WO2023168233A1

WO2023168233A1 - Genetically modified yeast and fermentation processes for the production of 3-hydroxypropionate

Info

Publication number: WO2023168233A1
Application number: PCT/US2023/063434
Authority: WO
Inventors: Keith Michael BRADY; Hans H. Liao; Brian Jeffrey RUSH
Original assignee: Cargill, Incorporated
Priority date: 2022-03-03
Filing date: 2023-03-01
Publication date: 2023-09-07

Abstract

Disclosed herein are genetically engineered yeast cells capable of producing 3-HP from sucrose. The genetically engineered yeast cells comprise an active 3-HP fermentation pathway; a polynucleotide encoding an exogenous invertase enzyme; a deletion or disruption of a native pyruvate decarboxylase (PDC) gene; and a genetic modification resulting in overexpression of a native hexokinase gene.

Description

GENETICALLY MODIFIED YEAST AND FERMENTATION PROCESSES FOR THE

PRODUCTION OF 3-HYDROXYPROPINATE

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims the benefit of U.S. Provisional Application No. 63/268,831, filed March 3, 2022, which is incorporated by reference herein in its entirety.

REFERENCE TO A SEQUENCE LISTING SUBMITTED VIA PATENT CENTER [0002] The content of the Sequence Listing XML file of the sequence listing named “PT- 1276-

WO-PCT.xml” which is 252,422 bytes in size created on March 1, 2023, and electronically submitted via Patent Center herewith the application is incorporated by reference in its entirety.

BACKGROUND

[0003] Fermentation processes are used commercially at large scale to produce organic molecules such as ethanol, citric acid, malonic acid, 3-hydroxypropinoic acid, and lactic acid. In those processes, a carbohydrate is fed to an organism that is capable of metabolizing it to the desired fermentation product. The carbohydrate and organism are selected together so that the organism is capable of efficiently digesting the carbohydrate to form the product desired in good yield. It is becoming more common to use genetically engineered organisms in these processes, in order to optimize yields and process variables, or to enable particular carbohydrates to be metabolized.

[0004] Sucrose is a possible carbohydrate feed for such commercial fermentation processes. However, many organisms are not capable of metabolizing sucrose and/or are not capable of metabolizing the fructose component of sucrose.

SUMMARY

[0005] The present disclosure provides a genetically engineered yeast cell capable of producing3-hydroxypropionate (3-HP) from sucrose, the engineered yeast cell comprising an active 3-HP fermentation pathway; a polynucleotide encoding an exogenous invertase enzyme; a deletion or disruption of a native pyruvate decarboxylase (PDC) gene; and a genetic modification resulting in overexpression of a native hexokinase gene. The yeast cell may be Crabtree negative. The yeast cell may be a yeast cell of the Issatchenkia orientalis /Pichia fermentans clade. The yeast may be an Issatchenkia orientalis cell. L0006J The disclosure also provides a genetically engineered Issatchenkia orientalis cell capable of producing 3-hydroxypropionate (3-HP) from sucrose, the engineered yeast cell comprising an active 3-HP fermentation pathway; a polynucleotide encoding an exogenous invertase enzyme; a deletion or disruption of a native pyruvate decarboxylase (PDC) gene, and a genetic modification resulting in overexpression of a native hexokinase gene, wherein the engineered I. orientalis cell is capable of producing 3-HP at a titer of at least 30, at least 80, at least 100, or at least 120 g/L.

[0007] The engineered yeast cell described herein may have hexokinase activity in the engineered yeast cell that is higher than hexokinase activity in an equivalent yeast cell lacking the genetic modification. Peak 3-HP production rate in the engineered yeast cell, when used in a fermentation process in the presence of sucrose, may be higher than peak 3-HP production rate of an equivalent yeast cell lacking the genetic modification. The genetic modification may comprise replacement of the native hexokinase gene promoter with a constitutive heterologous or artificial promoter. The constitutive heterologous or artificial promoter may be selected from the group consisting of pyruvate decarboxylase (PDC1), glyceraldehyde-3-phosphate dehydrogenase (TDH3), enolase (ENO1), and 3-phosphogly cerate kinase (PGK1). The genetic modification may comprise addition of an exogenous polynucleotide encoding the native hexokinase such that the genetically engineered yeast cell comprises at least one additional copy of a sequence encoding the native hexokinase. The native hexokinase may comprise a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs:24 and 25. The yeast cell may be an Issatchenkia orientalis cell and the native, overexpressed hexokinase comprises a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs:24 and 25. [0008] The engineered yeast cell may comprise a deletion or disruption of a glycerol-3- phosphate dehydrogenase (GPD) gene. The engineered yeast cell may comprise a deletion or disruption of an L-lactate: cytochrome c oxidoreductase (CYB2) gene. The exogenous invertase enzyme may comprise a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs: 12, 33, 34, and 35. The polynucleotide encodingthe exogenous invertase enzyme may be operably linked to a heterologous or artificial promoter. The promoter may be selected from the group consisting of pyruvate decarboxylase (PDC1), glyceraldehyde-3- phosphate dehydrogenase (TDH3), translational elongation factor (TEF), transaldolase (TAL), RPL16B, 3-phosphogly cerate kinase (PGK1), and enolase (EN01).

[0009] The yeast cell may additionally comprise an exogenous polynucleotide encoding a fructokinase. The fructokinase may comprise a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to SEQ ID NO: 26. The exogenous polynucleotide encoding the fructokinase may be operably linked to a heterologous or artificial promoter. The heterologous or artificial promoter may be selected from the group consisting of pyruvate decarboxylase (PDC1), glyceraldehyde-3- phosphate dehydrogenase (TDH3), translational elongation factor (TEF), transaldolase (TAL), RPL16B, 3-phosphogly cerate kinase (PGK1), and enolase (ENO1).

[0010] The active 3-HP fermentation pathway may comprise one or more exogenous polypeptides encoding a pyruvate carboxylase (PCY) enzyme, an aspartate aminotransferase (AAT) enzyme, an aspartate 1 -decarboxylase (ADC) enzyme, a [3-alanine aminotransferase (BAAT) enzyme, a 3-hydroxypropionic acid dehydrogenase (3-HPDH) enzyme, or combinations thereof. The PCY enzyme may comprise a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs:45, 46, 47, 48, 49, 50, or 51. The AAT enzy me may comprise a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs:57, 58, or 59. The ADC enzyme may comprise a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs:88-127, preferably at least one of SEQ ID NOs:94, 101, 102, or 103, most preferably SEQ ID NO: 102. The BAAT enzyme may comprise a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs:60, 62, 64, 66, or 67. The 3-HPDH enzyme may comprise a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs:70, 71 , 73, or 75. The one or more exogenous polynucleotides may be operably linked to a heterologous or artificial promoter selected from the group consisting of pyruvate decarboxylase (PDC1), glyceraldehyde-3-phosphate dehydrogenase (TDH3), translational elongation factor (TEF), transaldolase, RPL16B, 3-phosphoglycerate kinase (PGK1), and enolase (ENO1). LOO 11 J The disclosure also provides a method for producing 3 -hydroxy propionate (3-HP) from sucrose, the method comprising: contacting a substrate comprising sucrose with the engineered yeast cell described herein, wherein fermentation of the substrate by the engineered yeast produces 3-HP. The disclosure also provides a method for producing 3-hydroxypropionate (3-HP) from sucrose, the method comprising: contacting a substrate comprising sucrose with an engineered yeast cell comprising an active 3-HP fermentation pathway; a polynucleotide encoding an exogenous invertase enzyme; a deletion or disruption of a native pyruvate decarboxylase (PDC) gene; and a genetic modification resulting in overexpression of a native hexokinase gene, wherein fermentation of the substrate by the engineered yeast produces lactate. The volumetric oxygen uptake rate (OUR) of the method may be 0.5 to 40 mmol O2/(L • h), 1 to 35 mmol O2/(L • h), 3 to 30 mmol O2/(L • h), 6 to 27 mmol O2/(L • h), or 16-24 mmol O2/(L • h). The specific OUR of the method may be in the range of 0.2 to 13 mmol O2/(g cell dry weight • h), 0.3 to 10 mmol O2/(g cell dry weight • h), 1 to 7 mmol O2/(g cell dry weight • h), or 2 to 6 mmol O2/(g cell dry weight • h). The peak 3-HP production rate of the method may be at least 5 g L h’¹, at least 6 g L h’¹, at least 7 g L ¹ h’¹, or at least 8 g L ¹ h⁴. 3-HP may be produced at an average rate of at least 1.5 g L h⁴, at least 2.0 g L h⁴, at least 2.5 g L⁴ h⁴, at least 3.0 g L h⁴, or at least 3.5 g L h’¹. The fermentation temperature may be in the range of 25 °C to 45 °C, 20 °C to 40 °C, or 32 °C to 37 °C. The 3-HP titer of the method may be at least 30, at least 80, at least 100, or at least 120 g/L.

BRIEF DESCRIPTION OF THE FIGURES

[0012] This patent or application contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawings will be provided by the Office upon request and the payment of the necessary fee.

[0013] The drawings illustrate generally, by way of example, but not by way of limitation, various aspects discussed herein.

[0014] FIG. 1 shows metabolic pathways for the products of 3-HP.

[0015] FIG. 2 shows sugar profiles for the shake flask fermentations described in Example 2. [0016] FIG. 3 shows 3-HP production in the shake flask fermentations described in Example 2.

DETAILED DESCRIPTION

[0017] Reference will now be made in detail to certain aspects of the disclosed subject matter, examples of which are illustrated in part in the accompanying drawings. While the disclosed subject mater will be described in conjunction with the enumerated claims, it will be understood that the exemplified subject mater is not intended to limit the claims to the disclosed subject mater.

[0018] In this document, the terms “a,” “an,” or “the” are used to include one or more than one unless the context clearly dictates otherwise. The term “or” is used to refer to a nonexclusive “or” unless otherwise indicated. All publications, patents, and patent documents referred to in this document are incorporated by reference herein in their entirety, as though individually incorporated by reference. In the event of inconsistent usages between this document and those documents so incorporated by reference, the usage in the incorporated reference should be considered supplementary to that of this document; for irreconcilable inconsistencies, the usage in this document controls.

[0019] Values expressed in a range format should be interpreted in a flexible manner to include not only the numerical values explicitly recited as the limits of the range, but also to include all the individual numerical values or sub-ranges encompassed within that range as if each numerical value and sub-range were explicitly recited. For example, a range of “about 0. 1% to about 5%” or “about 0.1% to 5%” should be interpreted to include not just about 0.1% to about 5%, but also the individual values (e.g., 1%, 2%, 3%, and 4%) and the sub-ranges (e.g., 0.1% to 0.5%, 1.1% to 2.2%, 3.3% to 4.4%) within the indicated range. The statement “about X to Y” has the same meaning as “about X to about Y,” unless indicated otherwise. Likewise, the statement “about X, Y, or about Z” has the same meaning as “about X, about Y, or about Z,” unless indicated otherwise.

