Patent Application
20240352494
The present invention relates to metabolic-engineered yeast strains, such as metabolic-engineered Saccharomyces cerevisiae strains, producing high amounts of at least one, preferably all four natural cytokinins: trans-zeatin (tZ), trans-zeatin riboside (tZR), isopentenyladenine (iP) and isopentenyladenine riboside (iPR).
Cytokinins are a family of phytohormones that regulate plant growth processes. Cytokinins have a wide range of applications in crop improvement and management, such as micropropagation, general plant growth and health, and regulation of fruit size and quality (Aremu et al., 2020, Biomolecules, 10(9); Koprna et al., 2016, Bioorganic Med. Chem., 24:484-492). Trans-zeatin (tZ) and isopentenyladenine (iP) together with their sugar conjugates (glucosides and ribosides) are the most prevalent natural cytokinins. The free-base forms (tZ and iP) have stronger biological activities and higher receptor affinities than their sugar conjugates (Hoyerová and Hošek, 2020, Plant Sci., 11: 5-11; Kieber and Schaller, 2014, Arab. B., 12: c0168). However, cytokinin nucleosides such as trans-zeatin riboside (tZR) and isopentenyladenine riboside (iPR), have shown capacity to activate some specific receptors. Thus, these cytokinin nucleosides are considered as a translocation form of cytokinins between plant tissues, and can be converted into free-base forms (Sakakibara, 2006, Annu. Rev. Plant Biol., 57:431-449). Despite their potential benefits, the current high price of commercial cytokinins hampers wide applications in agriculture.
Some microorganisms, including various species of yeasts, naturally produce cytokinins. For example, Streletskii et al., (2019, PeerJ., 7: c6474), tested a collection of natural yeast strains and detected Z production in more than a half (55%) of studied strains. However, the production yields are very low (ng/g of biomass) and/or the microorganisms are not suitable for large-scale cultivation for commercial purposes.
Cytokinins precursors are obtained through the mevalonate pathway, which synthesizes isoprenoids used in a wide range of physiological processes in eukaryotes, archaea and some bacteria. A key enzyme in the isoprenoid and sterol synthesis is mevalonate kinase, which has been reported to participate in cytokinin-mediated growth and development as well as in substrate feedback and diurnal regulation (Miziorko, 2011, Archives of Biochemistry and Biophysics 505:131-143; Kasahara et al., 2004, Journal of Biological Chemistry 279:14049-14054; Åstot et al., 2000, PANS USA 97:14778-14783).
Takei et al. (2014, J. Biol. Chem., 279 (40): 41866-72) studied the biosynthesis of trans-zeatin and demonstrated that the cytokinin hydroxylases CYP735A1 and CYP735A2 are cytochrome P450 monooxygenases (P450s) that catalyze the biosynthesis of tZ. Takei et al. identified the genes from Arabidopsis using an adenosine phosphate isopentenyltransferase (AtIPT4)/P450 co-expression system in yeast. These strains were able to produce up to 3.36 mg/L of total cytokinins (tZ+(ZR+iP+iPR) in shake flask cultures.
European Patent Application Publication No. EP0248984 discloses the production of cytokinins, particularly tZ, by bacterial cells containing plasmids with insert DNA (tmr and/or tzs) isolated from Ti plasmids of Agrobacterium tumefaciens or with insert DNA isolated from a plasmid of Pseudomonas syringae pv. savastanoi (P. savastanoi). When both tmr and tza are included in the same plasmid, there is a substantial elevation in the tZ yield. This approach yielded a maximum concentration of 0.11 mg/L of tZ and 0.015 mg/L of iP.
These data reveal the necessity to improve the biosynthesis of cytokinins in microorganisms at high concentrations and productivities, enough to meet industrial standards and positioning as a feasible production method.
The present invention is directed to methodologies to produce natural cytokinins by assembly of plant-derived cytokinin pathway in yeast cells using synthetic biology and metabolic engineering tools. As exemplified hereinbelow, the genomic integration of four heterologous biosynthetic genes under galactose-inducible promoters enabled the production of large amounts of four cytokinins in yeast cells: trans-zeatin (tZ), trans-zeatin riboside (tZR), isopentenyladenine (iP), and isopentenyladenine riboside (iPR). Enhancement of precursor supply through overexpression of mevalonate pathway genes further increased cytokinin biosynthesis.
The present invention also discloses a fed-batch fermentation bioprocess of cytokinin-producing strains. The robust production method disclosed herein is based on a glucose growth phase followed by a galactose induction phase with intermittent ethanol pulses. This strategy yielded 1.5 g/L of total cytokinins with a volumetric productivity of 20 mg/L/h.
According to certain aspects, the present invention provides a genetically-modified yeast producing at least cytokinin selected from the group consisting of trans-zeatin, trans-zeatin riboside, isopentenyladenine tzar riboside and any combination thereof, the genetically modified yeast comprises a plurality of exogenous polynucleotides comprising:
According to certain embodiments, the encoded enzymes comprise amino acid sequence of plant enzymes, fungal enzymes, homologs thereof or any combination thereof. Each possibility represents a separate embodiment of the present invention.
According to certain embodiments, the encoded enzymes are of a plant origin or enzymes homologous thereto.
According to certain exemplary embodiments, the plant is Arabidopsis thaliana.
In some embodiments, the encoded isopentenyl transferase comprises an amino acid sequence having at least 80% identity to the amino acid sequence of A. thaliana IPT4. In some embodiments, the encoded isopentenyl transferase comprises the amino acid sequence of A. thaliana IPT4. In some embodiments, the A. thaliana IPT4 comprises the amino acid sequence set forth in SEQ ID NO:1.
In some embodiments, the encoded cytokinin hydroxylase comprises an amino acid sequence having at least 80% identity to the amino acid sequence of A. thaliana CYP735A1. In some embodiments, the encoded cytokinin hydroxylase comprises the amino acid sequence of A. thaliana CYP735A1. In some embodiments, the A. thaliana CYP735A1 comprises the amino acid sequence set forth in SEQ ID NO:2.
