Patent Application
20230374443
The invention relates to a yeast cell having the ability to produce a desired fermentation product and to a process for producing a fermentation product wherein said yeast cell is used.
Yeast-based fermentation processes are applied for industrial production of a broad and rapidly expanding range of chemical compounds from conventional and renewable carbohydrate feedstocks.
Especially in anaerobic fermentation processes, redox balancing of the cofactor couple NADH/NAD+ can cause important challenges for product yields. For example, a major challenge relating to the stoichiometry of yeast-based ethanol production is that substantial amounts of glycerol are invariably formed as a byproduct. It has been estimated that, in typical industrial ethanol processes, up to about 4 wt. % of the sugar feedstock is converted into glycerol (Nissen et al. Yeast 16 (2000) 463-474).
Glycerol production under anaerobic conditions is primarily linked to the redox balancing mechanisms in the yeast cell. During anaerobic growth of S. cerevisiae, sugar dissimilation occurs via so-called alcoholic fermentation. In this process, the NADH formed via the NAD+-dependent glycolytic glyceraldehyde-3-phosphate dehydrogenase reaction is reoxidized by converting acetaldehyde, formed by decarboxylation of pyruvate, to ethanol via NADH-dependent alcohol dehydrogenase. The fixed stoichiometry of this redox-neutral dissimilatory pathway causes problems when a net reduction of NAD+ to NADH occurs elsewhere in the metabolism. Under anaerobic conditions, in this situation, NADH reoxidation in S. cerevisiae is strictly dependent on reduction of sugar to glycerol. Glycerol formation is initiated by reduction of the glycolytic intermediate dihydroxyacetone phosphate (DHAP) to glycerol 3-phosphate (glycerol-3P), a reaction catalyzed by NADH-dependent glycerol 3-phosphate dehydrogenase. Subsequently, the glycerol 3-phosphate formed in this reaction is hydrolysed by glycerol-3-phosphatase to yield glycerol. Consequently, glycerol is a major by-product during anaerobic production of ethanol by S. cerevisiae. The production of glycerol is undesired as it reduces overall conversion of sugar to a desired fermentation product such as ethanol. Further, the presence of glycerol in effluents of fermentation plants may impose costs for waste-water treatment.
Nitrogen is a key nutrient for yeast cells. As described by Linder in his chapter 7 on Nitrogen Assimilation Pathways in Budding Yeasts, in the handbook “Non-conventional Yeasts: from Basic Research to Application”, edited by Sibirney, published by Springer Nature Switzerland AG (2019) pages 197 and following, ammonia (NH3) is one of the simplest nitrogen substrates used as a nitrogen source by budding yeasts.
According to Linder, the vast majority of biosynthetic pathways for nitrogen-containing biomolecules in yeast first require ammonia to be converted into L-glutamate and L-glutamine, which are then used as amino group donors in downstream anabolic transamination reactions. The enzyme NADP+-dependent glutamate dehydrogenase (EC 1.4.1.4; encoded by the GDH1 gene) catalyzes the amination of α-ketoglutarate to form I-glutamate, while the enzyme glutamine synthetase (EC 6.3.1.2; encoded by the GLN1 gene) catalyzes the amination of I-glutamate to form I-glutamine. A second copy of the GDH1 gene (termed GDH3) has been described in S. cerevisiae and appears to play a distinct physiological role in nitrogen metabolism.
According to Linder, the ability to assimilate inorganic nitrogen sources other than ammonia is thought to be rare among budding yeasts. Nitrate (NO3−) is said to be assimilated by a two-step reduction via nitrite (NO2−) to produce ammonia. The reduction of nitrate into nitrite is said to be carried out by the enzyme nitrate reductase (EC 1.7.1.2/EC 1.7.1.3), which is encoded by the YNR1 gene. Linder indicates that in addition to the presence of flavin adenine dinucleotide (FAD) and heme prosthetic groups, nitrate reductase is one of the few enzymes currently known in budding yeasts that require the molybdenum cofactor (MoCo) for its activity. Linder explains that the redox cofactor requirements for yeast nitrate reductase appear to differ between species. The nitrate reductase in Blastobotrys adeninivorans (family Trichomonascaceae) is thought specific for NADPH, while the nitrate reductases of Candida boidinii (family Pichiaceae), Cyberlindnera jadinii (family Phaffomycetaceae), and Ogataea polymorpha (family Pichiaceae) are thought to be able to use both NADH and NADPH. Nitrite is said to be further reduced to ammonia by the FAD-containing enzyme nitrite reductase (EC 1.7.1.4), which is encoded by the YNI1 gene. The redox cofactor specificity for budding yeast nitrite reductases is indicated by Linder to have not been studied in a comprehensive manner.
Also in the article by Siverio, titled “Assimilation of nitrate by yeasts”, published in FEMS Microbiology Reviews vol. 26 (2002) pages 277-284, it is mentioned that yeasts are able to use a great variety of compounds as nitrogen sources. However, the use of nitrate and nitrite is restricted to relatively few species of different genera. It is mentioned that yeasts of the genera Saccharomyces and Schizosaccharomyces are unable to use nitrate or nitrite as sole nitrogen source. The yeast studied by Siverio, Hansenula polymorpha, now renamed as Pichia angusta, was found to do comprise nitrate-reductase activity.
As indicated by Linder above, ammonia is a preferred nitrogen source for yeast cultivation. Urea can be a cheap source of ammonia. Urea can be easily broken down into two molecules of ammonium ion and one molecule of carbon dioxide. However, as indicated by Ingledew et al, in their article titled “Yeast foods and ethyl carbamate formation in wine”, published in the American Journal of Enology and Viticulture, (1987), vol. 38, pages 332-335, many countries have now banned the use of urea as a yeast food ingredient for potable alcohol manufacturing because it leads to the production of small amounts of urethane (ethyl carbamate) which is a suspected carcinogen in foods. Yoa et al, in their article titled “Quantitative Analysis of Ethyl Carbamate in Distillers Grains Coproducts and Bovine Plasma by Gas Chromatography—Mass Spectrometry”, published in the J. Agric. Food Chem. (2020), vol. 68, 10984-10991 have developed a gas chromatography—mass spectrometry assay to quantify ethyl carbamate (abbreviated as EC, mentioned to be a Group 2A probable human carcinogen) extracted from various distillers grains co-products and found that corn condensed distillers solubles contained the highest concentration of ethyl carbamate, ranging from 1618 to 2956 ng/g. Concentrations of ethyl carbamate in other types of distillers grains co-products varied from 17 to 917 ng/g. Cattle fed distillers grains coproducts that constituted 19-38% of the total feed (as-fed) were found to contain 2-3 ng/mL of ethyl carbamate in blood plasma.
WO2013/076144A2 describes a recombinant microorganism engineered for the production of 2,3-butanediol (BDO). The patent publication describes that 2,3-butanediol is a by-product of alcoholic fermentation by yeast and usually one of the most abundant minor constituent of wine. It is indicated that numerous attempts have been made to engineer Saccharomyces cerevisiae strains with reduced acetoin yields, by re-orienting carbons toward glycerol and 2,3-BDO to obtain low-alcohol yeasts with desirable organoleptic features, permitting the decrease of the ethanol contents in wines. WO2013076144A2 is related to a recombinant microorganism engineered to produce 2,3-butanediol (BDO) wherein said microorganism is chosen among bacterium or yeast and overexpresses at least one gene encoding a polypeptide involved in the conversion of pyruvate into 2,3-butanediol. Six different metabolic pathways are exemplified applying NADH-dependent butanediol dehydrogenase and/or NADH-dependent acetoin dehydrogenase.
In WO2013/076144A2 a number of optimizations of 2,3-butanediol production are described. In passing, as an example, it is mentioned that NADH-dependant glyceraldehyde-3-phosphate dehydrogenase can be replaced by an NADPH-dependant enzyme. It is noted that in this specific case the BDO producing organism will produce an excess of NADPH. It is mentioned that this NADPH in turn can be used via assimilatory nitrate reduction, requiring the introduction of nitrate reductase into certain yeast strains that lack this enzyme.
It would be an advancement in the art to provide a novel yeast cell, which is suitable for an anaerobic fermentation process for the production of a fermentation product, such as ethanol, which has a reduced glycerol production compared to its corresponding wild-type organism or which lacks glycerol production if the cell is used for the fermentative preparation of ethanol.
It would further be an advancement in the art to provide a novel yeast cell, the use of which leads to less contamination with lactic acid bacteria in an anaerobic fermentation process. Without wishing to be bound by any kind of theory, it is thought that contamination by lactic acid bacteria can reduce ethanol yield during fermentation of starch-based feedstocks by Saccharomyces yeast cells.
It would further be an advancement in the art to provide a novel yeast cell, which—when used in an anaerobic fermentation process—leads to the production of a commercially interesting yield of distillers grains co-products containing a reduced amount of ethylcarbamate and/or an otherwise improved quality as compared to distillers grains co-products obtained with its wild-type counterpart.
Accordingly this invention provides a Saccharomyces yeast cell, preferably a Saccharomyces cerevisae yeast cell, comprising one or more nucleic acid sequences encoding an enzyme having NADH-dependent nitrate reductase activity and/or one or more nucleic acid sequences encoding an enzyme having NADH-dependent nitrite reductase activity.
Preferably such Saccharomyces yeast cell further comprises one or more nucleic acid sequences encoding an enzyme having nitrate and/or nitrite transporter activity.
Further, such Saccharomyces yeast cell may preferably comprise flavin adenine dinucleotide (FAD), one or more heme prosthetic groups, and/or a molybdenum cofactor (MoCo) and/or one or more nucleic acid sequences encoding a flavin adenine dinucleotide (FAD), one or more heme prosthetic groups, and/or a molybdenum cofactor (MoCo).
Preferably the Saccharomyces yeast cell is a transgenic, recombinant and/or genetically modified Saccharomyces yeast cell. In such case, the above nucleic acid sequences are preferably nucleic acid sequences that are heterologous to the host cell that is used to construe such transgenic, recombinant and/or genetically modified Saccharomyces yeast cell.
Advantageously the Saccharomyces yeast cell, when used in a fermentation process, may produce less ethyl carbamate compared to corresponding wild-type cells.
Advantageously the Saccharomyces yeast cell, when used in a fermentation process, may produce less glycerol compared to corresponding wild-type cells. Preferably the Saccharomyces yeast cells may either be free of glycerol phosphate phosphatase activity or have reduced glycerol phosphate phosphatase activity compared to corresponding wild-type cells. More preferably the Saccharomyces yeast cells may comprise a genomic mutation in at least one gene selected from the group consisting of GPD1, GPD2, GPP1 and GPP2, preferably a deletion of one or more genes selected from the group consisting of GPD1, GPD2, GPP1 and GPP2.
Preferably the Saccharomyces yeast cell may further comprise:
In addition the invention provides an anaerobic fermentation process for the production of a fermentation product, comprising fermenting of a feed, which feed comprises an oxidized nitrogen source and a fermentable carbon source, using a Saccharomyces yeast cell as described herein.
Preferably the fermentable carbon source comprises or consists of one or more monosaccharides, disaccharides and/or polysaccharides, such as starch. Preferably the oxidized nitrogen source comprises or consists of:
Conveniently the oxidized nitrogen source may be part of a composition comprising nitrate and/or nitrite in combination with one or more other nitrogen sources selected from the group consisting of ammonium, ammonia and urea.
Advantageously a fermentation product may be produced selected from the group consisting of ethanol, n-butanol, isobutanol, lactic acid, 3-hydroxy-propionic acid, acrylic acid, acetic acid, succinic acid, fumaric acid, malic acid, itaconic acid, maleic acid, citric acid, adipic acid.
