Patent Application
20240309417
Not applicable.
The disclosure generally relates to the use of microorganisms with novel pathways for the conversion of short-chain hydrocarbons (e.g. methane, ethane, propane, butane, pentane) to fuels and chemicals (e.g. carboxylic acids, alcohols, hydrocarbons, and their alpha-, beta-, and omega-functionalized derivatives).
Global natural gas (CH4) resources that are technically recoverable with new horizontal drilling and efficient extraction technologies are estimated at 7.2×103 trillion cubic feet (Tcf), with estimates for the US ranging between 0.65×103 Tcf and up to 2×103 Tcf. Furthermore, about 5 trillion cubic feet (Tcf) of natural gas liquids or NGLs (primarily ethane, propane and butane) are produced annually in the United States and technically recoverable reserves of this resource are estimated at over 400 Tcf based on wet natural gas estimates.
The invention re-purposes native pathways for anaerobic and aerobic activation of medium- and long-chain hydrocarbons (C6-C20) to function with short-chain substrates (C1-C5). Through these engineered pathways, the short-chain hydrocarbon substrates are converted to central, intracellular metabolites such as acetyl-CoA, which can in turn be converted to a variety of fuels and chemicals through other native or engineered pathways.
SUMMARY OF THE DISCLOSURE
This invention demonstrates pathways that can be utilized for the conversion of short chain hydrocarbon feedstocks to a variety of fuels and chemicals. This is accomplished through key pathway modules for hydrocarbon activation and conversion to an acyl-CoA intermediate, generation of product precursor acetyl-CoA, which in certain cases also entails the generation of an addition acyl-CoA or keto-acid, and the formation of a desired product from acetyl-CoA. Dependent on the type of hydrocarbon activation pathway utilized, the regeneration of compounds required for activation from an acyl-CoA or keto-acid intermediate are also required.
Two main approaches for short chain hydrocarbon activation are exploited: 1) the oxygen-independent activation via fumarate addition, which given the need for fumarate during oxygen-independent activation also requires pathways for the regeneration of this intermediate for continued activation cycles, and 2) the oxygen-dependent activation via the terminal addition of a hydroxyl group to the alkane.
As used herein, an “oxygen-independent activation via fumarate addition” is the addition of fumarate to an alkane leading a 2-methyl-alkyl-succinate:
The enzyme that catalyzes this reaction is an “alkyl succinate synthase,” and more than 40 such examples are exemplified herein. Alkyl succinate synthases that are specific for methane as a substrate are called “methyl succinate synthases,” for ethane they are called “ethyl succinate synthases,” and so on, although there are of course enzymes with broader substrate specificity.
As used herein, an “oxygen-dependent activation” is the terminal addition of a hydroxyl group to the alkane to form a primary alcohol.
The enzyme that catalyzes this reaction is an “alkane monooxygenase” or “alkane hydroxylase”, and as above, they may sometimes be named according the alkane substrate specificity, although there are of course enzymes in both classes with broader substrate specificity. Several examples are provided herein.
Regardless of the activation pathway utilized, the resulting activated compound is then converted into an acyl-CoA intermediate through a series of reactions. Once the given acyl-CoA intermediate is produced, various pathways dependent on the type of acyl-CoA generated can be exploited for the generation of the product precursor acetyl-CoA.
Synthesis of the desired product(s) from acetyl-CoA can be accomplished through various engineered metabolic pathways, including a reversal of the beta-oxidation cycle (BOX-R) or the fatty acid biosynthesis (FAS) pathway. Following chain elongation through either of these pathways, the selection of a given termination pathway enables the synthesis of various product families.
As used herein “termination pathway” or “termination enzyme(s)” refers to one or more enzymes (or genes encoding same) that will pull reaction intermediates out the BOX-R or FAS cycle and produce the desired end product.
By “primary termination pathway” what is meant is an intermediate from the BOX-R or FAS cycle is pulled out of the BOX-R or FAS cycle by one (which can have more than one activity) or more termination enzymes and results in i) carboxylic acids, ii) primary alcohols, iii) hydrocarbons, or iv) primary amines, from CoA intermediates as described in
By “secondary termination pathway” what is meant is that the intermediate pulled out of the BOX-R or FAS cycle by a primary termination pathway enzyme is further modified by one or more enzymes.