In some embodiments, the NADPH-cytochrome P450 reductase comprises an amino acid sequence having at least 80% identity to the amino acid sequence of A. thaliana ATR1. In some embodiments, the encoded NADPH-cytochrome P450 reductase comprises the amino acid sequence of the A. thaliana ATR1. In some embodiments, the A. thaliana ATR1 comprises the amino acid sequence set forth in SEQ ID NO:3.
In some embodiments, the cytokinin riboside 5′-monophosphate phosphoribohydrolase comprises an amino acid sequence having at least 80% identity to the amino acid sequence of A. thaliana LOG7. In some embodiments, the encoded cytokinin riboside 5′-monophosphate phosphoribohydrolase comprises the amino acid sequence of A. thaliana LOG7. In some embodiments, the A. thaliana LOG7 comprises the amino acid sequence set forth in SEQ ID NO:4.
In some embodiments, the genetically-modified yeast comprises: (i) an exogenous polynucleotide encoding an isopentenyl transferase having at least 80% identity to the amino acid sequence of A. thaliana IPT4; (ii) an exogenous polynucleotide encoding a cytokinin hydroxylase having at least 80% identity to the amino acid sequence of A. thalianaCYP735A1; (iii) an exogenous polynucleotide encoding NADPH-cytochrome P450 reductase having at least 80% identity to the amino acid sequence of A. thaliana ATR1; and
In some embodiments, the genetically-modified yeast comprises: (i) an exogenous polynucleotide encoding A. thaliana IPT4; (ii) an exogenous polynucleotide encoding A. thaliana CYP735A1; (iii) an exogenous polynucleotide encoding A. thaliana ATR1; and (iv) an exogenous polynucleotide encoding A. thaliana LOG7.
In some embodiments, the yeast is Saccharomyces cerevisiae and the polynucleotides are optimized for expression in this yeast. In some embodiments, the yeast is Saccharomyces cerevisiae comprising an exogenous polynucleotide encoding A. thalianaIPT4 comprising the nucleic acid sequence set forth in SEQ ID NO:8. In some embodiments, the yeast is Saccharomyces cerevisiae comprising an exogenous polynucleotide encoding
A. thaliana CYP735A1 comprising the nucleic acid sequence set forth in SEQ ID NO:9. In some embodiments, the yeast is Saccharomyces cerevisiae comprising an exogenous polynucleotide encoding A. thaliana ATR1 comprising the nucleic acid sequence set forth in SEQ ID NO:10. In some embodiments, the yeast is Saccharomyces cerevisiae comprising an exogenous polynucleotide encoding A. thaliana LOG7 comprising the nucleic acid sequence set forth in SEQ ID NO: 11.
In some embodiments, the yeast is Saccharomyces cerevisiae comprising: an heterologous polynucleotide encoding A. thaliana IPT4 comprising the nucleic acid sequence set forth in SEQ ID NO:8; an heterologous polynucleotide encoding A. thaliana CYP735A1 comprising the nucleic acid sequence set forth in SEQ ID NO:9; an heterologous polynucleotide encoding A. thaliana ATR1 comprising the nucleic acid sequence set forth in SEQ ID NO:10; and a heterologous polynucleotide encoding A. thaliana LOG7 comprising the nucleic acid sequence set forth in SEQ ID NO:11.
In some embodiments, each of the plurality of the exogenous polynucleotides or a combination thereof is comprised within an expression cassette further comprising at least one regulatory element. The at least one regulatory element can be operably linked to each of the exogenous polynucleotides a combination of the exogenous polynucleotides can be operably linked to a single at least one regulatory element. The combination may include two, three or all four heterologous polynucleotides.
In some embodiments, the regulatory element is selected from a promoter, an enhancer, a termination sequence and any combination thereof.
In some embodiments, the promoter is an inducible promoter. In some particular embodiments, the promoter is a galactose-inducible promoter.
In some embodiments, the yeast is Saccharomyces cerevisiae comprising: an expression cassette encoding A. thaliana IPT4 comprising the nucleic acid sequence set forth in SEQ ID NO: 15; an expression cassette encoding A. thaliana CYP735A1 comprising the nucleic acid sequence set forth in SEQ ID NO: 16; an expression cassette encoding A. thaliana ATR1 comprising the nucleic acid sequence set forth in SEQ ID NO:17; and an expression cassette encoding A. thaliana LOG7 comprising the nucleic acid sequence set forth in SEQ ID NO:18. In some embodiments, the expression cassettes are arranged in a single polynucleotide molecule. In some particular embodiments, the single polynucleotide molecule comprises the nucleic acid sequence set forth in SEQ ID NO:25.
In some embodiments, a genetically-modified yeast of the present invention further comprises at least one additional exogenous polynucleotide selected from the group consisting of;
In some embodiments, the genetically-modified yeast further comprises: an exogenous polynucleotide encoding an amino-terminal truncated HMG-COA reductase having at least 80% identity to the amino acid sequence of Saccharomyces cerevisiae amino-terminal truncated HMG-COA reductase (Sc-tHMG1); and an exogenous polynucleotide encoding an amino-terminal truncated HMG-COA reductase 1 having at least 80% identity to the amino acid sequence of Xanthophyllomyces dendrorhous amino-terminal truncated HMG-COA reductase (Xd-tHMG1).
In some embodiments, the genetically-modified yeast further comprises an exogenous polynucleotide encoding Sc-tHMG1 and an exogenous polynucleotide encoding Xd-tHMG1.
In some exemplary embodiments, the Sc-tHMG1 comprises the amino acid sequence set forth in SEQ ID NO:5, and the Xd-tHMG1 comprises the amino acid sequence set forth in SEQ ID NO:6.
In some embodiments, the isopentenyl isomerase comprises an amino acid sequence having at least 80% identity to the amino acid sequence of S. cerevisiae isopentenyl isomerase (IDI1). In some embodiments, the isopentenyl isomerase is S. cerevisiae IDI1. In some particular embodiments, the S. cerevisiae IDI1 comprises the amino acid sequence set forth in SEQ ID NO:7.
