Abstract: Yeast cells with modified expression of certain enzyme activities in the mitochondria are described for isobutanol production. Modifications described provide an isobutanol biosynthesis pathway in the yeast mitochondria.

Abstract: The present invention relates to a deoxyribonucleic acid (DNA) comprising at least one promoter sequence, which is derived from a wild-type promoter of a methyltrophic yeast, whose transcription efficiency is modulated in comparison to the efficiency of the wild-type promoter by inserting or modifying a DNA binding site. The invention also relates to host cells, expression vectors, kits and methods for producing proteins while using the inventive DNA, as well as to different uses of the same and to a method for producing expression vectors.

Abstract: A microbial host cell is provided for the production of isobutanol. Carbon flux in the cell is optimized through the Entner-Doudoroff pathway.

Abstract: Provided are a recombinant gene associated with increased galactose catabolism, and a recombinant vector and microorganism including the gene. Also disclosed are a method of producing ethanol from a galactose-containing carbon source by culturing the microorganism including the gene in a galactose-containing carbon source such that ethanol is produced, and a method of screening a gene in yeast resulting in increased galactose catabolism when overexpressed.

Abstract: The present invention relates to fungal ?-15 fatty acid desaturases that are able to catalyze the conversion of linoleic acid (18:2, LA) to alpha-linolenic acid (18:3, ALA). Nucleic acid sequences encoding the desaturases, nucleic acid sequences which hybridize thereto, DNA constructs comprising the desaturase genes, and recombinant host plants and microorganisms expressing increased levels of the desaturases are described. Methods of increasing production of specific omega-3 and omega-6 fatty acids by over-expression of the ?-15 fatty acid desaturases are also described herein.

Abstract: The present invention relates to mutant ?8 desaturase genes, which have the ability to convert eicosadienoic acid [20:2 ?-6, EDA] to dihomo-?-linolenic acid [20:3, DGLA] and/or eicosatrienoic acid [20:3 ?-3, ETrA] to eicosatetraenoic acid [20:3 ?-3, ETA]. Isolated nucleic acid fragments and recombinant constructs comprising such fragments encoding ?8 desaturase along with methods of making long-chain polyunsaturated fatty acids (PUFAs) using these mutant ?8 desaturases in plants and oleaginous yeast are disclosed.

Abstract: Provided herein are a recombinant vector and microorganism including the isolated SNR84 gene, and a method of increasing volumetric productivity of biofuel from a galactose-containing carbon source using the isolated SNR84 gene, the recombinant vector or the recombinant microorganism. Also disclosed herein is a method of screening yeast for genes associated with increased galactose catabolism when the genes are overexpressed.

Abstract: The present invention relates to DNA encoding novel xylitol dehydrogenase and a method for using the same. Specifically, the present invention comprises providing the nucleic acid sequence of a xylitol dehydrogenase gene from Candida shehatae and introducing this gene into a host organism, thereby producing a microorganism having the ability to utilize xylose.

Abstract: The invention relates to an eukaryotic cell expressing nucleotide sequences encoding the ara A, ara B and ara D enzymes whereby the expression of these nucleotide sequences confers on the cell the ability to use L-arabinose and/or convert L-arabinose into L-ribulose, and/or xylulose 5-phosphate and/or into a desired fermentation product such as ethanol. Optionally, the eukaryotic cell is also able to convert xylose into ethanol.

Abstract: Yeast strains were engineered that have increased activity of heterologous proteins that require binding of an Fe—S cluster for their activity. The yeast strains have reduced activity of an endogenous Fe—S protein. Activities of heterologous fungal or plant 2Fe-2S dihydroxy-acid dehydratases and Fe—S propanediol dehydratase reactivase were increased for increased production of products made using biosynthetic pathways including these enzymes, such as valine, isoleucine, leucine, pantothenic acid (vitamin B5), isobutanol, 2-butanone and 2-butanol.

Abstract: Recombinant yeast strains that saccharify, ferment and grow on insoluble and crystalline forms of cellulose are disclosed herein. The yeast strains express tethered cellulases including cellobiohydrolase, endoglucanase and ?-glucosidase. The recombinant organisms are particularly suited for consolidated bioprocessing.