In addition a fermentation co-product may be produced, which fermentation co-product preferably comprises or consists of distillers grains, such as for example distillers wet grains and/or distillers dried grains, with or without solubles. Such fermentation co-product, such as such distillers grains, may advantageously comprise equal to or less than 17 ng/g of ethyl carbamate.
The invention further provides a product comprising distillers grains, obtained or obtainable by a fermentation process as described herein. In addition, the invention provides a product comprising distillers grains comprising equal to or less than 17 ng/g of ethyl carbamate. Such distillers grains may comprise or consist of distillers wet grains and/or distillers dried grains, with or without solubles.
The invention further provide a use of a fermentation co-product as described herein in an animal feed and/or in a fertilizer.
The Saccharomyces yeast cell according to the invention has in particular been found advantageous in that glycerol production and/or ethyl carbamate production may be considerably reduced or essentially eliminated and production of desired products, for example ethanol, may be increased. The invention allows one to increase the cytosolic NADH level in the Saccharomyces yeast cell. For example, in an ethanol fermentation process, this can advantageously lead to an improved yield of ethanol and/or a reduction in the formation of glycerol. These advantages are further detailed herein below.
In addition, the invention allows the Saccharomyces yeast cell to have an advantage over contaminants such as lactic acid bacteria, when fermentation is carried out with a feed or medium comprising an oxidized nitrogen source. Due to the capability of the Saccharomyces yeast cell to convert the oxidized nitrogen source, whereas the lactic acid bacteria may not have this capability or may have this capability to a lesser extent, the risk that the lactic acid bacteria reach a critical concentration is reduced.
This application contains a Sequence Listing in computer readable form, which is incorporated herein by reference. An overview is provided by Table 1 below:
Zea mays
Spinacia oleracea
Escherichia coli
Escherichia coli
Emericella nidulans
Pichia angusta
Escherichia coli
Escherichia coli
Escherichia coli
Escherichia coli
Escherichia coli
Escherichia coli
Escherichia coli
Escherichia coli
Escherichia coli
Escherichia coli
Escherichia coli
Escherichia coli
Escherichia coli
Escherichia coli
Escherichia coli
Saccharomyces cerevisiae
Arabidopsis thaliana
Arabidopsis thaliana
Arabidopsis thaliana
Arabidopsis thaliana
Arabidopsis thaliana
Arabidopsis thaliana
In the context of this patent application, each of the above protein/amino acid sequences is preferably encoded by a DNA/nucleic acid sequence that is codon-pair optimized for expression in S. cerevisiae. In order to reach an optimal expression one or more promoters may be added. Promoters may be regulated from strong to weak and may include one or more of TDH3, FBA1, ENO2, PGK1, TEF1, HTA1, HHF2, RPL8A, CHO1, RPS3, EFT2, HTA2, ACT1, PFY1, CUP1, ZUO1, VMA6 and/or ANB1, HEM13, YHK8, FET4, TIR4, AAC3.
Unless defined otherwise or clearly indicated by context, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art.
Throughout the present specification and the accompanying claims, the words “comprise” and “include” and variations such as “comprises”, “comprising”, “includes” and “including” are to be interpreted inclusively. That is, these words are intended to convey the possible inclusion of other elements or integers not specifically recited, where the context allows.
The articles “a” and “an” are used herein to refer to one or to more than one (i.e. to one or at least one) of the grammatical object of the article. By way of example, “an element” may mean one element or more than one element. When referring to a noun (e.g. a compound, an additive, etc.) in the singular, the plural is meant to be included. Thus, when referring to a specific moiety, e.g. “gene”, this means “at least one” of that gene, e.g. “at least one gene”, unless specified otherwise.
When referring to a compound of which several isomers exist (e.g. a D and an L enantiomer), the compound in principle includes all enantiomers, diastereomers and cis/trans isomers of that compound that may be used in the particular aspect of the invention; in particular when referring to such as compound, it includes the natural isomer(s).
The term “carbon source” refers to a source of carbon, preferably a compound or molecule comprising carbon. Preferably the carbon source is a carbohydrate. A carbohydrate is understood herein to be an organic compound made of carbon, oxygen and hydrogen. Suitably the carbon source may be selected from the group consisting of mono-, di- and/or polysaccharides, polyols, acids and acid salts. More preferably the carbon source is a compound selected from the group of glucose, arabinose, xylose, galactose, mannose, rhamnose, fructose, glycerol and acetic acid or a salt thereof.
The term “ferment”, and variations thereof such as “fermenting”, “fermentation” and/or “fermentative”, is used herein in a classical sense, i.e. to indicate that a process is or has been carried out under anaerobic conditions. An anaerobic fermentation is herein defined to be a fermentation carried out under anaerobic conditions. Anaerobic conditions are herein defined as conditions without any oxygen or in which essentially no oxygen is consumed by the yeast cell. Conditions in which essentially no oxygen is consumed suitably corresponds to an oxygen consumption of less than 5 mmol/l.h−1, in particular to an oxygen consumption of less than 2.5 mmol/l.h−1, or less than 1 mmol/l.h−1. More preferably 0 mmol/L/h is consumed (i.e. oxygen consumption is not detectable). This suitably corresponds to a dissolved oxygen concentration in a culture broth of less than 5% of air saturation, more suitably to a dissolved oxygen concentration of less than 1% of air saturation, or less than 0.2% of air saturation.
The term “cell” refers to a eukaryotic or prokaryotic organism, preferably occurring as a single cell. In the present invention the cell is a yeast cell. That is, the recombinant cell is selected from the group of genera consisting of yeast.
The terms “yeast” and “yeast cell” are used herein interchangeably and refer to a phylogenetically diverse group of single-celled fungi, most of which are in the division of Ascomycota and Basidiomycota. The budding yeasts (“true yeasts”) are classified in the order Saccharomycetales. The yeast cell according to the invention is a Saccharomyces yeast cell and is defined as a yeast cell derived from the genus of Saccharomyces. Preferably the yeast cell is a yeast cell of the species Saccharomyces cerevisiae.
The term “recombinant”, for example referring to a “recombinant yeast”, a “recombinant cell”, “recombinant micro-organism” and/or “recombinant strain” as used herein, refers to a yeast, cell, micro-organism or strain, respectively, containing nucleic acid which is the result of one or more genetic modifications. Simply put the yeast, cell, micro-organism or strain contains a different combination of nucleic acid from (either of) its parent(s). To construe a recombinant yeast, cell, micro-organism or strain recombinant DNA technique(s) and/or another mutagenic technique(s) can be used. In particular a recombinant yeast and/or a recombinant yeast cell may comprise nucleic acid not present in the corresponding wild-type yeast and/or cell, which nucleic acid has been introduced into that yeast and/or yeast cell using recombinant DNA techniques (i.e. a transgenic yeast and/or cell), or which nucleic acid not present in said wild-type yeast and/or cell is the result of one or more mutations—for example using recombinant DNA techniques or another mutagenesis technique such as UV-irradiation—in a nucleic acid sequence present in said wild-type yeast and/or yeast cell (such as a gene encoding a wild-type polypeptide) or wherein the nucleic acid sequence of a gene has been modified to target the polypeptide product (encoding it) towards another cellular compartment. Further, the term “recombinant” may suitably relate to a yeast, cell, micro-organism or strain from which nucleic acid sequences have been removed, for example using recombinant DNA techniques.
By a recombinant yeast comprising or having a certain activity is herein understood that the recombinant yeast may comprise one or more nucleic acid sequences encoding for an enzyme having such activity. Hence allowing the recombinant yeast to functionally express such a protein.
The term “transgenic” as used herein, for example referring to a “transgenic yeast” and/or a “transgenic cell”, refers to a yeast and/or cell, respectively, containing nucleic acid not naturally occurring in that yeast and/or cell and which has been introduced into that yeast and/or cell using recombinant DNA techniques, such as a recombinant yeast and/or cell.
The term “mutated” as used herein regarding proteins or polypeptides means that at least one amino acid in the wild-type or naturally occurring protein or polypeptide sequence has been replaced with a different amino acid, inserted or deleted from the sequence via mutagenesis of nucleic acids encoding these amino acids. Mutagenesis is a well-known method in the art, and includes, for example, site-directed mutagenesis by means of PCR or via oligonucleotide-mediated mutagenesis as described in Sambrook et al., Molecular Cloning-A Laboratory Manual, 2nd ed., Vol. 1-3 (1989). The term “mutated” as used herein regarding genes means that at least one nucleotide in the nucleic acid sequence of that gene or a regulatory sequence thereof, has been replaced with a different nucleotide, or has been deleted from the sequence via mutagenesis, resulting in the transcription of a protein sequence with a qualitatively of quantitatively altered function or the knock-out of that gene. In the context of this invention an “altered gene” has the same meaning as a mutated gene.
The term “gen” or “gene”, as used herein, refers to a nucleic acid sequence that can be transcribed into mRNAs that are then translated into protein. A gene encoding for a certain protein refers to the one or more nucleic acid sequence(s) encoding for such a protein.
The term “nucleic acid” as used herein, refers to a deoxyribonucleotide or ribonucleotide polymer, i.e. a polynucleotide, in either single or double-stranded form, and unless otherwise limited, encompasses known analogues having the essential nature of natural nucleotides in that they hybridize to single-stranded nucleic acids in a manner similar to naturally occurring nucleotides (e.g., peptide nucleic acids). A polynucleotide can be full-length or a subsequence of a native or heterologous structural or regulatory gene. Unless otherwise indicated, the term includes reference to the specified sequence as well as the complementary sequence thereof. Thus, DNAs or RNAs with backbones modified for stability or for other reasons are “polynucleotides” as that term is intended herein. Moreover, DNAs or RNAs comprising unusual bases, such as inosine, or modified bases, such as tritylated bases, to name just two examples, are polynucleotides as the term is used herein. It will be appreciated that a great variety of modifications have been made to DNA and RNA that serve many useful purposes known to those of skill in the art. The term polynucleotide as it is employed herein embraces such chemically, enzymatically or metabolically modified forms of polynucleotides, as well as the chemical forms of DNA and RNA characteristic of viruses and cells, including among other things, simple and complex cells.
The terms “polypeptide”, “peptide” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical analogue of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers. The essential nature of such analogues of naturally occurring amino acids is that, when incorporated into a protein, that protein is specifically reactive to antibodies elicited to the same protein but consisting entirely of naturally occurring amino acids. The terms “polypeptide”, “peptide” and “protein” are also inclusive of modifications including, but not limited to, glycosylation, lipid attachment, sulphation, gamma-carboxylation of glutamic acid residues, hydroxylation and ADP-ribosylation.
When an enzyme is mentioned with reference to an enzyme class (EC), the enzyme class is a class wherein the enzyme is classified or may be classified, on the basis of the Enzyme Nomenclature provided by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB), which nomenclature may be found at http://www.chem.qmul.ac.uk/iubmb/enzyme/. Other suitable enzymes that have not (yet) been classified in a specified class but may be classified as such, are meant to be included.
If referred herein to a protein or a nucleic acid sequence, such as a gene, by reference to a accession number, this number in particular is used to refer to a protein or nucleic acid sequence (gene) having a sequence as can be found via www.ncbi.nlm.nih.gov/, (as available on 1 Oct. 2020) unless specified otherwise.