In some embodiments, the genetically-modified yeast further comprises:
In some embodiments, the genetically-modified yeast further comprises:
In some embodiments, the genetically-modified yeast comprises: (i) an exogenous polynucleotide encoding A. thaliana IPT4; (ii) an exogenous polynucleotide encoding A. thaliana CYP735A1; (iii) an exogenous polynucleotide encoding A. thaliana ATR1; and (iv) an exogenous polynucleotide encoding A. thaliana LOG7; (v) an exogenous polynucleotide encoding Sc-tHMG1; (vi) an exogenous polynucleotide encoding Xd-tHMG1; and (vii) an exogenous polynucleotide encoding S. cerevisiae IDI1
In some embodiments, the yeast is Saccharomyces cerevisiae and the polynucleotides are codon optimized for expression in this yeast. In some embodiments, the yeast is Saccharomyces cerevisiae comprising an exogenous polynucleotide encoding Sc-tHMG1 comprising the nucleic acid sequence set forth in SEQ ID NO:12. In some embodiments, the yeast is Saccharomyces cerevisiae comprising an exogenous polynucleotide encoding Xd-tHMG1 comprising the nucleic acid sequence set forth in SEQ ID NO: 13. In some embodiments, the yeast is Saccharomyces cerevisiae comprising an exogenous polynucleotide encoding S. cerevisiae IDI1 comprising the nucleic acid sequence set forth in SEQ ID NO:14.
In some embodiments, the yeast is Saccharomyces cerevisiae further comprising: an exogenous polynucleotide encoding Sc-tHMG1 comprising the nucleic acid sequence set forth in SEQ ID NO:12; an exogenous polynucleotide encoding Xd-tHMG1 comprising the nucleic acid sequence set forth in SEQ ID NO:13; and an exogenous polynucleotide encoding S. cerevisiae IDI1 comprising the nucleic acid sequence set forth in SEQ ID NO: 14.
In some embodiments, each of the plurality of the exogenous polynucleotides or a combination thereof is comprised within an expression cassette further comprising at least one regulatory element. In some embodiments, the regulatory element is selected from a promoter, an enhancer, a termination sequence and any combination thereof. In some embodiments, the promoter is an inducible promoter. In some particular embodiments, the promoter is a galactose-inducible promoter. In other particular embodiments, the promoter is a constitutive promoter.
In some embodiments, the yeast is Saccharomyces cerevisiae further comprising: an expression cassette encoding Sc-tHMG1 comprising the nucleic acid sequence set forth in SEQ ID NO:22; an expression cassette encoding Xd-tHMG1 comprising the nucleic acid sequence set forth in SEQ ID NO:23; and an expression cassette encoding S. cerevisiae IDI1 comprising the nucleic acid sequence set forth in SEQ ID NO:24.
In some embodiments, the yeast is Saccharomyces cerevisiae further comprising: an expression cassette encoding Sc-tHMG1 comprising the nucleic acid sequence set forth in SEQ ID NO: 19; an expression cassette encoding Xd-tHMG1 comprising the nucleic acid sequence set forth in SEQ ID NO: 20; and an expression cassette encoding S. cerevisiaeIDI1 comprising the nucleic acid sequence set forth in SEQ ID NO: 21.
In some embodiments, the expression cassettes are arranged in a single polynucleotide molecule. In some particular embodiments, the single polynucleotide molecule comprises a nucleic acid sequence selected from SEQ ID NO: 27 and SEQ ID NO: 28. Each possibility represents a separate embodiment of the present invention.
In some embodiments, a genetically-modified yeast of the present invention comprises at least one additional copy of one or more of the exogenous polynucleotides encoding the cytokinin hydroxylase, NADPH-cytochrome P450 reductase and cytokinin riboside 5′-monophosphate phosphoribohydrolase.
In some embodiments, a genetically-modified yeast of the present invention comprises an additional copy of each of the exogenous polynucleotides encoding the cytokinin hydroxylase, NADPH-cytochrome P450 reductase and cytokinin riboside 5′-monophosphate phosphoribohydrolase.
In some embodiments, the additional copies of the heterologous polynucleotides encoding the cytokinin hydroxylase, NADPH-cytochrome P450 reductase and cytokinin riboside 5′-monophosphate phosphoribohydrolase are arranged in a single polynucleotide molecule. In some embodiments, the single polynucleotide molecule comprising the nucleic acid sequence set forth in SEQ ID NO:26.
In some embodiments, the yeast is Saccharomyces cerevisiae further comprising: an exogenous polynucleotide comprising the sequence set forth in SEQ ID NO:25 and an exogenous polynucleotide comprising the sequence set forth in SEQ ID NO:28. In some embodiments, the yeast further comprises an exogenous polynucleotide comprising the sequence set forth in SEQ ID NO:26.
According to another aspect, the present invention provides a method for producing at least one cytokinin selected from the group consisting of trans-zeatin, trans-zeatin riboside, isopentenyladenine and isopentenyladenine riboside and any combination thereof, the method comprising:
In some embodiments, step (A) comprises providing a genetically-modified yeast in which the exogenous polynucleotides are expressed under a galactose-inducible promoter, and the culturing in step (B) is performed by fed-batch fermentation process comprising a glucose growth phase followed by a galactose induction phase with intermittent ethanol pulses.
In some embodiments, at least 60% (w/w) of the produced cytokinins are trans-zeatin and isopentenyladenine. In additional embodiments, at least 70% (w/w) of the produced cytokinins are trans-zeatin and isopentenyladenine.
According to a further aspect, the present invention provides an expression cassette for genetically-modifying a yeast, comprising at least one regulatory element operably-linked to a nucleic acid sequence selected from the group consisting of:
According to certain embodiments, the encoded enzymes comprise amino acid sequence of plant enzymes, fungal enzymes, a combination thereof and homologs thereto. Each possibility represents a separate embodiment of the present invention.