Abstract: The present invention provides methods and related vectors and host cells for quantitative analysis of protein interactions in eukaryotic expression system. More specifically, the invention provides a yeast surface two-hybrid (YS2H) system that can express a pair of proteins, one protein (“bait”) as a fusion to a yeast cell wall protein, and the other (“prey”) in a secretory form. When two proteins interact in this system, they associate in the secretory pathway, and the prey that would otherwise be released into the media is captured on the cell surface by the bait. Expression of the bait and the prey proteins can be designed to promote a synchronized and comparable level of expression.

Abstract: The present invention relates to ?9 elongases, which have the ability to convert linoleic acid [18:2, LA] to eicosadienoic acid [20:2, EDA]. Isolated nucleic acid fragments and recombinant constructs comprising such fragments encoding ?9 elongase along with methods of making long-chain polyunsaturated fatty acids (PUFAs) using these ?9 elongases in plants and oleaginous yeast are disclosed.

Abstract: The invention provides variant phytase enzymes having increased thermal stability relative to their counterpart parent enzymes. The modifications to the enzymes include both single substitutions and various combinations of substitutions that provide improved stability and activity. The invention further provides nucleic acids encoding the variant phytase enzymes, host cells and vectors containing and expressing them, as well as feed compositions useful for providing improved nutrition, particularly with respect to the bioavailability of dietary phosphate, calcium, iron and zinc, among others.

Abstract: Methods of increasing the total lipid content in a eukaryotic cell, the total content of polyunsaturated fatty acids [“PUFAs”], and/or the ratio of desaturated fatty acids to saturated fatty acids by reducing the activity of the heterotrimeric SNF1 protein kinase are disclosed. Preferably, the chromosomal genes encoding the Snf1 ?-subunit, Gal83 ?-subunit or Snf4 ?-subunit of the SNF1 protein kinase, the upstream regulatory genes encoding Sak1, Hxk2, Glk1 or Reg1, or the downstream genes encoding Rme1, Cbr1 or Snf3 are manipulated in a PUFA-producing strain of the oleaginous yeast Yarrowia lipolytica, resulting in increased total lipid content, as compared to the parent strain comprising the heterotrimeric SNF1 protein kinase not having reduced activity.

Abstract: The present invention relates to ?6 desaturases, which have the ability to convert linoleic acid [“LA”; 18:2 ?-6] to ?-linolenic acid [“GLA”; 18:3 ?-6] and/or ?-linolenic acid [“ALA”; 18:3 ?-3] to stearidonic acid [“STA”; 18:4 ?-3]. Isolated nucleic acid fragments and recombinant constructs comprising such fragments encoding ?6 desaturases, along with methods of making long-chain polyunsaturated fatty acids [“PUFAs”] using these ?6 desaturases in oleaginous yeast, are disclosed.

Abstract: The present invention relates to host cells transformed with a nucleic acid sequence encoding a eukaryotic xylose isomerase obtainable from an anaerobic fungus. When expressed, the sequence encoding the xylose isomerase confers to the host cell the ability to convert xylose to xylulose which may be further metabolized by the host cell. Thus, the host cell is capable of growth on xylose as carbon source. The host cell preferably is a eukaryotic microorganism such as a yeast or a filamentous fungus. The invention further relates to processes for the production of fermentation products such as ethanol, in which a host cell of the invention uses xylose for growth and for the production of the fermentation product. The invention further relates to nucleic acid sequences encoding eukaryotic xylose isomerases and xylulose kinases as obtainable from anaerobic fungi.

Abstract: Cell lines having genetically modified glycosylation pathways that allow them to carry out a sequence of enzymatic reactions, which mimic the processing of glycoproteins in humans, have been developed. Recombinant proteins expressed in these engineered hosts yield glycoproteins more similar, if not substantially identical, to their human counterparts. The lower eukaryotes, which ordinarily produce high-mannose containing N-glycans, including unicellular and multicellular fungi are modified to produce N-glycans such as Man5GlcNAc2 or other structures along human glycosylation pathways.