[0020] Unless expressly stated, ppm (parts per million), percentage, and ratios are on a by weight basis. Percentage on a by weight basis is also referred to as wt% or % (wt) below.

[0021] This disclosure relates to various recombinant cells engineered to produce 3- hydroxypropinate which have improved sucrose consumption, in particular, improved fructose consumption. In general, the recombinant cells described herein have a deletion or disruption of a native pyruvate decarboxylase gene and have an active 3-HP fermentation pathway and are characterized by at least one of expression of an exogenous invertase enzyme, expression of an exogenous fructose transporter, expression of an exogenous hexokinase gene, and a genetic modification resulting in overexpression of a native hexokinase gene. The disclosure further provides fermentation methods for the production of 3-HP from sucrose using the genetically engineered cells described herein. L0022J As used herein, “3-hydroxypropionate” and “3-HP” are interchangeable and refer to the salt (3-hydroxypropionate) and acid (3-hydroxypropinoic acid) forms of 3-hydroxypropinoic acid. 3-HP is measured as the sum of free 3-hydroxypropionic acid and any 3-hydroxypropionate salts (excluding the portions attributable to any cation portion of said salt form present). In other words, “rate of 3-HP production,” “3-HP yield,” “3-HP titer,” and the like refer to the rate, yield, titer, respectively, of the sum of free 3-hydroxypropionic acid and any 3-hydroxylpropionate salts.

[0023] In general, recombinant cells described herein are yeast cells. Suitable yeast cells may include, but are not limited to, Saccharomyces cerevisiae, Issatchenkia orientalis, Pichia galeiformis, Pichia sp. YB-4149 (NRRL designation), Candida ethanolica, Pichia deserticola, Pichia membranifadens , ox Pichia fermentans. An ordinarily skilled artisan would understand the requirements for selection of a suitable yeast cell, and recombinant yeast cells of the present disclosure are not limited to those expressly recited herein.

[0024] The recombinant yeast cell may be a Crabtree negative yeast cell. As used herein, “Crabtree negative” refers to a yeast cell that does not exhibit the Crabtree effect of fermentative metabolism under aerobic conditions as a result of the inhibition of oxygen consumption by the microorganism when cultured at high specific grow th rates (long-term effect) or in the presence of high concentrations of glucose (short-term effect) due to the inhibition of the synthesis of respiratory enzymes. A Crabtree negative yeast cell will not exhibit this effect and is therefore able to consume oxygen even in the presence of high concentrations of glucose or at high growth rates. Methods for determining whether an organism is Crabtree negative or Crabtree positive are known and described in the art (e.g., See De Deken R.H. (1965) J. Gen. Microbiol., 44: 149-156). [0025] The recombinant cell may be a yeast cell of a species within the Issatchenkia orientalis /Pichia fermentans clade. This clade is the most terminal clade that contains at least the species Issatchenkia orientalis, Pichia galeiformis, Pichia sp. YB-4149 (NRRL designation), Candida ethanolica, Pichia deserticola, Pichia membranifadens, and Pichia fermentans. Identification and characterization of species within the I. orientalis/P. fermentans clade is known and described in the art. See, for example, Kurtzman et al. (“Identification and phylogeny of Ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences,” Antonie van Leeuwanhoek, 73:331-371, 1998) and W02007032792A2, each of which is incorporated herein by reference. Analysis of the variable D1/D2 domain of the 26S ribosomal DNA from hundreds of ascomycetes has shown that the I. orientalis/P. fermentans clade contains very closely related species. Members of the I. orientalis/P. fermentans clade exhibit greater similarity in the variable D1/D2 domain of the 26S ribosomal DNA to other members of the clade than to yeast species outside of the clade. Therefore, other members of the I. orientalis/P . fermentans clade can be identified by comparison of the D1/D2 domains of their respective ribosomal DNA and comparing to that of other members of the clade and closely related species outside of the clade, using Kurtzman and Robnetf s methods (see Kurtzman and Fell, The Yeasts, a Taxonomic Study, Section 35, Issatchenkia Kudryavtsev, pp. 222-223 (1998), which is hereby incorporated by reference). The recombinant cell may be a recombinant Issatchenkia orientalis, Pichia galeiformis, Pichia sp. YB-4149 (NRRL designation), Candida ethanolica, Pichia deserticola, Pichia membranifaden , or Pichia fermentans cell.

[0026] When first characterized, the species I. orientalis was assigned the name Pichia kudriavzevii . The anamorph (asexual form) of/, orientalis is known as Candida krusei. Examples of suitable/, orientalis strains may include, but are not limited to, /. orientalis strains ATCC 32196 and /, orientalis strain ATCC PTA-6658.

[0027] The recombinant cells described herein include one or more exogenous polynucleotide sequences encoding one or more exogenous polypeptides that, when expressed improve the fermentation of sucrose to 3-HP by the recombinant cells. The recombinant cell may alternatively or additionally include one or more genetic modifications that increases expression of a native polypeptide, wherein said increase in expression improves the fermentation of sucrose to 3-HP by the recombinant cell.

[0028] As used herein, “exogenous” refers to genetic material or an expression product thereof that originates from outside of the host organism. For example, the exogenous genetic material or expression product thereof can be a modified form of genetic material native to the host organism, it can be derived from another organism, it can be a modified form of a component derived from another organism, or it can be a synthetically derived component. For example, a K. lactis invertase gene is exogenous when introduced into /. orientalis.

[0029] As used herein, “native” refers to genetic material or an expression product thereof that is found, apart from individual-to-individual mutations which do not affect function or expression, within the genome of wild-type cells of the host cell.

[0030] As used herein, the terms “polypeptide” and “peptide” are used interchangeably and refer to the collective primary, secondary, tertiary, and quaternary amino acid sequence and structure necessary to give the recited macromolecule its function and properties. As used herein, “enzy me” or “biosynthetic pathway enzyme” refer to a protein that catalyzes a chemical reaction. The recitation of any particular enzyme, either independently or as part of a biosynthetic pathway is understood to include the co-factors, co-enzymes, and metals necessary for the enzyme to properly function. A summary of the ammo acids and their three and one leter symbols as understood in the art is presented in Table 1. The amino acid name, three leter symbol, and one leter symbol are used interchangeably herein.

Table 1: Amino Acid three and one leter symbols

[0031] Variants or sequences having substantial identity or homology with the polypeptides described herein can be utilized in the practice of the disclosed pigments, compositions, and methods. Such sequences can be referred to as variants or modified sequences. That is, a polypeptide sequence can be modified yet still retain the ability to exhibit the desired activity. Generally, the variant or modified sequence may include or greater than about 45%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, or 95% sequence identity with the wild-type, naturally occurring polypeptide sequence, or with a variant polypeptide as described herein.

[0032] As used herein, the phrases “% sequence identity,” “% identity,” and “percent identity,” are used interchangeably and refer to the percentage of residue matches betw een at least two amino acid sequences or at least two nucleic acid sequences aligned using a standardized algorithm. Methods of amino acid and nucleic acid sequence alignment are well-known. Sequence alignment and generation of sequence identity include global alignments and local alignments which are carried out using computational approaches. An alignment can be performed using BLAST (National Center for Biological Information (NCBI) Basic Local Alignment Search Tool) version 2.2.31 software with default parameters. Amino acid % sequence identity between amino acid sequences can be determined using standard protein BLAST with the following default parameters: Max target sequences: 100; Short queries: Automatically adjust parameters for short input sequences; Expect threshold: 10; Word size: 6; Max matches in a query range: 0; Matrix: BLOSUM62; Gap Costs: (Existence: 11, Extension: 1); Compositional adjustments: Conditional compositional score matrix adjustment; Filter: none selected; Mask: none selected. Nucleic acid % sequence identity between nucleic acid sequences can be determined using standard nucleotide BLAST with the following default parameters: Max target sequences: 100; Short queries: Automatically adjust parameters for short input sequences; Expect threshold: 10; Word size: 28; Max matches in a query range: 0; Match/Mismatch Scores: 1, -2; Gap costs: Linear; Filter: Low complexity regions; Mask: Mask for lookup table only. A sequence having an identity score of XX% (for example, 80%) with regard to a reference sequence using the NCBI BLAST version 2.2.31 algorithm with default parameters is considered to be at least XX% identical or, equivalently, have XX% sequence identity to the reference sequence.

[0033] Polypeptide or polynucleotide sequence identity may be measured over the length of an entire defined polypeptide sequence, for example, as defined by a particular SEQ ID number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined polypeptide sequence, for instance, a fragment of at least 15, at least 20, at least 30, at least 40, at least 50, at least 70 or at least 150 contiguous residues. Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in the tables, figures or Sequence Listing, may be used to describe a length over which percentage identity may be measured.

[0034] The polypeptides disclosed herein may include “variant” polypeptides, “mutants,” and “derivatives thereof. ” As used herein the term “wild-type” is a term of the art understood by skilled persons and means the typical form of a polypeptide as it occurs in nature as distinguished from variant or mutant forms. As used herein, a “variant,” “mutant,” or “derivative” refers to a polypeptide molecule having an amino acid sequence that differs from a reference protein or polypeptide molecule. A variant or mutant may have one or more insertions, deletions, or substitutions of an amino acid residue relative to a reference molecule.

[0035] The amino acid sequences of the polypeptide variants, mutants, derivatives, or fragments as contemplated herein may include conservative amino acid substitutions relative to a reference amino acid sequence. For example, a variant, mutant, derivative, or fragment polypeptide may include conservative amino acid substitutions relative to a reference molecule. “Conservative amino acid substitutions” are those substitutions that are a substitution of an amino acid for a different amino acid where the substitution is predicted to interfere least with the properties of the reference polypeptide. In other words, conservative amino acid substitutions substantially conserve the structure and the function of the reference polypeptide. Conservative ammo acid substitutions generally maintain (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a beta sheet or alpha helical conformation, (b) the charge and/or hydrophobicity of the molecule at the site of the substitution, and/or (c) the bulk of the side chain.

[0036] As used herein, terms “polynucleotide,” “polynucleotide sequence,” and “nucleic acid sequence,” and “nucleic acid,” are used interchangeably and refer to a sequence of nucleotides or any fragment thereof. These phrases also refer to DNA or RNA of natural or synthetic origin, which may be single-stranded or double-stranded and may represent the sense or the antisense strand. The DNA polynucleotides may be a cDNA or a genomic DNA sequence.