According to certain embodiments, the encoded enzymes are of a plant origin or enzymes homologous thereto.
According to certain embodiments, the plant is A. thaliana.
According to certain embodiments, the nucleic acid sequence encoding the A. thaliana enzyme is codon optimized for expression in Saccharomyces cerevisiae.
In some exemplary embodiments, the nucleic acid sequence is selected from the group consisting of:
In some embodiments, the at least one regulatory element comprises an inducible promoter. In some embodiments, the promoter is a galactose-inducible promoter. In some embodiments, the promoter is a galactose-inducible promoter and the expression cassette is selected from the group consisting of: an expression cassette for expressing A. thaliana IPT4 comprising the sequence set forth in SEQ ID NO:15; an expression cassette for expressing A. thaliana CYP735A1 comprising the sequence set forth in SEQ ID NO:16; an expression cassette for expressing A. thaliana ATR1 comprising the sequence set forth in SEQ ID NO: 17; and an expression cassette for expressing A. thaliana LOG7 comprising the sequence set forth in SEQ ID NO:18.
According to a further aspect, the present invention provides a nucleic acid construct for genetically-modifying a yeast to produce cytokinins comprising a plurality of expression cassettes, the plurality of expression cassettes comprising: an expression cassette for expressing A. thaliana IPT4 comprising the sequence set forth in SEQ ID NO: 15; an expression cassette for expressing A. thaliana CYP735A1 comprising the sequence set forth in SEQ ID NO:16; an expression cassette for expressing A. thaliana ATR1 comprising the sequence set forth in SEQ ID NO: 17; and an expression cassette for expressing A. thaliana LOG7 comprising the sequence set forth in SEQ ID NO:18.
In some embodiments, there is provided herein a vector for transforming a yeast cell to produce cytokinins, the vector comprising the nucleic acid construct, flanked by 5′ and 3′ yeast genomic integrating sequences. In some particular embodiments, the vector comprises a sequence selected from SEQ ID NO:29 and SEQ ID NO:30. Each possibility represents a separate embodiment of the present invention.
According a further aspect, the present invention provides a yeast that produces one or more of the following cytokinins: trans-zeatin, trans-zeatin riboside, isopentenyladenine and isopentenyladenine riboside, the method comprising transforming the yeast with a plurality of exogenous polynucleotides according to the present invention.
In some embodiments, the method further comprises transforming the yeast with at least one additional exogenous polynucleotide selected from the group consisting of: (A) one or more exogenous polynucleotide encoding an amino-terminal truncated HMG-COA reductase lacking the transmembrane domain; and (B) an exogenous polynucleotide encoding an isopentenyl isomerase.
In some embodiments, the yeast is further transformed with:
In some particular embodiments, the yeast is transformed with: an exogenous polynucleotide encoding Sc-tHMG1 comprising the nucleic acid sequence set forth in SEQ ID NO: 12; an exogenous polynucleotide encoding Xd-tHMG1 comprising the nucleic acid sequence set forth in SEQ ID NO:13; and an exogenous polynucleotide encoding S. cerevisiae IDI1 comprising the nucleic acid sequence set forth in SEQ ID NO: 14.
In some embodiments, the method further comprises transforming the yeast with an additional copy of each of the exogenous polynucleotides encoding the cytokinin hydroxylase, NADPH-cytochrome P450 reductase and cytokinin riboside 5′-monophosphate phosphoribohydrolase.
In some embodiments, the yeast is Saccharomyces cerevisiae.
These and further aspects and features of the present invention will become apparent from the detailed description, examples, and claims which follow.
The present invention provides metabolically-engineered yeast strains, such as metabolically-engineered Saccharomyces cerevisiae strains, producing high amounts of at least one natural cytokinins, preferably four natural cytokinins selected from the group consisting of:
Trans-zeatin ((Z), trans-zeatin riboside (tZR), isopentenyladenine (iP) and isopentenyladenine riboside (iPR) belongs to the isoprenoids cytokinin family. These cytokinins are prenylated derivatives of adenine (
In plants, cytokinins are biosynthesized starting from ATP or ADP. First, adenosine phosphate-isopentenyltransferases (IPT), catalyzes the N-prenylation of ADP or ATP using dimethylallyl diphosphate (DMAPP) as prenyl donor to form isopentenyl nucleotides (iPRTP, iPRDP). These isopentenyl nucleotides can be hydroxylated at the terminal carbon of prenyl side chain by specific cytokinin hydroxylase (cytochrome P450 monooxygenases family), generating trans-zeatin nucleotides (tZRTP, tZRDP, and (ZRMP). The tri-and di-phosphorylated iP and tZ nucleotides are dephosphorylated to iPRMP and tZRMP by enzymes of nucleotide metabolism. These monophosphate CK-nucleotides can be dephosphorylated again to yield the cytokinins nucleosides forms (tZR and iPR), or LOG enzymes can directly hydrolyze the phospho-ribose group to produce the free cytokinins (tZ and iP) (Kamada-Nobusada and Sakakibara, 2009, Phytochemistry, 70: 444-449; Kieber and Schaller, 2014, Arab. B., 12, c0168).
Several fungi species, particularly plant-pathogenic fungi, are also capable to produce cytokinins (e.g., Eisermann et al., 2020. Fungal Genetics and Biology 143:103436; Chanclud et al., 2016. PLOS Pathogens 12(2): e1005457).
The construction of cytokinin-producing yeast strains as disclosed herein comprises the expression of at least four heterologous, genes of plant origin: an isopentenyl transferase (EC 2.5.1.112), a cytokinin hydroxylase (EC 1.14.13), an NADPH-cytochrome P450 reductase (EC 1.6.2.4), and a cytokinin riboside 5′-monophosphate phosphoribohydrolase (EC 3.2.2.n1). The expression of an NADPH-cytochrome P450 reductase is intended to promote a more efficient electron transfer between NADPH and the cytokinin hydroxylase.