Abstract: A non-naturally occurring eukaryotic or prokaryotic organism includes one or more gene disruptions occurring in genes encoding enzymes imparting increased fumarate, malate or acrylate production in the organism when the gene disruption reduces an activity of the enzyme. The one or more gene disruptions confers increased production of acrylate onto the organism. Organisms that produce acrylate have an acrylate pathway that at least one exogenous nucleic acid encoding an acrylate pathway enzyme expressed in a sufficient amount to produce acrylate, the acrylate pathway comprising a decarboxylase. Methods of producing fumarate, malate or acrylate include culturing these organisms.

Abstract: Provided herein compositions and methods for producing isoprenoids, including squalene. In certain aspects and embodiments provided are genetically altered yeast and uses therefore. In some aspects and embodiments, the genetically altered yeast produce isoprenoids, preferably squalene. The genetically altered yeast may have alterations in the expression or activity of enzymes involved in squalene production. for example, acetyl-CoA carboxylase (or “ACCase”), HMG-CoA reductase, squalene epoxidase, and squalene synthase. One or more genes of a genetically altered yeast may be modified by gene repair oligonucleobases. Also are provided methods of producing squalene using a genetically altered yeast. The invention also provides squalene produced by genetically altered yeast.

Abstract: The invention relates to compositions, systems, and methods for producing fuels, such as ethanol and hydrogen, and related compounds. More specifically, compositions and methods are provided for making recombinant microorganisms for the production of fuels using genes from the Clostridium phytofermentans ethanol and hydrogen pathways disclosed herein.

Abstract: Recombinant materials, including DNA constructs, expression vectors, and host cells, and methods of identifying an environmental stimulus or a gene that alters the lifespan of an organism are identified. The recombinant DNA constructs include first and second chimeric genes that both encode substantially the same protein that is required for yeast replication, the first chimeric gene containing a promoter responsive to growth medium conditions and the second chimeric gene containing a promoter operable in mother cells but not daughter cells.

Abstract: Yeast cells with a reduced general control response to amino acid starvation were found to have increased tolerance to butanol in the growth medium. The reduced response was engineered by genetic modification of a gene involved in the response, a GCN gene, to eliminate activity of the encoded protein. Yeast strains with an engineered butanol biosynthetic pathway and a genetic modification in a gene involved in the general control response to amino acid starvation, which have increased butanol tolerance, are useful for production of butanol.

Abstract: Two acyltransferases are provided, suitable for use in the manufacture of microbial oils enriched in omega fatty acids in oleaginous yeast (e.g., Yarrowia lipolytica). Specifically, the genes encoding phophatidylcholine-diacylglycerol acyltransferase (PDAT) and diacylglycerol acyltransferase (DGAT2) have been isolated from Y. lipolytica. These genes encode enzymes that participate in the terminal step in oil biosynthesis in yeast. Each is expected to play a key role in altering the quantity of polyunsaturated fatty acids produced in oils of oleaginous yeasts.

Abstract: The present invention relates to methods and genetically engineered methylotrophic yeast strains for producing glycoproteins with mammalian-like glycosylation. The present invention also relates to vectors useful for generating methylotrophic yeast strains capable of producing glycoproteins with mammalian-like glycosylation. Glycoproteins produced from the genetically engineered methylotrophic yeast strains are also provided.

Abstract: Yeast cells having an exogenous lactate dehydrogenase gene ae modified by reducing L- or D-lactate:ferricytochrome c oxidoreductase activity in the cell. This leads to reduced consumption of lactate by the cell and can increase overall lactate yields in a fermentation process. Cells having the reduced I, or D-lactate:ferricytochrome c oxidoreductase activity can be screened for by resistance to organic acids such as lactic or glycolic acid.

Abstract: The present invention relates to eukaryotic host cells, especially lower eukaryotic host cells, having modified oligosaccharides which may be modified further by heterologous expression of a set of glycosyltransferases, sugar and sugar nucleotide transporters to become host-strains for the production of mammalian, e.g., human therapeutic glycoproteins. The process provides an engineered host cell which can be used to express and target any desirable gene(s) involved in glycosylation. Host cells with modified lipid-linked oligosaccharides are created or selected. N-glycans made in the engineered host cells exhibit GnTIII, GnTIV, GnTV, GnT VI or GnTIX activity, which produce bisected and/or multiantennary N-glycan structures and may be modified further by heterologous expression of one or more enzymes, e.g., glycosyltransferases, sugar, sugar nucleotide transporters, to yield human-like glycoproteins.

