curvata DGAT (RoTc; “Strain 3”); R. jostii PAP and T. curvata DGAT (RjTc; “Strain 4”); R. opacus PAP, T. curvata DGAT and Chimera 4 TE (Ch4RoTc; “Strain 5”); and R. opacus PAP, T. curvata (DGAT), and M. formatexigens (TE) (MfRoTc; “Strain 6”). Wild type R. opacus was used as a positive control since it is a model organism for natural TAG biosynthesis. In a Nile Red assay, observed fluorescence indicated lipid accumulation in all of the engineered strains (see e.g., FIG. 2A). The highest accumulation occurred in strains containing the A. baylyi DGAT. Optical density measurements indicated that strains containing the R. opacus PAP also grew to higher densities than those strains containing the R. jostii PAP (see e.g., FIG. 2B).

Growth of strain 1 (R. opacus PAP and A. baylyi DGAT (RoAb) in ΔphaC C. necator) resulted in a higher fatty acid content and an altered distribution compared to ΔphaC (see e.g., FIG. 3).

Without wishing to be bound by theory, it is estimated that the yield for TAG production using the engineered bacteria as described herein is about 10-20% (e.g., at least 10%, at least 11%, at least 12%, at least 13%, at least 14%, at least 15%, at least 16%, at least 17%, at least 18%, at least 19%, or at least 20% TAG yield). In some embodiments, percent yield can be calculated by dividing isolated lipids by total dry cell weight. In some embodiments, wild-type bacteria (e.g., C. necator) comprise at least 10% lipid yield. In some embodiments, engineered bacteria described herein comprise at least 20% lipid yield.

In some embodiments, percent yield can be calculated by dividing the actual yield (e.g., isolated amount of TAG) by the theoretical yield (which can be determined by the amount of each reactant and stoichiometric calculations to determine the expected amount of product).

Methods

FIGS. 2A and 2B: Strains were cultured on rich broth agar plates from glycerol stock at 30° C. for 2 days. Single colonies were incubated in rich broth liquid media with antibiotics (e.g., kanamycin) overnight. 1 mL of overnight culture was inoculated in 50 mL of minimal media comprising fructose (e.g., 20 g/L; 2%), cultured at 30° C. while shaking until OD 0.4-0.6. Then cells were induced with 0.1% arabinose and cultured for another ˜20 hours. OD600 was measured and 200 uL of culture was subjected to Nile Red assay. For the Nile Red assay, 5 uL of 0.025 mg/mL Nile Red in DMSO was added to the culture, incubated for 10 min at room temperature in the dark and fluorescence was measured (excitation: 550 nm, emission: 630 nm).

FIG. 3: 1 mL aliquot was inoculated in 300-600 mL rich broth with antibiotics (e.g., kanamycin) and incubated at 30° C. while shaking for 24 hr. The next day, cells were diluted 1:20 in 4 L or 10 L fermenter in minimal media comprising 20 g/L fructose and 1.5 g/L ammonium chloride. Cells were induced after ˜18 hr with 0.1% arabinose and cultured for another 24 hr. Cells were harvested and pellets lyophilized. Lyophilized cells were then subjected to direct methanolysis for whole cell fatty acid analysis. For that analysis, lyophilized cells were suspended in equal volumes of chloroform and acidified methanol, and heated for 2 hr at 100° C. The organic mixture was added to water, vortexed and separated via centrifugation. The chloroform phase was separated and analyzed for fatty acid methyl esters (FAMEs) via gas chromatography-mass spectrometry (GC-MS).

FIG. 7A-7B: For the PCR verification, standard PCR procedure was applied to cells diluted in ddH2O (see e.g., Table 6 below for strain designations used in FIG. 7A-7B).

TABLE 6

Exemplary Engineered TAG production strains.

Designation
strain
Genotype
Added enzymes

H16

Cupriavidus

wild type

necator H16

phaC

Cupriavidus

ΔphaC1

necator H16

873

Cupriavidus

ΔphaC1

R. opacus PAP,

necator H16

A. baylyi DGAT

875

Cupriavidus

ΔphaC1

R. jostii PAP,

necator H16

T. curvata DGAT

878

Cupriavidus

ΔphaC1

R. opacus PAP,

necator H16

T. curvata DGAT

881

Cupriavidus

ΔphaC1

R. opacus PAP,

necator H16

T. curvata DGAT,

Chimera 4 TE

884

Cupriavidus

ΔphaC1

R. jostii PAP,

necator H16

A. baylyi DGAT

887

Cupriavidus

ΔphaC1

R. opacus PAP,

necator H16

T. curvata DGAT,

M. formatexigens TE

FIG. 8: For TLC, lipids were extracted from strain 873 (see e.g., Table 6) via the Bligh Dyer method. Briefly, equal amounts of chloroform and methanol were added to lyophilized biomass. Lipids were extracted via vortexing and separated by adding potassium chloride solution and centrifuging. The chloroform layer was then loaded onto a thin layer chromatographie plate, evolved using a hexane:diethyl ether:acetic acid mobile phase and visualized using primuline.

FIG. 9: For HPLC, extracted TAGs were loaded onto C18 column and separated using two mobile phases, where one mobile phase consisted of acetonitrile, ammonium formate and formic acid and another mobile phase of isopropanol, water and formic acid.

FIG. 10: For GC-MS, TAGs extracted from strain 873 (see e.g., Table 6) were loaded onto AGILENT CP-TAP column and analyzed via Mass Spectrometry.

	Number	Date	Country
	63165941	Mar 2021	US
	63147496	Feb 2021	US

ENGINEERED BACTERIA AND METHODS OF PRODUCING TRIACYLGLYCERIDES

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