In some embodiments, the genes are Arabidopsis thaliana genes or polynucleotides homologous thereto. In certain embodiments, yeasts of the present invention comprise exogenous polynucleotides encoding enzymes having at least 80% identity to the amino acid sequence of A. thaliana enzymes, for example at least 85%, at least 90%, at least 95%, at least 97%, at least 99% or 100% identity to the amino acid sequence of A. thaliana enzymes. Each possibility represents a separate embodiment of the present invention.
In some embodiments, yeasts of the present invention comprise exogenous polynucleotides encoding A. thaliana enzymes.
In some particular embodiments, cytokinin-producing yeasts of the present invention comprise exogenous polynucleotides encoding the following A. thaliana enzymes: isopentenyl transferase 4 (IPT4), cytokinin hydroxylase CYP735A1, NADPH-cytochrome P450 reductase ATR1, and cytokinin riboside 5′-monophosphate phosphoribohydrolase 7 (LOG7).
As disclosed herein, product yield and productivities of cytokinin-producing yeasts of the present invention are improved by increasing DMAPP supply through MVA pathway enhancement. In some embodiments, cytokinin-producing yeasts of the present invention are further genetically modified by overexpression of amino-terminal truncated version of HMG-COA reductase (tHMG1) (EC 1.1.1.34) and isopentenyl isomerase (IDI1) (EC 5.3.3.2). In additional embodiments, cytokinin-producing yeasts of the present invention are further genetically modified by expression of additional copies of cytokinin biosynthetic genes. As disclosed herein, the latter is useful for controlling cytokinin proportions.
To further increase cytokinin concentrations and volumetric productivities, the cytokinin-producing yeasts of the present invention may be grown in a fed-batch fermentation process comprising a glucose growth phase followed by a galactose induction phase with intermittent ethanol pulses. A glucose exponential growth phase comprises culturing the cells in a medium containing glucose as a carbon source until high biomass is reached. A galactose induction phase with intermittent ethanol pulses comprises culturing the cells in a medium containing galactose as a carbon source, and providing ethanol to the medium at predefined intervals. In some embodiments, the intervals are defined based on an approximate consumption rate by the cell culture. In some embodiments, the intervals are between 5-15 hours, including each value within the range, for example between 10-12 hours, including each value within the range. In some exemplary embodiments, intervals of 10 hours are selected.
In some embodiments, at least 60% (w/w) of the total cytokinins produced according to the present invention are trans-zeatin and isopentenyladenine. In additional embodiments, 60-80% of the total cytokinins produced according to the present invention are trans-zeatin and isopentenyladenine. In additional embodiments, at least 70% (w/w) of the total cytokinins produced according to the present invention are trans-zeatin and isopentenyladenine, for example, at least 75%, at least 78%, between 70%-85%, between 75%-85%, between 70%-80% or between 75%-80% trans-zeatin and isopentenyladenine out of the total cytokinins (w/w). Each possibility represents a separate embodiment of the present invention.
Yeast species for use according to the present invention include S. cerevisiae, Pichia pastoris, Hansenula polymorpha, Kluyveromyces lactis and Yarrowia lipolytica. Each possibility represents a separate embodiment of the present invention. In some embodiments, a yeast of the present invention is S. cerevisiae.
In some embodiments, the genetically-modified yeasts of the present invention produce the cytokinins at increased amounts compared to a corresponding non-genetically modified yeast.
The term “heterologous”, when referring to a gene or a protein (polynucleotide or polypeptide), is used herein to describe a gene/polynucleotide or a protein/polypeptide that is not naturally found or expressed in the specific organism being referred to as expressing the polynucleotide or polypeptide, for example a yeast transformed according to the present invention.
The term “exogenous”, when referring to a polynucleotide, is used herein to describe a synthetic polynucleotide that is exogenously introduced into a yeast cell via transformation, so as to produce a ribonucleic acid (RNA) molecule and subsequently a polypeptide molecule. The exogenous polynucleotide can be heterologous polynucleotide as defined hereinabove or an endogenous polynucleotide exogenously introduced into the yeast cell, either under endogenous or exogenous regulatory elements. The exogenous polynucleotide may be introduced into the yeast in a stable or transient manner, so as to produce a ribonucleic acid (RNA) molecule and/or a polypeptide molecule. The term “endogenous” as used herein refers to a polynucleotide or polypeptide which is naturally present and/or naturally expressed within a specific organism.
The term “expression cassette” is used herein to describe an artificially assembled nucleic acid molecule which includes a nucleic acid sequence encoding a protein of interest and which is assembled such that the protein of interest is expressed in a target host cell. An expression cassette typically comprises appropriate regulatory sequences operably linked to the nucleic acid sequence encoding the protein of interest. An expression cassette may further include a nucleic acid sequence encoding a selection marker.
The terms “nucleic acid sequence”, “nucleotide sequence” and “polynucleotide” are used herein to refer to polymers of deoxyribonucleotides (DNA), ribonucleotides (RNA), and modified forms thereof in the form of a separate fragment or as a component of a larger construct. A nucleic acid sequence may be a coding sequence, i.e., a sequence that encodes for an end product in the cell, such as a protein. A nucleic acid sequence may also be a regulatory sequence, such as, for example, a promoter.
The terms “peptide”, “polypeptide” and “protein” are used herein to refer to a polymer of amino acid residues. The term “peptide” typically indicates an amino acid sequence consisting of 2 to 50 amino acids, while “protein” indicates an amino acid sequence consisting of more than 50 amino acid residues.
A sequence (such as a nucleic acid sequence and an amino acid sequence) that is “homologous” to a reference sequence refers herein to percent identity between the sequences, where the percent identity is at least 80%, at least 85%, at least 90%, at least 95%, at least 98% or at least 99%. Each possibility represents a separate embodiment of the present invention. Homologs of the sequences described herein are encompassed within the present invention. Protein homologs are encompassed as long as they maintain the activity of the original protein. Homologous nucleic acid sequences include variations related to codon usage and degeneration of the genetic code. Sequence identity may be determined using nucleotide/amino acid sequence comparison algorithms, as known in the art.