Every nucleic acid sequence herein that encodes a polypeptide also includes any conservatively modified variants thereof. This includes that, by reference to the genetic code, it describes every possible silent variation of the nucleic acid. The term “conservatively modified variants” applies to both amino acid and nucleic acid sequences. With respect to particular nucleic acid sequences, conservatively modified variants refers to those nucleic acids which encode identical or conservatively modified variants of the amino acid sequences due to the degeneracy of the genetic code. The term “degeneracy of the genetic code” refers to the fact that a large number of functionally identical nucleic acids encode any given protein. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine. Thus, at every position where an alanine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are “silent variations” and represent one species of conservatively modified variation.
Any exogenous gene coding for an enzyme herein comprises a nucleotide sequence coding for an amino acid sequence with at least 40, 50, 60, 65, 70, 75, 80, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99 or 100% amino acid sequence identity with any of SEQ ID's NO: X, wherein SEQ ID NO:X is any of the protein sequences in the sequence listing of this application. The exogenous gene coding for an enzyme may also comprises a nucleotide sequence coding for an amino acid sequence having one or several substitutions, insertions and/or deletions as compared to the amino acid sequence of any of SEQ ID NO: X. Preferably the amino acid sequence has no more than 300, 250, 200, 150, 100, 75, 50, 40, 30, 20, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 amino acid substitutions, insertions and/or deletions as compared to SEQ ID's NO: X.
Any exogenous gene coding for an enzyme herein comprises a nucleotide sequence with at least 40, 50, 60, 65, 70, 75, 80, 85, 86, 87, 88, 89, 90, 95, 96, 97, 98, 99% or 100% nucleotide (DNA) sequence identity with any of SEQ ID's NO: Y, wherein SEQ ID NO: Y is any of the nucleotide (DNA) sequences in the sequence listing of this application.
The term “functional homologue” (or in short “homologue”) of a polypeptide and/or amino acid sequence having a specific sequence (e.g. “SEQ ID NO: X”), as used herein, refers to a polypeptide and/or amino acid sequence comprising said specific sequence with the proviso that one or more amino acids are substituted, deleted, added, and/or inserted, and which polypeptide has (qualitatively) the same enzymatic functionality for substrate conversion. This functionality may be tested by use of an assay system comprising a recombinant cell comprising an expression vector for the expression of the homologue in yeast, said expression vector comprising a heterologous nucleic acid sequence operably linked to a promoter functional in the yeast and said heterologous nucleic acid sequence encoding the homologous polypeptide of which enzymatic activity for converting acetyl-Coenzyme A to acetaldehyde in the cell is to be tested, and assessing whether said conversion occurs in said cells. With respect to nucleic acid sequences, the term functional homologue is meant to include nucleic acid sequences which differ from another nucleic acid sequence due to the degeneracy of the genetic code and encode the same polypeptide sequence.
Sequence identity is herein defined as a relationship between two or more amino acid (polypeptide or protein) sequences or two or more nucleic acid (polynucleotide) sequences, as determined by comparing the sequences. Usually, sequence identities or similarities are compared over the whole length of the sequences compared. In the art, “identity” also means the degree of sequence relatedness between amino acid or nucleic acid sequences, as the case may be, as determined by the match between strings of such sequences.
Amino acid or nucleotide sequences are said to be homologous when exhibiting a certain level of similarity. Two sequences being homologous indicate a common evolutionary origin. Whether two homologous sequences are closely related or more distantly related is indicated by “percent identity” or “percent similarity”, which is high or low respectively. Although disputed, to indicate “percent identity” or “percent similarity”, “level of homology” or “percent homology” are frequently used interchangeably. A comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm. The skilled person will be aware of the fact that several different computer programs are available to align two sequences and determine the homology between two sequences (Kruskal, J. B. (1983) An overview of sequence comparison In D. Sankoff and J. B. Kruskal, (ed.), Time warps, string edits and macromolecules: the theory and practice of sequence comparison, pp. 1-44 Addison Wesley). The percent identity between two amino acid sequences can be determined using the Needleman and Wunsch algorithm for the alignment of two sequences. (Needleman, S. B. and Wunsch, C. D. (1970) J. Mol. Biol. 48, 443-453). The algorithm aligns amino acid sequences as well as nucleotide sequences. The Needleman-Wunsch algorithm has been implemented in the computer program NEEDLE. For the purpose of this invention the NEEDLE program from the EMBOSS package was used (version 2.8.0 or higher, EMBOSS: The European Molecular Biology Open Software Suite (2000) Rice, P. Longden, I. and Bleasby, A. Trends in Genetics 16, (6) pp 276-277, http://emboss.bioinformatics.nl/). For protein sequences, EBLOSUM62 is used for the substitution matrix. For nucleotide sequences, EDNAFULL is used. Other matrices can be specified. The optional parameters used for alignment of amino acid sequences are a gap-open penalty of 10 and a gap extension penalty of 0.5. The skilled person will appreciate that all these different parameters will yield slightly different results but that the overall percentage identity of two sequences is not significantly altered when using different algorithms.
The homology or identity is the percentage of identical matches between the two full sequences over the total aligned region including any gaps or extensions. The homology or identity between the two aligned sequences is calculated as follows: Number of corresponding positions in the alignment showing an identical amino acid in both sequences divided by the total length of the alignment including the gaps. The identity defined as herein can be obtained from NEEDLE and is labelled in the output of the program as “IDENTITY”.
The homology or identity between the two aligned sequences is calculated as follows: Number of corresponding positions in the alignment showing an identical amino acid in both sequences divided by the total length of the alignment after subtraction of the total number of gaps in the alignment. The identity defined as herein can be obtained from NEEDLE by using the NOBRIEF option and is labeled in the output of the program as “longest-identity”.
A variant of a nucleotide or amino acid sequence disclosed herein may also be defined as a nucleotide or amino acid sequence having one or several substitutions, insertions and/or deletions as compared to the nucleotide or amino acid sequence specifically disclosed herein (e.g. in de the sequence listing).
Optionally, in determining the degree of amino acid similarity, the skilled person may also take into account so-called “conservative” amino acid substitutions, as will be clear to the skilled person. Conservative amino acid substitutions refer to the interchangeability of residues having similar side chains. For example, a group of amino acids having aliphatic side chains is glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains is serine and threonine; a group of amino acids having amide-containing side chains is asparagine and glutamine; a group of amino acids having aromatic side chains is phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains is lysine, arginine, and histidine; and a group of amino acids having sulphur-containing side chains is cysteine and methionine. In an embodiment, conservative amino acids substitution groups are:
Nucleotide sequences of the invention may also be defined by their capability to hybridise with parts of specific nucleotide sequences disclosed herein, respectively, under moderate, or preferably under stringent hybridisation conditions. Stringent hybridisation conditions are herein defined as conditions that allow a nucleic acid sequence of at least about 25, preferably about 50 nucleotides, 75 or 100 and most preferably of about 200 or more nucleotides, to hybridise at a temperature of about 65° C. in a solution comprising about 1 M salt, preferably 6×SSC or any other solution having a comparable ionic strength, and washing at 65° C. in a solution comprising about 0.1 M salt, or less, preferably 0.2×SSC or any other solution having a comparable ionic strength. Preferably, the hybridisation is performed overnight, i.e. at least for 10 hours and preferably washing is performed for at least one hour with at least two changes of the washing solution. These conditions will usually allow the specific hybridisation of sequences having about 90% or more sequence identity.
Moderate conditions are herein defined as conditions that allow a nucleic acid sequences of at least 50 nucleotides, preferably of about 200 or more nucleotides, to hybridise at a temperature of about 45° C. in a solution comprising about 1 M salt, preferably 6×SSC or any other solution having a comparable ionic strength, and washing at room temperature in a solution comprising about 1 M salt, preferably 6×SSC or any other solution having a comparable ionic strength. Preferably, the hybridisation is performed overnight, i.e. at least for 10 hours, and preferably washing is performed for at least one hour with at least two changes of the washing solution. These conditions will usually allow the specific hybridisation of sequences having up to 50% sequence identity. The person skilled in the art will be able to modify these hybridisation conditions in order to specifically identify sequences varying in identity between 50% and 90%.
“Expression” refers to the transcription of a gene into structural RNA (rRNA, tRNA) or messenger RNA (mRNA) with subsequent translation into a protein. “Overexpression” refers to expression of a gene by a recombinant cell in excess to its expression in a corresponding wild-type cell. Such overexpression can for example be arranged for by: increasing the frequency of transcription of one or more nucleic acid sequences, for example by operational linking of the nucleic acid sequence to a promoter functional within the recombinant cell; and/or by increasing the number of copies of a certain nucleic acid sequence.
Nucleic acid sequences (i.e. polynucleotides) or proteins (i.e. polypeptides) may be homologous or heterologous to the genome of the host cell.
“Homologous” with respect to a host cell, means that the nucleic acid sequence does naturally occur in the genome of the host cell or that the protein is naturally produced by that cell. Homologous protein expression may e.g. be an overexpression or expression under control of a different promoter. In the present inventions the host cell is a yeast.
The term “heterologous”, with respect to the host cell, means that the polynucleotide does not naturally occur in the genome of the host cell or that the polypeptide is not naturally produced by that cell. Heterologous protein expression involves expression of a protein that is not naturally produced in the host cell. As used herein, “heterologous” may refer to a nucleic acid or protein is a nucleic acid or protein that originates from a foreign species, or, if from the same species, is substantially modified from its native form in composition and/or genomic locus by deliberate human intervention. For example, a promoter operably linked to a heterologous structural gene is from a species different from that from which the structural gene was derived, or, if from the same species, one or both are substantially modified from their original form. A heterologous protein may originate from a foreign species or, if from the same species, is substantially modified from its original form by deliberate human intervention.
The term “heterologous expression” refers to the expression of heterologous nucleic acids in a host cell. The expression of heterologous proteins in eukaryotic host cell systems such as yeast are well known to those of skill in the art. A polynucleotide comprising a nucleic acid sequence of a gene encoding an enzyme with a specific activity can be expressed in such a eukaryotic system. In some embodiments, transformed/transfected cells may be employed as expression systems for the expression of the enzymes. Expression of heterologous proteins in yeast is well known. Sherman, F., et al., Methods in Yeast Genetics, Cold Spring Harbor Laboratory (1982) is a well-recognized work describing the various methods available to express proteins in yeast. Two widely utilized yeasts are Saccharomyces cerevisiae and Pichia pastoris. Vectors, strains, and protocols for expression in Saccharomyces and Pichia are known in the art and available from commercial suppliers (e.g., Invitrogen). Suitable vectors usually have expression control sequences, such as promoters, including 3-phosphoglycerate kinase or alcohol oxidase, and an origin of replication, termination sequences and the like as desired.
As used herein “promoter” is a DNA sequence that directs the transcription of a (structural) gene. Typically, a promoter is located in the 5′-region of a gene, proximal to the transcriptional start site of a (structural) gene. Promoter sequences may be constitutive, inducible or repressible. In an embodiment there is no (external) inducer needed.
The term “vector” as used herein, includes reference to an autosomal expression vector and to an integration vector used for integration into the chromosome.
The term “expression vector” refers to a DNA molecule, linear or circular, that comprises a segment encoding a polypeptide of interest under the control of (i.e. operably linked to) additional nucleic acid segments that provide for its transcription. Such additional segments may include promoter and terminator sequences, and may optionally include one or more origins of replication, one or more selectable markers, an enhancer, a polyadenylation signal, and the like. Expression vectors are generally derived from plasmid or viral DNA, or may contain elements of both. In particular an expression vector comprises a nucleic acid sequence that comprises in the 5′ to 3′ direction and operably linked: (a) a yeast-recognized transcription and translation initiation region, (b) a coding sequence for a polypeptide of interest, and (c) a yeast-recognized transcription and translation termination region. “Plasmid” refers to autonomously replicating extrachromosomal DNA which is not integrated into a microorganism's genome and is usually circular in nature.
