WO2018132871A1 - Method of producing chemicals in yeast - Google Patents

Method of producing chemicals in yeast Download PDF

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Publication number
WO2018132871A1
WO2018132871A1 PCT/AU2018/050029 AU2018050029W WO2018132871A1 WO 2018132871 A1 WO2018132871 A1 WO 2018132871A1 AU 2018050029 W AU2018050029 W AU 2018050029W WO 2018132871 A1 WO2018132871 A1 WO 2018132871A1
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Prior art keywords
fructose
proteins
yeast cell
dihydroxyacetone
functional variants
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PCT/AU2018/050029
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French (fr)
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Thomas Williams
Ian PAULSEN
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Macquarie University
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Priority claimed from AU2017900129A external-priority patent/AU2017900129A0/en
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Publication of WO2018132871A1 publication Critical patent/WO2018132871A1/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N1/00—Microorganisms, e.g. protozoa; Compositions thereof; Processes of propagating, maintaining or preserving microorganisms or compositions thereof; Processes of preparing or isolating a composition containing a microorganism; Culture media therefor
    • C12N1/32—Processes using, or culture media containing, lower alkanols, i.e. C1 to C6
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/52—Genes encoding for enzymes or proenzymes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/80—Vectors or expression systems specially adapted for eukaryotic hosts for fungi
    • C12N15/81—Vectors or expression systems specially adapted for eukaryotic hosts for fungi for yeasts
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P19/00—Preparation of compounds containing saccharide radicals
    • C12P19/02—Monosaccharides
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P7/00—Preparation of oxygen-containing organic compounds
    • C12P7/24—Preparation of oxygen-containing organic compounds containing a carbonyl group
    • C12P7/26—Ketones
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P7/00—Preparation of oxygen-containing organic compounds
    • C12P7/24—Preparation of oxygen-containing organic compounds containing a carbonyl group
    • C12P7/26—Ketones
    • C12P7/28—Acetone-containing products