The phrase “codon optimization” refers to the selection of appropriate DNA nucleotides for use within a structural gene or fragment thereof that approaches codon usage within the organism of interest, and/or to a process of modifying a nucleic acid sequence for enhanced expression in the host cell of interest by replacing at least one codon (e.g., about or more than about 1, 2, 3, 4, 5, 10, 15, 20, 25, 50, or more codons) of the native sequence with codons that are more frequently or most frequently used in the genes of that host cell while maintaining the native amino acid sequence. Various species exhibit particular bias for certain codons of a particular amino acid. Accordingly, genes can be tailored for optimal gene expression in a given organism based on codon optimization. Therefore, an optimized gene or nucleic acid sequence refers to a gene in which the nucleotide sequence of a native or naturally occurring gene has been modified in order to utilize statistically preferred or statistically-favored codons within the organism. The present invention explicitly encompasses polynucleotides encoding an enzyme of interest as disclosed herein which are codon optimized for expression in a yeast to be transformed according to the present invention, e.g., in Saccharomyces cerevisiae.
The term “regulatory elements” or “regulatory sequences” are used herein to describe DNA sequences which control the expression (transcription) of coding sequences, such as promoters and terminators. The regulatory elements used herein are suitable for use in a yeast to be transformed according to the present invention (e.g., in Saccharomyces cerevisiae) namely, capable of directing gene expression in the yeast.
The term “promoter” is directed to a regulatory DNA sequence which controls or directs the transcription of another DNA sequence in vivo or in vitro. Usually, the promoter is located in the 5′ region (that is, precedes, located upstream) of the transcribed sequence.
Promoters may be derived in their entirety from a native source, or be composed of different elements derived from different promoters found in nature, or even comprise synthetic nucleotide segments. Promoters can be constitutive (i.e., promoter activation is not regulated by an inducing agent and hence rate of transcription is constant), or inducible (i.e., promoter activation is regulated by an inducing agent). In most cases the exact boundaries of regulatory sequences have not been completely defined, and in some cases cannot be completely defined, and thus DNA sequences of some variation may have identical promoter activity.
The term “terminator” is directed to another regulatory DNA sequence which regulates transcription termination. A terminator sequence is operably linked to the 3′ terminus of the nucleic acid sequence to be transcribed.
The term “operably linked” means that a selected nucleic acid sequence is in proximity with a regulatory element (promoter or terminator) to allow the regulatory element to regulate expression of the selected nucleic acid sequence.
A plurality of expression cassettes may be assembled together into a single nucleic acid construct. Expression cassettes/nucleic acid constructs are further constructed into vectors enabling transformation into the host cells.
Expression cassettes, constructs and vectors may be assembled by a variety of different methods, including conventional molecular biology methods such as polymerase chain reaction (PCR), restriction endonuclease digestion, in vitro and in vivo assembly methods, as well as gene synthesis methods, or a combination thereof. Exemplary expression cassettes, constructs and vectors, and methods for their construction, are provided below.
In some embodiments of the present invention, there is provided a design of heterologous cytokinin pathway in S. cerevisiae. The overall sequence of events in said pathway is as follows: Hexoses such as glucose and galactose are metabolized to pyruvate by the glycolytic pathway, which is then transformed to cytosolic acetyl-CoA in three sequential reactions. Acetyl-CoA is converted to isopentenyl diphosphate (IPP) and its isomer DMAPP by the endogenous mevalonate pathway (MVA). DMAPP and ATP/ADP are then incorporated to the cytokinin pathway by the expression of heterologous genes: IPT4, CYP735A1, ATR1, and LOG7 (dashed arrows,
A strong cytokinin pathway flux could dramatically deplete the total adenine nucleotides pool. In order to avoid possible negative impact on strain fitness and process robustness, expression of the cytokinin biosynthetic genes under the control of inducible promoters is currently preferred. With this approach, the yeast can achieve enough biomass before producing the cytokinins, reducing the metabolic burden in the growth phase. In some exemplary embodiments, an inducible promoter suitable for use according to the present invention is a galactose-inducible promoter. Additional inducible promoters that may be used include, for example: copper-inducible CUP1 in S. cerevisiae, methanol-inducible AOX1 in P. Pastoris, and erythritol-inducible EYD1/EYK1 or fatty acid-inducible POX2 in Y. lipolytica. Each possibility represents a separate embodiment of the present invention.
The following sections describe exemplary vectors and cloning for generating cytokinin-producing S. cerevisiae strains according to some embodiments of the present invention. The cytokinin-producing S. cerevisiae strains described below express the following A. thaliana enzymes: IPT4, CYP735A1, ATR1 and LOG7. Further described are exemplary vectors and cloning for generating cytokinin-producing S. cerevisiae strains that express amino-terminal truncated versions of HMG-COA reductase lacking the transmembrane domain (a truncated version of the endogenous S. cerevisiae HMG-COA reductase and a truncated version of the HMG-COA reductase of Xanthophyllomyces dendrorhous) and over-express the endogenous S. cerevisiae isopentenyl isomerase (IDI1). Further described are exemplary vectors and cloning for generating cytokinin-producing S. cerevisiae strains that also express additional copies of CYP735A1, ATR1, and LOG7.
The amino acid sequence of IPT4 is set forth as SEQ ID NO: 1 (UniProt accession no. Q9SB60). The amino acid sequence of CYP735A1 is set forth as SEQ ID NO: 2 (UniProt accession no. Q9FF18). The amino acid sequence of ATR1 is set forth as SEQ ID NO: 3 (UniProt accession no. Q9SB48). The amino acid sequence of LOG7 is set forth as SEQ ID NO: 4 (UniProt accession no. Q8GW29). The amino acid sequence of S. cerevisiae truncate-HMG1 (Sc-tHMG1) is set forth as SEQ ID NO: 5 (Partial sequence of UniProt accession no. P12683). The amino acid sequence of Xanthophyllomyces dendrorhous truncated-HMG1 (Xd-tHMG1) is set forth as SEQ ID NO: 6 (Partial sequence of UniProt accession no. A0A5B8KS46). The amino acid sequence of S. cerevisiae IDI1 is set forth as SEQ ID NO: 7 (UniProt accession no. P15496). Table 1 shows the amino acid and gene sequences used in this invention.