[0037] A polynucleotide is said to encode a polypeptide if, in its native state or when manipulated by methods know n to those skilled in the art, it can be transcribed and/or translated to produce the polypeptide or a fragment thereof. The anti-sense strand of such a polynucleotide is also said to encode the sequence.

[0038] Those of skill in the art understand the degeneracy of the genetic code and that a variety of polynucleotides can encode the same polypeptide. In some aspects, the polynucleotides (i.e., polynucleotides encoding a non-heme iron-binding protein polypeptide) may be codon-optimized for expression in a particular cell including, without limitation, a plant cell, bacterial cell, fungal cell, or animal cell. While polypeptides encoded by polynucleotide sequences found in coral are disclosed herein any polynucleotide sequences may be used which encodes a desired form of the polypeptides described herein. Thus, non-naturally occurring sequences may be used. These may be desirable, for example, to enhance expression in heterologous expression systems of polypeptides or proteins. Computer programs for generating degenerate coding sequences are available and can be used for this purpose. Pencil, paper, the genetic code, and a human hand can also be used to generate degenerate coding sequences.

[0039] The recombinant cells described herein may include deletions or disruptions in one or more native genes. The phase “deletion or disruption” refers to the status of a native gene in the recombinant cell that has either a completely eliminated coding region (deletion) or a modification of the gene, its promoter, or its terminator (such as be a deletion, insertion, or mutation) so that the gene no longer produces an active expression product, produces severely reduced quantities of the expression product (e.g., at least a 75% reduction or at least a 90% reduction) or produces an expression product with severely reduced activity (e.g., at least 75% reduced or at least 90% reduced). The deletion or disruption can be achieved by genetic engineering methods, forced evolution, mutagenesis, and/or selection and screening. The native gene to be deleted or disrupted may be replaced with an exogenous nucleic acid of interest for the expression of an exogenous gene product (e.g., polypeptide, enzyme, and the like).

[0040] The recombinant cell described herein may have a deletion or disruption of one or more native genes encoding an enzy me involved in ethanol fermentation or consumption. Deletion or disruption of one or more of these ethanol biosynthetic pathway enzymes decreases the ability of the cell to product ethanol, thereby increasing fermentation production of lactate.

[0041] The recombinant cells described herein include a deletion or disruption of a native pyruvate decarboxylase (PDC) gene. The native PDC gene encodes an enzyme that catalyzes the conversation of pyruvate to acetaldehyde and carbon dioxide. When the host cell contains multiple PDC genes, it is preferred to delete or disrupt at least one of them and more preferred to disrupt all of them to more completely eliminate the host cell’s ability to produce ethanol. When the recombinant cell is an/, orientalis cell, the recombinant cell may comprise a deletion or disruption of a PDC gene encoding an amino acid sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to SEQ ID NO:32. Methods for the deletion or disruption of the PDC genes of I. orientalis are known and described in the art. See, for example, W02007032792A2 and W02017091610A1, which are incorporated herein by reference.

[0042] The recombinant cells described herein may include a deletion or disruption of a native glycerol-3-phosphate dehydrogenase (GPD) gene. Deletion or disruption of a native GPD gene improves acetate consumption by providing the cell with a greater pool of reducing equivalents to assist in the oxido-reduction of acetate to ethanol. When the ethanol biosynthetic pathway is disrupted, this increased pool of reducing equivalents can improve production of a fermentation product, e.g., lactate. When the host cell contains multiple GPD genes, it is preferred to delete or disrupt at least one of them and more preferred to disrupt all of them.

[00431 The recombinant cells described herein may include a deletion or disruption of a native L-lactate: cytochrome c oxidoreductase gene (CYB2). When the host cell contains multiple CYB2 genes, it is preferred to delete or disrupt at least one of them and more preferred to disrupt all of them. For example, I. orientalis includes two alleles of the CYB2 gene (CYB2a and CYB2b) and both may be deleted or disrupted when I. orientalis is used as the host cell.

[0044] The recombinant cells described herein may include one or more genetic modifications in which an exogenous nucleic acid is integrated into the genome of the host cell. One of skill in the art know how to select suitable loci in a yest genome for integration of the exogenous nucleic acid. For example, in an/, orientalis host cells, suitable integraction loci may include, but are not limited to, the CYB2B loci (defined as the loci flanked by SEQ ID NO:38 and SEQ ID NO:39), the ato2 loci (defined as the loci flanked by SEQ ID NO:40 and SEQ ID NO:41), the adh9091 loci (defined as the loci flanked by SEQ ID NO:42 and SEQ ID NO:43), the pdc loci (defined as the loci flanked by SEQ ID NO:30 and SEQ ID NO:31), the gpd loci (defined as the loci flanked by SEQ ID NO:23 and SEQ ID NO: 128), the Ymr226c loci (defined as the loci flanked by SEQ ID NO: 129 and SEQ ID NO: 130), and the mdhb loci (defined as the loci flanked by SEQ ID NO: 131 and SEQ ID NO: 132). Other suitable integration loci may be determined one of skill in the art. Furthermore, one of skill in the art would recognize how to use sequences to design primers to verify correct gene integration at the chosen locus.

[0045J The recombinant cells described herein are capable of producing 3-HP and include an active 3-HP fermentation pathway. As used herein, “active 3-HP fermentation pathway ” refers to expression of one or more active enzymes which, together, convert PEP or pyruvate into 3-HP. For example, an active 3-HP fermentation pathway may proceed through PEP, pyruvate, oxaloacetate (OAA), aspartate, P-alanine, and malonate semialdehyde intermediates. The recombinant cells may include a set of 3-HP fermentation pathway s genes comprising one or more of pyruvate carboxylase (PYC), PEP carboxylase (PPC), aspartate aminotransferase (AAT), aspartate 1 -decarboxylase (ADC), P-alanine aminotransferase (BAAT), aminobutyrate aminotransferase (gabT), 3-HP dehydrogenase (3-HPDH), 3-hydroxyisobutyrate dehydrogenase (HIBADH), and 4-hydroxybutyrate dehydrogenase genes. The 3-HP fermentation pathway genes may also include a PEP carboxykinase (PCK) gene that has been modified to produce a polypeptide that preferably catalyzes the conversion of PEP to OAA (native PCK genes generally produce a polypeptide that preferably catalyzes the reverse reaction of OAA to PEP). Suitable active 3-HP fermentation pathways are known and described in the art, for example, in US 11,118,187 and US 9,845,484, each of which is incorporated herein by reference in its entirety.

[00461 A "pyruvate carboxylase gene" or "PYC gene" as used herein refers to any gene that encodes a polypeptide with pyruvate carboxylase activity. As used herein, “pyruvate carboxylase activity” refers to the ability to catalyze the conversion of pyruvate, CO2, and ATP to OAA, ADP, and phosphate. The PYC gene may be derived from a yeast source. For example, the PYC gene may be derived from an I. orientalis PY C gene encoding the amino acid sequence set forth in SEQ ID NO:45. The PYC gene may encode an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the amino acid sequence of SEQ ID NO:45. An I. orientalis -derived PYC gene may comprise the nucleotide sequence set forth in SEQ ID NO:44 or a nucleotide sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the nucleotide sequence set forth in SEQ ID NO:44. The PYC gene may be derived from a bacterial source. For example, the PYC gene may be derived from one of the few bacterial species that use only PY C and not PPC (see below) for anaplerosis, such as R. sphaer aides, or from a bacterial species that possesses both PYC and PPC, such as A. etli. The amino acid sequences encoded by the PYC genes of R. sphaer aides and A. etli are set forth in SEQ ID NOs:46 and 47, respectively. A PYC gene may be derived from a gene encoding the amino acid sequence of SEQ ID NOs:46 and 47, or from a gene encoding an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the ammo acid sequence of SEQ ID NOs:46 and 47.

[0047] Alternatively, the PY C gene may be derived from a PY C gene encoding an enzyme that does not have a dependence on acetyl-CoA for activation, such as a P. fluor escens PYC gene encoding the amino acid sequence set forth in SEQ ID NO:48 (carboxytransferase subunit) or SEQ ID NO:49 (biotin carboxylase subunit), a C. glutamicum PYC gene of encoding the amino acid sequence set forth in SEQ ID NO:50, or a gene encoding an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the amino acid sequence of SEQ ID NOs:48, 49, or 50. A PYC gene may also be derived from a PYC gene that encodes an enzyme that is not inhibited by aspartate, such as an S. meliloti PYC gene encoding the amino acid sequence set forth in SEQ ID N0:51 (Sauer FEMS Microbiol Rev 29:765 (2005)), or from a gene encoding an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the amino acid sequence of SEQ ID NO:51.

[0048] A "PEP carboxylase gene" or "PPC gene" as used herein refers to any gene that encodes a polypeptide with PEP carboxylase activity. As used herein, “PEP carboxylase activity,” refers to the ability to catalyze the conversion of PEP and CO2 to OAA and phosphate. A PPC gene may be derived from a bacterial PPC gene. For example, the PPC gene may be derived from an E. coli PPC gene encoding the amino acid sequence set forth in SEQ ID NO: 53 or an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the amino acid sequence of SEQ ID NO:53. In certain embodiments, an E. coli-derived PPC gene may comprise the nucleotide sequence set forth in SEQ ID NO:52 or a nucleotide sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the nucleotide sequence set forth in SEQ ID NO:52. A PPC gene may be derived from an “A” type PPC, found in many archea and a limited number of bacteria, that is not activated by acetyl CoA and is less inhibited by aspartate. For example, a PPC gene may be derived from an M. thermoautotrophicum PPC A gene encoding the amino acid sequence set forth in SEQ ID NO:54, a C. perfringens PPC A gene encoding the amino acid sequence set forth in SEQ ID NO:55, or a gene encoding an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the amino acid sequence of SEQ ID NOs:54 or 55. A PPC gene suitable for use in the engineered cells and methods described herein may have undergone one or more mutations versus the native gene in order to generate an enzyme with improved characteristics. For example, the gene may have been mutated to encode a PPC polypeptide with increased resistance to aspartate feedback versus the native polypeptide. The PPC gene may also be derived from a plant source.

[0049] An "aspartate aminotransferase gene" or "AAT gene" as used herein refers to any gene that encodes a polypeptide with aspartate aminotransferase activity. As used herein, “aspartate aminotransferase activity,” refers to the ability to catalyze the conversion of OAA to aspartate. Enzymes having aspartate aminotransferase activity are classified as EC 2.6.1.1. An AAT gene may be derived from a yeast source such as I. orientalis or S. cerevisiae. For example, the AAT gene may be derived from an I. orientalis AAT gene encoding the amino acid sequence set forth in SEQ ID NO: 57 or an S. cerevisiae AAT2 gene encoding the amino acid sequence set forth in SEQ ID NO:58. The ATT gene may encode an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the amino acid sequence of SEQ ID NOs:57 or 58. An I. orientalis- derived AAT gene may comprise the nucleotide sequence set forth in SEQ ID NO:56 or a nucleotide sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the nucleotide sequence set forth in SEQ ID NO: 56. The AAT gene may be derived from a bacterial source. For example, the AAT gene may be derived from an E. coli aspC gene encoding a polypeptide comprising the amino acid sequence set forth in SEQ ID NO:59. In other embodiments, the gene may encode an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the amino acid sequence of SEQ ID NO:59.

