# Patent

## Title
Acetate toxicity tolerance in recombinant microbial host cells

## Abstract

Acetate is a potent microbial inhibitor which can affect the performance of yeast in ethanolic fermentation. The present disclosure provides a recombinant microbial host cell having (i) a first genetic modification for increasing the activity of one or more proteins that function in a first metabolic pathway to convert acetate into an alcohol in the microbial host cell; (ii) a second genetic modification for increasing the activity of one or more proteins that function in a second metabolic pathway to import glycerol in the recombinant microbial host cell (iii) a third genetic modification for increasing the activity of one or more proteins that function in a third metabolic pathway to convert a C5 carbohydrate into ethanol in the microbial host cell. The recombinant microbial host cell comprises and natively expresses native proteins that function in a fourth native metabolic pathway to produce glycerol in the microbial host cell.

## Background
STATEMENT REGARDING SEQUENCE LISTING
The Sequence Listing associated with this application is provided in text format in lieu of a paper copy, and is hereby incorporated by reference into the specification. The name of the text file containing the Sequence Listing is 580127_410USPC_SEQUENCE_LISTING.txt. The text file is 90.7 KB, was created on Mar. 12, 2020, and is being submitted electronically via EFS-Web.
TECHNOLOGICAL FIELD
The present disclosure concerns recombinant microbial host cells with increased tolerance towards ethanol/robustness and capable of converting acetate into ethanol as well as methods of using such recombinant microbial host cells for the production of ethanol.
BACKGROUND
One of the main technical challenges in producing second-generation biochemicals from cellulosic feedstocks via fermentation is reducing the negative impact of microbial inhibitors released during feedstock hydrolysis, such as acetate. Wild-type strains of Saccharomyces cerevisiae are severely limited in their ability to anaerobically (co)-consume acetate, an important potent inhibitor in cellulosic hydrolysates. However, introducing a heterologous NADH-specific acetylating acetaldehyde dehydrogenase (AADH) makes it thermodynamically possible for yeasts to anaerobically convert acetate into ethanol during glucose fermentation (Guadalupe et al., 2010). The authors combined expression of an AADH with a gpd-strain background, which increased ethanol titers in two separate ways: additional ethanol is produced from acetate and the sugar that is no longer directed towards glycerol formation can be fermented to ethanol instead (Guadalupe et al., 2010). However, gpd-strains generally suffer from impaired robustness (Guadalupe et al., 2014), which can make them unsuitable for industrial fermentation of inhibitory hydrolysates. In addition, even if glycerol production is abolished, the amount of acetate that can be converted to ethanol with the amount of biosynthetic surplus NADH thus made available is limited and wild-type S. cerevisiae strains are severely restricted in their ability to generate additional cytosolic NADH anaerobically. AADH has also been expressed by itself in a wild-type GPD+ S. cerevisiae background, but this only resulted in decreased production of glycerol and acetate during glucose fermentation and did not lead to net acetate consumption (Zhang et al., 2011).
Some progress has already been made to engineer yeast strains that efficiently consume acetate during anaerobic fermentation and increase ethanol titers, while maintaining strong robustness and performance, especially on non-native substrates such as xylose and arabinose. It has been observed that S. cerevisiae strains engineered for xylose fermentation are particularly sensitive to acetic acid during xylose fermentation, a combination highly relevant to cellulosic hydrolysates. This effect has been recognized both in strains engineered to ferment xylose through the so-called fungal pathway, through xylose reductase (XR) and xylitol dehydrogenase (XDH), as well as in strains with the bacterial pathway, through xylose isomerase (XI).
Expression of AADH in an S. cerevisiae background, an XR/XDH xylose pathway and an ALD6 deletion significantly increased acetate consumption during anaerobic fermentation of a glucose/xylose mixture, while decreasing glycerol and xylitol formation (Wei et al., 2013). Further improvements with this approach were achieved by increasing the expression of AADH and the first enzyme in the acetate-to-ethanol pathway, acetyl-CoA synthetase (ACS) (Zhang et al., 2016). While these studies showed promising results, efficient conversion of acetate into ethanol in the reported strains depends on the redox-imbalanced combination of NAD(P)H-consuming XR and NADH-producing XDH to generate the NADH consumed in the acetate-to-ethanol pathway. This strategy is thus only applicable to XR/XDH strains during the fermentation of xylose. Using XR/XDH strains for xylose fermentation is furthermore complicated by their typical secretion of xylitol, which reduces product yields.
Expression of AADH has also been reported in xylose-fermenting S. cerevisiae strains overexpressing XI instead of XR/XDH (Onishi et al., 2016), although no modifications were explored to increase acetate consumption beyond a basic level.
In a distinct approach, conversion of acetate into ethanol was linked to consumption of exogenous glycerol through overexpression of NADH-specific glycerol dehydrogenase and dihydroxyacetone kinase (producing NADH) (WO2011/149353 and US2015/0176032). While this approach is not dependent on the cofermentation of a specific sugar, as is the case for the XR/XDH pathway discussed above (which requires xylose), it does require a significant amount of exogenous glycerol to be co-fed, which may not always be economical.
A further strategy to increase the anaerobic supply of redox equivalents for reducing acetate into ethanol, which relied on the expression of an NADPH-specific primary alcohol dehydrogenase (ADH), showed a significant increase in acetate consumption during glucose fermentation, presumably in part by allowing the yeast to anaerobically produce NADH while consuming NADPH (Henningsen et al., 2015). Acetate consumption was highest when NADPH-ADH expression was combined with overexpression of ACS and the first enzyme in the NADPH-forming oxidative pentose-phosphate pathway, glucose-6-phosphate dehydrogenase (G6PDH).
There thus remains a demand in industry for a metabolic engineering strategy for efficient anaerobic acetate consumption that maintains cellular robustness and that is independent of a particular co-substrate (glycerol for glycerol-consuming strains).
BRIEF SUMMARY
The present disclosure provides a microbial host cell which is especially suited to consume acetate in anaerobia by increasing the activity of one or more proteins that function in a first metabolic pathway (to convert acetate into an alcohol in the microbial host cell), in a second metabolic pathway (to import glycerol in the recombinant microbial host cell) and in a third metabolic pathway (to convert a C5 carbohydrate into the alcohol in the microbial host cell). The microbial host cell is capable of producing glycerol by natively expressing native proteins that function in a fourth native metabolic pathway to produce glycerol.
In a first aspect, the present disclosure provides a recombinant microbial host cell having (i) a first genetic modification for increasing the activity of one or more proteins that function in a first metabolic pathway to convert acetate into an alcohol in the microbial host cell; (ii) a second genetic modification for increasing the activity of one or more proteins that function in a second metabolic pathway to import glycerol in the recombinant microbial host cell; and (iii) a third genetic modification for increasing the activity of one or more proteins that function in a third metabolic pathway to convert a C5 carbohydrate into the alcohol in the microbial host cell. The recombinant microbial host cell comprises and natively expresses native proteins that function in a fourth native metabolic pathway to produce glycerol in the microbial host cell. In an embodiment, the alcohol is ethanol. In yet another embodiments, one or more proteins that function in the first metabolic pathway are heterologous proteins. In still another embodiment, the one or more proteins that function in the first metabolic pathway comprise a protein having acetylating acetaldehyde dehydrogenase activity. In yet a further embodiment, the protein having acetylating acetaldehyde dehydrogenase activity also has alcohol dehydrogenase activity and can be, for example, an ADHE polypeptide (for example from Bifidobacterium sp., including Bifidobacterium adolescentis). In still another embodiment, the one or more protein that function in the first metabolic pathway further comprises a protein having acetyl-CoA synthetase activity which can be, for example, an ACS2 polypeptide (for example from Saccharomyces sp., including Saccharomyces cerevisiae). In an embodiment, the one or more proteins that function in the second metabolic pathway are heterologous proteins. In still another embodiment, the protein having glycerol importing activity is an STL1 polypeptide (for example from Saccharomyces sp., including Saccharomyces cerevisiae or Pichia sp., including Pichia sorbitophila). In yet another embodiment, the one or more protein that function in the third metabolic pathway are heterologous proteins. In another embodiment, the C5 carbohydrate is xylose and/or arabinose. In still a further embodiment, one or more proteins that function in the third metabolic pathway comprise a protein having xylose isomerase activity, a protein having xylulokinase activity, a protein having transketolase activity, a protein having transaldolase activity, a protein having ribose-5-phosphate isomerase and/or a protein having ribulose-phosphate 3-epimerase activity. In a further embodiment, the one or more proteins that function in the third metabolic pathway comprise the protein having xylose isomerase activity which can be, for example, from Catonella sp., including Catonella morbi. In yet another embodiment, the one or more proteins that function in the third metabolic pathway comprises an arabinose transporter, an ARAA polypeptide, an ARAB polypeptide and/or an ARAD polypeptide. In an embodiment, the ARAA, ARAB or ARAD polypeptides can be from Bacteroides sp., including Bacteroides thetaiotaomicron. In another embodiment, the recombinant microbial host cell can further comprise at least one of a first additional genetic modification, wherein the first additional genetic modification is (a) a deletion in at least one an aldose reductase gene; (b) a mutation in a polypeptide encoded by an iron-sulfur cluster gene; and/or (c) a mutation in a RAS2 polypeptide. In an embodiment, the aldose reductase gene is a GRE3 gene and/or a YPR1 gene. In still another embodiment, the iron sulfur cluster gene is a YFH1 gene, a ISU1 gene and/or a NFS1 gene. In an embodiment, the native proteins that function in the fourth native metabolic pathway to produce glycerol comprise a GPD1 protein, a GPD2 protein, a GPP1 protein and a GPP2 protein. In some embodiment, the recombinant microbial host cell further comprises a fifth genetic modification for increasing the activity of one or more heterologous proteins that function in a fifth metabolic pathway for increasing the availability of electrons in the form of a reduced redox cofactor in the microbial host cell. In still another embodiment, the fifth genetic modification is for increasing the activity of a NADPH-dependent alcohol dehydrogenase. For example, the NADPH-dependent alcohol dehydrogenase from a bacteria or a eukaryotic source and can be an ADH1 polypeptide (for example from Entamoeba sp., including Entamoeba histolytica). In such embodiment, the recombinant microbial host cell can further comprise a second additional genetic modification for increasing the activity of a protein capable of producing NADPH. Such protein can be, for example, at least one of a ZWF1 protein, a SOL3 protein and/or a GND1 protein. In an embodiment, the recombinant microbial host cell can be a yeast host cell, for example from the genus Saccharomyces and, in some embodiments, from the species Saccharomyces cerevisiae. 



BRIEF DESCRIPTION OF THE DRAWINGS
Having thus generally described the nature of the invention, reference will now be made to the accompanying drawings, showing by way of illustration, a preferred embodiment thereof, and in which:
FIG. 1 compares the fermentation rate of different genetically engineered Saccharomyces cerevisiae strains on an industrial cellulosic medium. Results are shown as the accumulation of CO2 production (measured as pressure accumulation) in function of fermentation time (measured in hours) for strains M13446, M12623 and M12613.
FIG. 2 compares glucose, xylose and acetic acid consumption as well as glycerol and ethanol production in different strains of S. cerevisiae on an industrial cellulosic medium. Results are shown as the glucose, xylose, glycerol and acetate content (all provided as g/L, left axis) as well as the ethanol (▴) content (provided as g/L, right axis) in the culture medium of strains M12623, M12747 and M13446 at the end of the fermentation.
FIG. 3 compares glucose, xylose and acetic acid consumption as well as glycerol and ethanol production in different strains of S. cerevisiae on an industrial cellulosic medium. Results are shown as the glucose, xylose, glycerol and acetate content (all provided as g/L, left axis) as well as the ethanol (▴) content (provided as g/L, right axis) in the culture medium of strains M12623, M12747, M12932, M13446 and M13618 at the end of the fermentation.
FIG. 4 compares acetic acid consumption as well as glycerol and ethanol production in different strains of S. cerevisiae. Results are shown as the glycerol and acetate content (all provided as g/L, left axis) as well as the ethanol (▴) content (provided as g/L, right axis) in the culture medium of strains M12623, M14749, M14747, M14755, M14745, M14754, M14751, M13446 and M13618 at the end of the fermentation on a YPD80A4 (10 g/L yeast extract, 20 g/Lpeptone, 80 g/L glucose, 4 g/L acetate) medium.
FIG. 5 compares xylose and acetic acid consumption as well as glycerol and ethanol production in different strains of S. cerevisiae. Results are shown as the xylose, glycerol and acetate content (all provided as g/L, left axis) as well as the ethanol (1) content (provided as g/L, right axis) in the culture medium of strains M12623, M14749, M14747, M14755, M14745, M14754, M14751, M13446 and M13618 at the end of the fermentation on a YPX80A4 (10 g/L yeast extract, 20 g/Lpeptone, 80 g/L glucose, 4 g/L acetate) medium.
FIG. 6 compares xylose and acetic acid consumption as well as glycerol and ethanol production in different strains of S. cerevisiae on an industrial cellulosic medium. Results are shown as the xylose, and acetate content (all provided as g/L, left axis) as well as the ethanol (▴) content (provided as g/L, right axis) in the culture medium of strains M12623, M13618, M14615, M14712, M14716, and M14719 at the end of the fermentation.
FIG. 7 compares the fermentation rate of different S. cerevisiae strains. Results are shown as the cumulative CO2 production (measured as mL) in function of fermentation time (measured in hours) for strains M12623, M14712, M14716 and M14719.
FIG. 8 compares the fermentation rate of different S. cerevisiae strains. Results are shown as the cumulative CO2 production (measured as mL) in function of fermentation time (measured in hours) for strains M2390, M12623, M14718, M14837, M15339 and M15380 on a YPD60X60Ace9 (10 g/L yeast extract, 20 g/L peptone, 60 g/L dextrose, 60 g/L xylose, and 9 g/L acetic acid from potassium acetate set at an initial pH of 4.9 using sulfuric acid) medium.
FIG. 9 compares glucose, xylose and acetic acid consumption as well as glycerol and ethanol production in different strains of S. cerevisiae. Results are shown as the glucose, xylose, glycerol and acetate content (all provided as g/L, left axis) as well as the ethanol content (provided as g/L, right axis) in the culture medium of strains M2390, M12623, M14718, M14837, M15339, M15380 at the end of the fermentation on a YPD60X60Ace9 (10 g/L yeast extract, 20 g/L peptone, 60 g/L dextrose, 60 g/L xylose, and 9 g/L acetic acid from potassium acetate set at an initial pH of 4.9 using sulfuric acid) medium.
FIG. 10 compares the fermentation rate of different S. cerevisiae strains. Results are shown as the cumulative CO2 production (measured as mL) in function of fermentation time (measured in hours) for strains M2390, M11321 and M14507 in YPD20X10A10Ace4Gly1 (10 g/L yeast extract, 20 g/L peptone, 20 g/L glucose, 10 g/L xylose, 10 g/L arabinose, 4 g/L acetate from potassium acetate, and 1 g/L glycerol) medium.
FIG. 11 compares glucose, xylose, acetic acid and arabinose consumption as well as glycerol and ethanol production in different strains of S. cerevisiae. Results are shown as the glucose, xylose, glycerol, acetate, arabinose and ethanol content (all provided as g/L) in an unfermented medium (“Blank”) or the culture medium of strains M2390, M11321 and M14507 at the end of the fermentation on a YPD20X10A10Ace4Gly1 (10 g/L yeast extract, 20 g/L peptone, 20 g/L glucose, 10 g/L xylose, 10 g/L arabinose, 4 g/L acetate from potassium acetate, and 1 g/L glycerol) medium.
FIG. 12 compares the fermentation rate of different S. cerevisiae strains. Results are shown as the cumulative CO2 production (measured as PSI) in function of fermentation time (measured in hours) for strains M2390, M11321 and M14507 in a commercial corn fiber cellulosic substrate.