An “integration vector” refers to a DNA molecule, linear or circular, that can be incorporated in a microorganism's genome and provides for stable inheritance of a gene encoding a polypeptide of interest. The integration vector generally comprises one or more segments comprising a gene sequence encoding a polypeptide of interest under the control of (i.e. operably linked to) additional nucleic acid segments that provide for its transcription. Such additional segments may include promoter and terminator sequences, and one or more segments that drive the incorporation of the gene of interest into the genome of the target cell, usually by the process of homologous recombination. Typically, the integration vector will be one which can be transferred into the target cell, but which has a replicon which is nonfunctional in that organism. Integration of the segment comprising the gene of interest may be selected if an appropriate marker is included within that segment.
By “host cell” is herein understood a cell, such as a yeast cell, that is to be transformed with one or more nucleic acid sequences encoding for one or more heterologous proteins, to construe a transformed cell, also referred to as a recombinant cell. For example, the transformed cell may contain a vector and may support the replication and/or expression of the vector.
“Transformation” and “transforming”, as used herein, refers to the insertion of an exogenous polynucleotide (i.e. an exogenous nucleic acid sequence) into a host cell, irrespective of the method used for the insertion, for example, direct uptake, transduction, f-mating or electroporation. The exogenous polynucleotide may be maintained as a non-integrated vector, for example, a plasmid, or alternatively, may be integrated into the host cell genome.
By “disruption” is herein understood any disruption of activity, including, but not limited to, deletion, mutation and reduction of the affinity of the disrupted gene and expression of RNA complementary to such disrupted gene. It includes all nucleic acid modifications such as nucleotide deletions or substitutions, gene knock-outs, and other actions which affect the translation or transcription of the corresponding polypeptide and/or which affect the enzymatic (specific) activity, its substrate specificity, and/or or stability. It also includes modifications that may be targeted on the coding sequence or on the promotor of the gene. A gene disruptant is a cell that has one or more disruptions of the respective gene. Native to yeast herein is understood as that the gene is present in the yeast cell before the disruption.
The term “encoding” has the same meaning as “coding for”. Thus, by way of example, “one or more genes encoding a glycerol dehydrogenase” has the same meaning as “one or more genes coding for a glycerol dehydrogenase”. As far as genes encoding an enzyme are concerned, the phrase “one or more genes encoding a X”, wherein X denotes an enzyme, has the same meaning as “one or more genes encoding an enzyme having X activity”. Thus, by way of example, “one or more genes encoding a NADH-dependent nitrate reductase” has the same meaning as “one or more genes encoding an enzyme having NADH-dependent nitrate reductase activity”; and “one or more heterologous genes encoding a NADH-dependent nitrite reductase” has the same meaning as “one or more heterologous genes encoding an enzyme having NADH-dependent nitrite reductase activity”.
The abbreviation “NADH” refers to reduced, hydrogenated form of nicotinamide adenine dinucleotide. The abbreviation “NAD+” refers to the oxidized form of nicotinamide adenine dinucleotide. Nicotinamide adenine dinucleotide may act as a so-called cofactor, assisting in biochemical reactions and/or transformations in a cell.
“NADH dependent” is herein equivalent to NADH specific and “NADH dependency” is herein equivalent to NADH specificity.
By a NADH-dependent enzyme is herein understood an enzyme that is exclusively depended on NADH as a co-factor or that is predominantly dependent on NADH as a cofactor. By an “exclusive NADH-dependent” enzyme is herein understood an enzyme that has an absolute requirement for NADH over NADPH. That is, it is only active when NADH is applied as cofactor. By a “predominantly NADH-dependent” enzyme is herein understood an enzyme that has a higher specificity and/or a higher catalytic efficiency for NADH as a cofactor than for NADPH as a cofactor.
The enzyme's specificity characteristics can be described by the formula:
1<Km NADP+/KmNAD+<∞(infinity)
For a predominantly NADH-dependent enzyme, preferably KmNADP+/KmNAD+ is between 1 and 1000, between 1 and 500, between 1 and 200, between 1 and 100, between 1 and 50, between 1 and 10, between 5 and 100, between 5 and 50, between 5 and 20 or between 5 and 10. The Km's for the enzymes herein can be determined as enzyme specific, for NAD+ and NADP+ respectively, using know analysis techniques, calculations and protocols. These are described for instance in Lodish et al., Molecular Cell Biology 6th Edition, Ed. Freeman, pages 80 and 81, e.g.
For an predominantly NADH-dependent enzyme, preferably the ratio of the catalytic efficiency for NADPH/NADP+ as a cofactor (kcat/Km)NADP+ to NADH/NAD+ as cofactor (kcat/Km)NAD+, i.e. the catalytic efficiency ratio (kcat/Km)NADP+:(kcat/Km)NAD+, is more than 1:1, more preferably equal to or more than 2:1, still more preferably equal to or more than 5:1, even more preferably equal to or more than 10:1, yet even more preferably equal to or more than 20:1, even still more preferably equal to or more than 100:1, and most preferably equal to or more than 1000:1.
There is no upper limit, but for practical reasons the predominantly NADH-dependent enzyme may have a catalytic efficiency ratio (kcat/Km)NADP+:(kcat/Km)NAD+ of equal to or less than 1.000.000.000:1 (i.e. 1.109:1).
The Saccharomyces yeast cell is preferably a yeast cell derived from a yeast cell of the species Saccharomyces cerevisiae, herein also referred to as a Saccharomyces cerevisae yeast cell.
In an alternative embodiment, the Saccharomyces yeast cell as described herein may be replaced with a Schizosaccharomyces yeast cell, for example a Schizosaccharomyces pompe yeast cell, and such Schizosaccharomyces yeast cell may be used instead.
Preferably the Saccharomyces yeast cell is an industrial yeast cell. The living environments of yeast cells in industrial processes are significantly different from that in the laboratory. Industrial yeast cells must be able to perform well under multiple environmental conditions which may vary during the process. Such variations include changes in nutrient sources, pH, ethanol concentration, temperature, oxygen concentration, etc., which together have potential impact on the cellular growth and ethanol production of the yeast cell. An industrial yeast cell can be understood to refer to a yeast cell that, when compared to a laboratory counterpart, has a more robust performance. That is, when compared to a laboratory counterpart, the industrial yeast cell shows less variation in performance when one or more environmental conditions selected from the group of nutrient sources, pH, ethanol concentration, temperature, oxygen concentration, are varied during fermentation. Preferably, the Saccharomyces yeast cell is constructed on the basis of an industrial Saccharomyces yeast cell as a host, wherein the construction is conducted as described hereinafter. Examples of industrial Saccharomyces yeast cells are Ethanol Red® (Fermentis) Fermiol® (DSM) and Thermosacc® (Lallemand).
The Saccharomyces yeast cell comprises one or more genes encoding a NADH-dependent nitrate reductase and/or one or more genes encoding a NADH-dependent nitrite reductase. In addition, the Saccharomyces yeast cell described herein may comprise one or more genes encoding a nitrate and/or nitrite transporter and optionally one or more genes encoding further enzymes.
The Saccharomyces yeast cell described herein may be derived from any host cell capable of producing a fermentation product. Preferably the Saccharomyces yeast cell described herein is derived from a host cell having the ability to produce ethanol. Preferably the host cell is a Saccharomyces yeast cell, more preferably an industrial Saccharomyces yeast cell as described herein above.
The Saccharomyces yeast cell described herein may be derived from the host cell through any technique known by one skilled in the art to be suitable for incorporation of the desired genes. Such techniques may include any one or more of mutagenesis, recombinant DNA technology (including, but not limited to, CRISPR-CAS techniques), selective and/or adaptive evolution, mating, cell fusion, and/or cytoduction between yeast strains. Suitably the one or more genes encoding a NADH-dependent nitrate reductase and/or the one or more genes encoding a NADH-dependent nitrite reductase and/or any further genes are incorporated in the Saccharomyces yeast cell by a combination of one or more of the above techniques.
Nitrate reductase (NR) catalyzes the reduction of nitrate (NO3−) to nitrite (NO2−). Nitrite reductase catalyzes the reduction of nitrite to ammonia (NH3). Nitrate reductase and/or nitrite reductase can be part of a so-called nitrogen assimilation pathway in certain cells. Cells comprising nitrate reductase activity and/or nitrite reductase activity include certain plant cells and bacterial cells and a few yeast cells. As indicated by Linder, the ability to assimilate inorganic nitrogen sources other than ammonia is thought to be rare among budding yeasts. Among the few fungi that are naturally capable to assimilate nitrate or nitrite are Blastobotrys adeninivorans (family Trichomonascaceae) Candida boidinii (family Pichiaceae), Cyberlindnera jadinii (family Phaffomycetaceae), and Ogataea polymorpha (family Pichiaceae).
Preferably the Saccharomyces yeast cell as described herein comprises at least one or more genes encoding a NADH-dependent nitrate reductase.
By a NADH-dependent nitrate reductase is herein understood a nitrate reductase that is exclusively depended on NADH as a co-factor or that is predominantly dependent on NADH as a cofactor. Preferably the NADH-dependent nitrate reductase has a ratio of catalytic efficiency for NADPH/NADP+ as a cofactor (kcat/Km)NADP+ to NADH/NAD+ as cofactor (kcat/Km)NAD+, i.e. a catalytic efficiency ratio (kcat/Km)NADP+:(kcat/Km)NAD+, of more than 1:1, more preferably of equal to or more than 2:1, still more preferably of equal to or more than 5:1, even more preferably of equal to or more than 10:1, yet even more preferably of equal to or more than 20:1, even still more preferably of equal to or more than 100:1, and most preferably equal to or more than 1000:1. There is no upper limit, but for practical reasons the NADH-dependent nitrate reductase may have a catalytic efficiency ratio (kcat/Km)NADP+:(kcat/Km)NAD+ of equal to or less than 1.000.000.000:1 (i.e. 1.109). Most preferably the NADH-dependent nitrate reductase is exclusively depended on NADH/NAD+ as a co-factor. That is, most preferably the NADH-dependent nitrate reductase has an absolute requirement for NADH/NAD+ as a cofactor instead of NADPH/NADP+ as a cofactor.