Abstract: There is disclosed a method of producing isobutanol. In an embodiment, the method includes providing a microorganism transformed with an isobutanol producing pathway containing at least one exogenous gene. The microorganism is selected to produce isobutanol from a carbon source at a yield of at least 10 percent theoretical. The method includes cultivating the microorganism in a culture medium containing a feedstock providing the carbon source, until isobutanol is produced. The method includes recovering the isobutanol. In one embodiment, the microorganism is a yeast with a Crabtree-negative phenotype. In another embodiment, the microorganism is a yeast microorganism with a Crabtree-positive phenotype. There is disclosed a microorganism for producing isobutanol. In an embodiment, the microorganism includes an isobutanol producing pathway containing at least one exogenous gene, and is selected to produce a recoverable quantity of isobutanol from a carbon source at a yield of at least 10 percent theoretical.

Abstract: The present invention relates to eukaryotic host cells having modified oligosaccharides which may be modified further by heterologous expression of a set of glycosyltransferases, sugar transporters and mannosidases to become host-strains for the production of mammalian, e.g., human therapeutic glycoproteins. The invention provides nucleic acid molecules and combinatorial libraries which can be used to successfully target and express mammalian enzymatic activities such as those involved in glycosylation to intracellular compartments in a eukaryotic host cell. The process provides an engineered host cell which can be used to express and target any desirable gene(s) involved in glycosylation. Host cells with modified oligosaccharides are created or selected. N-glycans made in the engineered host cells have a Man5GlcNAc2 core structure which may then be modified further by heterologous expression of one or more enzymes, e.g.

Abstract: The invention relates to nucleic acid molecules encoding (poly)peptides having LPI (Lectin Pathway Inhibitor) activity, to recombinant vectors harboring such molecules, and the host cells carrying the vectors. The invention further relates to methods for preparing recombinant (poly)peptides having LPI activity and to the use of such recombinant (poly)peptides having LPI activity for diagnosis, prophylaxis and treatment, such as the treatment of inflammation reactions. In addition the invention provides therapeutic and diagnostic compositions comprising as the active ingredient the (poly)peptide having LPI activity.

Abstract: Bacterial polynucleotides and polypeptides are provided in which the polypeptides have a dehydrogenase activity, such as an alcohol dehydrogenase (ADH) activity, an uronate, a 4-deoxy-L-erythro-5-hexoseulose uronate (DEHU) ((4S,5S)-4,5 dihydroxy-2,6-dioxohexanoate) hydrogenase activity, a 2-keto-3-deoxy-D-gluconate dehydrogenase activity, a D-mannuronate hydrogenase activity, and/or a D-mannnonate dehydrogenase activity. Methods, enzymes, recombinant microorganism, and microbial systems are also provided for converting polysaccharides, such as those derived from biomass, into suitable monosaccharides or oligosaccharides, as well as for converting suitable monosaccharides or oligosaccharides into commodity chemicals, such as biofuels. Commodity chemicals produced by the methods described herein are also provided.

Abstract: Cell lines having genetically modified glycosylation pathways that allow them to carry out a sequence of enzymatic reactions, which mimic the processing of glycoproteins in humans, have been developed. Recombinant proteins expressed in these engineered hosts yield glycoproteins more similar, if not substantially identical, to their human counterparts. The lower eukaryotes, which ordinarily produce high-mannose containing N-glycans, including unicellular and multicellular fungi are modified to produce O-glycans or other structures along human glycosylation pathways.

Abstract: The present invention relates to methods for the production of ?-3 and/or ?-6 fatty acids in oleaginous yeast. Thus, desaturases and elongases able to catalyze the conversion of linoleic acid (LA) to ?-linolenic acid (GLA); ?-linoleic acid (ALA) to stearidonic acid (STA); GLA to dihomo-?-linoleic acid (DGLA); STA to eicosatetraenoic acid (ETA); DGLA to arachidonic acid (ARA); ETA to eicosapentaenoic acid (EPA); DGLA to ETA; EPA to docosapentaenoic acid (DPA); and ARA to EPA have been introduced into the genome of Yarrowia for synthesis of ARA and EPA.