[0050] A "P-alanine aminotransferase gene" or "BAAT gene" as used herein refers to any gene that encodes a polypeptide with P-alanine aminotransferase activity, meaning the ability to catalyze the conversion of P-alanine to malonate semialdehyde. Enzymes having P-alanine aminotransferase activity are classified as EC 2.6.1.19. In certain embodiments, a BAAT gene may be derived from a yeast source. For example, a BAAT gene may be derived from the I. orientcdis homolog to the pyd4 gene encoding the amino acid sequence set forth in SEQ ID NO:60. In some embodiments, the BAAT gene may encode an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the amino acid sequence of SEQ ID NO:60. In certain embodiments, an/. orzewto/A-derived BAAT gene may comprise the nucleotide sequence set forth in SEQ ID NO: 61 or a nucleotide sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the nucleotide sequence set forth in SEQ ID NO:61. In other embodiments, the BAAT gene may be derived from the S. kluyveri pyd4 gene encoding the amino acid sequence set forth in SEQ ID NO:62. In some embodiments, the BAAT gene may encode an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the amino acid sequence of SEQ ID NO: 62. In certain embodiments, a S. kluyveri-demed BAAT gene may comprise the nucleotide sequence set forth in SEQ ID NO:63 or a nucleotide sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the nucleotide sequence set forth in SEQ ID NO:63. In other embodiments, the BAAT gene may be derived from a bacterial source. For example, a BAAT gene may be derived from an S. avermitilis BAAT gene encoding the amino acid sequence set forth in SEQ ID NO:64. In some embodiments, the BAAT gene may encode an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the amino acid sequence of SEQ ID NO:64. In certain embodiments, a S. avermitilis-derived BAAT gene may comprise the nucleotide sequence set forth in SEQ ID NO:65 or a nucleotide sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the nucleotide sequence set forth in SEQ ID NO:65.

[0051] A BAAT gene may also be a "4-aminobutyrate aminotransferase" or "gabT gene" meaning that it has native activity on 4-aminobutyrate as well as P-alanine. Alternatively, a BAAT gene may be derived by random or directed engineering of a native gabT gene from a bacterial or yeast source to encode a polypeptide with BAAT activity. For example, a BAAT gene may be derived from the S', avermi Ulis gabT encoding the amino acid sequence set forth in SEQ ID N 0 : 66. In some embodiments, the S. avermitilis-derived BAAT gene may encode an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the amino acid sequence of SEQ ID NO:66. In other embodiments, a BAAT gene may be derived from the 5. cerevisiae gabT gene UGA1 encoding the amino acid sequence set forth in SEQ ID NO:67. In some embodiments, the S. cerevisiae-derived BAAT gene may encode an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the amino acid sequence of SEQ ID NO: 67. In certain embodiments, an S. cerevisiae-derived BAAT gene may comprise the nucleotide sequence set forth in SEQ ID NO:68 or a nucleotide sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the nucleotide sequence set forth in SEQ ID NO:68.

[0052] A "3-HP dehydrogenase gene" or "3-HPDH gene" as used herein refers to any gene that encodes a polypeptide with 3-HP dehydrogenase activity, meaning the ability to catalyze the conversion of malonate semialdehyde to 3-HP. Enzymes having 3-HP dehydrogenase activity are classified as EC 1.1.1.59 if they utilize an NAD(H) cofactor, and as EC 1.1.1.298 if they utilize an NADP(H) cofactor. Enzymes classified as EC 1.1.1.298 are alternatively referred to as malonate semialdehyde reductases. |0053J The 3-HPDH gene may be derived from a yeast source. For example, a 3-HPDH gene may be derived from the I. orientalis homolog to the YMR226C gene encoding the amino acid sequence set forth in SEQ ID NO:70. The 3-HPDH gene may encode an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the amino acid sequence of SEQ ID NO:70. In certain embodiments, an I. orientalis-dervved 3-HPDH gene may comprise the nucleotide sequence set forth in SEQ ID NO:69 or a nucleotide sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the nucleotide sequence set forth in SEQ ID NO:69. The 3-HPDH gene may be derived from the S. cerevisiae YMR226C gene encoding the amino acid sequence set forth in SEQ ID NO:71. The 3-HPDH gene may encode an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the amino acid sequence of SEQ ID NO:71. An 5. cerevisiae-derived 3- HPDH gene may comprise the nucleotide sequence set forth in SEQ ID NO: 72 or a nucleotide sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the nucleotide sequence set forth in SEQ ID NO:72.

[0054] The 3-HPDH gene may be derived from a bacterial source. For example, a 3-HPDH gene may be derived from an E. coli ydfG gene encoding the ammo acid sequence in SEQ ID NO:73. The gene may encode an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the amino acid sequence of SEQ ID NO:73. An E. co/z-derived 3-HPDH gene may comprise the nucleotide sequence set forth in SEQ ID NO:74 or a nucleotide sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the nucleotide sequence set forth in SEQ ID NO:74. The 3-HPDH gene may be derived from an M. sedula malonate semialdehyde reductase gene encoding the amino acid sequence set forth in SEQ ID NO:75. The 3-HPDH gene may encode an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the amino acid sequence set forth in SEQ ID NO:75. The M. seclula-dQvwQd 3-HPDH gene may comprise the nucleotide sequence set forth in SEQ ID NO:76 or a nucleotide sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity' to the nucleotide sequence set forth in SEQ ID NO:76. L0055J A "3-hydroxyisobutyrate dehydrogenase gene" or "HIBADH gene" as used herein refers to any gene that encodes a polypeptide with 3-hydroxyisobutyrate dehydrogenase activity, meaning the ability to catalyze the conversion of 3-hydroxyisobutyrate to methylmalonate semialdehyde. Enzymes having 3-hydroxyisobutyrate dehydrogenase activity are classified as EC 1.1.1.31. Some 3-hydroxyisobutyrate dehydrogenases also have 3-HPDH activity. The HIBADH gene may be derived from a bacterial source. For example, an HIBADH gene may be derived from an A. faecalis M3A gene encoding the amino acid sequence set forth in SEQ ID NO: 77, af. putida KT2440 or E23440 mmsB gene encoding the amino acid sequence set forth in SEQ ID NO:78 or SEQ ID NO:79, respectively, or aP. aeruginosa PAO1 mmsB gene encoding the amino acid sequence set forth in SEQ ID NO: 80. The HIBADH gene may encode an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the amino acid sequence set forth in SEQ ID NOs:77, 78, 79, or 80.

[0056] A "4-hydroxybutyrate dehydrogenase gene" as used herein refers to any gene that encodes a polypeptide with 4-hydroxybutyrate dehydrogenase activity, meaning the ability to catalyze the conversion of 4-hydroxybutanoate to succinate semialdehyde. Enzymes having 4- hydroxy butyrate dehydrogenase activity are classified as EC 1.1.1.61. Some 4-hydroxybutyrate dehydrogenases also have 3-HPDH activity. The 4-hydroxybutyrate dehydrogenase gene may be derived from a bacterial source. For example, a 4-hydroxybutyrate dehydrogenase gene may be derived from a R. eutropha Hl 6 4hbd gene encoding the amino acid sequence set forth in SEQ ID NO: 81 or a C. kluyveri DSM 555 hbd gene encoding the amino acid sequence set forth in SEQ ID NO: 82. In other embodiments, the gene may encode an amino acid sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the amino acid sequence set forth in SEQ ID NOs:81 or 82.

[0057] A "PEP carboxykinase gene" or "PCK gene" as used herein refers to any gene that encodes a polypeptide with PEP carboxykinase activity, meaning the ability to catalyze the conversion of PEP, CO2, and ADP or GDP to OAA and ATP or GTP, or vice versa. Enzy mes having PEP carboxykinase activity are classified as EC 4.1.1.32 (GTP/GDP utilizing) and EC 4.1. 1.49 (ATP/ ADP utilizing). The PCK gene may be derived from a yeast source. The PCK gene may be derived from a bacterial source, for example, the gene may be derived from a bacterium in which the PCK reaction favors the production of OAA rather than the more common form of the reaction where decarboxylation is dominant. For example, a PCK gene may be derived from an M. succiniciproducens PCK gene encoding the amino acid sequence set forth in SEQ ID NO: 83, an A. succiniciproducens PCK gene encoding the amino acid sequence set forth in SEQ ID NO:84, an A. succinogenes PCK gene encoding the amino acid sequence set forth in SEQ ID NO: 85, or an R. eutropha PCK gene encoding the amino acid sequence set forth in SEQ ID NO: 86. The PCK gene may have one or more mutations versus the native gene from which it was derived, such that the resultant gene encodes a polypeptide that preferably catalyzes the conversion of PEP to OAA. For example, a PCK gene may be derived from an E. coli KI 2 strain PCK gene encoding the amino acid sequence set forth in SEQ ID NO:87, where the gene has been mutated to preferably catalyze the conversion of PEP to OAA. Alternatively, the conversion of PEP to OAA may be catalyzed by a PEP carboxytransphosphorylase such as is found in propionic acid bacteria (e.g., P. shermanii, A. woodii) which use inorganic phosphate and diphosphate rather than ATP/ADP or GTP/GDP.

[0058] An "aspartate decarboxylase gene" or "ADC gene" as used herein refers to any gene that encodes a polypeptide with aspartate decarboxylase activity. As used herein, “aspartate decarboxylase activity” refers to the ability to catalyze the conversion of aspartate to P-alanme. Enzymes having aspartate decarboxylase activity are classified as EC 4.1. 1. 11. An ADC gene may be derived from a bacterial source. For example, the ADC gene may be derived from an S. avermitilis panD gene encoding the amino acid sequence set forth in SEQ ID NO: 88, a C. acetobutylicum panD gene encoding the amino acid sequence set forth in SEQ ID NO: 89, an H. pylori ADC gene encoding the amino acid sequence set forth in SEQ ID NO:90, a Bacillus sp. TS25 ADC gene encoding the amino acid sequence set forth in SEQ ID NO:91, a C. glutamicum ADC gene encoding the amino acid sequence set forth in SEQ ID NO: 92, a B. licheniformis ADC gene encoding the amino acid sequence set forth in SEQ ID NO:93. The ADC gene may encode an ammo acid sequence with at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% sequence identity to the amino acid sequence of at least one of SEQ ID NOs:88-93. Because an active aspartate decarboxylase may require proteolytic processing of an inactive proenzyme, in these embodiments the yeast host cell should be selected to support formation of an active enzyme coded by a bacterial ADC gene.