Definitions

  • the present invention relates to genetically modified strains of yeast which can be grown on alternative energy sources and used to produce industrial chemicals. Associated provisional application
  • Microorganisms can be engineered to produce valuable chemicals including fuels and pharmaceuticals as a sustainable and environmentally-friendly alternative to petroleum-based production of these products.
  • Feedstocks used to grow engineered microbes typically consist of a sugar or sugar-rich substrate.
  • the price of sugar from corn or sugarcane has thus far exceeded the cost of microbial chemical production processes.
  • the use of corn and sugarcane for the production of biofuels and other chemicals competes with the use of these resources in the human/animal food supply chain.
  • Methanol is a cheap and abundant potential carbon source for bioprocesses, as it can be chemically derived from methane from sources such as landfills, or from carbon monoxide and hydrogen generated from gasification of wood waste.
  • Engineering yeast to grow on methanol would therefore alleviate the economic strain on bioprocesses that depend on expensive feedstocks. While there are naturally occurring species of bacteria and yeast which are able to grow on methanol, these organisms have not been extensively characterised nor are they amendable to the genetic manipulation that is required for them to be suitable candidates for the production of industrial chemicals.
  • the present invention provides a yeast cell including a recombinant construct encoding one or more proteins that enable the cell to grow in a medium in which methanol is the only or main energy source for growth of the cell in the medium, wherein the one or more proteins is selected from the group consisting of: alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1 .3), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C.
  • alcohol oxidase E.C. 1 .1 .3.13
  • pyruvate carboxylase E.C. 6.4.1 .1
  • dihydroxyacetone synthase E.C. 2.2.1 .3
  • dihydroxyacetone kinase E.C. 2.7.1.29
  • fructose-1 -6-bisphophatase E.C. 3.1 .3.1 1
  • sedoheptulose bisphosphatase E.C. 3.1 .3.37
  • ribose-5-phosphate isomerase E.C. 5.3.1.6
  • D-ribulose-5-phosphate-3-epimerase E.C. 5.1 .3.1
  • transketolase 1 or 2 E.C. 2.2.1 .1
  • transaldolase EC 2.2.1.2
  • formaldehyde dehydrogenase E.C. 1.2.1 .46 or functional variants thereof.
  • the invention provides a method for forming a compound selected from the group consisting of xylulose-5-phosphate, glyceraldehyde-3- phosphate and dihydroxyacetone in a yeast cell comprising providing the yeast cell with a recombinant construct encoding one or more proteins selected from the group consisting of: alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1 .3), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C.
  • alcohol oxidase E.C. 1 .1 .3.13
  • pyruvate carboxylase E.C. 6.4.1 .1
  • dihydroxyacetone synthase E.C. 2.2.1 .3
  • dihydroxyacetone kinase E.C
  • fructose-1 -6-bisphophatase E.C. 3.1 .3.1 1
  • sedoheptulose bisphosphatase E.C. 3.1.3.37
  • ribose-5-phosphate isomerase E.C. 5.3.1.6
  • D-ribulose-5-phosphate-3-epimerase E.C. 5.1 .3.1
  • transketolase 1 or 2 E.C. 2.2.1.1
  • transaldolase EC 2.2.1 .2
  • formaldehyde dehydrogenase E.C.
  • the invention also provides a method for producing a chemical which can be used in an industrial process, the method comprising growing a yeast cell including a recombinant construct encoding one or more proteins that enable the cell to grow in a medium in which methanol is the only or main energy source for growth of the cell in the medium, wherein the one or more proteins is selected from the group consisting of: alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C.
  • transaldolase EC 2.2.1 .2
  • formaldehyde dehydrogenase E.C. 1.2.1 .46
  • functional variants thereof wherein the yeast cell includes a further construct enabling the production of the chemical.
  • the invention provides a recombinant construct encoding at least one protein for enabling a yeast cell to grow in a medium in which methanol is the only or main energy source for growth of the cell in the medium, wherein the one or more proteins is selected from the group consisting of: alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1.3), dihydroxyacetone kinase (E.C. 2.7.1 .29), fructose-1 -6-bisphosphate aldolase (E.C.
  • alcohol oxidase E.C. 1 .1 .3.13
  • pyruvate carboxylase E.C. 6.4.1 .1
  • dihydroxyacetone synthase E.C. 2.2.1.3
  • dihydroxyacetone kinase E.C. 2.7.1 .29
  • the invention provides a recombinant construct encoding at least one protein when used to enable a yeast cell to grow in a medium in which methanol is the only or main energy source for growth of the cell in the medium, wherein the one or more proteins is selected from the group consisting of: alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1.3), dihydroxyacetone kinase (E.C. 2.7.1 .29), fructose-1 -6-bisphosphate aldolase (E.C.
  • alcohol oxidase E.C. 1 .1 .3.13
  • pyruvate carboxylase E.C. 6.4.1 .1
  • dihydroxyacetone synthase E.C. 2.2.1.3
  • dihydroxyacetone kinase E.C. 2.7.1 .29
  • FIG. 1 Schematic of a synthetic methanol utilisation pathway according to the present invention. Enzymes (in dotted circles) catalysing reactions (arrows) between metabolites (black text) necessary for the assimilation of methanol into native yeast metabolism and growth on methanol as the sole carbon source. Underlined enzymes represent enzymes expressed in addition to native S. cerevisiae enzymes. Peroxisomal localisation of relevant proteins is indicated.
  • Enzyme abbreviations are as follows: AOD (alcohol oxidase), PYC (pyruvate carboxylase), CTA (catalase), pmp20 (peroxisomal membrane associated protein 20), DAS (dihydroxyacetone synthase), DAK (dihydroxyacetone kinase), FBA (Fructose-1 -6-bisphoshate aldolase), FBP (Fructose-1 - 6-bisphosphatase), SHB (Sedoheptulose bisphosphatase, also referred to herein as SBPase), RKI (Ribose-5-phosphate ketol isomerase), RPE (D-ribulose-5-phosphate-3- epimerase).
  • TAL1 , AOX1 , DAS1 , PYC1 genes to encode part of a synthetic methanol utilisation pathway in yeast.
  • Figure 3 pRS415 plasmid containing CTA1 , pmp20, and ADH1 genes for the detoxification of by-products of synthetic methylotrophic metabolism.
  • Figure 4 Vector map containing genes and promoters for methanol mediated gene expression in S. cerevisiae.
  • Figure 5 Growth over 30 hours with and without methanol.
  • An S. cerevisiae strain expressing peroxisome localised Pichia pastoris enzymes (alcohol oxidase, dihydroxyacetone synthase, catalase, pmp20), and cytosol localised alcohol dehydrogenase and pyruvate carboxylase, was cultured with and without methanol in yeast nitrogen base medium over 30 hours.
  • Optical density at 600 nm was measured to infer growth, with the percentage increase between 20 and 30 hours post inoculation shown.
  • Data and error bars represent mean and ⁇ 1 standard deviation from triplicate cultures.
  • Yeasts are commonly used in industrial technology and have been engineered to produce a variety of valuable chemicals and biofuels.
  • the reliance on carbon feedstocks derived from sugar from plant biomass for growth of these microorganisms represents a significant cost-impediment for the future large-scale reliance on microbial sources of industrially important chemicals.
  • Methanol is a cheap source of carbon and can be derived from landfill gas and wood-waste, making it a cost-effective and easily obtained source of carbon for the growth of yeasts used in the manufacture of industrial chemicals.
  • Methylotrophic yeasts i.e., yeasts that are able to metabolise methanol or methane
  • yeasts which are naturally methylotrophic do not generate sufficient energy to be able to drive synthesis of the metabolites required the production of industrial chemicals.
  • yeasts which have been exploited to date for the production of industrial chemicals are not naturally methylotrophic (i.e., do not have a natural capacity to utilise methane or methanol as a major source of energy).
  • Attempts to modify yeasts such as S. cerevisiae so that they are able to grow on methanol have thus far been unsuccessful, suggesting that more is required than simply genetically modifying the cells to express an enzyme capable of degrading methanol.
  • An advantage of the present invention is that it provides yeast which are not naturally methylotrophic with a novel metabolic pathway in the form of one or more proteins for enabling the yeast cells to grow where methanol is the only or main source of carbon source provided to the cells for growth.
  • the metabolic pathway is provided to yeast cells in the form of recombinant nucleic acid.
  • the constructs described herein encode proteins which enable yeast to utilise methanol as a major or sole source of carbon for the yeast to grow.
  • the proteins enable the production of metabolites from methanol which serve as a source of energy for the subsequent generation of industrial chemicals by the yeast cells.
  • the present invention has a significant advantage over previous attempts to provide yeasts, such as S. cerevisiae with a means to utilise methanol as a carbon source. This is because the present invention provides a minimum complement of the necessary proteins required to generate carbon metabolites that the yeast can utilise for growth (i.e., to generate a biomass of yeast) and excess energy to enable the yeast to synthesise the a chemical product. Thus, the present inventors have identified why others have previously failed to adapt non-methylotrophic yeasts to utilise methanol as a major source of carbon.
  • yeast with a single enzyme, e.g., alcohol oxidase, for metabolising methanol in order for the yeast to be able to utilise methanol as a source of energy.
  • a single enzyme e.g., alcohol oxidase
  • the term 'methylotroph' refers to any microorganism that, in its naturally occurring state (i.e., without genetic modification) can utilise reduced one- carbon compounds (such as methanol or methane) as a source of energy for growth and proliferation.
  • microorganisms of this type should not be confused with methanogens which on the contrary produce methane as a by-product from various one-carbon compounds such as carbon dioxide.
  • Some methylotrophs can also degrade the greenhouse gas methane, and in this case they are called methanotrophs. It follows that a non-methylotrophic yeast cell is one which, in its naturally occurring state, is unable to utilise one-carbon compounds such as methanol as a source of energy.
  • a non-methylotrophic yeast cell is a yeast cell which is unable to utilise methanol as a major or sole source of carbon, unless provided with a synthetic Methanol Utilisation Pathway, as herein described.
  • yeast cells include microorganisms of the species Saccharomyces cerevisiae (commonly known as bakers' yeast), Kluyveromyces lactis (and the related yeast Kluyveromyces marxianus), Yarrowia lipolytica, Schizosaccharomyces pombe and Arxula adeninivorans.
  • the yeast cell provided a recombinant construct encoding one or more proteins enabling growth of the cell in methanol can be any yeast which is not otherwise able to grow on methanol such as those described above.
  • the yeast cell is Saccharomyces cerevisiae.
  • carbon source is intended to mean a raw material input to a microbial culture that contains carbon atoms that can be used by the microorganism as a source of energy for growth and the manufacture of industrial chemicals in the culture.
  • the carbon source is preferably methanol.
  • the culture of microorganisms contains methanol as the major source of carbon, but other sources of carbon are also provided in the culture.
  • major carbon source is intended to mean that the culture media contains methanol as the main source of total carbon atoms in the media.
  • media comprising methanol as a major carbon source may be a medium where methanol represents at least about 50% or more of the total carbon atoms in the medium, preferably about 60% or more of the total carbon atoms in the medium, preferably 70% or more of the total carbon atoms in the medium, preferably about 80% or more of the total carbon atoms in the medium or preferably about 90% or more of the total carbon atoms in the medium.
  • methanol is the sole source of carbon in the culture medium
  • 100% of the total carbon atoms in the medium are derived from methanol.
  • 'methanol as a sole source of carbon' means that the microorganism must be able to be grown in media where the only source of carbon provided is methanol.
  • the present invention provides a yeast cell including a recombinant construct encoding one or more proteins that enable the cell to grow in a medium in which methanol is the only or main energy source for growth of the cell in the medium, wherein the one or more proteins is selected from the group consisting of: alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1 .3), transaldo!ase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1 .29), fructose-1 -6-bisphosphate aldolase (E.C.
  • alcohol oxidase E.C. 1 .1 .3.13
  • pyruvate carboxylase E.C. 6.4.1 .1
  • dihydroxyacetone synthase E.C. 2.2.1 .3
  • transaldo!ase
  • the present invention provides a synthetic microorganism, wherein the organism comprises a yeast cell that cannot grow if methanol is the only or major carbon source, wherein the yeast cell has been genetically modified to express one or more proteins which enable the yeast cell to utilise methanol as a source of carbon, the proteins being selected from the group consisting of alcohol oxidase (E.C. 1 .1.3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1 .3), transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C.
  • fructose-1 -6-bisphosphate aldolase E.C. 4.1 .2.13
  • fructose-1 -6-bisphophatase E.C. 3.1 .3.1 1
  • sedoheptulose bisphosphatase E.C. 3.1 .3.37
  • ribose-5-phosphate isomerase E.C. 5.3.1 .6
  • D-ribulose-5- phosphate-3-epimerase E.C. 5.1 .3.1
  • transketolase 1 or 2 E.C. 2.2.1 .1
  • functional variants thereof E.C. 2.2.1 .1
  • the yeast cell can be any of the species Saccharomyces cerevisiae, Kluyveromyces lactis, Kluyveromyces marxianus, Yarrowia lipolytica, Schizosaccharomyces pombe or Arxula adeninivorans.
  • the synthetic microorganism is a genetically modified Saccharomyces cerevisiae. It will be appreciated that any number of different strains of the above mentioned yeast species can be used.
  • suitable strains of S. cerevisiae include CEN.PK, S288c, BY4741 , and hybrid strains thereof.
  • the yeast cell has been transformed with one or more recombinant constructs that encode the proteins alcohol oxidase (E.C. 1.1 .3.13), dihydroxyacetone synthase (E.C. 2.2.1 .3) and pyruvate carboxylase (E.C. 6.4.1 .1 ), thereby enabling the cell to grow in a medium in which methanol is the major or sole source of carbon.
  • E.C. 1.1 .3.13 proteins alcohol oxidase
  • dihydroxyacetone synthase E.C. 2.2.1 .3
  • pyruvate carboxylase E.C. 6.4.1 .1
  • the yeast cell has been transformed with one or more recombinant constructs that encode the proteins: alcohol oxidase (E.C. 1.1 .3.13), pyruvate carboxylase (E.C. 6.4.1.1 ) and transaldolase (EC 2.2.1 .2), or functional variants thereof.
  • alcohol oxidase E.C. 1.1 .3.13
  • pyruvate carboxylase E.C. 6.4.1.1
  • transaldolase EC 2.2.1 .2
  • the yeast cell has been transformed with one or more recombinant constructs that encode the proteins: alcohol oxidase (E.C. 1.1 .3.13), pyruvate carboxylase (E.C. 6.4.1.1 ), dihydroxyacetone synthase (E.C. 2.2.1 .3), and transaldolase (EC 2.2.1 .2), or functional variants thereof.
  • alcohol oxidase E.C. 1.1 .3.13
  • pyruvate carboxylase E.C. 6.4.1.1
  • dihydroxyacetone synthase E.C. 2.2.1 .3
  • transaldolase EC 2.2.1 .2
  • the yeast cell has been transformed with one or more recombinant constructs that encode the proteins alcohol oxidase (E.C. 1.1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1 .3), dihydroxyacetone kinase (E.C. 2.7.1 .29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1 .2.13) and fructose-1 -6-bisphophatase (E.C. 3.1 .3.1 1 ), or functional variants thereof.
  • alcohol oxidase E.C. 1.1 .3.13
  • pyruvate carboxylase E.C. 6.4.1 .1
  • dihydroxyacetone synthase E.C. 2.2.1 .3
  • dihydroxyacetone kinase E.C. 2.7.1 .29
  • fructose-1 -6-bisphosphate aldolase E.
  • the yeast cell has been transformed with one or more recombinant constructs that encode the proteins alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1 .29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1 .2.13) and fructose- 1 -6-bisphophatase (E.C. 3.1.3.1 1 ), or functional variants thereof.
  • the yeast cell has been transformed with one or more recombinant constructs that encode the proteins alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1 .29), fructose-1 -6-bisphosphate ald
  • the yeast cell has been transformed with one or more recombinant constructs that encode the proteins alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) and dihydroxyacetone synthase (E.C. 2.2.1.3), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1.3.11) and sedoheptulose bisphosphatase (E.C.3.1.3.37), or functional variants thereof.
  • the proteins alcohol oxidase E.C. 1.1.3.13
  • pyruvate carboxylase E.C. 6.4.1.1
  • dihydroxyacetone synthase E.C. 2.2.1.3
  • dihydroxyacetone kinase E.C. 2.7.1.29
  • the yeast cell has been transformed with one or more recombinant constructs that encode the proteins alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C.2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C.4.1.2.13), fructose-1 -6- bisphophatase (E.C. 3.1.3.11) and sedoheptulose bisphosphatase (E.C. 3.1.3.37), or functional variants thereof.
  • alcohol oxidase E.C. 1.1.3.13
  • pyruvate carboxylase E.C. 6.4.1.1
  • transaldolase EC 2.2.1.2
  • dihydroxyacetone kinase E.C.2.7.1.29
  • fructose-1 -6-bisphosphate aldolase E.C.4.1.
  • the yeast cell has been transformed with one or more recombinant constructs that encode the proteins alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) dihydroxyacetone synthase (E.C. 2.2.1.3), transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6- bisphosphate aldolase (E.C.4.1.2.13), fructose-1 -6-bisphophatase (E.C.3.1.3.11) and sedoheptulose bisphosphatase (E.C.3.1.3.37), or functional variants thereof.
  • alcohol oxidase E.C. 1.1.3.13
  • pyruvate carboxylase E.C. 6.4.1.1
  • dihydroxyacetone synthase E.C. 2.2.1.3
  • transaldolase EC 2.2.1.2
  • the yeast cell has been transformed with one or more recombinant constructs that encode the proteins alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) and dihydroxyacetone synthase (E.C. 2.2.1.3), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1.3.11), sedoheptulose bisphosphatase (E.C. 3.1.3.37), ribose-5-phosphate isomerase (E.C.
  • the yeast cell has been transformed with one or more recombinant constructs that encode the proteins alcohol oxidase (E.C. 1.1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) and transaldolase (EC 2,2.1 .2), dihydroxyacetone kinase (E.C. 2.7.1 .29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1 .2.13), fructose-1 -6- bisphophatase (E.C.
  • the yeast cell has been transformed with one or more recombinant constructs that encode the proteins alcohol oxidase (E.C. 1.1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) and dihydroxyacetone synthase (E.C. 2.2.1 .3), transaldolase (EC 2.2.1 .2), dihydroxyacetone kinase (E.C. 2.7.1 .29), fructose-1 -6- bisphosphate aldolase (E.C. 4.1 .2.13), fructose-1 -6-bisphophatase (E.C. 3.1 .3.1 1 ), sedoheptulose bisphosphatase (E.C. 3.1.3.37), ribose-5-phosphate isomerase (E.C. 5.3.1 .6) and D-ribulose-5-phosphate-3-epimerase (E.C. 5.1 .3.1 ), or functional variants thereof.
  • alcohol oxidase E
  • the yeast cell has been transformed with one or more recombinant constructs that encode one or more of the proteins transketolase 1 or 2 (E.C. 2.2.1 .1 ), catalase (E.C. 1 .1 1.1 .6), glutathione peroxidase (E.C. 1 .1 1.1 .9) and methyl formate-synthesising alcohol dehydrogenase (E.C. 1 .1 .1.1 ), or functional variants thereof.
  • the proteins transketolase 1 or 2 E.C. 2.2.1 .1
  • catalase E.C. 1 .1 1.1 .6
  • glutathione peroxidase E.C. 1 .1 1.1 .9
  • methyl formate-synthesising alcohol dehydrogenase E.C. 1 .1 .1.1
  • the above-described yeast cells are strains of Saccharomyces cerevisiae.
  • the yeast cell may be transformed with a recombinant construct which encodes an endogenous protein from the yeast strain, for example for the purpose of over- expressing the endogenous protein in the cell.
  • a recombinant construct encoding the protein formaldehyde dehydrogenase (SFA1 , E.C. 1 .2.1 .46) to overexpress the native formaldehyde dehydrogenase gene from Saccharomyces cerevisiae in a cell transformed according to any one of the above embodiments.
  • the yeast cell can be any yeast cell which is unable to grow if methanol is the major or sole source of carbon provided to the yeast in the growing medium.
  • the yeast cell may comprise a genetic modification to the extent that it has some of the proteins which may be required for growth of the yeast on methanol, but does not yet have the full complement of proteins enabling growth on methanol as a major or sole carbon source.
  • the construct is essential for enabling the cell to grow in the medium and providing the yeast cell with the recombinant construct provided to the yeast cell is what is required to enable the cell to grow in the medium.
  • the present invention also provides a yeast cell including a recombinant construct as herein described, encoding one or more proteins that enable the cell to grow in a medium in which methanol is the only or main energy source for growth of the cell in the medium, wherein the cell contains a gene encoding a protein selected from the group consisting of alcohol oxidase (E.C. 1 .1.3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1 .3), transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C.
  • a protein selected from the group consisting of alcohol oxidase (E.C. 1 .1.3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1 .3), transaldolase (EC 2.2.1.2), dihydroxyacetone kinas
  • fructose-1 -6-bisphosphate aldolase E.C. 4.1 .2.13
  • fructose-1 -6-bisphophatase E.C. 3.1 .3.1 1
  • sedoheptulose bisphosphatase E.C. 3.1 .3.37
  • ribose-5-phosphate isomerase E.C. 5.3.1 .6
  • D-ribulose-5- phosphate-3-epimerase E.C. 5.1 .3.1
  • transketolase 1 or 2 E.C. 2.2.1 .1
  • functional variants thereof wherein the gene is not comprised in the recombinant construct.
  • the above listed genes are comprised in the genome of the cell but not in the construct such that the construct comprises the additional relevant genes which enable the cell to utilise methanol as a major or sole source of carbon.
  • the cell may have some of the components of a methanol utilisation pathway, it is unable to utilise methanol until it is provided with a construct of the invention.
  • yeast cells of the invention can be obtained by providing or inserting one or more recombinant constructs or nucleic acid fragments, as herein described, encoding proteins for enabling the yeast to grow on methanol.
  • any of the methods known conventionally in the art may be used to transform a yeast cell with the recombinant constructs herein described.
  • standard methods of yeast transformation using lithium acetate and polyethylene glycol will be well known to the skilled person for the purposes of generating stable transformants.
  • Successful transformants can be detected through the use of selectable markers, also encoded by the nucleic acid constructs.
  • selectable markers also encoded by the nucleic acid constructs.
  • Alternative methods for integrating the genes of interest into the genome can be used, for example, using CRISPR/Cas9 methods, or homologous recombination methods such that the yeast genome is permanently altered to encode genes required for methanol utilisation.
  • transforming yeast cells Suitable methods of transforming yeast cells are described in WO 00/71738A1 and WO 02/42471 A1 .
  • the terms "transforming” and “transformation” as used herein refers to a change in a cell's genetic characteristics, and a cell has been transformed when it has been modified to contain a new nucleic acid.
  • a cell is transformed where it is genetically modified from its native state.
  • transforming DNA may recombine with cellular genomic DNA by physically integrating into a chromosome of the cell.
  • the nucleic acid can be maintained transiently as an episomal element without being replicated, or may replicate independently as a plasmid. For example, in S.
  • expression vectors can be maintained stably in cells over many generations, provided that selection markers are continually selected for via the exclusion of relevant growth medium component.
  • some vectors include marker genes for leucine biosynthesis or uracil biosynthesis and thus, when a strain of yeast that does not express these genes is transformed with plasm ids encoding the relevant markers, transformants can be selected for using growth medium which does not contain uracil or leucine, or other component required for growth, as the case may be).
  • transfection is used to refer to the uptake of foreign or exogenous DNA by a cell, and a cell has been "transfected" when the exogenous DNA has been introduced inside the cell membrane.
  • transfection techniques are well known in the art. See, e.g., Graham et al., 1973. Virology 52:456; Sambrook et al., 2001 , MOLECULAR CLONING, A LABORATORY MANUAL, Cold Spring Harbor Laboratories; Davis et al., 1986, BASIC METHODS IN MOLECULAR BIOLOGY, Elsevier; and Chu et al., 1981 , Gene 13: 197. Such techniques can be used to introduce one or more exogenous polynucleotides into suitable host cells.
  • the one or more proteins which enable the yeast cells to grown in methanol as the main or sole energy source comprise, consist essentially of or consist of enzymes facilitating the conversion of methanol into downstream carbon-based metabolites.
  • the proteins may also comprise, consist essentially of, or consist of enzymes which facilitate the detoxification of bi-products formed during the metabolism of methanol (and its downstream metabolites) and/or proteins which enable the proper folding, localisation and function of key enzymes in the pathway.
  • enzyme is intended to refer to molecules that accelerate or catalyze chemical reactions. Almost all metabolic processes in the cell need enzymes in order to occur at rates fast enough to sustain life.
  • AOX alcohol oxidase
  • AOX1 AOX2
  • AOD E.C. 1 .1.3.13 any enzyme catalysing the reaction of a primary alcohol plus oxygen to an aldehyde plus hydrogen peroxide.
  • the alcohol oxidase catalyses the conversion of methanol to formaldehyde.
  • the AOX is AOX1 or AOX 2 from Pichia pastoris.
  • the AOX protein is AOX1 from Pichia pastoris.
  • An example of the protein sequence of AOX1 is shown in SEQ ID NO: 1 (AOX1 from Pichia pastoris)
  • SEQ ID NO: 2 sequence is codon optimised for expression in S. cerevisiae and also encodes a C-terminal PTS1 sequence
  • a - pyruvate carboxylase (PYC, PYC1 , E.C. 6.4.1 .1 ), being any enzyme catalysing the irreversible carboxylation of pyruvate to form oxaloacetate (OAA).
  • pyruvate carboxylase also functions to facilitate the folding, activity and subcellular localisation of AOX.
  • PYC1 from methylotrophic yeast is believed to facilitate binding of the cofactor FAD to AOX.
  • An example of a protein sequence of PYC is shown in SEQ ID NO: 3.
  • DAS1 D-xylulose-5-phosphate:formaldehyde glycolaldehydetransferase, E.C. 2.2.1 .3
  • DAS is also capable of converting fructose-6-phosphate (F6P) to erythrose-4- phosphate (E4P) and xylulose-5-phosphate (Xu5P).
  • DAS can catalyse the conversion of G3P and S7P to Xu5P and ribose-5-phosphate (R5P).
  • SEQ ID NO: 5 sequence from Pichia pastoris shown
  • MARIPKAVSTQDDIHELVIKTFRCYVLDLVEQYGGGHPGSAMGMVAIGIALWKYQMKY APNDPDYFNRDRFVLSNGHVCLFQYLFQHLTGLKEMTVKQLQSYHSSDYHSLTPGHP EIENPAVEVTTGPLGQGISNAVGMAIGSKNLAATYNRPGFPWDNTIYAIVGDACLQEG
  • C-terminal PTS1 show in underline.
  • SEQ ID NO: 6 also encodes C-terminal PTS1 signal and is codon optimised for expression in S. cerevisiae: ATGGCTAGAATTCCAAAGGCTGTTTCTACTCAAGACGACATTCACGAATTGGTTATT AAGACTTTCAGATGTTACGTTTTGGACTTGGTTGAACAATACGGTGGTGGTCACCC AGGTTCTGCTATGGGTATGGTTGCTATTGGTATTGCTTTGTGGAAGTACCAAATGA AGTACGCTCCAAACGACCCAGACTACTTCAACAGAGACAGATTCGTTTTGTCTAAC GGTCACGTTTGTTTGTTCCAATACTTGTTCCAACACTTGACTGGTTTGAAGGAAATG ACTGTTAAGCAATTGCAATCTTACCACTCTTCTGACTACCACTCTTTGACTCCAGGT C AC C C C C AG AAATTG AAAAC C C AG CTGTTG AAGTTACTACTG GTC C ATTG
  • DAK dihydroxyacetone kinase
  • E.C. 2.7.1.29 any enzyme which converts dihydroxyacetone into dihydroxyacetone phosphate (also called gylcerone phosphate or DHAP).
  • DAK is also known by the terms glycerone kinase, ATP:glycerone phosphotransferase and acetol kinase.
  • SEQ ID NO: 7 An example of the protein sequence of DAK is shown in SEQ ID NO: 7:
  • SEQ ID NO: 8 also encodes C-terminal PTS1 peptide; codon optimised: ATGTCCGCTAAATCGTTTGAAGTCACAGATCCAGTCAATTCAAGTCTCAAAG GGTTTGCCCTTGCTAACCCCTCCATTACGCTGGTCCCTGAAGAAAAAATTCTCTTC AG AAAGAC C G ATTC C G AC AAG ATC G C ATTAATTTCTG GTG GTG GTAGTG G AC ATG A ACCTACACACGCCGGTTTCATTGGTAAGGGTATGTTGAGTGGCGCCGTGGTTGGC GAAATTTTTGCATCCCCTTCAACAAAACAGATTTTAAATGCAATCCGTTTAGTCAAT GAAAATGCGTCTGGCGTTTTATTGATTGTGAAGAACTACACAGGTGATGTTTTGCAT TTTGGTCTGTCCGCTGAGAGCAAGCCTTGGGTATTAACTGCCGCGTTGCTG TCTG TC ATAG GTGATG
  • FBA1 -2 E.C. 4.1 .2.13
  • DHAP dihydroxyacetone phosphate
  • GAP glyceraldehyde-3-phosphate
  • F1 ,6BP fructose-1 -6-bisphosphate
  • FBA1 -2 is also capable of catalysing the reverse reaction (i.e., of fructose-1 -6-bisphosphate to DHAP and GAP) but it will be understood that for the purposes of the present invention, FBA1 -2 should catalyse the formation of fructose-1 -6-bisphosphate so that this molecule can be used as a substrate in downstream reactions of the methanol utilisation pathway. Further, FBA1 -2 can be used in accordance with the present invention for catalysing the conversion of erythrose 4-phosphate (E4P) and DHAP to sedoheptulose 1 ,7-bisphosphate (S1 ,7BP). An example of the protein sequence of FBA1 -2 is shown in SEQ ID NO: 9:
  • FBPase hexose diphosphatase, or fructose- bisphosphatase
  • E.C. 3.1 .3.1 1 is any enzyme catalysing the conversion of F1 ,6BP to fructose-6-phosphate (F6P).
  • FBPase hexose diphosphatase, or fructose- bisphosphatase
  • F6P fructose-6-phosphate
  • sedoheptulose bisphosphatase (sedoheptulose-1 ,7-bisphosphatase or SBPase, SBH17, E.C. 3.1 .3.37) is any enzyme catalysing the conversion of sedoheptulose 1 ,7- bisphosphate (S1 ,7BP) to sedoheptulose-7-phosphate (S7P).
  • SBPase An example of the protein sequence of SBPase is shown in SEQ ID NO: 13 (C-terminal PTS1 peptide underlined): MPSLTPRCIIVRHGQTEWSKSGQYTGLTDLPLTPYGEGQMLRTGESVFRNNQFLNPD NITYIFTSPRLRARQTVDLVLKPLSDEQRAKIRVWDDDLREWEYGDYEGMLTREIIELR KSRGLDKERPWNIWRDGCENGETTQQIGLRLSRAIARIQNLHRKHQSEGRASDIMVFA HGHALRYFAAIWFGLGVQKKCETIEEIQNVKSYDDDTVPYVKLESYRHLVDNPCFLLDA GGIGVLSYAHHNIDEPALELAGPFVSPPEEESQHGDVPEALIKSMTSKL
  • SBPase polypeptide An example of a polynucleotide encoding a SBPase polypeptide is shown in SEQ ID NO: 14 (codon optimised; also encodes PTS1 ):
  • TKL1 - transketolase
  • TLK2 E.C. 2.2.1 .1
  • PTS1 protein sequence of TKL
  • RKL1 ribose-5-phosphate ketol isomerase
  • Rpi D-ribose-5- phosphate aldose-ketose-isomerase
  • Ribose-5-phosphate isomerase E.C. 5.3.1.6 refers to any enzyme capable of catalysing the reaction of ribose-5-phosphate to ribulose-5-phosphate (RuL5P).
  • RKL1 protein sequence of RKL1 is shown in SEQ ID NO: 17 (PTS1 underlined):
  • SEQ ID NO: 18 An example of a polynucleotide encoding a RKL1 polypeptide is shown in SEQ ID NO: 18 (codon optimised; also encodes PTS1 ): ATGGCTGCCGGTGTCCCAAAAATTGATGCGTTAGAATCTTTGGGCAATCCTT TG G AG G ATGC C AAG AGAG CTG C AGC ATAC AG AG C AGTTGATG AAAATTTAAAATTT GATGATCACAAAATTATTGGAATTGGTAGTGGTAGCACAGTGGTTTATGTTGCCGA AAGAATTGGACAATATTTGCATGACCCTAAATTTTATGAAGTAGCGTCTAAATTCAT TTG C ATTC C AAC AG G ATTC C AATC AAG AAACTTG ATTTTG GATAAC AAGTTG C AATT AGGCTCCATTGAACAGTATCCTCGCATTGATATAGCGTTTGACGGTGCTGATGAAG TGGATGAGAATTTACAATTAATTAAAGGTGGTGGTGCTTGTCTATTTCAAGAAAA
  • RPE1 D-ribulose-5-phosphate
  • Xu5P D-xylulose-5-phosphate
  • Underlined sequence refers to C-terminal PTS1 peptide.
  • An example of a polynucleotide encoding a catalase polypeptide is shown in
  • SEQ ID NO: 22 sequence encoding Pichia pastoris CTA1 is shown; also encodes C- terminal PTS1 peroxisomal targeting peptide tag PEALIKSMTSKL, codon optimised for expression in Saccharomyces cerevisiae:
  • TPX E.C. 1 .1 1 .1 .9
  • SEQ ID NO: 23 Pichia pastoris sequence shown
  • Underlined sequence refers to C-terminal PTS1 peptide.
  • An example of a polynucleotide encoding a glutathione peroxidase polypeptide is shown in SEQ ID NO: 24 (also encodes C-terminal PTS1 ; codon optimised for expression in S. cerevisiae):
  • ADH1 - methyl formate-synthesising alcohol dehydrogenase
  • MFS a primary alcohol and NAD+ to an aldehyde, NADH and H+.
  • the enzyme catalyses the conversion of methanol and formaldehyde to methyl formate (for example, by dehydrogenation of the hydroxyl group of the hemiacetal adduct [CH2(OH)OCH3] of methanol and formaldehyde, leading to the formation of a stoichiometric amount of methyl formate).
  • An example of the protein sequence of methyl-formate synthesising alcohol dehydrogenase is shown in SEQ ID NO: 25:
  • TAL TALD01 EC 2.2.1.2
  • TAL TALD01 EC 2.2.1.2
  • EC 2.2.1.2 an enzyme which converts sedoheptulose 7-phosphate and giyceraldehyde 3-phosphate to erythrose 4- phosphate and fructose 6-phosphate.
  • SEQ ID NO: 27 An example of the protein sequence of transaidolase is shown in SEQ ID NO: 27:
  • SEQ ID NO: 38 An example of a protein sequence of formaldehyde dehydrogenase is shown in SEQ ID NO: 38:
  • the proteins are alcohol oxidase, pyruvate carboxylase and dihydroxyacetone synthase, or functional variants thereof.
  • the proteins which enable the cell to utilise methanol as a major or sole source of carbon are selected from the group consisting of: alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) and transaldolase (EC 2.2.1 .2), or functional variants thereof.
  • the proteins are alcohol oxidase, pyruvate carboxylase and dihydroxyacetone synthase, or functional variants thereof.
  • the proteins which enable the cell to utilise methanol as a major or sole source of carbon are selected from the group consisting of: alcohol oxidase (E.C. 1.1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ), dihydroxyacetone synthase (E.C. 2.2.1 .3), and transaldolase (EC 2.2.1.2), or functional variants thereof.
  • the proteins are alcohol oxidase, pyruvate carboxylase and dihydroxyacetone synthase, or functional variants thereof.
  • the proteins which enable the yeast cell to grow on methanol are alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1 .3), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13) and fructose-1 -6-bisphophatase (E.C.3.1.3.11), or functional variants thereof.
  • alcohol oxidase E.C. 1 .1 .3.13
  • pyruvate carboxylase E.C. 6.4.1 .1
  • dihydroxyacetone synthase E.C. 2.2.1 .3
  • dihydroxyacetone kinase E.C. 2.7.1.29
  • fructose-1 -6-bisphosphate aldolase E.C. 4.1.2.13
  • the proteins which enable the yeast cell to grow on methanol are alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) transaldo!ase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6- bisphosphate aldolase (E.C.4.1.2.13) and fructose-1 -6-bisphophatase (E.C.3.1.3.11), or functional variants thereof.
  • alcohol oxidase E.C. 1.1.3.13
  • pyruvate carboxylase E.C. 6.4.1.1
  • transaldo!ase EC 2.2.1.2
  • dihydroxyacetone kinase E.C. 2.7.1.29
  • fructose-1 -6- bisphosphate aldolase E.C.4.1.2.13
  • fructose-1 -6-bisphophatase E.C.3.1
  • the proteins which enable the yeast cell to grow on methanol are alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1), dihydroxyacetone synthase (E.C. 2.2.1.3), transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13) and fructose-1 -6-bisphophatase (E.C.3.1.3.11), or functional variants thereof.
  • alcohol oxidase E.C. 1.1.3.13
  • pyruvate carboxylase E.C. 6.4.1.1
  • dihydroxyacetone synthase E.C. 2.2.1.3
  • transaldolase EC 2.2.1.2
  • dihydroxyacetone kinase E.C. 2.7.1.29
  • the proteins which enable the yeast cell to grow on methanol are alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C.6.4.1.1) and dihydroxyacetone synthase (E.C. 2.2.1.3), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1.3.11) and sedoheptulose bisphosphatase (E.C. 3.1.3.37), or functional variants thereof.
  • alcohol oxidase E.C. 1.1.3.13
  • pyruvate carboxylase E.C.6.4.1.1
  • dihydroxyacetone synthase E.C. 2.2.1.3
  • dihydroxyacetone kinase E.C. 2.7.1.29
  • fructose-1 -6-bisphosphate aldolase E.C
  • the proteins which enable the yeast cell to grow on methanol are alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6- bisphosphate aldolase (E.C.4.1.2.13), fructose-1 -6-bisphophatase (E.C.3.1.3.11) and sedoheptulose bisphosphatase (E.C.3.1.3.37), or functional variants thereof.
  • alcohol oxidase E.C. 1.1.3.13
  • pyruvate carboxylase E.C. 6.4.1.1
  • transaldolase EC 2.2.1.2
  • dihydroxyacetone kinase E.C. 2.7.1.29
  • fructose-1 -6- bisphosphate aldolase E.C.4.1.2.13
  • the proteins which enable the yeast cell to grow on methanol are alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) dihydroxyacetone synthase (E.C. 2.2.1.3), transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1.3.11) and sedoheptulose bisphosphatase (E.C.3.1.3.37), or functional variants thereof.
  • alcohol oxidase E.C. 1.1.3.13
  • pyruvate carboxylase E.C. 6.4.1.1
  • dihydroxyacetone synthase E.C. 2.2.1.3
  • transaldolase EC 2.2.1.2
  • dihydroxyacetone kinase E.
  • the proteins which enable the yeast cell to grown on methanol are alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C.6.4.1.1) and dihydroxyacetone synthase (E.C. 2.2.1.3), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1.3.11), sedoheptulose bisphosphatase (E.C. 3.1.3.37), ribose-5-phosphate isomerase (E.C. 5.3.1.6) and D-ribulose-5-phosphate-3-epimerase (E.C. 5.1.3.1), or functional variants thereof.
  • alcohol oxidase E.C. 1.1.3.13
  • pyruvate carboxylase E.C.6.4.1.1
  • dihydroxyacetone synthase
  • the proteins which enable the yeast cell to grown on methanol are alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C.6.4.1.1) and transaldo!ase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6- bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1.3.11), sedoheptulose bisphosphatase (E.C. 3.1.3.37), ribose-5-phosphate isomerase (E.C.
  • the proteins which enable the yeast cell to grown on methanol are alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C.6.4.1.1) and dihydroxyacetone synthase (E.C. 2.2.1.3), transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C.
  • the proteins which enable the yeast cell to grown on methanol are alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C.6.4.1.1) and dihydroxyacetone synthase (E.C. 2.2.1.3), transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C.
  • the yeast cell may be provided with a nucleic acid construct which encodes transketolase 1 or 2 (E.C. 2.2.1 .1 ), catalase (E.C. 1.1 1 .1.6), glutathione peroxidase (E.C. 1 .1 1 .1 .9) and/or methyl formate-synthesising alcohol dehydrogenase (E.C. 1 .1.1 .1 ), or functional variants thereof.
  • the yeast cell may already have genes encoding proteins selected from the group consisting of alcohol oxidase (E.C. 1.1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ), dihydroxyacetone synthase (E.C. 2.2.1 .3), iransaldolase (EC 2.2.1 .2), dihydroxyacetone kinase (E.C. 2.7.1 .29), fructose-1 -6- bisphosphate aldolase (E.C. 4.1 .2.13), fructose-1 -6-bisphophatase (E.C. 3.1 .3.1 1 ), sedoheptulose bisphosphatase (E.C.
  • the present invention includes providing such cells with a recombinant construct encoding one or more proteins that enable the cell to grow in methanol, provided that the construct does not also contain the gene.
  • providing the recombinant construct to the yeast cell enables completion of the molecular pathway required to enable the yeast cells to grown in a medium where methanol is the sole or major carbon source.
  • the construct provides for increased expression (or over- expression) of a gene that is endogenous to the yeast cell, but for which increased expression is required in order for the cell to grow efficiently where methanol is the sole or major carbon source.
  • protein shall be taken to include a single polypeptide chain, i.e., a series of contiguous amino acids linked by peptide bonds or a series of polypeptide chains covalently or non-covalently linked to one another (i.e., a polypeptide complex).
  • the series of polypeptide chains can be covalently linked using a suitable chemical or a disulphide bond.
  • non-covalent bonds include hydrogen bonds, ionic bonds, Van der Waals forces, and hydrophobic interactions.
  • polypeptide or "polypeptide chain” will be understood from the foregoing paragraph to mean a series of contiguous amino acids linked by peptide bonds.
  • a polypeptide or peptidomimetic that may have, for example, at least 70%, at least 80%, at least 85%, at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% sequence identity to the recited sequences, which also retains the biological activity described.
  • the ability to determine enzymatic activity for each protein may be measured by any method as described herein or known in the art.
  • the biologically active variant or analog may contain one or more conservative amino acid substitutions, or non-native amino acid substitutions.
  • Percent (%) amino acid sequence identity or “percent (%) identical” with respect to a polypeptide sequence, i.e. a polypeptide, protein or fusion protein of the invention defined herein, is defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in the specific polypeptide of the invention, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity.
  • percent amino acid sequence identity X/Y100, where X is the number of amino acid residues scored as identical matches by the sequence alignment program's or algorithm's alignment of A and B and Y is the total number of amino acid residues in B.
  • the percent amino acid sequence identity of A to B will not equal the percent amino acid sequence identity of B to A.
  • the determination of percent identity between two sequences can be accomplished using a mathematical algorithm.
  • a nonlimiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin and Altschul (1990) Proc. Natl. Acad. Sci. USA 87:2264, modified as in Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-5877. Such an algorithm is incorporated into the BLASTN and BLASTX programs of Altschul et al. (1990) J. Mol. Biol.
  • Gapped BLAST in BLAST 2.0
  • PSI-Blast can be used to perform an iterated search that detects distant relationships between molecules. See Altschul et al. (1997) supra.
  • the default parameters of the respective programs e.g., BLASTX and BLASTN
  • Alignment may also be performed manually by inspection.