DNA polynucleotide sequences encoding the enzymes, codon-optimized for expression in S. cerevisiae (SEQ ID NO 8-14), were assembled in integrative yeast expression vectors. For this purpose, expression vectors were built employing Loop assembly method (Pollak et al., 2019, New Phytol., 222, 628-640; Pollak et al., 2020, Synth. Biol., 5 (1): ysaa001), which is based in Golden Gate cloning technique. The workflow included sequential assembly of DNA modules in different vectors termed Level 1 (L1), Level 2 (L2), and Level 3 (L3). Using this workflow, the polynucleotide sequences encoding the four enzymes were first cloned into entry vectors by the Gibson Assembly method. Then, transcriptional units for each gene (promoter-gene-terminator) were assembled into L1 vectors. For synthesizing L2 vectors, L1 units were joined together to arrange the whole biosynthetic pathway in a single construct. Finally, in L3 vectors, the L2 constructs were flanked between genomic integrating sequences. These L3 vectors were the final constructs used to transform the yeast cells and generate the cytokinin-producing strains. FIG. 3 illustrates an example map of L3 vectors. Table 2 shows the list and description of the constructed vectors, while Appendix I shows the sequences of the functional constructs which were assembled into these vectors.
A. thaliana IPT4 amino acid sequence
A. thaliana CYP735A1 amino acid sequence
A. thaliana ATR1 amino acid sequence
A. thaliana LOG7 amino acid sequence
S. cerevisiae truncated-HMG1 (Sc-tHMG1) amino acid
X. dendrorhous truncated-HMG1 (Xd-tHMG1) amino acid
S. cerevisiae IDI1 amino acid sequence
The L3 vectors were transformed into the parent yeast strain CEN.PK113-5D (genotype MATa ura3-52 HIS3, LEU2 TRP1 MAL2-8c SUC2) by CRISPR/Cas9 technology (Jakočiunas et al., 2016, Metab. Eng., 34:44-59; Shaw and Ellis, 2017, Quick and easy CRISPR engineering in Saccharomyces cerevisiae. This system requires incorporating three vectors into the yeast cells: a Cas9 containing vector, a guide RNA (gRNA) containing vector, and the cytokinin pathway L3 integrating vector. The three vectors were linearized by enzyme digestion and transformed by LiAc/PEG/ssDNA method (Gietz, 2014, Yeast transformation by the LiAc/SS carrier DNA/PEG method, in: Yeast Genetics. Humana Press, New York, pp. 1-12). Cas9 and sgRNA together carried out the double-strand break into the specific integrating site of the yeast genome. The latter facilitates the integration of the cytokinin pathway construct by homologous recombination in this specific site.
The transformants were selected in complete synthetic media without uracil (SC-URA). The isolation of the transformants that integrated the constructs were performed by genomic PCR of several colonies. These PCRs were carried out using primers which amplified regions between integration sites and different inner sites of the constructs (e.g., promoters and terminators). Three to five colonies of each constructed strain were selected and cultivated in shake flasks to test cytokinin production. Recycling of the selection marker was performed by serial cultivation of the strains in YPD until the loss of Cas9 episomal vectors, which carried the URA3 gene. Colonies that fail to grow in SC-URA were used for the next transformation rounds.
Table 3 summarizes the four constructed strains. CK1 strain contains the whole cytokinin pathway (IPT4, CYP735A1, ATR1, and LOG1) arranged in tandem transcriptional units and integrated at XI-5 site (chromosome XI, site 5). The four transcriptional units were placed under the control of galactose-inducible promoters. Different promoters and terminators were used for each transcriptional unit in order to avoid homologous recombination and ensure strain stability. CK1 was used as parent strain to construct CK2.1 by the integration of MVA enhancement construct in X-2 site. This construct consisted in two copies of tHMG1 gene (one from S. cerevisiae and other from X. dendrorhous) and one copy of IDI1 gene, all under the control of strong constitutive promoters. Similarly, CK.2.2 strains were built to enhance MVA pathway in CK1, but in this case, using a galactose-inducible version of the MVA enhancement construct. Finally, CK3.1 strain was generated by the transformation of CK2.1 with a construct that expressed additional copies of CYP735A1, ATR1, and LOG7, also under galactose-inducible promoters.
S cerevisiae strains constructed for the heterologous production of cytokinins
GAL1
CYP735A1_TCPS1
The following examples are presented in order to more fully illustrate certain embodiments of the invention. They should in no way, however, be construed as limiting the broad scope of the invention. One skilled in the art can readily devise many variations and modifications of the principles disclosed herein without departing from the scope of the invention.
By preliminary analysis of several transformants of CK1 strain generated as described above, two clearly differentiated cytokinin-producing phenotypes were detected, named as CK1-A and CK1-B. The sub-strains were grown in baffled shake flasks, containing YPDG medium (1% yeast extract, 2% peptone, 1% glucose, and 1% galactose) at 30° C. and 160 rpm. The cultures were sampled at 48 h and the fermented culture media was analyzed by HPLC-DAD. This method quantifies trans-zeatin (tZ), trans-zeatin riboside ((ZR), isopentenyladenine (iP), and isopentenyladenine riboside (iPR). The method is summarized as follow:
Exemplary HPLC-DAD analysis of fermented medium from CK1-B sub-strain in the presence or absence of induction is shown in
For a more detailed analysis of both phenotypes CK1-A and CK1-B, three independent transformants of each strain were cultivated in triplicate in baffled shake flasks, containing YPDG media with different glucose/galactose ratios. The cultures were sampled at 24 and 48 h (
Overall, CK-1B produced higher concentrations of total cytokinins than CK1-A. The strain production varied in response to the different induction strategies (namely, different ratios of glucose/galactose in the culture medium). As seen in
In order to characterize the kinetics of the CK-1B strain, a batch fermentation was carried out in benchtop bioreactor. The fermentation was performed in 700 mL of YPDG medium containing 2% peptone, 1.5% yeast extract, 1.5% of glucose, and 1.5% galactose. A SIMATIC PCS7 control system was used to monitor and control the cultivations at 30° C., pH=5.0, and dissolved oxygen above 2.8 mg/L. After 32 hours fermentation, the culture was supplemented with a pulse of 2% galactose. Culture samples were periodically collected for quantification of biomass, sugars, ethanol, and cytokinins.