Many examples of termination pathways are available and the following table provides several examples:
E. coli tesA E. coli tesB E. coli yciA E. coli fadM E. coli ydil E. coli ybgC Alcanivorax borkumensis tesB2
Fibrobacter succinogenes Fs2108
Prevotella rumincola Pr655
Prevotella ruminicola Pr1687
E. coli atoD
Clostridium kluyveri cat2
Clostridium acebotuylicum
E. coli ydiF
Clostridium acetobutylicum ptb
Enterococcus faecalis ptb
Salmonella enterica pduL
Clostridium acetobutylicum buk
Enterococcus faecalis buk
Salmonella enterica pduW
Clostridium acetobutylicum adhE2 Arabidopsis thaliana At3g11980 Arabidopsis thaliana At3g44560 Arabidopsis thaliana At3g56700 Arabidopsis thaliana At5g22500 Arabidopsis thaliana CER4
Marinobacter aquaeolei VTB
Marinobacter aquaeolei VTB
Acinetobacter calcoaceticus acr1 Acinetobacter sp Strain M-1 acrM Clostridium beijerinckii ald E. coli eut E Salmonella enterica eutE E. coli mhpF
E. coli betA E. coli dkgA E. coli eutG E. coli fucO E. coli upcA E. coli yahK E. coli ybbO
E. coli ybdH
E. coli yiaY
E. coli yjgB
Synechococcus elongatus PCC7942 orf1593 Nostoc punctiforme PCC73102 npun_R1711 Prochlorococcus marinus MIT9313 pmt1231
Arabidopsis thaliana At3g22200 Alcalgenes denitrificans AptA Bordetella bronchiseptica BB0869 Bordetella parapertussis BPP0784 Brucella melitensis BAWG_0478 Burkholderia pseudomallei BP1026B_I0669
Chromobacterium violaceum
Oceanicola granulosus
Paracoccus denitrificans PD1222
Pseudogulbenkiania ferrooxidans
Pseudomonas putida ω-TA
Ralstonia solanacearum ω-TA
Rhizobium meliloti SMc01534
Vibrio fluvialis ω-TA
Mus musculus abaT
E. coli gabT
Pseudomonas putida alkBGT Marinobacter aquaeolei CYP153A Mycobacterium marinum CYP153A16 Polaromonas sp. CYP153A Nicotiana tabacum CYP94A5 Vicia sativa CYP94A1 Vicia sativa CYP94A2 Arabidopsis thaliana CYP94B1 Arabidopsis thaliana CYP86A8 Candida tropicalis CYP52A1
Candida tropicalis CYP52A2
Homo sapiens CYP4A11
Rhodococcus ruber SC1 cddC Acinetobacter sp. SE19 chnD E. coli yah K E. coli yjgB
Rhodococcus ruber SC1 cddD Acinetobacter sp SE19 chnE
Myxococcus xanthus MXAN_0191 Stigmatella aurantiaca STIAU_3334
The synthetic pathway disclosed in this invention serves as a platform for the generation of valuable chemical products from less valuable and more abundant hydrocarbon feedstocks. Methane, for example, can be converted into liquid “drop in” fuels for use in the current transportation infrastructure. The methods, materials and systems herein thus allow for various chain length hydrocarbons to be activated and assimilated into central carbon metabolism allowing for product synthesis via numerous native and synthetic pathways.
The process involves performing traditional cultures using industrial organisms (such as E. coli, S. cerevisiae, Methylococcus capsulatus, or Pichia pastoris) that convert short-chain hydrocarbons (such as methane, ethane, propane, butane, or pentane) into chemical products. These organisms are considered workhorses of modern biotechnology, and are easy to genetically engineer, and scale up for industrial production levels of desired products.
The pathways in a living system are generally made by transforming the microbe with an expression vector encoding one or more of the proteins, but the genes can also be added to the chromosome by recombineering, homologous recombination, and similar techniques. Where the needed protein is endogenous, as is the case in some instances, it may suffice as is, but it is usually overexpressed using an inducible promoter for better functionality and user-control over the level of active enzyme.
As used herein, the expressions “microorganism,” “microbe,” “strain” and the like may be used interchangeably and all such designations include their progeny. It is also understood that all progeny may not be precisely identical in DNA content, due to deliberate or inadvertent mutations. Mutant progeny that have the same function or biological activity as screened for in the originally transformed cell are included. Where distinct designations are intended, it will be clear from the context.
As used herein, reference to a “cell” is generally understood to include a culture of such cells, as the work described herein is done in cultures having 109-15 cells.
As used herein, “growing” cells used it its art accepted manner, referring to exponential growth of a culture of cells, not the few cells that may not have completed their cell cycle at stationary phase or have not yet died in the death phase or after harvesting.
As used in the claims, “homolog” means an enzyme with at least 50% identity to one of the listed sequences and also having the same general catalytic activity. While higher identity (60%, 70%, 80%) and the like may be preferred, it is typical for bacterial sequences to diverge significantly (40-60%), yet still be identifiable as homologs, while mammalian species tend to diverge less (80-90%).
Reference to proteins herein can be understood to include reference to the gene encoding such protein. Thus, a claimed “permease” protein can include the related gene encoding that permease. However, it is preferred herein to refer to the protein by standard name per ecoliwiki or HUGO since both enzymatic and gene names have varied widely, especially in the prokaryotic arts.
Once an exemplary protein is obtained, many additional examples of proteins with similar activity can be identified by BLAST search. Further, every protein record is linked to a gene record, making it easy to design overexpression vectors. Many of the needed enzymes are already available in vectors, and can often be obtained from cell depositories or from the researchers who cloned them. But, if necessary, new clones can be prepared based on available sequence information using RT-PCR techniques. Thus, it should be easily possible to obtain all of the needed enzymes for overexpression.
Another way of finding suitable enzymes/proteins for use in the invention is to consider other enzymes with the same EC number, since these numbers are assigned based on the reactions performed by a given enzyme. An enzyme that thus be obtained, e.g., from AddGene or from the author of the work describing that enzyme, and tested for functionality as described herein. In addition, many sites provide lists of proteins that all catalyze the same reaction.
Understanding the inherent degeneracy of the genetic code allows one of ordinary skill in the art to design multiple nucleotides that encode the same amino acid sequence. NCBI™ provides codon usage databases for optimizing DNA sequences for protein expression in various species. Using such databases, a gene or cDNA may be “optimized” for expression in E. coli, yeast, algae or other species using the codon bias for the species in which the gene will be expressed.