Preferably the NADH-dependent nitrate reductase is a NADH-dependent nitrate reductase with enzyme classification EC 1.7.1.1. (i.e. with EC number EC 1.7.1.1) or enzyme classification EC.1.6.6.1 (i.e. with EC number 1.6.6.1). Suitably the NADH-dependent nitrate reductase, also referred to as NADH-dependent nitrate oxidoreductase, is an enzyme that catalyzes at least the following chemical reaction:
nitrate+NADH+H+→nitrite+NAD++H2O
Suitable NADH-dependent nitrate reductases may include one or more NADH-dependent nitrate reductases as obtained or derived from Agrostemma githago, Amaranthus hybridus, Amaranthus tricolor, Ankistrodesmus braunii, Arabidopsis thaliana, Aspergillus niger, Aspergillus nidulans, Auxenochlorella pyrenoidosa, Bradyrhizobium sp., Bradyrhizobium sp. 750, Brassica juncea, Brassica, oleracea, Camellia sinensis, Candida boidinii, Candida utilis, Capsicum frutescens, Chenopodium album, Cyberlindnera jadinii, Brassica juncea, Brassica oleracea, Camellia sinensis, Capsicum frutescens, Chenopodium album, Chlamydomonas reinhardtii, Chlorella fusca, Chlorella sp. Chlorella sp. Berlin, Chlorella vulgaris, Conticribra weissflogii, Cucumis sativus, Cucurbita maxima, Cucurbita pepo, Cucurbita sp., Dunaliella tertiolecta, Emiliania huxleyi, Emericella nidulans, Fusarium oxysporum, Fusarium oxysporum JCM 11502, Glyceria maxima, Glycine max, Gossypium hirsutum, Gracilaria chilensis, Gracilaria tenuistipitata, Helianthus annuus, Hordeum vulgare, Lactuca sativa, Lemna minor, Lupinus albus, Mycobactyerium tuberculosis, Nicotiana plumbaginifolia, Nicotiana tabacum, Ogataea angusta, Ogataea polymorpha, Oryza sativa, Phaeocystis Antarctica, Phragmites australis, Physcomitrella patens, Pisum arvense, Polytrichum commune, Pyropia yezoensis, Raphanus sativus, Rhodobacter capsulatus, Rhodobacter capsulatus E1F1, Ricinus communis, Selaginella kraussiana, Sinapis alba, Skeletonema costatum, Skeletonema tropicum, Solanum lycopersicum, Spinacia oleracea, Suaeda maritima, Tetraselmis gracilis, Thalassia Testudinum, Thalassiosira Antarctica, Thalassiosira pseudonana, Triticum aestivum, Triticum turgidum subsp durum, Ulva sp. And/or Zea mays; and/or functional homologues of such NADH-dependent nitrate reductases comprising an amino acid sequence with at least 50, 60, 65, 70, 75, 80, 85, 90, 95, 98 or at least 99% amino acid sequence identity with one or more of such aforementioned NADH-dependent nitrate reductases; and/or functional homologues of such NADH-dependent nitrate reductases comprising an amino acid sequence having one or several substitutions, insertions and/or deletions as compared to the amino acid sequence of one or more of such aforementioned NADH-dependent nitrate reductases, wherein preferably the amino acid sequence of any of the above functional homologues has no more than 300, 250, to such aforementioned NADH-dependent nitrate reductases.
Preferred NADH-dependent nitrate reductases include the NADH-dependent nitrate reductases as obtained or derived from Candida boidinii (a nitrate reductase capable of utilizing both NADH and NADPH as electron donors), Candida utilis (a nitrate reductase capable of utilizing both NADH and NADPH as electron donors), Fusarium oxysporum (as described by Fujii et al, in their article titled “Denitrification by the Fungus Fusarium oxysporum Involves NADH-Nitrate Reductase” published in Biosci. Biotechnol. Biochem., 72 (2), pages 412-420, 2008, incorporated herein by reference), Spinacia oleracea and Zea Mays.
Preferred NADH-dependent nitrate reductases hence include: NADH-dependent nitrate reductases comprising a polypeptide having an amino acid sequence of SEQ ID NO:1 and/or SEQ ID NO:2, as described herein; and/or functional homologues of SEQ ID NO:1 and/or SEQ ID NO:2 comprising an amino acid sequence with at least 40, 50, 60, 65, 70, 75, 80, 85, 90, 95, 98 or at least 99% amino acid sequence identity with one or more of SEQ ID NO:1 and/or SEQ ID NO:2 respectively; and/or functional homologues of SEQ ID NO:1 and/or SEQ ID NO:2 comprising an amino acid sequence having one or several substitutions, insertions and/or deletions as compared to the amino acid sequence of one or more of SEQ ID NO:1 and/or SEQ ID NO:2 respectively. Preferably the amino acid sequence of any of the above functional homologues has no more than 300, 250, 200, 150, 100, 75, 50, 40, 30, 20, 10 or 5 amino acid substitutions, insertions and/or deletions as compared to SEQ ID NO:1 and/or SEQ ID NO:2 respectively.
Preferably the Saccharomyces yeast cell comprises an exogenous gene coding for an enzyme with NADH-dependent nitrate reductase activity. More preferably the Saccharomyces yeast cell comprises an exogenous gene coding for an enzyme with NADH-dependent nitrate reductase activity selected from the group consisting of NADH-dependent nitrate reductases as obtained or derived from Agrostemma githago, Amaranthus hybridus, Amaranthus tricolor, Ankistrodesmus braunii, Arabidopsis thaliana, Aspergillus niger, Aspergillus nidulans, Auxenochlorella pyrenoidosa, Bradyrhizobium sp., Bradyrhizobium sp. 750, Brassica juncea, Brassica, oleracea, Camellia sinensis, Candida boidinii, Candida utilis, Capsicum frutescens, Chenopodium album, Cyberlindnera jadinii, Brassica juncea, Brassica oleracea, Camellia sinensis, Capsicum frutescens, Chenopodium album, Chlamydomonas reinhardtii, Chlorella fusca, Chlorella sp. Chlorella sp. Berlin, Chlorella vulgaris, Conticribra weissflogii, Cucumis sativus, Cucurbita maxima, Cucurbita pepo, Cucurbita sp., Dunaliella tertiolecta, Emiliania huxleyi, Emericella nidulans, Fusarium oxysporum, Fusarium oxysporum JCM 11502, Glyceria maxima, Glycine max, Gossypium hirsutum, Gracilaria chilensis, Gracilaria tenuistipitata, Helianthus annuus, Hordeum vulgare, Lactuca sativa, Lemna minor, Lupinus albus, Mycobactyerium tuberculosis, Nicotiana plumbaginifolia, Nicotiana tabacum, Ogataea angusta, Ogataea polymorpha, Oryza sativa, Phaeocystis Antarctica, Phragmites australis, Physcomitrella patens, Pisum arvense, Polytrichum commune, Pyropia yezoensis, Raphanus sativus, Rhodobacter capsulatus, Rhodobacter capsulatus E1F1, Ricinus communis, Selaginella kraussiana, Sinapis alba, Skeletonema costatum, Skeletonema tropicum, Solanum lycopersicum, Spinacia oleracea, Suaeda maritima, Tetraselmis gracilis, Thalassia Testudinum, Thalassiosira Antarctica, Thalassiosira pseudonana, Triticum aestivum, Triticum turgidum subsp durum, Ulva sp. and Zea mays, and functional homologues of such NADH-dependent nitrate reductases comprising an amino acid sequence with at least 50, 60, 65, 70, 75, 80, 85, 90, 95, 98 or at least 99% amino acid sequence identity with one or more of such aforementioned NADH-dependent nitrate reductases; and functional homologues of such NADH-dependent nitrate reductases comprising an amino acid sequence having one or several substitutions, insertions and/or deletions as compared to the amino acid sequence of one or more of such aforementioned NADH-dependent nitrate reductases, wherein preferably the amino acid sequence of any of the above functional homologues has no more than 300, 250, 200, 150, 100, 75, 50, 40, 30, 20, 10 or 5 amino acid substitutions, insertions and/or deletions as compared to such aforementioned NADH-dependent nitrate reductases.
Suitably the Saccharomyces yeast cell may comprise a nucleotide sequence coding for an amino acid sequence of any of SEQ ID NO:1 and/or SEQ ID NO:2 or an amino acid sequence having one or several substitutions, insertions and/or deletions as compared to the amino acid sequence of any of SEQ ID NO:1 and/or SEQ ID NO:2. Preferably the amino acid sequence has no more than 300, 250, 200, 150, 100, 75, 50, 40, 30, 20, 10 or 5 amino acid substitutions, insertions and/or deletions as compared to SEQ ID NO:1 and/or SEQ ID NO:2 respectively.
The Saccharomyces yeast cell may combine one or more genes encoding the above NADH-dependent nitrate reductase with one or more genes encoding an NADPH-dependent nitrite reductase. Preferably, however, the Saccharomyces yeast cell combines one or more genes encoding the above NADH-dependent nitrate reductase with one or more genes encoding a NADH-dependent nitrite reductase.
Examples of suitable NADH-dependent nitrate reductases, their UniProt Database Accession number (as can be found on the Uniprot website (https://www.uniprot.org/ as per 4 Oct. 2020), their description, the organism from which they may be derived, and their amino acid sequence identity with SEQ ID NO:1, are listed in Table 2 below.
Zea mays
Oryza meyeriana var.
granulata
Actinidia chinensis var.
chinensis
Olea europaea var.
sylvestris
Daucus carota subsp.
sativus
Glycine subgen. Soja
Glycine subgen. Soja
As indicated above, nitrite reductase catalyzes the reduction of nitrite to ammonia (NH3).
Preferably the Saccharomyces yeast cell as described herein comprises at least one or more genes encoding a NADH-dependent nitrite reductase.
By a NADH-dependent nitrite reductase is herein understood a nitrite reductase that is exclusively depended on NADH as a co-factor or that is predominantly dependent on NADH as a cofactor. Preferably the NADH-dependent nitrite reductase has a ratio of catalytic efficiency for NADPH/NADP+ as a cofactor (kcat/Km)NAD+ to NADH/NAD+ as cofactor (kcat/Km)NAD+, i.e. a catalytic efficiency ratio (kcat/Km)NADP+:(kcat/Km)NAD+, of more than 1:1, more preferably of equal to or more than 2:1, still more preferably of equal to or more than 5:1, even more preferably of equal to or more than 10:1, yet even more preferably of equal to or more than 20:1, even still more preferably of equal to or more than 100:1, and most preferably equal to or more than 1000:1. There is no upper limit, but for practical reasons the NADH-dependent nitrite reductase may have a catalytic efficiency ratio (kcat/Km)NADP+:(kcat/Km)NAD+ of equal to or less than 1.000.000.000:1 (i.e. 1.109). Most preferably the NADH-dependent nitrite reductase is exclusively depended on NADH/NAD+ as a co-factor. That is, most preferably the NADH-dependent nitrite reductase has an absolute requirement for NADH/NAD+ as a cofactor instead of NADPH/NADP+ as a cofactor.
Preferably the NADH-dependent nitrite reductase is a NADH-dependent nitrite reductase with enzyme classification EC 1.7.1.15 (i.e. with EC number EC 1.7.1.15). Suitably the NADH-dependent nitrite reductase, also referred to as NADH-dependent nitrite oxidoreductase, is an enzyme that catalyzes at least the following chemical reaction:
nitrite+3NADH+5H+→ammonia+3NAD++2H2O
The person skilled in the art will understand that the ammonia may also be present and/or referred to as so-called ammonium hydroxide NH4OH
Suitable NADH-dependent nitrite reductases may include one or more NADH-dependent nitrite reductases as derived from Aspergillus nidulans (also called Emericella nidulans), Arcobacter ellisii, Arcobacter pacificus Bacillus subtilis, Bacillus subtilis JH642, Cupriavidus taiwanensis Escherichia coli, Ralstonia taiwanensis, Ralstonia syzygii, Ralstonia solanacearum, Rhodobacter capsulatus, Rhodobacter capsulatus, Paraburkholderia ribeironis; and/or functional homologues of such NADH-dependent nitrite reductases comprising an amino acid sequence with at least 40, 50, 60, 65, 70, 75, 80, 85, 90, 95, 98 or at least 99% amino acid sequence identity with one or more of such aforementioned NADH-dependent nitrite reductases; and/or functional homologues of such NADH-dependent nitrite reductases comprising an amino acid sequence having one or several substitutions, insertions and/or deletions as compared to the amino acid sequence of one or more of such aforementioned NADH-dependent nitrite reductases, wherein preferably the amino acid sequence of any of the above functional homologues has no more than 300, 250, to such aforementioned NADH-dependent nitrite reductases.