DETAILED DESCRIPTION
i) Definitions
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Also, unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular. All publications, patents and other references mentioned herein are incorporated by reference in their entireties for all purposes.
The term “increasing” when used in reference to the activity of one or more proteins encompasses both providing activity of the protein in the recombinant microbial host cell (in embodiments in which the protein was not natively expressed by the recombinant microbial host cell) and augmenting the activity of the protein in the recombinant microbial host cell (in embodiments in which the protein was natively expressed by the recombinant microbial host cell). Therefore the expression “increasing the activity” generally refers to an heightened activity of the one or more proteins, which can be heterolgous or native to the microbial host cell.
The term “heterologous” when used in reference to a polynucleotide, a gene, a protein, a polypeptide or an enzyme refers to a nucleic acid, a polynucleotide, a gene, a protein, a polypeptide, or an enzyme not normally found in the host organism. “Heterologous” also includes a native coding region, or portion thereof, that is reintroduced into the source organism in a form that is different from the corresponding native gene, e.g., not in its natural location in the organism's genome or not with its native regulatory elements (i.e. promoter and terminator). The heterologous polynucleotide or gene may be introduced into the host organism by, e.g., gene transfer. A heterologous gene/polynucleotide may include a native coding region that is a portion of a chimeric gene including non-native regulatory regions that is reintroduced into the native host. Foreign genes can comprise native genes inserted into a non-native organism, or chimeric genes. The term “heterologous” when used in reference to a nucleic acid molecule (such as a promoter, a terminator or a coding sequence) or a protein refers to a nucleic acid molecule or a protein that is not natively found in the recombinant host cell. For example, a heterologous element could be derived from a different strain of host cell, or from an organism of a different taxonomic group (e.g., different kingdom, phylum, class, order, family genus, or species, or any subgroup within one of these classifications). A heterologous element may be derived from any source, e.g., eukaryotes, prokaryotes, viruses, or synthetic polynucleotide fragments.
The heterologous nucleic acid molecules or polynucleotides present in the recombinant host cell can be integrated in the host cell's genome. The term “integrated” as used herein refers to genetic elements that are placed, through molecular biology techniques, into the genome of a host cell. For example, genetic elements can be placed into the chromosomes of the host cell as opposed to in a vector such as a plasmid carried by the host cell. Methods for integrating genetic elements into the genome of a host cell are well known in the art and include homologous recombination. The heterologous nucleic acid molecule can be present in one or more copies (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12 or even more copies) in the microbial host cell's genome (at the same or different loci). The heterologous nucleic acid molecule(s) can be integrated at a neutral integration site, e.g., a genomic location which does not negatively affect the growth, robustness, viability or fermentation performances of the recombinant microbial host cell. Alternatively, the heterologous nucleic acid molecule can be independently replicating from the yeast's genome. In such embodiment, the nucleic acid molecule can be stable and/or self-replicating.
In some embodiments, heterologous nucleic acid/polynucleotide molecules which can be introduced into the recombinant microbial host cells are codon-optimized with respect to the intended recipient recombinant microbial host cell. As used herein the term “codon-optimized coding region” means a nucleic acid coding region that has been adapted for expression in the cells of a given organism by replacing at least one, or more than one, codons with one or more codons that are more frequently used in the genes of that organism. In general, highly expressed genes in an organism are biased towards codons that are recognized by the most abundant tRNA species in that organism. One measure of this bias is the “codon adaptation index” or “CAI,” which measures the extent to which the codons used to encode each amino acid in a particular gene are those which occur most frequently in a reference set of highly expressed genes from an organism. The CAI of codon optimized heterologous nucleic acid molecules described herein corresponds to between about 0.8 and 1.0, between about 0.8 and 0.9, or about 1.0.
The heterologous nucleic acid molecule can be introduced in the recombinant microbial host cell using a vector. A “vector,” e.g., a “plasmid”, “cosmid” or “artificial chromosome” (such as, for example, a yeast artificial chromosome) refers to an extra chromosomal element and is usually in the form of a circular double-stranded DNA molecule. Such vectors may be autonomously replicating sequences, genome integrating sequences, phage or nucleotide sequences, linear, circular, or supercoiled, of a single- or double-stranded DNA or RNA, derived from any source, in which a number of nucleotide sequences have been joined or recombined into a unique construction which is capable of introducing a promoter fragment and DNA sequence for a selected gene product along with appropriate 3′ untranslated sequence into a cell.
The heterologous polypeptides of the present disclosure can be encoded by a gene ortholog or a gene paralog. In the context of the present disclosure, a “gene ortholog” is understood to be a gene in a different species that evolved from a common ancestral gene by speciation. It is understood that the protein encoded by a gene ortholog retains the same function as the protein encoded by the original gene. Alternatively, a “gene paralog” is understood to be a gene related by duplication within the genome. In the context of the present invention, a gene paralog encodes an enzyme that could exhibit additional biological function than the native enzyme.
The heterologous nucleic acid molecules/polynucleotides described herein can comprise transcriptional and/or translational control regions. “Transcriptional and translational control regions” are DNA regulatory regions, such as promoters, enhancers, terminators, and the like, that provide for the expression of a coding region in a host cell. In eukaryotic cells, polyadenylation signals are control regions.
The terms “promoter” is intended to include a polynucleotide that can transcriptionally control a gene-of-interest that it does not transcriptionally control in nature. In certain embodiments, the transcriptional control of a promoter results in an increase in expression of the gene-of-interest under certain circumstances. In certain embodiments, a promoter is placed 5′ to the gene-of-interest. A promoter may be used to replace the natural promoter, or may be used in addition to the natural promoter. A surrogate promoter may be endogenous with regard to the host cell in which it is used, or it may be a heterologous polynucleotide sequence introduced into the host cell, e.g., exogenous with regard to the host cell in which it is used.
The terms “gene(s)” or “polynucleotide(s)” or “polynucleotide sequence(s)” are intended to include nucleic acid molecules, e.g., polynucleotides which include an open reading frame encoding a polypeptide, and can further include non-coding regulatory sequences, and introns. In addition, the terms are intended to include one or more genes that map to a functional locus. In addition, the terms are intended to include a specific gene for a selected purpose. The gene may be endogenous to the host cell or may be recombinantly introduced into the host cell, e.g., as a plasmid maintained episomally or a plasmid (or fragment thereof) that is stably integrated into the genome. In addition to the plasmid form, a gene may, for example, be in the form of linear DNA. In certain embodiments, the gene or polynucleotide is involved in at least one step in the bioconversion of biomass to, e.g., ethanol.
The heterologous proteins or polypeptides of the present disclosure can be a variant of a known/native protein or polypeptide. A variant comprises at least one amino acid difference when compared to the amino acid sequence of the native protein or polypeptide. As used herein, a variant refers to alterations in the amino acid sequence that do not adversely affect the biological functions of the protein or polypeptide. A substitution, insertion or deletion is said to adversely affect the protein when the altered sequence prevents or disrupts a biological function associated with the native protein or polypeptide. For example, the overall charge, structure or hydrophobic-hydrophilic properties of the protein can be altered without adversely affecting a biological activity. Accordingly, the amino acid sequence can be altered, for example to render the peptide more hydrophobic or hydrophilic, without adversely affecting the biological activities of the food and/or feed enzyme. The protein or polypeptides variants have at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identity to the native proteins and polypeptides described herein. The term “percent identity”, as known in the art, is a relationship between two or more polypeptide sequences or two or more polynucleotide sequences, as determined by comparing the sequences. The level of identity can be determined conventionally using known computer programs. Identity can be readily calculated by known methods, including but not limited to those described in: Computational Molecular Biology (Lesk, A4. M., ed.) Oxford University Press, N Y (1988); Biocomputing: Informatics and Genome Projects (Smith, D. W., ed.) Academic Press, N Y (1993); Computer Analysis of Sequence Data, Part I (Griffin, A. M., and Griffin, H. G., eds.) Humana Press, N J (1994); Sequence Analysis in Molecular Biology (von Heinje, G., ed.) Academic Press (1987); and Sequence Analysis Primer (Gribskov, M. and Devereux, J., eds.) Stockton Press, NY (1991). Preferred methods to determine identity are designed to give the best match between the sequences tested. Methods to determine identity and similarity are codified in publicly available computer programs. Sequence alignments and percent identity calculations may be performed using the MegAlign program of the Lasergene bioinformatics computing suite (DNASTAR Inc., Madison, Wis.). Multiple alignments of the sequences disclosed herein were performed using the Clustal method of alignment (Higgins and Sharp (1989) CABIOS. 5:151-153) with the default parameters (GAP PENALTY=10, GAP LENGTH PEN ALT Y=10). Default parameters for pairwise alignments using the Clustal method were KTUPLB 1, GAP PENALTY=3, WINDOW=5 and DIAGONALS SAVED=5.
The variant proteins or polypeptides described herein may be (i) one in which one or more of the amino acid residues are substituted with a conserved or non-conserved amino acid residue (preferably a conserved amino acid residue) and such substituted amino acid residue may or may not be one encoded by the genetic code, or (ii) one in which one or more of the amino acid residues includes a substituent group, or (iii) one in which the mature polypeptide is fused with another compound, such as a compound to increase the half-life of the polypeptide (for example, polyethylene glycol), or (iv) one in which the additional amino acids are fused to the mature polypeptide for purification of the polypeptide. A “variant” of the protein or polypeptide can be a conservative variant or an allelic variant.
The heterologous proteins or polypeptides can be a fragment of a known/native/variant protein or polypeptide. A fragment comprises at least one fewer amino acid residue when compared to the amino acid sequence of the known/native/variant protein or polypeptide and still possesses the biological activity of the native protein or polypeptide. In some embodiments, protein or polypeptide “fragments” have at least at least 100, 200, 300, 400, 500, 600, 700 or more consecutive amino acids of the known/native/variant protein or polypeptide. In some embodiments, fragments have at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98% or 99% identity to the known/native/variant proteins and polypeptides described herein. In some embodiments, fragments can be employed for producing the corresponding full-length protein or polypeptide by peptide synthesis. Therefore, the fragments can be employed as intermediates for producing the full-length proteins.
The term “transcriptional control” is intended to include the ability to modulate gene expression at the level of transcription. In certain embodiments, transcription, and thus gene expression, is modulated by replacing or adding a surrogate promoter near the 5′ end of the coding region of a gene-of-interest, thereby resulting in altered gene expression. In certain embodiments, the transcriptional control of one or more genes is engineered to result in the optimal expression of such genes, e.g., in a desired ratio. The term also includes inducible transcriptional control as recognized in the art.
In the context of the present disclosure, the recombinant host cell is a microorganism and includes, without limitations, bacteria, yeasts, fungi, plant and mammalian cells. In an embodiment, the recombinant microbial host cell is a yeast and, in some additional embodiments, the yeast can be used in the production of biofuels. Suitable yeast host cells can be, for example, from the genus Saccharomyces, Kluyveromyces, Arxula, Debaryomyces, Candida, Pichia, Phaffia, Schizosaccharomyces, Hansenula, Kloeckera, Schwanniomyces, Torula, Issatchenkia or Yarrowia. Suitable yeast species can include, for example, S. cerevisiae, S. bulderi, S. barnetti, S. exiguus, S. uvarum, S. diastaticus, C. utilis, K. lactis, K. marxianus or K. fragilis. In some embodiments, the yeast is selected from the group consisting of Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans, Issatchenkia orientalis (Candida krusei), Pichia pastoris, Scheffersomyces stipitis, Yarrowia lipolytica, Ogataea polymorpha, Phaffia rhodozyma, Candida utilis, Arxula adeninivorans, Debaryomyces hansenii, Debaryomyces polymorphus, Schizosaccharomyces pombe and Schwanniomyces occidentalis. In some embodiment, the host cell can be an oleaginous yeast cell. For example, the oleaginous yeast host cell can be from the genus Blakeslea, Candida, Cryptococcus, Cunninghamella, Lipomyces, Mortierella, Mucor, Phycomyces, Pythium, Rhodosporidum, Rhodotorula, Trichosporon or Yarrowia. In some alternative embodiment, the host cell can be an oleaginous microalgae host cell (e.g., for example, from the genus Thraustochytrium or Schizochytrium). In an embodiment, the recombinant yeast host cell is from the genus Saccharomyces and, in some embodiments, from the species Saccharomyces cerevisiae. 
ii) First Metabolic Pathway
In the context of the present disclosure, the recombinant microbial host cell comprises at least one first genetic modification for increasing the activity of one or more native and/or heterologous protein in a first (engineered) metabolic pathway to convert acetate into an alcohol such as ethanol or isopropanol. In some embodiments, this allows the recombinant microbial host cell to comprise one or more recombinantly expressed heterologous proteins that function in a first engineered metabolic pathway to convert acetate into an alcohol in the microbial host cell. For example, in an embodiment in which the one or more protein is a native protein, the first genetic modification can comprise including an heterologous promoter which increases the expression (and ultimately the activity) of the native protein to convert acetate into an alcohol. In still another example, the first genetic modification can include a mutation in the coding sequence of the protein that functions to increase the conversion of acetate into an alcohol which increases the activity of the mutated protein (when compared to the native protein). In yet another example, in an embodiment in which the one or more protein is a heterologous protein, the first genetic modification can include one or more copies of the heterologous protein to increase the expression (and ultimately the activity) of the heterologous protein to convert acetate into an alcohol. Increasing the conversion of acetate into ethanol is advantageous to reduce acetate toxicity as well as to increase ethanol production, while maintaining robustness.
In order to increase the activity of the one or more protein functioning to convert acetate into ethanol, it is possible to include, in the recombinant microbial host cell, one or more copies of a heterologous nucleic acid molecule encoding the protein functioning to convert acetate into an alcohol. For example, the recombinant microbial host cell can have one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve or more copies of the heterologous nucleic acid molecule encoding the protein functioning to convert acetate into an alcohol. In an embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) one copy of the heterologous nucleic acid molecule encoding the protein functioning to convert acetate into an alcohol. In an embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) two copies of the heterologous nucleic acid molecule encoding the protein functioning to convert acetate into an alcohol. In another embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) three copies of the heterologous nucleic acid molecule encoding the protein functioning to convert acetate into an alcohol. In yet another embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) four copies of the heterologous nucleic acid molecule encoding the protein functioning to convert acetate into an alcohol. In still another embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) five copies of the heterologous nucleic acid molecule encoding the protein functioning to convert acetate into an alcohol. In a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) six copies of the heterologous nucleic acid molecule encoding the protein functioning to convert acetate into an alcohol. In yet a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) seven copies of the heterologous nucleic acid molecule encoding the protein functioning to convert acetate into an alcohol. In still a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) eight copies of the heterologous nucleic acid molecule encoding the protein functioning to convert acetate into an alcohol. In still a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) nine copies of the heterologous nucleic acid molecule encoding the protein functioning to convert acetate into an alcohol. In still a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) ten copies of the heterologous nucleic acid molecule encoding the protein functioning to convert acetate into an alcohol. In still a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) eleven copies of the heterologous nucleic acid molecule encoding the protein functioning to convert acetate into an alcohol. In still a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) twelve copies of the heterologous nucleic acid molecule encoding the protein functioning to convert acetate into an alcohol. In an embodiment, the recombinant microbial host cell comprises twelve copies of the heterologous nucleic acid molecule encoding the protein functioning to convert acetate into an alcohol. The heterologous nucleic acid molecule can be independently replicating or integrated in the recombinant microbial host cell. When the heterologous nucleic acid molecule is integrated in the recombinant microbial host cell, it can be positioned at neutral integration site. When more than one copy of the heterologous nucleic acid molecule encoding the protein functioning to convert acetate is introduced in the recombinant microbial host cell, each of the copies can be integrated at one or more (the same or different) integration sites.
Acetate can be converted in ethanol by first converting acetate into acetyl-coA by the enzymatic activity of an acetyl-coA synthase (ACS). Acetyl-coA can then be converted to acetaldehyde by the enzymatic activity of an acetylating acetaldehyde dehydrogenase (AADH). Finally, acetaldehyde can be converted to ethanol by the enzymatic activity of an alcohol dehydrogenase (ADH).
As indicated above, an exemplary protein capable of functioning to convert acetate into ethanol can be an acetyl-coA synthase (ACS). Acetyl-coA synthases (ACS) catalyze the conversion of acetate into acetyl-coA and are classified in the Enzyme Commission Number class 6.2.1.1. As such, the one or more proteins that function to convert acetate into ethanol can be an acetyl-coA synthase, an acetyl-coA synthase variant, an acetyl-coA synthase fragment or be encoded by a gene ortholog of the gene encoding the acetyl-coA synthase. Exemplary proteins having acetyl-coA synthase activity can be encoded, for example by one of the following genes Saccharomyces cerevisiae Gene ID: 850846, Arabidopsis thaliana Gene ID: 837082, Solanum lycopersicum Gene ID: 606304, Sugiyamaella lignohabitans Gene ID: 30035839 and 30034559, Triticum aestivum Gene ID: 543237, Scheffersomyces stipitis Gene ID: 4840021, Volvox carteri f. nagariensis Gene ID: 9624764, Chlamydomonas reinhardtii Gene ID: 5725731 and Candida albicans Gene ID: 3644710. In an embodiment, the protein having acetyl-coA synthase activity is an ACS2 protein (derived from Saccharomyces cerevisiae for example) that can have the amino acid sequence of SEQ ID NO: 3, an ACS2 protein variant, an ACS2 protein fragment or a protein encoded by an ACS2 gene ortholog/paralog. In yet another embodiment, the heterologous gene coding for the ACS2 protein is present in a single copy in the recombinant microbial host cell.
In addition, the one or more proteins that function to convert acetate into ethanol can be an acetylating acetaldehyde dehydrogenase, an acetylating acetaldehyde dehydrogenase variant, an acetylating acetaldehyde dehydrogenase fragment or be encoded by a gene ortholog of the gene encoding the acetylating acetaldehyde dehydrogenase. Exemplary proteins having acetaldehyde dehydrogenase can be encoded, for example by one of the following genes Escherichia coli Gene ID: 945837, Shewanella oneidensis Gene ID: 1169879, Streptococcus mutans Gene ID: 1029722, Clostridium acetobutylicum Gene ID: 1116040, Enterococcus faecalis Gene ID: 1199789, Yersinia pestis Gene ID: 1175014, Lactobacillus acidophilus Gene ID: 3252921, Lactobacillus plantarum Gene ID: 1061605, Clostridioides difficile Gene ID: 4915990 and 4913165, Vibrio fischeri Gene ID: 3278124, Yersinia enterocolitica subsp. enterocolitica Gene ID: 4715506, Streptococcus mitis Gene ID: 8797547, Streptococcus suis Gene ID: 8154061, Streptococcus pneumoniae Gene ID: 933809, Streptococcus sanguinis Gene ID: 4808056, Lactococcus lactis subsp. lactis Gene ID: 1115832, Streptococcus agalactiae Gene ID: 1012803, Clostridium botulinum Gene ID: 5400197, Shigella dysenteriae Gene ID: 3796690, Salmonella enterica subsp. enterica serovar Typhimurium Gene ID: 1253268, Shigella flexneri Gene ID: 1024221, Escherichia coli Gene ID: 7158044, 7151810, 7150297 and 7150296, Clostridium botulinum Gene ID: 5184600, Gossypium hirsutum Gene ID: 107924008 and 107911678, Gossypium raimondii Gene ID: 105802323, Cryptosporidium parvum Gene ID: 3374407, Danio rerio Gene ID: 492710, Alligator sinensis Gene ID: 102375576, Odobenus rosmarus divergens Gene ID: 101383414, Felis catus Gene ID: 101082028, Staphylococcus epidermidis (GenBank Accession Number WP_002505668.1), Shewanella oneidensis (GenBank Accession Number WP_011072193.10), Citrobacter pasteurii (GenBank Accession Number WP_005126398.1), Lactobacillus sakei (GenBank Accession Number WP_011374088.1), Lactobacillus plantarum (GenBank Accession Number WP_003643605.1), Brevibacillus laterosporus (GenBank Accession Number WP_003339465.1), Olsenella uli (GenBank Accession Number WP_013251192.1), Lactobacillus plantarum (GenBank Accession Number WP_015379735.1), Entamoeba histolytica (GenBank Accession Number Q24803.1), Clostridium ljungdahlii (GenBank Accession Number WP_013238313.1), Piromyces sp. (GenBank Accession Number AAQ22352) and Bifidobacterium adolescentis (GenBank Accession Number CUN50402 or SEQ ID NO: 1). In embodiments, the one or more proteins that function to convert acetate into ethanol is a bifunctional acetaldehyde-coA/alcohol dehydrogenase.
As indicated above, the protein having acetylating acetaldehyde dehydrogenase activity can be a bifunctional protein which can also exhibit an alcohol dehydrogenase activity such as, for example, an ADHE protein from Bifidobacterium adolescentis. The protein having acetylating acetaldehyde dehydrogenase activity can be an ADHE protein (such as, for example, the one having the amino acid sequence of SEQ ID NO: 1), an ADHE protein variant, an ADHE protein fragment or a protein encoded by an ADHE gene ortholog/paralog. In yet another embodiment, the heterologous gene coding for the ADHE protein can be present in one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve copies or more copies in the recombinant microbial host cell. In an embodiment, the heterologous gene coding for the ADHE protein can be present in four copies in the recombinant microbial host cell. In another embodiment, the heterologous gene coding for the ADHE protein can be present in eight copies in the recombinant microbial host cell. In a further embodiment, the heterologous gene coding for the ADHE protein can be present in ten copies in the recombinant microbial host cell. In still another embodiment, the heterologous gene coding for the ADHE protein can be present in twelve copies in the recombinant microbial host cell.