Initial cloning experiments have proceeded in E. coli for convenience since most of the required genes are already available in plasmids suitable for bacterial expression, but the addition of genes to bacteria is of nearly universal applicability. Indeed, since recombinant methods were invented in the 70's and are now so commonplace, even school children perform genetic engineering experiments using bacteria. Such species include e.g., Bacillus, Streptomyces, Azotobacter, Trichoderma, Rhizobium, Pseudomonas, Micrococcus, Nitrobacter, Proteus, Lactobacillus, Pediococcus, Lactococcus, Salmonella, Streptococcus, Paracoccus, Methanosarcina, and Methylococcus, or any of the completely sequenced bacterial species. Indeed, hundreds of bacterial genomes have been completely sequenced, and this information greatly simplifies both the generation of vectors encoding the needed genes, as well as the planning of a recombinant engineering protocol. Such species are listed along with links at en.wikipedia.org/wiki/List_of_sequenced_bacterial genomes.
Additionally, yeast, such as Saccharomyces, are a common species used for microbial manufacturing, and many species can be successfully transformed. Indeed, yeast are already available that express recombinant thioesterases—one of the termination enzymes described herein—and the reverse beta oxidation pathway has also been achieved in yeast. Other species include but are not limited to Candida, Aspergillus, Arxula adeninivorans, Candida boidinii, Hansemula polymorpha (Pichia angusta), Kluyveromyces lactis, Pichia pastoris, and Yarrowia lipolytica, to name a few.
It is also possible to genetically modify many species of algae, including e.g., Spirulina, Apergillus, Chlamydomonas, Laminaria japonica, Undaria pinnatifida, Porphyra, Eucheuma, Kappaphycus, Gracilaria, Monostroma, Enteromorpha, Arthrospira, Chlorella, Dunaliella, Aphanizomenon, Isochrysis, Pavlova, Phaeodactylum, Ulkenia, Haematococcus, Chaetoceros, Nannochloropsis, Skeletonema, Thalassiosira, and Laminaria japonica, and the like. Indeed, the microalga Pavlova lutheri is already being used as a source of economically valuable docosahexaenoic (DHA) and eicosapentaenoic acids (EPA), and Crypthecodinium cohnii is the heterotrophic algal species that is currently used to produce the DHA used in many infant formulas.
Furthermore, a number of databases include vector information and/or a repository of vectors and can be used to choose vectors suitable for the chosen host species. See e.g., AddGene.org which provides both a repository and a searchable database allowing vectors to be easily located and obtained from colleagues. See also Plasmid Information Database (PlasmID) and DNASU having over 191,000 plasmids. A collection of cloning vectors of E. coli is also kept at the National Institute of Genetics as a resource for the biological research community. Furthermore, vectors (including particular ORFS therein) are usually available from colleagues.
The enzymes can be added to the genome or via expression vectors, as desired. Preferably, multiple enzymes are expressed in one vector or multiple enzymes can be combined into one operon by adding the needed signals between coding regions. Further improvements can be had by overexpressing one or more, or even all of the enzymes, e.g., by adding extra copies to the cell via plasmid or other vector. Initial experiments may employ expression plasmids hosting 3 or more ORFs for convenience, but it may be preferred to insert operons or individual genes into the genome for long term stability.
Still further improvements in yield can be had by reducing competing pathways, such as those pathways for making e.g., acetate, formate, ethanol, and lactate, and it is already well known in the art how to reduce or knockout these pathways. See e.g., the Rice patent portfolio by Ka-Yiu San and George Bennett (U.S. Pat. Nos. 7,569,380, 7,262,046, 8,962,272, 8,795,991) and patents by these inventors (U.S. Pat. Nos. 8,129,157 and 8,691,552) (each incorporated by reference herein in its entirety for all purposes). Many others have worked in this area as well.
In calculating “% identity” the unaligned terminal portions of the query sequence are not included in the calculation. The identity is calculated over the entire length of the reference sequence, thus short local alignments with a query sequence are not relevant (e.g., % identity=number of aligned residues in the query sequence/length of reference sequence). Alignments are performed using BLAST homology alignment as described by Tatusova T A & Madden T L (1999) FEMS Microbiol. Lett. 174:247-250, and available through the NCBI website. The default parameters were used, except the filters were turned OFF.
“Operably associated” or “operably linked”, as used herein, refer to functionally coupled nucleic acid or amino acid sequences.
“Recombinant” is relating to, derived from, or containing genetically engineered material. In other words, the genetics of an organism was intentionally manipulated in some way.
“Reduced activity” is defined herein to be at least a 75% reduction in protein activity, as compared with an appropriate control species (e.g., the wild type gene in the same host species). Preferably, at least 80, 85, 90, 95% reduction in activity is attained, and in the most preferred embodiment, the activity is eliminated (100%). Proteins can be inactivated with inhibitors, by mutation, or by suppression of expression or translation, by knock-out, by adding stop codons, by frame shift mutation, and the like. All reduced activity genes or proteins are signified herein by “−”.
By “null” or “knockout” what is meant is that the mutation produces undetectable active protein. A gene can be completely (100%) reduced by knockout or removal of part of all of the gene sequence. Use of a frame shift mutation, early stop codon, point mutations of critical residues, or deletions or insertions, and the like, can also completely inactivate (100%) gene product by completely preventing transcription and/or translation of active protein. All null mutants herein are signified by A.