  • Another non- limiting example of a mathematical algorithm utilized for the comparison of sequences is the ClustalW algorithm (Higgins et al.
  • ClustalW compares sequences and aligns the entirety of the amino acid or DNA sequence, and thus can provide data about the sequence conservation of the entire amino acid sequence.
  • the ClustalW algorithm is used in several commercially available DNA/amino acid analysis software packages, such as the ALIGNX module of the Vector NTI Program Suite (Invitrogen Corporation, Carlsbad, CA). After alignment of amino acid sequences with ClustalW, the percent amino acid identity can be assessed.
  • a non-limiting examples of a software program useful for analysis of ClustalW alignments is GENEDOCTM or JalView (http://www.jalview.org/). GENEDOCTM allows assessment of amino acid (or DNA) similarity and identity between multiple proteins.
  • the polypeptide desirably comprises an amino end and a carboxyl end.
  • the polypeptide can comprise D-amino acids, L-amino acids or a mixture of D- and L-amino acids.
  • the D-form of the amino acids is particularly preferred since a polypeptide comprised of D-amino acids is expected to have a greater retention of its biological activity in vivo.
  • the polypeptide can be prepared by any of a number of conventional techniques.
  • the polypeptide can be isolated or purified from a naturally occurring source or from a recombinant source. Recombinant production is preferred.
  • a DNA fragment encoding a desired peptide can be subcloned into an appropriate vector using well-known molecular genetic techniques (see, e.g., Maniatis et al., Molecular Cloning: A Laboratory Manual, 2nd ed. (Cold Spring Harbor Laboratory, 1982); Sambrook et al., Molecular Cloning A Laboratory Manual, 2nd ed. (Cold Spring Harbor Laboratory, 1989).
  • the fragment can be transcribed and the polypeptide subsequently translated in vitro.
  • kits also can be employed (e.g., such as manufactured by Clontech, Palo Alto, Calif.; Amersham Pharmacia Biotech Inc., Piscataway, N.J.; InVitrogen, Carlsbad, Calif., and the like).
  • the polymerase chain reaction optionally can be employed in the manipulation of nucleic acids.
  • conservative substitution refers to the replacement of an amino acid present in the native sequence in the peptide or polypeptide with a naturally or non- naturally occurring amino acid or a peptidomimetic having similar steric properties.
  • side-chain of the native amino acid to be replaced is either polar or hydrophobic
  • the conservative substitution should be with a naturally occurring amino acid, a non- naturally occurring amino acid or with a peptidomimetic moiety which is also polar or hydrophobic (in addition to having the same steric properties as the side- chain of the replaced amino acid).
  • conservative substitutions by naturally occurring amino acids can be determined bearing in mind the fact that replacement of charged amino acids by sterically similar non-charged amino acids are considered as conservative substitutions.
  • amino acid analogs synthetic amino acids
  • a peptidomimetic of the naturally occurring amino acid is well documented in the literature known to the skilled person and non-natural or unnatural amino acids are described further below.
  • the substituting amino acid should have the same or a similar functional group in the side chain as the original amino acid.
  • Alterations of the native amino acid sequence to produce mutant polypeptides can be done by a variety of means known to those skilled in the art.
  • site-specific mutations can be introduced by ligating into an expression vector a synthesized oligonucleotide comprising the modified site.
  • oligonucleotide-directed site-specific mutagenesis procedures can be used, such as disclosed in Walder et al., Gene 42: 133 (1986); Bauer et al., Gene 37: 73 (1985); Craik, Biotechniques, 12-19 (January 1995); and U.S. Pat. Nos. 4,518,584 and 4,737,462.
  • a preferred means for introducing mutations is the QuikChange Site-Directed Mutagenesis Kit (Stratagene, La Jolla, Calif.).
  • the proteins which are described herein may also include targeting sequences.
  • the targeting sequences present in the protein sequences may facilitate subcellular localisation of the proteins, for example, to the peroxisome or mitochondria of the yeast.
  • PTS1 peroxisomal targeting sequences
  • the consensus sequence for the type 2 peroxisomal targeting sequence (PTS2) in yeast is: (R/K)-(L/V/I)-(XXXX)-(H/Q)-(I_/A/F).
  • catalase Sigma Aldrich catalogue number CAT100
  • dihydroxyacetone synthase and other peroxisomally targeted enzymes in the invention can also be assayed using available kits.
  • Fructose-1 -6-bisphosphate aldolase https://www.sigmaaldrich.com/content/dam/sigma- aldrich/docs/Sigma/Enzyme_Assay/a881 1 enz.pdf
  • Fructose-6-phosphatase (http://www.sigmaaldrich.com/content/dam/sigma- aldrich/docs/Sigma/Bulletin/1/mak020bul.pdf), RKI1 and RPE1 (https://www.sigmaaldrich.com/content/dam/sigma- aldrich/docs/Sigma/Enzyme_Assay/phosphoriboisomerase.pdf).
  • proteins which enable a yeast cell to utilise methanol as a source of energy can be provided to a yeast cell by genetically modifying the yeast cell so that it is able to synthesise the relevant proteins.
  • Genetically engineered or “genetically modified” refers to any cell modified by any recombinant DNA or RNA technology.
  • the cell has been transfected, transformed, or transduced with a recombinant polynucleotide molecule, and thereby been altered so as to cause the cell to alter expression of a desired protein.
  • Methods and vectors for genetically engineering host cells are well known in the art; for example, various techniques are illustrated in Current Protocols in Molecular Biology, Ausubel et al., eds. (Wiley & Sons, New York, 1988, and quarterly updates).
  • Genetic engineering techniques include but are not limited to expression vectors, targeted homologous recombination, and gene activation (see, for example, U.S. Pat. No. 5,272,071 ), and trans-activation by engineered transcription factors (see, for example, Segal et al., 1999, Proc Natl Acad Sci USA 96(6):2758-63).
  • the genetic modifications described herein result in an increase in gene expression or function and can be referred to as amplification, overproduction, overexpression, activation, enhancement, addition, or up-regulation of a gene.
  • reference to increasing the action (or activity) of enzymes or other proteins discussed herein generally refers to any genetic modification in the microorganism in question that results in increased expression and/or functionality (biological activity) of the enzymes or proteins and includes higher activity of the enzymes (e.g., specific activity or in vivo enzymatic activity), reduced inhibition or degradation of the enzymes, and overexpression of the enzymes.
  • gene copy number can be increased, expression levels can be increased by use of a promoter that gives higher levels of expression than that of the native promoter, or a gene can be altered by genetic engineering or classical mutagenesis to increase the biological activity of an enzyme. Combinations of some of these modifications are also possible.
  • exogenous polynucleotides is intended to mean polynucleotides that are not derived from naturally occurring polynucleotides in a given organism. Exogenous polynucleotides may be derived from polynucleotides present in a different organism.
  • a yeast cell may be genetically modified with a nucleic acid construct which contains one or more exogenous polynucleotides, encoding one or more enzymes which enable the yeast cell to utilise methanol as a main source of energy.
  • the exogenous polynucleotides may be heterologous or homologous.
  • heterologous refers to a molecule or activity derived from a source other than the referenced species whereas “homologous” refers to a molecule or activity derived from the host microbial organism. Accordingly, exogenous expression of a nucleic acid molecule of the invention can be through the use of either or both a heterologous or homologous nucleic acid molecule.
  • the exogenous polynucleotides as herein described may be expressed from one or more chromosomal locations or from one or more plasmid locations. In other words, the polynucleotides encoding the proteins enabling growth on methanol may be provided on a single nucleic acid molecule, or multiple nucleic acid molecules.
  • the exogenous polynucleotides are derived from nucleic acid sequences found in the genome of methylotrophic organisms.
  • the exogenous nucleic acid may encode a protein from a methylotrophic organism such as from the genera Pichia, Candida, Hansen ula and Torulpsis.
  • the exogenous polynucleotides are derived from Pichia pastoris, Pichia methanolica, Candida boidinii and/or Hansenula polymorpha (also called Pichia augusta). In a preferred embodiment, the exogenous polynucleotides are from Pichia pastoris.
  • the exogenous polynucleotides may be provided in one or more expression constructs (plasmid vectors). Accordingly, in yet a further embodiment, the present invention provides a recombinant construct encoding at least one protein for enabling a yeast cell to grow in a medium in which methanol is the only or main energy source for growth of the cell in the medium, wherein the one or more proteins is selected from the group consisting of: alcohol oxidase (E.C. 1 .1.3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1 .3), dihydroxyacetone kinase (E.C.
  • alcohol oxidase E.C. 1 .1.3.13
  • pyruvate carboxylase E.C. 6.4.1 .1
  • dihydroxyacetone synthase E.C. 2.2.1 .3
  • dihydroxyacetone kinase E.C.
  • fructose-1 -6- bisphosphate aldolase E.C. 4.1 .2.13
  • fructose-1 -6-bisphophatase E.C. 3.1 .3.1 1
  • sedoheptulose bisphosphatase E.C. 3.1 .3.37
  • ribose-5-phosphate isomerase E.C. 5.3.1 .6
  • D-ribulose-5-phosphate-3-epimerase E.C. 5.1 .3.1
  • transketolase 1 or 2 E.C. 2.2.1.1
  • functional variants thereof E.C. 2.2.1.1
  • the exogenous polynucleotides are all provided on a single low-copy plasmid.
  • suitable plasmids include pRS415 and pRS416.
  • the present invention provides a plasmid which encodes one or more of AOX1 , PYC1 , DAS1 , DAK, FBA2, FBP1 , RKI1 , RPE1 , SHB17, TAL1 , AOX1 , DAS1 , PYC1 genes to encode part of a synthetic methanol utilisation pathway in yeast.
  • the plasmid encodes AOX1 , DAS1 and PYC1 genes.
  • the plasmid encodes AOX1 , DAS1 , PYC1 , DAK, FBA2, FBP1 , and SHB17 genes.
  • the plasmid encodes AOX1 , DAS1 , PYC1 , DAK, FBA2, FBP1 , SBPase, RPE1 and RKL1 genes and optionally also TAL1 .
  • nucleic acid constructs of the present invention include nucleic acid sequences encoding one or more of the subject proteins described herein.
  • the nucleic acid constructs also encode targeting sequences, to enable localisation of the encoded proteins to the desired subcellular organelle to facilitate optimal utilisation of methanol by the yeast cell.
  • the targeting sequence may be for targeting of a protein to the peroxisomes or mitochondria of the yeast.
  • the nucleic acid constructs may include nucleic acid sequences encoding peroxisomal targeting sequences adjacent to the sequence encoding the relevant protein, such that the synthesised protein includes an N-terminal, C-terminal or internal targeting sequence.
  • sequence encoding the subcellular targeting sequence may encode a type 1 or type 2 peroxisomal-targeting sequence (PTS1 or PTS2). Examples of PTS1 and PTS2 sequences are described above.
  • the polynucleotide encoding the subcellular targeting sequence may be an endogenous or exogenous sequence.
  • the sequence encoding the targeting sequence may be from the yeast cell which will be provided with the recombinant construct. Alternatively, an exogenous targeting sequence may be used.
  • localisation to the peroxisome may be desirable to ensure proper activity of the relevant protein.
  • catabolism of methanol results in the formation of oxidation products and toxins such as hydrogen peroxide and formaldehyde
  • This may also facilitate the compartmentalisation and detoxification of such toxins by proteins which are naturally found in the peroxisomes of the non- methylotrophic yeast cell.
  • proteins which are useful for detoxifying products of methanol catabolism include catalase, glutathione peroxidase.
  • the nucleic acids of the present invention are preferably operably linked to promoters such that the subject enzymes are expressed in the cell when cultured under suitable conditions.
  • the promoters may be specific for individual yeast cell species.
  • promoter refers to a non-coding sequence located upstream (i.e., 5') to the translation start codon of a structural gene (generally within about 1 to 1000 bp, preferably 1 -500 bp, especially 1 -100 bp) and which controls the start of transcription of a structural gene.
  • the promoter may be native to the host cell or exogenous.
  • the promoters can be those that control the expression of genes that are involved in central carbon metabolism, e.g., glycolytic promoters or TCA cycle gene promoters.
  • Suitable promoters include the non-limiting examples of promoters from yeast genes phosphoglycerate kinase (PGK), glyceraldehyde-3-phosphate dehydrogenase (TDH, including TDH3), pyruvate decarboxylase (PDC1 ), triose phosphate isomerase (TP1 ), Transcription enhancer factor-1 (TEF-1 ) (TEF2), purinecytosine permease (PCPL3), alcohol dehydrogenase (ADH), the SSA promoter, YEF3 promoter and PPI1 promoter.
  • Preferred promoters of the invention include the TEF-1 , TDH3, SSA, YEF3 and PPI1 (S.
  • PGK S. cerevisiae
  • PDCI S. cerevisiae, K. marxianus
  • galactose inducible GAL1 or glucose de-repressible SUC2 promoters may be used.
  • the promoters used in the nucleic acid constructs of the present invention are inducible promoters, for enabling expression of proteins under specific circumstances. For example, it may be desirable for the proteins to only be expressed by the yeast cell when the cell is exposed to high levels of methanol. In such circumstances, it may be desirable to utilise promoters which are induced by methanol. Some promoters may be induced by one substrate, by repressed by another. For example the P A ox promoter from Pichia pastoris is strongly induced by the presence of methanol, but repressed by the presence of glucose or ethanol.
  • the present invention also provides for nucleic acid constructs comprising one or more polynucleotides encoding any enzyme, as herein described, wherein the polynucleotide is operably linked to an inducible promoter, for inducing expression of the enzyme upon exposure to methanol.
  • the promoter is the P A ox promoter from Pichia pastoris.
  • the PMOX promoter from H. polymorpha
  • the PAODI promoter from C. boidinii
  • PMODI promoter from P. methanolica.
  • the activity and regulation of certain promoters described herein can be further controlled by the provision of one or more transcription factors to the yeast cell.
  • the present invention includes transforming the yeast cells with constructs expressing one or more transcription factors which activate or regulate any of the promoters used in accordance with the present invention.
  • the one or more transcription factors may activate a native S. cerevisiae promoter.
  • the native promoter that is activated by the one or more transcription factors may be operably linked to an endogenous S. cerevisiae gene sequence.
  • the native promoter may be operably linked to an exogenous polynucleotide that encodes an enzyme enabling methanol utilisation by a yeast cell.
  • the one or more transcription factors may activate a heterologous promoter that is operably linked to a polynucleotide encoding an enzyme enabling a yeast cell to utilise methanol as a source of energy.
  • the heterologous promoter is a Pichia pastoris promoter, and the one or more transcription factors activates the Pichia pastoris promoter.
  • the promoter is the P A ox promoter from Pichia pastoris, and the transcription factor is any one of the transcription factors Mit1 , Mxr1 and Prm 1 .
  • two or more of the transcription factors which activate the P A ox promoter from Pichia pastoris are used.
  • all three of the transcription factors Mit1 , Mxr1 and Prm1 are used. It will be clear that the present invention includes constructs and exogenous polynucleotides encoding said transcription factors.
  • Said constructs may be transformed into the yeast cells separately to the constructs which encode enzymes for enabling methanol utilisation by the yeast cell.
  • the polynucleotides encoding the transcription factors may be included in the same construct that encodes enzymes enabling methanol utilisation by the yeast cell.
  • the promoter sequence may be homologous to the promoter sequence of the gene where insertion is targeted.
  • the constructs may include sequences which enable integration of the polynucleotides into the yeast cells genome using CRE recombinase.
  • CRE recombinase CRE recombinase
  • the recombinant nucleic acid construct can and preferably does contain other elements as well, including (a) a terminator sequence; (b) one or more selection marker gene(s) (including an associated promoter and terminator); (c) one or more homologous flanking sequences for inserting the fragment at a particular locus in the genome of the host cell; (d) one or more restriction sites which enable it to be cut to form a linear fragment containing the gene encoding a relevant protein as herein described, its promoters and flanking sequences, marker genes and associated promoters and terminators, etc., for insertion into the genome of the yeast cell; and/or (e) a backbone portion.
  • nucleic acid is used herein to refer to any molecule (e.g., nucleic acid, plasmid or virus) used to transfer protein-coding information to the host cell.
  • Methods of transforming cells are well known in the art, and can include such non- limiting examples as electroporation, calcium chloride-, or lithium acetate-based methods.
  • the DNA used in the transformations can either be cut with particular restriction enzymes or uncut.
  • selection marker genes refer to genetic material that encodes a protein necessary for the survival and/or growth of a host cell grown in a selective culture medium.
  • Typical selection marker genes encode proteins that (a) confer resistance to antibiotics or other toxins, e.g., zeocin (sh ble gene from Streptoalloteichus hindustanus), G418 (kanamycin-resistance gene of Tn903), hygromycin (aminoglycoside antibiotic resistance gene from E.
  • coli coli
  • ampicillin tetracycline
  • kanamycin for host cells
  • kanamycin for host cells
  • b complement auxotrophic deficiencies of the cell and/or supply critical nutrients not available from simple media, such as amino acid leucine deficiency (K. marxianus Leu2 gene); or a K. marxianus ura3 gene that gives uracil to orotidine-5'-phosphate decarboxylase negative cells.
  • Preferred selectable markers include the non-limiting examples of zeocin resistance gene, G418 resistance gene, and the hygromycin resistance gene.
  • terminal refers to an untranscribed sequence located downstream
  • the terminator can be exogenous or native to the yeast species. Suitable exogenous terminators include the GAL10, CYC-1 ADH1 t, STE2, MFA1 , PHO5t and TPI1 terminators from S. cerevisiae or other yeast species.
  • the terminator sequence is homologous to a terminator sequence of the encoded gene.
  • Each nucleic acid sequence encoding the desired protein can be incorporated into an expression vector.
  • "Expression vector” or “vector” refers to a compound and/or composition that transduces, transforms, or infects a host cell, thereby causing the cell to express nucleic acids and/or proteins other than those endogenous to the cell, or in a manner not naturally occurring in the cell.
  • An expression vector contains a sequence of nucleic acids (ordinarily RNA or DNA) to be expressed by the host cell (in this case a yeast cell).
  • the expression vector also comprises materials to aid in achieving entry of the nucleic acid into the host microorganism, such as a virus, liposome, protein coating, or the like.
  • the expression vectors contemplated for use in the present invention include those into which a nucleic acid sequence can be inserted, along with any preferred or required operational elements. Further, the expression vector must be one that can be transferred into a host cell and replicated therein.
  • Preferred expression vectors are plasmids, particularly those with restriction sites that have been well-documented and that contain the operational elements preferred or required for transcription of the nucleic acid sequence. Such plasmids, as well as other expression vectors, are well known to those of ordinary skill in the art.
  • any suitable expression vector may be used to incorporate the desired sequences
  • readily-available expression vectors include, without limitation, plasmids, such as pSCIOI, pBR322, pBBRIMCS-3, pUR, pEX, pMRIOO, pCR4, pBAD24, pUC19, and bacteriophages, such as Ml 3 phage and ⁇ phage.
  • Yeast episomal plasmids (YEPs) and Yeast integrated plasmids (YIPs) may also be used.
  • the plasmids used are yeast centromeric plasmids containing selectable markers.
  • the plasmids used are yeast centromeric plasmids with LEU2 and/or URA3 genes as selectable markers.
  • expression vectors may only be suitable for particular host cells.
  • the expression vector can be introduced into the host cell, which is then monitored for viability and expression of the sequences contained in the vector.
  • the plasm id may be adapted for integration of the exogenous polynucleotides into the genome of the yeast cell.
  • the present invention provides a method for forming a metabolite derived from methanol in a yeast cell comprising providing the yeast cell with a recombinant construct encoding one or more proteins selected from the group consisting of: alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1 .3), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C.
  • alcohol oxidase E.C. 1 .1 .3.13
  • pyruvate carboxylase E.C. 6.4.1 .1
  • dihydroxyacetone synthase E.C. 2.2.1 .3
  • dihydroxyacetone kinase E.C. 2.
  • a P. pastoris pyruvate carboxylase is required for correct folding and import of alcohol oxidase protein monomers via the loading of a flavin adenine dinucleotide cofactor (FAD).
  • FAD flavin adenine dinucleotide cofactor
  • 3 moles of methanol are required to generate 1 mole of glyceraldehyde-3-phosphate, as 3 moles of xylulose-5-phosphate are required as input for dihydroxyacetone synthase mediated conversion of formaldehyde into dihydroxyaceyone synthase and glyceraldehyde-3- phosphate.
  • the present inventors have found that there are certain metabolites downstream of methanol which are key to providing the excess energy required to product industrial chemicals.
  • the present invention provides a method for forming a compound selected from the group consisting of xylulose-5- phosphate, glyceraldehyde-3-phosphate and dihydroxyacetone, in a yeast cell comprising providing the yeast cell with a recombinant construct encoding one or more proteins selected from the group consisting of: alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1 .3), dihydroxyacetone kinase (E.C.
  • fructose-1 -6-bisphosphate aldolase E.C. 4.1.2.13
  • fructose-1 -6-bisphophatase E.C. 3.1 .3.1 1
  • sedoheptulose bisphosphatase E.C. 3.1.3.37
  • ribose-5-phosphate isomerase E.C. 5.3.1.6
  • D-ribulose-5-phosphate-3-epimerase E.C. 5.1 .3.1
  • transketolase 1 or 2 E.C. 2.2.1 .1
  • transaldolase EC 2.2.1 .2
  • formaldehyde dehydrogenase E.C. 1.2.1 .46
  • biomass is intended to mean the collection of biological matter, made up of cells, that results from the culturing process of a microorganism under suitable conditions for the growth of that organism in culture.
  • the biomass includes simply the cells and their contents and in some cases, the biomass includes additionally any macromolecules, such as proteins, that are secreted into the culture, outside the boundary of the cell membrane.
  • culturing is intended to mean the growth or maintenance of microorganisms under laboratory or industrial conditions.
  • microorganisms can be cultured using liquid or solid media as a source of nutrients for the microorganisms.
  • some microorganisms can be cultured in defined media, in which the liquid or solid media are generated by preparation using purified chemical components.
  • the composition of the culture media can be adjusted to suit the microorganism or the industrial purpose for the culture.
  • Culturing parameters may include, but are not limited to, such features as the temperature of the culture media, the dissolved oxygen concentration, the dissolved carbon dioxide concentration, the rate of stirring of the liquid media, the pressure in the vessel, etc.
  • the yeast cells described herein are provided with methanol as either the major source or sole source of carbon.
  • methanol is a low-cost chemical which can also be derived from fossil sources (natural gas, coal, oil shale, tar sands, etc.), or from agricultural products and municipal waste, wood and varied biomass (via syngas, a CO- and H 2 - containing gas mixture generated by gasification of organic matter).
  • Methanol can also be made from chemical recycling of carbon dioxide by catalytic hydrogenation of CO2 with H 2 where the hydrogen has been obtained from water electrolysis. Methanol may also be produced through CO2 electrochemical reduction. While methanol may be added directly to the culture medium, the skilled person will appreciate that the methods of the present invention include the growth of yeast on or in a medium in which methanol is a crude component.
  • the source of methanol may be provided in the form of an agricultural waste product, in which methanol is the principal carbon component, but wherein other materials are present.
  • the present invention is useful for further metabolising waste from distillation of wood.
  • Additional nutrients may also be provided in the culture medium, such as sources of nitrogen, phosphorus, sulfur, trace minerals, etc. that promote the viability of the cells.
  • sources of nitrogen, phosphorus, sulfur, trace minerals, etc. that promote the viability of the cells.
  • the following may be provided in the culture medium:
  • Nicotinic acid 400 g/L
  • Citric acid 0.1 g/L
  • the media utilised can be commercially obtained (for example, Yeast Nitrogen Base without Amino Acids from Sigma Aldrich, supplemented with 0.5 -2 % w/v methanol).
  • the media utilised can be commercially obtained (for example, Yeast Nitrogen Base without Amino Acids from Sigma Aldrich, supplemented with 0.5 -2 % w/v methanol).
  • methanol is provided as the major, but not the sole source of carbon to the cell
  • any number of carbohydrates may be used to 'supplement' the carbon source.
  • examples of such carbohydrates are: hexose sugars such as glucose and fructose, oligomers of glucose such as maltose, isomaltose, maltotriose, starch, and sucrose, maltodextrins and xylose (a pentose sugar) are preferred.
  • Less preferred carbohydrates include galactose, mannose and arabinose.
  • the temperature during culturing of the microorganisms can be from about room temperature, more preferably from about 30°C, more preferably from about 35°C. Preferably the temperature does not exceed 40 °C.
  • the maximum temperature will depend on the particular yeast cell.
  • the yeast cell is K. marxianus, for example, the recombinant cell can tolerate relatively high temperatures (such as above 40°C and up to 50°C, especially up to 45°C).
  • the concentration of cells in the culture medium is typically in the range of about 1 -150, preferably about 3-10, even more preferably about 3-6 g dry cells/liter of culture medium.
  • the skilled person will be familiar with methods for determining the growth rate of the yeast cells, as a means for determining the ability of the cells to utilise methanol as a sole or major source of carbon.
  • the maximum specific growth rate for lab S. cerevisiae yeast strains when provided with glucose is around 0.45 h "1 (as compared with no growth when provided only with methanol; wherein the specific growth rate h "1 is defined as the rate of increase in biomass in grams of cells, per gram of cells, per hour).
  • the specific growth rate h "1 is defined as the rate of increase in biomass in grams of cells, per gram of cells, per hour.
  • evidence of methanol utilisation will be growth of the yeast strain at a rate somewhere between that of a typical S. cerevisiae lab strain in methanol and when provided with glucose.
  • the growth rate observed for the synthetic yeast strains of the present invention is approximately the same or greater than the growth rate observed for a methylotrophic strain, when grown under the same conditions.
  • the term "chemical” is broadly meant include any substance used in or resulting from a reaction involving changes to atoms or molecules, especially one derived according to any of the processes set forth herein.
  • a chemical is intended to mean a substance obtained by a chemical process or a substance having a chemical effect.
  • Examples of chemicals contemplated by the invention are dicarboxylic acid, malic acid, fumaric acid, succinic acid, malic acid salt, fumaric acid salt, succinic acid salt, L-malic acid, D-malic acid, maleic acid, lactic acid, adipic acid, 1 ,3-propanediol, 2,3-butanediol, 1 ,4-butanediol, butadiene, fatty acid derivatives, fatty alcohols, fatty acids, fatty acid esters, fatty acid methyl esters, fatty acid ethyl esters, branched fatty acids, branched fatty acid derivatives, omega-3 fatty acids, isoprenoids, isoprene, farnesene, farnesane, squalene, squalane, carotenoids, amino acids, alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, monoso
  • chemicals include, but are not limited to, ethanol, propanol, isopropanol, butanol, fatty alcohols, fatty acid esters, ethyl esters, wax esters; hydrocarbons and alkanes such as propane, octane, diesel, Jet Propellant 8 (JP8); polymers such as terephthalate, 1 ,3-propanediol, 1 ,4-butanediol, polyols, Polyhydroxyalkanoates (PHA), poly-beta-hydroxybutyrate (PHB), acrylate, adipic acid, ⁇ -caprolactone, isoprene, caprolactam, rubber; commodity chemicals such as lactate, docosahexaenoic acid (DHA), 3-hydroxypropionate, ⁇ -valerolactone, lysine, serine, aspartate, aspartic acid, sorbitol, ascorbate, ascorbic acid, isopenten
  • the methods of the present invention can be exploited to provide yeast strains which can be used to produce farnesene, farnesane, propanol, butanol, or octanol.
  • Other examples of chemical include, without limitation, all compounds that can be produced with the methods set forth herein. Such compounds are intended to include all molecules that can be constructed with the methods set forth herein including, for example without limitation, all organic and inorganic molecules that can be made with the methods set forth herein.
  • the term chemical is intended to include natural and non-natural compounds.
  • natural molecules include, but are not limited to, amino acids, nucleic acids, nucleotides and polynucleotides and all related biological molecules.
  • Non-natural compounds include, but are not limited to, amino acids and nucleotides that are modified in a way differently than they are normally modified in biological systems.
  • a chemical such as listed above, simply by growing the synthetic microorganisms described herein, under suitable conditions to produce the chemical.
  • the yeast can produce certain industrially relevant chemicals.
  • An example of this is ethanol, which is metabolite produced in abundance by yeast.
  • Other examples include glycerol and acetate.
  • yeast cells described herein can be further modified to express pathways capable of producing a number of useful products, including commodity chemicals such as those described herein.
  • the present invention provides a method for producing a chemical which can be used in an industrial process, the method comprising growing a yeast cell including a recombinant construct encoding one or more proteins that enable the cell to grow in a medium in which methanol is the only or main energy source for growth of the cell in the medium, wherein the one or more proteins is selected from the group consisting of: alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1 .3), dihydroxyacetone kinase (E.C.
  • fructose-1 -6-bisphosphate aldolase E.C. 4.1.2.13
  • fructose-1 -6-bisphophatase E.C. 3.1 .3.1 1
  • sedoheptulose bisphosphatase E.C. 3.1.3.37
  • ribose-5-phosphate isomerase E.C. 5.3.1.6
  • D-ribulose-5-phosphate-3-epimerase E.C. 5.1 .3.1
  • transketolase 1 or 2 E.C.
  • transaldolase EC 2.2.1 .2
  • formaldehyde dehydrogenase E.C, 1.2.1 .46
  • functional variants thereof wherein the yeast cell includes a further construct enabling the production of the chemical.
  • yeast cells described herein can function as 'platform strains' which can be grown on methanol as either a major or sole source of carbon. These platform strains can then be further manipulated using known methods to express biosynthetic pathways for the production of a chemical.
  • biosynthetic pathway also referred to as “metabolic pathway” refers to a set of anabolic or catabolic biochemical reactions for converting one chemical species into another.
  • biosynthetic pathways include: lactic acid production pathways, as described for example in US 7,405,068 (van Maris et al); malic acid and succinic acid production pathways, as described for example in WO 2007/06159 (Winkler et al); dicarboxylic acid production pathways, as described for example in WO2009/065780, WO 2009/101 180 and US 2012/0040422; cis,cis-muconic acid production pathways, for example, as described in Weber et al., (2012) Appl. Environ. Microbiol. 78: 8421 and Curran et al.,(2013) Metab. Eng. 15: 55-66); propionic acid (US 1898329) and para-hydroxybenzoic acid pathways (EP 2957629)
  • Example 1 Synthetic Methylotroph derived from S. cerevisiae
  • a genetically modified strain of S. cerevisiae is obtained by standard molecular cloning and metabolic engineering. Genes encoding proteins from P. pastoris are cloned and introduced into S. cerevisiae for enabling the S. cerevisiae to grow in a medium in which methanol is the main carbon source.
  • the genes encoding the enzymes alcohol oxidase, (EC 1 .1 .3.13, Aoxl, Aox2), dihydroxyacetone synthase (EC 2.2.1 .3, Dhas), and pyruvate carboxylase (EC 6.4.1 .1 , Pyc) are expressed from chromosomal integrated loci or from plasmids or both, wherein the enzymes are encoded by polynucleotides that are operably linked to a S. cerevisiae promoter, such as Pcycl, Padhl, Ptef2, Pgall.
  • S. cerevisiae promoter such as Pcycl, Padhl, Ptef2, Pgall.
  • the resultant strains containing these genes are tested for growth in minimal media supplemented with methanol. Strains that grow on methanol have functional methanol-consumption pathways.
  • Example 2 Induction of gene expression in S. cerevisiae
  • a genetically modified strain of S. cerevisiae is obtained by standard molecular cloning and metabolic engineering. Genes encoding proteins from P. pastoris are cloned and introduced into S. cerevisiae for enabling the S. cerevisiae to grow in a medium in which methanol is the main carbon source.
  • the genes encoding the enzymes alcohol oxidase, (EC 1 .1 .3.13, Aoxl, Aox2), dihydroxyacetone synthase (EC 2.2.1 .3, Dhas), and pyruvate carboxylase (EC 6.4.1 .1 , Pyc) are expressed from chromosomal integrated loci or from plasm ids or both using the Pichia pastoris promoter P A ox- The resultant strains containing these genes are tested for growth in minimal media supplemented with methanol. Strains that grow on methanol have functional methanol-consumption pathways.
  • a genetically modified strain of S. cerevisiae is obtained by standard molecular cloning and metabolic engineering. Genes encoding proteins from P. pastoris are cloned and introduced into S. cerevisiae for enabling the S. cerevisiae to grow in a medium in which methanol is the main carbon source.
  • the genes encoding the enzymes DAK, FBA2, FBP1 , RKI1 , RPE1 , SBPase, TAL1 , AOX1 , DAS1 , PYC1 are provided in a plasmid construct (see Figure 2).
  • the genes CTA1 , pmp20, and ADH1 genes for the detoxification of by-products of synthetic methylotrophic metabolism are provided in a separate construct (see Figure 3).
  • the resultant cells containing the construct are tested for growth in minimal media supplemented with methanol. Strains that grow on methanol have functional methanol- consumption pathways.
  • Example 4 Induction of gene expression in yeast A genetically modified strain of S. cerevisiae is obtained as described in Example
  • the strain is transformed with a construct containing polynucleotides encoding the transcription factors PRM1 , MIT1 , and MXR1 which were codon optimised for expression in S. cerevisiae, and had nuclear localisation sequences added to their C-termini.
  • MIT1 and PRM1 are expressed from their native P. pastoris promoters, while MXR1 is expressed from the S. cerevisiae PDA1 promoter.
  • the sequences for these parts are shown below.
  • An annotated vector map is shown in Figure 4.
  • the construct encoding the transcription factors is transformed into S. cerevisiae harbouring constructs encoding enzymes for methanol utilisation, where the polynucleotides encoding the enzymes are operably linked to the AOX promoter from Pichia pastoris.
  • the resultant strains containing these genes are tested for growth in minimal media supplemented with methanol.
  • P. pastoris PRM1 protein sequence with S. cerevisiae MATalpha2 nuclear localisation signal (KIPIK) (SEQ ID NO: 29)
  • P. pastoris PRM1 DNA sequence, codon optimised for expression in S. cerevisiae (SEQ ID NO: 30)
  • P. pastoris PRM1 promoter sequence (SEQ ID NO: 31 )
  • P. pastoris MIT1 protein sequence with S. cerevisiae MATalpha2 nuclear localisation signal (KIPIK) (SEQ ID NO: 32) MSTAAPIKEESQFAHLTLMNKDLPSNAKQAKSKVSAAPAKTSSRSAGGSGNNN AAPVKKRVRTGCLTCRKKHKKCDENRNPKCDFCTLKGLECVWPENNKKNIFVNNSMK DFLGKKPVEGADSLNLAMNLQQQQSSNAMGNQSLSSIGLESFGYGSGIKNEFNFQDLI GSNSGSSDPTFTVDADEAQKFDISSKNSRKRQKLGLLPVGNAASHLNGFNGISNGKSH SFSSPSGTNDDELSGLMFNSPSFNPLTVNDSTNNSNHNIGLSPMSCLFSTVQEASQKK HANSSRHFSYPSGPEDLWFNEFQKQALTANGENAVQQGDDASKDTTVIPKDESSNSS IFSSRSSAASSNSGDDVGRMGPFSKGPEIEFNYDSFLESL
  • P. pastoris MIT1 DNA sequence, codon optimised for expression in S. cerevisiae (SEQ ID NO: 33)
  • P. pastoris MXR1 protein sequence with S. cerevisiae SV40 nuclear localisation signal (PKKKRKV) (SEQ ID NO: 35)
  • P. pastoris MXR1 DNA sequence, codon optimised for expression in S. cerevisiae (SEQ ID NO: 36) ATGTCTCAAAAAAGACCAACTTCTTTGAGATTTATTACTTCTTTTCCAAGATTT CCAAAAAGATCTTTTTTTACTATGCCAGTTGTTTCTTCTTTGATTTCTTCTAATATTAA AAAATCTCCACAAGATAAAGTTGTTACTGTTGCTGGTGGTTGTTTTTGGGGTTTGGA ATATATTTATAAAATGCATTTTAAAGATAGAATTGTTGATACTCAAGTTGGTTGCT AATGGTAATTTGTCTAATCCAACTTATAAAGAAGTTTGTCAAGGTTTGACTTATCATG CTGAAGTTTTGCAAATTGCTTATAATCCAGAAGTTATTTCTTATAAAGAATTGATTGA TTTTTTTTTTGGTTCATGATCCAACTCAAGATGATGGTCAAGGTCCAGATATTGG TACTCAATATAAAAGATGATGGTCAACTCAAGATGATGGTCAAGATATTGG TACTCAATATA
  • Example 5 Assessing synthetic methanol assimilation pathway in Saccharomyces cerevisiae
  • the genes encoding peroxisomally-targetted alcohol oxidase, dihydroxyacetone synthase, catalase, pmp20), and cytosol localised alcohol dehydrogenase and pyruvate carboxylase, were introduced into an S. cerevisiae BY4741 strain. This strain had methionine and histidine autotrophies repaired such that growth without any amino acids added to the media was possible.
  • the methanol utilisation pathway genes were encoded on plasmids ScMOX3a and ScMOX2b ( Figures 6 and 3, respectively).
  • the strain was pre-cultured twice on minimal medium (Yeast nitrogen base without amino acids) with glucose as the sole carbon source prior to inoculation into either minimal medium without any carbon source ('without methanol', Figure 5), or minimal medium with 2% methanol as the sole carbon source ('with methanol', Figure 5). Both conditions were tested in triplicate.
  • the population density (optical density at 600nm, or OD600nm') was measured at 20 hours after residual glucose from the inoculum has been exhausted, and then again after 50 hours to analyse any potential growth due to the presence of methanol in the medium ( Figure 5).
  • the plasm ids ScMOX3a and ScMOX2b are also transformed into S. cerevisiae strain BY4741/CEN.PK2-1 c (a diploid hybrid). Strains of this background, with or without the plasm id-encoded methylotrophy genes are grown to exponential phase in glucose minimal medium, serially diluted to 10,000 fold, and each dilution spotted onto agar plates. Agar plates contain yeast nitrogen base with either; no carbon source, 1 % glucose, 1 % methanol, or 2% methanol. Growth of the control and methylotrophic strains are assessed according to the rate of single colony appearance over 5 -7 days at 30° Celsius.
  • Example 6 SCRaMbLE of ScMOX3a, ScMOX2b, and ScMOX3c genes onto synthetic chromosome XIV in a BY4741/CEN.PK2-1c diploid hybrid
  • the 'SCRaMbLE' system (Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution), is used to randomly integrate and duplicate LoxPSym flanked genes from the ScMOX3a, ScMOX2b, and ScMOX3c plasmids onto synthetic chromosome XIV in a diploid BY4741/CEN.PK2-1 c hybrid.
  • the SCRaMbLE system is disclosed in Dymon and Boeke (2012) Bioenginered Buds 3: 168-171 ; Jovicevic et al., (2014) Bioessays 36: 855-860; and Shen et al., (2016) Genome Res. 26: 36-49, the contents of which are hereby incorporated by reference in their entirety.
  • the "Synthetic Yeast Genome Project” involves the chemical synthesis, re-design, and replacement of the entire Saccharomyces cerevisiae genome.
  • One of the features of the synthetic yeast genome is the incorporation of 34 bp 'LoxPsym' motifs ( ATAACTTC GTATAATGTAC ATTATAC GAAGTTAT) 3bp after the stop codon of every non-essential gene in the genome.
  • Cre-recombinase enzyme When a heterologous Cre- recombinase enzyme is inducible expressed in a synthetic chromosome containing yeast strain, the LoxPSym sites are targeted for recombination by the Cre enzyme. This process results in every LoxPSym-flanked gene having a chance to be inverted, translocated, deleted, or duplicated, and creates a extreme genotypic and phenotypic diversity within a typical laboratory-scale yeast culture.
  • SCRaMbLE'd populations of the yeast cells produced according to the invention are plated onto agar plates with methanol as the only carbon source such that yeast cells with superior combinations and ratios of synthetic methylotrophy genes and chromosome XIV genes are selected for. Any fast-growing colonies derived from this process are then whole-genome re- sequenced to determine the content and ratio of methylotrophy and chromosome XIV genes. They are also used for adaptive laboratory evolution in liquid culture with methanol as the sole carbon source to additionally select for single nucleotide polymorphisms resulting in protein structural changes and altered promoter activity of native and synthetic genes.