In addition, the one or more proteins that function to convert acetate into ethanol can be an alcohol dehydrogenase, an alcohol dehydrogenase variant, an alcohol dehydrogenase fragment or be encoded by a gene ortholog of the gene encoding the alcohol dehydrogenase. Exemplary proteins having alcohol dehydrogenase can be encoded, for example by one of the following genes Mus musculus Gene ID: 11522, Saccharomyces cerevisiae Gene ID: 854068, Rattus norvegicus Gene ID: 24172, Arabidopsis thaliana Gene ID: 844047, Zea mays Gene ID: 542363, Schizosaccharomyces pombe Gene ID: 2538902, Chlamydomonas reinhardtii Gene ID: 5729132, Solanum tuberosum Gene ID: 102577519, Xenopus tropicalis Gene ID: 496861, Vitis vinifera Gene ID: 100232853, Candida albicans Gene ID: 3636489, Volvox carteri f. nagariensis Gene ID: 9620963, Cucumis melo Gene ID: 103500074, Lactobacillus plantarum Gene ID: 1061600, Aquifex aeolicus Gene ID: 1192812, Scheffersomyces stipitis Gene ID: 4836752, Spathaspora passalidarum Gene ID: 18875210, Serpula lacrymans var. lacrymans Gene ID: 18820813, Glycine max Gene ID: 100801552, Neurospora crassa Gene ID: 3873329, Drosophila virilis Gene ID: 6634390, Drosophila mojavensis Gene ID: 6576953, Homo sapiens Gene ID: 124, Rattus norvegicus Gene ID: 29646, Gallus gallus Gene ID: 771920, Bos taurus Gene ID: 280982, Oryctolagus cuniculus Gene ID: 100009283, Oryza sativa Gene ID: 4350053, Hipposideros armiger Gene ID: 109392935, Anas platyrhynchos Gene ID: 101804666, Xenopus laevis Gene ID: 398377, Ceratitis capitata Gene ID: 101454300, Oryza brachyantha Gene ID: 102719808, Gorilla gorilla Gene ID: 101142845, Bactrocera oleae Gene ID: 106621040, Musa acuminata Gene ID: 103995941 and 103982733, Castor canadensis Gene ID: 109695326, Rhinolophus sinicus Gene ID: 109461442, Brassica napus Gene ID: 106392161, Brassica oleracea Gene ID: 106300708, Brassica rapa Gene ID: 103832166, Pelodiscus sinensis Gene ID: 102452388, Mus musculus 110997 and 110991, Saccharomyces eubayanus Gene ID: 28931457, Schizosaccharomyces cryophilus Gene ID: 25036848 and 25036707, Schizosaccharomyces octosporus Gene ID: 25031898, Schizosaccharomyces japonicus Gene ID: 7050092, 7049104 and 7048162, Candida orthopsilosis Gene ID: 14541766, Aspergillus nidulans Gene ID: 2868277, Xenopus laevis Gene ID: 373778, Pyrococcus furiosus Gene ID: 1467904, Clostridioides difficile Gene ID: 31354717, Clostridioides difficile Gene ID: 31351817, Methanococcus maripaludis Gene ID: 2762190, Thermotoga petrophila Gene ID: 29653443, Vibrio tubiashii Gene ID: 23447604, Clostridium botulinum Gene ID: 19965636, Pyrococcus furiosus Gene ID: 13301033, Methanococcus maripaludis Gene ID: 10982346, Vibrio orientalis Gene ID: 25686470, Bacteroides vulgatus Gene ID: 5301727, Caldicellulosiruptor bescii Gene ID: 31773596, Brachyspira hyodysenteriae Gene ID: 31720359, Methanobrevibacter sp. Gene ID: 1579878, Vibrio tasmaniensis Gene ID: 7159841, Clostridioides difficile Gene ID: 4916648 and 4913210, Thermotoga maritima Gene ID: 896938, Desulfovibrio vulgaris str. Hildenborough Gene ID: 2793915, Bacteroides cellulosilyticus Gene ID: 29610521, Eisenbergiella tayi Gene ID: 31715080, Clostridium beijerinckii Gene ID: 31665570, Dictyoglomus turgidum Gene ID: 7083157, Homo sapiens Gene ID: 125, Mus musculus Gene ID: 26876, Saccharomyces cerevisiae Gene ID: 852442, Mus musculus Gene ID: 11668, Homo sapiens Gene ID: 131, Mus musculus Gene ID: 11529, Saccharomyces cerevisiae Gene ID: 852636 and 851386, Schizosaccharomyces pombe Gene ID: 2542714, Streptomyces coelicolor Gene ID: 1095683, Nicotiana tabacum Gene ID: 107830910, Morus notabilis Gene ID: 21387053 and 21384487, Candida dubliniensis Gene ID: 8048415, 8045940 and 8044976, Nicotiana attenuata Gene ID: 109208159 and 109207487, Zeugodacus cucurbitae Gene ID: 105211861, Bactrocera latifrons Gene ID: 108965731, Malus domestica Gene ID: 103428551 and 103409572 and Entamoeba histolytica (SEQ ID NO: 4).
As indicated above, in an embodiment, the protein having alcohol dehydrogenase activity can be a bifunctional protein which can also exhibit an acetaldehyde dehydrogenase activity such as, for exam, an ADHE protein from Bifidobacterium adolescentis. The protein having alcohol dehydrogenase activity can be an ADHE protein (such as, for example, the one having the amino acid sequence of SEQ ID NO: 1), an ADHE protein variant, an ADHE protein fragment or a protein encoded by an ADHE gene ortholog/paralog. In yet another embodiment, the heterologous gene coding for the ADHE protein can be present in one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve copies in the recombinant microbial host cell.
Acetate can be converted to isopropanol by first converting acetate into acetyl-coA by the enzymatic activity of an acetyl-coA synthase (ACS). Acetyl-coA can then be converted into acetoacetyl-coA by the enzymatic activity of an acetyl-coA acetyltransferase (AcoAAT). Acetoacetyl-coA can then be converted into acetoacetate by the enzymatic activity of an acetoacetyl-coA transferase (ACoAT). Acetoacetate can then be converted into acetone by the enzymatic activity of an acetaacetate decarboxylase (ADC). Acetone can then be converted into isopropanol by the enzymatic activity of a secondary alcohol dehydrogenase (SADH). As such, the one of more proteins that function to convert acetate into isopropanol can be an acetyl-coA synthase (ACS), an acetyl-coA acetyltransferase (AcoAAT), an acetoacetyl-coA transferase (ACoAT), an acetaacetate decarboxylase (ADC) and/or a secondary alcohol dehydrogenase (SADH) as well as corresponding variants and fragments thereof.
iii) Second Metabolic Pathway
In the context of the present disclosure, the recombinant microbial host cell has a second genetic modification for increasing the activity of one or more native and/or heterologous proteins that function in a second (engineered) metabolic pathway to import glycerol inside the recombinant microbial host cell. In some embodiments, this allows the recombinant microbial host cell to comprise one or more recombinantly expressed heterologous proteins that function in a second engineered metabolic pathway to import glycerol in the recombinant microbial host cell. For example, in an embodiment in which the one or more protein is a native protein, the second genetic modification can comprise including an heterologous promoter which increases the expression (and ultimately the activity) of the native protein capable of importing glycerol. In still another example, the second genetic recombination can cause a mutation in the coding sequence of the protein that function to import glycerol which increases the activity of the mutated protein (when compared to the native protein). In yet another example, in an embodiment in which the one or more protein is an heterologous protein, the second genetic modification can comprising introducing one or more copies of the heterologous protein to increase the expression (and ultimately the activity) of the heterologous protein to increase the import of glycerol. As shown in the Examples below, increasing the import of glycerol is advantageous to decrease glycerol production while maintaining adequate robustness (growth rates in the presence of acetate). In the context of the present disclosure, the one or more proteins that function to import glycerol specifically excludes the proteins of the fourth native metabolic pathway (described below).
In order to increase the activity of the protein functioning to import glycerol, it is possible to include, in the recombinant microbial host cell, one or more copies of an heterologous nucleic acid molecule encoding the protein functioning to import glycerol. For example, the recombinant microbial host cell can have one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve or more copies of the heterologous nucleic acid molecule encoding the protein functioning to import glycerol. In an embodiment, the recombinant microbial host cell comprises between four and eight copies of the heterologous nucleic acid molecule encoding the protein functioning to import glycerol. In an embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) two copies of the heterologous nucleic acid molecule encoding the protein functioning to import glycerol. In another embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) three copies of the heterologous nucleic acid molecule encoding the protein functioning to import glycerol. In yet another embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) four copies of the heterologous nucleic acid molecule encoding the protein functioning to import glycerol. In still another embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) five copies of the heterologous nucleic acid molecule encoding the protein functioning to import glycerol. In a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) six copies of the heterologous nucleic acid molecule encoding the protein functioning to import glycerol. In yet a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) seven copies of the heterologous nucleic acid molecule encoding the protein functioning to import glycerol. In still a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) eight copies of the heterologous nucleic acid molecule encoding the protein functioning to import glycerol. In an embodiment, the recombinant microbial host cell comprises four copies of the heterologous nucleic acid molecule encoding the protein functioning to import glycerol. The heterologous nucleic acid molecule can be independently replicating or integrated in the recombinant microbial host cell. When the heterologous nucleic acid molecule is integrated in the recombinant microbial host cell, it is preferably positioned at neutral integration site. When more than one copy of the heterologous nucleic acid molecule encoding the protein functioning to import glycerol is introduced in the recombinant microbial host cell, each of the copy can be integrated at one or more (the same or different) integration sites.
Exemplary proteins capable of functioning to import glycerol include aquaporins as well as glycerol facilitators. The FPS1/FPS2 protein (encoded by Gene ID 850683 in Saccharomyces cerevisiae) is a glycerol facilitator capable of importing glycerol inside the cell. As such, the protein capable of functioning to import glycerol can be a FPS1 protein, a FPS1 protein variant, a FPS1 protein fragment or a protein encoded by a FPS1 gene ortholog. The FPS1 protein can be derived, for example, from Saccharomyces cerevisiae or a corresponding ortholog found in Pachysolen tannophilus, Komagataella pastoris, Yarrowia lipolytica and/or Cyberlindnera jadinii. 
Another exemplary protein capable of functioning to import glycerol is the glucose-inactivated glycerol/proton symporter STL1. The native function of the STL1 protein is the uptake of glycerol from the extracellular environment. STL1 is a member of the Sugar Porter Family which is part of the Major Facilitator Superfamily (MFS). STL1 transports glycerol by proton symport meaning that the glycerol and protons are cotransported through STL1 into the cell. In S. cerevisiae, STL1 expression and glycerol uptake is typically repressed when carbon sources such as glucose are available. When the cells undergo high osmotic shock, STL1 is expressed in order to help deal with the osmotic shock by transporting the osmoprotectant glycerol into the cell and increasing the intracellular glycerol concentration. In the context of the present disclosure, the protein functioning to import glycerol can be the STL1 protein, a variant of the STL1 protein, a fragment of the STL1 protein or a protein encoded by a STL1 gene ortholog/paralog.
The heterologous protein functioning to import glycerol can be encoded by a STL1 gene. The STL1 protein is natively expressed in yeasts and fungi, therefore the heterologous protein functioning to import glycerol can be derived from yeasts and fungi. STL1 genes encoding the STL1 protein include, but are not limited to, Saccharomyces cerevisiae Gene ID: 852149, Candida albicans Gene ID 3703976, Kluyveromyces lactis Gene ID: 2896463, Ashbya gossypii Gene ID: 4620396, Eremothecium sinecaudum Gene ID: 28724161, Torulaspora delbrueckii Gene ID: 11505245, Lachancea thermotolerans Gene ID: 8290820, Phialophora attae Gene ID: 28742143, Penicillium digitatum Gene ID: 26229435, Aspergillus oryzae Gene ID: 5997623, Aspergillus fumigatus Gene ID: 3504696, Talaromyces atroroseus Gene ID: 31007540, Rasamsonia emersonii Gene ID: 25315795, Aspergillus flavus Gene ID: 7910112, Aspergillus terreus Gene ID: 4322759, Penicillium chrysogenum Gene ID: 8310605, Alternaria alternata Gene ID: 29120952, Paraphaeosphaeria sporulosa Gene ID: 28767590, Pyrenophora tritici-repentis Gene ID: 6350281, Metarhizium robertsii Gene ID: 19259252, Isaria fumosorosea Gene ID: 30023973, Cordyceps militaris Gene ID: 18171218, Pochonia chlamydosporia Gene ID: 28856912, Metarhizium majus Gene ID: 26274087, Neofusicoccum parvum Gene ID: 19029314, Diplodia corticola Gene ID: 31017281, Verticillium dahliae Gene ID: 20711921, Colletotrichum gloeosporioides Gene ID: 18740172, Verticillium albo-atrum Gene ID: 9537052, Paracoccidioides lutzii Gene ID: 9094964, Trichophyton rubrum Gene ID: 10373998, Nannizzia gypsea Gene ID: 10032882, Trichophyton verrucosum Gene ID: 9577427, Arthroderma benhamiae Gene ID: 9523991, Magnaporthe oryzae Gene ID: 2678012, Gaeumannomyces graminis var. tritici Gene ID: 20349750, Togninia minima Gene ID: 19329524, Eutypa lata Gene ID: 19232829, Scedosporium apiospermum Gene ID: 27721841, Aureobasidium namibiae Gene ID: 25414329, Sphaerulina musiva Gene ID: 27905328 as well as Pachysolen tannophilus GenBank Accession Numbers JQ481633 and JQ481634, Saccharomyces paradoxus STL1 (encoded by SEQ ID NO: 5 and shown in SEQ ID NO: 6) and Pichia sorbitophila (encoded by SEQ ID NO: 7 and shown in SEQ ID NO: 8). In an embodiment, the STL1 protein is encoded by Saccharomyces cerevisiae Gene ID: 852149 and can have, for example, the amino acid sequence of SEQ ID: 2 (a variant thereof or a fragment thereof). In still another embodiment, one, two, three, four, five, six, seven, eight, nine, ten, eleven or twelve copies of a heterologous gene coding for the STL1 protein are included in the recombinant microbial host cell. In yet another embodiment, four copies of a heterologous gene coding for the STL1 protein are included in the recombinant microbial host cell.
The heterologous protein functioning to import glycerol can be encoded by a STL1 gene as indicated herein or a STL1 gene ortholog. The heterologous protein functioning to import glycerol can be a STL1 protein as defined herein, a variant of the STL1 protein and/or a fragment of the STL1 protein. In addition, when more than one copy of the heterologous STL1 is included in the recombinant microbial cell, the plurality of heterologous nucleic acid molecules encoding the STL1 protein could be the same or different, integrated at the same or different integration sites.
Optionally, the microbial host can have a further genetic modification for decreasing the (biological) activity of a protein which functions to export glycerol (e.g., actively transport glycerol from inside the cell). The recombinant microbial host cells can have at least one genetic modification allowing it to decrease the (biological) activity of a protein which functions to export glycerol (e.g., actively transport glycerol to outside the cell). Still in the context of the present disclosure, the activity of the protein functioning to export glycerol in the recombinant microbial host cell is decreased in glycolytic conditions. The FPS1 protein is an exemplary protein which functions to export glycerol. The FPS1 protein is a channel protein located in the plasma membrane that controls the accumulation and release of glycerol in yeast osmoregulation. As such, the first genetic modification can include reducing or deleting the expression of the gene encoding the FPS1 protein during glycolytic conditions.
iv) Third Metabolic Pathway
In the context of the present disclosure, the recombinant microbial host cell comprises a third genetic modification for increasing the activity of one or more native and/or heterologous protein in a third (engineered) metabolic pathway to convert C5 carbohydrate (such as arabinose, xylose or a combination thereof) into ethanol. In some embodiments, this allows the recombinant microbial host cell to comprise one or more recombinantly expressed heterologous proteins that function in a third metabolic pathway to convert a C5 carbohydrate into the alcohol in the microbial host cell.
In an embodiment, the C5 carbohydrate is xylose and the recombinant microbial host cell is capable of converting xylose into ethanol. Xylose is a five-carbon monosaccharide that can be metabolized into useful products by a variety of organisms. There are two main pathways of xylose metabolism, each unique in the characteristic enzymes they utilize. One pathway is called the “Xylose Reductase-Xylitol Dehydrogenase” or XR-XDH pathway. Xylose reductase (XR) and xylitol dehydrogenase (XDH) are the two main enzymes used in this method of xylose degradation. XR is responsible for the reduction of xylose to xylitol and is aided by cofactors NADH or NADPH. Xylitol is then oxidized to xylulose by XDH and accomplished generally with the cofactor NAD+ (this can be done, for example, by the activity of an L-xylulose reductase (E.C. 1.1.1.10)). The second pathway is called “Xylose Isomerase” or XI pathway. The enzyme XI is responsible for direct conversion of xylose into xylulose and does not proceed via xylitol as an intermediate. Both pathways create xylulose, although the enzymes utilized are different. After production of xylulose both the XR-XDH and XI pathways proceed through enzyme xylulokinase (XKS), to further modify xylulose into xylulose-5-phosphate where it then enters the pentose phosphate pathway for further catabolism, and e.g. generate ethanol.
As such, the present disclosure provides that the microbial recombinant host cells comprises a third genetic modification for increasing the activity of one or more native or heterologous proteins that function in the third engineered metabolic pathway to convert xylose into ethanol. For example, in an embodiment in which the one or more protein is a native protein, the third genetic modification can include an heterologous promoter which increases the expression (and ultimately the activity) of the native protein to convert xylose into ethanol. In still another example, in an embodiment in which the one or more protein is a native protein, the third genetic modification can cause a mutation in the coding sequence of the protein that function to convert xylose into ethanol which increases the activity of the mutated protein (when compared to the native protein). In yet another example, in an embodiment in which the one or more protein is an heterologous protein, the third genetic modification can include one or more copies of the heterologous protein to increase the expression (and ultimately the activity) of the heterologous protein to convert xylose into ethanol.
In order to increase the activity of the protein functioning to convert xylose into ethanol, it is possible to include, in the recombinant microbial host cell, one or more copies of an heterologous nucleic acid molecule encoding the protein functioning to convert xylose into ethanol. For example, the recombinant microbial host cell can have one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, sixteen or more copies of the heterologous nucleic acid molecule encoding the protein functioning to convert xylose into ethanol. In an embodiment, the recombinant microbial host cell comprises between four and eight copies of the heterologous nucleic acid molecule encoding the protein functioning to convert xylose into ethanol. In an embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) two copies of the heterologous nucleic acid molecule encoding the protein functioning to convert xylose into ethanol. In another embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) three copies of the heterologous nucleic acid molecule encoding the protein functioning to convert xylose into ethanol. In yet another embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) four copies of the heterologous nucleic acid molecule encoding the protein functioning to convert xylose into ethanol. In still another embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) five copies of the heterologous nucleic acid molecule encoding the protein functioning to convert xylose into ethanol. In a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) six copies of the heterologous nucleic acid molecule encoding the protein functioning to convert xylose into ethanol. In yet a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) seven copies of the heterologous nucleic acid molecule encoding the protein functioning to convert xylose into ethanol. In still a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) eight copies of the heterologous nucleic acid molecule encoding the protein functioning to convert xylose into ethanol. In still a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) nine copies of the heterologous nucleic acid molecule encoding the protein functioning to convert xylose into ethanol. In still a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) ten copies of the heterologous nucleic acid molecule encoding the protein functioning to convert xylose into ethanol. In still a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) eleven copies of the heterologous nucleic acid molecule encoding the protein functioning to convert xylose into ethanol. In still a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) twelve copies of the heterologous nucleic acid molecule encoding the protein functioning to convert xylose into ethanol. In still a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) thirteen copies of the heterologous nucleic acid molecule encoding the protein functioning to convert xylose into ethanol. In still a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) fourteen copies of the heterologous nucleic acid molecule encoding the protein functioning to convert xylose into ethanol. In still a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) fifteen copies of the heterologous nucleic acid molecule encoding the protein functioning to convert xylose into ethanol. In still a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) sixteen copies of the heterologous nucleic acid molecule encoding the protein functioning to convert xylose into ethanol. In an embodiment, the recombinant microbial host cell comprises sixteen copies of the heterologous nucleic acid molecule encoding the protein functioning to convert xylose into ethanol. The heterologous nucleic acid molecule can be independently replicating or integrated in the recombinant microbial host cell. When the heterologous nucleic acid molecule is integrated in the recombinant microbial host cell, it is preferably positioned at neutral integration site. When more than one copy of the heterologous nucleic acid molecule encoding the protein functioning to convert xylose into ethanol is introduced in the recombinant microbial host cell, each of the copy can be integrated at one or more (the same or different) integration sites.