“Overexpression” or “overexpressed” is defined herein to be at least 150% of protein activity as compared with an appropriate control species, or any expression in a species that lacks the activity altogether. Preferably, the activity is increased 100-500% or even ten fold. Overexpression can be achieved by mutating the protein to produce a more active form or a form that is resistant to inhibition, by removing inhibitors, or adding activators, and the like. Overexpression can also be achieved by removing repressors, adding multiple copies of the gene to the cell, or up-regulating the endogenous gene, and the like. All overexpressed genes or proteins are signified herein by “+”.
In certain species it is possible to genetically engineer the endogenous protein to be overexpressed by changing the regulatory sequences or removing repressors. However, overexpressing the gene by inclusion on selectable plasmids or other vectors that exist in hundreds of copies in the cell may be preferred due to its simplicity and ease of exerting externals controls, although permanent modifications to the genome may be preferred in the long term for stability reasons.
The terms “operably associated” or “operably linked,” as used herein, refer to functionally coupled nucleic acid sequences.
As used herein “recombinant” is relating to, derived from, or containing genetically engineered material. In other words, the genome was intentionally manipulated by the hand of man in some way.
The term “endogenous” or “native” means that a gene originated from the species in question, without regard to subspecies or strain, although that gene may be naturally or intentionally mutated, or placed under the control of a promoter that results in overexpression or controlled expression of said gene. Thus, genes from Clostridia would not be endogenous to Escherichia, but a plasmid expressing a gene from E. coli or would be considered to be endogenous to any genus of Escherichia, even though it may now be overexpressed.
“Expression vectors” are used in accordance with the art accepted definition of a plasmid, virus or other propagatable sequence designed for protein expression in cells. There are thousands of such vectors commercially available, and typically each has an origin of replication (ori); a multiple cloning site; a selectable marker; ribosome binding sites; a promoter and often enhancers; and the needed termination sequences. Most expression vectors are inducible, although constitutive expressions vectors also exist.
As used herein, “inducible” means that gene expression can be controlled by the hand of man, by adding e.g., a ligand to induce expression from an inducible promoter. Exemplary inducible promoters include the lac operon, inducible by IPTG, the yeast AOX1 promoter inducible with methanol, the strong LAC4 promoter inducible with lactate, and the like. Low level of constitutive protein synthesis may occur even in expression vectors with tightly controlled promoters.
As used herein, an “integrated sequence” means the sequence has been integrated into the host genome, as opposed to being maintained on an expression vector. It will still be expressable, and preferably is inducible as well.
The use of the word “a” or “an” when used in conjunction with the term “comprising” in the claims or the specification means one or more than one, unless the context dictates otherwise.
The term “about” means the stated value plus or minus the margin of error of measurement or plus or minus 10% if no method of measurement is indicated.
The use of the term “or” in the claims is used to mean “and/or” unless explicitly indicated to refer to alternatives only or if the alternatives are mutually exclusive.
The terms “comprise”, “have”, “include” and “contain” (and their variants) are open-ended linking verbs and allow the addition of other elements when used in a claim. The following abbreviations are used herein:
The activation of the short chain hydrocarbon substrates, such as methane of LNG components, requires the high stability and low reactivity of hydrocarbon compounds to be overcome through the cleavage of an inert C—H bond. Two main biological approaches can be exploited here for this purpose, 1) the oxygen-independent activation through the addition of fumarate to form a 2-methyl-alkyl-succinyl-CoA, or 2) the oxygen-dependent activation through the terminal addition of a hydroxyl group to the alkane to form a primary alcohol.
The first approach leverages a native pathway for anaerobic hydrocarbon activation used by certain microorganisms for the degradation of C6-C20 alkanes (Callaghan, 2013). In this pathway, an alkyl-succinate synthase first forms a branched methyl-alkyl-succinate adduct from the addition of fumarate to the alkane, with further metabolism and fumarate regeneration steps resulting in the conversion of hydrocarbon substrates to central, intracellular metabolites (
In order to meet ATP requirements of this cycle, native hydrocarbon degrading microorganisms utilize the electrons generated during substrate oxidation for anaerobic respiration with nitrate, metal ions, or sulfate, thereby making hydrocarbon degradation thermodynamically favorable (Mbadinga et al., 2011). An example of this type of process is found in strain H×N1, which can grow anaerobically on alkanes such as hexane when coupled to denitrification, with the key genes required for initial alkane activation proposed (Grundmann et al., 2008). Reports also have suggested similar activation with shorter chain hydrocarbons in bacterial consortiums, although the enzymes responsible have not been identified (Duncan et al., 2009; Kniemeyer et al., 2007).