Escherichia coli utilizes several distinct enzymes in its nitrite assimilation pathway. The nirD gene encodes a NADH-dependent nitrite reductase (NADH) small subunit, whilst the nirB gene encodes a NADH-dependent nitrite reductase (NADH) large subunit.
Preferred NADH-dependent nitrite reductases include the NADH-dependent nitrite reductases as derived from Aspergillus nidulans (also called Emericella nidulans), a nitrite reductase capable of utilizing both NADH and NADPH as electron donors, and/or Escherichia coli. At high nitrate and/or nitrite concentrations, the nitrite reductase encoded by the nirB gene of Escherichia coli is especially preferred.
Preferred NADH-dependent nitrite reductases hence include: NADH-dependent nitrite reductases comprising a polypeptide having an amino acid sequence of SEQ ID NO:3 (E. coli nitrate reductase small subunit encoded by nirD) and/or SEQ ID NO:4 (E. coli nitrate reductase large subunit encoded by nirB) and/or SEQ ID NO:5 (Emericella nidulans nitrate reductase encoded by niiA), as described herein; and/or functional homologues of SEQ ID NO:3 and/or SEQ ID NO:4 and/or SEQ ID NO:5 comprising an amino acid sequence with at least 40, 50, 60, 65, 70, 75, 80, 85, 90, 95, 98 or at least 99% amino acid sequence identity with one or more of SEQ ID NO:3 and/or SEQ ID NO:4 and/or SEQ ID NO:5 respectively; and/or functional homologues of SEQ ID NO:3 and/or SEQ ID NO:4 and/or SEQ ID NO:5 comprising an amino acid sequence having one or several substitutions, insertions and/or deletions as compared to the amino acid sequence of one or more of SEQ ID NO:3 and/or SEQ ID NO:4 and/or SEQ ID NO:5 respectively. Preferably the amino acid sequence of any of the above functional homologues has no more than 300, 250, 200, 150, 100, 75, 50, 40, 30, 20, 10 or 5 amino acid substitutions, insertions and/or deletions as compared to SEQ ID NO:3 and/or SEQ ID NO:4 and/or SEQ ID NO:5 respectively.
Preferably the Saccharomyces yeast cell comprises an exogenous gene coding for an enzyme with NADH-dependent nitrite reductase activity. More preferably the Saccharomyces yeast cell comprises an exogenous gene coding for an enzyme with NADH-dependent nitrite reductase activity selected from the group consisting of NADH-dependent nitrite reductases as derived from Aspergillus nidulans (also called Emericella nidulans), Arcobacter ellisii, Arcobacter pacificus Bacillus subtilis, Bacillus subtilis JH642, Cupriavidus taiwanensis Escherichia coli, Ralstonia taiwanensis, Ralstonia syzygii, Ralstonia solanacearum, Rhodobacter capsulatus, Rhodobacter capsulatus, Paraburkholderia ribeironis; and/or functional homologues of such NADH-dependent nitrite reductases comprising an amino acid sequence with at least 40, 50, 60, 65, 70, 75, 80, 85, 90, 95, 98 or at least 99% amino acid sequence identity with one or more of such aforementioned NADH-dependent nitrite reductases; and/or functional homologues of such NADH-dependent nitrite reductases comprising an amino acid sequence having one or several substitutions, insertions and/or deletions as compared to the amino acid sequence of one or more of such aforementioned NADH-dependent nitrite reductases, wherein preferably the amino acid sequence of any of the above functional homologues has no more than 300, 250, 200, 150, 100, 75, 50, 40, 30, 20, 10 or 5 amino acid substitutions, insertions and/or deletions as compared to such aforementioned NADH-dependent nitrite reductases.
Suitably the Saccharomyces yeast cell may comprise a nucleotide sequence coding for an amino acid sequence of any of SEQ ID NO:3 (E. coli nitrate reductase small subunit encoded by nirD) and/or SEQ ID NO:4 (E. coli nitrate reductase large subunit encoded by nirB) and/or SEQ ID NO:5 (Emericella nidulans nitrate reductase encoded by niiA), or an amino acid sequence having one or several substitutions, insertions and/or deletions as compared to the amino acid sequence of any of SEQ ID NO:3 and/or SEQ ID NO:4 and/or SEQ ID NO:5. Preferably the amino acid sequence has no more than 300, 250, 200, 150, 100, 75, 50, 40, 30, 20, 10 or 5 amino acid substitutions, insertions and/or deletions as compared to SEQ ID NO:3 and/or SEQ ID NO:4 and/or SEQ ID NO:5 respectively.
The Saccharomyces yeast cell may combine one or more genes encoding one or more of the above NADH-dependent nitrite reductases with one or more genes encoding an NADPH-dependent nitrate reductase. Preferably, however, the Saccharomyces yeast cell combines one or more genes encoding one or more of the above NADH-dependent nitrite reductases with one or more genes encoding a NADH-dependent nitrate reductase.
Examples of suitable NADH-dependent nitrite reductases, their UniProt Database Accession number (as can be found on the Uniprot website (https://www.uniprot.org/ as per 4 Oct. 2020), their description, the organism from which they may be derived, and their amino acid sequence identity with SEQ ID NO:3 (small subunit encoded by nirD), are listed in Table 3 below.
Examples of suitable NADH-dependent nitrite reductases, their UniProt Database Accession number (as can be found on the Uniprot website (https://www.uniprot/org/ as per 4 Oct. 2020), their description, the organism from which they may be derived, and their amino acid sequence identity with SEQ ID NO:4 (large subunit encoded by nirB), are listed in Table 4 below.
Enterobacter sp.
Enterobacter sp.
Enterobacter sp. kpr-6
Enterobacter sp.
Enterobacter sp.
Erwinia sp. CPCC
Orbus sp. IPMB12
Pantoea sp. LMG
Vibrio sp. qd031
Vibrio sp. E4404
Pantoea sp.
Vibrio sp.
Vibrio sp.
Pantoea sp. IMH
Nissabacter sp.
Rahnella sp. SAP-1
Orbus sp.
Pantoea sp.
Motilimonas sp.
Vibrio sp.
Schmidhempelia bombi
Vibrio sp. H11
Erwinia sp.
Preferably, the Saccharomyces yeast cell further comprises one or more genetic modifications that result in an increased transport of oxidized nitrogen source, such as nitrate or nitrite, into the yeast cell. More preferably the Saccharomyces yeast cell further comprising one or more genes encoding a nitrate and/or nitrite transporter.
Suitable transporters may include the sulphite transporters Ssu1 and SSu2 (as described by Cabrera et al in their article titled “Molecular Components of Nitrate and Nitrite Efflux in Yeast”, published February 2014 Volume 13 Number 2 Eukaryotic Cell p. 267-278, herein incorporated by reference); and the nitrate/nitrite transporter YNT1 derived from Pichia angusta (also referred to as Hansenula polymorpha) and/or a functional homologues of one or more of such nitrate/nitrite transporters comprising an amino acid sequence with at least 40, 50, 60, 65, 70, 75, 80, 85, 90, 95, 98 or at least 99% amino acid sequence identity with one or more of the aforementioned nitrate/nitrite transporters; and/or functional homologues of one or more of such nitrate/nitrite transporters comprising an amino acid sequence having one or several substitutions, insertions and/or deletions as compared to the amino acid sequence of one or more of such aforementioned nitrate/nitrite transporters, wherein preferably the amino acid sequence of any of the above functional homologues has no more than 300, 250, 200, 150, 100, 75, 50, 40, 30, 20, 10 or 5 amino acid substitutions, insertions and/or deletions as compared to such aforementioned nitrate/nitrite transporter YNT1.
Preferably the Saccharomyces yeast cell comprises a nucleic acid sequence encoding the nitrate/nitrite transporter YNT1 derived from Pichia angusta and/or a functional homologues of such nitrate/nitrite transporter YNT1 comprising an amino acid sequence with at least 50, 60, 65, 70, 75, 80, 85, 90, 95, 98 or at least 99% amino acid sequence identity with nitrate/nitrite transporter YNT1; and/or functional homologues of such nitrate/nitrite transporter YNT1 comprising an amino acid sequence having one or several substitutions, insertions and/or deletions as compared to the amino acid sequence of one or more of such aforementioned nitrate/nitrite transporter YNT1, wherein preferably the amino acid sequence of any of the above functional homologues has no more than 300, 250, 200, 150, 100, 75, 50, 40, 30, 20, 10 or 5 amino acid substitutions, insertions and/or deletions as compared to such aforementioned nitrate/nitrite transporter YNT1.
Preferred nitrate/nitrite transporter hence include: nitrate/nitrite transporters comprising a polypeptide having an amino acid sequence of SEQ ID NO:6, as described herein; and/or functional homologues of SEQ ID NO:6 comprising an amino acid sequence with at least 40, 50, 60, 65, 70, 75, 80, 85, 90, 95, 98 or at least 99% amino acid sequence identity with SEQ ID NO:6; and/or functional homologues of SEQ ID NO:6 comprising an amino acid sequence having one or several substitutions, insertions and/or deletions as compared to the amino acid sequence of SEQ ID NO:6. Preferably the amino acid sequence of any of the above functional homologues has no more than 300, 250, 200, 150, 100, 75, 50, 40, 30, 20, 10 or 5 amino acid substitutions, insertions and/or deletions as compared to SEQ ID NO:6.
Suitably the Saccharomyces yeast cell may comprise a nucleotide sequence coding for an amino acid sequence of SEQ ID NO:6 or an amino acid sequence having one or several substitutions, insertions and/or deletions as compared to the amino acid sequence of any of SEQ ID NO:6. Preferably the amino acid sequence has no more than 300, 250, 200, 150, 100, 75, 50, 40, 30, 20, 10 or 5 amino acid substitutions, insertions and/or deletions as compared to SEQ ID NO:6 respectively.
Examples of suitable nitrite/nitrate transporters, their UniProt Database Accession number (as can be found on the Uniprot website (https://www.uniprot.org/ as per 4 Oct. 2020), their description, the organism from which they may be derived, and their amino acid sequence identity with SEQ ID NO:6 are listed in Table 5 below.
Pseudogymnoascus
Marssonina brunnea f.
Preferably the Saccharomyces yeast cell further comprises suitable co-factors to enhance the activity of the above mentioned NADH-dependent nitrate reductase and/or NADH-dependent nitrite reductase. Preferred cofactors include flavin adenine dinucleotide (FAD), heme prosthetic groups, and/or molybdenum cofactor (MoCo). Preferably the Saccharomyces yeast cell may therefore further comprise one or more genes encoding enzymes for the synthesis of one or more of flavin adenine dinucleotide (FAD), heme prosthetic groups, and/or molybdenum cofactor (MoCo). For example, the Saccharomyces yeast cell may comprise one or more genes encoding for an enzyme having FAD synthase activity.
Preferably the Saccharomyces yeast cell is therefore a Saccharomyces yeast cell further comprising:
A suitable set of genes encoding enzymes for the synthesis of a molybdenum cofactor (MoCo) is described in PCT patent application PCT/NL2020/050241, published as WO2020/209718 in the name of the Technische Universiteit Delft. For example, the Saccharomyces yeast cell may suitably further comprise a recombinant Moco pathway gene set that allows the yeast to produce Molybdenum co-factor, wherein the Moco pathway gene set comprises:
Suitably, the Saccharomyces yeast cell may further comprise a deletion or disruption of one or more endogenous nucleotide sequence encoding a glycerol 3-phosphate phosphohydrolase gene and/or encoding a glycerol 3-phosphate dehydrogenase gene.