[0059] Alternatively, the ADC can be an insect ADC (e g., of the Class Insecta). Unlike bacterial ADCs that self-cleave to generate a pyruvoyl moiety for catalysis, insect ADCs use pyridoxal- 5'-phosphate (PLP) as a cofactor and share considerably higher sequence identity to glutamate decarboxylases (GDCs) compared to bacterial ADCs (see Liu et al., 2012, Insect Biochem. Mai. Bio. 42: 396-403). As demonstrated in US Patent 9,845,484, which is incorporated herein by reference in its entirety, expression of an insect aspartate 1- decarboxylase (ADC), such as the Aedes aegypti ADC of SEQ ID NO: 94, the Drosophila melanogaster ADC of SEQ ID NO: 101, the Danaus plexippus ADC of SEQ ID NO: 102, or the Apis mellifera ADC of SEQ ID NO: 113, in a recombinant yeast host cell significantly enhances the production of metabolic 3-HP compared to other heterologous ADC enzymes. [0060] Accordingly, recombinant cell described herein may comprise a heterologous polynucleotide encoding an aspartate 1 -decarboxyl se (ADC) of the Class Insecta and is capable of producing 3-HP. The recombinant cell may additionally or alternatively comprise a heterologous polynucleotide encoding an aspartate 1 -decarboxylase (ADC) of the Class Bivalvia, Branchiopoda, Gastropoda, or Leptocardii and is capable of producing 3-HP. The ADC may be pyridoxal-5 '-phosphate (PLP) dependent. The expressed ADC may be present in the cytosol of the host cells.

[0061] The recombinant cell described herein may comprise a heterologous polynucleotide encoding an ADC with a sequence at least at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% identical to any one of SEQ ID NOs:94-127. SEQ IDNOs:94-127 are described in detail in at least Tables 1 and 2 of US Patent No. 9,845,484, which is incorporated herein by reference in its entirety'. Preferably, the heterologous polynucleotide encodes an ADC with a sequence at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% identical to at least one of SEQ ID NOs:94, 101, 102, or 113. Most preferably, the the heterologous polynucleotide encodes an ADC with a sequence at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, or at least 99% identical to SEQ ID NO: 102.

[0062] The recombinant yeast cells described herein compnsing a heterologous polynucleotide encoding an ADC of the Class Insecta, Bivalvia, Branchiopoda, Gastropoda, or Leptocardii have an increased levels of ADC activity compared to the host cells without the heterologous polynucleotide encoding the ADC, when cultivated under the same conditions. For example, the recombinant yeast cells may have an increased level of ADC activity of at least 5%, e.g., at least 10%, at least 15%, at least 20%, at least 25%, at least 50%, at least 100%, at least 150%, at least 200%, at least 300%, or at 500% compared to the host cells without the heterologous polynucleotide encoding the ADC of the Class Insecta, Bivalvia, Branchiopoda, Gastropoda, or Leptocardii, when cultivated under the same conditions.

[0063] The recombinant cells described herein may include an exogenous nucleic acid encoding an invertase enzyme. The invertase enzyme may be expressed from an exogenous nucleic acid on a plasmid or an exogenous nucleic acid integrated into the genome of the recombinant host cell. The invertase enzyme may be any suitable enzyme with invertase activity. As used herein, “invertase activity” refers to the ability to catalyze the hydrolysis of sucrose to fructose and glucose. Suitable invertase enzymes may include, but are not limited to, enzymes categorized under EC number 3.2. 1.26. The invertase may be from any suitable organism or may be synthetic. Suitable invertase enzymes may be invertase enzymes from Kluyveromyces lactis (SEQ ID NO: 12), Saccharomyces cerevisiae (SEQ ID NO:33), Schizosaccharomyces pombe (SEQ ID NO:34), Aspergillus niger (SEQ ID NO:35), and the like. The recombinant cell may include an invertase enzyme with a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs:12, 33, 34, and 35. The recombinant cell capable of producing lactate may include an exogenous nucleic acid encoding an invertase enzyme with a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs:12, 33, 34, and 35.

[0064] The recombinant cells described herein may include an exogenous nucleic acid encoding a fructokinase. The fructokinase enzyme may be expressed from an exogenous nucleic acid on a plasmid or an exogenous nucleic acid integrated into the genome of the recombinant host cell. The fructokinase enzyme may be any suitable enzyme with fructokinase activity. As used herein, “fructokinase activity” refers to the ability to catalyze the transfer of a phosphate group from adenosine triphosphate (ATP) to fructose. Suitable fructokinase enzymes may include, but are not limited to, enzymes categorized under EC number 2.7.1.4. The fructokinase may be from any suitable organisms or may be synthetic. For example, the fructokmase enzyme may the fructokinase enzyme from Clostridium acetobutylicum (UniProt Ref. Q9L8G5; SEQ ID NO:26). The recombinant cell may include a fructokinase enzyme with a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to SEQ ID NO:26. The recombinant cell may include an exogenous nucleic acid encoding a fructokinase enzyme with a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to SEQ ID NO:26.

[0065] The recombinant cells described herein may include an exogenous nucleic acid encoding a native or exogenous hexokinase or may have a genetic modification resulting in overexpression of a native hexokinase. The hexokinase may be any suitable enzyme with hexokinase activity. As used herein, “hexokinase activity” refers to the ability to catalyze the phosphorylation of a hexose by ATP to a hexose phosphate. For example, the hexokinase enzyme may catalyze the addition of a phosphate from ATP to glucose to form glucose-6-phosphate. Suitable hexokinase enzymes may include, but are not limited to, enzymes categorized under EC number 2.7. 1. 1. The hexokinase may be a hexokinase I, hexokinase II, or hexokinase III isozyme. The hexokinase may a hexokinase native to host cell or the hexokinase may be an exogenous hexokinase. For example, when the host organism is I. orientalis, the hexokinase may be an enzyme with a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs:24 and 25. The recombinant cell may comprise an exogenous nucleic acid encoding a hexokinase at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs:24 and 25. The recombinant cell may include a genetic modification that increases expression of a hexokinase at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs:24 and 25. The genetic modification may include, but is not limited to, insertion of additional copies of a nucleic acid encoding the native hexokinase into the cell, insertion of a constitutive promoter upstream of the coding region of the native hexokinase gene in the genome of the host cell, and/or modification of the existing promoter upstream of the coding region of the native hexokinase gene in the genome of the host cell. One of skill in the art will recognize that expression of a native hexokinase gene may be increased by a number of methods known in the art and will be able to select and apply such methods as appropriate.

L0066J The recombinant cells described herein may include an exogenous nucleic acid encoding a fructose transporter. The fructose transporter may be expressed from an exogenous nucleic acid on a plasmid or an exogenous nucleic acid integrated into the genome of the recombinant host cell. The fructose transporter may be any suitable enzyme with fructose transporter activity. As used herein, "fructose transporter activity” refers to the ability to catalyze the transfer of fructose through a plasmid membrane. Enzymes with fructose transporter activity may also be referred to in the art as transferase, symporters, facilitators, and the like. The fructose transporter may be from any suitable organism or may be synthetic. For example, the fructose transporter may be a fructose transporter from K. lactis (UniProt Ref. F2Z6G6, SEQ ID NO: 27), Zygosaccharomyces bailii (UniProt Ref. Q70WR7, SEQ ID NO:28), Saccharomyces carlsbergensis (GenBank Ref. EHN03988.1; SEQ ID NO:29), Botryotinia fuckeliana (UniProt Ref. Q5XTQ5; SEQ ID NO: 36), or Ganoderma boninense (GenBank Ref. VWO95402.1; SEQ ID NO:37). The recombinant cell may include a fructose transporter with a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to one of SEQ ID NOs:27, 28, 29, 36, and 37. The recombinant cell may include an exogenous polynucleotide encoding a fructose transporter with a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to ate least one of SEQ ID NOs:27, 28, 29, 36, and 37. A recombinant cell including a fructose transporter as described herein will have an increased rate of fructose consumption (e g., fructose uptake by the cell and/or fermentation of fructose to one or more end products) compared to an equivalent cell lacking said fructose transporter. Similarly, a recombinant cell including a fructose transporter as described herein will have a glucose consumption rate that is equivalent or greater than the glucose consumption rate in an equivalent cell lacking said fructose transporter. In other words, while the presence of the fructose transporter increases the rate of fructose consumption, it will not decrease the rate of glucose consumption.

[0067] The exogenous nucleic acids in the recombinant cells described herein may be under the control of a promoter. For example, the exogenous nucleic acid may be operably linked to a heterologous or artificial promoter. Suitable promoters are known and described in the art. Promoters may include, but are not limited to, RPL16B (SEQ ID NO: 14), pyruvate decarboxylase (PDC1; SEQ ID NO: 13), glyceraldehyde-3-phosphate dehydrogenase (TDH3; SEQ ID NO: 17), translational elongation factor (TEF; SEQ ID NO: 18), transaldolase (TAL; SEQ ID NO: 16), enolase (ENO1; SEQ ID N0: 19), 3-phosphoglycerate kinase (PGK1; SEQ ID NO:15).

[0068] The exogenous nucleic acids in the recombinant cells described herein may be under the control of a terminator. For example, the exogenous nucleic acid may be operably linked to a heterologous or artificial terminator. Suitable terminators are known and described in the art. Terminators may include, but are not limited to, PDC (SEQ ID NO:20), and ScGALlO (SEQ ID NO:21).

[0069] A promoter or terminator is “operably linked” to a given polynucleotide (e g., a gene) if its position in the genome or expression cassette relative to said polynucleotide is such that the promoter or terminator, as the case may be, perfomrs its transcriptional control function.

[0070] The polypeptides described herein may be provided as part of a construct. As used herein, the term “construct” refers to recombinant polynucleotides including, without limitation, DNA and RNA, which may be single-stranded or double-stranded and may represent the sense or the antisense strand. Recombinant polynucleotides are polynucleotides formed by laboratory methods that include polynucleotide sequences derived from at least two different natural sources or they may be synthetic. Constructs thus may include new modifications to endogenous genes introduced by, for example, genome editing technologies. Constructs may also include recombinant polynucleotides created using, for example, recombinant DNA methodologies. The construct may be a vector including a promoter operably linked to the polynucleotide encoding the thermolabile non-heme iron-binding polypeptide. As used herein, the term “vector” refers to a polynucleotide capable of transporting another polynucleotide to which it has been linked. The vector may be a plasmid, which refers to a circular double-stranded DNA loop into which additional DNA segments may be integrated.