Furthermore, several potential variations of this pathway exist in which various biological reactions can be utilized to convert the 2-methyl-alkyl-succinate adduct formed via fumarate addition into central metabolic intermediates (
Considering the use of fumarate in the alkane activation cycle, this oxygen-independent activation approach also requires pathways for the regeneration of this compound from an acyl-CoA or keto-acid. Details on the pathways leading to the regeneration of fumarate from an acyl-CoA, such as propionyl-CoA, or a keto-acid, such as pyruvate, are shown in
In contrast to hydrocarbon activation via fumarate addition, an alternative pathway for the cleavage of an inert C—H bond is the use of an oxygen-dependent activation mechanism in which an alkane hydroxylase/monooxygenase adds a terminal alcohol group to the hydrocarbon, which is then further oxidized (
Once the product precursor acetyl-CoA has been formed through the above described approaches, the desired products can then be synthesized through various native or engineered metabolic pathways. These include both the reversal of the β-oxidation cycle and the fatty acid biosynthesis pathway, which both proceed from acetyl-CoA as the starting compound. While the type of condensation reaction for chain elongation varies between the 2 pathways (reversal of the β-oxidation cycle utilizes a non-decarboxylative condensation while the fatty acid biosynthesis pathway employs a decarboxylative condensation), both proceed through a series of condensation, reduction, dehydration, and reduction reactions that result in an intermediate 2 carbons longer than the starting unit. As such, each of these pathways can be exploited for the synthesis of a wide range of products through the selection of termination pathways that convert cycle intermediates to products such as carboxylic acids and alcohols among others.
Thus, either of these product synthesis pathways, combined with the key pathway modules for hydrocarbon activation and conversion to an acyl-CoA intermediate, generation of product precursor acetyl-CoA, and generation of an addition acyl-CoA or keto-acid for fumarate when required, and the formation of a desired product from acetyl-CoA enables an engineered microorganism capable of the conversion of short-chain hydrocarbons (e.g. methane, ethane, propane, butane, pentane) to fuels and chemicals (e.g. carboxylic acids, alcohols, hydrocarbons, and their alpha-, beta-, and omega-functionalized derivatives).
The following description provides additional details, any one of which can be subject to patenting in combination with any other. The specification in its entirety is to be treated as providing a variety of details that can be used interchangeably with other details, as the specification would be of inordinate length if one were to list every possible combination of genes/vectors/enzymes/hosts that can be made to convert short chain hydrocarbons to desired fuels and chemicals of interest. Some possible combinations are listed in Table G, however, (
Enzymes of interest can be expressed from vectors such as pETDuet-1 or pCDFDuet-1 (MERCK, Germany), which makes use of the DE3 expression system. Genes can be codon optimized according to the codon usage frequencies of the host organism and synthesized by a commercial vendor or in-house. However, thousands of expression vectors and hosts are available, and this is a matter of convenience.
The genes can be amplified by PCR using primers designed with 15-22 base pairs of homology for the appropriate vector cut site. For enzymes that will not require a 6×-histadine tag fusion for purification, pCDFDuet-1 can be linearized with NcoI and EcoRI. Enzymes that will be purified by Ni-NTA column will make use of the 6×-HIS tag in pCDFDuet-1. The vector can be linearized using only EcoRI in this case.
The PCR product can be inserted into the vector using e.g., the In-Fusion HD EcoDry Cloning System and the vector transformed by heat shock into competent E. coli cells. Transformants can be selected on solid media containing the appropriate antibiotic. Plasmid DNA can be isolated using any suitable method, including QIAprep Spin Miniprep Kit (QIAGEN, Limburg), and the construct confirmed by PCR and sequencing. Confirmed constructs can be transformed by e.g., electroporation into a host strain such as E. coli for expression, but other host species can be used with suitable expression vectors and possible codon optimization for that host species.
Expression of the desired enzymes from the constructed strain can be conducted in liquid culture, e.g., shaking flasks, bioreactors, chemostats, fermentation tanks and the like. Gene expression is typically induced by the addition of a suitable inducer, when the culture reaches an OD550 nm of approximately 0.5-0.8. Induced cells can be grown for about 4-8 hours, at which point the cells can be pelleted and saved to −20° C. Expression of the desired protein can be confirmed by running samples on SDS-PAGE.
The expressed enzyme can be directly assayed in crude cell lysates, simply by breaking the cells by chemical, enzymatic, heat or mechanical means. Depending on the expression level and activity of the enzyme, however, purification may be required to be able to measure enzyme activity over background levels. Purified enzymes can also allow for the in vitro assembly of the pathway, allowing for its controlled characterization.
N- or C-terminal HIS-tagged proteins can be purified using e.g., a Ni-NTA Spin Kit (Qiagen, Venlo, Limburg) following the manufacturer's protocol, or other methods could be used. The HIS-tag system was chosen for convenience only, and other tags are available for purification uses. Further, the proteins in the final assembled pathway need not be tagged if they are for in vivo use. Tagging was convenient, however, for the enzyme characterization work performed hereunder.
Reaction conditions for enzyme assays can vary greatly with the type of enzyme to be tested. In general, however, enzyme assays follow a similar general protocol. Purified enzyme or crude lysate is added to suitable reaction buffer. Reaction buffers typically contain salts, necessary enzyme cofactors, and are at the proper pH. Buffer compositions often change depending on the enzyme or reaction type. The reaction is initiated by the addition of substrate, and some aspect of the reaction related either to the consumption of a substrate or the production of a product is monitored.
Choice of the appropriate monitoring method depends on the compound to be measured. Spectrophotometric assays are convenient because they allow for the real time determination of enzyme activity by measuring the concentration dependent absorbance of a compound at a certain wavelength. There are not always compounds with a measureable absorbance at convenient wavelengths in the reaction, unfortunately. In these situations, other methods of chemical analysis may be necessary to determine the concentration of the involved compounds.