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Abstract

The present invention relates to methods for engineering yeast strains which can be used in the production of industrially important chemicals. Nucleic acids encoding components of the methanol utilization pathway are used to modify yeast cells such as Saccharomyces cerevisiae to enable them to grow in media in which methanol is the only or main energy source. The nucleic acids may encode proteins including alcohol oxidase, dihydroxyacetone synthase, dihydroxyacetone kinase, fructose- 1-6-bisphosphate aldolase, fructose-1-6-bisphosphatase, sedoheptulose bisphosphatase, ribose-5-phosphate isomerase, D-ribulose-5-phosphate-3-epimerase, transketolase 1 or 2, transaldolase and formaldehyde dehydrogenase.

Description

METHOD OF PRODUCING CHEMICALS IN YEAST
Field of the invention
The present invention relates to genetically modified strains of yeast which can be grown on alternative energy sources and used to produce industrial chemicals. Associated provisional application
This application claims priority from Australian provisional application AU2017900129, the contents of which are hereby incorporated by reference in their entirety.
Background of the invention Microorganisms can be engineered to produce valuable chemicals including fuels and pharmaceuticals as a sustainable and environmentally-friendly alternative to petroleum-based production of these products.
Feedstocks used to grow engineered microbes typically consist of a sugar or sugar-rich substrate. However, the price of sugar from corn or sugarcane has thus far exceeded the cost of microbial chemical production processes. Furthermore, the use of corn and sugarcane for the production of biofuels and other chemicals, competes with the use of these resources in the human/animal food supply chain.
An attractive alternative to the use of expensive sugar-based substrates is to utilise waste materials as a source of energy for yeast to grow. Methanol is a cheap and abundant potential carbon source for bioprocesses, as it can be chemically derived from methane from sources such as landfills, or from carbon monoxide and hydrogen generated from gasification of wood waste. Engineering yeast to grow on methanol would therefore alleviate the economic strain on bioprocesses that depend on expensive feedstocks. While there are naturally occurring species of bacteria and yeast which are able to grow on methanol, these organisms have not been extensively characterised nor are they amendable to the genetic manipulation that is required for them to be suitable candidates for the production of industrial chemicals. Moreover, the methanol utilisation of these organisms has evolved out of a need to survive in environments of low energy supply, which means that when these organisms are grown on methanol, there is insufficient excess metabolic energy remaining to drive the production of industrially important chemicals. There is a need to develop alternative methods for growing microorganisms so that they can be used in the production of industrially important chemicals. In particular, there is a need to develop microorganisms such as yeasts to utilise alternative feedstocks as a source of energy.
Reference to any prior art in the specification is not an acknowledgment or suggestion that this prior art forms part of the common general knowledge in any jurisdiction or that this prior art could reasonably be expected to be understood, regarded as relevant, and/or combined with other pieces of prior art by a skilled person in the art.
Summary of the invention The present invention provides a yeast cell including a recombinant construct encoding one or more proteins that enable the cell to grow in a medium in which methanol is the only or main energy source for growth of the cell in the medium, wherein the one or more proteins is selected from the group consisting of: alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1 .3), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1 .3.1 1 ), sedoheptulose bisphosphatase (E.C. 3.1 .3.37), ribose-5-phosphate isomerase (E.C. 5.3.1.6) and D-ribulose-5-phosphate-3-epimerase (E.C. 5.1 .3.1 ), transketolase 1 or 2 (E.C. 2.2.1 .1 ), transaldolase (EC 2.2.1.2), formaldehyde dehydrogenase (E.C. 1.2.1 .46) or functional variants thereof.
In a further aspect, the invention provides a method for forming a compound selected from the group consisting of xylulose-5-phosphate, glyceraldehyde-3- phosphate and dihydroxyacetone in a yeast cell comprising providing the yeast cell with a recombinant construct encoding one or more proteins selected from the group consisting of: alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1 .3), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1 .3.1 1 ), sedoheptulose bisphosphatase (E.C. 3.1.3.37), ribose-5-phosphate isomerase (E.C. 5.3.1.6) and D-ribulose-5-phosphate-3-epimerase (E.C. 5.1 .3.1 ), transketolase 1 or 2 (E.C. 2.2.1.1 ), transaldolase (EC 2.2.1 .2), formaldehyde dehydrogenase (E.C. 1.2.1 .46) or functional variants thereof; and growing the yeast cell in a medium in which methanol is the only or main energy source for growth of the cell in the medium. The invention also provides a method for producing a chemical which can be used in an industrial process, the method comprising growing a yeast cell including a recombinant construct encoding one or more proteins that enable the cell to grow in a medium in which methanol is the only or main energy source for growth of the cell in the medium, wherein the one or more proteins is selected from the group consisting of: alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1.3), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1 .3.1 1 ), sedoheptulose bisphosphatase (E.C. 3.1.3.37), ribose-5-phosphate isomerase (E.C. 5.3.1.6) and D-ribulose-5-phosphate-3-epimerase (E.C. 5.1 .3.1 ), transketolase 1 or 2 (E.C. 2.2.1.1 ), transaldolase (EC 2.2.1 .2), formaldehyde dehydrogenase (E.C. 1.2.1 .46) or functional variants thereof, wherein the yeast cell includes a further construct enabling the production of the chemical.
The invention provides a recombinant construct encoding at least one protein for enabling a yeast cell to grow in a medium in which methanol is the only or main energy source for growth of the cell in the medium, wherein the one or more proteins is selected from the group consisting of: alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1.3), dihydroxyacetone kinase (E.C. 2.7.1 .29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1 .2.13), fructose-1 -6-bisphophatase (E.C. 3.1 .3.1 1 ), sedoheptulose bisphosphatase (E.C. 3.1 .3.37), ribose-5-phosphate isomerase (E.C. 5.3.1 .6) and D- ribulose-5-phosphate-3-epimerase (E.C. 5.1 .3.1 ), transketolase 1 or 2 (E.C. 2.2.1.1 ), iransaldolase (EC 2.2.1 .2), formaldehyde dehydrogenase (E.C. 1 .2.1 .46) or functional variants thereof.
The invention provides a recombinant construct encoding at least one protein when used to enable a yeast cell to grow in a medium in which methanol is the only or main energy source for growth of the cell in the medium, wherein the one or more proteins is selected from the group consisting of: alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1.3), dihydroxyacetone kinase (E.C. 2.7.1 .29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1 .2.13), fructose-1 -6-bisphophatase (E.C. 3.1 .3.1 1 ), sedoheptulose bisphosphatase (E.C. 3.1 .3.37), ribose-5-phosphate isomerase (E.C. 5.3.1 .6) and D- ribulose-5-phosphate-3-epimerase (E.C. 5.1 .3.1 ), transketolase 1 or 2 (E.C. 2.2.1.1 ), iransaldolase (EC 2.2.1 .2), formaldehyde dehydrogenase (E.C. 1 .2.1 .46) or functional variants thereof. As used herein, except where the context requires otherwise, the term
"comprise" and variations of the term, such as "comprising", "comprises" and "comprised", are not intended to exclude further additives, components, integers or steps.
It will be understood that the invention disclosed and defined in this specification extends to all alternative combinations of two or more of the individual features mentioned or evident from the text or drawings. All of these different combinations constitute various alternative aspects of the invention.
Further aspects of the present invention and further embodiments of the aspects described in the preceding paragraphs will become apparent from the following description, given by way of example and with reference to the accompanying drawings.
Brief description of the drawings
Figure 1 : Schematic of a synthetic methanol utilisation pathway according to the present invention. Enzymes (in dotted circles) catalysing reactions (arrows) between metabolites (black text) necessary for the assimilation of methanol into native yeast metabolism and growth on methanol as the sole carbon source. Underlined enzymes represent enzymes expressed in addition to native S. cerevisiae enzymes. Peroxisomal localisation of relevant proteins is indicated. Enzyme abbreviations are as follows: AOD (alcohol oxidase), PYC (pyruvate carboxylase), CTA (catalase), pmp20 (peroxisomal membrane associated protein 20), DAS (dihydroxyacetone synthase), DAK (dihydroxyacetone kinase), FBA (Fructose-1 -6-bisphoshate aldolase), FBP (Fructose-1 - 6-bisphosphatase), SHB (Sedoheptulose bisphosphatase, also referred to herein as SBPase), RKI (Ribose-5-phosphate ketol isomerase), RPE (D-ribulose-5-phosphate-3- epimerase). The following metabolite abbreviations were used: DHA (dihydroxyacetone), Xu5P (xylulose-5-phosphate), GA3P (glyceraldehyde-3- phosphate), DHAP (dihydroxyacetone phosphate), F1 ,5BP (fructose-1 -5-bisphosphate), F6P (fructose-6-phosphate), E4P (erythrose-4-phosphate), S1 ,7BP (sedoheptulose 1 ,7- bisphosphate), S7P (sedoheptulose-7-phosphate), R5P (ribose-5-phosphate), Rul5P (ribulose-5-phosphate), RCOOOH (alkyl hydroperoxide), RCOOH (reduced alkyl hydroperoxide), GSSG (oxidised glutathione), GSH (oxidised form of glutathione). Figure 2: pRS416 plasmid containing DAK, FBA2, FBP1 , RKI1 , RPE1 , SBPase,
TAL1 , AOX1 , DAS1 , PYC1 genes to encode part of a synthetic methanol utilisation pathway in yeast.
Figure 3: pRS415 plasmid containing CTA1 , pmp20, and ADH1 genes for the detoxification of by-products of synthetic methylotrophic metabolism. Figure 4: Vector map containing genes and promoters for methanol mediated gene expression in S. cerevisiae.
Figure 5: Growth over 30 hours with and without methanol. An S. cerevisiae strain expressing peroxisome localised Pichia pastoris enzymes (alcohol oxidase, dihydroxyacetone synthase, catalase, pmp20), and cytosol localised alcohol dehydrogenase and pyruvate carboxylase, was cultured with and without methanol in yeast nitrogen base medium over 30 hours. Optical density at 600 nm was measured to infer growth, with the percentage increase between 20 and 30 hours post inoculation shown. Data and error bars represent mean and ± 1 standard deviation from triplicate cultures. Detailed description of the embodiments
Reference will now be made in detail to certain embodiments of the invention. While the invention will be described in conjunction with the embodiments, it will be understood that the intention is not to limit the invention to those embodiments. On the contrary, the invention is intended to cover all alternatives, modifications, and equivalents, which may be included within the scope of the present invention as defined by the claims.
One skilled in the art will recognize many methods and materials similar or equivalent to those described herein, which could be used in the practice of the present invention. The present invention is in no way limited to the methods and materials described. It will be understood that the invention disclosed and defined in this specification extends to all alternative combinations of two or more of the individual features mentioned or evident from the text or drawings. All of these different combinations constitute various alternative aspects of the invention. All of the patents and publications referred to herein are incorporated by reference in their entirety.
For purposes of interpreting this specification, terms used in the singular will also include the plural and vice versa.
Yeasts are commonly used in industrial technology and have been engineered to produce a variety of valuable chemicals and biofuels. However, the reliance on carbon feedstocks derived from sugar from plant biomass for growth of these microorganisms represents a significant cost-impediment for the future large-scale reliance on microbial sources of industrially important chemicals.
Methanol is a cheap source of carbon and can be derived from landfill gas and wood-waste, making it a cost-effective and easily obtained source of carbon for the growth of yeasts used in the manufacture of industrial chemicals. Methylotrophic yeasts (i.e., yeasts that are able to metabolise methanol or methane) are not readily amendable to the genetic modification required for the production of industrial chemicals. Moreover, yeasts which are naturally methylotrophic do not generate sufficient energy to be able to drive synthesis of the metabolites required the production of industrial chemicals. On the other hand, the yeasts which have been exploited to date for the production of industrial chemicals, such as Saccharomyces cerevisiae, are not naturally methylotrophic (i.e., do not have a natural capacity to utilise methane or methanol as a major source of energy). Attempts to modify yeasts such as S. cerevisiae so that they are able to grow on methanol have thus far been unsuccessful, suggesting that more is required than simply genetically modifying the cells to express an enzyme capable of degrading methanol.
An advantage of the present invention is that it provides yeast which are not naturally methylotrophic with a novel metabolic pathway in the form of one or more proteins for enabling the yeast cells to grow where methanol is the only or main source of carbon source provided to the cells for growth. The metabolic pathway is provided to yeast cells in the form of recombinant nucleic acid. The constructs described herein encode proteins which enable yeast to utilise methanol as a major or sole source of carbon for the yeast to grow. In addition, the proteins enable the production of metabolites from methanol which serve as a source of energy for the subsequent generation of industrial chemicals by the yeast cells.
The present invention has a significant advantage over previous attempts to provide yeasts, such as S. cerevisiae with a means to utilise methanol as a carbon source. This is because the present invention provides a minimum complement of the necessary proteins required to generate carbon metabolites that the yeast can utilise for growth (i.e., to generate a biomass of yeast) and excess energy to enable the yeast to synthesise the a chemical product. Thus, the present inventors have identified why others have previously failed to adapt non-methylotrophic yeasts to utilise methanol as a major source of carbon. Contrary to the approach adopted by others, the inventors have determined that it is simply not enough to provide yeast with a single enzyme, e.g., alcohol oxidase, for metabolising methanol in order for the yeast to be able to utilise methanol as a source of energy.
As used herein, the term 'methylotroph' refers to any microorganism that, in its naturally occurring state (i.e., without genetic modification) can utilise reduced one- carbon compounds (such as methanol or methane) as a source of energy for growth and proliferation. Microorganisms of this type should not be confused with methanogens which on the contrary produce methane as a by-product from various one-carbon compounds such as carbon dioxide. Some methylotrophs can also degrade the greenhouse gas methane, and in this case they are called methanotrophs. It follows that a non-methylotrophic yeast cell is one which, in its naturally occurring state, is unable to utilise one-carbon compounds such as methanol as a source of energy.
As used herein, a non-methylotrophic yeast cell is a yeast cell which is unable to utilise methanol as a major or sole source of carbon, unless provided with a synthetic Methanol Utilisation Pathway, as herein described.
Commonly known non-methylotrophic yeast cells include microorganisms of the species Saccharomyces cerevisiae (commonly known as bakers' yeast), Kluyveromyces lactis (and the related yeast Kluyveromyces marxianus), Yarrowia lipolytica, Schizosaccharomyces pombe and Arxula adeninivorans. In any embodiment of the present invention, the yeast cell provided a recombinant construct encoding one or more proteins enabling growth of the cell in methanol, can be any yeast which is not otherwise able to grow on methanol such as those described above. In a preferred embodiment, the yeast cell is Saccharomyces cerevisiae.
As used herein, the term "carbon source" is intended to mean a raw material input to a microbial culture that contains carbon atoms that can be used by the microorganism as a source of energy for growth and the manufacture of industrial chemicals in the culture. As provided herein, the carbon source is preferably methanol.
The skilled person will appreciate the distinction between the ability of a microorganism to metabolise a substrate to provide energy and the ability of the microorganism to use that substrate as a sole source of carbon for energy. For example, in some embodiments, the culture of microorganisms contains methanol as the major source of carbon, but other sources of carbon are also provided in the culture. As such, as used herein, "major carbon source" is intended to mean that the culture media contains methanol as the main source of total carbon atoms in the media. For example, media comprising methanol as a major carbon source may be a medium where methanol represents at least about 50% or more of the total carbon atoms in the medium, preferably about 60% or more of the total carbon atoms in the medium, preferably 70% or more of the total carbon atoms in the medium, preferably about 80% or more of the total carbon atoms in the medium or preferably about 90% or more of the total carbon atoms in the medium.
Where methanol is the sole source of carbon in the culture medium, 100% of the total carbon atoms in the medium are derived from methanol. As used herein, 'methanol as a sole source of carbon' means that the microorganism must be able to be grown in media where the only source of carbon provided is methanol.
Yeast cells of the invention
The present invention provides a yeast cell including a recombinant construct encoding one or more proteins that enable the cell to grow in a medium in which methanol is the only or main energy source for growth of the cell in the medium, wherein the one or more proteins is selected from the group consisting of: alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1 .3), transaldo!ase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1 .29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1 .2.13), fructose-1 -6-bisphophatase (E.C. 3.1 .3.1 1 ), sedoheptulose bisphosphatase (E.C. 3.1 .3.37), ribose-5-phosphate isomerase (E.C. 5.3.1 .6) and D-ribulose-5- phosphate-3-epimerase (E.C. 5.1 .3.1 ), transketolase 1 or 2 (E.C. 2.2.1 .1 ), or functional variants thereof.
In yet a further embodiment, the present invention provides a synthetic microorganism, wherein the organism comprises a yeast cell that cannot grow if methanol is the only or major carbon source, wherein the yeast cell has been genetically modified to express one or more proteins which enable the yeast cell to utilise methanol as a source of carbon, the proteins being selected from the group consisting of alcohol oxidase (E.C. 1 .1.3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1 .3), transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1 .29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1 .2.13), fructose-1 -6-bisphophatase (E.C. 3.1 .3.1 1 ), sedoheptulose bisphosphatase (E.C. 3.1 .3.37), ribose-5-phosphate isomerase (E.C. 5.3.1 .6) and D-ribulose-5- phosphate-3-epimerase (E.C. 5.1 .3.1 ), transketolase 1 or 2 (E.C. 2.2.1 .1 ), or functional variants thereof. The yeast cell can be any of the species Saccharomyces cerevisiae, Kluyveromyces lactis, Kluyveromyces marxianus, Yarrowia lipolytica, Schizosaccharomyces pombe or Arxula adeninivorans. Preferably, the synthetic microorganism is a genetically modified Saccharomyces cerevisiae. It will be appreciated that any number of different strains of the above mentioned yeast species can be used. For example, suitable strains of S. cerevisiae include CEN.PK, S288c, BY4741 , and hybrid strains thereof.
In one example, the yeast cell has been transformed with one or more recombinant constructs that encode the proteins alcohol oxidase (E.C. 1.1 .3.13), dihydroxyacetone synthase (E.C. 2.2.1 .3) and pyruvate carboxylase (E.C. 6.4.1 .1 ), thereby enabling the cell to grow in a medium in which methanol is the major or sole source of carbon.
In one example, the yeast cell has been transformed with one or more recombinant constructs that encode the proteins: alcohol oxidase (E.C. 1.1 .3.13), pyruvate carboxylase (E.C. 6.4.1.1 ) and transaldolase (EC 2.2.1 .2), or functional variants thereof.
In one example, the yeast cell has been transformed with one or more recombinant constructs that encode the proteins: alcohol oxidase (E.C. 1.1 .3.13), pyruvate carboxylase (E.C. 6.4.1.1 ), dihydroxyacetone synthase (E.C. 2.2.1 .3), and transaldolase (EC 2.2.1 .2), or functional variants thereof.
In one example, the yeast cell has been transformed with one or more recombinant constructs that encode the proteins alcohol oxidase (E.C. 1.1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1 .3), dihydroxyacetone kinase (E.C. 2.7.1 .29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1 .2.13) and fructose-1 -6-bisphophatase (E.C. 3.1 .3.1 1 ), or functional variants thereof.
In one example, the yeast cell has been transformed with one or more recombinant constructs that encode the proteins alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1 .29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1 .2.13) and fructose- 1 -6-bisphophatase (E.C. 3.1.3.1 1 ), or functional variants thereof. In one example, the yeast cell has been transformed with one or more recombinant constructs that encode the proteins alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1), dihydroxyacetone synthase (E.C. 2.2.1.3), transaldo!ase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6- bisphosphate aldolase (E.C.4.1.2.13) and fructose-1 -6-bisphophatase (E.C.3.1.3.11), or functional variants thereof.
In one example, the yeast cell has been transformed with one or more recombinant constructs that encode the proteins alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) and dihydroxyacetone synthase (E.C. 2.2.1.3), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1.3.11) and sedoheptulose bisphosphatase (E.C.3.1.3.37), or functional variants thereof.
In one example, the yeast cell has been transformed with one or more recombinant constructs that encode the proteins alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C.2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C.4.1.2.13), fructose-1 -6- bisphophatase (E.C. 3.1.3.11) and sedoheptulose bisphosphatase (E.C. 3.1.3.37), or functional variants thereof.
In one example, the yeast cell has been transformed with one or more recombinant constructs that encode the proteins alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) dihydroxyacetone synthase (E.C. 2.2.1.3), transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6- bisphosphate aldolase (E.C.4.1.2.13), fructose-1 -6-bisphophatase (E.C.3.1.3.11) and sedoheptulose bisphosphatase (E.C.3.1.3.37), or functional variants thereof. In one example, the yeast cell has been transformed with one or more recombinant constructs that encode the proteins alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) and dihydroxyacetone synthase (E.C. 2.2.1.3), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1.3.11), sedoheptulose bisphosphatase (E.C. 3.1.3.37), ribose-5-phosphate isomerase (E.C. 5.3.1.6) and D-ribulose-5- phosphate-3-epimerase (E.C.5.1.3.1), or functional variants thereof. In one example, the yeast cell has been transformed with one or more recombinant constructs that encode the proteins alcohol oxidase (E.C. 1.1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) and transaldolase (EC 2,2.1 .2), dihydroxyacetone kinase (E.C. 2.7.1 .29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1 .2.13), fructose-1 -6- bisphophatase (E.C. 3.1.3.1 1 ), sedoheptulose bisphosphatase (E.C. 3.1 .3.37), ribose-5- phosphate isomerase (E.C. 5.3.1 .6) and D-ribulose-5-phosphate-3-epimerase (E.C. 5.1 .3.1 ), or functional variants thereof.
In one example, the yeast cell has been transformed with one or more recombinant constructs that encode the proteins alcohol oxidase (E.C. 1.1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) and dihydroxyacetone synthase (E.C. 2.2.1 .3), transaldolase (EC 2.2.1 .2), dihydroxyacetone kinase (E.C. 2.7.1 .29), fructose-1 -6- bisphosphate aldolase (E.C. 4.1 .2.13), fructose-1 -6-bisphophatase (E.C. 3.1 .3.1 1 ), sedoheptulose bisphosphatase (E.C. 3.1.3.37), ribose-5-phosphate isomerase (E.C. 5.3.1 .6) and D-ribulose-5-phosphate-3-epimerase (E.C. 5.1 .3.1 ), or functional variants thereof.
In addition to the above combinations of enzymes, the yeast cell has been transformed with one or more recombinant constructs that encode one or more of the proteins transketolase 1 or 2 (E.C. 2.2.1 .1 ), catalase (E.C. 1 .1 1.1 .6), glutathione peroxidase (E.C. 1 .1 1.1 .9) and methyl formate-synthesising alcohol dehydrogenase (E.C. 1 .1 .1.1 ), or functional variants thereof.
In particularly preferred embodiments, the above-described yeast cells are strains of Saccharomyces cerevisiae.
Still further, and in addition to the combinations of genes described above, the yeast cell may be transformed with a recombinant construct which encodes an endogenous protein from the yeast strain, for example for the purpose of over- expressing the endogenous protein in the cell. One example of this is the use of a recombinant construct encoding the protein formaldehyde dehydrogenase (SFA1 , E.C. 1 .2.1 .46) to overexpress the native formaldehyde dehydrogenase gene from Saccharomyces cerevisiae in a cell transformed according to any one of the above embodiments. In yet further aspects of the invention, the yeast cell can be any yeast cell which is unable to grow if methanol is the major or sole source of carbon provided to the yeast in the growing medium. In some embodiments, the yeast cell may comprise a genetic modification to the extent that it has some of the proteins which may be required for growth of the yeast on methanol, but does not yet have the full complement of proteins enabling growth on methanol as a major or sole carbon source. In other words, the construct is essential for enabling the cell to grow in the medium and providing the yeast cell with the recombinant construct provided to the yeast cell is what is required to enable the cell to grow in the medium. For example, the present invention also provides a yeast cell including a recombinant construct as herein described, encoding one or more proteins that enable the cell to grow in a medium in which methanol is the only or main energy source for growth of the cell in the medium, wherein the cell contains a gene encoding a protein selected from the group consisting of alcohol oxidase (E.C. 1 .1.3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1 .3), transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1 .29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1 .2.13), fructose-1 -6-bisphophatase (E.C. 3.1 .3.1 1 ), sedoheptulose bisphosphatase (E.C. 3.1 .3.37), ribose-5-phosphate isomerase (E.C. 5.3.1 .6) and D-ribulose-5- phosphate-3-epimerase (E.C. 5.1 .3.1 ), transketolase 1 or 2 (E.C. 2.2.1 .1 ), or functional variants thereof; and wherein the gene is not comprised in the recombinant construct. In other words, in certain embodiments, the above listed genes are comprised in the genome of the cell but not in the construct such that the construct comprises the additional relevant genes which enable the cell to utilise methanol as a major or sole source of carbon. In other words, while the cell may have some of the components of a methanol utilisation pathway, it is unable to utilise methanol until it is provided with a construct of the invention.
The terms "recombinant microorganism," "synthetic microorganism", "modified microorganism," and "recombinant host cell" are used interchangeably herein and refer to microorganisms, especially yeast, that have been genetically modified to include a recombinant construct as herein described, for example to express or to overexpress endogenous polynucleotides, to express heterologous polynucleotides, such as those included in a vector, in an integration construct, or which have an alteration in expression of an endogenous gene. The yeast cells of the invention can be obtained by providing or inserting one or more recombinant constructs or nucleic acid fragments, as herein described, encoding proteins for enabling the yeast to grow on methanol.
Any of the methods known conventionally in the art may be used to transform a yeast cell with the recombinant constructs herein described. For example, standard methods of yeast transformation using lithium acetate and polyethylene glycol will be well known to the skilled person for the purposes of generating stable transformants. Successful transformants can be detected through the use of selectable markers, also encoded by the nucleic acid constructs. Again, the skilled person will be familiar with such methods for determining successful transformation of a nucleic acid construct into a microorganism. Alternative methods for integrating the genes of interest into the genome can be used, for example, using CRISPR/Cas9 methods, or homologous recombination methods such that the yeast genome is permanently altered to encode genes required for methanol utilisation.
Suitable methods of transforming yeast cells are described in WO 00/71738A1 and WO 02/42471 A1 . The terms "transforming" and "transformation" as used herein refers to a change in a cell's genetic characteristics, and a cell has been transformed when it has been modified to contain a new nucleic acid. Thus, a cell is transformed where it is genetically modified from its native state. For example, following transfection, transforming DNA may recombine with cellular genomic DNA by physically integrating into a chromosome of the cell. Alternatively, the nucleic acid can be maintained transiently as an episomal element without being replicated, or may replicate independently as a plasmid. For example, in S. cerevesiae, expression vectors can be maintained stably in cells over many generations, provided that selection markers are continually selected for via the exclusion of relevant growth medium component. (By way of further example, some vectors include marker genes for leucine biosynthesis or uracil biosynthesis and thus, when a strain of yeast that does not express these genes is transformed with plasm ids encoding the relevant markers, transformants can be selected for using growth medium which does not contain uracil or leucine, or other component required for growth, as the case may be).
The term "transfection" is used to refer to the uptake of foreign or exogenous DNA by a cell, and a cell has been "transfected" when the exogenous DNA has been introduced inside the cell membrane. A number of transfection techniques are well known in the art. See, e.g., Graham et al., 1973. Virology 52:456; Sambrook et al., 2001 , MOLECULAR CLONING, A LABORATORY MANUAL, Cold Spring Harbor Laboratories; Davis et al., 1986, BASIC METHODS IN MOLECULAR BIOLOGY, Elsevier; and Chu et al., 1981 , Gene 13: 197. Such techniques can be used to introduce one or more exogenous polynucleotides into suitable host cells.
Proteins enabling yeast to utilise methanol
The one or more proteins which enable the yeast cells to grown in methanol as the main or sole energy source comprise, consist essentially of or consist of enzymes facilitating the conversion of methanol into downstream carbon-based metabolites. The proteins may also comprise, consist essentially of, or consist of enzymes which facilitate the detoxification of bi-products formed during the metabolism of methanol (and its downstream metabolites) and/or proteins which enable the proper folding, localisation and function of key enzymes in the pathway. As used herein, the term "enzyme" is intended to refer to molecules that accelerate or catalyze chemical reactions. Almost all metabolic processes in the cell need enzymes in order to occur at rates fast enough to sustain life.
The proteins which may be encoded by the recombinant constructs described herein and which are useful in the invention are described below: - alcohol oxidase (AOX, AOX1 , AOX2, AOD E.C. 1 .1.3.13), being any enzyme catalysing the reaction of a primary alcohol plus oxygen to an aldehyde plus hydrogen peroxide. In a preferred embodiment, the alcohol oxidase catalyses the conversion of methanol to formaldehyde. In certain embodiments, the AOX is AOX1 or AOX 2 from Pichia pastoris. Preferably, the AOX protein is AOX1 from Pichia pastoris. An example of the protein sequence of AOX1 is shown in SEQ ID NO: 1 (AOX1 from Pichia pastoris)
MAIPEEFDILVLGGGSSGSCIAGRLANLDHSLKVGLIEAGENNLNNPWVYLPGIYPRNM KLDSKTASFYTSNPSPHLNGRRAIVPCANVLGGGSSINFMMYTRGSASDYDDFQAEG WKTKDLLPLMKKTETYQRACNNPDIHGFEGPIKVSFGNYTYPVCQDFLRASESQGIPY VDDLEDLVTAHGAEHWLKWINRDTGRRSDSAHAFVHSTMRNHDNLYLICNTKVDKIIV EDGRAAAVRTVPSKPLNPKKPSHKIYRARKQIVLSCGTISSPLVLQRSGFGDPIKLRAA GVKPLVNLPGVGRNFQDHYCFFSPYRIKPQYESFDDFVRGDAEIQKRVFDQWYANGT GPLATNGIEAGVKIRPTPEELSQMDESFQEGYREYFEDKPDKPVMHYSIIAGFFGDHTK IPPGKYMTMFHFLEYPFSRGSIHITSPDPYAAPDFDPGFMNDERDMAPMVWAYKKSR ETARRMDHFAGEVTSHHPLFPYSSEARALEMDLETSNAYGGPLNLSAGLAHGSWTQP LKKPTAKNEGHVTSNQVELHPDIEYDEEDDKAIENYIREHTETTWHCLGTCSIGPREGS KIVKWGGVLDHRSNVYGVKGLKVGDLSVCPDNVGCNTYTTALLIGEKTATLVGEDLGY SGEALDMTVPQFKLGTYEKTGLARFPEALIKSMTSKL. Underlined sequence refers to a type 1 peroxisomal targeting sequence (PTS1 ).
An example of a polynucleotide encoding an AOX1 polypeptide is shown in SEQ ID NO: 2 (sequence is codon optimised for expression in S. cerevisiae and also encodes a C-terminal PTS1 sequence):
ATGGCTATTCCAGAAGAATTCGACATTTTGGTTTTGGGTGGTGGTTCTTCTGGTTCT TGTATTGCTGGTAGATTGGCTAACTTGGACCACTCTTTGAAGGTTGGTTTGATTGAA GCTGGTGAAAACAACTTGAACAACCCATGGGTTTACTTGCCAGGTATTTACCCAAG AAACATGAAGTTGGACTCTAAGACTGCTTCTTTCTACACTTCTAACCCATCTCCACA CTTGAACGGTAGAAGAGCTATTGTTCCATGTGCTAACGTTTTGGGTGGTGGTTCTT CTATTAACTTCATGATGTACACTAGAGGTTCTGCTTCTGACTACGACGACTTCCAAG CTGAAGGTTGGAAGACTAAGGACTTGTTGCCATTGATGAAGAAGACTGAAACTTAC CAAAGAGCTTGTAACAACCCAGACATTCACGGTTTCGAAGGTCCAATTAAGGTTTC TTTC G GTAACTAC ACTTAC C C AGTTTGTC AAG ACTTCTTG AG AG CTTCTG AATCTC A AGGTATTCCATACGTTGACGACTTGGAAGACTTGGTTACTGCTCACGGTGCTGAAC ACTGGTTGAAGTGGATTAACAGAGACACTGGTAGAAGATCTGACTCTGCTCACGCT TTCGTTCACTCTACTATGAGAAACCACGACAACTTGTACTTGATTTGTAACACTAAG GTTGACAAGATTATTGTTGAAGACGGTAGAGCTGCTGCTGTTAGAACTGTTCCATC TAAGC C ATTG AAC C C AAAG AAG C C ATCTC AC AAG ATTTAC AG AG CTAG AAAG C AAA TTGTTTTGTCTTGTGGTACTATTTCTTCTCCATTGGTTTTGCAAAGATCTGGTTTCG GTGACCCAATTAAGTTGAGAGCTGCTGGTGTTAAGCCATTGGTTAACTTGCCAGGT GTTGGTAGAAACTTCCAAGACCACTACTGTTTCTTCTCTCCATACAGAATTAAGCCA C AATAC G AATCTTTC G AC G ACTTC GTTAG AG GTG AC G CTG AAATTC AAAAGAG AGT TTTCGACCAATGGTACGCTAACGGTACTGGTCCATTGGCTACTAACGGTATTGAAG CTG GTGTTAAG ATTAG AC C AACTC C AG AAGAATTGTCTC AAATG G AC G AATCTTTC C AAG AAG GTTAC AG AG AATACTTC G AAG AC AAG C C AG AC AAG C C AGTTATG C ACTA CTCTATTATTGCTGGTTTCTTCGGTGACCACACTAAGATTCCACCAGGTAAGTACAT GACTATGTTCCACTTCTTGGAATACCCATTCTCTAGAGGTTCTATTCACATTACTTC TC C AG AC C C ATAC G CTG CTC C AG ACTTC GAC C C AG GTTTC ATG AAC G AC G AAAG A GACATGGCTCCAATGGTTTGGGCTTACAAGAAGTCTAGAGAAACTGCTAGAAGAAT GGACCACTTCGCTGGTGAAGTTACTTCTCACCACCCATTGTTCCCATACTCTTCTG AAG CTAG AG CTTTG G AAATG G ACTTGG AAACTTCTAAC G CTTAC GGTG GTC C ATTG AACTTGTCTGCTGGTTTGGCTCACGGTTCTTGGACTCAACCATTGAAGAAGCCAAC TG CTAAG AAC G AAG GTC AC GTTACTTCTAAC C AAGTTG AATTG C AC C C AG AC ATTG AATAC GAC G AAG AAG AC G AC AAG G CTATTGAAAACTAC ATTAG AG AAC AC ACTG AA ACTACTTGGCACTGTTTGGGTACTTGTTCTATTGGTCCAAGAGAAGGTTCTAAGATT GTTAAGTGGGGTGGTGTTTTGGACCACAGATCTAACGTTTACGGTGTTAAGGGTTT GAAGGTTGGTGACTTGTCTGTTTGTCCAGACAACGTTGGTTGTAACACTTACACTA CTGCTTTGTTGATTGGTGAAAAGACTGCTACTTTGGTTGGTGAAGACTTGGGTTAC TCTGGTGAAGCTTTGGACATGACTGTTCCACAATTCAAGTTGGGTACTTACGAAAA GACTGGTTTGGCTAGATTCCCAGAAGCTTTGATTAAGTCTATGACTTCTAAGTTGTA