[0071] The disclosure also provides fermentation methods for the production of lactate using the recombinant cells described herein. The fermentation methods include the step of fermenting a substrate using the genetically engineered yeasts described herein to product lactate. The fermentation method can include additional steps, as would be understood by a person skilled in the art. Non-limiting examples of additional process steps include maintaining the temperature of the fermentation broth within a predetermined range, adjusting the pH during fermentation, and isolating the lactate from the fermentation broth. The fermentation process may be a microaerobic process.

[0072] The fermentation method can be run using sucrose as a substrate, as a result of the genetic modifications to the recombinant cell described herein. The substrate of the fermentation method can also include other components in addition to sucrose. The fermentation substrate can also include glucose, xylose, fructose, hydrozylates of starch, lignocellulosic hydrozylates, or a combination thereof. As contemplated herein, the sucrose component of the substrate will be hydrolyzed into glucose and fructose via the activity' of an invertase and/or sucrase. Accordingly, the fermentation substrate may not contain any sucrose per se because all of the sucrose may be hydrolyzed at some point during the process.

[0073] The fermentation process can be run under various conditions. The fermentation temperature, i.e., the temperature of the fermentation broth during processing, may be ambient temperature. Alternatively, or additionally, the fermentation temperature may be maintained within a predetermined range. For example, the fermentation temperature can be maintained in the range of 25 °C to 45 °C, 20 °C to 40 °C, or 32 °C to 37 °C. However, a skilled artisan will recognize that the fermentation temperature is not limited to any specific range recited herein and may be modified as appropriate. 100741 The fermentation process can be run within certain oxygen uptake rate (OUR) ranges. The volumetric OUR of the fermentation process can be in the range of 0.5 to 40, 1 to 35, 3 to 30, 6 to 27, or 16-24 mmol O2/(L • h). In some embodiments, the specific OUR can be in the range of 0.2 to 13, 0.3 to 10, 1 to 7, or 2 to 6 mmol O2/(g cell dry weight • h). However, the volumetric or specific OURs of the fermentation process are not limited to any specific rates or ranges recited herein.

[0075] The fermentation process can be run at various cell concentrations. In some embodiments, the cell dry weight at the end of fermentation can be 1 to 20, 1 to 13, 2 to 10, or 3 to 8 g cell dry weight/L. Further, the pitch density or pitching rate of the fermentation process can vary. In some embodiments, the pitch density can be 0.05 to 5, 0.05 to 4, or 0.05 to 2 g cell dry weight/L.

[0076] The fermentation process can be associated with various characteristics, such as, but not limited to, fermentation production rate, pathway fermentation yield, final titer, and peak fermentation rate. These characteristics can be affected by the selection of the yeast and/or genetic modification of the yeast used in the fermentation process. These characteristics can be affected by adjusting the fermentation process conditions. These characteristics can be adjusted via a combination of yeast selection or modification and the selection of fermentation process conditions.

[0077] The 3-HP production rate of the process may be at least 1.0, at least 1.5, or at least 2.0, at least 2.5, at least 3.0, or at least 3.5 g L^_1h⁴. The 3-HP mass yield of the process may be at least 55 percent, at least 65 percent, at least 70 percent, at least 75 percent, at least 80 percent, or at least 85 percent. The final 3-HP titer of the process may be at least 30, at least 80, at least 100, or at least 120 g/hter. The fermentation process may have a peak 3-HP production rate of at least 5, at least 6, at least 7, or at least 8 g L'¹ h’¹.

[0078] In some aspects, the fermentation process can include sucrose as a substrate for only a portion of the process. For example, the fermentation process can include the step of generating a yeast seed culture using sucrose as substrate, then running the full production batch with a hydrolysate, a hydrolysate supplemented with sucrose, or other substrate instead of sucrose. The fermentation process can be run as a sucrose-fed batch. Further, the fermentation process can be a batch process, continuous process, or semi-continuous process, as would be understood by a person skilled in the art. EXAMPLES

[0079] The invention is further described in detail by reference to the following experimental examples. These examples are provided for purposes of illustration only and are not intended to be limiting unless otherwise specified. Thus, the invention should in no way be construed as being limited to the following examples, but rather should be construed to encompass any and all variations which become evident as a result of the teaching provided herein.

Example 1 : Genetically Modified Y east Strains

Strain 1-1

[0080] Strain 1-1 is an Issatchenkia orientalis host strain in which

(i) both alleles of the pyruvate decarboxylase (PDC) gene are knocked out and replaced with the native pyruvate carboxylase (PY C) gene from Issatchenkia orientalis under the control of the PDC promoter and TAL terminator, the native aspartate amino transferase gene (AAT) from Issatchenkia orientalis under the control of the ENO1 promoter and RK1 terminator, a gene encoding the aspartate 1 -decarboxylase (ADC) from Danaus plexippus under the control of the PGK1 promoter and the TKL terminator, and the native [l-alanine aminotransferase (BAAT) gene pyd4 from Issatchenkia orientalis under the control of the TDH3 promoter and the PDC terminator;

(ii) both alleles of the glyceraldehyde-3-phosphate dehydrogenase gene (GPD) are knocked out and replaced with six copies of genes encoding the ADC from Danaus plexippus under the control of the TDH3 or PDC promoter and the TKL, TAL, or PDC terminator. The Hygromycin B antibiotic resistance marker (HPH) from E. coli is also integrated at one allele of the GPD locus under the control of the PGK1 promoter and the GAL10 terminator;

(iii) both alleles of the ymr226c gene are knocked out and replaced with four copies of genes encoding the native YMR226c 3-HP dehydrogenase (3-HPDH) from Issatchenkia orientalis under the control of the ENO1, PDC, TDH3, or TEF2 promoters, respectively, and the ENO1, PDC, TDH3, or TEF2 terminators, respectively; and

(iv) both alleles of the malate dehydrogenase B (mdhB) gene are knocked out and replaced with four copies of genes encoding the D. plexippus ADC under the control of the PDC promoter and TKL terminator.

[0081] Strain 1-1 therefore has a total of 22 copies of genes encoding the D. plexippus ADC, 8 copies of genes encoding the I. orientalis YMR226c 3-HPDH, 2 copies of the native PCY gene from I. orientalis, 2 copies of the AAT gene from I. orientalis, and 2 copies of the BAAT gene pyd4 from/. orientalis.

Strain 1-2

[0082] Strain 1-1 was transformed with SEQ ID NO:2. SEQ ID NO:2 is a segment of SEQ ID NO: 1 , a plasmid containing the invertase gene from K. lactis (KIINV', SEQ ID NO: 11 ) encoding the amino acid sequence of SEQ ID NO: 12. SEQ ID NO:2 contains i) an expression cassette for KIINV, encoding the amino acid sequence SEQ ID NO: 12, under the control of the RPL16b promoter SEQ ID NO: 14 and the PDC terminator SEQ ID NO:20; and ii) flanking DNA for targeted chromosomal integration into the CYB2B loci. Transformants are selected on YNB + Sucrose plates. Resulting transformants are streaked for single colony isolation on YNB + Sucrose plates. A single colony is selected. Correct integration of SEQ ID NO:2 into the selected colony is verified by PCR. A PCR verified isolate is designated Strain 1-2.

Strain 1-3

[0083] Strain 1-1 was transformed with SEQ ID NO:3. SEQ ID NO:3 contains i) an expression cassette for KIINV, encoding the amino acid sequence of SEQ ID NO: 12, under the control of the ENO1 promoter SEQ ID NO: 19 and the tScGALlO terminator SEQ ID NO:21; and (ii) flanking DNA for targeted chromosomal integration into the CYB2B loci. Transformants are selected on YNB + Sucrose plates. Resulting transformants are streaked for single colony isolation on YNB + Sucrose plates. A single colony is selected. Correct integration of SEQ ID NO:3 into the selected colony is verified by PCR. A PCR verified isolate is designated Strain 1-3.

Prophetic Strains 1 -4a and l-4b

[0084] Strain 1-2 or 1-3 can be transformed with SE ID NO: 4. SEQ ID NO:4 contains i) an expression cassette for the selectable marker gene melibiase from S. cerevisiae (ScMEL5) including the PGK promoter SEQ ID NO: 15 and the MEL5 terminator SEQ ID NO:22 and flanked by LoxP sites; ii) an expression cassette for the hexokinase gene from I. orientalis, encoding the amino acid sequence SEQ ID NO:25, under the control of the PDC promoter SEQ ID NO: 13 and the S. cerevisiae GAL10 terminator SEQ ID NO:21; and iii) flanking DNA for targeted chromosomal integration into the ato2 loci. Transformants can be selected on YNB plates containing 2% melibiose as sole carbon source and 32ug/mL x-alpha-gal (5-bromo-4-chloro-3- indoxyl-a-D-galactopyranoside) which provides colorimetric indication of the presence of the ScMEL5 marker gene. Resulting transformants can be streaked for single colony isolation on YPD containing 32pg/mL x-alpha-gal. Single blue colonies may be selected. Correct integration of SEQ ID NO:4 into the selected blue colonies was verified by PCR. PCR verified isolates are designated Strains l-4a (transformation of strain 1-2) and l-4b (transformation of strain 1-3).

Prophetic Strains 1 -5a and 1 -5b

[0085] Strain 1-2 or 1-3 can be transformed with SEQ ID NO:5. SEQ ID NO:5 contains i) an expression cassette for the selectable marker gene melibiase from S. cerevisiae (ScMEL5) including the PGK promoter SEQ ID NO: 15 and the MEL5 terminator SEQ ID NO:22 and flanked by LoxP sites; ii) an expression cassette for the fructokinase gene from Clostridium acetobutylicum (CaScrK), encoding the amino acid sequence SEQ ID NO:26, under the control of the PDC promoter SEQ ID NO: 13 and the S. cerevisiae GAL 10 terminator SEQ ID NO:21; and iii) flanking DNA for targeted chromosomal integration into the ato2 loci. Transformants can be selected on YNB plates containing 2% melibiose as sole carbon source and 32pg/mL x-alpha-gal which provides colorimetric indication of the presence of the ScMEL5 marker gene. Resulting transformants can be streaked for single colony isolation on YPD containing 32pg/mL x-alpha- gal. A single blue colony may be selected. Correct integration of SEQ ID NO:5 into the selected blue colony can be verified by PCR. PCR verified isolates are designated strains 1-5 a (transformation of strain 1-2) and 1 -5b (transformation of strain 1-3).