As an example, cultures for enzymatic assays were conducted in 125 ml Erlenmeyer flasks containing 25 mL LB media inoculated at 3% from an overnight culture. E. coli strains containing constructs expressing genes of interest were grown under appropriate conditions until an optical density of ˜0.5 was reached, at which point inducer(s) were added and the cells incubated for an additional 4 hrs. Cell harvesting and preparation of crude cell extracts for enzyme assays was conducted as described elsewhere (Dellomonaco et al., 2011). Enzymatic reactions were then monitored on either a Synergy HT plate reader (BioTek Instruments, Inc., Winooski, VT) or a Biomate 5 Spectrophotometer (Thermo Scientific, Waltham, MA) according to established protocols.
Furthermore, whole cell biotransformations represent another method to determine enzyme/pathway functionality. As an example, biotransformations for alkane activation were conducted using E. coli BL21(DE3) with appropriate vectors. 750 μL of an overnight LB culture with appropriate antibiotics was used to inoculate 25 mL LB media with 10 μM FeSO4 in a 125 mL Pyrex Erlenmeyer flask. Flasks were incubated at 37° C. and 200 rpm in an NBS Benchtop Incubator Shaker until an optical density of ˜0.5 was reached, at which point appropriate inducers were added. Cultures were grown for 4 hrs post-induction and then centrifuged (8000 rpm, 22° C., 5 min) and re-suspended to an optical density ˜12 in 100 mM KPi buffer (pH 7.0) with 1% glycerol (Koch et al., 2009). 250 μL alkane was then added to a 2 mL cell suspension in a 5 mL glass vial and incubated with rotation (60 rpm) at 30° C. for 2 hrs. Following the biotransformations, products (alcohols) were extracted and analyzed as previously described (Kim et al., 2015).
Gas chromatography (GC) is convenient for the quantification of volatile substances, of which fatty acids and alcohols are of particular relevance. Internal standards, typically one or more molecules of similar type not involved in the reaction, are added to the reaction mixture, and the reaction mixture is extracted with an organic solvent, such as hexane. Fatty acid samples, for example, can be dried under a stream of nitrogen and converted to their trimethylsilyl derivatives using N,O-Bis(trimethylsilyl)trifluoroacetamide (BSTFA) and pyridine in a 1:1 ratio. After 30 minutes incubation, the samples are once again dried and resuspended in hexane to be applied to the gas chromatograph (GC). Aldehyde samples do not need to be derivatized. Samples can be run e.g., on a Varian CP-3800 gas chromatograph (VARIAN ASSOCIATES, Palo Alto, CA) equipped with a flame ionization detector and HP-5 capillary column (AGILENT TECH., CA).
Once pathways have been fully studied in vitro, they can be constructed in vivo with greater confidence. The strain construction for the in vivo pathway operation should allow for the well-defined, controlled expression of the enzymes of the pathway. As before, E. coli or yeast will be a host of choice for the in vivo pathway, but other hosts could be used. The Duet system, for example, allows for the simultaneous expression of up to eight proteins by induction with IPTG in E. coli, and initial experiments will use this host.
Pathway enzymes can also be inserted into the host chromosome, allowing for the maintenance of the pathway without requiring antibiotics to ensure the continued upkeep of plasmids. A large number of genes that can be placed on the chromosome, as chromosomal expression does not require separate origins of replication as is the case with plasmid expression.
DNA constructs for chromosomal integration usually include an antibiotic resistance marker with flanking FRT sites for removal, as described by Datsenko and Wanner, a well characterized promoter, a ribosome binding site, the gene of interest, and a transcriptional terminator. The overall product is a linear DNA fragment with 50 base pairs of homology for the target site on the chromosome flanking each side of the construct.
However, the Flp-FRT recombination method is only one system for adding genes to a chromosome, and other systems are available, such as the RecBCD pathway, the RecF pathway, RecA recombinase, non-homologous end joining (NHEJ), Cre-Lox recombination, TYR recombinases and integrases, SER resolvases/invertases, SER integrases, PhiC31 Integrase, and the like. Chromosomal modifications in E. coli can also achieved by the method of recombineering, as originally described by Datsenko and Wanner.
In a recombineering method, for example, the cells are prepared for electroporation following standard techniques, and the cells transformed with linear DNA that contains flanking 50 base pair targeting homology for the desired modification site. For seamless integration of a DNA construct, a two-step approach can be taken using a cassette that contains both positive and negative selection markers, such as the combination of cat and sacB. In the first round of recombineering, the cat-sacB cassette with targeting homology for the desired modification site is introduced to the cells. The cat gene provides resistance to chloramphenicol, which allows for positive recombinants to be selected for on solid media containing chloramphenicol.
A positive isolate can be subjected to a second round of recombineering introducing the desired DNA construct with targeting homology for sites that correspond to the removal of the cat-sacB cassette. The sacB gene encodes for an enzyme that provides sensitivity to sucrose. Thus, growth on media containing sucrose allows for the selection of recombinants in which the cat-sacB construct was removed. Pl phage lysates can be made from isolates confirmed by PCR and sequencing. The lysates can be used to transduce the modification into desired strains, as described previously.
Engineered strains expressing the designed pathway can be cultured under the following or similar conditions. Overnight cultures started from a single colony can be used to inoculate flasks containing appropriate media. Cultures are grown for a set period of time, and the culture media analyzed. The conditions will be highly dependent on the specifications of the actual pathway and what exactly is to be tested. For example, the ability for the pathway to be used for hydrocarbon utilization can be tested by the use of short-chain alkanes as a substrate in MOPS minimal media, as described by Neidhardt, supplemented with appropriate antibiotics, and inducers.