Preferably enzymatic activity needed for the NADH-dependent glycerol synthesis in the yeast cell is reduced or deleted. The reduction or deletion of the enzymatic activity of glycerol 3-phosphate phosphohydrolase and/or glycerol 3-phosphate dehydrogenase can be achieved by modifying one or more genes encoding a NAD-dependent glycerol 3-phosphate dehydrogenase (GPD) and/or one or more genes encoding a glycerol phosphate phosphatase (GPP), such that the enzyme is expressed considerably less than in the wild-type or such that the gene encodes a polypeptide with reduced activity. Such modifications can be carried out using commonly known biotechnological techniques, and may in particular include one or more knock-out mutations or site-directed mutagenesis of promoter regions or coding regions of the structural genes encoding GPD and/or GPP. Alternatively, yeast strains that are defective in glycerol production may be obtained by random mutagenesis followed by selection of strains with reduced or absent activity of GPD and/or GPP. S. cerevisiae GPD1, GPD2, GPP1 and GPP2 genes are shown in WO2011010923, and are disclosed in SEQ ID NO: 24-27 of that application.
Preferably at least one gene encoding a GPD and/or at least one gene encoding a GPP is entirely deleted, or at least a part of the gene is deleted that encodes a part of the enzyme that is essential for its activity. In particular, good results have been achieved with a S. cerevisiae cell, wherein the open reading frames of the GPD1 gene and of the GPD2 gene have been inactivated. Inactivation of a structural gene (target gene) can be accomplished by a person skilled in the art by synthetically synthesizing or otherwise constructing a DNA fragment consisting of a selectable marker gene flanked by DNA sequences that are identical to sequences that flank the region of the host cell's genome that is to be deleted. In particular, good results have been obtained with the inactivation of the GPD1 and GPD2 genes in Saccharomyces cerevisiae by integration of the marker genes kanMX and hphMX4. Subsequently this DNA fragment is transformed into a host cell. Transformed cells that express the dominant marker gene are checked for correct replacement of the region that was designed to be deleted, for example by a diagnostic polymerase chain reaction or Southern hybridization.
Thus, in the Saccharomyces yeast cells of the invention, glycerol 3-phosphate phosphohydrolase activity and/or glycerol 3-phosphate dehydrogenase activity is advantageously reduced. In the cells of the invention, the specific glycerolphosphate dehydrogenase activity is preferably reduced by at least a factor 0.8, 0.5, 0.3, 0.1, 0.05 or 0.01 as compared to a strain which is genetically identical except for the genetic modification causing the reduction in specific activity, preferably under anaerobic conditions. Glycerolphosphate dehydrogenase activity may be determined as described by Overkamp et al. (2002, Yeast 19:509-520).
Preferably the Saccharomyces yeast cell may further comprise:
More preferably the Saccharomyces yeast cell may comprise: one or more nucleic acid sequences encoding a glycerol dehydrogenase; and/or one or more nucleic acid sequences encoding a dihydroxyacetone kinase; and/or one or more nucleic acid sequences encoding a glycerol transporter, each as described and exemplified in WO 2019/063507 A1 (hereby incorporated by reference).
The enzyme glycerol dehydrogenase catalyzes at least the following reaction:
glycerol+NAD+<->glycerone+NADH+H+
Thus, the two substrates of this enzyme are glycerol and NAD+, whereas its three products are glycerone, NADH, and H+. Glycerone and dihydroxyacetone are herein synonyms. This enzyme belongs to the family of oxidoreductases, specifically those acting on the CH—OH group of donor with NAD+ or NADP+ as acceptor. The systematic name of this enzyme class is glycerol:NAD+2-oxidoreductase. Other names in common use include glycerin dehydrogenase, and NAD+-linked glycerol dehydrogenase. This enzyme participates in glycerolipid metabolism. Structural studies have shown that the enzyme is zinc-dependent with the active site lying between the two domains of the protein. In an embodiment the enzyme having glycerol dehydrogenase activity is preferably a NAD+ linked glycerol dehydrogenase (EC 1.1.1.6). Such enzyme may be from bacterial origin or for instance from fungal origin. An example is gldA from E. coli. The enzyme having glycerol dehydrogenase activity may also be a NADP+ linked glycerol dehydrogenase (EC 1.1.1.72). When a recombinant yeast is used for ethanol production, which typically takes place under anaerobic conditions, NAD+ linked glycerol dehydrogenases are preferred.
Preferably the Saccharomyces yeast cell may also comprise a nucleic acid coding for an enzyme having dihydroxyacetone kinase activity. The Saccharomyces yeast cell preferably comprises one or more genes coding for an enzyme having dihydroxyacetone kinase activity with EC codes E.C. 2.7.1.28 and/or E.C. 2.7.1.29. The enzyme dihydroxyacetone kinase catalyzes at least one of the following reactions:
This family of enzymes may include examples of the single chain form of dihydroxyacetone kinase (also called glycerone kinase) that uses ATP (EC 2.7.1.29 or EC 2.7.1.28) as the phosphate donor, rather than a phosphoprotein as in Escherichia coli. This form has separable domains homologous to the K and L subunits of the E. coli enzyme, and is found in yeasts and other eukaryotes and in some bacteria, including Citrobacter freundii. The member from tomato has been shown to phosphorylate dihydroxyacetone, 3,4-dihydroxy-2-butanone, and some other aldoses and ketoses. Members from mammals have been shown to catalyse both the phosphorylation of dihydroxyacetone and the splitting of ribonucleoside diphosphate-X compounds among which FAD is the best substrate. In yeast there are two isozymes of dihydroxyacetone kinase (Dak1 and Dak2). In an embodiment the Saccharomyces yeast cell may comprises endogenous DAK which is overexpressed. The enzyme having dihydroxy acetone kinase activity may be encoded by an endogenous gene, e.g. a DAK1, which endogenous gene is preferably placed under control of a constitutive promoter. The recombinant cell may comprise a genetic modification that increases the specific activity of dihydroxyacetone kinase in the cell.
In an embodiment the Saccharomyces yeast cell may further comprise one or more genes coding for a glycerol transporter or an enzyme having an amino acid sequence listed for such in WO 2019/063507 A1 (i.e. WO 2019/063507 A1 refers to SEQ ID NO: 16 and SEQ ID NO: 17 therein for the glycerol transporter which are incorporated by reference herewith) or a functional homologue thereof having a sequence identity of at least 50%, preferably at least 60%, 70%, 75%, 80%. 85%, 90%, 95%, or at least 99%. Any glycerol that is externally available in the medium (e.g. from the backset in corn mash) or secreted after internal cellular synthesis may be transported into the cell and converted to ethanol.
The invention further provides an anaerobic fermentation process for the production of a fermentation product, comprising fermenting of a feed, which feed comprises an oxidized nitrogen source and a fermentable carbon source, using a saccharomyces yeast cell as described above.
The fermentable carbon source preferably comprises or is consisting of one or more fermentable carbohydrates. More preferably, the fermentable carbon source comprises one or more mono-saccharides, disaccharides and/or polysaccharides. For example, the fermentable carbon source may comprise one or more carbohydrates selected from the group consisting of glucose, fructose, sucrose, maltose, xylose, arabinose, galactose, mannose and trehalose. The fermentable carbon source, preferably comprising or consisting of one or more carbohydrates, may suitably be obtained from starch, cellulose, hemicellulose lignocellulose, and/or pectin. Suitably the fermentable carbon source may be in the form of a, preferably aqueous, slurry, suspension, or a liquid.
The concentration of fermentable carbohydrate, such as for example glucose, during fermentation is preferably equal to or more than 80 g/L. That is, the initial concentration of glucose at the start of the fermentation, is preferably equal to or more than 80 g/L, more preferably equal to or more than 90 g/L, even more preferably equal to or more than 100 g/L, still more preferably equal to or more than 110 g/L, yet even more preferably equal to or more than 120 g/L, equal to or more than 130 g/L, equal to or more than 140 g/L, equal to or more than 150 g/L, equal to or more than 160 g/L, equal to or more than 170 g/L, or equal to or more than 180 g/L. The start of the fermentation may be the moment when the fermentable fermentable carbohydrate is brought into contact with the recombinant cell of the invention.
The fermentable carbon source may be prepared by contacting starch, lignocellulose, and/or pectin with an enzyme composition, wherein one or more mono-saccharides, disaccharides and/or polysaccharides are produced, and wherein the produced mono-saccharides, disaccharides and/or polysaccharides are subsequently fermented to give a fermentation product.
In one embodiment the fermentable carbohydrate is, or is comprised by a biomass hydrolysate, such as a corn stover or corn fiber hydrolysate. Such biomass hydrolysate may in its turn comprise, or be derived from corn stover and/or corn fiber.
By a “hydrolysate” is herein understood a polysaccharide-comprising material (such as corn stover, corn starch, corn fiber, or lignocellulosic material, which polysaccharides have been depolymerized through the addition of water to form mono and oligosaccharide sugars. Hydrolysates may be produced by enzymatic or acid hydrolysis of the polysaccharide-containing material.
A biomass hydrolysate may be a lignocellulosic biomass hydrolysate. Lignocellulose herein includes hemicellulose and hemicellulose parts of biomass. Also lignocellulose includes lignocellulosic fractions of biomass. Suitable lignocellulosic materials may be found in the following list: orchard primings, chaparral, mill waste, urban wood waste, municipal waste, logging waste, forest thinnings, short-rotation woody crops, industrial waste, wheat straw, oat straw, rice straw, barley straw, rye straw, flax straw, soy hulls, rice hulls, rice straw, corn gluten feed, oat hulls, sugar cane, corn stover, corn stalks, corn cobs, corn husks, switch grass, miscanthus, sweet sorghum, canola stems, soybean stems, prairie grass, gamagrass, foxtail; sugar beet pulp, citrus fruit pulp, seed hulls, cellulosic animal wastes, lawn clippings, cotton, seaweed, trees, softwood, hardwood, poplar, pine, shrubs, grasses, wheat, wheat straw, sugar cane bagasse, corn, corn husks, corn hobs, corn kernel, fiber from kernels, products and by-products from wet or dry milling of grains, municipal solid waste, waste paper, yard waste, herbaceous material, agricultural residues, forestry residues, municipal solid waste, waste paper, pulp, paper mill residues, branches, bushes, canes, corn, corn husks, an energy crop, forest, a fruit, a flower, a grain, a grass, a herbaceous crop, a leaf, bark, a needle, a log, a root, a sapling, a shrub, switch grass, a tree, a vegetable, fruit peel, a vine, sugar beet pulp, wheat midlings, oat hulls, hard or soft wood, organic waste material generated from an agricultural process, forestry wood waste, or a combination of any two or more thereof. Lignocellulose, which may be considered as a potential renewable feedstock, generally comprises the polysaccharides cellulose (glucans) and hemicelluloses (xylans, heteroxylans and xyloglucans). In addition, some hemicellulose may be present as glucomannans, for example in wood-derived feedstocks. The enzymatic hydrolysis of these polysaccharides to soluble sugars, including both monomers and multimers, for example glucose, cellobiose, xylose, arabinose, galactose, fructose, mannose, rhamnose, ribose, galacturonic acid, glucuronic acid and other hexoses and pentoses occurs under the action of different enzymes acting in concert. In addition, pectins and other pectic substances such as arabinans may make up considerably proportion of the dry mass of typically cell walls from non-woody plant tissues (about a quarter to half of dry mass may be pectins). Lignocellulosic material may be pretreated. The pretreatment may comprise exposing the lignocellulosic material to an acid, a base, a solvent, heat, a peroxide, ozone, mechanical shredding, grinding, milling or rapid depressurization, or a combination of any two or more thereof. This chemical pretreatment is often combined with heat-pretreatment, e.g. between 150-220° C. for 1 to 30 minutes.