Abstract: The present invention is directed to a yeast cell for producing a recombinant collagen like protein. The present invention is further directed to a kit of parts or a co-expression system for use in the production of such a protein and to a method of producing said recombinant protein and a thread made therefrom. Furthermore, the invention pertains to proteins or threads obtainable by these methods as well as their use in various fields of technology and medicine.

Abstract: The present invention generally relates to methods of modifying the glycosylation structures of recombinant proteins expressed in fungi or other lower eukaryotes, to more closely resemble the glycosylation of proteins from higher mammals, in particular humans. The present invention also relates to novel enzymes and, nucleic acids encoding them and, hosts engineered to express the enzymes, methods for producing modified glycoproteins in hosts and modified glycoproteins so produced.

Abstract: The present invention is directed to a method of modifying a spider silk protein and a spider silk protein obtainable by said method. The invention further pertains to a nucleic acid sequence coding for a modified spider silk protein, a vector containing said sequences and host cells transformed with this vector. The invention furthermore is directed to a pharmaceutical or cosmetical composition containing a modified spider silk protein as defined herein and the use of said modified sequences in various fields, in particular in the fields of medicine, cosmetics and technical applications.

Abstract: This invention relates to a method for utilizing less purified starch in fermentation processes. One example is a recombinant E. coli containing a exogenous extracellular isoamylase activity that is capable of utilizing small oligomers containing (1,6) linkages (including but not limited to isomaltose and panose) in fermentations to produce useful products. The invention is useful in large-scale industrial biofermentations by reducing the cost of the substrate carbohydrate.

Abstract: The invention provides methods of modifying the lipids produced by microbial organisms through genetic engineering. The invention also provides genetically engineered microbes and methods of fermenting microbes for oil production. Also provided are oils, fuels, oleochemicals, chemical precursors, and other compounds manufactured by such modified microorganisms. Exemplary oil-bearing organisms include organisms containing one or more exogenous genes encoding a fatty acyl-ACP thioesterase, fatty acyl-CoA/aldehyde reductase, fatty acyl-CoA reductase, fatty aldehyde reductase, fatty aldehyde decarbonylase, and/or an acyl carrier protein.

Abstract: There can be provided a fungal antigen which is an insoluble fraction obtainable from fungal cells of which cell wall has been substantially removed or at least partially removed; a process for producing the same; a nucleic acid encoding the fungal antigen; a biologic product containing the fungal antigen; a method of stimulating immunological responses by using the biologic product; a method of suppressing allergic reaction to fungi in a vertebrate; and a method for diagnosing a disease caused by fungi in a vertebrate.

Abstract: The invention relates to an improved nucleic acid molecule encoding fungal immunomodulatory protein (FIP) that is better expressed in fungi, to vectors comprising the nucleic acid molecule, to hosts transformed with said vectors, to processes of expressing the protein of the invention in said transformed hosts, to the protein of the invention produced by said processes, to uses of said hosts comprising the protein of the invention and to a process of purifying FIP. The protein of the invention has wide immunomodulatory activity. Thus, the present invention further relates to uses of the protein of the invention in cosmetic or pharmaceutical compositions and to food or feed additives comprising the protein of the invention. Finally, the invention relates to the method of modulating immunological activities by orally administering FIP or proteins fused with FIP to a subject.

Abstract: The invention provides methods of manufacturing oils and oil-based products such as transportation fuels, industrial chemicals, edible oils, lubricants and plastics using sugar cane, sugar beets, and cane/beet agricultural processing byproducts as a feedstock for bioproduction processes. The disclosed processes utilize oil-bearing microbes as a conversion technology to convert chemical energy produced by sugar cane and sugar beets into energy-containing oils and oil derivatives. Also provided herein are oil-bearing microbes containing one or more exogenous sucrose utilization genes.

Abstract: The present invention provides screening procedures for identifying inhibitors of components of regulatory networks by a positive phenotype and modified yeast cell lines suitable for said screening. The screening procedures are especially suited to screen for substances that re-sensitize resistant pathogenic microorganisms or tumor cells by suspending the expression of resistance-relevant genes. The invention further provides methods for constructing said cell lines and their use in screening systems.