As indicated above, an exemplary protein capable of functioning to convert xylose into ethanol is a xylose reductase. Xylose reductases catalyze the conversion of xylose and NADP+ to NADPH and xylitol and are classified in Enzyme Commission Number class 1.1.1.307. The protein having xylose reductase activity can be native or heterologous to the recombinant microbial host cell. As such, the one or more proteins that function to convert xylose into ethanol can be a xylose reductase, a xylose reductase variant, a xylose reductase fragment or be encoded by a gene ortholog of the gene encoding the xylose reductase. Exemplary proteins having xylose reductase activity can be encoded, for example, by one of the following genes Saccharomyces cerevisiae Gene ID: 856504, Candida albicans Gene ID: 3637811, Spathaspora passalidarum Gene ID: 18873850, Spathaspora passalidarum Gene ID: 18873849, Neurospora crassa Gene ID: 3880080, Rhodotorula graminis Gene ID: 28979189, Rhodotorula toruloides Gene ID: 27367976, Coccidioides posadasii Gene ID: 9696920, Neurospora tetrasperma Gene ID: 20825713, Eutypa lata Gene ID: 19231177, Brugia malayi Gene ID: 6102456, Cyberlindnera jadinii Gene ID: 30989853, Cyberlindnera jadinii Gene ID: 30987720, Gloeophyllum trabeum Gene ID: 19299660, Dichomitus squalens Gene ID: 18845177, Sugiyamaella lignohabitans Gene ID: 30035130, Escherichia coli Gene ID: 14575, Enterobacter aerogenes Gene ID: 10792723, Shigella dysenteriae Gene ID: 3799695, Klebsiella pneumoniae subsp. pneumoniae Gene ID: 11849430, Klebsiella pneumoniae subsp. pneumoniae Gene ID: 11846109, Chaetomium globosum Gene ID: 4387651, Xylona heveae Gene ID: 28894354, Sphaerulina musiva Gene ID: 27899106, Aspergillus fumigatus Gene ID: 3507406, Phialocephala scopiformis Gene ID: 28822177, Scheffersomyces stipitis Gene ID: 4839234, Marssonina brunnea f. sp. ‘multigermtubi’ Gene ID: 18765662, Marssonina brunnea f. sp. ‘multigermtubi’ Gene ID: 18760177, Fusarium verticillioides Gene ID: 30067248, Fusarium oxysporum f. sp. lycopersici Gene ID: 28952604, Magnaporthe oryzae Gene ID: 2679231, Magnaporthe oryzae Gene ID: 2676633, Metarhizium robertsii Gene ID: 19254828, Salmo salar Gene ID: 100196319, Scedosporium apiospermum Gene ID: 27728550, Grosmannia clavigera Gene ID: 25974877, Chaetomium thermophilum var. thermophilum Gene ID: 18259733, Penicillium digitatum Gene ID: 26230358, Fusarium graminearum Gene ID: 23548958, Togninia minima Gene ID: 19327575, Togninia minima Gene ID: 19324058, Eutypa lata Gene ID: 19225623, Colletotrichum fioriniae Gene ID: 1903145, Trichoderma reesei Gene ID: 18481522, Coprinopsis cinerea okayama Gene ID: 6016721, Aspergillus oryzae Gene ID: 5991970, Purpureocillium lilacinum Gene ID: 28891088, Pochonia chlamydosporia Gene ID: 28845024, Phialocephala scopiformis Gene ID: 28819819, Moniliophthora roreri Gene ID: 19287580, Candida tropicalis Gene ID: 8298564, Candida tropicalis Gene ID: 8298550, Aspergillus clavatus Gene ID: 4701691, Neosartorya fischeri Gene ID: 4591084, Fusarium verticillioides Gene ID: 30065949, Fusarium oxysporum f. sp. lycopersici Gene ID: 28944059, Metarhizium majus Gene ID: 26274458, Metarhizium brunneum Gene ID: 26242741, Hyphopichia burtonii Gene ID: 30995750, Trametes versicolor Gene ID: 19410447, Gloeophyllum trabeum Gene ID: 19308234, Pichia kudriavzevii Gene ID: 31691310, Diplodia corticola Gene ID: 31011414, Talaromyces atroroseus Gene ID: 31005086, Colletotrichum higginsianum Gene ID: 28864958, Debaryomyces fabryi Gene ID: 26839549, Aspergillus nomius Gene ID: 26811375, Ogataea parapolymorpha Gene ID: 25770833, Wickerhamomyces ciferrii Gene ID: 23465359, Verticillium dahliae Gene ID: 20706550, 20702536 and 20701874, Gaeumannomyces graminis Gene ID: 20348746 and 20344199, Exophiala dermatitidis Gene ID: 20305335, Coniosporium apollinis Gene ID: 19904082, Pestalotiopsis fici Gene ID: 19272170, Pestalotiopsis fici Gene ID: 19269538, Pestalotiopsis fici Gene ID: 19266700, Capronia epimyces Gene ID: 19168745, Colletotrichum gloeosporioides Nara Gene ID: 18744050, 18735990 and 18735559, Candida orthopsilosis Gene ID: 14541546, Nannizzia gypsea Gene ID: 10029154 and 10025413, Verticillium albo-atrum Gene ID: 9537026, 9536837 and 9530694, Arthroderma otae Gene ID: 9229156 and 9223336, Ajellomyces dermatitidis Gene ID: 8508433, Uncinocarpus reesii Gene ID: 8444043, Talaromyces stipitatus Gene ID: 8100993, Candida dubliniensis Gene ID: 8048448, Aspergillus flavus Gene ID: 7917889, Talaromyces marneffei Gene ID: 7027728, Pyrenophora tritici-repentis Gene ID: 6347932, Ajellomyces capsulatus Gene ID: 5446848, Aspergillus niger Gene ID: 88 4977114, Coccidioides immitis Gene ID: 4563516, Aspergillus terreus Gene ID: 4317317, Legionella pneumophila subsp. pneumophila Gene ID: 19833631, Drosophila serrata Gene ID: 110180493, Drosophila kikkawai Gene ID: 108085888, Drosophila biarmipes Gene ID: 108031656, Lingula anatina Gene ID: 106181656, Lingula anatina Gene ID: 106171375, Wasmannia auropunctata Gene ID: 105461757, Aspergillus nidulans Gene ID: 2876201 and Gossypium arboreum Gene ID: 108452823.
As indicated above, an exemplary protein capable of functioning to convert xylose into ethanol is a xylitol dehydrogenase. Xylitol dehydrogenases catalyze the conversion of xylitol and NAD(P)+ to NAD(P)H and xylulose and are classified in Enzyme Commission Number classes 1.1.1.9, 1.1.1.10, and 1.1.1.B19. The protein having xylitol dehydrogenase activity can be native or heterologous to the recombinant microbial host cell. As such, the one or more proteins that function to convert xylose into ethanol can be a xylitol dehydrogenase, a xylitol dehydrogenase variant, a xylitol dehydrogenase fragment or be encoded by a gene ortholog of the gene encoding the xylitol dehydrogenase. Exemplary proteins having xylitol dehydrogenase activity can be encoded, for example, by one of the following genes Scheffersomyces stipitis Gene ID: 4852013, Aspergillus fumigatus Gene ID: 3504379, Neosartorya fischeri Gene ID: 4588723, Aspergillus flavus Gene ID: 7916321, Burkholderia pseudomallei Gene ID: 3096519, Spathaspora passalidarum Gene ID: 18873119, Marssonina brunnea f. sp. ‘multigermtubi’ Gene ID: 18762909, Aspergillus fumigatus Gene ID: 3510018, Trichosporon asahii var. asahii Gene ID: 25989339, Grosmannia clavigera Gene ID: 25976562, Togninia minima Gene ID: 19323828, Eutypa lata Gene ID: 19231523, Zymoseptoria tritici Gene ID: 13400430, Metarhizium acridum Gene ID: 19248315, Metarhizium brunneum Gene ID: 26237334, Colletotrichum gloeosporioides Gene ID: 18746313, Colletotrichum gloeosporioides Gene ID: 18744455, Trichophyton verrucosum Gene ID: 9581453, Candida tenuis Gene ID: 18248090, Neurospora crassa Gene ID: 3880931, Kalmanozyma brasiliensis Gene ID: 27418672, Rhodotorula toruloides Gene ID: 27365983, Pseudozyma antarctica Gene ID: 26304285, Grosmannia clavigera Gene ID: 25977209, Grosmannia clavigera Gene ID: 25977138, Tilletiaria anomala Gene ID: 25266716, Tilletiaria anomala Gene ID: 25262877, Cryptococcus neoformans var. grubii Gene ID: 23890423 and 23888063, Ustilago maydis Gene ID: 23562964 and 23561726, Cryptococcus gattii Gene ID: 10189635 and 10186924, Cryptococcus neoformans var. neoformans Gene ID: 3256238 and 3254324, Penicillium digitatum Gene ID: 26232154, Beauveria bassiana Gene ID: 19887394, Togninia minima Gene ID: 19329338, Togninia minima Gene ID: 19326215, Eutypa lata Gene ID: 19232345, Neofusicoccum parvum Gene ID: 19019499, Spathaspora passalidarum Gene ID: 18872743, Trichoderma reesei Gene ID: 18489305, Cordyceps militaris Gene ID: 18169004, 18167411 and 18165647, Aspergillus fumigatus Gene ID: 3510395, Aspergillus fumigatus Gene ID: 3504124, Moniliophthora roreri Gene ID: 19295526, Paracoccidioides lutzii Gene ID: 9096001, Aspergillus clavatus Gene ID: 4700891, Neosartorya fischeri Gene ID: 4591951, Metarhizium majus Gene ID: 26277956 and 26273006, Metarhizium brunneum Gene ID: 26244190, Trametes versicolor Gene ID: 19409382, Coniophora puteana Gene ID: 19200989, Punctularia strigosozonata Gene ID: 18887059, Auricularia subglabra Gene ID: 18846596, Dichomitus squalens Gene ID: 18844667 and 18835513, Fomitiporia mediterranea Gene ID: 18674855, 18670465 and 8670457, Colletotrichum gloeosporioides Gene ID: 18748503, 18748273 and 18737879, Salpingoeca rosetta Gene ID: 16074109, Ajellomyces dermatitidis Gene ID: 8506409, Talaromyces stipitatus Gene ID: 8110045, Aspergillus flavus Gene ID: 7910668, Talaromyces marneffei Gene ID: 7023775, Botryotinia fuckeliana Gene ID: 5432604, Cryptococcus gattii Gene ID: 10190105, Penicillium digitatum Gene ID: 26233981, Neofusicoccum parvum Gene ID: 19029447, Coprinopsis cinerea Gene ID: 6013820, Moniliophthora roreri Gene ID: 19281434, Aspergillus clavatus Gene ID: 4704682, Trichophyton rubrum Gene ID: 10375531, Arthroderma benhamiae Gene ID: 9522667, Arthroderma otae Gene ID: 9228403, Talaromyces stipitatus Gene ID: 8105295, Candida dubliniensis CD36Gene ID: 8049664, Aspergillus flavus Gene ID: 7910657, Talaromyces marneffei Gene ID: 7030599, Agrobacterium fabrum Gene ID: 1136192, Serratia fonticola Gene ID: 32347422, Salmonella sp. Gene ID: 13920602, Aspergillus flavus Gene ID: 7914649, Candida dubliniensis Gene ID: 8048370, Gluconobacter oxydans Gene ID: 29878874, Ruegeria mobilis Gene ID: 28251902, Gluconobacter oxydans Gene ID: 29878967, Aspergillus terreus Gene ID: 4317086, Malassezia pachydermatis Gene ID: 28726616, Rhodotorula graminis Gene ID: 28974966, Xylona heveae Gene ID: 28900298, Candida auris Gene ID: 28880885, Galdieria sulphuraria Gene ID: 17088923, Isaria fumosorosea Gene ID: 30026285 and 30021036, Purpureocillium lilacinum Gene ID: 28892276 and 28891262, Pochonia chlamydosporia Gene ID: 28851412 and 28851146, Metarhizium majus Gene ID: 26277955, Metarhizium brunneum Gene ID: 26237333, Hyphopichia burtonii Gene ID: 30993894, Ascoidea rubescens Gene ID: 30968501, Kwoniella bestiolae Gene ID: 30208129 and 30205267, Tsuchiyaea wingfieldii Gene ID: 30196836 and 30189647, Kwoniella pini Gene ID: 30175369 and 30171228, Kwoniella mangroviensis Gene ID: 30165268 and 30161756, Cutaneotrichosporon oleaginosus Gene ID: 28983728 and 28981978, Kwoniella dejecticola Gene ID: 28966656 and 28965491, Aspergillus nidulans Gene ID: 2868103, Aspergillus terreus Gene ID: 4317242, Gluconobacter oxydans Gene ID: 29878913 and Saccharomyces cerevisiae Gene ID: 850759.
As indicated above, an exemplary protein capable of functioning to convert xylose into ethanol is a xylose isomerase. Xyloses isomerases catalyze the conversion of D-xylose to D-xylulose and are classified with the Enzymatic Commission class 5.3.1.5. The protein having xylose isomerase activity can be native or heterologous to the recombinant microbial host cell. As such, the one or more proteins that function to convert xylose into ethanol can be a xylose isomerase, a xylose isomerase variant, a xylose isomerase fragment or be encoded by a gene ortholog of the gene encoding the xylose isomerase. The xylose isomeras can be derived from a prokaryotic or a eukaryotic cell such as, for example, Bacteroides thetaiotamicron, Parabacteroides distasonis, Cyllamyces aberensis, Abiotrophia defectiva, Chitinophaga pinensis, Prevotella ruminicola, Piromyces equi, Lachnoclostridium phytofermentans, Clostridium phytofermentans and/or Catonella morbi. Exemplary proteins having xylose isomerase activity can be encoded, for example, by one of the following genes Escherichia coli Gene ID: 948141, Streptomyces coelicolor Gene ID: 1096592, Bacillus licheniformis Gene ID: 3030684, Pseudomonas syringae Gene ID: 1184658, Yersinia enterocolitica subsp. enterocolitica Gene ID: 4716464, Piromyces sp. (GenBank Accession Number CAB76571), Catonella morbi (GenBank Accession Number WP_023355929) and Bacteroides thetaiotamicron (GenBank Accession Number WP_055217966). In some embodiments, the protein having xylose isomerase activity can be provided in a chimeric form (e.g., a chimeric xylose isomerase), such as, for example, those described in US Patent Application published under 2016/040152. In an embodiment, the xylose isomerase can be from Catonella morbi (GenBank Accession Number WP_023355929 or SEQ ID NO: 9, a variant thereof or a fragment thereof).
As indicated above, an exemplary protein capable of functioning to convert xylose into ethanol is an xylulokinase (XKS). Xylulokinases catalyze the conversion of ATP and D-xylulose into ADP and D-xylulose 5-phosphate and are classified in the Enzyme Commission Number class 2.7.1.17. The protein having xylulokinase activity can be native or heterologous to the recombinant microbial host cells. As such, the one or more proteins that function to convert xylose into ethanol can be a xylulokinase, a xylulokinase variant, a xylulokinase fragment or be encoded by a gene ortholog of the gene encoding the xylulokinase. Exemplary proteins having xylulokinase activity can be encoded, for example by one of the following genes Saccharomyces cerevisiae Gene ID: 853108, Candida albicans Gene ID: 3648306, Scheffersomyces stipitis Gene ID: 4850923, Spathaspora passalidarum Gene ID: 18872670, Sugiyamaella lignohabitans Gene ID: 30034300, Saccharomyces eubayanus Gene ID: 28931298, Candida orthopsilosis Gene ID: 14538150 and Candida dubliniensis Gene ID: 8047525. In an embodiment, the protein having xylulokinase activity is a XKS1 protein, a XKS1 protein variant, a XKS1 protein fragment or a protein encoded by a XKS1 gene ortholog/paralog. In still another embodiment, the XKS1 protein is derived from Saccharomyces cerevisiae. In still a further embodiment, the XKS1 protein has the amino acid sequence of SEQ ID NO: 19, is a variant thereof or is a fragment thereof. In yet another embodiment, the heterologous gene coding for the XKS1 protein is present in two copies in the recombinant microbial host cell.
Once D-xylulose 5-phosphate is formed, it can enter the pentose phosphate pathway and be processed (directly or indirectly) by one or more of a transketolase, a transaldolase, a ribose-5-phosphate isomerase and ribulose-5-phosphate epimerase.
As indicated above, an exemplary protein capable of functioning to convert xylose into ethanol is a transketolase (TLK). Transketolases catalyze the conversion of D-xylulose-5-phosphate and aldose erythrose-4-phosphate into fructose 6-phosphate and glyceraldehyde-3-phosphate as well as the conversion of D-xylulose-5-phosphate and D-ribose-5-phosphate into sedoheptulose-7-phosphate and glyceraldehyde-3-phosphate. Transketolases are classified in the Enzyme Commission Number class 2.2.1.1. The protein having transketolase activity can be native or heterologous to the recombinant microbial host cell. As such, the one or more proteins that function to convert xylose into ethanol can be a transketolase, a transketolase variant, a transketolase fragment or be encoded by a gene ortholog/paralog of the gene encoding the transketolase. Exemplary proteins having transketolase activity can be encoded, for example by one of the following genes Saccharomyces cerevisiae Gene ID: 856188 and Saccharomyces cerevisiae Gene ID: 852414. In an embodiment, the protein having transketolase activity is a TLK1 protein, a TLK1 protein variant, a TLK1 protein fragment or a protein encoded by a TLK1 gene ortholog. In still another embodiment, the TLK1 protein is derived from Saccharomyces cerevisiae. In still a further embodiment, the TLK1 protein has the amino acid sequence of SEQ ID NO: 18, is a variant thereof or is a fragment thereof. In yet another embodiment, the heterologous gene coding for the TLK1 protein is present in a single copy in the recombinant microbial host cell.
As indicated above, an exemplary protein capable of functioning to convert xylose into ethanol is a transaldolase (TAL), such as, for example a sedoheptulose-7-phosphate:D-glyceraldehyde-3-phosphate transaldolase. Transaldolases catalyze the conversion of sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate into erythrose 4-phosphate and fructose 6-phosphate and are classified in the Enzyme Commission Number class 2.2.1.2. The protein having transaldose activity can be native or endogenous to the recombinant microbial host cell. As such, the one or more proteins that function to convert xylose into ethanol can be encoded, for example, by one of the following genes Saccharomyces cerevisiae Gene ID: 851068 and 852934. In an embodiment, the protein having transaldose activity is a TAL1 protein, a TAL1 protein variant, a TAL1 protein fragment or a protein encoded by a TAL1 gene ortholog/paralog. In still another embodiment, the TAL1 protein is derived from Saccharomyces cerevisiae. In still another embodiment, the TAL1 protein has the amino acid sequence of SEQ ID NO: 17, is a variant thereof or a fragment thereof. In yet another embodiment, the heterologous gene coding for the TAL1 protein is present in a single copy in the recombinant microbial host cell.
As indicated above, an exemplary protein capable of functioning to convert xylose into ethanol is a ribose-5-phosphate isomerase. Ribose-5-phosphate isomerases catalyze the conversion between ribose-5-phosphate and ribulose-5-phosphate and are classified in the Enzyme Commission Number class 5.3.1.6. The protein having ribose-5-phosphate isomerase can be native or heterologous to the recombinant microbial host cell. As such, the one or more proteins that function to convert xylose into ethanol can be encoded, for example, by one of the following genes Saccharomyces cerevisiae Gene ID: 854262, Sugiyamaella lignohabitans Gene ID: 30035791, Spathaspora passalidarum Gene ID: 18870249, Candida albicans Gene ID: 3636574, Scheffersomyces stipitis Gene ID: 4837111 and Zymoseptoria tritici Gene ID: 13398936. In an embodiment, the protein having ribose-5-phosphate isomerase activity is a RKI1 protein, a RKI1 protein variant, a RKI1 protein fragment or a protein encoded by a RKI1 gene ortholog/paralog. In still another embodiment, the RKI1 protein is derived from Saccharomyces cerevisiae. In a further embodiment, the RKI1 protein has the amino acid sequence of SEQ ID NO 13, is a variant thereof or a fragment thereof. In yet another embodiment, the heterologous gene coding for the RKI1 protein is present in a single copy in the recombinant microbial host cell.
As indicated above, an exemplary protein capable of functioning to convert xylose into ethanol is a ribulose-phosphate 3-epimerase. Ribulose-phosphate 3-epimerases catalyze the conversion of conversion between D-ribulose 5-phosphate and D-xylulose 5-phosphate and are classified in the Enzyme Commission Number class 5.1.3.1. The protein having ribulose-phosphate 3-epimerase activity can be native or heterologous to the recombinant microbial host cell. As such, the one or more proteins that function to convert xylose into ethanol can be encoded, for example, by one of the following genes Saccharomyces cerevisiae Gene ID: 853322, Sugiyamaella lignohabitans Gene ID: 30033351, Thalassiosira pseudonana Gene ID: 7446232, Chlamydomonas reinhardtii Gene ID: 5716597, Scheffersomyces stipitis Gene ID: 4840854, Aureococcus anophagefferens Gene ID: 20229018 and Zymoseptoria tritici Gene ID: 13398961. In an embodiment, the protein having ribulose-5-phosphate 3-epimerase activity is a RPE1 protein, a RPE1 protein variant, a RPE1 protein fragment or a protein encoded by a RPE1 gene ortholog. In still another embodiment, the RPE1 protein is derived from Saccharomyces cerevisiae. In still another embodiment, the RPE1 protein has the amino acid sequence of SEQ ID NO: 15, is a variant thereof or is a fragment thereof. In yet another embodiment, the heterologous gene coding for the RPE1 protein is present in a single copy in the recombinant microbial host cell.
In another complementary or alternative embodiment, the C5 carbohydrate is arabinose. Much like xylose, arabinose can be metabolized into useful products by a variety of organisms. The conversion of arabinose into xylose may require the activity of one or more of an arabinose transporter, an arabinose isomerase (AI), a ribulokinase (RK) and a ribulose 5-phosphate epimerase (RSPE).
As such, the present disclosure provides a third genetic modification for increasing the activity of one or more proteins that function in the third engineered metabolic pathway to convert arabinose into ethanol. For example, in an embodiment in which the one or more protein is a native protein, the third genetic modification can include an heterologous promoter which increases the expression (and ultimately the activity) of the native protein to convert arabinose into ethanol. In still another example, in an embodiment in which the one or more protein is a native protein, the third genetic modification can cause a mutation in the coding sequence of the protein that function to convert arabinose into ethanol which increases the activity of the mutated protein (when compared to the native protein). In yet another example, in an embodiment in which the one or more protein is an heterologous protein, the third genetic modification can include one or more copies of the heterologous protein to increase the expression (and ultimately the activity) of the heterologous protein to convert arabinose into ethanol.
In order to increase the activity of the protein functioning to convert arabinose into ethanol, it is possible to include, in the recombinant microbial host cell, one or more copies of an heterologous nucleic acid molecule encoding the protein functioning to convert arabinose into ethanol. For example, the recombinant microbial host cell can have one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, thirteen, fourteen, fifteen, sixteen or more copies of the heterologous nucleic acid molecule encoding the protein functioning to convert arabinose into ethanol. In an embodiment, the recombinant microbial host cell comprises between four and eight copies of the heterologous nucleic acid molecule encoding the protein functioning to convert arabinose into ethanol. In an embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) two copies of the heterologous nucleic acid molecule encoding the protein functioning to convert arabinose into ethanol. In another embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) three copies of the heterologous nucleic acid molecule encoding the protein functioning to convert arabinose into ethanol. In yet another embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) four copies of the heterologous nucleic acid molecule encoding the protein functioning to convert arabinose into ethanol. In still another embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) five copies of the heterologous nucleic acid molecule encoding the protein functioning to convert arabinose into ethanol. In a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) six copies of the heterologous nucleic acid molecule encoding the protein functioning to convert arabinose into ethanol. In yet a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) seven copies of the heterologous nucleic acid molecule encoding the protein functioning to convert arabinose into ethanol. In still a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) eight copies of the heterologous nucleic acid molecule encoding the protein functioning to convert arabinose into ethanol. In still a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) nine copies of the heterologous nucleic acid molecule encoding the protein functioning to convert arabinose into ethanol. In still a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) ten copies of the heterologous nucleic acid molecule encoding the protein functioning to convert arabinose into ethanol. In still a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) eleven copies of the heterologous nucleic acid molecule encoding the protein functioning to convert arabinose into ethanol. In still a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) twelve copies of the heterologous nucleic acid molecule encoding the protein functioning to convert arabinose into ethanol. In still a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) thirteen copies of the heterologous nucleic acid molecule encoding the protein functioning to convert arabinose into ethanol. In still a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) fourteen copies of the heterologous nucleic acid molecule encoding the protein functioning to convert arabinose into ethanol. In still a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) fifteen copies of the heterologous nucleic acid molecule encoding the protein functioning to convert arabinose into ethanol. In still a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) sixteen copies of the heterologous nucleic acid molecule encoding the protein functioning to convert arabinose into ethanol. In an embodiment, the recombinant microbial host cell comprises sixteen copies of the heterologous nucleic acid molecule encoding the protein functioning to convert arabinose into ethanol. The heterologous nucleic acid molecule can be independently replicating or integrated in the recombinant microbial host cell. When the heterologous nucleic acid molecule is integrated in the recombinant microbial host cell, it is preferably positioned at neutral integration site. When more than one copy of the heterologous nucleic acid molecule encoding the protein functioning to convert arabinose into ethanol is introduced in the recombinant microbial host cell, each of the copy can be integrated at one or more (the same or different) integration sites.
As indicated above, an exemplary protein capable of functioning to convert arabinose into ethanol is an arabinose transporter. An “arabinose transporter” as used herein is meant to refer to an enzyme that is capable of efficiently transporting arabinose across a membrane. In general, arabinose transporters are transmembrane proteins that selectively transport pentoses, specifically arabinose, into the cell. In the context of the present disclosure, the one or more protein for converting arabinose into ethanol can be an arabinose transporter, an arabinose transporter variant or an arabinose transporter fragment. Arabinose transporters can be derived from a number of species. These include without limitations transporters derived from Saccharomyces cerevisiae (GAL2), Ambrosiozyma monospora, Candida arabinofermentans, Ambrosiozyma monospora, Kluveromyces marxianus, Pichia guillermondii (LAT1), Pichia guillermondii (LAT2), Pichia stipites, Ambrosiozyma monospora (LAT2), Debaryomyces hensenii, Apergillus flavus, Aspergillus terreus, Neosartorya fischeri, Aspergillus niger, Penicillium marneffei, Coccidioides posadasii, Gibberella zeae, Magnaporthe oryzae, Schizophyllum commune, Pichia stipites, Saccaharomyces cerevisiae (HXT2), Aspergillus clavatus (ACLA_032060), Sclerotinia sclerotiorum (SS 1G_01302), Arthroderma benhamiae (ARB 03323), Trichophyton equinum (TEQG_03356), Trichophyton tonsurans (G_04876), Coccidioides immitis (CIMG_09387), Coccidioides posadasii (CPSG_03942), Coccidioides posadasii (CPC735_017640), Botryotinia fuckeliana (BC1G_08389), Pyrenophora tritici-repentis (PTRG_10527), Ustilago maydis (UM03895.1), Clavispora lusitaniae (CLUG_02297), Pichia guillermondii (LAT1), Pichia guillermondii (LAT2), Debaryomyces hansenii (DEHA2E01 166 g), Pichia stipites, Candida albicans, Debaryomyces hansenii (DEHA2B 16082g), Kluveromyces marxianus (LAT1), Kluyveromyces lactis (KLLA-ORF10059), Lachancea thermotolerans (KLTH0H13728g), Kluveromyces thermotolerans, Vandenvaltozyma polyspora (Kpol_281p3), Zygosaccharomyces rouxii (ZYRO0E03916g), Pichia pastoris (0.1833), Candida arabinofermentans (0.1378), Ambrosiozyma monospora (LAT1), Aspergillus clavatus (ACLA_044740), Neosartorya fischeri (NFIA_094320), Aspergillus flavus (AFLA_1 16400), Aspergillus terreus (ATEG_08609), Aspergillus niger (ANI_1 1064034), Telaromyces stipitatus (TSTA_124770), Penicillium chrysogenum (Pc20g01790), Penicillium chrysogenum (Pc20g01790) #2, Gibberella zeae (FG10921.1), Nectria hematococco, Glomerella graminicola (GLRG_10740), Arabidopsis thaliana, Vandenvaltozyma polyspora, Debaryomyces hanseii, Aspergillus niger, Penicillium chrysogenum, Pichia guilermondii, Aspergillus flavus, Candida lusitnaea, Candida albicans, Kluveromyces marxianus, Pichia stipites, Candida arabinofermentans or any suitable source of the enzyme.