In addition to the fermentable carbon source, the fermentation feed and/or fermentation medium also comprises an oxidized nitrogen source. Examples of oxidized nitrogen sources include alkali metal salts and alkaline earth metal salts of nitrite and nitrate, such as for example sodium nitrate, sodium nitrite, potassium nitrate, potassium nitrite, calcium nitrate, calcium nitrite, magnesium nitrate and/or magnesium nitrite. The oxidized nitrogen source may also be present as a dissolved or dissociated salt, that it, it may also be present as a nitrite NO2− ion or nitrate NO3− ion. Suitably the oxidized nitrogen source, such as a nitrate salt or a nitrite salt, may be present in combination with ammonium. For example ammonium nitrate or ammonium nitrite may be used as an oxidized nitrogen source. However, ammonium nitrate can be explosive and would need to be provided in a composition mitigating such risk.
Another example of an oxidized nitrogen source is the so-called Urea Ammonium Nitrate, also abbreviates as UAN (UAN is for example supplied by producer YARA in Norway). UAN provides four distinct forms of nitrogen: NH4, NO3, Urea and NH3. Even though UAN still comprises urea, the percentage urea used can be greatly reduced by using UAN instead of urea. Advantageously, though UAN contains ammonium nitrate, UAN is not explosive and is not classified as a “dangerous good” during air, land or sea transport.
The anaerobic fermentation process produces one or more fermentation products. Suitable fermentation products include alcohols and organic acids. Preferred fermentation products include ethanol, butanol, lactic acid and succinic acid. In addition, the process also provides dried distillers grains (DDG).
Such dried distillers grains (DDG) may advantageously be used as animal feed, for example as part of the feed for cattle, pigs or poultry. Due to the use of the Saccharomyces yeast cell according to the invention, the quality of the dried distillers grains (DDG) may be improved. The amount of ethyl carbamate and/or lactic acid therein may be reduced and the type and concentration of nitrogen-containing components therein may be improved. Advantageously the dried distillers grains may comprise no or a reduced amount of urethane (ethyl carbamate).
Advantageously the invention provides a product comprising distillers grains comprising equal to or less than 17 ng/g of ethyl carbamate, more preferably equal to or less than 10 ng/g of ethyl carbamate, even more preferably equal to or less than 5 ng/g and most preferably equal to or less than 1 ng/g. There is no lower limit, but practical reasons the distillers grains may comprise equal to or more than 0.001 ng/g. The distillers grains can be wet or dried and can be with or without solubles.
All patent and literature references cited in the present specification are hereby incorporated by reference in their entirety.
The following examples are offered for illustrative purposes only, and are not intended to limit the scope of the present invention in any way.
In order to incorporate an NADH-dependent nitrate and/or nitrite assimilation pathway in a Saccharomyces yeast cell, alternative gene combinations are to be tested. For a number of enzymes in the pathway, i.e. nitrate and/or nitrite transporters, NADH dependent nitrate reductase and/or NADH dependent nitrite reductase, multiple alternative genes are to be tested that could allow the Saccharomyces yeast cell to convert an external oxidized nitrogen source into intracellular ammonia, in parallel with a conversion of pentose and/or hexose sugars into ethanol, under anaerobic conditions.
Unless indicated otherwise, the methods used are standard biochemical techniques. Examples of suitable general methodology textbooks include Sambrook et al., Molecular Cloning, a Laboratory Manual (1989) and Ausubel et al., Current Protocols in Molecular Biology (1995), John Wiley & Sons, Inc.
Ethanol Red, a commercial Saccharomyces cerevisiae yeast available from LeSaffre (France) can be used to express various NADH-dependent nitrate reductases (EC 1.7.1.1), NADH-dependent nitrite reductases (EC 1.7.1.15) and/or a nitrate transporter and/or a molybdenum cofactor pathway. For example, this modified yeast can contain a NADH-dependent nitrate reductases from Zea mays (SEQ ID NO:1), NADH-dependent nitrite reductases from E. coli coding for the small subunit NirD (SEQ ID NO:3) and large subunit NirB (SEQ ID NO:4), and Siroheme synthase CysG from E. coli (SEQ ID NO:22) or overexpression of the S. cerevisiae MET8 Bifunctional dehydrogenase and ferrochelatase (YBR213W) (SEQ ID NO:23):
cerevisiae (strain ATCC 204508/S288c) OX = 559292 GN = MET8 PE = 1 SV = 1
Furthermore, this modified yeast can express a functional pathway to produce the molybdopterin cofactor. The genes and corresponding enzymes for molybdopterin pathway from GTP can be downloaded from the MetaCyc website (https://metacyc.org as available on 5 Oct. 2020).
The E. coli molybdopterin pathway has been described by Leimkühler S, Wuebbens M M, Rajagopalan K V., in their article “The History of the Discovery of the Molybdenum Cofactor and Novel Aspects of its Biosynthesis in Bacteria”, published in Coord Chem Rev. (2011); Vol. 255(9-10): pages 1129-1144. (doi:10.1016/j.ccr.2010.12.003). The following enzymes of the molybdopterin cofactor pathway can be expressed: MoaA (SEQ ID NO:7), MoaC (SEQ ID NO:8), MoaD (SEQ ID NO:9), MoaE (SEQ ID NO:10), MoeB (SEQ ID NO:19), MogA (SEQ ID NO:20), MoeA (SEQ ID NO:18), MobA (SEQ ID NO:11), MobB (SEQ ID NO:12), MocA (SEQ ID NO13) and/or IscS (SEQ ID NO:21) and/or ModA, ModB and/or ModC for molybdate transport (SEQ ID NO:14, SEQ ID NO:15 and SEQ ID NO:16, respectively) and/or ModE (SEQ ID NO:17).
This modified yeast can in addition or alternatively express a functional pathway to produce the molybdopterin cofactor from plants as described for example by Mendel R R, in its article titled “Biology of the molybdenum cofactor”, published in J Exp Bot. (2007); Vol. 58(9): pages 2289-2296. (doi: 10.1093/jxb/erm024. Epub 2007 Mar. 9. PMID: 17351249.). Suitably the following enzymes from Arabidopsis thaliana can be expressed in yeast to produce the Cnx1 (SEQ ID NO:24), Cnx2 (SEQ ID NO: 25), Cnx3 (SEQ ID NO: 26), Cnx5=MOCS3 (SEQ ID NO:27), Cnx6=Moc2B (SEQ ID NO:28), Cnx7=Moc2A (SEQ ID NO:29):
thaliana OX = 3702 GN = CNX1 PE = 1 SV = 2
thaliana OX = 3702 GN = CNX2 PE = 1 SV = 1
Arabidopsis thaliana OX = 3702 GN = MOCS2 PE = 2 SV = 1
Arabidopsis thaliana OX = 3702 GN = At4g10100 PE = 3 SV = 1
Escherichia coli (strain K12) OX = 83333 GN = moaC PE = 1 SV = 2
Escherichia coli (strain K12) OX = 83333 GN = moaD PE = 1 SV = 2
Escherichia coli (strain K12) OX = 83333 GN = moaE PE = 1 SV = 3
coli (strain K12) OX = 83333 GN = moeA PE = 1 SV = 1
Escherichia coli (strain K12) OX = 83333 GN = moeB PE = 1 SV = 1
coli (strain K12) OX = 83333 GN = mobA PE = 1 SV = 1
Escherichia coli (strain K12) OX = 83333 GN = mocA PE = 1 SV = 1
Enterobacteria phage T4 OX = 10665 GN = modB PE = 1 SV = 2
Escherichia coli (strain K12) OX = 83333 GN = modC PE = 3 SV = 4
The strain construction approach is described in WO2013144257A1 (publication of patent application PCT/EP2013/056623) and WO 2015/028582. Expression cassettes from various genes of interest are recombined in vivo into a pathway at a specific locus upon transformation of this yeast (U.S. Pat. No. 9,738,890 B2).
The open reading frames (ORFs), are synthesized at TWIST (South San Francisco, CA 94080, 35 USA). The promoter, ORF and terminator sequences are assembled into expression cassettes with Golden Gate technology, as described by Engler et al (2011) and ligated into BsaI-digested backbone vectors that decorated the expression cassettes with the connectors for the in vivo recombination step. The expression cassettes including connectors are amplified by PCR. In addition, a 5′- and a 3′-DNA fragment of approximately 500 by of the up- and downstream part of the integration locus is amplified using PCR and decorated by a connector sequence. Upon transformation of yeast cells with these DNA fragments, in vivo recombination and integration into the genome takes place at the desired location. CRISPR-Cas9 technology is used to make a unique double stranded break at the integration locus to target the pathway to this specific locus (DiCarlo et al., 2013, Nucleic Acids Res 41:4336-4343) and WO16110512.
The strains are tested in anaerobic fermentation. Corn mash (30% (w/w) solids) is prepared by mixing 333 g corn flour (Limagrain, Belgium) per kg mash, with 300 ml/kg thin stillage and 367 ml/kg demineralized water. The pH is adjusted to 5.5 with 2M KOH solution. Starch in the mixture is liquefied by adding 0.02 g/kg of a commercial alpha-amylase (Termamyl, Novozymes), and incubated for 4 hours at 80′C in a rotary shaker. After liquefaction the pH is adjusted to 4.5 with 2M H2SO4 solution. The strains are pre-cultured by inoculating 200 ml YepH (20 g/l phytone peptone, 10 g/l yeast extract) supplemented with 2% w/v glucose, from a cryovial and incubated in a 500 ml shake flask. To determine the inoculation volume of the yeast, the dry cell weight (DCW) content of the culture is determined by filtration and drying via a CEM-SMART microwave. A quantity of the preculture corresponding to the required inoculation size for the propagations are centrifuged (3 min, 4500×g), washed once with sterile demineralized water, centrifuged once more, resuspended in propagation medium and transferred to the propagation flasks. Propagations are performed in 100 ml Erlenmeyer shake flasks with a foam stopper for 6h at 32′C, 150 rpm, creating a semi-aerobic environment. The propagation medium is diluted to a 70% (v/v) solution, checked for pH 4.5 and is supplied with 4.2 g/l KNO3 and antibiotics (neomycin and PenG). For each strain 0.088 g/l commercial amyloglucosidase enzyme (Spirizyme Excel, novozymes) is added. Fermentations were performed in simultaneous saccharification fermentation (SSF) mode, using 500 ml schott bottles filled with 200 ml of corn mash and fitted with an Ankom gas production system cap (Ankom, Macedon, NY, USA), effectively rendering the fermentations anaerobic. The corn mash is used as such, with addition of 3.4 g/l KNO3 and antibiotics, pH 4.5. The inoculation of the fermenters is done by transferring 10% of the propagation medium to the fermenters, reaching 400 ml of volume. The pH is not controlled during the fermentations, while temperature is controlled at 32° C. Fermentation samples were taken throughout the run and different components were measured by HPLC analysis using a Dionex Ultimate 3000 HPLC system with column oven TCC-3400 and Autosampler WPS-3000 equipped with a guard column (Bio-Rad H cartridge) and an Aminex HPX-87H column (300×7.8 mm; Bio-Rad, Hercules, USA); elution took place at 65′C with 5 mM H2804 at 0.55 ml/min; the eluate is monitored using a Refractive Index detector RefractoMax 521. CO2 is measured online during the fermentation.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2021/077334 | 10/5/2021 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 63087642 | Oct 2020 | US |