Abstract: The present invention relates to an isolated nucleic acid molecule encoding a mutant phytase and the isolated mutant phytase itself. The present invention further relates to methods of using the isolated nucleic acid molecule and the isolated mutant phytase of the present invention.

Abstract: This invention relates generally to the discovery of a novel control of sorbose utilization (CSU) genes. The invention further relates to the detection of these genes and their use in the diagnosis and treatment of fungal infections.

Abstract: The invention relates to a novel double hybrid system and to the uses thereof. This system provides, in particular, a tool that enables the detection of the interruption of a protein-protein interaction. The developed system uses transcription interference as a mechanism for detecting a breaking up of interacting protein pairs. The developed double hybrid system can be applied to the screening of molecules enabling the detection of molecules breaking up a protein-protein interaction as well as enabling the identification of alleles lacking in the interaction of proteins involved in the protein-protein interactions.

Abstract: The present invention relates to a fungal C16/18 fatty acid elongase that is able to catalyze the conversion of palmitate (16:0) to stearic acid (18:0). Specifically, the nucleotide sequence of a Mortierella alpina C16/18 fatty acid elongase is provided (designated as “ELO3”). Methods of increasing microbial oil production, increasing carbon flux into the polyunsaturated fatty acid biosynthetic pathway and increasing the content of polyunsaturated fatty acids by over-expression of the C16/18 fatty acid elongase are described herein. Most desirably, the substrate specificity of the instant ELO3 will be particularly useful to enable accumulation of long-chain polyunsaturated fatty acids in oleaginous yeast, such as Yarrowia lipolytica.

Abstract: The present invention provides cells having more than two drug resistance genes and at least two different resistance genes that have been recombined into the chromosome of a cell. It also teaches the processes for preparing cells by recombining two or more different drug resistance genes into the chromosome of a cell. The invention further shows a screening method using the cells of described herein that may be used to accomplish high throughput screening of, among other things, natural products and/or whole cells isolated from the environment.

Abstract: In an embodiment, there is disclosed a recombinant microbial host cell having each of the DNA molecules encoding a polypeptide or group of polypeptides that catalyze the conversion: (i) Acetyl-CoA to Acetate and CoA ??(conversion 1) (ii) Acetyl-CoA to Acetoacetyl-CoA and CoA ??(conversion 2) (iii) Acetoacetyl-CoA and Acetate to Acetoacetate and Acetyl-CoA ??(conversion 3.1) (iv) Acetoacetate to Acetone and CO2 ??(conversion 4) (v) Acetone and NAD(P)H and H+ to Isopropanol and NAD(P)+ ??(conversion 5) wherein at least one DNA molecule is heterologous to the microbial host cell and wherein the microbial host cell produces isopropanol. In another embodiment, a method is disclosed for the production of isopropanol including providing a recombinant microbial host cell, the host cell of (i) with a fermentable carbon substrate in a fermentation medium under conditions whereby isopropanol is produced, and recovering the isopropanol.

Abstract: The present invention relates to ?5 desaturases, which have the ability to convert dihomo-?-linolenic acid (DGLA; 20:3 ?-6) to arachidonic acid (ARA; 20:4 ?-6) and/or eicosatetraenoic acid (ETA; 20:4 ?-3) to eicosapentaenoic acid (EPA; 20:5 ?-3). Isolated nucleic acid fragments and recombinant constructs comprising such fragments encoding ?5 desaturases along with a method of making long-chain polyunsaturated fatty acids (PUFAs) using these ?5 desaturases in oleaginous yeast are disclosed.

Abstract: The present invention relates to ?8 desaturase genes, which have the ability to convert eicosadienoic acid (EDA; 20:2 ?-6) to dihomo-?-linolenic acid (DGLA; 20:3 ?-6) and/or eicosatrienoic acid (ETrA; 20:3 ?-3) to eicosatetraenoic acid (ETA; (20:3 ?-3). Isolated nucleic acid fragments and recombinant DNA constructs comprising such fragments encoding ?8 desaturases along with a method of making long-chain polyunsaturated fatty acids (PUFAs) using these ?8 desaturases in oleaginous yeast are disclosed.