In an embodiment, the one or more protein for converting arabinose into ethanol can be an inhibitor of an arabinose transporter and the third genetic modification is for decreasing or preventing the expression of such inhibitor. For example, the inhibitor can be a transcription factor which limits the expression of the arabinose transporter under certain circumstances. In some embodiments, the inhibitor is a GAL2 inhibitor, for example, a GAL80 transcription factor protein which limits the expression of the GAL2 protein. The third genetic modification can thus be a deletion in the gal80 gene which would cause a constitutive expression of the GAL2 protein (an arabinose transporter).
As indicated above, an exemplary protein capable of functioning to convert arabinose into ethanol is an arabinose isomerase (AI). An arabinose isomerase refers to an enzyme that is capable of catalyzing the chemical conversion of arabinose to ribulose (EC 5.3.1.3). Arabinose isomerase belongs to the oxidoreductase family of enzymes capable of interconverting aldoses and ketoses. In an embodiment, the arabinose isomerase can be an L-arabinose isomerase. Arabinose isomerases of the present disclosure include those derived from various species including both prokaryotic and eukaryotic species. Arabinose isomerases may be derived from Bacillus subtilis, Mycobacterium smegmatis, Bacillus licheniformis, Lactobacillus plantarum (AraA), Arthrobacter aurescens (AraA), Clavibacter michiganensis (AraA), Gramella forsetii (AraA), Bacteroides thetaiotamicron (AraA), Escherichia coli (AraA) or any other suitable source of the enzyme. In an embodiment, the arabinose isomerase is AraA from Bacteroides thetaiotamicron and can have the amino acid sequence of SEQ ID NO: 10 (a variant thereof or a fragment thereof). In an embodiment, the heterologous AraA is present in a single copy in the recombinant microbial host cell's genome.
As indicated above, an exemplary protein capable of functioning to convert arabinose into ethanol is a ribulokinase (RK). A ribulokinase refers to an enzyme that is capable of catalyzing the chemical reaction that phosphorylates ribulose to yield ribulose-5-phosphate (EC 2.7.1.16). In an embodiment, the ribulokinase can be an L-ribulokinase. Ribulokinases of the present disclosure include those derived from various species including both prokaryotic and eukaryotic species. Ribulokinases may be derived from Escherichia coli (AraB), Lactobacillus plantarum (AraB), Arthrobacter aurescens (AraB), Clavibacter michiganensis (AraB), Gramella forsetii (AraB), Bacteroides thetaiotamicron (AraB) or any other suitable source of the enzyme. In an embodiment, the ribulokinase is AraB from Bacteroides thetaiotamicron and can have the amino acid sequence of SEQ ID NO: 11 (a variant thereof or a fragment thereof). In an embodiment, the heterologous AraB is present in a single copy in the recombinant microbial host cell's genome.
As indicated above, an exemplary protein capable of functioning to convert arabinose into ethanol is and a ribulose 5-phosphate epimerase (RSPE). The ribulose 5-phosphate epimerase enzyme capable of catalyzing the interconversion of ribulose-5-phosphate and xylulose-5-phosphate (EC 5.1.3.4). In an embodiment, the ribulose 5-phosphate epimerase can be an L-ribulose 5-phosphate epimerase. Ribulose 5-phosphate epimerases of the present disclosure include those derived from various species including both prokaryotic and eukaryotic species. Ribulose 5-phosphate epimerases may be derived from Escherichia coli (AraD), Lactobacillus plantarum (AraD), Arthrobacter aurescens (AraD), Clavibacter michiganensis (AraD), Gramella forsetti (AraD), Bacteroides thetaiotamicron (AraD) or any other suitable source of the enzyme. In an embodiment, the R5PE is AraD from Bacteroides thetaiotamicron and can have the amino acid sequence of SEQ ID NO: 12 (a variant thereof or a fragment thereof). In an embodiment, the heterologous AraB is present in a single copy in the recombinant microbial host cell's genome.
Further genetic modifications can be introduced in the microbial host cell to facilitate or increase the conversion of a C5 carbohydrate into ethanol in genes which are not directly associated with the conversion of the carbohydrate into ethanol. Such modifications have been described in WO 2016/024215 and include one or more deletion in an aldose reductase gene (such as, form example, the GRE3 gene and/or the YPR1 gene), a mutation in a polypeptide encoded by an iron-sulfur cluster gene (such as, for example, the YFH1 polypeptide (including the T163P mutation), the ISU1 polypeptide (including the D71N, the D71G and/or the S98F mutation(s)) as well as the NFS1 polypeptide (including the L115W and/or the E458D mutation(s))) as well as a mutation in a RAS2 polypeptide (including the A66T mutation, such as, for example, those described in PCT/EP2017/056456).
v) Fourth Native Metabolic Pathway
In the context of the present disclosure, the recombinant microbial host cell comprises all native proteins that function in a fourth native metabolic pathway to produce glycerol. In the recombinant microbial host cell of the present disclosure, the biological activity of the one or more native proteins functioning to produce glycerol are not genetically modified or engineered and as such, the recombinant microbial host cell expresses natively the proteins involved in the production of glycerol. As shown in the Examples below, maintaining the native ability of the microbial host cell to produce glycerol allows it to also maintain adequate robustness (growth rate kinetics in the presence of acetate).
As used in the context of the present disclosure, the proteins that function to produce glycerol specifically excludes the proteins of the second engineered metabolic pathway. The one or more proteins that function to produce glycerol are involved in the conversion of DHAP to glycerol-3-phosphate (G3P) and the conversion of G3P to glycerol. The proteins that function to produce glycerol can be involved in the conversion of dihydroxyacetone phosphate (DHAP also known as glycerone phosphate) to G3P (such as, for example, the GPD proteins). The term “glycerol-3-phosphate dehydrogenase” or “GPD” is intended to include the enzymes capable of converting dihydroxyacetone phosphate to glycerol-3-phosphate. GPD includes those enzymes that correspond to Enzyme Commission Number 1.1.1.8. Alternatively or in combination, the one or more proteins that function to produce glycerol can be involved in the conversion of G3P to glycerol (such as, for example, the GPP proteins). The term “glycerol-3-phosphate phosphatase” or “GPP” is intended to include the enzymes capable of converting glycerol-3-phosphate to glycerol. GPP includes those enzymes that corresponding to Enzyme Commission Number 3.1.3.21.
Most eukaryotic cells express two different glycerol-3-phosphate dehydrogenases (GPDs) which are necessary for glycerol production and they are expressed in response to different cellular signals: the GPD1 and the GPD2 proteins. Both proteins share 75% amino acid identity and, while they catalyze the same reaction, the differences in their promoter sequence make them more efficient enzymes under the environmental conditions that induce their expression.
The recombinant microbial host cell of the present disclosure can natively express the NAD-dependent glycerol-3-phosphate dehydrogenase GPD1 protein or a GPD1 gene ortholog. The GPD1 protein is natively expressed in yeasts, fungi, mammalian and plant cells. GPD1 genes encoding the GPD1 protein include, but are not limited to Saccharomyces cerevisiae Gene ID: 851539, Schizosaccharomyces pombe Gene ID: 2540547, Schizosaccharomyces pombe Gene ID: 2540455, Neurospora crassa Gene ID: 3873099, Candida albicans Gene ID: 3643924, Scheffersomyces stipitis Gene ID: 4840320, Spathaspora passalidarum Gene ID: 18874668, Trichoderma reesei Gene ID: 18482691, Nectria haematococca Gene ID: 9668637, Candida dubliniensis Gene ID: 8046432, Chlamydomonas reinhardtii Gene ID: 5716580, Brassica napus Gene ID: 106365675, Chlorella variabilis Gene ID: 17355036, Brassica napus Gene ID: 106352802, Mus musculus Gene ID: 14555, Homo sapiens Gene ID: 2819, Rattus norvegicus Gene ID: 60666, Sus scrofa Gene ID: 100153250, Gallus gallus Gene ID: 426881, Bos taurus Gene ID: 525042, Xenopus tropicalis Gene ID: 448519, Pan troglodytes Gene ID: 741054, Canis lupus familiaris Gene ID: 607942, Callorhinchus milii Gene ID: 103188923, Columba livia Gene ID: 102088900, Macaca fascicularis Gene ID: 101865501, Myotis brandtii Gene ID: 102257341, Heterocephalus glaber Gene ID: 101702723, Nannospalax galili Gene ID: 103746543, Mustela putorius furo Gene ID: 101681348, Callithrix jacchus Gene ID: 100414900, Labrus bergylta Gene ID: 109980872, Monopterus albus Gene ID: 109969143, Castor canadensis Gene ID: 109695417, Paralichthys olivaceus Gene ID: 109635348, Bos indicus Gene ID: 109559120, Hippocampus comes Gene ID: 109507993, Rhinolophus sinicus Gene ID: 109443801, Hipposideros armiger Gene ID: 109393253, Crocodylus porosus Gene ID: 109324424, Gavialis gangeticus Gene ID: 109293349, Panthera pardus Gene ID: 109249099, Cyprinus carpio Gene ID: 109094445, Scleropages formosus Gene ID: 108931403, Nanorana parkeri Gene ID: 108789981, Rhinopithecus bieti Gene ID: 108543924, Lepidothrix coronata Gene ID: 108509436, Pygocentrus nattereri Gene ID: 108444060, Manis javanica Gene ID: 108406536, Cebus capucinus imitator Gene ID: 108316082, Ictalurus punctatus Gene ID: 108255083, Kryptolebias marmoratus Gene ID: 108231479, Miniopterus natalensis Gene ID: 107528262, Rousettus aegyptiacus Gene ID: 107514265, Coturnix japonica Gene ID: 107325705, Protobothrops mucrosquamatus Gene ID: 107302714, Parus major Gene ID: 107215690, Marmota marmota marmota Gene ID: 107148619, Gekko japonicus Gene ID: 107122513, Cyprinodon variegatus Gene ID: 107101128, Acinonyx jubatus Gene ID: 106969233, Poecilia latipinna Gene ID: 106959529, Poecilia mexicana Gene ID: 106929022, Calidris pugnax Gene ID: 106891167, Sturnus vulgaris Gene ID: 106863139, Equus asinus Gene ID: 106845052, Thamnophis sirtalis Gene ID: 106545289, Apteryx australis mantelli Gene ID: 106499434, Anser cygnoides domesticus Gene ID: 106047703, Dipodomys ordii Gene ID: 105987539, Clupea harengus Gene ID: 105897935, Microcebus murinus Gene ID: 105869862, Propithecus coquereli Gene ID: 105818148, Aotus nancymaae Gene ID: 105709449, Cercocebus atys Gene ID: 105580359, Mandrillus leucophaeus Gene ID: 105527974, Colobus angolensis palliates Gene ID: 105507602, Macaca nemestrina Gene ID: 105492851, Aquila chrysaetos canadensis Gene ID: 105414064, Pteropus vampyrus Gene ID: 105297559, Camelus dromedarius Gene ID: 105097186, Camelus bactrianus Gene ID: 105076223, Esox lucius Gene ID: 105016698, Bison bison bison Gene ID: 105001494, Notothenia coriiceps Gene ID: 104967388, Larimichthys crocea Gene ID: 104928374, Fukomys damarensis Gene ID: 04861981, Haliaeetus leucocephalus Gene ID: 104831135, Corvus cornix cornix Gene ID: 104683744, Rhinopithecus roxellana Gene ID: 104679694, Balearica regulorum gibbericeps Gene ID: 104630128, Tinamus guttatus Gene ID: 104575187, Mesitornis unicolor Gene ID: 104539793, Antrostomus carolinensis Gene ID: 104532747, Buceros rhinoceros silvestris Gene ID: 104501599, Chaetura pelagica Gene ID: 104385595, Leptosomus discolor Gene ID: 104353902, Opisthocomus hoazin Gene ID: 104326607, Charadrius vociferus Gene ID: 104284804, Struthio camelus australis Gene ID: 104144034, Egretta garzetta Gene ID: 104132778, Cuculus canorus Gene ID: 104055090, Nipponia nippon Gene ID: 104011969, Pygoscelis adeliae Gene ID: 103914601, Aptenodytes forsteri Gene ID: 103894920, Serinus canaria Gene ID: 103823858, Manacus vitellinus Gene ID: 103760593, Ursus maritimus Gene ID: 103675473, Corvus brachyrhynchos Gene ID: 103613218, Galeopterus variegatus Gene ID: 103598969, Equus przewalskii Gene ID: 103546083, Calypte anna Gene ID: 103536440, Poecilia reticulata Gene ID: 103464660, Cynoglossus semilaevis Gene ID: 103386748, Stegastes partitus Gene ID: 103355454, Eptesicus fuscus Gene ID: 103285288, Chlorocebus sabaeus Gene ID: 103238296, Orycteropus afer afer Gene ID: 103194426, Poecilia formosa Gene ID: 103134553, Erinaceus europaeus Gene ID: 103118279, Lipotes vexillifer Gene ID: 103087725, Python bivittatus Gene ID: 103049416, Astyanax mexicanus Gene ID: 103021315, Balaenoptera acutorostrata scammoni Gene ID: 103006680, Physeter catodon Gene ID: 102996836, Panthera tigris altaica Gene ID: 102961238, Chelonia mydas Gene ID: 102939076, Peromyscus maniculatus bairdii Gene ID: 102922332, Pteropus alecto Gene ID: 102880604, Elephantulus edwardii Gene ID: 102844587, Chrysochloris asiatica Gene ID: 102825902, Myotis davidii Gene ID: 102754955, Leptonychotes weddellii Gene ID: 102730427, Lepisosteus oculatus Gene ID: 102692130, Alligator mississippiensis Gene ID: 102576126, Vicugna pacos Gene ID: 102542115, Camelus ferus Gene ID: 102507052, Tupaia chinensis Gene ID: 102482961, Pelodiscus sinensis Gene ID: 102446147, Myotis lucifugus Gene ID: 102420239, Bubalus bubalis Gene ID: 102395827, Alligator sinensis Gene ID: 102383307, Latimeria chalumnae Gene ID: 102345318, Pantholops hodgsonii Gene ID: 102326635, Haplochromis burtoni Gene ID: 102295539, Bos mutus Gene ID: 102267392, Xiphophorus maculatus Gene ID: 102228568, Pundamilia nyererei Gene ID: 102192578, Capra hircus Gene ID: 102171407, Pseudopodoces humilis Gene ID: 102106269, Zonotrichia albicollis Gene ID: 102070144, Falco cherrug Gene ID: 102047785, Geospiza fortis Gene ID: 102037409, Chinchilla lanigera Gene ID: 102014610, Microtus ochrogaster Gene ID: 101990242, Ictidomys tridecemlineatus Gene ID: 101955193, Chrysemys picta Gene ID: 101939497, Falco peregrinus Gene ID: 101911770, Mesocricetus auratus Gene ID: 101824509, Ficedula albicollis Gene ID: 101814000, Anas platyrhynchos Gene ID: 101789855, Echinops telfairi Gene ID: 101641551, Condylura cristata Gene ID: 101622847, Jaculus jaculus Gene ID: 101609219, Octodon degus Gene ID: 101563150, Sorex araneus Gene ID: 101556310, Ochotona princeps Gene ID: 101532015, Maylandia zebra Gene ID: 101478751, Dasypus novemcinctus Gene ID: 101446993, Odobenus rosmarus divergens Gene ID: 101385499, Tursiops truncatus Gene ID: 101318662, Orcinus orca Gene ID: 101284095, Oryzias latipes Gene ID: 101154943, Gorilla gorilla Gene ID: 101131184, Ovis aries Gene ID: 101119894, Felis catus Gene ID: 101086577, Takifugu rubripes Gene ID: 101079539, Saimiri boliviensis Gene ID: 101030263, Papio anubis Gene ID: 101004942, Pan paniscus Gene ID: 100981359, Otolemur garnettii Gene ID: 100946205, Sarcophilus harrisii Gene ID: 100928054, Cricetulus griseus Gene ID: 100772179, Cavia porcellus Gene ID: 100720368, Oreochromis niloticus Gene ID: 100712149, Loxodonta africana Gene ID: 100660074, Nomascus leucogenys Gene ID: 100594138, Anolis carolinensis Gene ID: 100552972, Meleagris gallopavo Gene ID: 100542199, Ailuropoda melanoleuca Gene ID: 100473892, Oryctolagus cuniculus Gene ID: 100339469, Taeniopygia guttata Gene ID: 100225600, Pongo abelii Gene ID: 100172201, Ornithorhynchus anatinus Gene ID: 100085954, Equus caballus Gene ID: 100052204, Mus musculus Gene ID: 100198, Xenopus laevis Gene ID: 399227, Danio rerio Gene ID: 325181, Danio rerio Gene ID: 406615, Melopsittacus undulatus Gene ID: 101872435, Ceratotherium simum simum Gene ID: 101408813, Trichechus manatus latirostris Gene ID: 101359849 and Takifugu rubripes Gene ID: 101071719).
The recombinant microbial host cells of the present disclosure can natively express the NAD-dependent glycerol-3-phosphate dehydrogenase GPD2 protein or a GPD2 gene ortholog. The GPD2 protein is expressed in bacteria, yeasts, fungi, mammalian and plant cells. GPD2 genes encoding the GPD2 protein include, but are not limited to Mus musculus Gene ID: 14571, Homo sapiens Gene ID: 2820, Saccharomyces cerevisiae Gene ID: 854095, Rattus norvegicus Gene ID: 25062, Schizosaccharomyces pombe Gene ID: 2541502, Mus musculus Gene ID: 14380, Danio rerio Gene ID: 751628, Caenorhabditis elegans Gene ID: 3565504, Mesocricetus auratus Gene ID: 101825992, Xenopus tropicalis Gene ID: 779615, Macaca mulatta Gene ID: 697192, Bos taurus Gene ID: 504948, Canis lupus familiaris Gene ID: 478755, Cavia porcellus Gene ID: 100721200, Gallus gallus Gene ID: 424321, Pan troglodytes Gene ID: 459670, Oryctolagus cuniculus Gene ID: 100101571, Candida albicans Gene ID: 3644563, Xenopus laevis Gene ID: 444438, Macaca fascicularis Gene ID: 102127260, Ailuropoda melanoleuca Gene ID: 100482626, Cricetulus griseus Gene ID: 100766128, Heterocephalus glaber Gene ID: 101715967, Scheffersomyces stipitis Gene ID: 4838862, Ictalurus punctatus Gene ID: 108273160, Mustela putorius furo Gene ID: 101681209, Nannospalax galili Gene ID: 103741048, Callithrix jacchus Gene ID: 100409379, Lates calcarifer Gene ID: 108873068, Nothobranchius furzeri Gene ID: 07384696, Acanthisitta chloris Gene ID: 103808746, Acinonyx jubatus Gene ID: 106978985, Alligator mississippiensis Gene ID: 102562563, Alligator sinensis Gene ID: 102380394, Anas platyrhynchos, Anolis carolinensis Gene ID: 100551888, Anser cygnoides domesticus Gene ID: 106043902, Aotus nancymaae Gene ID: 105719012, Apaloderma vittatum Gene ID: 104281080, Aptenodytes forsteri Gene ID: 103893867, Apteryx australis mantelli Gene ID: 106486554, Aquila chrysaetos canadensis Gene ID: 105412526, Astyanax mexicanus Gene ID: 103029081, Austrofundulus limnaeus Gene ID: 106535816, Balaenoptera acutorostrata scammoni Gene ID: 103019768, Balearica regulorum gibbericeps, Bison bison bison Gene ID: 104988636, Bos indicus Gene ID: 109567519, Bos mutus Gene ID: 102277350, Bubalus bubalis Gene ID: 102404879, Buceros rhinoceros silvestris Gene ID: 104497001, Calidris pugnax Gene ID: 106902763, Callorhinchus milii Gene ID: 103176409, Calypte anna Gene ID: 103535222, Camelus bactrianus Gene ID: 105081921, Camelus dromedarius Gene ID: 105093713, Camelus ferus Gene ID: 102519983, Capra hircus Gene ID: 102176370, Cariama cristata Gene ID: 104154548, Castor canadensis Gene ID: 109700730, Cebus capucinus imitator Gene ID: 108316996, Cercocebus atys Gene ID: 105576003, Chaetura pelagica Gene ID: 104391744, Charadrius vociferus Gene ID: 104286830, Chelonia mydas Gene ID: 102930483, Chinchilla lanigera Gene ID: 102017931, Chlamydotis macqueenii Gene ID: 104476789, Chlorocebus sabaeus Gene ID: 103217126, Chrysemys picta Gene ID: 101939831, Chrysochloris asiatica Gene ID: 102831540, Clupea harengus Gene ID: 105902648, Colius striatus Gene ID: 104549356, Colobus angolensis palliates Gene ID: 105516852, Columba livia Gene ID: 102090265, Condylura cristata Gene ID: 101619970, Corvus brachyrhynchos, Coturnix japonica Gene ID: 107316969, Crocodylus porosus Gene ID: 109322895, Cuculus canorus Gene ID: 104056187, Cynoglossus semilaevis Gene ID: 103389593, Dasypus novemcinctus Gene ID: 101428842, Dipodomys ordii Gene ID: 105996090, Echinops telfairi Gene ID: 101656272, Egretta garzetta Gene ID: 104135263, Elephantulus edwardii Gene ID: 102858276, Eptesicus fuscus Gene ID: 103283396, Equus asinus Gene ID: 106841969, Equus caballus Gene ID: 100050747, Equus przewalskii Gene ID: 103558835, Erinaceus europaeus Gene ID: 103114599, Eurypyga helias Gene ID: 104502666, Falco cherrug Gene ID: 102054715, Falco peregrinus Gene ID: 101912742, Felis catus Gene ID: 101089953, Ficedula albicollis Gene ID: 101816901, Fukomys damarensis Gene ID: 104850054, Fundulus heteroclitus Gene ID: 105936523, Galeopterus variegatus Gene ID: 103586331, Gavia stellata Gene ID: 104250365, Gavialis gangeticus Gene ID: 109301301, Gekko japonicus Gene ID: 107110762, Geospiza fortis Gene ID: 102042095, Gorilla gorilla Gene ID: 101150526, Haliaeetus albicilla Gene ID: 104323154, Haliaeetus leucocephalus Gene ID: 104829038, Haplochromis burtoni Gene ID: 102309478, Hippocampus comes Gene ID: 109528375, Hipposideros armiger Gene ID: 109379867, ktidomys tridecemlineatus Gene ID: 101965668, Jaculus jaculus Gene ID: 101616184, Kryptolebias marmoratus Gene ID: 108251075, Labrus bergylta Gene ID: 109984158, Larimichthys crocea Gene ID: 104929094, Latimeria chalumnae Gene ID: 102361446, Lepidothrix coronata Gene ID: 108501660, Lepisosteus oculatus Gene ID: 102691231, Leptonychotes weddellii Gene ID: 102739068, Leptosomus discolor Gene ID: 104340644, Lipotes vexillifer Gene ID: 103074004, Loxodonta africana Gene ID: 100654953, Macaca nemestrina Gene ID: 105493221, Manacus vitellinus Gene ID: 103757091, Mandrillus leucophaeus Gene ID: 105548063, Manis javanica Gene ID: 108392571, Marmota marmota marmota Gene ID: 107136866, Maylandia zebra Gene ID: 101487556, Mesitornis unicolor Gene ID: 104545943, Microcebus murinus Gene ID: 105859136, Microtus ochrogaster Gene ID: 101999389, Miniopterus natalensis Gene ID: 107525674, Monodelphis domestica Gene ID: 100014779, Monopterus albus Gene ID: 109957085, Myotis brandtii Gene ID: 102239648, Myotis davidii Gene ID: 102770109, Myotis lucifugus Gene ID: 102438522, Nanorana parkeri Gene ID: 108784354, Nestor notabilis Gene ID: 104399051, Nipponia nippon Gene ID: 104012349, Nomascus leucogenys Gene ID: 100590527, Notothenia coriiceps Gene ID: 104964156, Ochotona princeps Gene ID: 101530736, Octodon degus Gene ID: 101591628, Odobenus rosmarus divergens Gene ID: 101385453, Oncorhynchus kisutch Gene ID: 109870627, Opisthocomus hoazin Gene ID: 104338567, Orcinus orca Gene ID: 101287409, Oreochromis niloticus Gene ID: 100694147, Ornithorhynchus anatinus Gene ID: 100081433, Orycteropus afer afer Gene ID: 103197834, Oryzias latipes Gene ID: 101167020, Otolemur garnettii Gene ID: 100966064, Ovis aries Gene ID: 443090, Pan paniscus Gene ID: 100970779, Panthera pardus Gene ID: 109271431, Panthera tigris altaica Gene ID: 102957949, Pantholops hodgsonii Gene ID: 102323478, Papio anubis Gene ID: 101002517, Paralichthys olivaceus Gene ID: 109631046, Pelodiscus sinensis Gene ID: 102454304, Peromyscus maniculatus bairdii Gene ID: 102924185, Phaethon lepturus Gene ID: 104624271, Phalacrocorax carbo Gene ID: 104049388, Physeter catodon Gene ID: 102978831, Picoides pubescens Gene ID: 104296936, Poecilia latipinna Gene ID: 106958025, Poecilia mexicana Gene ID: 106920534, Poecilia reticulata Gene ID: 103473778, Pongo abelii Gene ID: 100452414, Propithecus coquereli Gene ID: 105807399, Protobothrops mucrosquamatus Gene ID: 107289584, Pseudopodoces humilis Gene ID: 102109711, Pterocles gutturalis Gene ID: 104461236, Pteropus alecto Gene ID: 102879110, Pteropus vampyrus Gene ID: 105291402, Pundamilia nyererei Gene ID: 102200268, Pygocentrus nattereri Gene ID: 108411786, Pygoscelis adeliae Gene ID: 103925329, Python bivittatus Gene ID: 103059167, Rhincodon typus Gene ID: 109920450, Rhinolophus sinicus Gene ID: 109445137, Rhinopithecus bieti Gene ID: 108538766, Rhinopithecus roxellana Gene ID: 104654108, Rousettus aegyptiacus Gene ID: 107513424, Saimiri boliviensis Gene ID: 101027702, Salmo salar Gene ID: 106581822, Sarcophilus harrisii Gene ID: 100927498, Scleropages formosus Gene ID: 108927961, Serinus canaria Gene ID: 103814246, Sinocyclocheilus grahamiGene ID: 107555436, Sorex araneus Gene ID: 101543025, Stegastes partitus Gene ID: 103360018, Struthio camelus australis Gene ID: 104138752, Sturnus vulgaris Gene ID: 106861926, Sugiyamaella lignohabitans Gene ID: 30033324, Sus scrofa Gene ID: 397348, Taeniopygia guttata Gene ID: 100222867, Takifugu rubripes Gene ID: 101062218, Tarsius syrichta Gene ID: 103254049, Tauraco erythrolophus Gene ID: 104378162, Thamnophis sirtalis Gene ID: 106538827, Tinamus guttatus Gene ID: 104572349, Tupaia chinensis Gene ID: 102471148, Tursiops truncatus Gene ID: 101330605, Ursus maritimus Gene ID: 103659477, Vicugna pacos Gene ID: 102533941, Xiphophorus maculatus Gene ID: 102225536, Zonotrichia albicollis Gene ID: 102073261, Ciona intestinalis Gene ID: 100183886, Meleagris gallopavo Gene ID: 100546408, Trichechus manatus latirostris Gene ID: 101355771, Ceratotherium simum simum Gene ID: 101400784, Melopsittacus undulatus Gene ID: 101871704, Esox lucius Gene ID: 10502249 and Pygocentrus nattereri Gene ID: 108411786. In an embodiment, the GPD2 protein is encoded by Saccharomyces cerevisiae Gene ID: 854095.
The recombinant microbial host cells of the present disclosure can natively express the glycerol-1-phosphatase 1 (GPP1) protein or a GPP1 gene ortholog/paralog. The GPP1 protein is expressed in eukaryotic cells (including yeasts, animals and humans) as well as in plants. GPP1 genes encoding the GPP1 protein include, but are not limited to Saccharomyces cerevisiae Gene ID: 854758, Arabidopsis thaliana Gene ID: 828690, Scheffersomyces stipitis Gene ID: 4836794, Chlorella variabilis Gene ID: 17352997, Solanum tuberosum Gene ID: 102585195, Homo sapiens Gene ID: 7316, Millerozyma farinosa Gene ID: 14521241, 14520178, 1451927 and 14518181, Sugiyamaella lignohabitans Gene ID: 30035078, Candida dubliniensis Gene ID: 8046759.
The recombinant microbial host cells of the present disclosure can natively express the glycerol-1-phosphatase GPP2 protein or a GPP2 gene ortholog/paralog. The GPP2 protein is expressed in eukaryotic cells (including yeasts) as well as in plants. GPP2 genes encoding the GPP2 protein include, but are not limited to Saccharomyces cerevisiae Gene ID: 856791, Sugiyamaella lignohabitans Gene ID: 30035078, Arabidopsis thaliana Gene ID: 835849, Nicotiana attenuata Gene ID: 109234217, Candida albicans Gene ID: 3640236, Candida glabrata Gene ID: 2891433, 2891243 and 2889223.
In an embodiment, the recombinant microbial host cell natively expresses at least one (and in an embodiment no more than one) of the GPD1, GPD2, GPP1 and/or GPP2 protein. In another embodiment, the recombinant microbial host cell natively expresses has at least two (and in an embodiment no more than two) of the GPD1, GPD2, GPP1 and/or GPP2 protein. In a further embodiment, the recombinant microbial host cell natively expresses has at least three (and in an embodiment no more than three) of the GPD1, GPD2, GPP1 and/or GPP2 protein. In a further embodiment, the recombinant microbial host cell natively expresses the GPD1, GPD2, GPP1 and GPP2 proteins.