A - pyruvate carboxylase (PYC, PYC1 , E.C. 6.4.1 .1 ), being any enzyme catalysing the irreversible carboxylation of pyruvate to form oxaloacetate (OAA). As described herein, pyruvate carboxylase also functions to facilitate the folding, activity and subcellular localisation of AOX. For example, PYC1 from methylotrophic yeast is believed to facilitate binding of the cofactor FAD to AOX. An example of a protein sequence of PYC is shown in SEQ ID NO: 3.
MAEEDYLPVYQLRRDSSLLGTMNKILVANRGEIPIRIFRTAHELSMNTVAIYSHEDRLSM HRLKADEAYVIGERGQYSPVQAYLAIDEIIKIAVKHNVNMIHPGYGFCSENSEFARKVEE NGILWVGPSDTVIDAVGDKVSARNLAYAANVPTVPGTPGPIEDVAQATAFVEEYGYPVI IKAAFGGGGRGMRWREGDDIEDAFLRASSEAKTAFGNGTVFIERFLDKPKHIEVQLLA DNYGNVIHLFERDCSVQRRHQKVARNCSAKTLPVEVRNAILNDAVKLAKTANYRNAGT AEFLVDSQNRHYFIEINPRIQVEHTITEEITGVDIVAAQIQIAAGASLEQLGLLQEKITTRG FAIQCRITTEDPTKNFQPDTGKIEVYRSSGGNGVRLDGGNGFAGAVISPHYDSMLVKC STSGSNYEIRRRKMIRALVEFRIRGVKTNIPFLLALLTHPVFMTSECWTTFIDDTPELFKI LTSQNRAQKLLAYLGDLAVNGSSIKGQIGLPKLHKEADIPSITDINGDVIDVSIPPPDGW RQFLLEKGPEQFAQQVRAFPGLMIMDTTWRDAHQSLLATRVRTHDLLNIAPATSYALH HAFALECWGGATFDVSMRFLHEDPWQRLRKLRKAVPNIPFSMLLRGGNGVAYYSLPD NAIDHFLKQAKDTGVDVFRVFDALNDIEQLKVGVDAVKKAGGWEATMCYSGDMLKP GKKYNLEYYINLATEIVEMGTHILAVKDMAGTLKPTAAKQLISALRRKFPSLPIHVHTHDS AGTGVASMVACARAGADVVTVRVNSMSGMTSQPSMSAFIASLDGEIETGIPEANAREI DAYWAEMRLLYSCFEADLKGPDPEVYQHEIPGGQLTNLLFQAQQVGLGEKWVETKKA YEAANRLLGDIVKVTPTSKWGDLAQFMVSNKLSSEDVERLASELDFPDSVLDFFEGL MGTPYGGFPEPLRTNVISGKRRKLTSRPGLTLEPYNIPAIREDLEARFSKVTENDVASY NMYPKVYEAYKKQQELYGDLSVLPTRNFLSPPKIDEERHVTIVTIETRKTLIIKCMAEGE LSQSSGTREVYFELNGEMRKVTVEDKNGAVETITRPKADAHNPNEIGAPMAGVWEV RVHENGEVKKGDPIAVLSAMKMEMVISSPVAGRIGQIAVKENDSVDASDLIPKSSRLSK LLMFIILIILY An example of a polynucleotide encoding a PYC polypeptide is shown in SEQ ID
NO: 4 (codon optimised for expression in S. cerevisiae):
ATG G CTG AAG AAG ACTACTTG C C AGTTTAC C AATTG AG AAG AG ACTCTTCTTTGTT G G GTACTATG AAC AAG ATTTTG GTTG CTAAC AG AG GTG AAATTC C AATTAG AATTTT CAGAACTGCTCACGAATTGTCTATGAACACTGTTGCTATTTACTCTCACGAAGACA GATTGTCTATGCACAGATTGAAGGCTGACGAAGCTTACGTTATTGGTGAAAGAGGT CAATACTCTCCAGTTCAAGCTTACTTGGCTATTGACGAAATTATTAAGATTGCTGTT AAG C AC AAC GTTAAC ATG ATTC AC C C AG GTTAC G GTTTCTGTTCTG AAAACTCTG AA TTCGCTAGAAAGGTTGAAGAAAACGGTATTTTGTGGGTTGGTCCATCTGACACTGT TATTGACGCTGTTGGTGACAAGGTTTCTGCTAGAAACTTGGCTTACGCTGCTAACG TTCCAACTGTTCCAGGTACTCCAGGTCCAATTGAAGACGTTGCTCAAGCTACTGCT TTCGTTGAAGAATACG GTTAC CCAGTTATTATTAAGG CTG CTTTCG GTG GTG GTG G TAG AGGTATG AG AGTTGTTAG AG AAG GTG AC G AC ATTG AAG AC G CTTTCTTGAG AG CTTCTTCTGAAGCTAAGACTGCTTTCGGTAACGGTACTGTTTTCATTGAAAGATTCT TGGACAAGCCAAAGCACATTGAAGTTCAATTGTTGGCTGACAACTACGGTAACGTT ATTCACTTGTTCGAAAGAGACTGTTCTGTTCAAAGAAGACACCAAAAGGTTGCTAG AAACTGTTCTGCTAAGACTTTGCCAGTTGAAGTTAGAAACGCTATTTTGAACGACG CTGTTAAGTTGGCTAAGACTGCTAACTACAGAAACGCTGGTACTGCTGAATTCTTG GTTGACTCTCAAAACAGACACTACTTCATTGAAATTAACCCAAGAATTCAAGTTGAA CACACTATTACTGAAGAAATTACTGGTGTTGACATTGTTGCTGCTCAAATTCAAATT GCTGCTGGTGCTTCTTTGGAACAATTGGGTTTGTTGCAAGAAAAGATTACTACTAG AGGTTTCGCTATTCAATGTAGAATTACTACTGAAGACCCAACTAAGAACTTCCAACC AG AC ACTG GTAAG ATTG AAGTTTAC AG ATCTTCTG GTG GTAAC G GTGTTAG ATTG G ACGGTGGTAACGGTTTCGCTGGTGCTGTTATTTCTCCACACTACGACTCTATGTTG GTTAAGTGTTCTACTTCTGGTTCTAACTACGAAATTAGAAGAAGAAAGATGATTAGA G CTTTG GTTG AATTC AG AATTAG AG GTGTTAAG ACTAAC ATTC C ATTCTTGTTG G CT TTGTTG ACTC AC C C AGTTTTC ATG ACTTCTG AATGTTG G ACTACTTTC ATTG AC G AC ACTC C AG AATTGTTC AAG ATTTTG ACTTCTC AAAAC AG AG CTC AAAAGTTGTTG G CT TACTTGGGTGACTTGGCTGTTAACGGTTCTTCTATTAAGGGTCAAATTGGTTTGCCA AAGTTGCACAAGGAAGCTGACATTCCATCTATTACTGACATTAACGGTGACGTTATT GACGTTTCTATTCCACCACCAGACGGTTGGAGACAATTCTTGTTGGAAAAGGGTCC AG AAC AATTC G CTC AAC AAGTTAG AG CTTTC C C AG GTTTG ATG ATTATG G AC ACTA CTTGGAGAGACGCTCACCAATCTTTGTTGGCTACTAGAGTTAGAACTCACGACTTG TTGAACATTGCTCCAGCTACTTCTTACGCTTTGCACCACGCTTTCGCTTTGGAATGT TGGGGTGGTGCTACTTTCGACGTTTCTATGAGATTCTTGCACGAAGACCCATGGCA AAGATTGAGAAAGTTGAGAAAGGCTGTTCCAAACATTCCATTCTCTATGTTGTTGAG AGGTGGTAACGGTGTTGCTTACTACTCTTTGCCAGACAACGCTATTGACCACTTCT TGAAGCAAGCTAAGGACACTGGTGTTGACGTTTTCAGAGTTTTCGACGCTTTGAAC GACATTGAACAATTGAAGGTTGGTGTTGACGCTGTTAAGAAGGCTGGTGGTGTTGT TGAAGCTACTATGTGTTACTCTGGTGACATGTTGAAGCCAGGTAAGAAGTACAACT TGGAATACTACATTAACTTGGCTACTGAAATTGTTGAAATGGGTACTCACATTTTGG CTGTTAAGGACATGGCTGGTACTTTGAAGCCAACTGCTGCTAAGCAATTGATTTCT GCTTTGAGAAGAAAGTTCCCATCTTTGCCAATTCACGTTCACACTCACGACTCTGC TGGTACTGGTGTTGCTTCTATGGTTGCTTGTGCTAGAGCTGGTGCTGACGTTGTTA CTGTTAGAGTTAACTCTATGTCTGGTATGACTTCTCAACCATCTATGTCTGCTTTCA TTG CTTCTTTG G AC G GTG AAATTG AAACTG GTATTC C AG AAG CTAAC G CTAG AG AA ATTGACGCTTACTGGGCTGAAATGAGATTGTTGTACTCTTGTTTCGAAGCTGACTT G AAG G GTC C AG AC C C AGAAGTTTAC C AAC AC G AAATTC C AG GTG GTC AATTG ACTA ACTTGTTGTTCCAAGCTCAACAAGTTGGTTTGGGTGAAAAGTGGGTTGAAACTAAG AAG G CTTAC G AAG CTGCTAAC AG ATTGTTGG GTG AC ATTGTTAAG GTTACTC C AAC TTCTAAGGTTGTTGGTGACTTGGCTCAATTCATGGTTTCTAACAAGTTGTCTTCTGA AGACGTTGAAAGATTGGCTTCTGAATTGGACTTCCCAGACTCTGTTTTGGACTTCTT C G AAG GTTTG ATG G GTACTC C ATAC G GTG GTTTC C C AG AAC C ATTG AG AACTAAC G TTATTTCTG GTAAG AG AAG AAAGTTG ACTTCTAG AC C AG GTTTG ACTTTG G AAC CAT ACAACATTCCAGCTATTAGAGAAGACTTGGAAGCTAGATTCTCTAAGGTTACTGAAA AC G AC GTTG CTTCTTAC AAC ATGTAC C C AAAG GTTTAC G AAGCTTAC AAG AAG C AA CAAGAATTGTACGGTGACTTGTCTGTTTTGCCAACTAGAAACTTCTTGTCTCCACCA AAGATTGACGAAGAAAGACACGTTACTATTGTTACTATTGAAACTAGAAAGACTTTG ATTATTAAGTGTATGGCTGAAGGTGAATTGTCTCAATCTTCTGGTACTAGAGAAGTT TACTTC GAATTG AAC G GTG AAATGAG AAAG GTTACTGTTGAAG AC AAG AAC G GTG C TGTTGAAACTATTACTAGACCAAAGGCTGACGCTCACAACCCAAACGAAATTGGTG CTCCAATGGCTGGTGTTGTTGTTGAAGTTAGAGTTCACGAAAACGGTGAAGTTAAG AAGGGTGACCCAATTGCTGTTTTGTCTGCTATGAAGATGGAAATGGTTATTTCTTCT CCAGTTGCTGGTAGAATTGGTCAAATTGCTGTTAAGGAAAACGACTCTGTTGACGC TTCTGACTTGATTCCAAAGTCTTCTAGATTGTCTAAGTTGTTGATGTTCATTATTTTG ATTATTTTGTACTAA
- dihydroxyacetone synthase (also referred to as formaldehyde transketolase, DAS1 , D-xylulose-5-phosphate:formaldehyde glycolaldehydetransferase, E.C. 2.2.1 .3), referring to any enzyme capable of catalysing the reaction of formaldehyde and xylulose-5-phosphate to glyceraldehyde 3-phosphate and glycerone. As described herein, DAS is also capable of converting fructose-6-phosphate (F6P) to erythrose-4- phosphate (E4P) and xylulose-5-phosphate (Xu5P). Yet further, DAS can catalyse the conversion of G3P and S7P to Xu5P and ribose-5-phosphate (R5P). An example of the protein sequence of DAS is shown in SEQ ID NO: 5 (sequence from Pichia pastoris shown): MARIPKAVSTQDDIHELVIKTFRCYVLDLVEQYGGGHPGSAMGMVAIGIALWKYQMKY APNDPDYFNRDRFVLSNGHVCLFQYLFQHLTGLKEMTVKQLQSYHSSDYHSLTPGHP EIENPAVEVTTGPLGQGISNAVGMAIGSKNLAATYNRPGFPWDNTIYAIVGDACLQEG PALESISLAGHLALDNLIVIYDNNQVCCDGSVDVNNTEDISAKFRAQNWNVIDIVDGSRD VATIVKAIDWAKAETERPTLINVRTEIGQDSAFGNHHAAHGSALGEEGIRELKTKYGFN PAQKFWFPKEVYDFFAEKPAKGDELVKNWKKLVDSYVKEYPREGQEFLSRVRGELPK NWRTYIPQDKPTEPTATRTSAREIVRALGKNLPQVIAGSGDLSVSILLNWDGVKYFFNP KLQTFCGLGGDYSGRYIEFGIREHSMCAIANGLAAYNKGTFLPITSTFYMFYLYAAPAL RMAALQELKAIHIATHDSIGAGEDGPTHQPIALSSLFRAMPNFYYMRPADATEVAALFE VAVELEHSTLLSLSRHEVDQYPGKTSAQGAKRGGYWEDCEGKPDVQLIGTGSELEFA IKTARLLRQQKGWKVRVLSFPCQRLFDEQSITYRRSVLRRGEVPTWVEAYVAYGWE RYATAGYTM NTFG KS LPVE DVYKYFGYTP E Kl GE RWQYVN S I KAS P Q I LYE F H D LKG K PKHDKLPEALIKSMTSKL
C-terminal PTS1 show in underline.
An example of a polynucleotide encoding a DAS polypeptide is shown in SEQ ID NO: 6 (also encodes C-terminal PTS1 signal and is codon optimised for expression in S. cerevisiae): ATGGCTAGAATTCCAAAGGCTGTTTCTACTCAAGACGACATTCACGAATTGGTTATT AAGACTTTCAGATGTTACGTTTTGGACTTGGTTGAACAATACGGTGGTGGTCACCC AGGTTCTGCTATGGGTATGGTTGCTATTGGTATTGCTTTGTGGAAGTACCAAATGA AGTACGCTCCAAACGACCCAGACTACTTCAACAGAGACAGATTCGTTTTGTCTAAC GGTCACGTTTGTTTGTTCCAATACTTGTTCCAACACTTGACTGGTTTGAAGGAAATG ACTGTTAAGCAATTGCAATCTTACCACTCTTCTGACTACCACTCTTTGACTCCAGGT C AC C C AG AAATTG AAAAC C C AG CTGTTG AAGTTACTACTG GTC C ATTG G GTC AAG G TATTTCTAACGCTGTTGGTATGGCTATTGGTTCTAAGAACTTGGCTGCTACTTACAA CAGACCAGGTTTCCCAGTTGTTGACAACACTATTTACGCTATTGTTGGTGACGCTT GTTTGCAAGAAGGTCCAGCTTTGGAATCTATTTCTTTGGCTGGTCACTTGGCTTTG GACAACTTGATTGTTATTTACGACAACAACCAAGTTTGTTGTGACGGTTCTGTTGAC GTTAACAACACTGAAGACATTTCTGCTAAGTTCAGAGCTCAAAACTGGAACGTTATT GACATTGTTGACGGTTCTAGAGACGTTGCTACTATTGTTAAGGCTATTGACTGGGC TAAGGCTGAAACTGAAAGACCAACTTTGATTAACGTTAGAACTGAAATTGGTCAAG ACTCTGCTTTCGGTAACCACCACGCTGCTCACGGTTCTGCTTTGGGTGAAGAAGGT ATTAGAGAATTGAAGACTAAGTACGGTTTCAACCCAGCTCAAAAGTTCTGGTTCCC AAAG G AAGTTTAC G ACTTCTTC G CTG AAAAG C C AG CTAAG G GTG AC G AATTG GTTA AGAACTGGAAGAAGTTGGTTGACTCTTACGTTAAGGAATACCCAAGAGAAGGTCAA GAATTCTTGTCTAGAGTTAGAGGTGAATTGCCAAAGAACTGGAGAACTTACATTCC ACAAGACAAGCCAACTGAACCAACTGCTACTAGAACTTCTGCTAGAGAAATTGTTA GAGCTTTGGGTAAGAACTTGCCACAAGTTATTGCTGGTTCTGGTGACTTGTCTGTT TCTATTTTGTTG AACTG G G AC G GTGTTAAGTACTTCTTC AAC C C AAAGTTG C AAACT TTCTGTG GTTTG G GTG GTG ACTACTCTG GTAG ATAC ATTG AATTC G GTATTAG AG A ACACTCTATGTGTGCTATTGCTAACGGTTTGGCTGCTTACAACAAGGGTACTTTCTT GCCAATTACTTCTACTTTCTACATGTTCTACTTGTACGCTGCTCCAGCTTTGAGAAT GGCTGCTTTGCAAGAATTGAAGGCTATTCACATTGCTACTCACGACTCTATTGGTG CTGGTGAAGACGGTCCAACTCACCAACCAATTGCTTTGTCTTCTTTGTTCAGAGCT ATGCCAAACTTCTACTACATGAGACCAGCTGACGCTACTGAAGTTGCTGCTTTGTT CGAAGTTGCTGTTGAATTGGAACACTCTACTTTGTTGTCTTTGTCTAGACACGAAGT TGACCAATACCCAGGTAAGACTTCTGCTCAAGGTGCTAAGAGAGGTGGTTACGTTG TTGAAGACTGTGAAGGTAAGCCAGACGTTCAATTGATTGGTACTGGTTCTGAATTG GAATTCGCTATTAAGACTGCTAGATTGTTGAGACAACAAAAGGGTTGGAAGGTTAG AGTTTTGTCTTTCCCATGTCAAAGATTGTTCGACGAACAATCTATTACTTACAGAAG ATCTGTTTTGAGAAGAGGTGAAGTTCCAACTGTTGTTGTTGAAGCTTACGTTGCTTA CGGTTGGGAAAGATACGCTACTGCTGGTTACACTATGAACACTTTCGGTAAGTCTT TG C C AGTTG AAG AC GTTTAC AAGTACTTC G GTTAC ACTC C AG AAAAG ATTG GTG AA AGAGTTGTTCAATACGTTAACTCTATTAAGGCTTCTCCACAAATTTTGTACGAATTC CACGACTTGAAGGGTAAGCCAAAGCACGACAAGTTGCCAGAAGCTTTGATTAAGTC TATGACTTCTAAGTTGTAA
- dihydroxyacetone kinase (DAK; E.C. 2.7.1.29), being any enzyme which converts dihydroxyacetone into dihydroxyacetone phosphate (also called gylcerone phosphate or DHAP). DAK is also known by the terms glycerone kinase, ATP:glycerone phosphotransferase and acetol kinase. An example of the protein sequence of DAK is shown in SEQ ID NO: 7:
MSAKSFEVTDPVNSSLKGFALANPSITLVPEEKILFRKTDSDKIALISGGGSGHEPTHAG FIGKGMLSGAWGEIFASPSTKQILNAIRLVNENASGVLLIVKNYTGDVLHFGLSAERAR ALGINCRVAVIGDDVAVGREKGGMVGRRALAGTVLVHKIVGAFAEEYSSKYGLDGTAK VAKIINDNLVTIGSSLDHCKVPGRKFESELNEKQMELGMGIHNEPGVKVLDPIPSTEDLI SKYMLPKLLDPNDKDRAFVKFDEDDEVVLLVNNLGGVSNFVISSITSKTTDFLKENYNIT PVQTIAGTLMTSFNGNGFSITLLNATKATKALQSDFEEIKSVLDLLNAFTNAPGWPIADF EKTSAPSVNDDLLHNEVTAKAVGTYDFDKFAEWMKSGAEQVIKSEPHITELDNQVGDG DCGYTLVAGVKGITENLDKLSKDSLSQAVAQISDFIEGSMGGTSGGLYSILLSGFSHGLI QVCKSKDEPVTKEIVAKSLGIALDTLYKYTKARKGSSTMIDALEPFVKEFTASKDFNKAV KAAEEGAKSTATFEAKFGRASYVGDSSQVEDPGAVGLCEFLKGVQSALPEALIKSMTS KL
C-terminal PTS1 signal peptide shown in underline.
An example of a polynucleotide encoding a DAK polypeptide is shown in SEQ ID NO: 8 (also encodes C-terminal PTS1 peptide; codon optimised): ATGTCCGCTAAATCGTTTGAAGTCACAGATCCAGTCAATTCAAGTCTCAAAG GGTTTGCCCTTGCTAACCCCTCCATTACGCTGGTCCCTGAAGAAAAAATTCTCTTC AG AAAGAC C G ATTC C G AC AAG ATC G C ATTAATTTCTG GTG GTG GTAGTG G AC ATG A ACCTACACACGCCGGTTTCATTGGTAAGGGTATGTTGAGTGGCGCCGTGGTTGGC GAAATTTTTGCATCCCCTTCAACAAAACAGATTTTAAATGCAATCCGTTTAGTCAAT GAAAATGCGTCTGGCGTTTTATTGATTGTGAAGAACTACACAGGTGATGTTTTGCAT TTTGGTCTGTCCGCTGAGAGAGCAAGAGCCTTGGGTATTAACTGCCGCGTTGCTG TC ATAG GTGATG ATGTTG C AGTTG G C AGAG AAAAG G GTG GTATG GTTG GTAG AAG AGCATTGGCAGGTACCGTTTTGGTTCATAAGATTGTAGGTGCCTTCGCAGAAGAAT ATTCTAGTAAGTATGGCTTAGACGGTACAGCTAAAGTGGCTAAAATTATCAACGAC AATTTGGTGACCATTGGATCTTCTTTAGACCATTGTAAAGTTCCTGGCAGGAAATTC GAAAGTGAATTAAACGAAAAACAAATGGAATTGG GTATG GGTATTCATAACGAACC TGGTGTGAAAGTTTTAGACCCTATTCCTTCTACCGAAGACTTGATCTCCAAGTATAT GCTACCAAAACTATTGGATCCAAACGATAAGGATAGAGCTTTTGTAAAGTTTGATGA AGATGATGAAGTTGTCTTGTTAGTTAACAATCTCGGCGGTGTTTCTAATTTTGTTAT TAGTTCTATCACTTCCAAAACTACGGATTTCTTAAAGGAAAATTACAACATAACCCC G GTTC AAAC AATTG CTG GC AC ATTG ATG AC CTC CTTC AATG GTAATG G GTTC AGTA TCACATTACTAAACGCCACTAAGGCTACAAAGGCTTTGCAATCTGATTTTGAGGAG ATCAAATCAGTACTAGACTTGTTGAACGCATTTACGAACGCACCGGGCTGGCCAAT TGCAGATTTTGAAAAGACTTCTGCCCCATCTGTTAACGATGACTTGTTACATAATGA AGTAACAGCAAAGGCCGTCGGTACCTATGACTTTGACAAGTTTGCTGAGTGGATGA AG AGTG GTGCTG AAC AAGTTATC AAG AG C G AAC C G C AC ATTAC G G AACTAG AC AAT C AAGTTG GTG ATG GTGATTGTG GTTAC ACTTTAGTG G C AG G AGTTAAAG G CATC AC CGAAAACCTTGACAAGCTGTCGAAGGACTCATTATCTCAGGCGGTTGCCCAAATTT CAGATTTCATTGAAGGCTCAATGGGAGGTACTTCTGGTGGTTTATATTCTATTCTTT TGTCGGGTTTTTCACACGGATTAATTCAGGTTTGTAAATCAAAGGATGAACCCGTC ACTAAGGAAATTGTGGCTAAGTCACTCGGAATTGCATTGGATACTTTATACAAATAT ACAAAGGCAAGGAAGGGATCATCCACCATGATTGATGCTTTAGAACCATTCGTTAA AGAATTTACTGCATCTAAGGATTTCAATAAGGCGGTAAAAGCTGCAGAGGAAGGTG CTAAATCCACTGCTACATTCGAGGCCAAATTTGGCAGAGCTTCGTATGTCGGCGAT TCATCTCAAGTAGAAGATCCTGGTGCAGTAGGCCTATGTGAGTTTTTGAAGGGGGT TCAAAGCGCCTTGCCAGAAGCTTTGATTAAGTCTATGACTTCTAAGTTGTAA
- fructose-1 -6-bisphophate aldolase (FBA1 -2, E.C. 4.1 .2.13), referring to any enzyme catalyzing the conversion of dihydroxyacetone phosphate (glycerone phosphate or DHAP) and glyceraldehyde-3-phosphate (also called triose phosphate or 3-phosphoglyceraldehyde, GAP) into fructose-1 -6-bisphosphate (F1 ,6BP). FBA1 -2 is also capable of catalysing the reverse reaction (i.e., of fructose-1 -6-bisphosphate to DHAP and GAP) but it will be understood that for the purposes of the present invention, FBA1 -2 should catalyse the formation of fructose-1 -6-bisphosphate so that this molecule can be used as a substrate in downstream reactions of the methanol utilisation pathway. Further, FBA1 -2 can be used in accordance with the present invention for catalysing the conversion of erythrose 4-phosphate (E4P) and DHAP to sedoheptulose 1 ,7-bisphosphate (S1 ,7BP). An example of the protein sequence of FBA1 -2 is shown in SEQ ID NO: 9:
MGVEQILKRKTGVIVGEDVHNLFTYAKEHKFAIPAINVTSSSTAVAALEAARDSKSPIILQ TSNGGAAYFAGKGISNEGQNASIKGAIAAAHYIRSIAPAYGIPWLHSDHCAKKLLPWFD GMLEADEAYFKEHGEPLFSSHMLDLSEETDEENISTCVKYFKRMAAMDQWLEMEIGIT GGEEDGVNNENADKEDLYTKPEQVYNVYKALHPISPNFSIAAAFGNCHGLYAGDIALR PEILAEHQKYTREQVGCKEEKPLFLVFHGGSGSTVQEFHTGIDNGVVKVNLDTDCQYA YLTGIRDYVLNKKDYIMSPVGNPEGPEKPNKKFFDPRVVWREGEKTMGAKITKSLETF RTTNTLPEALIKSMTSKL
C-terminal PTS1 peptide shown in underline An example of a polynucleotide encoding a FBA1 -2 polypeptide is shown in SEQ Id NO: 10: (also encodes C-terminal PTS1 ; codon optimised):
ATGGGTGTTGAACAAATCTTAAAGAGAAAGACCGGTGTCATCGTTGGTGAAGATGT CCACAACTTATTCACTTACGCTAAGGAACACAAGTTCGCTATTCCAGCTATTAACGT CACCTCTTCTTCTACTGCCGTCGCTGCTTTAGAAGCTGCTAGAGACAGCAAGTCCC CAATCATTTTGCAAACCTCTAACGGTGGTGCTGCTTACTTCGCTGGTAAGGGTATC TCTAACGAAGGTCAAAATGCTTCCATCAAGGGTGCTATTGCCGCTGCCCACTACAT CAGATCCATTGCTCCAGCTTACGGTATCCCAGTTGTCTTACACTCTGACCACTGTG CCAAGAAGTTGTTGCCATGGTTCGATGGTATGTTGGAAGCTGATGAAGCTTACTTC AAGGAACACGGTGAACCATTATTCTCCTCCCACATGTTGGATTTGTCTGAAGAAAC C G ATG AAG AAAAC ATCTCTACTTGTGTC AAGTACTTC AAG AG AATG G C C G CTATG G ACCAATGGTTAGAAATGGAAATCGGTATTACCGGTGGTGAAGAAGATGGTGTTAAC AAC G AAAAC G CTG AC AAG G AAG ACTTGTAC AC C AAG C C AG AAC AAGTTTAC AAC GT CTACAAGGCTTTGCACCCAATCTCTCCAAACTTCTCCATTGCTGCTGCTTTCGGTAA CTGTCACGGTTTGTACGCTGGTGACATCGCTTTGAGACCAGAAATCTTGGCTGAAC AC C AAAAGTAC AC C AG AG AAC AAGTTG GTTG C AAG G AAG AAAAG C C ATTGTTCTTG GTCTTCCACGGTGGTTCCGGTTCTACTGTCCAAGAATTCCACACTGGTATTGACAA CGGTGTTGTCAAGGTCAACTTGGACACTGACTGTCAATACGCTTACTTGACTGGTA TCAGAGACTACGTCTTGAACAAGAAGGACTACATAATGTCCCCAGTCGGTAACCCA GAAGGTCCAGAAAAGCCAAACAAGAAGTTCTTCGACCCAAGAGTCTGGGTTAGAG AAG GTG AAAAG AC C ATG G GTG CTAAG ATC AC C AAGTCTTTG GAAACTTTC C GTAC C ACTAACACTTTACCAGAAGCTTTGATTAAGTCTATGACTTCTAAGTTGTAA
- fructose-1 -6-bisphosphatase (FBPase, hexose diphosphatase, or fructose- bisphosphatase, E.C. 3.1 .3.1 1 ) is any enzyme catalysing the conversion of F1 ,6BP to fructose-6-phosphate (F6P). An example of the protein sequence of FBPase is shown in SEQ ID NO: 1 1 :
MPTLVNGPRRDSTEGFDTDIITLPRFIIEHQKQFKNATGDFTLVLNALQFAFKFVSHTIR RAELVNLVGLAGASNFTGDQQKKLDVLGDEIFINAMRASGIIKVLVSEEQEDLIVFPTNT GSYAVCCDPIDGSSNLDAGVSVGTIASIFRLLPDSSGTINDVLRCGKEMVAACYAMYG SSTHLVLTLGDGVDGFTLDTNLGEFILTHPNLRIPPQKAIYSINEGNTLYWNETIRTFIEK VKQPQADNNNKPFSARYVGSMVADVHRTFLYGGLFAYPCDKKSPNGKLRLLYEAFPM AFLMEQAGGKAVNDRGERILDLVPSHIHDKSSIWLGSSGEIDKFLDHIGKSQPEALIKS MTSKL
C-terminal PTS1 shown in underline.
An example of a polynucleotide encoding an FBPase polypeptide is shown in SEQ ID NO: 12 (codon optimised; also encodes PTS1 ):
ATGCCAACTCTAGTAAATGGACCAAGAAGAGACTCTACCGAAGGGTTTGATACCGA TATCATCACTCTTCCTAGATTCATAATCGAGCACCAGAAGCAATTTAAGAACGCTAC TGGTGATTTCACATTAGTACTGAATGCCTTGCAATTCGCGTTCAAATTTGTATCTCA CACCATCAGACGTGCTGAATTGGTTAACTTGGTTGGGTTAGCAGGCGCTTCCAACT TCACTGGTGACCAGCAAAAGAAGTTGGACGTTCTAGGTGATGAAATATTTATCAAT GCCATGAGGGCTAGTGGGATCATCAAGGTCCTTGTATCTGAAGAACAGGAAGACT TG ATC GTTTTTC C C AC AAAC AC G G G CTC ATAC G C AGTGTGTTGTG ATC CTATTG AT GGCTCCTCAAATTTGGACGCCGGTGTCTCCGTTGGAACTATCGCGTCTATATTCAG ACTGCTACCAGACTCATCAGGTACTATAAACGACGTACTGAGATGTGGTAAAGAAA TGGTAGCCGCTTGCTATGCCATGTACGGATCCTCTACGCATCTAGTATTGACATTG G GTG ATG G AGTTG ATG G GTTTAC CTTAG AC AC AAACTTG G G C G AATTC ATCTTGAC TCATCCTAACTTAAGAATTCCGCCTCAAAAGGCCATCTACTCAATTAATGAAGGTAA C AC C CTCTACTG G AAC G AG ACTATAAG AAC ATTTATTG AG AAAGTC AAAC AAC C C C AAGCAGACAACAACAACAAGCCTTTCTCGGCTAGGTATGTTGGATCCATGGTTGCT G ATGTTC AC AG G AC GTTTCTTTAC G GTG G C CTTTTC GC ATAC C CTTG C G AC AAG AA GAGCCCCAACGGAAAACTGAGGTTGCTTTATGAGGCCTTCCCAATGGCTTTCTTAA TG G AAC AAG C AG G G G G AAAAG C G GTC AAC G ATC G C G G AG AG AG AATCTTG GATTT GGTGCCAAGTCATATCCATGACAAATCTTCTATTTGGTTGGGTTCTTCAGGTGAAAT TGACAAATTTTTAGACCATATTGGCAAGTCACAGCCAGAAGCTTTGATTAAGTCTAT GACTTCTAAGTTGTAA
- sedoheptulose bisphosphatase (sedoheptulose-1 ,7-bisphosphatase or SBPase, SBH17, E.C. 3.1 .3.37) is any enzyme catalysing the conversion of sedoheptulose 1 ,7- bisphosphate (S1 ,7BP) to sedoheptulose-7-phosphate (S7P). An example of the protein sequence of SBPase is shown in SEQ ID NO: 13 (C-terminal PTS1 peptide underlined): MPSLTPRCIIVRHGQTEWSKSGQYTGLTDLPLTPYGEGQMLRTGESVFRNNQFLNPD NITYIFTSPRLRARQTVDLVLKPLSDEQRAKIRVWDDDLREWEYGDYEGMLTREIIELR KSRGLDKERPWNIWRDGCENGETTQQIGLRLSRAIARIQNLHRKHQSEGRASDIMVFA HGHALRYFAAIWFGLGVQKKCETIEEIQNVKSYDDDTVPYVKLESYRHLVDNPCFLLDA GGIGVLSYAHHNIDEPALELAGPFVSPPEEESQHGDVPEALIKSMTSKL
An example of a polynucleotide encoding a SBPase polypeptide is shown in SEQ ID NO: 14 (codon optimised; also encodes PTS1 ):
ATGCCTTCGCTAACCCCCAGATGTATCATTGTCAGACACGGTCAAACTGAATGGTC CAAGTCAGGCCAGTATACTGGTTTGACAGATCTACCGTTAACGCCCTACGGTGAG GGCCAAATGTTGAGGACCGGTGAGAGTGTTTTCCGCAATAATCAGTTTTTGAATCC AGACAACATCACTTATATCTTCACCTCTCCACGTTTGCGTGCCAGGCAAACTGTGG ATTTG GTTTTG AAAC C ATTAAG C G AC GAG C AAAG AG CTAAG ATC CGTGTGGTGGTA GACGACGACTTGCGAGAGTGGGAGTACGGTGACTACGAGGGAATGCTGACTCGA G AAATC ATTG AATTG AG AAAGTC AC G C G GTTTG G AC AAG GAG AG G C C ATG G AATAT CTGGAGAGATGGGTGTGAGAACGGTGAGACTACTCAGCAAATTGGGTTGAGACTT TC C C G C G CTATTG C C AGAATC C AG AACTTG C AC C GC AAG C AC C AG AGTG AG G G C A GAGCATCAGACATCATGGTCTTTGCGCACGGACATGCATTGCGTTATTTTGCTGCT ATTTG GTTTG GACTG G GTGTG C AAAAG AAGTGTG AG AC G ATTG AAG AAATTCAAAA TGTCAAATCTTATGATGACGACACAGTTCCATATGTGAAATTGGAATCTTACAGACA TTTGGTAGACAATCCATGTTTCTTACTGGACGCCGGTGGGATTGGTGTTTTGTCAT AC G CTC AC C AC AAC ATTG AC G AAC CTG C ATTG G AATTAG C AG GTC C ATTTGTCTC A CCACCAGAGGAGGAATCCCAGCATGGCGATGTGCCAGAAGCTTTGATTAAGTCTA TGACTTCTAAGTTGTAA
- transketolase (TKL1 , TLK2, E.C. 2.2.1 .1 ) is any enzyme catalysing the conversion of fructose-6-phosphate to erythrose-4-phosphate and xylulose-5-phospate. An example of the protein sequence of TKL is shown in SEQ ID NO: 15 (PTS1 underlined):
MSNSLEQLKAAGTWVTDTGEFESIAKYTPQDATTNPSLILAASNKAEYAKLIDIAVDYA KKQGGSVEEQANIALDRLLIEFGKEILKIVPGRVSTEVDARLSFDKEATIKKALEIIELYKS VGVEKDRILIKIASTWEGIQAARELEAKYGIHCNLTLLFSFVQAVACAEAKVTLISPFVGR ILDWYKASTGKDYKGDEDPGVQSVKAIFNYYKKFGYDTIVMGASFRNTGEIKALAGCD FLTIAPKLLEELLNSKEPVPQKLDASAASSLDIERVSYIDDEAAFRFGLNEDAMSTEKLS EGIRKFSADCVTLLNLLKEKVQAPEALIKSMTSKL
An example of a polynucleotide encoding a TKL polypeptide is shown in SEQ ID NO: 16 (codon optimised; also encodes PTS1 ): ATGTCTAACTCTTTGGAACAATTGAAGGCTGCTGGTACTGTTGTTGTTACTGACACT GGTGAATTCGAATCTATTGCTAAGTACACTCCACAAGACGCTACTACTAACCCATCT TTGATTTTGGCTGCTTCTAACAAGGCTGAATACGCTAAGTTGATTGACATTGCTGTT GACTACGCTAAGAAGCAAGGTGGTTCTGTTGAAGAACAAGCTAACATTGCTTTGGA CAGATTGTTGATTGAATTCGGTAAGGAAATTTTGAAGATTGTTCCAGGTAGAGTTTC TACTGAAGTTGACGCTAGATTGTCTTTCGACAAGGAAGCTACTATTAAGAAGGCTTT GGAAATTATTGAATTGTACAAGTCTGTTGGTGTTGAAAAGGACAGAATTTTGATTAA GATTGCTTCTACTTGGGAAGGTATTCAAGCTGCTAGAGAATTGGAAGCTAAGTACG GTATTCACTGTAACTTGACTTTGTTGTTCTCTTTCGTTCAAGCTGTTGCTTGTGCTG AAGCTAAGGTTACTTTGATTTCTCCATTCGTTGGTAGAATTTTGGACTGGTACAAGG CTTCTACTGGTAAGGACTACAAGGGTGACGAAGACCCAGGTGTTCAATCTGTTAAG GCTATTTTCAACTACTACAAGAAGTTCGGTTACGACACTATTGTTATGGGTGCTTCT TTCAGAAACACTGGTGAAATTAAGGCTTTGGCTGGTTGTGACTTCTTGACTATTGCT CCAAAGTTGTTGGAAGAATTGTTGAACTCTAAGGAACCAGTTCCACAAAAGTTGGA C G CTTCTG CTGCTTCTTCTTTG G AC ATTG AAAG AGTTTCTTAC ATTG AC GAC G AAG C TGCTTTCAGATTCGGTTTGAACGAAGACGCTATGTCTACTGAAAAGTTGTCTGAAG GTATTAGAAAGTTCTCTGCTGACTGTGTTACTTTGTTGAACTTGTTGAAGGAAAAGG TTCAAGCTCCAGAAGCTTTGATTAAGTCTATGACTTCTAAGTTGTAA
- ribose-5-phosphate ketol isomerase (also referred to as RKL1 , Rpi, D-ribose-5- phosphate aldose-ketose-isomerase, Ribose-5-phosphate isomerase E.C. 5.3.1.6) refers to any enzyme capable of catalysing the reaction of ribose-5-phosphate to ribulose-5-phosphate (RuL5P). An example of the protein sequence of RKL1 is shown in SEQ ID NO: 17 (PTS1 underlined):
MAAGVPKIDALESLGNPLEDAKRAAAYRAVDENLKFDDHKIIGIGSGSTWYVAE RIGQYLHDPKFYEVASKFICIPTGFQSRNLILDNKLQLGSIEQYPRIDIAFDGADEVDENL QLIKGGGACLFQEKLVSTSAKTFIWADSRKKSPKHLGKNWRQGVPIEIVPSSYVRVKN DLLEQLHAEKVDIRQGGSAKAGPWTDNNNFIIDADFGEISDPRKLHREIKLLVGWETG LFIDNASKAYFGNSDGSVEVTEKPEALIKSMTSKL
An example of a polynucleotide encoding a RKL1 polypeptide is shown in SEQ ID NO: 18 (codon optimised; also encodes PTS1 ): ATGGCTGCCGGTGTCCCAAAAATTGATGCGTTAGAATCTTTGGGCAATCCTT TG G AG G ATGC C AAG AGAG CTG C AGC ATAC AG AG C AGTTGATG AAAATTTAAAATTT GATGATCACAAAATTATTGGAATTGGTAGTGGTAGCACAGTGGTTTATGTTGCCGA AAGAATTGGACAATATTTGCATGACCCTAAATTTTATGAAGTAGCGTCTAAATTCAT TTG C ATTC C AAC AG G ATTC C AATC AAG AAACTTG ATTTTG GATAAC AAGTTG C AATT AGGCTCCATTGAACAGTATCCTCGCATTGATATAGCGTTTGACGGTGCTGATGAAG TGGATGAGAATTTACAATTAATTAAAGGTGGTGGTGCTTGTCTATTTCAAGAAAAAT TGGTTAGTACTAGTGCTAAAACCTTCATTGTCGTTGCTGATTCAAGAAAAAAGTCAC CAAAACATTTAGGTAAGAACTGGAGGCAAGGTGTTCCCATTGAAATTGTACCTTCC TCATACGTGAGGGTCAAGAATGATCTATTAGAACAATTGCATGCTGAAAAAGTTGA CATCAGACAAGGAGGTTCTGCTAAAGCAGGTCCTGTTGTAACTGACAATAATAACT TC ATTATC G ATG C G G ATTTC G GTG AAATTTC C G ATC C AAG AAAATTG C ATAGAG AAA TCAAACTGTTAGTGGGCGTGGTGGAAACAGGTTTATTCATCGACAACGCTTCAAAA GCCTACTTCGGTAATTCTGACGGTAGTGTTGAAGTTACCGAAAAGCCAGAAGCTTT GATTAAGTCTATGACTTCTAAGTTGTAA - D-ribulose-5-phosphate-3-epimerase (RPE1 , phosphopentose epimerase, ribulose-phosphate 3-epimerase, E.C. 5.1 .3.1 ) is any enzyme catalysing the conversion of D-ribulose-5-phosphate (RuL5P) to D-xylulose-5-phosphate (Xu5P). An example of the protein sequence of RPE1 is shown in SEQ ID NO: 19 (PTS1 underlined):
MVKPIIAPSILASDFANLGCECHKVINAGADWLHIDVMDGHFVPNITLGQPIVTSLRRSV PRPGDASNTEKKPTAFFDCHMMVENPEKVWDDFAKCGADQFTFHYEATQDPLHLVK LIKSKGIKAACAIKPGTSVDVLFELAPHLDMALVMTVEPGFGGQKFMEDMMPKVETLR AKFPHLNIQVDGGLGKETIPKAAKAGANVIVAGTSVFTAADPHDVISFMKEEVSKELRS RDLLDPEALIKSMTSKL
.An example of a polynucleotide encoding a RPE1 polypeptide is shown in SEQ ID NO: 20 (codon optimised; also encodes PTS1 ): ATGGTCAAACCAATTATAGCTCCCAGTATCCTTGCTTCTGACTTCGCCAACTTGGG TTG C G AATGTC ATAAG GTC ATC AAC G C C G G C G C AG ATTG GTTAC ATATC GATGTC A TGGACGGCCATTTTGTTCCAAACATTACTCTGGGCCAACCAATTGTTACCTCCCTA CGTCGTTCTGTGCCACGCCCTGGCGATGCTAGCAACACAGAAAAGAAGCCCACTG CGTTCTTCGATTGTCACATGATGGTTGAAAATCCTGAAAAATGGGTCGACGATTTT GCTAAATGTGGTGCTGACCAATTTACGTTCCACTACGAGGCCACACAAGACCCTTT GCATTTAGTTAAGTTGATTAAGTCTAAGGGCATCAAAGCTGCATGCGCCATCAAAC CTGGTACTTCTGTTGACGTTTTATTTGAACTAGCTCCTCATTTGGATATGGCTCTTG TTATG ACTGTG GAAC CTG G GTTTG GAG G C C AAAAATTC ATG G AAG AC ATGATG C C A AAAGTGGAAACTTTGAGAGCCAAGTTCCCCCATTTGAATATCCAAGTCGATGGTGG TTTG G G C AAG G AGAC C ATC C C G AAAG C C G C C AAAG C C G GTG C C AAC GTTATTGTC GCTGGTACCAGTGTTTTCACTGCAGCTGACCCGCACGATGTTATCTCCTTCATGAA AGAAGAAGTCTCGAAGGAATTGCGTTCTAGAGATTTGCTAGATCCAGAAGCTTTGA TTAAGTCTATGACTTCTAAGTTGTAA - catalase (CAT, CTA equilase, caperase, optidase, catalase-peroxidase, E.C.
1 .1 1 .1 .6), being any enzyme catalysing the decomposition of hydrogen peroxide to water and oxygen. An example of the protein sequence of catalase is shown in SEQ ID NO: 21 (sequence for Pichia pastoris shown):
MSQPPKWTTSNGAPVSDVFATERATFDNANHANNAPKVGPLLLQDFQLIDSLAHFDR ERIPERVVHAKGAGAFGEFEVTDDISDVCAAKFLDTIGKKTRIFTRFSTVGGEKGSADS ARDPRGFSTKFYTEEGNLDLVYNNTPIFFIRDPSKFPHFIHTQKRNPATNLKDANMFWD YLVNNQESIHQVMYLFSDRGTPASLRKMNGYSGHTYKWYNKKGEWVYVQVHFKSDL GVVNFNNEEAGKLAGEDPDYHTGDLFNAIERGEYPSWTCYIQTMTQEQAAKQPFSVF DLTKVWPHKDFPLRRFGKFTLNENPKNYFAEVEQAAFSPSHTIPSMQPSADPVLQSRL FSYPDTHRHRLGVNYQQIPVNCPVAPVFTPQMRDGSMTVNGNLGSTPNYKSSFCPFS TEAQIQTNSHTPEEVLAAHTEKFHWGGILDSKSYDFEQPRALWKVFGKTPGQQRNFC HNVAVHVAAANHEIQDRVFEYFSKVYPEIGDQIRKEVLQLSPRGDSAARLPEALIKSMT SKL
Underlined sequence refers to C-terminal PTS1 peptide. An example of a polynucleotide encoding a catalase polypeptide is shown in
SEQ ID NO: 22 (sequence encoding Pichia pastoris CTA1 is shown; also encodes C- terminal PTS1 peroxisomal targeting peptide tag PEALIKSMTSKL, codon optimised for expression in Saccharomyces cerevisiae):
ATGTCTCAACCACCAAAGTGGACTACTTCTAACGGTGCTCCAGTTTCTGACGTTTT CGCTACTGAAAGAGCTACTTTCGACAACGCTAACCACGCTAACAACGCTCCAAAGG TTG GTC C ATTGTTGTTG C AAG ACTTC C AATTG ATTG ACTCTTTG G CTC ACTTC G AC A GAGAAAGAATTCCAGAAAGAGTTGTTCACGCTAAGGGTGCTGGTGCTTTCGGTGA ATTCGAAGTTACTGACGACATTTCTGACGTTTGTGCTGCTAAGTTCTTGGACACTAT TGGTAAGAAGACTAGAATTTTCACTAGATTCTCTACTGTTGGTGGTGAAAAGGGTT CTGCTGACTCTGCTAGAGACCCAAGAGGTTTCTCTACTAAGTTCTACACTGAAGAA GGTAACTTGGACTTGGTTTACAACAACACTCCAATTTTCTTCATTAGAGACCCATCT AAGTTC C C AC ACTTC ATTC AC ACTC AAAAG AG AAAC C C AG CTACTAACTTG AAG G A C G CTAAC ATGTTCTG G G ACTACTTG GTTAAC AAC C AAG AATCTATTC AC C AAGTTAT GTACTTGTTCTCTGACAGAGGTACTCCAGCTTCTTTGAGAAAGATGAACGGTTACT CTGGTCACACTTACAAGTGGTACAACAAGAAGGGTGAATGGGTTTACGTTCAAGTT C ACTTC AAGTCTGACTTGGGTGTTGTTAACTTC AAC AAC G AAG AAG CTGGTAAGTT G G CTG GTG AAG AC C C AG ACTAC C AC ACTG GTG ACTTGTTC AAC G CTATTG AAAG A G GTG AATAC C C ATCTTG GACTTGTTAC ATTC AAACTATG ACTC AAG AAC AAG CTG CT AAGCAACCATTCTCTGTTTTCGACTTGACTAAGGTTTGGCCACACAAGGACTTCCC ATTG AG AAGATTCGGTAAGTTCACTTTG AAC GAAAACCC AAAG AACTACTTCG CTG AAGTTGAACAAGCTGCTTTCTCTCCATCTCACACTATTCCATCTATGCAACCATCTG CTG AC C C AGTTTTG C AATCTAG ATTGTTCTCTTAC C C AG AC ACTC AC AG AC AC AG AT TGGGTGTTAACTACC AAC AAATTCCAGTTAACTGTCCAGTTG CTC CAGTTTTC ACTC CACAAATGAGAGACGGTTCTATGACTGTTAACGGTAACTTGGGTTCTACTCCAAAC TACAAGTCTTCTTTCTGTCCATTCTCTACTGAAGCTCAAATTCAAACTAACTCTCACA CTCCAGAAGAAGTTTTGGCTGCTCACACTGAAAAGTTCCACTGGGGTGGTATTTTG GACTCTAAGTCTTACGACTTCGAACAACCAAGAGCTTTGTGGAAGGTTTTCGGTAA GACTCCAGGTCAACAAAGAAACTTCTGTCACAACGTTGCTGTTCACGTTGCTGCTG CTAACCACGAAATTCAAGACAGAGTTTTCGAATACTTCTCTAAGGTTTACCCAGAAA TTGGTGACCAAATTAGAAAGGAAGTTTTGCAATTGTCTCCAAGAGGTGACTCTGCT GCTAGATTGCCAGAAGCTTTGATTAAGTCTATGACTTCTAAGTTGTAA
The skilled person will appreciate that while many yeasts have endogenous catalase enzymes, the provision of additional catalase may assist in the detoxification of excess hydrogen peroxide produced as a result of providing the microorganism with a construct as herein described which encodes proteins which the yeast cell does not yet have to enable it to utilise methanol as a major carbon source.
- glutathione peroxidase (pmp20, GSH peroxidase, selenium-glutathione peroxidase, reduced glutathione peroxidase, Ahpl p or type II thioredoxin peroxidase,
TPX, E.C. 1 .1 1 .1 .9), referring to an enzyme which catalyses the conversion of 2 glutathione molecules and one hydrogen peroxide molecule to glutathione disulfide and two water molecules. An example of the protein sequence of glutathione peroxidase is shown in SEQ ID NO: 23 (Pichia pastoris sequence shown): MSRNFQTVKRGDRFPTDATMFHIPSSGGGPAPFNLRETVQGKRFIWAAPGAFTSTC HEEHLPPYIKNLPTFLKKGIDFILVITANDAFVLNSWKKALGADSDKIIFASDTNLELANKL G LTLD LS VAG LGQ RTG RFAL I VG KD GVVQ NVFAE KG P EVKH S SAD RVLAKL PEAL IKS MTSKL
Underlined sequence refers to C-terminal PTS1 peptide. An example of a polynucleotide encoding a glutathione peroxidase polypeptide is shown in SEQ ID NO: 24 (also encodes C-terminal PTS1 ; codon optimised for expression in S. cerevisiae):
ATGTCTAGAAACTTCCAAACTGTTAAGAGAGGTGACAGATTCCCAACTGACGCTAC TATGTTCCACATTCCATCTTCTGGTGGTGGTCCAGCTCCATTCAACTTGAGAGAAA CTGTTCAAGGTAAGAGATTCATTGTTGTTGCTGCTCCAGGTGCTTTCACTTCTACTT GTC AC G AAG AAC ACTTG C C AC C ATAC ATTAAG AACTTG C C AACTTTCTTG AAG AAG GGTATTGACTTCATTTTGGTTATTACTGCTAACGACGCTTTCGTTTTGAACTCTTGG AAGAAGGCTTTGGGTGCTGACTCTGACAAGATTATTTTCGCTTCTGACACTAACTT GGAATTGGCTAACAAGTTGGGTTTGACTTTGGACTTGTCTGTTGCTGGTTTGGGTC AAAGAACTGGTAGATTCGCTTTGATTGTTGGTAAGGACGGTGTTGTTCAAAACGTT TTCGCTGAAAAGGGTCCAGAAGTTAAGCACTCTTCTGCTGACAGAGTTTTGGCTAA GTTGCCAGAAGCTTTGATTAAGTCTATGACTTCTAAGTTGTAA
- methyl formate-synthesising alcohol dehydrogenase (ADH1 , MFS, E.C. 1 .1 .1 .1 ), referring to an enzyme which converts a primary alcohol and NAD+ to an aldehyde, NADH and H+. In a preferred embodiment, the enzyme catalyses the conversion of methanol and formaldehyde to methyl formate (for example, by dehydrogenation of the hydroxyl group of the hemiacetal adduct [CH2(OH)OCH3] of methanol and formaldehyde, leading to the formation of a stoichiometric amount of methyl formate). An example of the protein sequence of methyl-formate synthesising alcohol dehydrogenase is shown in SEQ ID NO: 25:
MSPTIPTTQKAVIFETNGGPLEYKDIPVPKPKSNELLINVKYSGVCHTDLHAWKGDWPL DNKLPLVGGHEGAGVWAYGENVTGWEIGDYAGIKWLNGSCLNCEYCIQGAESSCAK ADLSGFTHDGSFQQYATADATQAARIPKEADLAEVAPILCAGITVYKALKTADLRIGQW VAISGAGGGLGSLAVQYAKALGLRVLGIDGGADKGEFVKSLGAEVFVDFTKTKDVVAE VQKLTNGGPHGVINVSVSPHAINQSVQYVRTLGKWLVGLPSGAVVNSDVFWHVLKSI EIKGSYVGNREDSAEAIDLFTRGLVKAPIKIIGLSELAKVYEQMEAGAIIGRYWDTSK
An example of a polynucleotide encoding a methyl-formate synthesising alcohol dehydrogenase polypeptide is shown in SEQ ID NO: 26 (codon optimised):
ATGTCTCCAACTATTCCAACTACTCAAAAGGCTGTTATTTTCGAAACTAACGGTGGT CCATTGGAATACAAGGACATTCCAGTTCCAAAGCCAAAGTCTAACGAATTGTTGATT AACGTTAAGTACTCTGGTGTTTGTCACACTGACTTGCACGCTTGGAAGGGTGACTG GCCATTGGACAACAAGTTGCCATTGGTTGGTGGTCACGAAGGTGCTGGTGTTGTT GTTGCTTACGGTGAAAACGTTACTGGTTGGGAAATTGGTGACTACGCTGGTATTAA GTGGTTGAACGGTTCTTGTTTGAACTGTGAATACTGTATTCAAGGTGCTGAATCTTC TTGTGCTAAGGCTGACTTGTCTGGTTTCACTCACGACGGTTCTTTCCAACAATACG CTACTGCTGACGCTACTCAAGCTGCTAGAATTCCAAAGGAAGCTGACTTGGCTGAA GTTGCTCCAATTTTGTGTGCTGGTATTACTGTTTACAAGGCTTTGAAGACTGCTGAC TTGAGAATTGGTCAATGGGTTGCTATTTCTGGTGCTGGTGGTGGTTTGGGTTCTTT GGCTGTTCAATACGCTAAGGCTTTGGGTTTGAGAGTTTTGGGTATTGACGGTGGTG CTGACAAGGGTGAATTCGTTAAGTCTTTGGGTGCTGAAGTTTTCGTTGACTTCACT AAGACTAAGGACGTTGTTGCTGAAGTTCAAAAGTTGACTAACGGTGGTCCACACGG TGTTATTAACGTTTCTGTTTCTCCACACGCTATTAACCAATCTGTTCAATACGTTAGA ACTTTGGGTAAGGTTGTTTTGGTTGGTTTGCCATCTGGTGCTGTTGTTAACTCTGAC GTTTTCTGGCACGTTTTGAAGTCTATTGAAATTAAGGGTTCTTACGTTGGTAACAGA GAAGACTCTGCTGAAGCTATTGACTTGTTCACTAGAGGTTTGGTTAAGGCTCCAAT TAAGATTATTGGTTTGTCTGAATTGGCTAAGGTTTACGAACAAATGGAAGCTGGTG CTATTATTGGTAGATACGTTGTTGACACTTCTAAGTAA
- transaidolase (TAL TALD01 , EC 2.2.1.2) referring to an enzyme which converts sedoheptulose 7-phosphate and giyceraldehyde 3-phosphate to erythrose 4- phosphate and fructose 6-phosphate.
An example of the protein sequence of transaidolase is shown in SEQ ID NO: 27:
MSNSLEQLKAAGTWVTDTGEFESIAKYTPQDATTNPSLILAASNKAEYAKLIDIAVDYA KKQGGSVEEQANIALDRLLIEFGKEILKIVPGRVSTEVDARLSFDKEATIKKALEIIELYKS VGVEKDRILIKIASTWEGIQAARELEAKYGIHCNLTLLFSFVQAVACAEAKVTLISPFVGR ILDWYKASTGKDYKGDEDPGVQSVKAIFNYYKKFGYDTIVMGASFRNTGEIKALAGCD FLTIAPKLLEELLNSKEPVPQKLDASAASSLDIERVSYIDDEAAFRFGLNEDAMSTEKLS EGIRKFSADCVTLLNLLKEKVQAPEALIKSMTSKL
An example of a polynucleotide encoding a transaidolase is shown in SEQ ID NO: 28: ATGTCTAACTCTTTGGAACAATTGAAGGCTGCTGGTACTGTTGTTGTTACTGACACT GGTGAATTCGAATCTATTGCTAAGTACACTCCACAAGACGCTACTACTAACCCATCT TTGATTTTGGCTGCTTCTAACAAGGCTGAATACGCTAAGTTGATTGACATTGCTGTT GACTACGCTAAGAAGCAAGGTGGTTCTGTTGAAGAACAAGCTAACATTGCTTTGGA CAGATTGTTGATTGAATTCGGTAAGGAAATTTTGAAGATTGTTCCAGGTAGAGTTTC TACTGAAGTTGACGCTAGATTGTCTTTCGACAAGGAAGCTACTATTAAGAAGGCTTT GGAAATTATTGAATTGTACAAGTCTGTTGGTGTTGAAAAGGACAGAATTTTGATTAA GATTGCTTCTACTTGGGAAGGTATTCAAGCTGCTAGAGAATTGGAAGCTAAGTACG GTATTCACTGTAACTTGACTTTGTTGTTCTCTTTCGTTCAAGCTGTTGCTTGTGCTG AAGCTAAGGTTACTTTGATTTCTCCATTCGTTGGTAGAATTTTGGACTGGTACAAGG CTTCTACTGGTAAGGACTACAAGGGTGACGAAGACCCAGGTGTTCAATCTGTTAAG GCTATTTTCAACTACTACAAGAAGTTCGGTTACGACACTATTGTTATGGGTGCTTCT TTCAGAAACACTGGTGAAATTAAGGCTTTGGCTGGTTGTGACTTCTTGACTATTGCT CCAAAGTTGTTGGAAGAATTGTTGAACTCTAAGGAACCAGTTCCACAAAAGTTGGA C G CTTCTG CTG CTTCTTCTTTG G AC ATTG AAAG AGTTTCTTAC ATTG AC GAC G AAGC TGCTTTCAGATTCGGTTTGAACGAAGACGCTATGTCTACTGAAAAGTTGTCTGAAG GTATTAGAAAGTTCTCTGCTGACTGTGTTACTTTGTTGAACTTGTTGAAGGAAAAGG TTCAAGCTCCAGAAGCTTTGATTAAGTCTATGACTTCTAAGTTGTAA formaldehyde dehydrogenase (SFA1 , s-nitrosoglutathione reducatase, GSNO reductase, NAD+-dependent formaldydhe dehydrogenase, S- (hydroxymethyl)glutathione dehydrogenase, E.C. 1 .2.1.46), referring to an enzyme which catalyses the conversion of formaldehyde, NAD+ and water to formate and NADH and H+.
An example of a protein sequence of formaldehyde dehydrogenase is shown in SEQ ID NO: 38:
MSAATVGKPIKCIAAVAYDAKKPLSVEEITVDAPKAHEVRIKIEYTAVCHTDAYTL SGSDPEGLFPCVLGHEGAGIVESVGDDVITVKPGDHVIALYTAECGKCKFCTSGKTNL CGAVRATQGKGVMPDGTTRFHNAKGEDIYHFMGCSTFSEYTWADVSVVAIDPKAPL DAACLLGCGVTTGFGAALKTANVQKGDTVAVFGCGTVGLSVIQGAKLRGASKIIAIDIN NKKKQYCSQFGATDFVNPKEDLAKDQTIVEKLIEMTDGGLDFTFDCTGNTKIMRDALE ACHKGWGQSIIIGVAAAGEEISTRPFQLVTGRVWKGSAFGGIKGRSEMGGLIKDYQKG ALKVEEFITHRRPFKEINQAFEDLHNGDCLRTVLKSDEIK
An example of a polynucleotide sequence encoding a formaldehyde dehydrogenase is shown in SEQ ID NO: 39:
ATGTCCGCCGCTACTGTTGGTAAACCTATTAAGTGCATTGCTGCTGTTGCGT ATGATGCGAAGAAACCATTAAGTGTTGAAGAAATCACGGTAGACGCCCCAAAAGC GCACGAAGTACGTATCAAAATTGAATATACTGCTGTATGCCACACTGATGCGTACA CTTTATCAGGCTCTGATCCAGAAGGACTTTTCCCTTGCGTTCTGGGCCACGAAGGA GCCGGTATCGTAGAATCTGTAGGCGATGATGTCATAACAGTTAAGCCTGGTGATCA TGTTATTGCTTTGTACACTGCTGAGTGTGGCAAATGTAAGTTCTGTACTTCCGGTAA AACCAACTTATGTGGTGCTGTTAGAGCTACTCAAGGGAAAGGTGTAATGCCTGATG GGACCACAAGATTTCATAATGCGAAAGGTGAAGATATATACCATTTCATGGGTTGC TCTACTTTTTCCGAATATACTGTGGTGGCAGATGTCTCTGTGGTTGCCATCGATCC AAAAGCTCCCTTGGATGCTGCCTGTTTACTGGGTTGTGGTGTTACTACTGGTTTTG GGGCGGCTCTTAAGACAGCTAATGTGCAAAAAGGCGATACCGTTGCAGTATTTGG CTGCGGGACTGTAGGACTCTCCGTTATCCAAGGTGCAAAGTTAAGGGGCGCTTCC AAGATCATTGCCATTGACATTAACAATAAGAAAAAACAATATTGTTCTCAATTTGGT GCCACGGATTTTGTTAATCCCAAGGAAGATTTGGCCAAAGATCAAACTATCGTTGA AAAGTTAATTGAAATGACTGATGGGGGTCTGGATTTTACTTTTGACTGTACTGGTAA TACCAAAATTATGAGAGATGCTTTGGAAGCCTGTCATAAAGGTTGGGGTCAATCTA TTATCATTGGTGTGGCTGCCGCTGGTGAAGAAATTTCTACAAGGCCGTTCCAGCTG GTCACTGGTAGAGTGTGGAAAGGCTCTGCTTTTGGTGGCATCAAAGGTAGATCTG AAATGGGCGGTTTAATTAAAGACTATCAAAAAGGTGCCTTAAAAGTCGAAGAATTTA TCACTCACAGGAGACCATTCAAAGAAATCAATCAAGCCTTTGAAGATTTGCATAAC GGTGATTGCTTAAGAACCGTCTTGAAGTCTGATGAAATAAAATAG In certain embodiments, the proteins which enable the cell to utilise methanol as a major or sole source of carbon, are selected from the group consisting of: alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) and dihydroxyacetone synthase (E.C. 2.2.1 .3), or functional variants thereof. In a preferred embodiment, the proteins are alcohol oxidase, pyruvate carboxylase and dihydroxyacetone synthase, or functional variants thereof.
In certain embodiments, the proteins which enable the cell to utilise methanol as a major or sole source of carbon, are selected from the group consisting of: alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) and transaldolase (EC 2.2.1 .2), or functional variants thereof. In a preferred embodiment, the proteins are alcohol oxidase, pyruvate carboxylase and dihydroxyacetone synthase, or functional variants thereof.
In certain embodiments, the proteins which enable the cell to utilise methanol as a major or sole source of carbon, are selected from the group consisting of: alcohol oxidase (E.C. 1.1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ), dihydroxyacetone synthase (E.C. 2.2.1 .3), and transaldolase (EC 2.2.1.2), or functional variants thereof. In a preferred embodiment, the proteins are alcohol oxidase, pyruvate carboxylase and dihydroxyacetone synthase, or functional variants thereof.