Prophetic Strains l-6a and l-6b

[0086] Strain 1-2 or 1-3 can be transformed with SEQ ID NO: 6. SEQ ID NO: 6 contains i) an expression cassette for the selectable marker gene melibiase from S. cerevisiae (ScMEL5) including the PGK promoter SEQ ID NO: 15 and the MEL5 terminator SEQ ID NO:22 and flanked by LoxP sites; ii) an expression cassette for the fructose transporter gene from Kluyveromyces lactis (KlFrtl), encoding the amino acid sequence SEQ ID NO:27, under the control of the PDC promoter SEQ ID NO: 13 and the S. cerevisiae GAL 10 terminator SEQ ID NO:21; and iii) flanking DNA for targeted chromosomal integration into the ato2 loci. Transformants can be selected on YNB plates containing 2% melibiose as sole carbon source and 32pg/mL x-alpha-gal which provides colorimetric indication of the presence of the ScMEL5 marker gene. Resulting transformants can be streaked for single colony isolation on YPD containing 32pg/mL x-alpha- gal. A single blue colony can be selected. Correct integration of SEQ ID NO:6 into the selected blue colony can be verified by PCR. PCR verified isolates are designated strains l-6a (transformation of strain 1-2) and l-6b (transformation of strain 1-3).

Prophetic Strains l-7a and l-7b

[0087] Strain 1-2 or 1-3 can be transformed with SEQ ID NO: 7. SEQ ID NO: 7 contains i) an expression cassette for the selectable marker gene melibiase from S. cerevisiae (ScMEL5) including the PGK promoter SEQ ID NO: 15 and the MEL5 terminator SEQ ID NO:22 and flanked by LoxP sites; ii) an expression cassette for the fructokinase gene from Clostridium acetobutylicum (CaScrK), encoding the amino acid sequence SEQ ID NO:26, under the control of the PDC promoter SEQ ID NO: 13 and the S. cerevisiae GAL 10 terminator SEQ ID NO:21; and iii) flanking DNA for targeted chromosomal integration into the adh9091 loci. Transformants can be selected on YNB plates containing 2% melibiose as sole carbon source and 32pg/mL x-alpha- gal which provides colorimetric indication of the presence of the ScMEL5 marker gene. Resulting transformants can be streaked for single colony isolation on YPD containing 32pg/mL x-alpha- gal. A single blue colony can be selected. Correct integration of SEQ ID NO:7 into the selected blue colony can be verified by PCR. PCR verified isolates are designated strains l-7a (transformation of strain 1-2) and 1 -7b (transformation of strain 1-3).

Prophetic Strains l-8a and l-8b

[0088] Strain 1-2 or 1-3 can be transformed with SEQ ID NO: 8. SEQ ID NO: 8 contains i) an expression cassette for the selectable marker gene melibiase from S. cerevisiae (ScMEL5) including the PGK promoter SEQ ID NO: 15 and the MEL5 terminator SEQ ID NO:22 and flanked by LoxP sites; n) an expression cassette for the fructose transporter gene from Kluyveromyces lactis (KlFrtl), encoding the amino acid sequence SEQ ID NO:27, under the control of the PDC promoter SEQ ID NO: 13 and the S. cerevisiae GAL 10 terminator SEQ ID NO:21; and iii) flanking DNA for targeted chromosomal integration into the adh9091 loci. Transformants can be selected on YNB plates containing 2% melibiose as sole carbon source and 32pg/mL x-alpha-gal which provides colorimetric indication of the presence of the ScMEL5 marker gene. Resulting transformants can be streaked for single colony isolation on YPD containing 32pg/mL x-alpha- gal. A single blue colony can be selected. Correct integration of SEQ ID NO: 8 into the selected blue colony can be verified by PCR. PCR verified isolates are designated strains l-8a (transformation of strain 1-2) and 1 -8b (transformation of strain 1-3). Prophetic Strains l-9a and l-9b

[0089] Strain 1-2 or 1-3 can be transformed with SEQ ID NO: 9. SEQ ID NO: 9 contains i) an expression cassette for the selectable marker gene melibiase from S. cerevisiae (ScMEL5) including the PGK promoter SEQ ID NO: 15 and the MEL5 terminator SEQ ID NO:22 and flanked by LoxP sites; ii) an expression cassette for the fructose transporter gene from Zygosaccharomyces bailii (ZbFfzl), encoding the amino acid sequence SEQ ID NO:28, under the control of the PDC promoter SEQ ID NO: 13 and the S. cerevisiae GAL 10 terminator SEQ ID NO:21; and iii) flanking DNA for targeted chromosomal integration into the adh9091 loci. Transformants can be selected on YNB plates containing 2% melibiose as sole carbon source and 32pg/mL x-alpha-gal which provides colorimetric indication of the presence of the ScMEL5 marker gene. Resulting transformants can be streaked for single colony isolation on YPD containing 32pg/mL x-alpha- gal. A single blue colony can be selected. Correct integration of SEQ ID NO:9 into the selected blue colony can be verified by PCR. PCR verified isolates are designated strains l-9a (transformation of strain 1-2) and 1 -9b (transformation of strain 1-3).

Prophetic Strains l-10a and l-10b

[0090] Strain 1-2 or 1-3 can be transformed with SEQ ID NO: 10. SEQ ID NO: 10 contains i) an expression cassette for the selectable marker gene melibiase from S. cerevisiae (ScMEL5) including the PGK promoter SEQ ID NO: 15 and the MEL5 terminator SEQ ID NO:22 and flanked by LoxP sites; ii) an expression cassette for the fructose transporter gene from Saccharomyces carlsbergensis (ScarlFsyl), encoding the amino acid sequence SEQ ID NO:29, under the control of the PDC promoter SEQ ID NO: 13 and the S. cerevisiae GAL 10 terminator SEQ ID NO:21; and iii) flanking DNA for targeted chromosomal integration into the adh.9091 loci. Transformants can be selected on YNB plates containing 2% melibiose as sole carbon source and 32pg/mL x-alpha- gal which provides colorimetric indication of the presence of the ScMEL5 marker gene. Resulting transformants can be streaked for single colony isolation on YPD containing 32pg/mL x-alpha- gal. A single blue colony can be selected. Correct integration of SEQ ID NO:9 into the selected blue colony can be verified by PCR. PCR verified isolates are designated strain l -10a (transformation of strain 1-2) are strain 1-10b (transformation of strain 1-3)

Example 2: Fermentations with 3-HP producing strains 1-2 and 1-3

[0091] The 3-HP producing strains 1-1, 1-2, and 1-3 were run shake flasks to assess sucrose, dextrose, and fructose consumption as well as 3-HP production. Strains 1-1, 1-2, and 1-3 were streaked out for single colonies on YPD plates (bacteriological peptone 20g/L, yeast extract 10 g/L, glucose 20 g/L, and agar 15 g/L) and incubated until single colonies were visible. Incubation at room temperature resulted in single colony growth in about 72 hours and incubation at 30 °C resulted in single colony growth in about 18 hours. Cells from plates were scraped into production medium (Table 2) and the optical density (ODeoo) was measured. Optical density is measured at a wavelength of 600 nm with a 1 cm path length cuvette using a model Genesys20 spectrophotometer (Thermo Scientific).

[0092] A 250 mL non-baffled shake flask containing 0.26g CaCOi was inoculated with the production medium culture to reach an initial ODeoo of 0.2. Immediately prior to inoculation, 18 mL of the production medium was added to the 250 mL shake flask. The production medium is sterilized, pH to 5.5, and contains the components outlined in Table 4.1. After inoculation, shake flasks are incubated at 34 °C with a relative humidity of 80% and shaking at 150 rpm for approximately 72 hours.

[0093] Samples were taken periodically throughout the fermentation and at the end of the batch. Samples were analyzed for sucrose, dextrose, fructose, and 3-HP concentration by high performance liquid chromatography with refractive index detector. Fermentation results are reported in FIGS. 2 and 3.

[0094] Overall, both strains 1-2 and 1-3 showed improved sucrose and fructose consumption relative to control strain 1-1 (FIG. 2). Similarly, when sucrose was used as a substrate, strains 1- 2 and 1-3 were able to produce 3-HP, while strain 1-1 did not produce 3-HP with the sucrose substrate. Strain 1-1 only produced 3-HP in the presence of dextrose as a substrate.

Table 2: Production Medium

Example 3: Prophetic fermentations with 3-HP producing strains

[0095] The 3-HP producing yeast strains l-4a, l-4b, l-5a, l-5b, l-6a, l-6b, l-7a, l-7b, l-8a, l-8b, l-9a, l-9b, l-10a, and/or l-10b can be run in fermenters to assess sucrose, glucose, and fructose consumption as well as 3-HP production. Strains l-4a, l-4b, l-5a, 1 -5b, l-6a, 1 -6b, l-7a, l-7b, l-8a, l-8b, l-9a, l-9b, l-10a, and/or 1-1 Ob can be streaked out for single colonies on asterile YPD plate (bacteriological peptone 20g/L, yeast extract 10 g/L, glucose 20 g/L, and agar 15 g/L) and incubated until single colonies are visible. Incubation at room temperature results in single colony growth in about 72 hours and incubation at 30 °C results in single colony growth in about 18 hours. Cells from plates can be scraped into sterile seed medium (Table 3) to for a slurry and the optical density (ODeoo) measured. Optical density is measured at a wavelength of 600 nm with a 1 cm path length cuvette using a model Genesys20 spectrophotometer (Thermo Scientific). The target ODeoo of the slurry is approximately 0.4. A quantity of the slurry is inoculated into a first seed culture to result in a starting ODeoo of 0.1. Seed cultures are incubated in 500 mL shake flasks containing 50 mL seed medium at 34 °C and 250 RPM until they reach an ODeoo of 4-8.

[0096] A second seed culture is inoculated with a quantity of a first seed culture to result in a starting ODeoo of 1.0. Second seed cultures are incubated in 500 mL shake flasks containing 50 mL seed medium at 34 °C and 250 RPM until they reach an ODeoo of 4-8.

[0097] A 2L capacity fermenter is inoculated with a quantity of the second seed culture to reach on initial ODeoo of 0.2. Separate fermenters are inoculated with seed cultures for each of the strains. Immediately prior to inoculating, 1.45 L of fermentation medium is added to each fermenter. The fermentation medium has been sterilized, the pH adjusted to 5.5, and contains the components outlined in Table 5.