In still another embodiment, the recombinant microbial host cell natively expresses at least one NAD-dependent glycerol-3-phosphate dehydrogenase GPD protein and at least one glycerol-1-phosphatase (GPP) protein. For example, the recombinant microbial host cell can natively express the GPD1 and the GPP1 proteins but not the GPD2 and the GPP2 proteins. In another example, the recombinant microbial host cell can natively express the GPD1 and GPP2 proteins but not the GPD2 and GPP1 proteins. In still another example, the recombinant microbial host cell can natively express the GPD2 and GPP1 proteins but not the GPD1 and the GPP2 proteins. In still a further example, the recombinant microbial host cell can natively express the GPD2 and GPP2 proteins but not the GPD1 and GPP1 proteins. In another embodiment, the recombinant microbial host cell can natively express both GPD proteins (GPD1 and GPD2) and only one GPP protein (GPP1 or GPP2). In still a further embodiment, the recombinant microbial host cell can natively express only one GPD protein (GPD1 or GPD2) and both GPP proteins (GPP1 and GPP2).
vi) Fifth Metabolic Pathway
In the context of the present disclosure, the recombinant microbial host cell can have a fifth and optional genetic modification for increasing the activity of one or more native and/or heterologous proteins that function in a fifth (engineered) metabolic pathway to increase the availability of electrons in the form of reduced redox cofactors such as, for example, NADH or NAD(P)H. In some embodiments, this allows the recombinant microbial host cell to comprise one or more recombinantly expressed heteterologous proteins that function in the fifth metabolic pathway. The heterologous proteins that function in the fifth engineered metabolic pathway were described in WO2014074895. For example, in an embodiment in which the one or more protein is a native protein, the fifth genetic modification can include an heterologous promoter which increases the expression (and ultimately the activity) of the native protein to increase the availability of electrons in the form of reduced redox cofactors. In still another example, in an embodiment in which the one or more protein is a native protein, the fifth genetic modification can include a mutation in the coding sequence of the protein that function to increase the availability of electrons in the form or reduced redox cofactors which increases the activity of the mutated protein (when compared to the native protein). In yet another example, in an embodiment in which the one or more protein is an heterologous protein, the fifth genetic modification can include one or more copies of the heterologous protein to increase the expression (and ultimately the activity) of the heterologous protein to increase the availability of electrons in the form of a reduced redox cofactors.
When the microbial recombinant host cell includes a first genetic modification for increasing the activity of a protein having both acetylating acetaldehyde dehydrogenase activity and alcohol dehydrogenase activity, the fifth genetic modification can be made to increase the activity of an NADPH-dependent alcohol dehydrogenase. The protein having NADPH-dependent alcohol dehydrogenase activity can be an ADH1 polypeptide (for example from Entamoeba sp., including Entamoeba histolytica (such as, for example, the one having the amino acid sequence of SEQ ID NO: 4), an ADH1 polypeptide variant, an ADH1 polypeptide fragment or a polypeptide encoded by an ADH1 gene ortholog/paralog. In yet another embodiment, the heterologous gene coding for the NADPH-dependent alcohol dehydrogenase protein is present in one, two, three, four or more copies in the recombinant microbial host cell.
In order to increase the activity of one or more proteins functioning to increase the availability of electrons in the form of a reduced redox cofactor, it is possible to include, in the recombinant microbial host cell, one or more copies of an heterologous nucleic acid molecule encoding the protein functioning in the fifth engineered metabolic pathway. For example, the recombinant microbial host cell can have one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve or more copies of the heterologous nucleic acid molecule encoding the protein in the fifth engineered metabolic pathway. In an embodiment, the recombinant microbial host cell comprises between one and four copies of the heterologous nucleic acid molecule encoding the protein functioning in the fifth engineered metabolic pathway. In an embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) one copy of the heterologous nucleic acid molecule encoding the protein functioning in the fifth engineered metabolic pathway. In an embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) two copies of the heterologous nucleic acid molecule encoding the protein functioning in the fifth engineered metabolic pathway. In another embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) three copies of the heterologous nucleic acid molecule encoding the protein functioning in the fifth engineered metabolic pathway. In yet another embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) four copies of the heterologous nucleic acid molecule encoding the protein functioning in the fifth engineered metabolic pathway. In still another embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) five copies of the heterologous nucleic acid molecule encoding the protein functioning in the fifth engineered metabolic pathway. In a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) six copies of the heterologous nucleic acid molecule encoding the protein functioning in the fifth engineered metabolic pathway. In yet a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) seven copies of the heterologous nucleic acid molecule encoding the protein functioning in the fifth engineered metabolic pathway. In still a further embodiment, the recombinant microbial host cell comprises at least (and in some additional embodiments no more than) eight copies of the heterologous nucleic acid molecule encoding the protein functioning in the fifth engineered metabolic pathway. In an embodiment, the recombinant microbial host cell comprises one copy of the heterologous nucleic acid molecule encoding the protein functioning in the fifth engineered metabolic pathway. The heterologous nucleic acid molecule can be independently replicating or integrated in the recombinant microbial host cell. When the heterologous nucleic acid molecule is integrated in the recombinant microbial host cell, it is preferably positioned at neutral integration site. When more than one copy of the heterologous nucleic acid molecule encoding the protein functioning in the fifth engineered metabolic pathway is introduced in the recombinant microbial host cell, each of the copy can be integrated at one or more (the same or different) integration sites.
In some instances, it may be advisable to support the enzymatic activity of the protein having NADPH-dependent alcohol dehydrogenase activity by increasing the activity of one or more proteins capable of producing NADPH by introducing a second additional genetic modification. For example, the second additional genetic modification can be made to one or more proteins capable of increasing the flux through an oxidative pentose phosphate pathway. As shown in the Examples below, increasing the flux through an oxidative pentose phosphate pathway is advantageous to increase conversion of acetate into ethanol while maintaining adequate robustness (growth rates, kinetics in the presence of acetate).
The one or more proteins capable of producing NADPH can be involved in the conversion of glucose-6-phosphate to ribulose-5-phosphate. The one or more proteins capable of producing NADPH can include a glucose-6-phosphate dehydrogenase which catalyzes the conversion of glucose-6-phosphate to D-6-phospho-glucono-δ-lactone and thereby produces NAD(P)H. Existing glucose-6-phosphate dehydrogenases are classified in the Enzyme Commission Number class 1.1.1.49. The glucose-6-phosphate dehydrogenases that can be overexpressed include, but are not limited to, Saccharomyces cerevisiae Gene ID: 855480, Schizosaccharomyces pombe Gene ID: 2543200, Mycobacterium tuberculosis Gene ID: 885817, Candida albicans Gene ID: 3634913, Scheffersomyces stipitis Gene ID: 4840428, Spathaspora passalidarum Gene ID: 18873881, Trichoderma reesei Gene ID: 18488529, Sugiyamaella lignohabitans Gene ID: 30033743, Pseudomonas syringae Gene ID: 1182936, Saccharomyces eubayanus Gene ID: 28933643, Tilletiaria anomala Gene ID: 25263324, Candida orthopsilosis Gene ID: 14536750, Candida dubliniensis Gene ID: 8045036, Ashbya gossypii Gene ID: 4618820, Yarrowia lipolytica Gene ID: 2912994, Debaryomyces hansenii Gene ID: 2900295, Eremothecium sinecaudum Gene ID: 28721758, Lachancea thermotolerans Gene ID: 8294207, Vandenvaltozyma polyspora Gene ID: 5543493, Torulaspora delbrueckii Gene ID: 11503674, Naumovozyma dairenensis Gene ID: 11497048, Naumovozyma dairenensis Gene ID: 11496104, Candida glabrata Gene ID: 2889898, Millerozyma farinosa Gene ID: 14524780, Millerozyma farinosa Gene ID: 14523985, Tetrapisispora blattae Gene ID: 14497097, Kazachstania africana Gene ID: 13886105, Kazachstania africana Gene ID: 13885322, Tetrapisispora phaffii Gene ID: 11530753 and/or Kluyveromyces lactis Gene ID: 3293693. In an embodiment, the glucose-6-phosphate dehydrogenase is a ZWF1 protein (for example from Saccharomyces sp., including Saccharomyces cerevisiae for example), a ZWF1 protein variant, a ZWF1 protein fragment or a protein encoded by a ZWF1 gene ortholog/paralog. In still a further embodiment, the ZWF1 protein has the amino acid sequence of SEQ ID NO: 20, is a variant thereof or is a fragment thereof. In yet another embodiment, a single copy of an heterologous gene coding for the ZWF1 protein is included in the recombinant microbial host cell.
The one or more proteins capable of producing NADPH can include a 6-phosphogluconolactonase which catalyzes the conversion of D-6-phospho-glucono-δ-lactone in 6-phospho-D-gluconate. Existing 6-phosphogluconolactonases are classified in the Enzyme Commission Number class 3.1.1.31. The 6-phosphogluconolactonases that can be overexpressed include, but are not limited to Saccharomyces cerevisiae Gene ID: 856568, Candida albicans Gene ID: 3646625, Saccharomyces eubayanus Gene ID: 28931703, Candida orthopsilosis Gene ID: 14540431, Saccharomyces cerevisiae Gene ID: 853163, Millerozyma farinosa Gene ID: 14522418, Saccharomyces cerevisiae S288c Gene ID: 853155, Saccharomyces eubayanus Gene ID: 28931348. In an embodiment, the 6-phosphogluconolactonase is a SOL3 or SOL4 protein (from Saccharomyces cerevisiae for example), a SOL3 or SOL4 protein variant, a SOL3 or SOL4 protein fragment or a protein encoded by a SOL3 or SOL4 gene ortholog. In another embodiment, the 6-phosphogluconolactonase is a SOL3 protein, a SOL3 protein variant, a SOL3 protein fragment or a protein encoded by a SOL3 gene ortholog/paralog. In still another embodiment, the 6-phosphogluconolactonase is a SOL3 protein (for example from Saccharomyces sp., including Saccharomyces cerevisiae for example). In yet another embodiment, the SOL3 protein has the amino acid sequence of SEQ ID NO: 16, a variant thereof or a fragment thereof. In still another embodiment, a single copy of a heterologous gene coding for a SOL3 protein is included in the recombinant microbial host cell.
The one or more proteins capable of producing NADPH can include a 6-phosphogluconate dehydrogenase which catalyzes the conversion of 6-phospho-D-gluconate in ribulose-5-phosphate and thus produces CO2. Existing 6-phosphogluconate dehydrogenases are classified in the Enzyme Commission Number class 1.1.1.44. The 6-phosphogluconate dehydrogenases that can be overexpressed include, but are not limited to Saccharomyces cerevisiae Gene ID: 856589, Mycobacterium tuberculosis Gene ID: 885755, Candida albicans Gene ID: 3636131, Scheffersomyces stipitis Gene ID: 4851939, Spathaspora passalidarum Gene ID: 18871521, Zymoseptoria tritici Gene ID: 13402018, Ascoidea rubescens Gene ID: 30968350, Aspergillus fumigatus Gene ID: 3508701, Saitoella complicata Gene ID: 30186746, Sphaerulina musiva Gene ID: 27902722, Candida orthopsilosis Gene ID: 14540072, Talaromyces stipitatus Gene ID: 8102542, Aspergillus flavus Gene ID: 7913831, Talaromyces marneffei Gene ID: 7024375, Saccharomyces eubayanus Gene ID: 28931722, Clavispora lusitaniae Gene ID: 8496367, Clavispora lusitaniae Gene ID: 8496118, Saccharomyces cerevisiae Gene ID: 853172, Sugiyamaella lignohabitans Gene ID: 30035723, Mycobacterium tuberculosis Gene ID: 885820, Lactobacillus plantarum Gene ID: 1062157, Gardnerella vaginalis Gene ID: 9904914, Enterococcus faecium Gene ID: 13000204, Mycobacterium leprae Gene ID: 909952, Saccharomyces eubayanus Gene ID: 28931358, Synechococcus phage Gene ID: 4239176 and Meyerozyma guilliermondii Gene ID: 5124800. In an embodiment, the 6-phosphogluconate dehydrogenase is a GND1 or GND2 protein (from Saccharomyces cerevisiae for example), a GND1 or GND2 protein variant, a GND1 or GND2 protein fragment or a protein encoded by a GND1 or GND2 gene ortholog/paralog. In another embodiment, the 6-phosphogluconate dehydrogenase is a GND1 protein, a GND1 protein variant, a GND1 protein fragment or a protein encoded by a GND1 gene ortholog/paralog. In still another embodiment, the GND1 protein has the amino acid sequence of SEQ ID NO: 13, is a variant thereof or is a fragment thereof. In yet another embodiment, a single copy of an heterologous gene coding for the GND1 protein is included in the recombinant microbial host cell.
The recombinant microbial host cell of the present disclosure can include a second additional genetic modification to express at least one of a glucose-6-phosphate dehydrogenase (the ZWF1 protein for example), a 6-phosphogluconolactonase (the SOL3 protein for example) and a 6-phosphogluconate dehydrogenase (the GND1 protein for example). In still another embodiment, the recombinant microbial host cell of the present disclosure can include a second additional genetic modification to express at least two of a glucose-6-phosphate dehydrogenase (the ZWF1 protein for example), a 6-phosphogluconolactonase (the SOL3 protein for example) and a 6-phosphogluconate dehydrogenase (the GND1 protein for example). In yet another embodiment, the microbial host cell of the present disclosure can include of a second additional genetic modification to express a glucose-6-phosphate dehydrogenase (the ZWF1 protein for example), a 6-phosphogluconolactonase (the SOL3 protein for example) and a 6-phosphogluconate dehydrogenase (the GND1 protein for example) In such embodiments, one or more of these proteins can be derived from S. cerevisiae. In addition, the nucleic acid sequences encoding these one or more heterologous proteins can be present in a single copy or more in the microbial recombinant host cell.
In yet another example, the second additional genetic modification for increasing the activity of one or more proteins capable of making NADPH can be made (i) for increasing the activity of one or more proteins in a xylose fermentation pathway (for example by upregulating the expression of the native and/or heterologous xylose reductase (XR) and xylitol dehydrogenase (XDH) enzymes), (ii) for modulating the activity of transcription factors that regulate expression of enzymes of the pentose phosphate pathway (PPP), (iii) for decreasing the activity of the native enzyme glucose-6-P isomerase that competes with the oxidative branch of the PPP, (iv) for increasing the activity of one or more proteins in the ribulose-monophosphate pathway (RuMP, for the conversion fructose-6-P into ribulose-5-P and formaldehyde), (v) for increasing the activity of one or more proteins that function in the dihydroxyacetone (DHA) pathway (for the interconversion of dihydroxyacetone and glyceraldehyde-3-P into xylose-5-P and formaldehyde) and/or (vi) for decreasing the activity of a native dihydroxyacetone kinase enzyme.
vii) Process for Making Ethanol
The recombinant microbial host cell of the present disclosure can advantageously be used in a process for making ethanol. As described herein and shown in the Examples, the recombinant microbial host cell has an increased tolerance towards acetate. As such, the recombinant microbial host cell of the present disclosure can be used to make ethanol in the presence, for example, of less than 20 g/l of acetate (and in some embodiments between 4 to 14 g/l of acetate). In some embodiments, the recombinant microbial cell produces more ethanol than a corresponding strain, due to the direct conversion of acetate to ethanol, and optionally also due to the reduced need to produce glycerol for reoxidizing surplus NADH, which can now be consumed in the conversion of acetate to ethanol, which provides an alternative anaerobic redox sink for NADH.
A further advantage of using the recombinant microbial host cell is that it does not require exogenous glycerol addition to produce ethanol from acetate. As such, the recombinant microbial host cell of the present disclosure are used in a process in which no exogenous glycerol in included in the fermentable substrate.
In the present disclosure the recombinant microorganism can be used to produce ethanol from biomass, which is referred to herein as lignocellulosic material, lignocellulosic substrate, or cellulosic biomass.
In addition, to producing ethanol, the recombinant microorganisms as described herein can be combined, either as recombinant host cells or as engineered metabolic pathways in recombinant host cells, alone, with additional purified enzymes and/or with additional microorganisms (recombinant or not).
Numerous cellulosic substrates can be used in accordance with the present invention. Substrates for cellulose activity assays can be divided into two categories, soluble and insoluble, based on their solubility in water. Soluble substrates include cellodextrins or derivatives, carboxymethyl cellulose (CMC), or hydroxyethyl cellulose (HEC). Insoluble substrates include crystalline cellulose, microcrystalline cellulose (Avicel), amorphous cellulose, such as phosphoric acid swollen cellulose (PASC), dyed or fluorescent cellulose, and pretreated lignocellulosic biomass. These substrates are generally highly ordered cellulosic material and thus only sparingly soluble.
The terms “lignocellulosic material”, “lignocellulosic substrate” and “cellulosic biomass” mean any type of biomass comprising cellulose, hemicellulose, lignin, or combinations thereof, such as but not limited to woody biomass, forage grasses, herbaceous energy crops, non-woody-plant biomass, agricultural wastes and/or agricultural residues, forestry residues and/or forestry wastes, paper-production sludge and/or waste paper sludge, waste-water-treatment sludge, municipal solid waste, corn fiber from wet and dry mill corn ethanol plants, and sugar-processing residues. The terms “hemicellulosics”, “hemicellulosic portions” and “hemicellulosic fractions” mean the non-lignin, non-cellulose elements of lignocellulosic material, such as but not limited to hemicellulose (i.e., comprising xyloglucan, xylan, glucuronoxylan, arabinoxylan, mannan, glucomannan, and galactoglucomannan, among others), pectins (e.g., homogalacturonans, rhamnogalacturonan I and II, and xylogalacturonan), and proteoglycans (e.g., arabinogalactan-protein, extensin, and proline-rich proteins).
In a non-limiting example, the lignocellulosic material can include, but is not limited to, woody biomass, such as recycled wood pulp fiber, sawdust, hardwood, softwood, and combinations thereof; grasses, such as switch grass, cord grass, rye grass, reed canary grass, miscanthus, or a combination thereof; sugar-processing residues, such as but not limited to sugar cane bagasse; agricultural wastes, such as but not limited to rice straw, rice hulls, barley straw, corn cobs, cereal straw, wheat straw, canola straw, oat straw, oat hulls, and corn fiber; stover, such as but not limited to soybean stover, corn stover; succulents, such as but not limited to, Agave; and forestry wastes, such as but not limited to, recycled wood pulp fiber, sawdust, hardwood (e.g., poplar, oak, maple, birch, willow), softwood, or any combination thereof. Lignocellulosic material may comprise one species of fiber; alternatively, lignocellulosic material may comprise a mixture of fibers that originate from different lignocellulosic materials. Other lignocellulosic materials are agricultural wastes, such as cereal straws, including wheat straw, barley straw, canola straw and oat straw; corn fiber; stovers, such as corn stover and soybean stover; grasses, such as switch grass, reed canary grass, cord grass, and miscanthus; or combinations thereof.
Paper sludge is also a viable feedstock for ethanol production. Paper sludge is solid residue arising from pulping and paper-making, and is typically removed from process wastewater in a primary clarifier. At a disposal cost of $30/wet ton, the cost of sludge disposal equates to $5/ton of paper that is produced for sale. The cost of disposing of wet sludge is a significant incentive to convert the material for other uses, such as conversion to ethanol.
It will be appreciated that suitable lignocellulosic material may be any feedstock that contains soluble and/or insoluble cellulose, where the insoluble cellulose may be in a crystalline or non-crystalline form. In various embodiments, the lignocellulosic biomass comprises, for example, wood, corn, corn stover, sawdust, bark, leaves, agricultural and forestry residues, grasses such as switchgrass, ruminant digestion products, municipal wastes, paper mill effluent, newspaper, cardboard or combinations thereof.
In some embodiments, the recombinant microbial host cell of the present disclosure can be used for hydrolyzing a cellulosic substrate, for example a cellulosic substrate as described above, by contacting the cellulosic substrate with a recombinant microorganism of the invention. In some embodiments, the recombinant microbial host cell of the present disclosure can be used for hydrolyzing a cellulosic substrate, for example a cellulosic substrate as described above, by contacting the cellulosic substrate with a co-culture comprising yeast cells expressing heterologous cellulases.
In some embodiments, the recombinant microbial host cell of the present disclosure can be used for fermenting cellulose. Such methods can be accomplished, for example, by culturing a host cell or co-culture in a medium that contains insoluble cellulose to allow saccharification and fermentation of the cellulose.
The production of ethanol can, according to the present process, be performed at temperatures of at least about 20° C., 21° C., 22° C., 23° C., 24° C., 25° C., 26° C., 27° C., 28° C., 29° C., 30° C., about 31° C., about 32° C., about 33° C., about 34° C., about 35° C., about 36° C., about 37° C., about 38° C., about 39° C., about 40° C., about 41° C., about 42° C., about 43° C., about 44° C., about 45° C., about 46° C., about 47° C., about 48° C., about 49° C., or about 50° C.
In some embodiments, the processes can comprise contacting a cellulosic substrate with a recombinant microorganism or co-culture of the invention and additionally contacting the cellulosic substrate with externally produced cellulase enzymes. Exemplary externally produced cellulase enzymes are commercially available and are known to those of skill in the art.
In some embodiments, the methods comprise producing ethanol at a particular rate. For example, in some embodiments, ethanol is produced at a rate of at least about 0.1 mg per hour per liter, at least about 0.25 mg per hour per liter, at least about 0.5 mg per hour per liter, at least about 0.75 mg per hour per liter, at least about 1.0 mg per hour per liter, at least about 2.0 mg per hour per liter, at least about 5.0 mg per hour per liter, at least about 10 mg per hour per liter, at least about 15 mg per hour per liter, at least about 20.0 mg per hour per liter, at least about 25 mg per hour per liter, at least about 30 mg per hour per liter, at least about 50 mg per hour per liter, at least about 100 mg per hour per liter, at least about 200 mg per hour per liter, at least about 300 mg per hour per liter, at least about 400 mg per hour per liter, or at least about 500 mg per hour per liter.
In some embodiments, the recombinant microbial host cells can produce ethanol at a rate of at least about 0.1 mg per hour per liter, at least about 0.25 mg per hour per liter, at least about 0.5 mg per hour per liter, at least about 0.75 mg per hour per liter, at least about 1.0 mg per hour per liter, at least about 2.0 mg per hour per liter, at least about 5.0 mg per hour per liter, at least about 10 mg per hour per liter, at least about 15 mg per hour per liter, at least about 20.0 mg per hour per liter, at least about 25 mg per hour per liter, at least about 30 mg per hour per liter, at least about 50 mg per hour per liter, at least about 100 mg per hour per liter, at least about 200 mg per hour per liter, at least about 300 mg per hour per liter, at least about 400 mg per hour per liter, or at least about 500 mg per hour per liter more than a control strain (lacking heterologous cellulases) and grown under the same conditions. In some embodiments, the ethanol can be produced in the absence of any externally added cellulases.
Ethanol production can be measured using any method known in the art. For example, the quantity of ethanol in fermentation samples can be assessed using HPLC analysis. Many ethanol assay kits are commercially available that use, for example, alcohol oxidase enzyme based assays. Methods of determining ethanol production are within the scope of those skilled in the art from the teachings herein. The U.S. Department of Energy (DOE) provides a method for calculating theoretical ethanol yield.
The present invention will be more readily understood by referring to the following examples which are given to illustrate the invention rather than to limit its scope.
EXAMPLE