The results are presented in
Cytokinin production parameters achieved in this fermentation are presented in Table 4. The strain CK1-B produced up to 94.6 mg/L of total cytokinins after 73 hours of fermentation with predominance of tZ (68.6 mg/L). The volumetric productivities were 1.67 mg/L/h of total cytokinins and 1.13 mg/L/h of tZ.
The carbon flux through the native MVA pathway could be restricting the DMAPP availability and consequently limiting the cytokinin biosynthesis in CK1 strains. To increase MVA pathway flux, two copies of tHMG1 gene were overexpressed. Additionally, IDI1 gene was overexpressed to enhances IPP/DMAPP isomerization. The expression of these genes was carried out by the integration of the MVA enhancement construct (Table 3) in both constitutive and galactose-inducible variants to generate the strains CK2.1 and CK2.2, respectively. The strains were cultivated in triplicate in baffled shake flasks containing YPDG (1% glucose, 1% galactose).
The results are shown in
As an example of how cytokinin proportion can be redistributed by the expression of additional copies of the cytokinin pathway, a construct harboring CYP735A, ATR1 and LOG7 was integrated in CK2.1 strain. The resulting strain, CK3.1, showed a 1.6-fold increase in tZ and a 1.3-fold decrease iP concentrations. The expression of an extra copy of cytokinin hydroxylase system (CYP735A/ATR1) without extra expression of IPT4 redirected the flux to hydroxylated cytokinins. This result illustrates how the pathway can be adjusted in order to control the cytokinin ratios depending on the desired application of the product.
To further increase cytokinin production, the highest producing strain CK2.2 was scaled to high-density cultures in 1 L bioreactors. A SIMATIC PCS7 control system was used to monitor and control the cultivations at 30° C., pH=5.0, and dissolved oxygen above 2.8 mg/L. Ammonium hydroxide (25% m/m) was used to automatically control the pH. Excessive foam formation was prevented by the use of liquid silicone 10% v/v when required. The dissolved oxygen was maintained above 2.6 mg/L by an automatic algorithm which controls agitation (160-280 rpm), air flux, and pure oxygen flux. The total gas flux was maintained between 0.4-0.5 L/min, varying the percent of air and pure oxygen depending on the culture demand. Gas outflux was measured using a Blue Vary gas sensor (BlueSens). The media employed for the fermentation are detailed in Table 5. The growth medium was used to obtain high cell densities while the induction medium was applied to induce the production of cytokinins after the growth phase.
The bioreactor was inoculated with 300 mL of shake flask cultures of CK2.2 strain.
The growth phase strategy consisted in a glucose-limited exponential feeding using the growth medium (Table 5). The growth rate was maintained at μ=0.12 h−1. In order to adapt the cells to galactose before the induction, a pulse of 15 g/L of galactose was administered at 22 h of the growth phase. The growth medium was replaced by the induction medium at 30 h of fermentation, and the latter was administered at a constant feeding rate of 0.14 mL/min. In order to increase the supply of cytosolic acetyl-CoA and boost cytokinin production, periodic pulses of 15 g/L of ethanol were supplied every 10 h during the whole induction phase (
The culture reached 65 g/L at the end of the growth phase (30 h). Yeast cells started to produce cytokinins at 28 h, six hours after the galactose adaptation pulse. This adaptation strategy facilitated the transition from the growth medium to the induction medium and speeded up the production of cytokinins. The fed-batch process reached 1.2 g/L of total cytokinins in the culture medium after 75 h of fermentation (
Table 6 presents the final cytokinin composition in the culture medium and biomass after 75 h of fermentation. Table 7 shows the detailed production parameters.
The bioactivity of the produced cytokinins was tested in A. thaliana by hypocotyl length assay. This assay is based on the capacity of cytokinins to inhibit hypocotyl elongation in A. thaliana seedlings (Cary et al., 1995, Plant Physiol., 107 (4): 1075-1082). Seeds of A. thaliana Col-0 were surface sterilized, sown on 0.5× Murashige and Skoog (MS) medium (Murashige and Skoog, 1962, Physiol. Plant., 15(13):473-497) (0.7% agar) without sucrose, and stratified in darkness for 3 days at 4° C. Seedlings were grown in complete darkness in a growth cabinet at 21°° C. Hypocotyl lengths were determined after 8 days of growth, and at least 15 seedlings were measured for each treatment. The culture medium obtained by the fed-batch fermentation of CK2.2 strain (Example 4) was diluted 1/10000 to a final concentration 0.12 mg/L of total cytokinins for the assay. Trans-zeatin chemical standard was used as positive control and fermented YPDG medium of CEN.PK113-5D strain was used as a negative control
The foregoing description of the specific embodiments will so fully reveal the general nature of the invention that others can, by applying current knowledge, readily modify and/or adapt for various applications such specific embodiments without undue experimentation and without departing from the generic concept, and therefore, such adaptations and modifications should and are intended to be comprehended within the meaning and range of equivalents of the disclosed embodiments. It is to be understood that the phraseology or terminology employed herein is for the purpose of description and not of limitation. The means, materials, and steps for carrying out various disclosed chemical structures and functions may take a variety of alternative forms without departing from the invention.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/IB2022/057603 | 8/15/2022 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 63233272 | Aug 2021 | US |