In a further embodiment, the proteins which enable the yeast cell to grow on methanol are alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1 .3), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13) and fructose-1 -6-bisphophatase (E.C.3.1.3.11), or functional variants thereof.
In a further embodiment, the proteins which enable the yeast cell to grow on methanol are alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) transaldo!ase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6- bisphosphate aldolase (E.C.4.1.2.13) and fructose-1 -6-bisphophatase (E.C.3.1.3.11), or functional variants thereof.
In a further embodiment, the proteins which enable the yeast cell to grow on methanol are alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1), dihydroxyacetone synthase (E.C. 2.2.1.3), transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13) and fructose-1 -6-bisphophatase (E.C.3.1.3.11), or functional variants thereof.
In another embodiment, the proteins which enable the yeast cell to grow on methanol are alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C.6.4.1.1) and dihydroxyacetone synthase (E.C. 2.2.1.3), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1.3.11) and sedoheptulose bisphosphatase (E.C. 3.1.3.37), or functional variants thereof.
In another embodiment, the proteins which enable the yeast cell to grow on methanol are alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6- bisphosphate aldolase (E.C.4.1.2.13), fructose-1 -6-bisphophatase (E.C.3.1.3.11) and sedoheptulose bisphosphatase (E.C.3.1.3.37), or functional variants thereof.
In another embodiment, the proteins which enable the yeast cell to grow on methanol are alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) dihydroxyacetone synthase (E.C. 2.2.1.3), transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1.3.11) and sedoheptulose bisphosphatase (E.C.3.1.3.37), or functional variants thereof. In yet a further embodiment, the proteins which enable the yeast cell to grown on methanol are alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C.6.4.1.1) and dihydroxyacetone synthase (E.C. 2.2.1.3), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1.3.11), sedoheptulose bisphosphatase (E.C. 3.1.3.37), ribose-5-phosphate isomerase (E.C. 5.3.1.6) and D-ribulose-5-phosphate-3-epimerase (E.C. 5.1.3.1), or functional variants thereof.
In yet a further embodiment, the proteins which enable the yeast cell to grown on methanol are alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C.6.4.1.1) and transaldo!ase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6- bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1.3.11), sedoheptulose bisphosphatase (E.C. 3.1.3.37), ribose-5-phosphate isomerase (E.C. 5.3.1.6) and D-ribulose-5-phosphate-3-epimerase (E.C. 5.1.3.1), or functional variants thereof. In yet a further embodiment, the proteins which enable the yeast cell to grown on methanol are alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C.6.4.1.1) and dihydroxyacetone synthase (E.C. 2.2.1.3), transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1.3.11), sedoheptulose bisphosphatase (E.C. 3.1.3.37), ribose-5-phosphate isomerase (E.C. 5.3.1.6) and D-ribulose-5- phosphate-3-epimerase (E.C.5.1.3.1), or functional variants thereof.
In yet a further embodiment, the proteins which enable the yeast cell to grown on methanol are alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C.6.4.1.1) and dihydroxyacetone synthase (E.C. 2.2.1.3), transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1.3.11), sedoheptulose bisphosphatase (E.C.3.1.3.37), ribose-5-phosphate isomerase (E.C.5.3.1.6) , D-ribulose-5-phosphate- 3-epimerase (E.C. 5.1.3.1), and formaldehyde dehydrogenase (E.C. 1.2.1.46) or functional variants thereof. In addition to the above combinations of enzymes, the yeast cell may be provided with a nucleic acid construct which encodes transketolase 1 or 2 (E.C. 2.2.1 .1 ), catalase (E.C. 1.1 1 .1.6), glutathione peroxidase (E.C. 1 .1 1 .1 .9) and/or methyl formate-synthesising alcohol dehydrogenase (E.C. 1 .1.1 .1 ), or functional variants thereof.
In certain embodiments, the yeast cell may already have genes encoding proteins selected from the group consisting of alcohol oxidase (E.C. 1.1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ), dihydroxyacetone synthase (E.C. 2.2.1 .3), iransaldolase (EC 2.2.1 .2), dihydroxyacetone kinase (E.C. 2.7.1 .29), fructose-1 -6- bisphosphate aldolase (E.C. 4.1 .2.13), fructose-1 -6-bisphophatase (E.C. 3.1 .3.1 1 ), sedoheptulose bisphosphatase (E.C. 3.1.3.37), ribose-5-phosphate isomerase (E.C. 5.3.1 .6), D-ribulose-5-phosphate-3-epimerase (E.C. 5.1 .3.1 ), or functional variants thereof. The present invention includes providing such cells with a recombinant construct encoding one or more proteins that enable the cell to grow in methanol, provided that the construct does not also contain the gene. In other words, in certain embodiments of the present invention, providing the recombinant construct to the yeast cell enables completion of the molecular pathway required to enable the yeast cells to grown in a medium where methanol is the sole or major carbon source.
Alternatively, the construct provides for increased expression (or over- expression) of a gene that is endogenous to the yeast cell, but for which increased expression is required in order for the cell to grow efficiently where methanol is the sole or major carbon source.
The term "protein" shall be taken to include a single polypeptide chain, i.e., a series of contiguous amino acids linked by peptide bonds or a series of polypeptide chains covalently or non-covalently linked to one another (i.e., a polypeptide complex). For example, the series of polypeptide chains can be covalently linked using a suitable chemical or a disulphide bond. Examples of non-covalent bonds include hydrogen bonds, ionic bonds, Van der Waals forces, and hydrophobic interactions.
The term "polypeptide" or "polypeptide chain" will be understood from the foregoing paragraph to mean a series of contiguous amino acids linked by peptide bonds. Also contemplated for use in the invention is a biologically active variant or analog of the proteins listed above, a polypeptide or peptidomimetic that may have, for example, at least 70%, at least 80%, at least 85%, at least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98% or at least 99% sequence identity to the recited sequences, which also retains the biological activity described. The ability to determine enzymatic activity for each protein may be measured by any method as described herein or known in the art. The biologically active variant or analog may contain one or more conservative amino acid substitutions, or non-native amino acid substitutions. "Percent (%) amino acid sequence identity" or "percent (%) identical" with respect to a polypeptide sequence, i.e. a polypeptide, protein or fusion protein of the invention defined herein, is defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in the specific polypeptide of the invention, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity.
Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms (non-limiting examples described below) needed to achieve maximal alignment over the full-length of the sequences being compared. When amino acid sequences are aligned, the percent amino acid sequence identity of a given amino acid sequence A to, with, or against a given amino acid sequence B (which can alternatively be phrased as a given amino acid sequence A that has or comprises a certain percent amino acid sequence identity to, with, or against a given amino acid sequence B) can be calculated as: percent amino acid sequence identity = X/Y100, where X is the number of amino acid residues scored as identical matches by the sequence alignment program's or algorithm's alignment of A and B and Y is the total number of amino acid residues in B. If the length of amino acid sequence A is not equal to the length of amino acid sequence B, the percent amino acid sequence identity of A to B will not equal the percent amino acid sequence identity of B to A. In calculating percent identity, typically exact matches are counted. The determination of percent identity between two sequences can be accomplished using a mathematical algorithm. A nonlimiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin and Altschul (1990) Proc. Natl. Acad. Sci. USA 87:2264, modified as in Karlin and Altschul (1993) Proc. Natl. Acad. Sci. USA 90:5873-5877. Such an algorithm is incorporated into the BLASTN and BLASTX programs of Altschul et al. (1990) J. Mol. Biol. 215:403. To obtain gapped alignments for comparison purposes, Gapped BLAST (in BLAST 2.0) can be utilized as described in Altschul et al. (1997) Nucleic Acids Res. 25:3389. Alternatively, PSI-Blast can be used to perform an iterated search that detects distant relationships between molecules. See Altschul et al. (1997) supra. When utilizing BLAST, Gapped BLAST, and PSI-Blast programs, the default parameters of the respective programs (e.g., BLASTX and BLASTN) can be used. Alignment may also be performed manually by inspection. Another non- limiting example of a mathematical algorithm utilized for the comparison of sequences is the ClustalW algorithm (Higgins et al. (1994) Nucleic Acids Res. 22:4673-4680). ClustalW compares sequences and aligns the entirety of the amino acid or DNA sequence, and thus can provide data about the sequence conservation of the entire amino acid sequence. The ClustalW algorithm is used in several commercially available DNA/amino acid analysis software packages, such as the ALIGNX module of the Vector NTI Program Suite (Invitrogen Corporation, Carlsbad, CA). After alignment of amino acid sequences with ClustalW, the percent amino acid identity can be assessed. A non-limiting examples of a software program useful for analysis of ClustalW alignments is GENEDOC™ or JalView (http://www.jalview.org/). GENEDOC™ allows assessment of amino acid (or DNA) similarity and identity between multiple proteins. Another non- limiting example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller (1988) CABIOS 4: 1 1 - 17. Such an algorithm is incorporated into the ALIGN program (version 2.0), which is part of the GCG Wisconsin Genetics Software Package, Version 10 (available from Accelrys, Inc., 9685 Scranton Rd., San Diego, CA, USA). When utilizing the ALIGN program for comparing amino acid sequences, a PAM 120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used. The polypeptide desirably comprises an amino end and a carboxyl end. The polypeptide can comprise D-amino acids, L-amino acids or a mixture of D- and L-amino acids. The D-form of the amino acids, however, is particularly preferred since a polypeptide comprised of D-amino acids is expected to have a greater retention of its biological activity in vivo.
The polypeptide can be prepared by any of a number of conventional techniques. The polypeptide can be isolated or purified from a naturally occurring source or from a recombinant source. Recombinant production is preferred. For instance, in the case of recombinant polypeptides, a DNA fragment encoding a desired peptide can be subcloned into an appropriate vector using well-known molecular genetic techniques (see, e.g., Maniatis et al., Molecular Cloning: A Laboratory Manual, 2nd ed. (Cold Spring Harbor Laboratory, 1982); Sambrook et al., Molecular Cloning A Laboratory Manual, 2nd ed. (Cold Spring Harbor Laboratory, 1989). The fragment can be transcribed and the polypeptide subsequently translated in vitro. Commercially available kits also can be employed (e.g., such as manufactured by Clontech, Palo Alto, Calif.; Amersham Pharmacia Biotech Inc., Piscataway, N.J.; InVitrogen, Carlsbad, Calif., and the like). The polymerase chain reaction optionally can be employed in the manipulation of nucleic acids.
The term "conservative substitution" as used herein, refers to the replacement of an amino acid present in the native sequence in the peptide or polypeptide with a naturally or non- naturally occurring amino acid or a peptidomimetic having similar steric properties. Where the side-chain of the native amino acid to be replaced is either polar or hydrophobic, the conservative substitution should be with a naturally occurring amino acid, a non- naturally occurring amino acid or with a peptidomimetic moiety which is also polar or hydrophobic (in addition to having the same steric properties as the side- chain of the replaced amino acid).
Conservative amino acid substitution tables providing functionally similar amino acids are well known to one of ordinary skill in the art. The following six groups are examples of amino acids that may be considered to be conservative substitutions for one another:
1 ) Alanine (A), Serine (S), Threonine (T);
2) Aspartic acid (D), Glutamic acid 3) Asparagine (N), Glutamine (Q); 4) Arginine (R), Lysine (K);
5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); and
6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W).
As naturally occurring amino acids are typically grouped according to their properties, conservative substitutions by naturally occurring amino acids can be determined bearing in mind the fact that replacement of charged amino acids by sterically similar non-charged amino acids are considered as conservative substitutions. For producing conservative substitutions by non-naturally occurring amino acids it is also possible to use amino acid analogs (synthetic amino acids) well known in the art. A peptidomimetic of the naturally occurring amino acid is well documented in the literature known to the skilled person and non-natural or unnatural amino acids are described further below. When affecting conservative substitutions the substituting amino acid should have the same or a similar functional group in the side chain as the original amino acid. Alterations of the native amino acid sequence to produce mutant polypeptides, such as by insertion, deletion and/or substitution, can be done by a variety of means known to those skilled in the art. For instance, site-specific mutations can be introduced by ligating into an expression vector a synthesized oligonucleotide comprising the modified site. Alternately, oligonucleotide-directed site-specific mutagenesis procedures can be used, such as disclosed in Walder et al., Gene 42: 133 (1986); Bauer et al., Gene 37: 73 (1985); Craik, Biotechniques, 12-19 (January 1995); and U.S. Pat. Nos. 4,518,584 and 4,737,462. A preferred means for introducing mutations is the QuikChange Site-Directed Mutagenesis Kit (Stratagene, La Jolla, Calif.).
The proteins which are described herein may also include targeting sequences. The targeting sequences present in the protein sequences may facilitate subcellular localisation of the proteins, for example, to the peroxisome or mitochondria of the yeast.
It will be understood, therefore, that the sequences shown herein may be further modified to include additional targeting sequences at either N or C- termini, or at an internal region of the protein sequence. Examples of type 1 peroxisomal targeting sequences (PTS1 ), which are typically located at the C-terminus of a protein are:
- SKL, ARY,ARF, GRF, AKL,NKF, SKI, NHL, NKL
The consensus sequence for the type 2 peroxisomal targeting sequence (PTS2) in yeast is: (R/K)-(L/V/I)-(XXXXX)-(H/Q)-(I_/A/F).
The skilled person will be familiar with methods for confirming successful transformation of relevant constructs, as well as methods for determining whether the transformants possess the relevant enzyme activity provided by the encoded protein. For example, alcohol oxidase activity (and therefore inferring correct protein folding of the encoded protein) can be inferred using a commercially available enzyme assay kit (http://www.sigmaaldrich.com/technical-documents/protocols/biology/enzymatic-assay- of-alcohol-oxidase. htm I).
Activity of catalase (Sigma Aldrich catalogue number CAT100), dihydroxyacetone synthase, and other peroxisomally targeted enzymes in the invention can also be assayed using available kits. For example: Fructose-1 -6-bisphosphate aldolase (https://www.sigmaaldrich.com/content/dam/sigma- aldrich/docs/Sigma/Enzyme_Assay/a881 1 enz.pdf),
Fructose-6-phosphatase: (http://www.sigmaaldrich.com/content/dam/sigma- aldrich/docs/Sigma/Bulletin/1/mak020bul.pdf), RKI1 and RPE1 (https://www.sigmaaldrich.com/content/dam/sigma- aldrich/docs/Sigma/Enzyme_Assay/phosphoriboisomerase.pdf).
Constructs encoding proteins enabling yeast to utilise methanol
The skilled person will appreciate that proteins which enable a yeast cell to utilise methanol as a source of energy, as described herein, can be provided to a yeast cell by genetically modifying the yeast cell so that it is able to synthesise the relevant proteins.
"Genetically engineered" or "genetically modified" refers to any cell modified by any recombinant DNA or RNA technology. In other words, the cell has been transfected, transformed, or transduced with a recombinant polynucleotide molecule, and thereby been altered so as to cause the cell to alter expression of a desired protein. Methods and vectors for genetically engineering host cells are well known in the art; for example, various techniques are illustrated in Current Protocols in Molecular Biology, Ausubel et al., eds. (Wiley & Sons, New York, 1988, and quarterly updates). Genetic engineering techniques include but are not limited to expression vectors, targeted homologous recombination, and gene activation (see, for example, U.S. Pat. No. 5,272,071 ), and trans-activation by engineered transcription factors (see, for example, Segal et al., 1999, Proc Natl Acad Sci USA 96(6):2758-63).
In certain embodiments, the genetic modifications described herein result in an increase in gene expression or function and can be referred to as amplification, overproduction, overexpression, activation, enhancement, addition, or up-regulation of a gene. More specifically, reference to increasing the action (or activity) of enzymes or other proteins discussed herein generally refers to any genetic modification in the microorganism in question that results in increased expression and/or functionality (biological activity) of the enzymes or proteins and includes higher activity of the enzymes (e.g., specific activity or in vivo enzymatic activity), reduced inhibition or degradation of the enzymes, and overexpression of the enzymes. For example, gene copy number can be increased, expression levels can be increased by use of a promoter that gives higher levels of expression than that of the native promoter, or a gene can be altered by genetic engineering or classical mutagenesis to increase the biological activity of an enzyme. Combinations of some of these modifications are also possible.
As used herein, the term "exogenous polynucleotides" is intended to mean polynucleotides that are not derived from naturally occurring polynucleotides in a given organism. Exogenous polynucleotides may be derived from polynucleotides present in a different organism. In accordance with the present invention, a yeast cell may be genetically modified with a nucleic acid construct which contains one or more exogenous polynucleotides, encoding one or more enzymes which enable the yeast cell to utilise methanol as a main source of energy. The exogenous polynucleotides may be heterologous or homologous. The term
"heterologous" refers to a molecule or activity derived from a source other than the referenced species whereas "homologous" refers to a molecule or activity derived from the host microbial organism. Accordingly, exogenous expression of a nucleic acid molecule of the invention can be through the use of either or both a heterologous or homologous nucleic acid molecule. The exogenous polynucleotides as herein described, may be expressed from one or more chromosomal locations or from one or more plasmid locations. In other words, the polynucleotides encoding the proteins enabling growth on methanol may be provided on a single nucleic acid molecule, or multiple nucleic acid molecules.
In certain embodiments, the exogenous polynucleotides are derived from nucleic acid sequences found in the genome of methylotrophic organisms. For example, the exogenous nucleic acid may encode a protein from a methylotrophic organism such as from the genera Pichia, Candida, Hansen ula and Torulpsis.
In certain embodiments, the exogenous polynucleotides are derived from Pichia pastoris, Pichia methanolica, Candida boidinii and/or Hansenula polymorpha (also called Pichia augusta). In a preferred embodiment, the exogenous polynucleotides are from Pichia pastoris.
The exogenous polynucleotides may be provided in one or more expression constructs (plasmid vectors). Accordingly, in yet a further embodiment, the present invention provides a recombinant construct encoding at least one protein for enabling a yeast cell to grow in a medium in which methanol is the only or main energy source for growth of the cell in the medium, wherein the one or more proteins is selected from the group consisting of: alcohol oxidase (E.C. 1 .1.3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1 .3), dihydroxyacetone kinase (E.C. 2.7.1 .29), fructose-1 -6- bisphosphate aldolase (E.C. 4.1 .2.13), fructose-1 -6-bisphophatase (E.C. 3.1 .3.1 1 ), sedoheptulose bisphosphatase (E.C. 3.1 .3.37), ribose-5-phosphate isomerase (E.C. 5.3.1 .6) and D-ribulose-5-phosphate-3-epimerase (E.C. 5.1 .3.1 ), transketolase 1 or 2 (E.C. 2.2.1.1 ), or functional variants thereof.
In certain embodiments, the exogenous polynucleotides are all provided on a single low-copy plasmid. Examples of suitable plasmids include pRS415 and pRS416. For example, in certain embodiments, the present invention provides a plasmid which encodes one or more of AOX1 , PYC1 , DAS1 , DAK, FBA2, FBP1 , RKI1 , RPE1 , SHB17, TAL1 , AOX1 , DAS1 , PYC1 genes to encode part of a synthetic methanol utilisation pathway in yeast. In a further embodiment, the plasmid encodes AOX1 , DAS1 and PYC1 genes. In yet a further embodiment, the plasmid encodes AOX1 , DAS1 , PYC1 , DAK, FBA2, FBP1 , and SHB17 genes. In a particularly preferred embodiment, the plasmid encodes AOX1 , DAS1 , PYC1 , DAK, FBA2, FBP1 , SBPase, RPE1 and RKL1 genes and optionally also TAL1 .
The nucleic acid constructs of the present invention include nucleic acid sequences encoding one or more of the subject proteins described herein.
In certain embodiments, the nucleic acid constructs also encode targeting sequences, to enable localisation of the encoded proteins to the desired subcellular organelle to facilitate optimal utilisation of methanol by the yeast cell. The targeting sequence may be for targeting of a protein to the peroxisomes or mitochondria of the yeast. For example, in certain embodiments, the nucleic acid constructs may include nucleic acid sequences encoding peroxisomal targeting sequences adjacent to the sequence encoding the relevant protein, such that the synthesised protein includes an N-terminal, C-terminal or internal targeting sequence. For example, sequence encoding the subcellular targeting sequence may encode a type 1 or type 2 peroxisomal-targeting sequence (PTS1 or PTS2). Examples of PTS1 and PTS2 sequences are described above.
The polynucleotide encoding the subcellular targeting sequence may be an endogenous or exogenous sequence. In other words, while the polynucleotide encoding the protein enabling growth of the yeast cell on methanol may be exogenous (derived from a methylotroph), the sequence encoding the targeting sequence may be from the yeast cell which will be provided with the recombinant construct. Alternatively, an exogenous targeting sequence may be used.
The skilled person will appreciate that localisation to the peroxisome may be desirable to ensure proper activity of the relevant protein. For example, given that catabolism of methanol results in the formation of oxidation products and toxins such as hydrogen peroxide and formaldehyde, it may be desirable to ensure that the proteins which are involved in the formation or detoxification of these toxic products are localised to the peroxisome. This may also facilitate the compartmentalisation and detoxification of such toxins by proteins which are naturally found in the peroxisomes of the non- methylotrophic yeast cell. Alternatively, it may be desirable to provide additional proteins for ensuring the detoxification of toxins in the yeast cell. Examples of proteins which are useful for detoxifying products of methanol catabolism include catalase, glutathione peroxidase.
The nucleic acids of the present invention are preferably operably linked to promoters such that the subject enzymes are expressed in the cell when cultured under suitable conditions. The promoters may be specific for individual yeast cell species.
As used herein, the term "promoter" refers to a non-coding sequence located upstream (i.e., 5') to the translation start codon of a structural gene (generally within about 1 to 1000 bp, preferably 1 -500 bp, especially 1 -100 bp) and which controls the start of transcription of a structural gene. The promoter may be native to the host cell or exogenous. The promoters can be those that control the expression of genes that are involved in central carbon metabolism, e.g., glycolytic promoters or TCA cycle gene promoters. Suitable promoters include the non-limiting examples of promoters from yeast genes phosphoglycerate kinase (PGK), glyceraldehyde-3-phosphate dehydrogenase (TDH, including TDH3), pyruvate decarboxylase (PDC1 ), triose phosphate isomerase (TP1 ), Transcription enhancer factor-1 (TEF-1 ) (TEF2), purinecytosine permease (PCPL3), alcohol dehydrogenase (ADH), the SSA promoter, YEF3 promoter and PPI1 promoter. Preferred promoters of the invention include the TEF-1 , TDH3, SSA, YEF3 and PPI1 (S. cerevisiae), PGK (S. cerevisiae), and PDCI (S. cerevisiae, K. marxianus) promoters. In addition, the galactose inducible GAL1 , or glucose de-repressible SUC2 promoters may be used.
In certain embodiments, the promoters used in the nucleic acid constructs of the present invention are inducible promoters, for enabling expression of proteins under specific circumstances. For example, it may be desirable for the proteins to only be expressed by the yeast cell when the cell is exposed to high levels of methanol. In such circumstances, it may be desirable to utilise promoters which are induced by methanol. Some promoters may be induced by one substrate, by repressed by another. For example the PAox promoter from Pichia pastoris is strongly induced by the presence of methanol, but repressed by the presence of glucose or ethanol. Accordingly, the present invention also provides for nucleic acid constructs comprising one or more polynucleotides encoding any enzyme, as herein described, wherein the polynucleotide is operably linked to an inducible promoter, for inducing expression of the enzyme upon exposure to methanol. In certain embodiments, the promoter is the PAox promoter from Pichia pastoris. The skilled person will appreciate that it is also possible to utilise a promoter from another methylotrophic organism, for example, the PMOX promoter from H. polymorpha, the PAODI promoter from C. boidinii or the PMODI promoter from P. methanolica.
In yet further embodiments, the activity and regulation of certain promoters described herein, can be further controlled by the provision of one or more transcription factors to the yeast cell. For example, in certain embodiments, the present invention includes transforming the yeast cells with constructs expressing one or more transcription factors which activate or regulate any of the promoters used in accordance with the present invention. The one or more transcription factors may activate a native S. cerevisiae promoter. The native promoter that is activated by the one or more transcription factors may be operably linked to an endogenous S. cerevisiae gene sequence. Alternatively, the native promoter may be operably linked to an exogenous polynucleotide that encodes an enzyme enabling methanol utilisation by a yeast cell.
Alternatively, the one or more transcription factors may activate a heterologous promoter that is operably linked to a polynucleotide encoding an enzyme enabling a yeast cell to utilise methanol as a source of energy.
In certain embodiments, the heterologous promoter is a Pichia pastoris promoter, and the one or more transcription factors activates the Pichia pastoris promoter. In yet further embodiments, the promoter is the PAox promoter from Pichia pastoris, and the transcription factor is any one of the transcription factors Mit1 , Mxr1 and Prm 1 . In certain embodiments, two or more of the transcription factors which activate the PAox promoter from Pichia pastoris are used. In yet further embodiments, all three of the transcription factors Mit1 , Mxr1 and Prm1 are used. It will be clear that the present invention includes constructs and exogenous polynucleotides encoding said transcription factors. Said constructs may be transformed into the yeast cells separately to the constructs which encode enzymes for enabling methanol utilisation by the yeast cell. Alternatively, the polynucleotides encoding the transcription factors may be included in the same construct that encodes enzymes enabling methanol utilisation by the yeast cell.
In certain embodiments it may be desired to integrate the polynucleotides encoding the proteins at a targeted locus of the yeast cell's genome. In such cases, the promoter sequence may be homologous to the promoter sequence of the gene where insertion is targeted.
For example, in certain embodiments, the constructs may include sequences which enable integration of the polynucleotides into the yeast cells genome using CRE recombinase. The skilled person will be familiar with the use of such techniques, including for example, the use of the SCRaMbLe system for synthetic chromosome recombination and modification (Dymon and Boeke (2012) Bioenginered Buds 3: 168- 171 ; Jovicevic et al., (2014) Bioessays 36: 855-860; and Shen et al., (2016) Genome Res. 26: 36-49).
The recombinant nucleic acid construct can and preferably does contain other elements as well, including (a) a terminator sequence; (b) one or more selection marker gene(s) (including an associated promoter and terminator); (c) one or more homologous flanking sequences for inserting the fragment at a particular locus in the genome of the host cell; (d) one or more restriction sites which enable it to be cut to form a linear fragment containing the gene encoding a relevant protein as herein described, its promoters and flanking sequences, marker genes and associated promoters and terminators, etc., for insertion into the genome of the yeast cell; and/or (e) a backbone portion.
The term "recombinant nucleic acid" is used herein to refer to any molecule (e.g., nucleic acid, plasmid or virus) used to transfer protein-coding information to the host cell. Methods of transforming cells are well known in the art, and can include such non- limiting examples as electroporation, calcium chloride-, or lithium acetate-based methods. The DNA used in the transformations can either be cut with particular restriction enzymes or uncut.
As used herein, the term "selection marker genes" refer to genetic material that encodes a protein necessary for the survival and/or growth of a host cell grown in a selective culture medium. Typical selection marker genes encode proteins that (a) confer resistance to antibiotics or other toxins, e.g., zeocin (sh ble gene from Streptoalloteichus hindustanus), G418 (kanamycin-resistance gene of Tn903), hygromycin (aminoglycoside antibiotic resistance gene from E. coli), ampicillin, tetracycline, or kanamycin for host cells; (b) complement auxotrophic deficiencies of the cell and/or supply critical nutrients not available from simple media, such as amino acid leucine deficiency (K. marxianus Leu2 gene); or a K. marxianus ura3 gene that gives uracil to orotidine-5'-phosphate decarboxylase negative cells. Preferred selectable markers include the non-limiting examples of zeocin resistance gene, G418 resistance gene, and the hygromycin resistance gene. The term "terminator" refers to an untranscribed sequence located downstream
(i.e., 3') to the translation STOP codon of a structural gene (generally within about 1 to 1000 bp, more typically 1 -500 base pairs and especially 1 -100 base pairs) and which controls the end of transcription of the structural gene. The terminator can be exogenous or native to the yeast species. Suitable exogenous terminators include the GAL10, CYC-1 ADH1 t, STE2, MFA1 , PHO5t and TPI1 terminators from S. cerevisiae or other yeast species.
As with the promoters, in certain embodiments, the terminator sequence is homologous to a terminator sequence of the encoded gene.
Each nucleic acid sequence encoding the desired protein can be incorporated into an expression vector. "Expression vector" or "vector" refers to a compound and/or composition that transduces, transforms, or infects a host cell, thereby causing the cell to express nucleic acids and/or proteins other than those endogenous to the cell, or in a manner not naturally occurring in the cell. An expression vector contains a sequence of nucleic acids (ordinarily RNA or DNA) to be expressed by the host cell (in this case a yeast cell). Optionally, the expression vector also comprises materials to aid in achieving entry of the nucleic acid into the host microorganism, such as a virus, liposome, protein coating, or the like. The expression vectors contemplated for use in the present invention include those into which a nucleic acid sequence can be inserted, along with any preferred or required operational elements. Further, the expression vector must be one that can be transferred into a host cell and replicated therein. Preferred expression vectors are plasmids, particularly those with restriction sites that have been well-documented and that contain the operational elements preferred or required for transcription of the nucleic acid sequence. Such plasmids, as well as other expression vectors, are well known to those of ordinary skill in the art.
Methods for designing and making nucleic acid constructs and expression vectors are well known to those skilled in the art.
Although any suitable expression vector may be used to incorporate the desired sequences, readily-available expression vectors include, without limitation, plasmids, such as pSCIOI, pBR322, pBBRIMCS-3, pUR, pEX, pMRIOO, pCR4, pBAD24, pUC19, and bacteriophages, such as Ml 3 phage and λ phage. Yeast episomal plasmids (YEPs) and Yeast integrated plasmids (YIPs) may also be used.
In a preferred embodiment, the plasmids used are yeast centromeric plasmids containing selectable markers. In a more preferred embodiment, the plasmids used are yeast centromeric plasmids with LEU2 and/or URA3 genes as selectable markers. Of course, such expression vectors may only be suitable for particular host cells. One of ordinary skill in the art, however, can readily determine through routine experimentation whether any particular expression vector is suited for any given host cell. For example, the expression vector can be introduced into the host cell, which is then monitored for viability and expression of the sequences contained in the vector.
The plasm id may be adapted for integration of the exogenous polynucleotides into the genome of the yeast cell.
The skilled person will appreciate that it is possible to generate suitable amounts of polynucleotide constructs in non-host cells (for example, in E. coli or other bacterial systems), prior to eventual transformation of the yeast cell into which the construct is to be introduced. The skilled person will be familiar with the use of bacterial systems for producing recombinant expression vectors for ultimate use in eukaryotic microorganisms.
Metabolite production