Analysis of culture media after fermentation provides insight into the performance of the engineered pathway. Quantification of hydrocarbons and longer chain fatty acid and alcohol products can be analyzed by GC. Other metabolites, such as short chain organic acids and alcohols can be analyzed by high pressure liquid chromatograph (HPLC). Once the pathway is fully functional, the cultures can be grown in chemostat, providing continuous uninterrupted production of product if desired.
Various—omics techniques, such as microarray or 2D-PAGE can give information about gene expression or protein expression, respectively. Genome scale modeling allows for the identification of additional modifications to the host strain that might lead to improved performance. Deletion of competing pathways, for example, might increase carbon flux through the engineered pathway for product production.
Standard molecular biology techniques were used for gene cloning, plasmid isolation, and E. coli transformation. Native E. coli genes were amplified from E. coli MG1655 genomic DNA using primers to append 15 bp of homology on each end of the gene insert for recombination into the vector backbone. Genes from other organisms were codon optimized and synthesized by either GeneArt (LIFE TECH., CA or GENSCRIPT, NJ). Plasmids were linearized by the appropriate restriction enzymes and recombined with the gene inserts using the In-Fusion HD Eco-Dry Cloning system (CLONTECH LAB. CA,). The mixture was subsequently transformed into Stellar competent cells (CLONTECH LAB.).
Transformants that grew on solid media (LB+Agar) supplemented with the appropriate antibiotic were isolated and screened for the gene insert by PCR. Plasmid was isolated from the verified transformants and the sequence of the gene insert was further confirmed by DNA sequencing (LONE STAR LABS, TX). Plasmids (also referred to as vectors) in each case contain at least one promoter, a ribosome binding site for each gene, the gene(s) of interest, at least one terminator, an origin of replication, and an antibiotic resistance marker. Exemplary plasmids are shown in
Genes that encode the enzymes of the engineered pathway were cloned and expressed as described above. The crude protein extracts or purified enzymes were assessed for their ability to catalyze the proposed reactions. Tables β-F below describe the characterization of enzymes for required pathway steps depicted in
TABLE B describes the characterization of enzymes involved in hydrocarbon activation/utilization and conversion to acyl-CoA intermediates through the fumarate addition pathway as depicted in
T. aromatica
R. Sphaeroides
M. musculus
M. sedula Pcc
S. coelicolor Pcc
P. horikoshii Mce
P. freudenreichii
E. coli SucCD
E. coli SdhCDAB
E. coli FadE
E. coli FadB
E. coli FadB
E. coli AtoB
E. coli FadA
R. eutropha BktB
S. collinus FadA
P. putida FadAx
Additional details on alkylsuccinate synthase enzymes, required for the activation of hydrocarbons via fumarate addition are provided in TABLE C:
Desulfosarcina sp. BuS5
Desultosarcina sp. BuS5
Azoarcus sp. H × N1
Azoarcus sp. H × N1
Azoarcus sp. H × N1
Azoarcus sp. H × N1
Included in these alkylsuccinate synthase enzymes are those from Azoarcus sp. H×N1 (Grundmann et al., 2008) and Desulfosarcina sp. BuS5 (Kniemeyer et al., 2007) for which the catalytic subunit, and associated subunits for the case of Azoarcus sp. H×N1, have been proposed. Genes encoding the proposed subunits of the Azoarcus sp. H×N1 alkylsuccinate synthase have been cloned into required expression vectors as shown in
Furthermore, several candidate alkylsuccinate synthase subunits and associated proteins have been identified through a BLAST search of Azoarcus sp. H×N1 alkylsuccinate synthase subunits against the recently sequenced Desulfosarcina sp. BuS5 genome, a strain that degrades propane and butane via fumarate addition. This search identified several enzymes within close physical proximity to the large catalytic MasD subunit (WP_027352796.1), including 2 enzymes with high similarity to the Azoarcus sp. H×N1MasE subunit (WP_027352794.1 and WP_027352793.1), a protein with similarity to alkylsuccinate synthase gamma subunits from Desulfatibacillum alkenivorans AK-01 and Smithella sp. SCADC (WP_027352795.1), and enzymes with similarity to the Azoarcus sp. H×N1 MasG activating enzyme (WP_051374532.1) and other radical SAM enzymes (WP_027352800.1). In all, 13 proteins appear to be encoded from an operon within the Desulfosarcina sp. BuS5 genome spanning the locus from 66239-79342 in the associated genome sequence NZ_AXAM01000003.1. Genes encoding potential subunits of the alkylsuccinate synthase (WP_027352793.1, WP_027352794.1, WP_027352795.1, and WP_027352796.1) and activation enzyme (WP_051374532.1 and WP_027352800.1) have been cloned into required expression vectors as shown in
This type of homology search can be further exploited to identify other potential alkylsuccinate synthase enzymes/operons through a BLAST search of these enzymes against other hydrocarbon degrading species. For example, a search of the Desulfosarcina sp. BuS5 MasD subunit (WP_027352796.1) was used to identify potential MasD subunits from species such as Peptococcaceae bacterium SCADC1_2_3 (WP_036734374.1), Desulfoglaeba alkanexedens ALDC (ADJ51097.1), and Peptococcaceae bacterium BRH_c4a (KJS01634.1), among others.