[0098] pH in the fermenters starts at 5.5 and as 3-HP is produced it free falls to 4.45 where it is maintained by controlled addition of a 30% suspension of lime (calcium hydroxide) until 84 g of the 30% lime suspension has been added, after which no further pH control occurs. The fermenters are sparged with 0.25 SLPM (standard liters per minute) air through a sparge ring at the base of the vessel. An oxygen uptake rate of 20 mmol O2/ (L* h) is achieved by selecting an appropriate agitation speed. Alternative or additional oxygen uptake rates may also be used (e.g., 15-17 mmol O2/ (L* h),). These fermentations are operated such that after the cells achieve a sufficient density, oxygen limitation is achieved and subsequently maintained throughout the rest of the fermentation (e.g., dissolved oxygen less than about 10% of atmospheric air saturation.) Dissolved oxygen is measured using Mettler Toledo InPro® 6800 sensor (Mettler-Toledo GmbH, Urdorf, Switzerland), calibrated prior to inoculation. 0% is calibrated by unplugging the probe and measuring a null signal, 100% is calibrated under atmospheric air using air sparging according to the run conditions in the vessel as detailed above (prior to inoculation). For this example, the inlet and outlet concentrations of Oxygen, N2 and CO2 values are measured by a mass spectrometer. Oxygen uptake rate (“OUR”) is calculated from these measurements using methods known to those in the art as described above.

[0099] Samples are taken immediately after inoculation, at the end of the batch, and periodically throughout the fermentation. Samples are analyzed for 3-HP, glucose, fructose, sucrose, and arabitol concentration by high performance liquid chromatography with refractive index detector.

Table 3: Seed Medium

Table 4: DMu salts 25x

Table 5: Fermentation Medium

Table 6: Trace Composition

Claims

CLAIMS What is claimed is:

1. A genetically engineered yeast cell capable of producing 3-hydroxypropionate (3-HP) from sucrose, the engineered yeast cell comprising an active 3-HP fermentation pathway; a polynucleotide encoding an exogenous invertase enzyme; a deletion or disruption of a native pyruvate decarboxylase (PDC) gene; and a genetic modification resulting in overexpression of a native hexokinase gene.

2. The engineered yeast cell of claim 1, wherein the yeast cell is Crabtree negative.

3. The engineered yeast cell of claim 1 or 2, wherein the yeast cell is a yeast of the Issatchenkia orientalis IPichia fermentans clade.

4. The engineered yeast cell of any one of claims 1-3, wherein the yeast cell is an Issatchenkia orientalis cell.

5. A genetically engineered Issatchenkia orientalis cell capable of producing 3- hydroxypropionate (3-HP) from sucrose, the engineered yeast cell comprising an active 3-HP fermentation pathway; a polynucleotide encoding an exogenous invertase enzyme; a deletion or disruption of a native pyruvate decarboxylase (PDC) gene; and a genetic modification resulting in overexpression of a native hexokinase gene, wherein the engineered I. orientalis cell is capable of producing 3-HP at a titer of at least 30, at least 80, at least 100, or at least 120 g/L.

6 The engineered yeast cell of any one of claims 1-5, wherein hexokinase activity in the engineered yeast cell is higher than hexokinase activity in an equivalent yeast cell lacking the genetic modification.

7. The engineered yeast cell of any one of claims 1-6, wherein peak 3-HP production rate in the engineered yeast cell, when used in a fermentation process in the presence of sucrose, is higher than peak 3-HP production rate of an equivalent yeast cell lacking the genetic modification.

8. The engineered yeast cell of any one of claim 1-7, wherein the genetic modification comprises replacement of the native hexokinase gene promoter with a constitutive heterologous or artificial promoter.

9. The engineered yeast cell of claim 8, wherein the constitutive heterologous or artificial promoter is selected from the group consisting of pyruvate decarboxy lase (PDC1), glyceraldehyde-3 -phosphate dehydrogenase (TDH3), enolase (EN01), and 3-phosphogly cerate kinase (PGK1).

10. The engineered yeast cell of any one of claims 1-9, wherein the genetic modification comprises addition of an exogenous polynucleotide encoding the native hexokinase such that the genetically engineered yeast cell comprises at least one additional copy of a sequence encoding the native hexokinase.

11. The engineered yeast cell of any one of claims 1-10, wherein the native hexokinase comprises a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs:24 and 25.

12. The engineered yeast cell of any one of claims 1-11, wherein the engineered yeast cell comprises a deletion or disruption of a glycerol-3-phosphate dehydrogenase (GPD) gene.

13. The engineered yeast cell of any one of claims 1-12, wherein the engineered yeast cell comprises a deletion or disruption of an L-lactate:cytochrome c oxidoreductase (CYB2) gene.

14. The engineered yeast cell of any one of claims 1-13, wherein the exogenous invertase enzyme comprises a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs: 12, 33, 34, and 35.

15. The engineered yeast cell of any one of claims 1-14, wherein the polynucleotide encoding the exogenous invertase enzyme is operably linked to a heterologous or artificial promoter.

16. The engineered yeast cell of claim 15, wherein the promoter is selected from the group consisting of pyruvate decarboxylase (PDC1 ), glyceraldehyde-3-phosphate dehydrogenase (TDH3), translational elongation factor (TEF), transaldolase (TAL), RPL16B, 3- phosphoglycerate kinase (PGK1), and enolase (EN01).

17. The engineered yeast cell of any one of claims 1-16, wherein the yeast cell is an Issatchenkia orientalis cell and the native, overexpressed hexokinase comprises a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs:24 and 25.

18. The engineered yeast cell of any one of claims 1-17, wherein the yeast cell additionally comprises an exogenous polynucleotide encoding a fructokinase.

19. The engineered yeast cell of claim 18, wherein the fructokinase comprises a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to SEQ ID NO: 26.

20. The engineered cell of claim 18 or 19, wherein the exogenous polynucleotide encoding the fructokinase is operably linked to a heterologous or artificial promoter.

21. The engineered cell of claim 20, wherein the heterologous or artificial promoter is selected from the group consisting of pyruvate decarboxylase (PDC1), glyceraldehyde-3- phosphate dehydrogenase (TDH3), translational elongation factor (TEF), transaldolase (TAL), RPL16B, 3-phosphogly cerate kinase (PGK1), and enolase (ENO1).

22. The engineered cell of any one of claims 1-21, wherein the active 3 -HP fermentation pathway comprises one or more exogenous polypeptides encoding a pyruvate carboxylase (PCY) enzyme, an aspartate aminotransferase (AAT) enzyme, an aspartate 1 -decarboxylase (ADC) enzyme, a -alamne aminotransferase (BAAT) enzyme, a 3 -hydroxy propionic acid dehydrogenase (3-HPDH) enzyme, or combinations thereof.

23. The engineered cell of claim 22, wherein i) the PCY enzyme comprises a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs:45, 46, 47, 48, 49, 50, or 51; ii) the AAT enzyme comprises a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs:57, 58, or 59; iii) the ADC enzyme comprises a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs: 88-127, preferably at least one of SEQ ID NOs:94, 101, 102, or 103, most preferably SEQ ID NO:102; iv) the BAAT enzyme comprises a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs: 60, 62, 64, 66, or 67; or v) the 3-HPDH enzyme comprises a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs:70, 71, 73, or 75.

24. The engineered cell of claim 22 or 23, wherein the one or more exogenous polynucleotides is operably linked to a heterologous or artificial promoter selected from the group consisting of pyruvate decarboxylase (PDC1), glyceraldehyde-3 -phosphate dehydrogenase (TDH3), translational elongation factor (TEF), transaldolase, RPL16B, 3- phosphoglycerate kinase (PGK1), and enolase (ENO1).

25. A method for producing 3-hydroxypropionate (3-HP) from sucrose, the method comprising: contacting a substrate comprising sucrose with the engineered yeast cell of any one of claims 1-24, wherein fermentation of the substrate by the engineered yeast produces 3-HP.

26. A method for producing 3-hydroxypropionate (3-HP) from sucrose, the method comprising: contacting a substrate comprising sucrose with an engineered yeast cell comprising an active 3-HP fermentation pathway; a polynucleotide encoding an exogenous invertase enzyme; a deletion or disruption of a native pyruvate decarboxylase (PDC) gene; and a genetic modification resulting in overexpression of a native hexokinase gene, wherein fennentation of the substrate by the engineered yeast produces lactate.

27. The method of claim 26, wherein the active 3-HP fermentation pathway comprises one or more exogenous polypeptides encoding a pyruvate carboxylase (PCY) enzyme, an aspartate aminotransferase (AAT) enzyme, an aspartate 1 -decarboxylase (ADC) enzyme, a P-alanine aminotransferase (BAAT) enzyme, a 3-hydroxypropionic acid dehydrogenase (3-HPDH) enzyme, or combinations thereof.

28. The method of claim 27, wherein i) the PCY enzyme comprises a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs:45, 46, 47, 48, 49, 50, or 51; ii) the AAT enzyme comprises a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs:57, 58, or 59; in) the ADC enzyme comprises a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs: 88-127, preferably at least one of SEQ ID NOs:94, 101, 102, or 103, most preferably SEQ ID NO:102; iv) the BAAT enzyme comprises a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs: 60, 62, 64, 66, or 67; or v) the 3-HPDH enzyme comprises a sequence at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 98%, at least 99%, or 100% identical to at least one of SEQ ID NOs:70, 71, 73, or 75.

29. The method of claim 27 or 28, wherein the one or more exogenous polynucleotides is operably linked to a heterologous or artificial promoter selected from the group consisting of pyruvate decarboxylase (PDC1), glyceraldehyde-3 -phosphate dehydrogenase (TDH3), translational elongation factor (TEF), transaldolase, RPL16B, 3-phosphogly cerate kinase (PGK1), and enolase (ENO1).

30. The method of any one of claims 25-29, wherein the volumetric oxygen uptake rate (OUR) is 0.5 to 40 mmol O2/(L • h), 1 to 35 mmol O2/(L • h), 3 to 30 mmol O2/(L • h), 6 to 27 mmol O₂/(L • h), or 16-24 mmol O2/(L • h).

31. The method of any one of claims 25-30, wherein the specific OUR is in the range of 0.2 to 13 mmol O2/(g cell dry weight • h), 0.3 to 10 mmol C>2/(g cell dry weight • h), 1 to 7 mmol O2/(g cell dry weight • h), or 2 to 6 mmol O2/(g cell dry weight • h).

32. The method of any one of claims 25-31, wherein peak 3-HP production rate is at least 5 g L'¹ h'¹, at least 6 g L'¹ h'¹, at least 7 g L'¹ h’¹, or at least 8 g L ¹ h’¹.

33. The method of any one of claims 25-32, wherein 3-HP is produced at a rate of at least 1.5 g L ¹ h’¹, at least 2.0 g L'¹ h’¹, at least 2.5 g L'¹ h’¹, at least 3.0 g L ¹ h’¹, or at least 3.5 g L'¹ h" i

34. The method of any one of claims 25-33, wherein the fermentation temperature is in the range of 25 °C to 45 °C, 20 °C to 40 °C, or 32 °C to 37 °C.

35. The method of any one of claims 25-34, wherein the 3-HP titer is at least 30, at least 80, at least 100, or at least 120 g/L.