The present invention provides a method for forming a metabolite derived from methanol in a yeast cell comprising providing the yeast cell with a recombinant construct encoding one or more proteins selected from the group consisting of: alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1 .3), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1 .3.1 1 ), sedoheptulose bisphosphatase (E.C. 3.1.3.37), ribose-5-phosphate isomerase (E.C. 5.3.1.6) and D-ribulose-5-phosphate-3-epimerase (E.C. 5.1 .3.1 ), transketolase 1 or 2 (E.C. 2.2.1 .1 ), transa!dolase (EC 2.2.12), or functional variants thereof; and culturing the yeast cell in a medium in which methanol is the only or main energy source for growth of the cell in the medium.
As explained above, previous attempts have been made to genetically modify yeasts which do not normally utilise methanol as a main source of energy (such as S. cerevisiae), for use in a process involving the production of an industrially important chemical. Without wishing to be bound by theory, the inventors believe that the reason these previous attempts have failed is because the yeasts do not derive sufficient excess energy from the metabolism of methanol to then be able to produce the desired chemical product. (In fact, these attempts have failed to provide a strain of S. cerevisiae that is capable of growing at a sufficient rate using methanol as the sole source of energy, let alone provide a strain that can then be used to drive production of industrially important chemicals). In other words, more than simply growing on methanol is required for the yeast to be useful for producing an industrial chemical; the yeast must have sufficient energy reserves to drive production of the chemical.
In certain embodiments of the present invention, a P. pastoris pyruvate carboxylase is required for correct folding and import of alcohol oxidase protein monomers via the loading of a flavin adenine dinucleotide cofactor (FAD). 3 moles of methanol are required to generate 1 mole of glyceraldehyde-3-phosphate, as 3 moles of xylulose-5-phosphate are required as input for dihydroxyacetone synthase mediated conversion of formaldehyde into dihydroxyaceyone synthase and glyceraldehyde-3- phosphate. The present inventors have found that there are certain metabolites downstream of methanol which are key to providing the excess energy required to product industrial chemicals.
Accordingly, in yet a further embodiment, the present invention provides a method for forming a compound selected from the group consisting of xylulose-5- phosphate, glyceraldehyde-3-phosphate and dihydroxyacetone, in a yeast cell comprising providing the yeast cell with a recombinant construct encoding one or more proteins selected from the group consisting of: alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1 .3), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1 .3.1 1 ), sedoheptulose bisphosphatase (E.C. 3.1.3.37), ribose-5-phosphate isomerase (E.C. 5.3.1.6) and D-ribulose-5-phosphate-3-epimerase (E.C. 5.1 .3.1 ), transketolase 1 or 2 (E.C. 2.2.1 .1 ), transaldolase (EC 2.2.1 .2), formaldehyde dehydrogenase (E.C. 1.2.1 .46) or functional variants thereof; and growing the yeast cell in a medium in which methanol is the only or main energy source for growth of the cell in the medium.
The skilled person will appreciate that growing a yeast cell as described above is a suitable approach for generating a biomass of yeast cells which can be used in downstream applications, such as the production of an industrially important chemical. As used herein, the term "biomass" is intended to mean the collection of biological matter, made up of cells, that results from the culturing process of a microorganism under suitable conditions for the growth of that organism in culture. In some cases, the biomass includes simply the cells and their contents and in some cases, the biomass includes additionally any macromolecules, such as proteins, that are secreted into the culture, outside the boundary of the cell membrane. As used herein, the term "culturing" is intended to mean the growth or maintenance of microorganisms under laboratory or industrial conditions. The culturing of microorganisms is a standard practice in the field of microbiology. Microorganisms can be cultured using liquid or solid media as a source of nutrients for the microorganisms. In addition, some microorganisms can be cultured in defined media, in which the liquid or solid media are generated by preparation using purified chemical components. The composition of the culture media can be adjusted to suit the microorganism or the industrial purpose for the culture.
The skilled person will be familiar with the required culturing parameters that provide the microorganism with an environment that enables the culture to consume the available nutrients. In so doing, the microbiological culture may grow and/or produce chemicals or by-products. Culturing parameters may include, but are not limited to, such features as the temperature of the culture media, the dissolved oxygen concentration, the dissolved carbon dioxide concentration, the rate of stirring of the liquid media, the pressure in the vessel, etc.
During the growth phase, the yeast cells described herein are provided with methanol as either the major source or sole source of carbon. This enables large amounts of yeast biomass to be produced, at a relatively low cost since expensive sources of carbohydrate (sugars) are not needed for the yeast cells to proliferate. The skilled person will be familiar with means for obtaining a suitable source of methanol for use in culture of the yeast strains described herein. Methanol is a low-cost chemical which can also be derived from fossil sources (natural gas, coal, oil shale, tar sands, etc.), or from agricultural products and municipal waste, wood and varied biomass (via syngas, a CO- and H2- containing gas mixture generated by gasification of organic matter).
Methanol can also be made from chemical recycling of carbon dioxide by catalytic hydrogenation of CO2 with H2 where the hydrogen has been obtained from water electrolysis. Methanol may also be produced through CO2 electrochemical reduction. While methanol may be added directly to the culture medium, the skilled person will appreciate that the methods of the present invention include the growth of yeast on or in a medium in which methanol is a crude component. For example, the source of methanol may be provided in the form of an agricultural waste product, in which methanol is the principal carbon component, but wherein other materials are present. Thus, the present invention is useful for further metabolising waste from distillation of wood.
Additional nutrients may also be provided in the culture medium, such as sources of nitrogen, phosphorus, sulfur, trace minerals, etc. that promote the viability of the cells. For example, the following may be provided in the culture medium:
Nitrogen Sources:
• Ammonium sulfate, 5.0 g/L
Vitamins:
Biotin, 2.0 pg/L
Calcium pantothenate, 400 g/L
Folic acid, 2.0 g/L
Inositol, 2.0 mg/L
Nicotinic acid, 400 g/L
p-Aminobenzoic acid, 200 g/L
Pyridoxine HCI, 400 pg/L
Riboflavin, 200 pg/L
Thiamine HCL, 400 pg/L
Citric acid, 0.1 g/L
Trace Elements:
Boric acid, 500 g/L
Copper sulfate, 40 g/L
Potassium iodide, 100 g/L
Ferric chloride, 200 g/L • Magnesium sulfate, 400 g/L
• Sodium molybdate, 200 g/L
• Zinc sulfate, 400 g/L
Salts: · Potassium phosphate monobasic, 1.0 g/L
• Magnesium sulfate, 0.5 g/L
• Sodium chloride, 0.1 g/L
• Calcium chloride, 0.1 g/L
In certain embodiments, the media utilised can be commercially obtained (for example, Yeast Nitrogen Base without Amino Acids from Sigma Aldrich, supplemented with 0.5 -2 % w/v methanol).
In certain embodiments, the media utilised can be commercially obtained (for example, Yeast Nitrogen Base without Amino Acids from Sigma Aldrich, supplemented with 0.5 -2 % w/v methanol). In circumstances where methanol is provided as the major, but not the sole source of carbon to the cell, any number of carbohydrates may be used to 'supplement' the carbon source. Examples of such carbohydrates are: hexose sugars such as glucose and fructose, oligomers of glucose such as maltose, isomaltose, maltotriose, starch, and sucrose, maltodextrins and xylose (a pentose sugar) are preferred. Less preferred carbohydrates include galactose, mannose and arabinose.
The temperature during culturing of the microorganisms can be from about room temperature, more preferably from about 30°C, more preferably from about 35°C. Preferably the temperature does not exceed 40 °C.
The maximum temperature will depend on the particular yeast cell. When the yeast cell is K. marxianus, for example, the recombinant cell can tolerate relatively high temperatures (such as above 40°C and up to 50°C, especially up to 45°C). During culturing, the concentration of cells in the culture medium is typically in the range of about 1 -150, preferably about 3-10, even more preferably about 3-6 g dry cells/liter of culture medium.
The skilled person will be familiar with methods for determining the growth rate of the yeast cells, as a means for determining the ability of the cells to utilise methanol as a sole or major source of carbon. For example, the maximum specific growth rate for lab S. cerevisiae yeast strains when provided with glucose is around 0.45 h"1 (as compared with no growth when provided only with methanol; wherein the specific growth rate h"1 is defined as the rate of increase in biomass in grams of cells, per gram of cells, per hour). Thus, evidence of methanol utilisation will be growth of the yeast strain at a rate somewhere between that of a typical S. cerevisiae lab strain in methanol and when provided with glucose. In certain embodiments, the growth rate observed for the synthetic yeast strains of the present invention is approximately the same or greater than the growth rate observed for a methylotrophic strain, when grown under the same conditions.
Chemicals
As used herein, the term "chemical" is broadly meant include any substance used in or resulting from a reaction involving changes to atoms or molecules, especially one derived according to any of the processes set forth herein. As such, a chemical is intended to mean a substance obtained by a chemical process or a substance having a chemical effect.
Examples of chemicals contemplated by the invention, without limitation, are dicarboxylic acid, malic acid, fumaric acid, succinic acid, malic acid salt, fumaric acid salt, succinic acid salt, L-malic acid, D-malic acid, maleic acid, lactic acid, adipic acid, 1 ,3-propanediol, 2,3-butanediol, 1 ,4-butanediol, butadiene, fatty acid derivatives, fatty alcohols, fatty acids, fatty acid esters, fatty acid methyl esters, fatty acid ethyl esters, branched fatty acids, branched fatty acid derivatives, omega-3 fatty acids, isoprenoids, isoprene, farnesene, farnesane, squalene, squalane, carotenoids, amino acids, alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, monosodium glutamate, glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine, ornithine, proline, selenocysteine, serine, tyrosine, ethanol, propanol, 1 -butanol, 2-butanol, isobutanol (2-methylpropan-l-ol), alcohols, alkanes, alkenes, olefins, animal feed additives, mixtures of amino acids, and proteins.
Other examples of chemicals include, but are not limited to, ethanol, propanol, isopropanol, butanol, fatty alcohols, fatty acid esters, ethyl esters, wax esters; hydrocarbons and alkanes such as propane, octane, diesel, Jet Propellant 8 (JP8); polymers such as terephthalate, 1 ,3-propanediol, 1 ,4-butanediol, polyols, Polyhydroxyalkanoates (PHA), poly-beta-hydroxybutyrate (PHB), acrylate, adipic acid, ε-caprolactone, isoprene, caprolactam, rubber; commodity chemicals such as lactate, docosahexaenoic acid (DHA), 3-hydroxypropionate, γ-valerolactone, lysine, serine, aspartate, aspartic acid, sorbitol, ascorbate, ascorbic acid, isopentenol, lanosterol, omega-3 DHA, lycopene, itaconate, 1 ,3-butadiene, ethylene, propylene, succinate, citrate, citric acid, glutamate, malate, 3-hydroxypropionic acid (HPA), lactic acid, THF, gamma butyrolactone, pyrrolidones, hydroxybutyrate, glutamic acid, levulinic acid, acrylic acid, malonic acid; specialty chemicals such as carotenoids, isoprenoids, itaconic acid; pharmaceuticals and pharmaceutical intermediates such as 7- aminodeacetoxycephalosporanic acid (7-ADCA)/cephalosporin, erythromycin, polyketides, statins, paclitaxel, docetaxel, terpenes, peptides, steroids, omega fatty acids and other such suitable products of interest. Such products are useful in the context of biofuels, industrial and specialty chemicals, as intermediates used to make additional products, such as nutritional supplements, nutraceuticals, polymers, paraffin replacements, personal care products and pharmaceuticals.
Preferably, the methods of the present invention can be exploited to provide yeast strains which can be used to produce farnesene, farnesane, propanol, butanol, or octanol. Other examples of chemical include, without limitation, all compounds that can be produced with the methods set forth herein. Such compounds are intended to include all molecules that can be constructed with the methods set forth herein including, for example without limitation, all organic and inorganic molecules that can be made with the methods set forth herein. The term chemical is intended to include natural and non-natural compounds.
Examples of natural molecules include, but are not limited to, amino acids, nucleic acids, nucleotides and polynucleotides and all related biological molecules. Non-natural compounds include, but are not limited to, amino acids and nucleotides that are modified in a way differently than they are normally modified in biological systems.
The skilled person will appreciate that it is possible to produce a chemical, such as listed above, simply by growing the synthetic microorganisms described herein, under suitable conditions to produce the chemical. For example, provided that an appropriate carbon source is provided to the microorganisms (in the form of methanol) and appropriate trace elements and vitamins, the yeast can produce certain industrially relevant chemicals. An example of this is ethanol, which is metabolite produced in abundance by yeast. Other examples include glycerol and acetate.
In alternative embodiments the yeast cells described herein can be further modified to express pathways capable of producing a number of useful products, including commodity chemicals such as those described herein.
Accordingly, in a further embodiment, the present invention provides a method for producing a chemical which can be used in an industrial process, the method comprising growing a yeast cell including a recombinant construct encoding one or more proteins that enable the cell to grow in a medium in which methanol is the only or main energy source for growth of the cell in the medium, wherein the one or more proteins is selected from the group consisting of: alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1 .3), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1 .3.1 1 ), sedoheptulose bisphosphatase (E.C. 3.1.3.37), ribose-5-phosphate isomerase (E.C. 5.3.1.6) and D-ribulose-5-phosphate-3-epimerase (E.C. 5.1 .3.1 ), transketolase 1 or 2 (E.C. 2.2.1.1 ), transaldolase (EC 2.2.1 .2), formaldehyde dehydrogenase (E.C, 1.2.1 .46) or functional variants thereof, wherein the yeast cell includes a further construct enabling the production of the chemical.
The skilled person will appreciate that in this way, the yeast cells described herein can function as 'platform strains' which can be grown on methanol as either a major or sole source of carbon. These platform strains can then be further manipulated using known methods to express biosynthetic pathways for the production of a chemical.
The term "biosynthetic pathway", also referred to as "metabolic pathway", refers to a set of anabolic or catabolic biochemical reactions for converting one chemical species into another.
Similarly to the case for generating the synthetic microorganisms described herein, the skilled person will be familiar with methods for further modifying the platform, synthetic yeast strains of the present invention to express one or more biosynthetic pathways of interest. Examples are such biosynthetic pathways include: lactic acid production pathways, as described for example in US 7,405,068 (van Maris et al); malic acid and succinic acid production pathways, as described for example in WO 2007/06159 (Winkler et al); dicarboxylic acid production pathways, as described for example in WO2009/065780, WO 2009/101 180 and US 2012/0040422; cis,cis-muconic acid production pathways, for example, as described in Weber et al., (2012) Appl. Environ. Microbiol. 78: 8421 and Curran et al.,(2013) Metab. Eng. 15: 55-66); propionic acid (US 1898329) and para-hydroxybenzoic acid pathways (EP 2957629).
Examples
Example 1: Synthetic Methylotroph derived from S. cerevisiae A genetically modified strain of S. cerevisiae is obtained by standard molecular cloning and metabolic engineering. Genes encoding proteins from P. pastoris are cloned and introduced into S. cerevisiae for enabling the S. cerevisiae to grow in a medium in which methanol is the main carbon source. In one example, the genes encoding the enzymes alcohol oxidase, (EC 1 .1 .3.13, Aoxl, Aox2), dihydroxyacetone synthase (EC 2.2.1 .3, Dhas), and pyruvate carboxylase (EC 6.4.1 .1 , Pyc) are expressed from chromosomal integrated loci or from plasmids or both, wherein the enzymes are encoded by polynucleotides that are operably linked to a S. cerevisiae promoter, such as Pcycl, Padhl, Ptef2, Pgall. The resultant strains containing these genes are tested for growth in minimal media supplemented with methanol. Strains that grow on methanol have functional methanol-consumption pathways. Example 2: Induction of gene expression in S. cerevisiae
A genetically modified strain of S. cerevisiae is obtained by standard molecular cloning and metabolic engineering. Genes encoding proteins from P. pastoris are cloned and introduced into S. cerevisiae for enabling the S. cerevisiae to grow in a medium in which methanol is the main carbon source. In one example, the genes encoding the enzymes alcohol oxidase, (EC 1 .1 .3.13, Aoxl, Aox2), dihydroxyacetone synthase (EC 2.2.1 .3, Dhas), and pyruvate carboxylase (EC 6.4.1 .1 , Pyc) are expressed from chromosomal integrated loci or from plasm ids or both using the Pichia pastoris promoter PAox- The resultant strains containing these genes are tested for growth in minimal media supplemented with methanol. Strains that grow on methanol have functional methanol-consumption pathways.
Example 3: Induction of gene expression in S. cerevisiae
A genetically modified strain of S. cerevisiae is obtained by standard molecular cloning and metabolic engineering. Genes encoding proteins from P. pastoris are cloned and introduced into S. cerevisiae for enabling the S. cerevisiae to grow in a medium in which methanol is the main carbon source. In this example, the genes encoding the enzymes DAK, FBA2, FBP1 , RKI1 , RPE1 , SBPase, TAL1 , AOX1 , DAS1 , PYC1 are provided in a plasmid construct (see Figure 2). In addition, the genes CTA1 , pmp20, and ADH1 genes for the detoxification of by-products of synthetic methylotrophic metabolism, are provided in a separate construct (see Figure 3). The resultant cells containing the construct are tested for growth in minimal media supplemented with methanol. Strains that grow on methanol have functional methanol- consumption pathways.
Example 4: Induction of gene expression in yeast A genetically modified strain of S. cerevisiae is obtained as described in Example
2. In addition, the strain is transformed with a construct containing polynucleotides encoding the transcription factors PRM1 , MIT1 , and MXR1 which were codon optimised for expression in S. cerevisiae, and had nuclear localisation sequences added to their C-termini. MIT1 and PRM1 are expressed from their native P. pastoris promoters, while MXR1 is expressed from the S. cerevisiae PDA1 promoter. The sequences for these parts are shown below. An annotated vector map is shown in Figure 4.
The construct encoding the transcription factors is transformed into S. cerevisiae harbouring constructs encoding enzymes for methanol utilisation, where the polynucleotides encoding the enzymes are operably linked to the AOX promoter from Pichia pastoris.
The resultant strains containing these genes are tested for growth in minimal media supplemented with methanol.
P. pastoris PRM1 protein sequence with S. cerevisiae MATalpha2 nuclear localisation signal (KIPIK) (SEQ ID NO: 29)
MVSGGTIFKAEGIWRQMVKHYHMHSNSFINFKEGCVQTTLINRYNWIVLFIIKIK LFQALFNSSLAVLRQSSLGLCSQINRFQTEYKSMVDESLDSLSLFIHEMTNKSIQVLGSI FNFIVDLFIGTYVCLLDLLITSTTRVSATVAEEIVDVVNNTITTTATELNKQLSSVASVINR VGNFFSDDNFKAIDLTIDSLKNWQIPSSVDEKIRSLNNVDVNLDGLLDGVVSNVTDKIIK TRSLPEKRVVNGSFALNEACSSDTVSDFYDSLHTSSNRMFTLILILSVGSIWITLVQLW LQSRSFRHIQEIDEKRPNMEWSTFENRYIHKYCGSGYIKWLMLYICSSPSINILVLFFFS LFSYIIQVAIVNKVQNLSNDWLADGESYNNDNLNQYVQYQAKSYETYINDNMTLASIHN TFSSVNSTMNDFITDVNGGINGIFRDSIVGDMVNGWYCVIGRKLEAVNKGFDWLTKST ELKIPTENYVISNQDQDDLMSKMAEGISALCKYYKQNLTWELWQCLLFGLLWTFQLMI GILISKFQRQPEQRYDDNPFIHPEFIPFKPYETYHHTKNDVIAETLNRIKRNESVPSFKAD SLSLSSMLDNSARRPKKIPIK
P. pastoris PRM1 DNA sequence, codon optimised for expression in S. cerevisiae (SEQ ID NO: 30)
ATGGTTTCTGGTGGTACTATTTTTAAAGCTGAAGGTATTTGGAGACAAATGG TTAAACATTATCATATGCATTCTAATTCTTTTATTAATTTTAAAGAAGGTTGTGTTCAA ACTACTTTGATTAATAGATATAATGTTGTTATTGTTTTGTTTATTATTAAAATTAAATT GTTTCAAGCTTTGTTTAATTCTTCTTTGGCTGTTTTGAGACAATCTTCTTTGGGTTTG TGTTCTCAAATTAATAGATTTCAAACTGAATATAAATCTATGGTTGATGAATCTTTGG ATTCTTTGTCTTTGTTTATTCATGAAATGACTAATAAATCTATTCAAGTTTTGGGTTC TATTTTTAATTTTATTGTTGATTTGTTTATTGGTACTTATGTTTGTTTGTTGGATTTGT TGATTACTTCTACTACTAGAGTTTCTGCTACTGTTGCTGAAGAAATTGTTGATGTTG TTAATAATACTATTACTACTACTGCTACTGAATTGAATAAACAATTGTCTTCTGTTGC TTCTGTTATTAATAGAGTTGGTAATTTTTTTTCTGATGATAATTTTAAAGCTATTGATT TGACTATTGATTCTTTGAAAAATTGGCAAATTCCATCTTCTGTTGATGAAAAAATTAG ATCTTTGAATAATGTTGATGTTAATTTGGATGGTTTGTTGGATGGTGTTGTTTCTAAT GTTACTGATAAAATTATTAAAACTAGATCTTTGCCAGAAAAAAGAGTTGTTAATGGTT CTTTTGCTTTGAATGAAGCTTGTTCTTCTGATACTGTTTCTGATTTTTATGATTCTTT GCATACTTCTTCTAATAGAATGTTTACTTTGATTTTGATTTTGTCTGTTGGTTCTATT GTTGTTATTACTTTGGTTCAATTGTGGTTGCAATCTAGATCTTTTAGACATATTCAAG AAATTGATGAAAAAAGACCAAATATGGAAGTTGTTTCTACTTTTGAAAATAGATATAT TCATAAATATTGTGGTTCTGGTTATATTAAATGGTTGATGTTGTATATTTGTTCTTCT CCATCTATTAATATTTTGGTTTTGTTTTTTTTTTCTTTGTTTTCTTATATTATTCAAGTT GCTATTGTTAATAAAGTTCAAAATTTGTCTAATGATTGGTTGGCTGATGGTGAATCT TATAATAATGATAATTTGAATCAATATGTTCAATATCAAGCTAAATCTTATGAAACTT ATATTAATGATAATATGACTTTGGCTTCTATTCATAATACTTTTTCTTCTGTTAATTCT ACTATGAATGATTTTATTACTGATGTTAATGGTGGTATTAATGGTATTTTTAGAGATT CTATTGTTGGTGATATGGTTAATGGTGTTGTTTATTGTGTTATTGGTAGAAAATTGG AAGCTGTTAATAAAGGTTTTGATTGGTTGACTAAATCTACTGAATTGAAAATTCCAA CTGAAAATTATGTTATTTCTAATCAAGATCAAGATGATTTGATGTCTAAAATGGCTGA AGGTATTTCTGCTTTGTGTAAATATTATAAACAAAATTTGACTTGGGAATTGTGGCA ATGTTTGTTGTTTGGTTTGTTGTGGACTTTTCAATTGATGATTGGTATTTTGATTTCT AAATTTCAAAGACAACCAGAACAAAGATATGATGATAATCCATTTATTCATCCAGAA TTTATTCCATTTAAACCATATGAAACTTATCATCATACTAAAAATGATGTTATTGCTG AAACTTTGAATAGAATTAAAAGAAATGAATCTGTTCCATCTTTTAAAGCTGATTCTTT GTCTTTGTCTTCTATGTTGGATAATTCTGCTAGAAGACCAAAAAAAATTCCAATTAAA TAA
P. pastoris PRM1 promoter sequence (SEQ ID NO: 31 )
G C AAATC ATG G ACTG G ATG C G GC C AG C AC ATC C CATC AG C C ATG AATAAC A CCAGACAAGAATTGTGGTGTACTTGTACTCATATACTGGATACAAACTATCCACAAT ACCCTCCCCGCGCTGGTACGGGGTCTGCTCGTCGTTCTATTTCCGAGTAGGATAA CTTGATATTGAAGTCTATGGGTCATGAGTTGATGAATAACTGAGTTGGGGAAGTTC ACCAGATGAGTTAGTAAGGGTTTCAATGTGTGTAGGATGAAATATATGGTTCTTGAT GGACGATTGCCGTAGCATCAAATTTCTGATACCCCGAGCCGTGATGTCTTCGTTAT CTGGTGTTGTTGTTATCAGTTATCTGTGCGGCTGCTATCTTTTCTAGGTTTTCTACG TAAGCTTTCTAAGC C GC AC G AC ATG C C G AATGTTG C GTG AG ATG AG AATAG ATG AT AGATGTCTGAAGGAAAAAAGACGAATAGTAATCTTCGTAGAAGTTTTAAAGGTGATA GCAAATAATTGATCAGTGGAAAAAATTGCACAATGAGTGGAAAATGGTTTGCAATG AG C AATTATG AGTTTAAG C CTCTTGG AAACTGTC AAG GTG AAAG ATTG AG CTTTAG ACGAATGTGATTGTATACTGTTTCAGG
P. pastoris MIT1 protein sequence with S. cerevisiae MATalpha2 nuclear localisation signal (KIPIK) (SEQ ID NO: 32) MSTAAPIKEESQFAHLTLMNKDLPSNAKQAKSKVSAAPAKTSSRSAGGSGNNN AAPVKKRVRTGCLTCRKKHKKCDENRNPKCDFCTLKGLECVWPENNKKNIFVNNSMK DFLGKKPVEGADSLNLAMNLQQQQSSNAMGNQSLSSIGLESFGYGSGIKNEFNFQDLI GSNSGSSDPTFTVDADEAQKFDISSKNSRKRQKLGLLPVGNAASHLNGFNGISNGKSH SFSSPSGTNDDELSGLMFNSPSFNPLTVNDSTNNSNHNIGLSPMSCLFSTVQEASQKK HANSSRHFSYPSGPEDLWFNEFQKQALTANGENAVQQGDDASKDTTVIPKDESSNSS IFSSRSSAASSNSGDDVGRMGPFSKGPEIEFNYDSFLESLKAESPSSSKYNLPDTLKEY MTLSSSYLNTQHSDTLANGTNGNYASTVSNNLSLSLNSFSFSDKFSLSPPTITDAEKFS LMRNFIDNISPWFDTFDNTKQFGTKIPILAKKCSSLYYAILAISSRQRERIRKEHNEKTLQ CYQYSLQQLIPTVQSSNNIEYIITCILLSVFHIMSSEPSTQRDIIASLAKYIQSCNINGFTSN DKLEKSIFWNYVNLDLATCTIGEESMVIPFSYWVKETTDYKTIQDVKPFFTKKTSTTTDD DLDDMYAIYILYISGRIINLLNCRDAKLNFEPKWEFLWNELNEWELNKPLTFQSIVQFKA NDESQGGSTFPTVLFSNSRSCYSNQLYHMSYIILVQNKPRLYKIPFTTVSASMSSPSDN RAGASASSTPASDHHASGDHLSPRSIEPSVSTTLSPPPNANGGGNKFRSTLWHAKQIC GISINNNHNSNLAAKVNSLQPLWHAGKLISSKSEHTQLLKLLNNLECATGWPMNWKGK ELIDYWNVEEKIPIK
P. pastoris MIT1 DNA sequence, codon optimised for expression in S. cerevisiae (SEQ ID NO: 33)
ATGTCTACTGCTGCTCCAATTAAAGAAGAATCTCAATTTGCTCATTTGACTTT GATGAATAAAGATTTGCCATCTAATGCTAAACAAGCTAAATCTAAAGTTTCTGCTGC TCCAGCTAAAACTTCTTCTAGATCTGCTGGTGGTTCTGGTAATAATAATGCTGCTCC AGTTAAAAAAAGAGTTAGAACTGGTTGTTTGACTTGTAGAAAAAAACATAAAAAATG TGATGAAAATAGAAATCCAAAATGTGATTTTTGTACTTTGAAAGGTTTGGAATGTGT TTG G C C AG AAAATAATAAAAAAAATATTTTTGTTAATAATTCTATG AAAG ATTTTTTG GGTAAAAAACCAGTTGAAGGTGCTGATTCTTTGAATTTGGCTATGAATTTGCAACAA CAACAATCTTCTAATGCTATGGGTAATCAATCTTTGTCTTCTATTGGTTTGGAATCTT TTGGTTATGGTTCTGGTATTAAAAATGAATTTAATTTTCAAGATTTGATTGGTTCTAA TTCTGGTTCTTCTGATCCAACTTTTACTGTTGATGCTGATGAAGCTCAAAAATTTGA TATTTCTTCTAAAAATTCTAGAAAAAGACAAAAATTGGGTTTGTTGCCAGTTGGTAAT GCTGCTTCTCATTTGAATGGTTTTAATGGTATTTCTAATGGTAAATCTCATTCTTTTT CTTCTCCATCTGGTACTAATGATGATGAATTGTCTGGTTTGATGTTTAATTCTCCAT CTTTTAATCCATTGACTGTTAATGATTCTACTAATAATTCTAATCATAATATTGGTTTG TCTCCAATGTCTTGTTTGTTTTCTACTGTTCAAGAAGCTTCTCAAAAAAAACATGCTA ATTCTTCTAGACATTTTTCTTATCCATCTGGTCCAGAAGATTTGTGGTTTAATGAATT TCAAAAACAAGCTTTGACTGCTAATGGTGAAAATGCTGTTCAACAAGGTGATGATG CTTCTAAAGATACTACTGTTATTCCAAAAGATGAATCTTCTAATTCTTCTATTTTTTCT TCTAGATCTTCTGCTGCTTCTTCTAATTCTGGTGATGATGTTGGTAGAATGGGTCCA TTTTCTAAAGGTCCAGAAATTGAATTTAATTATGATTCTTTTTTGGAATCTTTGAAAG CTGAATCTCCATCTTCTTCTAAATATAATTTGCCAGATACTTTGAAAGAATATATGAC TTTGTCTTCTTCTTATTTGAATACTCAACATTCTGATACTTTGGCTAATGGTACTAAT GGTAATTATGCTTCTACTGTTTCTAATAATTTGTCTTTGTCTTTGAATTCTTTTTCTTT TTCTGATAAATTTTCTTTGTCTCCACCAACTATTACTGATGCTGAAAAATTTTCTTTG ATGAGAAATTTTATTGATAATATTTCTCCATGGTTTGATACTTTTGATAATACTAAAC AATTTGGTACTAAAATTCCAATTTTGGCTAAAAAATGTTCTTCTTTGTATTATGCTAT TTTGGCTATTTCTTCTAGACAAAGAGAAAGAATTAGAAAAGAACATAATGAAAAAAC TTTGCAATGTTATCAATATTCTTTGCAACAATTGATTCCAACTGTTCAATCTTCTAAT AATATTGAATATATTATTACTTGTATTTTGTTGTCTGTTTTTCATATTATGTCTTCTGA ACCATCTACTCAAAGAGATATTATTGCTTCTTTGGCTAAATATATTCAATCTTGTAAT ATTAATG GTTTTACTTCTAATG ATAAATTG G AAAAATCTATTTTTTG G AATTATGTTAA TTTGGATTTGGCTACTTGTACTATTGGTGAAGAATCTATGGTTATTCCATTTTCTTAT TGGGTTAAAGAAACTACTGATTATAAAACTATTCAAGATGTTAAACCATTTTTTACTA AAAAAACTTCTACTACTACTGATGATGATTTGGATGATATGTATGCTATTTATATTTT GTATATTTCTGGTAGAATTATTAATTTGTTGAATTGTAGAGATGCTAAATTGAATTTT G AAC C AAAATG G G AATTTTTGTG G AATG AATTG AATG AATGG G AATTG AATAAAC C A TTGACTTTTCAATCTATTGTTCAATTTAAAGCTAATGATGAATCTCAAGGTGGTTCTA CTTTTCCAACTGTTTTGTTTTCTAATTCTAGATCTTGTTATTCTAATCAATTGTATCAT ATGTCTTATATTATTTTGGTTCAAAATAAACCAAGATTGTATAAAATTCCATTTACTA CTGTTTCTGCTTCTATGTCTTCTCCATCTGATAATAGAGCTGGTGCTTCTGCTTCTT CTACTCCAGCTTCTGATCATCATGCTTCTGGTGATCATTTGTCTCCAAGATCTATTG AACCATCTGTTTCTACTACTTTGTCTCCACCACCAAATGCTAATGGTGGTGGTAATA AATTTAGATCTACTTTGTGGCATGCTAAACAAATTTGTGGTATTTCTATTAATAATAA TCATAATTCTAATTTGGCTGCTAAAGTTAATTCTTTGCAACCATTGTGGCATGCTGG TAAATTGATTTCTTCTAAATCTGAACATACTCAATTGTTGAAATTGTTGAATAATTTG GAATGTGCTACTGGTTGGCCAATGAATTGGAAAGGTAAAGAATTGATTGATTATTG G AATGTTG AAG AAAAG ATTC C AATTAAGTAA
P. pastoris MIT1 promoter sequence (SEQ ID NO: 34)
G C AGTC AAAAATG G C AAC C C C C G G ATATTG GAG G G AAGAAG AGTGTG G G G GAGACACCTGTCACTGCAGCTATGAGGAGTTTGATTTATTGGAAGCATTTGTTAAT GTGGGTGAATTCTCTGCGACCTACATAATACGTGCATAATATGTGCATGAAAAGAC AACAAGATAAATTTAGTAAAATATGGGGTAATAGAGAGGGCTGGACTGAACGTTGA TGGCAAGACTGAGGGAGAAAACATAAAAGCAAGTGGAATTAGTACACAATTAGTGC TGGATTGTTGGACTGTATAGGGGTTCTGTATTCGTAGGTCCCTGATTGATAGTAAT GTGTGTAAGTGAAGGGAAAAAAAAAAAAAAAAAATTCAAAAACTGGGGAAAAGAAC TCCTTAAAAATTTTCATATGTATGATGAAAGACTGCTGCAGGAGATGTTCAAGATTG AAAAATTAAAGCTAGCGACCTACGAGTCCATATAGTGTTGGAACGGAATCTGGAGG TGTG AAC AC C GTC ATTC C CTAATCTAAGTTTCTGTC GAG C C GTTTG AAAAGTTC CTC TTCGTCAATAAAGTTTGACTTTGATCGACAGAGTTGAGCTAATCGGAAATACTCCC G AAG ATAC AC C C GAG C AGTG AAG C G G G G C ATC AGTAAAAATTAAG G G GTGTTG AG TGCGGTTTGCGCGCAGTAGTTAGCATCAATGCCAGACGTAGAAATCATACATTCTG GTTTC AG AATC AG AC G AC ATC G AGAG AG ATAC AC C AG C AC C ACTTG AACTC C C C C A ATGACGGTGCGGTGGTGGGGGTGAACAGGTAGAACTGTAGATGTGACCAATCACT GTCACGTATTATATTACAGAGAACGGGGGTTACAGAAAGGGTGGAAACGAACGTC G GAG G AGG AATGAG GAG AG AG GAG G AAAG AG G AG GTAG ATC G AG C AG ATTGATG TGATAAAAACCACCCCTCCAAAACTGTTATTATGCCCCCAAGTTTACGATTTTTCTC CTCCTTCAGCCTCGCTCGCTGGCCAATATCTTTGATCCTCCGTCCATGGATTCTTC CCGTTCCGCTCTATCCGATAAGAGGTTGGCTTCCGAGAAGGTTGGTTATTGGAGAT G AC GTAC AAAGTG C AC AAC AAAC C AGATGTTGTTTAG C G C G ATC G G C C C AAC C C C TCTTGTTGTTAGAGAGTCTTATGCATATTTCGTAGACCCGGGACTGTACATTCGTCC GTCCTCAGCTATTGGTCATTTGATACCACTCAAAGGACTGCCCCAACCCTGATTTC CCCAAACAGCATACTAGTCATTCATTCAGCATAACGGGGTTTTTTTTGTTTCAACCC TCCCATTATATATAATCAAGGAAGCCCTCCTGGCACCTTCCCTCTCTTCTTCCCTCT CTATAACCATTTCACTCTGAGTTGCTTTATAAACATAGATTACGTCGCAGCAGACAC TCACGCACCACCCCCTCTTTCCCCTGCTCTCAAAGATTCTATATAACAGCCA
P. pastoris MXR1 protein sequence with S. cerevisiae SV40 nuclear localisation signal (PKKKRKV) (SEQ ID NO: 35)
MSQKRPTSLRFITSFPRFPKRSFFTMPWSSLISSNIKKSPQDKWTVAGGCFW GLEYIYKMHFKDRIVDTQVGFANGNLSNPTYKEVCQGLTYHAEVLQIAYNPEVISYKELI DFFFLVHDPTQDDGQGPDIGTQYRSAVFYLDEEEKEIAEQSLAETQKKWFPHHEIVTQ VEKLTSYWDAEDYHQEYLIKNADGYHCPTHVLRTEPKAISVPKKKRKV
P. pastoris MXR1 DNA sequence, codon optimised for expression in S. cerevisiae (SEQ ID NO: 36) ATGTCTCAAAAAAGACCAACTTCTTTGAGATTTATTACTTCTTTTCCAAGATTT CCAAAAAGATCTTTTTTTACTATGCCAGTTGTTTCTTCTTTGATTTCTTCTAATATTAA AAAATCTCCACAAGATAAAGTTGTTACTGTTGCTGGTGGTTGTTTTTGGGGTTTGGA ATATATTTATAAAATGCATTTTAAAGATAGAATTGTTGATACTCAAGTTGGTTTTGCT AATGGTAATTTGTCTAATCCAACTTATAAAGAAGTTTGTCAAGGTTTGACTTATCATG CTGAAGTTTTGCAAATTGCTTATAATCCAGAAGTTATTTCTTATAAAGAATTGATTGA TTTTTTTTTTTTGGTTCATGATCCAACTCAAGATGATGGTCAAGGTCCAGATATTGG TACTCAATATAGATCTGCTGTTTTTTATTTGGATGAAGAAGAAAAAGAAATTGCTGA ACAATCTTTGGCTGAAACTCAAAAAAAATGGTTTCCACATCATGAAATTGTTACTCA AGTTGAAAAATTGACTTCTTATTGGGATGCTGAAGATTATCATCAAGAATATTTGATT AAAAATGCTGATGGTTATCATTGTCCAACTCATGTTTTGAGAACTGAACCAAAAGCT ATTTCTGTTC C AAAG AAG AAG AG AAAG GTTTAA
S. cerevisiae PDA1 promoter sequence, used for regulation of MXR1 expression (SEQ ID NO: 37)
TAAGCTTGATATCGAATTCCTGCAGCCCGTATTCTGATAAATCTAAAGAGAA ATTACTAAAAAAAAG AAAAAAAAAAGAAC G G G G GTGTAATAATTTGTAGTTC ATTAT TGCAATTATATATCTATATCTATATATGTATATAACATTAACATGTGCATGTACACAC GTAATCGCGCGTGTACATGTCTATATGTGTTACTTGAACTATACTGTTTTGACGTGT ATGTTTATTTATCTCTCTTCTGATTCCTCCACCCCTTCCTTACTCAACCGGGTAAAT GTCGCATCATGACTCCCGACAATAATCCCCTCTGGTATAGCGAGAAGCAACTTTAG CTTCTTAACGGCAAGAACTTTTTTATGTTTGTCGCACCTGTATCTTCACAAAAGTTG G ATAC AG C AATAAG AAAG G AAAC C AC ATTTGTG C C A
Example 5: Assessing synthetic methanol assimilation pathway in Saccharomyces cerevisiae
The genes encoding peroxisomally-targetted alcohol oxidase, dihydroxyacetone synthase, catalase, pmp20), and cytosol localised alcohol dehydrogenase and pyruvate carboxylase, were introduced into an S. cerevisiae BY4741 strain. This strain had methionine and histidine autotrophies repaired such that growth without any amino acids added to the media was possible. The methanol utilisation pathway genes were encoded on plasmids ScMOX3a and ScMOX2b (Figures 6 and 3, respectively). The strain was pre-cultured twice on minimal medium (Yeast nitrogen base without amino acids) with glucose as the sole carbon source prior to inoculation into either minimal medium without any carbon source ('without methanol', Figure 5), or minimal medium with 2% methanol as the sole carbon source ('with methanol', Figure 5). Both conditions were tested in triplicate. The population density (optical density at 600nm, or OD600nm') was measured at 20 hours after residual glucose from the inoculum has been exhausted, and then again after 50 hours to analyse any potential growth due to the presence of methanol in the medium (Figure 5). When no carbon source was present in the growth medium, there was an average of 4.25 ± 3.74% increase in growth (OD600nm) over 30 hours, reflecting the utilisation of trace amounts of glucose in the medium, or of cellular storage carbohydrates such as trehalose. In contrast, when methanol was present in the growth medium, there was an 18.01 ± 6.88 % increase in growth (Figure 5). Therefore, the synthetic methanol assimilation pathway results in a significant 422% increase in growth over the 30 hour period measured when methanol is present in the medium (p = 0.04, two-sided t-test with equal variance). These results show that the expressed metabolic pathway functions in S. cerevisiae to enable growth with methanol as the sole carbon source.
The plasm ids ScMOX3a and ScMOX2b are also transformed into S. cerevisiae strain BY4741/CEN.PK2-1 c (a diploid hybrid). Strains of this background, with or without the plasm id-encoded methylotrophy genes are grown to exponential phase in glucose minimal medium, serially diluted to 10,000 fold, and each dilution spotted onto agar plates. Agar plates contain yeast nitrogen base with either; no carbon source, 1 % glucose, 1 % methanol, or 2% methanol. Growth of the control and methylotrophic strains are assessed according to the rate of single colony appearance over 5 -7 days at 30° Celsius.
Example 6: SCRaMbLE of ScMOX3a, ScMOX2b, and ScMOX3c genes onto synthetic chromosome XIV in a BY4741/CEN.PK2-1c diploid hybrid
The 'SCRaMbLE' system (Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution), is used to randomly integrate and duplicate LoxPSym flanked genes from the ScMOX3a, ScMOX2b, and ScMOX3c plasmids onto synthetic chromosome XIV in a diploid BY4741/CEN.PK2-1 c hybrid.
The SCRaMbLE system is disclosed in Dymon and Boeke (2012) Bioenginered Buds 3: 168-171 ; Jovicevic et al., (2014) Bioessays 36: 855-860; and Shen et al., (2016) Genome Res. 26: 36-49, the contents of which are hereby incorporated by reference in their entirety. Briefly, the "Synthetic Yeast Genome Project" involves the chemical synthesis, re-design, and replacement of the entire Saccharomyces cerevisiae genome. One of the features of the synthetic yeast genome is the incorporation of 34 bp 'LoxPsym' motifs ( ATAACTTC GTATAATGTAC ATTATAC GAAGTTAT) 3bp after the stop codon of every non-essential gene in the genome. When a heterologous Cre- recombinase enzyme is inducible expressed in a synthetic chromosome containing yeast strain, the LoxPSym sites are targeted for recombination by the Cre enzyme. This process results in every LoxPSym-flanked gene having a chance to be inverted, translocated, deleted, or duplicated, and creates a extreme genotypic and phenotypic diversity within a typical laboratory-scale yeast culture. SCRaMbLE'd populations of the yeast cells produced according to the invention are plated onto agar plates with methanol as the only carbon source such that yeast cells with superior combinations and ratios of synthetic methylotrophy genes and chromosome XIV genes are selected for. Any fast-growing colonies derived from this process are then whole-genome re- sequenced to determine the content and ratio of methylotrophy and chromosome XIV genes. They are also used for adaptive laboratory evolution in liquid culture with methanol as the sole carbon source to additionally select for single nucleotide polymorphisms resulting in protein structural changes and altered promoter activity of native and synthetic genes.
It will be understood that the invention disclosed and defined in this specification extends to all alternative combinations of two or more of the individual features mentioned or evident from the text or drawings. All of these different combinations constitute various alternative aspects of the invention.