Furthermore, additional enzymes required for conversion of fumarate activated hydrocarbon intermediates to product precursors have been investigated. Enzymes such as T. aromatica succinyl-CoA:(R)-benzylsuccinate CoA-transferase (Q9KJF0, Q9KJE9), R. sphaeroides (2S)-methylsuccinyl-CoA dehydrogenase (ADC44452.1), and R. sphaeroides mesaconyl-coenzyme A hydratase (Q3IZ78) enable the conversion of the fumarate activated hydrocarbons to product precursors, which can then be converted to desired products. Genes encoding the above proteins have been cloned into required expression vectors (
The above described enzymes for hydrocarbon activation/utilization and conversion to acyl-CoA intermediates through the fumarate addition pathway provide a route for the bioconversion of short-chain hydrocarbons of varying chain length. For the specific case of methane activation/utilization, the pathways depicted in
T. aromatica
R. sphaeroides
C. aurantiacus
C. aurantiacus
C. aurantiacus
E. coli MaeA
E. coli FumA
T. aromatica
R. sphaeroides
R. sphaeroides
R. sphaeroides
M. sedula Pcc
S. coelicolor
P. horikoshii
freudenreichii
E. coli SucCD
E. coli
E. coli Gcl
E. coli GarR
E. coli GlxK
Together, these enzymatic components described above provide a full route for the conversion of short chain hydrocarbons to acyl-CoA (e.g. acetyl-CoA) product precursors, which can subsequently be converted into fuels and chemicals (e.g. carboxylic acids, alcohols, hydrocarbons, and their alpha-, beta-, and omega-functionalized derivatives) through numerous product synthesis pathways, such as beta-oxidation reversal (BOX-R) or fatty acid biosynthesis. BOX-R is not described in great detail herein, since it has been described in the inventor's prior patents and publications.
The use of an oxygen-dependent activation mechanism in which an alkane hydroxylase adds a terminal alcohol group to the hydrocarbon can also be exploited for the bioconversion of short chain hydrocarbons to fuels and chemicals as depicted in
M. capsulatus (Bath)
M. capsulatus (Bath)
Thauera butanivorans
Thauera butanivorans
P. putida AlkBFG
Mycobacterium sp.
Thauera butanivorans
P. putida AlkBFG
Mycobacterium sp.
Thauera butonivorans
P. putida AlkBGT
P. putida AlkBGT
E. coli FucO
L. Reuteri PduP
E. coli Acs
P. Aeruginosa butyryl-
E. coli AdhE
E. coli MhpF
E. coli FadE
E. coli FadB
E. coli FadB
E. coli AtoB
E. coli FadA
R. eutropha BktB
S. collinus FadA
P. putida FadAx
In addition to the demonstrated activation of hydrocarbon such as pentane and hexane to the associated alcohols, the enzymes required for the conversion of these alcohols to product precursors have also been characterized. The combination of these enzymatic components provide a full route for the conversion of short chain hydrocarbons to acyl-CoA (e.g. acetyl-CoA) product precursors, which can subsequently be converted into fuels and chemicals (e.g. carboxylic acids, alcohols, hydrocarbons, and their alpha-, beta-, and omega-functionalized derivatives) through numerous product synthesis pathways, such as beta-oxidation reversal or fatty acid biosynthesis.
The enzymes described in TABLE F represent a number of examples of enzymes with required pathway activity, however this list is not representative of all available enzymes. Many additional enzymes have been shown to possess the required activities in literature and as such, can easily be integrated with the pathway framework. Furthermore, sequence similarity can also be used for the identification of additional enzymes. As an example, components of putative alkane monooxygenase system in Rhodobacter sphaeroides were identified through a BLAST using the soluble methane monoxygenase (sMMO) system of Methylococcus capsulatus (Bath). Required hydroxylase alpha (YP_352924.1) and reductase (YP_352923.1) subunits were identified, which are part of a 4 gene operon also including a hydroxylase beta subunit (YP_352922.1) and a regulatory protein (YP_352921.1). Genes encoding potential subunits this putative alkane monooxygenase have been cloned into required expression vectors as shown in
By exploiting either of these hydrocarbon activation described above, various fuels and chemicals (e.g. carboxylic acids, alcohols, hydrocarbons, and their alpha-, beta-, and omega-functionalized derivatives) can be synthesized from short-chain hydrocarbons through the metabolic pathways described and demonstrated herein.
Each of the following is incorporated by reference herein in its entirety for all purposes:
All accession numbers (generally in brackets after a gene or protein) are expressly incorporated by reference for all purposes herein. Inclusion of the information at each accession entry, would render the patent of inordinate length, and thus, incorporation of all sequences (and other information found therein) by reference is preferred. A person of ordinary skill in the art will recognize the accession numbers and be able to access them from a variety of databases.
This application is a divisional application of U.S. application Ser. No. 16/878,032, filed May 10, 2020, which is a continuation of U.S. application Ser. No. 15/562,606, filed Sep. 28, 2017, now abandoned, which is a 371 application of International Application No. PCT/US16/25103, published in English and filed on Mar. 31, 2016, which claims priority to U.S. Ser. No. 62/140,628, filed Mar. 31, 2015. The entire teachings of the above applications are incorporated herein by reference.
| Number | Date | Country | |
|---|---|---|---|
| 62140628 | Mar 2015 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 16878032 | May 2020 | US |
| Child | 18413954 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 15562606 | Sep 2017 | US |
| Child | 16878032 | US |