TABLE 1







Description of the genotypes of the Saccharomyces cerevisiae strains used


in this Example. All strains, except M2390 shared expression of the


heterologous xylose isomerase from Catonella morbi (SEQ ID NO: 9)


overexpression of XKS1 (SEQ ID NO: 19), the pentose phosphate pathway


genes RPE1 (SEQ ID NO: 15), TAL1 (SEQ ID NO: 17), TLK1 (SEQ ID


NO: 18), RKI1 (SEQ ID NO: 14), deletions of gre3 and ypr1 (to reduce


xylitol formation) and introduction of the YFH1-T163P allele (to


benefit the xylose fermentation rate).








Strains
Genotype





M2390
Non-engineered host strain


M11321
No additional modification


M12613
gpd1Δ, B. adolescentis adhE (4x), STL1 (4x), ACS2


M12623
RAS2-A66T


M12747
RAS2-A66T, gpd2Δ, B. adolescentis adhE (4x), STL1 (4x), ACS2


M12932
RAS2-A66T, gpd2Δ, B. adolescentis adhE (8x), STL1 (4x), ACS2, E. histolytica



ADH1 (4x)


M13446
RAS2-A66T, B. adolescentis adhE (4x), STL (4x), ACS2


M13618
RAS2-A66T, B. adolescentis adhE (8x), STL1 (4x), ACS2, E. histolytica ADH1


M14507
B. adolescentis adhE (4x), STL1 (4x), ASC2, Bacteriodes thetaiotaomicron araA,



araB, araD


M14615
RAS2-A66T, B. adolescentis adhE (10x), STL1 (4x), ACS2, E. histolytica ADH1


M14718
RAS2-A66T, B. adolescentis adhE (10x), STL1 (4x), ACS2, E. histolytica ADH1,



ZWF1, SOL3, GND1


M14745
RAS2-A66T, B. adolescentis adhE (4x), STL1 (4x)


M14747
RAS2-A66T, STL1(4x)


M14749
RAS2-A66T, B. adolescentis adhE (4x)


M14751
RAS2-A66T, B. adolescentis adhE (4x), STL1 (4x), ACS2


M14754
RAS2-A66T, B. adolescentis adhE (4x), ACS2


M14755
RAS2-A66T, ACS2


M14712
RAS2-A66T, B. adolescentis adhE (12x), STL1 (4x), ACS2, E. histolytica ADH1


M14716
RAS2-A66T, B. adolescentis adhE (10x), STL1 (4x), ACS2, E. histolytica ADH1,



ZWF1


M14719
RAS2-A66T, B. adolescentis adhE (10x), STL1 (4x), ASCS2, E. histolytica



ADH1, ZWF1, SOL3, GND1


M14837
RAS2-A66T, B. adolescentis adhE (10x), STL1 (4x), ACS2, E. histolytica ADH1,



ZWF1, SOL3, GND1, gpd2Δ


M15339
RAS2-A66T, B. adolescentis adhE (10x), STL1 (4x), ACS2, E. histolytica ADH1,



ZWF1, SOL3, GND1, gpd2Δ, gpd1Δ


M15380
RAS2-A66T, B. adolescentis adhE (10x), STL1 (4x), ACS2, E. histolytica ADH1,