Claims

1 . A yeast cell including a recombinant construct encoding one or more proteins that enable the cell to grow in a medium in which methanol is the only or main energy source for growth of the cell in the medium,
wherein the one or more proteins is selected from the group consisting of:
alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 )
dihydroxyacetone synthase (E.C. 2.2.1 .3), dihydroxyacetone kinase (E.C.
2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1 .2.13), fructose-1 -6- bisphophatase (E.C. 3.1 .3.1 1 ), sedoheptulose bisphosphatase (E.C. 3.1 .3.37), ribose-5-phosphate isomerase (E.C. 5.3.1 .6) and D-ribulose-5-phosphate-3- epimerase (E.C. 5.1 .3.1 ), transketolase 1 or 2 (E.C. 2.2.1 .1 ), transaldolase (EC 2.2.1 .2), formaldehyde dehydrogenase (E.C. 1.2.1 .46) or functional variants thereof.
2. The yeast cell of claim 1 , wherein the construct is essential for enabling the cell to grow in the medium.
3. The yeast cell of claim 2, wherein the cell contains a gene encoding a protein selected from the group consisting of alcohol oxidase (E.C. 1 .1.3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1 .3),
dihydroxyacetone kinase (E.C. 2.7.1 .29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1 .3.1 1 ), sedoheptulose bisphosphatase (E.C. 3.1 .3.37), ribose-5-phosphate isomerase (E.C. 5.3.1 .6) and D-ribulose-5-phosphate-3-epimerase (E.C. 5.1 .3.1 ), transketolase 1 or 2 (E.C. 2.2.1.1 ), transaldolase (EC 2.2.1 .2), formaldehyde dehydrogenase (E.C. 1 .2.1.46) or functional variants thereof wherein the gene is not comprised in the recombinant construct.
4. The yeast cell of any one of claims 1 to 3, wherein the recombinant construct encodes the proteins alcohol oxidase (E.C. 1.1 .3.13), dihydroxyacetone synthase (E.C. 2.2.1 .3) and pyruvate carboxylase (E.C. 6.4.1 .1 ).
5. The yeast cell of any one of claims 1 to 3, wherein the recombinant construct encodes the proteins: alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C.6.4.1.1) and transaldolase (EC 2.2.1.2), or functional variants thereof.
6. The yeast cell of any one of claims 1 to 3, wherein the recombinant construct encodes the proteins: alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C.6.4.1.1), dihydroxyacetone synthase (E.C.2.2.1.3), and transaldolase (EC 2.2.1.2), or functional variants thereof.
7. The yeast cell of any one of claims 1 to 3, wherein the recombinant construct encodes the proteins: alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) dihydroxyacetone synthase (E.C. 2.2.1.3), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13) and fructose-1 -6-bisphophatase (E.C.3.1.3.11), or functional variants thereof.
8. The yeast cell of any one of claims 1 to 3, wherein the recombinant construct encodes the proteins: alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13) and fructose-1 -6- bisphophatase (E.C.3.1.3.11), or functional variants thereof.
9. The yeast cell of any one of claims 1 to 3, wherein the recombinant construct encodes the proteins: alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1), dihydroxyacetone synthase (E.C. 2.2.1.3), transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13) and fructose-1 -6-bisphophatase (E.C. 3.1.3.11), or functional variants thereof.
10. The yeast cell of any one of claims 1 to 3, wherein the recombinant construct encodes the proteins: alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) and dihydroxyacetone synthase (E.C. 2.2.1.3), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1.3.11) and sedoheptulose bisphosphatase (E.C.3.1.3.37), or functional variants thereof.
11. The yeast cell of any one of claims 1 to 3, wherein the recombinant construct encodes the proteins: alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase
(E.C. 6.4.1.1) transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6- bisphophatase (E.C. 3.1.3.11) and sedoheptulose bisphosphatase (E.C. 3.1.3.37), or functional variants thereof.
12. The yeast cell of any one of claims 1 to 3, wherein the recombinant construct encodes the proteins: alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) dihydroxyacetone synthase (E.C. 2.2.1.3), transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1.3.11) and sedoheptulose bisphosphatase (E.C.3.1.3.37), or functional variants thereof.
13. The yeast cell of any one of claims 1 to 3, wherein the recombinant construct encodes the proteins: alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) and dihydroxyacetone synthase (E.C. 2.2.1.3), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C.3.1.3.11), sedoheptulose bisphosphatase (E.C. 3.1.3.37), ribose-5-phosphate isomerase (E.C. 5.3.1.6) and D-ribulose-5- phosphate-3-epimerase (E.C.5.1.3.1), or functional variants thereof.
14. The yeast cell of any one of claims 1 to 3, wherein the recombinant construct encodes the proteins: alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) and transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6- bisphophatase (E.C. 3.1.3.11), sedoheptulose bisphosphatase (E.C. 3.1.3.37), ribose-5-phosphate isomerase (E.C. 5.3.1.6) and D-ribulose-5-phosphate-3- epimerase (E.C.5.1.3.1), or functional variants thereof.
15. The yeast cell of any one of claims 1 to 3, wherein the recombinant construct encodes the proteins: alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1), dihydroxyacetone synthase (E.C. 2.2.1.3), transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1.3.11), sedoheptulose bisphosphatase (E.C. 3.1.3.37), ribose-5-phosphate isomerase (E.C. 5.3.1.6) and D-ribulose-5-phosphate-3-epimerase (E.C. 5.1.3.1), or functional variants thereof.
16. The yeast cell of any one of claims 1 to 15, wherein the cell also comprises a recombinant construct encoding one or more of the proteins transketolase 1 or 2 (E.C. 2.2.1.1), catalase (E.C. 1.11.1.6), glutathione peroxidase (E.C. 1.11.1.9) and methyl formate-synthesising alcohol dehydrogenase (E.C. 1.1.1.1), or functional variants thereof.
17. The yeast cell of any one of claims 1 to 15, wherein the cell also comprises a recombinant construct encoding catalase (E.C.1.11.1.6), glutathione peroxidase (E.C. 1.11.1.9) and methyl formate-synthesising alcohol dehydrogenase (E.C. 1.1.1.1), or functional variants thereof.
18. The yeast cell of any one of the preceding claims, wherein the construct includes an inducible promoter enabling the production of said proteins when the cell is contacted with methanol.
19. The yeast cell of any one of the preceding claims wherein the recombinant
construct encodes one or more proteins from the yeast Pichia pastoris, Pichia angusta.
20. The yeast cell of any one of the preceding claims wherein the construct is
integrated into the genome of the cell.
21 . The yeast cell of any one of the preceding claims wherein the construct encodes sequences for targeting of the one or more proteins to a subcellular organelle of the cell.
22. A genetically modified yeast cell, wherein the cell comprises one or more nucleic acid molecules encoding one or more proteins that enable the cell to grow in a medium in which methanol is the only or main energy source for growth of the cell in the medium,
wherein the one or more proteins is selected from the group consisting of:
alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 )
dihydroxyacetone synthase (E.C. 2.2.1 .3), dihydroxyacetone kinase (E.C.
2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1 .2.13), fructose-1 -6- bisphophatase (E.C. 3.1.3.1 1 ), sedoheptulose bisphosphatase (E.C. 3.1 .3.37), ribose-5-phosphate isomerase (E.C. 5.3.1.6) and D-ribulose-5-phosphate-3- epimerase (E.C. 5.1 .3.1 ), transketolase 1 or 2 (E.C. 2.2.1.1 ), transaldolase (EC
2.2.1 .2) , formaldehyde dehydrogenase (E.C. 1.2.1 ,46) or functional variants thereof.
23. The yeast cell of claim 22, wherein the one or more nucleic acid molecules
encode alcohol oxidase (E.C. 1 .1 .3.13), dihydroxyacetone synthase (E.C.
2.2.1.3) and pyruvate carboxylase (E.C. 6.4.1 .1 ).
24. The yeast cell of claim 22, wherein the one or more nucleic acid molecules encode alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) and transaldolase (EC 2.2.1 .2), or functional variants thereof.
25. The yeast cell of claim 22, wherein the one or more nucleic acid molecules encode the proteins: alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C.
6.4.1 .1 ) , dihydroxyacetone synthase (E.C. 2.2.1 .3), and transaldolase (EC
2.2.1 .2) , or functional variants thereof.
26. The yeast cell of claim 22, wherein the one or more nucleic acid molecules encode alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1.3), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13) and fructose-1 -6- bisphophatase (E.C.3.1.3.11), or functional variants thereof.
27. The yeast cell of claim 22, wherein the one or more nucleic acid molecules encode the proteins: alcohol oxidase (E.C.1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13) and fructose-1 -6- bisphophatase (E.C.3.1.3.11), or functional variants thereof.
28. The yeast cell of claim 22, wherein the one or more nucleic acid molecules encode the proteins: alcohol oxidase (E.C.1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1), dihydroxyacetone synthase (E.C.2.2.1.3), transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13) and fructose-1 -6-bisphophatase (E.C. 3.1.3.11), or functional variants thereof.
29. The yeast cell of claim 22, wherein the one or more nucleic acid molecules encode the proteins: alcohol oxidase (E.C.1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) and dihydroxyacetone synthase (E.C.2.2.1.3), dihydroxyacetone kinase
(E.C.2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C.4.1.2.13), fructose-1 -6- bisphophatase (E.C. 3.1.3.11) and sedoheptulose bisphosphatase (E.C. 3.1.3.37), or functional variants thereof.
30. The yeast cell of claim 22, wherein the one or more nucleic acid molecules encode the proteins: alcohol oxidase (E.C.1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C.3.1.3.11) and sedoheptulose bisphosphatase (E.C.3.1.3.37), or functional variants thereof.
31. The yeast cell of claim 22, wherein the one or more nucleic acid molecules encode the proteins: alcohol oxidase (E.C.1.1.3.13), pyruvate carboxylase (E.C.
6.4.1.1) dihydroxyacetone synthase (E.C. 2.2.1.3), transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1.3.11) and sedoheptulose bisphosphatase (E.C.3.1.3.37), or functional variants thereof.
32. The yeast cell of claim 22, wherein the one or more nucleic acid molecules encode the proteins: alcohol oxidase (E.C.1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) and dihydroxyacetone synthase (E.C.2.2.1.3), dihydroxyacetone kinase (E.C.2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C.4.1.2.13), fructose-1 -6- bisphophatase (E.C. 3.1.3.11), sedoheptulose bisphosphatase (E.C. 3.1.3.37), ribose-5-phosphate isomerase (E.C. 5.3.1.6) and D-ribulose-5-phosphate-3- epimerase (E.C.5.1.3.1), or functional variants thereof.
33. The yeast cell of claim 22, wherein the one or more nucleic acid molecules encode the proteins: alcohol oxidase (E.C.1.1.3.13), pyruvate carboxylase (E.C.
6.4.1.1) and transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6- bisphophatase (E.C. 3.1.3.11), sedoheptulose bisphosphatase (E.C. 3.1.3.37), ribose-5-phosphate isomerase (E.C. 5.3.1.6) and D-ribulose-5-phosphate-3- epimerase (E.C.5.1.3.1), or functional variants thereof.
34. The yeast cell of claim 22, wherein the one or more nucleic acid molecules encode the proteins: alcohol oxidase (E.C.1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1), dihydroxyacetone synthase (E.C.2.2.1.3), transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase
(E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1.3.11), sedoheptulose bisphosphatase (E.C. 3.1.3.37), ribose-5-phosphate isomerase (E.C. 5.3.1.6) and D-ribulose-5-phosphate-3-epimerase (E.C. 5.1.3.1), or functional variants thereof.
35. The yeast cell of any one of claims 22 to 34 wherein the cell also comprises one or more nucleic acid molecules encoding one or more of the proteins transketolase 1 or 2 (E.C. 2.2.1.1), catalase (E.C. 1.11.1.6), glutathione peroxidase (E.C. 1.1 1 .1 .9) and methyl formate-synthesising alcohol dehydrogenase (E.C. 1 .1 .1 .1 ), or functional variants thereof.
36. The yeast cell of any one of claims 22 to 34 wherein the cell also comprises one or more nucleic acid molecules encoding catalase (E.C. 1 .1 1 .1 .6), glutathione peroxidase (E.C. 1.1 1 .1 .9) and methyl formate-synthesising alcohol dehydrogenase (E.C. 1 .1 .1 .1 ), or functional variants thereof.
37. The yeast cell of any one of claims 22 to 36, wherein any one of the proteins is expressed under the control of an inducible promoter enabling the production of said protein when the cell is contacted with methanol.
38. The yeast cell of any one of the preceding claims, wherein the cell does not
include said proteins when the cell is not contacted with methanol.
39. The yeast cell of any one of the preceding claims, wherein the cell includes a further construct enabling the formation of a chemical which can be used in an industrial process.
40. The yeast cell of any one of the preceding claims wherein the yeast cell is a cell of Saccharomyces cerevisiae, Kluyveromyces lactis, Kluyveromyces marxianus, Yarrowia lipolytica, Schizosaccharomyces pombe or Arxula adeninivorans.
41 . A method for forming a compound selected from the group consisting of xylulose- 5-phosphate, glyceraldehyde-3-phosphate and dihydroxyacetone in a yeast cell including growing a yeast cell of any one of the preceding claims on a medium including methanol.
42. A method for producing a chemical which can be used in an industrial process, the method including growing a yeast cell of claim 39 in a medium including methanol.
43. A recombinant construct encoding at least one protein for enabling a yeast cell to grow in a medium in which methanol is the only or main energy source for growth of the cell in the medium,
wherein the one or more proteins is selected from the group consisting of:
alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 )
dihydroxyacetone synthase (E.C. 2.2.1 .3), dihydroxyacetone kinase (E.C.
2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1 .2.13), fructose-1 -6- bisphophatase (E.C. 3.1.3.1 1 ), sedoheptulose bisphosphatase (E.C. 3.1 .3.37), ribose-5-phosphate isomerase (E.C. 5.3.1.6) and D-ribulose-5-phosphate-3- epimerase (E.C. 5.1 .3.1 ), transketolase 1 or 2 (E.C. 2.2.1.1 ), transaldolase (EC
2.2.1 .2) , catalase (E.C. 1 .1 1 .1 .6), glutathione peroxidase (E.C. 1 .1 1 .1 .9) and methyl formate-synthesising alcohol dehydrogenase (E.C. 1 .1.1 .1 ), or functional variants thereof.
44. The recombinant construct according to claim 43, wherein the construct encodes the proteins alcohol oxidase (E.C. 1 .1.3.13), dihydroxyacetone synthase (E.C.
2.2.1.3) and pyruvate carboxylase (E.C. 6.4.1 .1 ).
45. The recombinant construct according to claim 43, wherein the recombinant construct encodes the proteins: alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) and transaldolase (EC 2.2.1 .2), or functional variants thereof.
46. The recombinant construct according to claim 43, wherein the recombinant construct encodes the proteins: alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ), dihydroxyacetone synthase (E.C. 2.2.1 .3), and transaldolase (EC 2.2.1 .2), or functional variants thereof.
47. The recombinant construct according to claim 43, wherein the recombinant construct encodes the proteins: alcohol oxidase (E.C. 1 .1 .3.13), pyruvate carboxylase (E.C. 6.4.1 .1 ) dihydroxyacetone synthase (E.C. 2.2.1 .3), dihydroxyacetone kinase (E.C. 2.7.1 .29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13) and fructose-1 -6-bisphophatase (E.C. 3.1.3.11), or functional variants thereof.
48. The recombinant construct according to claim 43, wherein the recombinant construct encodes the proteins: alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C.6.4.1.1), transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C.2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C.4.1.2.13) and fructose- 1 -6-bisphophatase (E.C.3.1.3.11), or functional variants thereof.
49. The recombinant construct according to claim 43, wherein the recombinant construct encodes the proteins: alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1), dihydroxyacetone synthase (E.C. 2.2.1.3), transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C.2.7.1.29), fructose-1- 6-bisphosphate aldolase (E.C. 4.1.2.13) and fructose-1 -6-bisphophatase (E.C. 3.1.3.11 ), or functional variants thereof.
50. The recombinant construct according to claim 43, wherein the recombinant construct encodes the proteins: alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) and dihydroxyacetone synthase (E.C. 2.2.1.3), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase
(E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1.3.11) and sedoheptulose bisphosphatase (E.C.3.1.3.37), or functional variants thereof.
51. The recombinant construct according to claim 43, wherein the recombinant construct encodes the proteins: alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C.6.4.1.1) transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C.2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C.4.1.2.13), fructose-1 -6- bisphophatase (E.C. 3.1.3.11) and sedoheptulose bisphosphatase (E.C. 3.1.3.37), or functional variants thereof.
52. The recombinant construct according to claim 43, wherein the recombinant construct encodes the proteins: alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) dihydroxyacetone synthase (E.C. 2.2.1.3), transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C.2.7.1.29), fructose-1 - 6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1.3.11) and sedoheptulose bisphosphatase (E.C. 3.1.3.37), or functional variants thereof.
53. The recombinant construct according to claim 43, wherein the recombinant construct encodes the proteins: alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) and dihydroxyacetone synthase (E.C. 2.2.1.3), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1.3.11), sedoheptulose bisphosphatase (E.C. 3.1.3.37), ribose-5-phosphate isomerase (E.C. 5.3.1.6) and D-ribulose-5-phosphate-3-epimerase (E.C. 5.1.3.1), or functional variants thereof.
54. The recombinant construct according to claim 43, wherein the recombinant construct encodes the proteins: alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) and transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C. 2.7.1.29), fructose-1 -6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C.3.1.3.11), sedoheptulose bisphosphatase (E.C. 3.1.3.37), ribose-5-phosphate isomerase (E.C. 5.3.1.6) and D-ribulose-5- phosphate-3-epimerase (E.C.5.1.3.1), or functional variants thereof.
55. The recombinant construct according to claim 43, wherein the recombinant construct encodes the proteins: alcohol oxidase (E.C. 1.1.3.13), pyruvate carboxylase (E.C. 6.4.1.1) and dihydroxyacetone synthase (E.C. 2.2.1.3), transaldolase (EC 2.2.1.2), dihydroxyacetone kinase (E.C.2.7.1.29), fructose-1 - 6-bisphosphate aldolase (E.C. 4.1.2.13), fructose-1 -6-bisphophatase (E.C. 3.1.3.11), sedoheptulose bisphosphatase (E.C. 3.1.3.37), ribose-5-phosphate isomerase (E.C.5.3.1.6) and D-ribulose-5-phosphate-3-epimerase (E.C.5.1.3.1), or functional variants thereof.
56. The recombinant construct according to claim 43, wherein the construct encodes one or more of the proteins transketolase 1 or 2 (E.C.2.2.1.1), catalase (E.C.
1.11.1.6), glutathione peroxidase (E.C. 1.11.1.9) and methyl formate- synthesising alcohol dehydrogenase (E.C.1.1.1.1), or functional variants thereof.
57. The recombinant construct according to claim 56, wherein the construct encodes the proteins transketolase 1 or 2 (E.C.2.2.1.1), catalase (E.C.1.11.1.6), glutathione peroxidase (E.C.1.11.1.9) and methyl formate-synthesising alcohol dehydrogenase (E.C.1.1.1.1), or functional variants thereof.
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Cited By (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
KR102080886B1 (en) * 2019-05-21 2020-02-24 씨제이제일제당 주식회사 ribulose-phosphate 3-epimerases comprising motifs having lower side reactions
WO2023056256A1 (en) * 2021-09-29 2023-04-06 Lpoxy Therapeutics, Inc. Enteric aerobization therapy
US11883428B2 (en) 2020-04-03 2024-01-30 Lpoxy Therapeutics, Inc. Enteric aerobization therapy
WO2024068845A1 (en) * 2022-09-29 2024-04-04 Vib Vzw New loxpsym sites for large-scale orthogonal cre-mediated recombination
US12036239B2 (en) 2023-02-14 2024-07-16 Lpoxy Therapeutics, Inc. Treatment of inflammatory bowel diseases through administration of enteric aerobization therapy

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2015160848A1 (en) * 2014-04-15 2015-10-22 Industrial Microbes, Inc. Synthetic methanotrophic and methylotrophic microorganisms

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2015160848A1 (en) * 2014-04-15 2015-10-22 Industrial Microbes, Inc. Synthetic methanotrophic and methylotrophic microorganisms

Non-Patent Citations (8)

* Cited by examiner, † Cited by third party
Title
CREGG, J.M. ET AL.: "Functional characterization of the two alcohol oxidase genes from the yeast Pichia pastoris", MOLECULAR AND CELLULAR BIOLOGY, vol. 9, no. 3, 1989, pages 1316 - 1323, XP000106699 *
DAI, Z. ET AL.: "Metabolic construction strategies for direct methanol utilization in Saccharomyces cerevisiae", BIORESOURCE TECHNOLOGY, vol. 245, 2017, pages 1407 - 1412, XP085238067, [retrieved on 20170519] *
HORIGUCHI, H. ET AL.: "Antioxidant system within yeast peroxisome", THE JOURNAL OF BIOLOGICAL CHEMISTRY, vol. 276, no. 17, 2001, pages 14279 - 14288, XP055504825 *
KRAINER, F.W. ET AL.: "Recombinant protein expression in Pichia pastoris strains with an engineered methanol utilization pathway", MICROBIAL CELL FACTORIES, vol. 11, no. 1, 2012, pages 22, XP021118475 *
KUSANO, M. ET AL.: "Hemiacetal dehydrogenation activity of alcohol dehydrogenases in Saccharomyces cerevisiae", BIOSCIENCE, BIOTECHNOLOGY AND BIOCHEMISTRY, vol. 62, no. 10, 1998, pages 1956 - 1961, XP055504828 *
OZIMEK, P. ET AL.: "Pyruvate carboxylase is an essential protein in the assembly of yeast peroxisomal oligomeric alcohol oxidase", MOLECULAR BIOLOGY OF THE CELL, vol. 14, no. 2, 18 November 2002 (2002-11-18), pages 786 - 797, XP002594066 *
YURIMOTO, H. ET AL.: "Alcohol dehydrogenases that catalyse methyl formate synthesis participate in formaldehyde detoxification in the methylotrophic yeast Candida boidinii", YEAST, vol. 21, no. 4, 2004, pages 341 - 350, XP055136490 *
ZHANG, W. ET AL.: "Guidance for engineering of synthetic methylotrophy based on methanol metabolism in methylotrophy", RSC ADVANCES, vol. 7, no. 7, 2017, pages 4083 - 4091, XP055392694 *

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KR102080886B1 (en) * 2019-05-21 2020-02-24 씨제이제일제당 주식회사 ribulose-phosphate 3-epimerases comprising motifs having lower side reactions
WO2020235830A1 (en) * 2019-05-21 2020-11-26 씨제이제일제당 (주) Ribulose-phosphate 3-epimerase motif having lower side reactivity and enzyme comprising same
JP2022522693A (en) * 2019-05-21 2022-04-20 シージェイ チェイルジェダン コーポレーション Ribulose-phosphate 3-epimerase motif with low side reactivity and enzymes containing it
AU2020279663B2 (en) * 2019-05-21 2023-04-13 Cj Cheiljedang Corporation Ribulose-Phosphate 3-Epimerase Motif Having Low Side Reactivity And Enzyme Including The Same
JP7410162B2 (en) 2019-05-21 2024-01-09 シージェイ チェイルジェダン コーポレーション Ribulose phosphate 3-epimerase motif with low side reactivity and enzyme containing it
US11883428B2 (en) 2020-04-03 2024-01-30 Lpoxy Therapeutics, Inc. Enteric aerobization therapy
US11944641B2 (en) 2020-04-03 2024-04-02 Lpoxy Therapeutics, Inc. Treatment of inflammatory bowel diseases through administration of enteric aerobization therapy
US11975023B2 (en) 2020-04-03 2024-05-07 Lpoxy Therapeutics, Inc Methods for inhibiting anaerobic microorganisms
WO2023056256A1 (en) * 2021-09-29 2023-04-06 Lpoxy Therapeutics, Inc. Enteric aerobization therapy
WO2024068845A1 (en) * 2022-09-29 2024-04-04 Vib Vzw New loxpsym sites for large-scale orthogonal cre-mediated recombination
US12036239B2 (en) 2023-02-14 2024-07-16 Lpoxy Therapeutics, Inc. Treatment of inflammatory bowel diseases through administration of enteric aerobization therapy

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