ZWF1, SOL3, GND1, gpd1Δ









Strain construction. Engineered strains (Table 1) were constructed in a wild-type diploid industrial S. cerevisiae M2390 strain background, using standard transformation and selection techniques known to those skilled in the art, with scarless genomic integrations using integration cassettes that were targeted through homologous recombination. In the genotype descriptions in Table 1, heterologous genes are preceded by the name of their donor organism. All heterologous genes were codon-optimized for expression in S. cerevisiae. Unless noted otherwise, each integration cassette only contained a single copy of each listed gene (making for a total of two gene copies for both chromosome copies of the diploid strain). In the case of exceptions to this rule, the total gene copy number in the strain at the integration site is listed after the gene name in parenthesis (e.g., “(4×)” means that the integration cassette contained two copies of the listed gene, making for a total of four gene copies for both chromosome copies). All genes in integration cassettes were expressed through the use of endogenous promoters and terminators and integrated at neutral integration sites.
Cell culture and subsequent analysis. Strains were maintained in glycerol stocks at −80° C. To create a fermentation inoculum, freezer stocks were first struck to YPD plates (yeast extract, peptone, dextrose), which were then used to inoculate 5 ml YPD40 media in 14 ml capped round-bottom tubes. After 24 hours incubation at 35° C. in a rotary drum, 2 mL culture was spun down and resuspended in water to 300 μl, which was then used to inoculate a fermentation bottle. Fermentations took place in 60 mL sealed serum bottles, filled with either 20 mL or 30 mL of media, which were then incubated at 32° C. in a rotary shaker. The initial pH of the fermentation media was adjusted to 5.5. Off-gas production was continuously monitored through either accumulated pressure (which was periodically vented) or continuous mass flow (with no pressure buildup). Once the fermentations had reached their end, final high performance liquid chromatography (HPLC) measurements were taken.
Fermentation on YPD60X60Ace9 medium. Strains to be tested were struck out onto a YPD40 (10 g/L yeast extract, 20 g/L peptone, 40 g/L dextrose, and 15 g/L agarose) agar plate and incubated for 2 days at 30° C. A 10 uL inoculum loop sized cell mass scraped of the agar plate was then used to inoculate one 250 mL erlenmeyer flask for each strain with a 55 mL volume of YPD40 and incubated at 32° C. and 200 RPM for 20 hours. A 50 mL volume of the liquid cultures were spun down at 4000 RPM for 3 minutes in 50 mL tubes, decanted, and reconstituted with a 3 mL volume of sterile water. To determine the dry cell weight (DCW) of each of the samples for inoculation, a 1 mL volume of each sample was analyzed using a Sartorius LMA200 moisture meter. The fermentation medium YPD60X60Ace9 (10 g/L yeast extract, 20 g/L peptone, 60 g/L dextrose, 60 g/L xylose, and 9 g/L acetic acid from potassium acetate set at an initial pH of 4.9 using sulfuric acid) was aliquoted at a volume of 30 mL into 60 mL serum bottles in a laminar flow hood. Each strain was then inoculated at an initial DCW of 0.1 g/L in triplicate and the serum bottles were then sealed with grey butyl rubber stoppers with aluminum crimps. Bottles were vented with 23g needles and placed in an incubator (32° C. and 150 RPM), monitored with a mass flow meter for CO2 production and sampled for HPLC at 24 and 48 hours looking at carbohydrates, ethanol, glycerol, and organic acids.
Fermentation on YPD20X10A10Ace4Gly1 medium. Strains to be tested were struck out onto a YPD40 (10 g/L yeast extract, 20 g/L peptone, 40 g/L dextrose, and 15 g/L agarose) agar plate and incubated for 2 days at 30° C. A 10 uL inoculum loop sized cell mass scraped of the agar plate was then used to inoculate one 250 mL erlenmeyer flask for each strain with a 55 mL volume of YPD40 and incubated at 32° C. and 200 RPM for 20 hours. A 50 mL volume of the liquid cultures were spun down at 4000 RPM for 3 minutes in 50 mL tubes, decanted, and reconstituted with a 3 mL volume of sterile water. To determine the dry cell weight (DCW) of each of the samples for inoculation, a 1 mL volume of each sample was analyzed using a Sartorius LMA200 moisture meter. The fermentation medium YPD20X10A10Ace4Gly1 (10 g/L yeast extract, 20 g/L peptone, 20 g/L glucose, 10 g/L xylose, 10 g/L arabinose, 4 g/L acetate from potassium acetate, and 1 g/L glycerol) was aliquoted at a volume of 30 mL into 60 mL serum bottles in a laminar flow hood. Each strain was then inoculated at an initial DCW of 0.1 g/L in triplicate and the serum bottles were then sealed with grey butyl rubber stoppers with aluminum crimps. Bottles were vented with 23g needles and placed in an incubator at 32° C. and 150 RPM monitored for mass flow via Automated CO2 Analysis (ACAN) taking HPLC samples the end of fermentation looking at carbohydrates, ethanol, glycerol, and organic acids.
Corn fermentation. Fermentations were run using a commercially produced pretreated corn fiber cellulosic substrate. These fermentations were set up essentially the same as those described above (Fermentation on YPD20X10A10Ace4Gly1 medium section) except a 0.3 g/L DCW inoculum was used and the 30 mL corn fiber substrate was approximately 20% total solids.
Strain M12623 is engineered to utilize xylose and was used as the parent strain for engineering of all strains expressing the RAS2-A66T mutation (as described in WO2017/158189). Strain M13446 additionally expresses the heterologous ADHE enzyme from B. adolescentis (SEQ ID NO: 1) and overexpress the native glycerol transporter STL1 (SEQ ID NO: 2) and acetyl-CoA synthetase ACS2 (SEQ ID NO: 3). Strain M13446 exhibits acetate consumption, reduced glycerol production and increased ethanol production in a challenging industrial cellulosic substrate compare to M12623 (FIG. 2) without any negative impact on fermentation rates (FIG. 1). FIG. 1 also shows that a strain with a gpd1 deletion (M12613) showed a decreased fermentation rate in relation to a GPD+ strain with otherwise comparable genotypes (M13446). Strain M12747, containing a deletion of GPD2 in addition to the modifications found in M13446, exhibited similar acetate consumption and increased ethanol titers indicating that a gpd2 deletion is not always necessary for, or beneficial to, conversion of acetate into ethanol (FIG. 2).
Strains M12747 and M13446 were further engineered to also express a heterologous NADPH-specific ADH from Entamoeba histolytica (EhADH1, SEQ ID NO: 4), resulting in strains M12932 and M13618, respectively. This was done in an attempt to increase anaerobic NADH availability for the acetate utilization pathway and glycerol production. Although the incorporation of E. histolytica ADH1 increased glycerol biosynthesis more in the GPD2+ M13618 than in the d2-M12932 in a cellulosic substrate derived from a thermochemically and enzymatically pretreated plant material substrate, M13618 still produced less glycerol than the M12623 parent strain, and similar improvements in final ethanol and acetate titers were obtained with or without the gpd2 deletion (FIG. 3). Thus, overexpression of ADHE, STL1 and ACS2 can increase ethanol titers through acetate utilization, even in strains overproducing NADH (through the overexpression of EhADH1), without causing glycerol overproduction beyond the wild-type level.
The impact of the various genetic modifications in YP acetate media, with either glucose as the main carbon source, was then investigated. The combination of ADHE and STL1 overexpression (see strain M14745) was effective in reducing glycerol titers and increasing ethanol titers in both media, but acetate uptake was not apparent in the YPD media. Nevertheless, the results in the YPX medium indicated that adhE and STL1 alone enable acetate consumption with the addition of ACS2 providing additional benefit (compare strains M12623, M14745, and M14751 in FIG. 5). The highest acetate uptake was observed in strain M13618, with increased expression of adhE (8 copies) and introduction of the E. histolytica ADH1, although improvements in ethanol titer above the parent strain M12623 were modest in both media. These results also show that M13618 supported increased acetate conversion in media without addition of a co-substrate such as glycerol.
It was then determined if ADHE expression was limited in M13618 and if ADHE could effectively compete with the glycerol synthesis pathway for the additional NADH generated through expression of EhADH1. The ADHE copy number was thus increased from 8 (M13618) to 10 (M14615) to 12 (M14712), which significantly improved ethanol titers in industrial hydrolysate by reducing glycerol production and increasing acetate consumption (FIG. 6). The strains with the engineered acetate-to-ethanol pathway also showed improved xylose fermentation compared to the M12623 parent strain, perhaps due to increased media detoxification and increased strain robustness.
It was then tested if acetate conversion could be further stimulated by increasing the availability of NADPH, by increasing the expression of genes in the oxidative pentose phosphate pathway (ZWF, GND1, SOL3). Interestingly, the results in FIG. 6 using an industrial cellulosic medium show that ZWF1 overexpression by itself (M14716) improved acetate consumption but resulted in decreased xylose-utilization. When ZWF1 overexpression was combined with SOL3 and GND1 overexpression (M14719), acetate consumption further increased and xylose-utilization improved (FIG. 6). The fermentation rates mirror the results seen in the HPLC analysis (FIG. 7).
Having improved the acetate conversion and strain robustness through increased adhE expression, expression of EhADH1 and overexpression of ZWF1, GND1, and SOL3, the question of the benefit of modifying native glycerol production was revisited. Strain M14718 was used as the parent to create strains with gpd2 deleted (M14837), gpd1 deleted (M15380), or both gpd1 and gpd2 deleted (M15339). The deletion of either gpd1 or gpd2 resulted in a slower fermentation than M14718 on YPD60X60Ace9 media (10 g/L yeast extract, 20 g/L peptone, 60 g/L glucose, 60 g/L xylose, 9 g/L acetate, FIG. 8). M14718 also had faster fermentation kinetics than the unengineered strain M2390 and the strain containing only the modifications enabling xylose-utilization (M12623). The HPLC results show M14718 consumed more acetate, glucose and xylose than either M14837 (gpd2 deletion), M15380 (gpd1 deletion), or M15339 (gpd1 and gpd2 deletions) and produced the highest ethanol titer (FIG. 9). This data indicates that the presence of GPD1 and GPD2 (i.e., the native glycerol pathway) in a strain provides increased robustness and improved strain performance in challenging substrates.
The ability to combine technology for fermenting arabinose with acetate conversion was demonstrated using strain M14507 (engineered to express the B. thetaiotaomicron araA, araB, and araD genes). M14507 also contains the pathway for xylose fermentation found in the other strains described above as well as expression of Ba adhE and overexpression of STL1 and ACS2. In defined media YPD20X10A10Ace4Gly1 (10 g/L yeast extract, 20 g/L peptone, 20 g/L glucose, 10 g/L xylose, and 10 g/L arabinose, 4 g/L acetate, and 1 g/L glycerol) strain M14507 consumed all available glucose, xylose, and arabinose as well as  ̃0.3 g/L acetate resulting in the highest ethanol titer of the tested strains (FIG. 11) and also the highest ethanol yield on gram sugar consumed (Table 2). Strain M14507 also had the lowest glycerol of the three strains despite having consumed 10 and 20 g/L more sugar and generating the greatest amount of cell mass (FIG. 11). The fermentation rate and lag time for M14507 was similar to M2390 and M11321 indicating no negative interactions of the additional arabinose engineering on strain performance (FIG. 10).







TABLE 2







Summary of yield on glucose, xylose, and arabinose


(YPD20X10A10Ace4Gly1) under anaerobic conditions.


Yield is calculated as gram of product produced per


gram of sugar consumed (glucose + xylose + arabinose).









YPD20X10A10Ace4Gly1











M2390
M11321
M14507
















Yield (g/g)
Ethanol
0.440
0.457
0.461




Glycerol
0.026
0.022
0.011




Acetic acid
−0.004
−0.005
−0.009




DCW
0.140
0.109
0.104










Max Ethanol (g/L)
9.13
14.10
18.84









When used to ferment a corn fiber cellulosic substrate, strain M14507 appeared to have largely completed the fermentation after about 54 hours (FIG. 12). Strain M2390 stopped fermenting after about 24 hours at a significantly lower CO2 level than M11321 and M14507 with M11321's fermentation ending around 48 hours with a lower CO2 level than M14507 (FIG. 12). The 72 hours HPLC samples showed that M14507 consumed the majority of the xylose and arabinose resulting in about 18 g/L more ethanol produced than the control strain M2390 and about 8 g/L more ethanol produced than M11321, with a  ̃109% and  ̃33% increase in ethanol titer respectively in this corn fiber fermentation (Table 3). A slight decrease in xylose concentration is observed for M2390 and is most likely due partly to the conversion of xylose into xylitol by endogenous aldose reductases enzymes as well as consumption of other compounds which cannot be distinguished from xylose using our HPLC analysis methods. Strains M11321 and M14507 consumed the same amount of glucose and xylose with M14507 producing 0.7 g/L less glycerol (20% reduction) and consuming 0.5 g/L more acetate compared to M11321.







TABLE 3







HPLC results for samples taken at 72 hours from the corn fiber


cellulosic substrate fermentation. All values are in g/L.














Glucose
Xylose
Arabinose
Glycerol
Acetic Acid
Ethanol

















Substrate
33.0
28.8
17.8
6.2
4.0
0.0


M2390
0.0
27.0
17.1
8.2
4.1
16.2


M11321
0.7
8.1
17.1
9.6
4.5
25.6


M14507
0.0
3.8
1.1
8.9
4.0
34.0









While the invention has been described in connection with specific embodiments thereof, it will be understood that the scope of the claims should not be limited by the preferred embodiments set forth in the examples, but should be given the broadest interpretation consistent with the description as a whole.
REFERENCES


    De Bont, J. A. M., Teunissen, A. W. R. H., 2011. Yeast Strains Engineered to Produce Ethanol from Acetic Acid and Glycerol. WO2011149353 (A1).
    De Bont, J. A. M., Teunissen, A. W. R. H., Klaassen, P., Hartman, W. W. A., Van Beusekom, S., 2015. Yeast strains engineered to produce ethanol from acetic acid and glycerol. US2015176032 (A1).
    Guadalupe Medina, V., Almering, M. J. H., van Maris, A. J. A., Pronk, J. T., 2010. Elimination of glycerol production in anaerobic cultures of a Saccharomyces cerevisiae strain engineered to use acetic acid as an electron acceptor. Appl Env. Microbiol 76, 190-195. doi:10.1128/AEM.01772-09.
    Guadalupe Medina, V., Metz, B., Oud, B., van der Graaf, C. M., Mans, R., Pronk, J. T., van Maris, A. J. A., 2014. Evolutionary engineering of a glycerol-3-phosphate dehydrogenase-negative, acetate-reducing Saccharomyces cerevisiae strain enables anaerobic growth at high glucose concentrations. Microb. Biotechnol. 7, 44-53. doi:10.1111/1751-7915.12080.
    Henningsen, B. M., Hon, S., Covalla, S. F., Sonu, C., Argyros, D. A., Barrett, T. F., Wiswall, E., Froehlich, A. C., Zelle, R. M., 2015. Increasing anaerobic acetate consumption and ethanol yield in Saccharomyces cerevisiae with NADPH-specific alcohol dehydrogenase. Appl. Environ. Microbiol. 81, 8108-8117. doi:10.1128/AEM.01689-15.
    Onishi, T., Tada, N., Yasutani, N., Katahira, S., Ishida, N., Nagura, R., 2016. Method for Producing Ethanol Using Recombinant Yeast. US2016002674 (A1).
    US Patent Application published under 2016/040152.
    Wei, N., Quarterman, J., Kim, S. R., Cate, J. H. D., Jin, Y.-S., 2013. Enhanced biofuel production through coupled acetic acid and xylose consumption by engineered yeast. Nat. Commun. 4, 2580. doi:10.1038/ncomms3580.
    Zhang, G.-C., Kong, I. I., Wei, N., Peng, D., Turner, T. L., Sung, B. H., Sohn, J.-H., Jin, Y.-S., 2016. Optimization of an acetate reduction pathway for producing cellulosic ethanol by engineered yeast. Biotechnol. Bioeng. 113, 2587-2596. doi:10.1002/bit.26021.
    Zhang, L., Tang, Y., Guo, Z., Ding, Z., Shi, G., 2011. Improving the ethanol yield by reducing glycerol formation using cofactor regulation in Saccharomyces cerevisiae. Biotechnol. Lett. 33, 1375-1380. doi:10.1007/s10529-011-0588-6.

## Claims

1. A recombinant microbial host cell comprising:
a first genetic modification for increasing, when compared to a control microbial host cell lacking the first genetic modification, the activity of one or more proteins that function in a first metabolic pathway to convert acetate into an alcohol in the microbial host cell, wherein the one or more proteins that function in the first metabolic pathway comprise a protein having acetylating acetaldehyde dehydrogenase activity or a protein having acetylating acetaldehyde dehydrogenase activity and alcohol dehydrogenase activity (ADHE);
a second genetic modification for increasing, when compared to the control microbial host cell lacking the second genetic modification, the activity of one or more proteins that function in a second metabolic pathway to import glycerol in the recombinant microbial host cell, wherein the protein that function in the second metabolic pathway is an STL1 polypeptide; and
a third genetic modification for increasing, when compared to the control microbial host cell lacking the third genetic modification, the activity of one or more proteins that function in a third metabolic pathway to convert a C5 carbohydrate into the alcohol in the microbial host cell, wherein the one or more proteins that function in the third metabolic pathway comprise a protein having xylose isomerase activity from the genus Catonella sp.; and
wherein the recombinant microbial host cell comprises and natively expresses native proteins that function in a fourth native metabolic pathway to produce glycerol in the microbial host cell, wherein the native proteins that function in the fourth native metabolic pathway to produce glycerol comprise a GPD1 protein, a GPD2 protein, a GPP1 protein and a GPP2 protein.

2. The recombinant microbial host cell of claim 1, wherein the alcohol is ethanol.

3. The recombinant microbial host cell of claim 1, wherein the one or more proteins that function in the first, second or third metabolic pathway are heterologous proteins.

4. The recombinant microbial host cell of claim 1, wherein the one or more protein that function in the first metabolic pathway further comprises a protein having acetyl-CoA synthetase activity or is an ACS2 polypeptide.

5. The recombinant microbial host cell of claim 1, further comprising at least one of a first additional genetic modification, wherein the first additional genetic modification is:
a deletion in at least one an aldose reductase gene;
a mutation in a polypeptide encoded by an iron-sulfur cluster gene; or
a mutation in a RAS2 polypeptide.

6. The recombinant microbial host cell of claim 5, wherein the aldose reductase gene is a GRE3 gene and/or a YPR1 gene.

7. The recombinant microbial host cell of claim 5, wherein the iron sulfur cluster gene is a YFH1 gene, a ISU1 gene and/or a NFS1 gene.

8. The recombinant microbial host cell of claim 1 further comprising a fifth genetic modification for increasing the activity of one or more heterologous proteins that function in a fifth metabolic pathway for increasing the availability of electrons in the form of a reduced redox cofactor in the microbial host cell.

9. The recombinant microbial host cell of claim 8, wherein the fifth genetic modification is for increasing the activity of a NADPH-dependent alcohol dehydrogenase.

10. The recombinant microbial host cell of claim 9, wherein the NADPH-dependent alcohol dehydrogenase is an ADH1 polypeptide.

11. The recombinant microbial host cell of claim 9, further comprising a second additional genetic modification for increasing the activity of a protein capable of producing NADPH.

12. The recombinant microbial host cell of claim 11, wherein the protein capable of producing NADPH is at least one of a ZWF1 protein, a SOL3 protein and/or a GND1 protein.

13. The recombinant microbial host cell of claim 1 which is a yeast host cell.

14. The recombinant microbial host cell of claim 13 wherein the yeast host cell is a yeast of genus Saccharomyces.

15. The recombinant microbial host cell of claim 14, wherein the yeast of genus Saccharomyces is a yeast of species Saccharomyces cerevisiae.

16. The recombinant microbial host cell of claim 1, wherein the protein having acetylating acetaldehyde dehydrogenase and alcohol dehydrogenase activity is an ADHE polypeptide from the genus Bifidobacterium sp. or from Bifidobacterium adolescentis.

17. The recombinant microbial host cell of claim 4, wherein the ACS2 polypeptide is from the genus Saccharomyces sp. or from Saccharomyces cerevisiae.

18. The recombinant microbial host cell of claim 1, wherein the STL1 polypeptide is from the genus Saccharomyces sp. or Pichia sp.; or from Saccharomyces cerevisiae or Pichia sorbitophila.

19. The recombinant microbial host cell of claim 1, wherein the protein having xylose isomerase activity is from Catonella morbi.

20. The recombinant microbial host cell of claim 1, wherein the one or more proteins that function in the third metabolic pathway further comprise a protein having xylulokinase activity, a protein having transketolase activity, a protein having transaldolase activity, a protein having ribose-5-phosphate isomerase activity, and/or a protein having ribulose-phosphate 3-epimerase activity.

21. The recombinant microbial host cell of claim 1, wherein the one or more proteins that function in the third metabolic pathway further comprise an arabinose transporter, an ARAA polypeptide, an ARAB polypeptide, and/or an ARAD polypeptide.

22. The recombinant microbial host cell of claim 21, wherein at least one of the ARAA, ARAB or ARAD is from the genus Bacteroides sp. or from Bacteroides thetaiotaomicron.