Patent Grant
9382563
The sequence listing submitted via EFS, in compliance with 37 C.F.R. §1.52(e), is incorporated herein by reference. The sequence listing text file submitted via EFS contains the file “30820US-C1-D1-D1_SEQLIST.txt” created on Nov. 18, 2013, which is 41,146 bytes in size.
The present invention relates to filamentous fungal host cells useful for the production of granular starch hydrolyzing enzymes having glucoamylase activity (GSHE), wherein the GSHE is derived from a strain of Humicola grisea or a strain of Aspergillus awamori. More specifically, the invention relates to the expression of a heterologous polynucleotide encoding a GSHE in a Trichoderma host and particularly in a Trichoderma reesei host.
Industrial fermentations predominately use glucose as a feed stock for the production of a multitude of proteins, enzymes, alcohols and other chemicals. In many applications, the glucose is produced by the enzymatic conversion of starch. This conversion is frequently accomplished by a two-step process. The first step is a liquefaction step, wherein an insoluble granular starch substrate is slurried in water, gelatinized with heat and hydrolyzed by a thermostable alpha amylase (e.g., E.C. 3.2.1.1: 1,4-alpha-D-glucan glucanohydrolase) in the presence of calcium. The second step is a saccharification step, wherein the soluble dextrins (sugars) produced in the first step are further hydrolyzed to glucose by an enzyme having glucoamylase (e.g., E.C. 3.2.1.3: 1,4-alpha-D-glucan glucohydrolase) activity. Glucoamylases catalyze the release of glucose from the non-reducing ends of starch. Glucose may then be used as an end product or used as a precursor to be converted to other commercially important end products, such as fructose, ethanol, ascorbic acid (ASA) intermediates and/or 1,3-propanediol.
Therefore, glucoamylases, which are involved in the conversion of starch to sugar are extremely important industrial enzymes. Glucoamylases may be obtained from bacteria, plants and fungi. However, preferred glucoamylases are derived from fungal strains. Examples of fungal glucoamylases include those obtained from strains of Aspergillus, Rhizopus, Humicola and Mucor (See, WO 92/00381 and WO 00/04136).
Various glucoamylases have been commercialized, including Aspergillus niger glucoamylase (e.g., trade name OPTIDEX L-400® from Genencor International Inc. and trade name AMG from Novo Nordisk) and Rhizopus (e.g., trade name CU.CONC from Shin Nihon Chemicals, Japan and trade name GLUCZYME from Amano Pharmaceuticals, Japan).
Certain thermophilic and mesophilic fungi, and particularly strains of Humicola grisea and Aspergillus awamori, produce an enzyme having both glucoamylase activity and the ability to hydrolyze raw starch. These glucoamylases are referred to as granular starch hydrolyzing enzymes (GSHE) and are also known in the art as raw starch hydrolyzing (RSH) enzymes. Additionally, while these enzymes will hydrolyze thinned starch hydrolyzate to glucose in a manner similar to other known glucoamylases, they frequently have a pH optimum in the range of 5.0 to 7.0 as compared to a pH optimum of less than 5.0 for widely used glucoamylase preparations (See, Tosi et al., (1993) Can. J. Microbiol., 39: 846-851).
Since glucoamylases and in particular granular starch hydrolyzing enzymes are important enzymes used industrially for the conversion of starch to glucose, processes providing increased expression and production of these enzymes are highly desirable. In addition, granular starch hydrolyzing enzymes having improved characteristics, such as increased specific activity, different pH ranges, and/or different levels of glycosylation may be particularly advantageous in industrial processes.
It is a primary object of this invention to provide a filamentous fungal strain transformed with a heterologous polynucleotide encoding a granular starch hydrolyzing enzyme, especially a Trichoderma strain and more specifically a strain of T. reesei, which expresses and secretes granular starch hydrolyzing enzyme into its culture medium.
In one aspect, the invention provides a recombinant Trichoderma cell comprising a heterologous polynucleotide encoding a granular starch hydrolyzing enzyme (GSHE). In one embodiment, the recombinant Trichoderma cell includes a heterologous polynucleotide encoding a GSHE having at least 80% sequence identity to the sequence set forth in SEQ ID NO: 3 or the sequence set forth in SEQ ID NO: 6. In a second embodiment, the recombinant Trichoderma cell includes a heterologous polynucleotide encoding a GSHE having at least 90% sequence identity to the sequence set forth in SEQ ID NO: 3 or the sequence set forth in SEQ ID NO: 6. In a third embodiment, the recombinant Trichoderma cell includes a heterologous polynucleotide encoding a GSHE having at least 95% sequence identity to the sequence set forth in SEQ ID NO: 3 or the sequence set forth in SEQ ID NO: 6. In a fourth embodiment, the recombinant Trichoderma cell includes a heterologous polynucleotide encoding a GSHE having the sequence set forth in SEQ ID NO: 3 or the sequence set forth in SEQ ID NO: 6. In another embodiment, the recombinant Trichoderma cell includes a heterologous polynucleotide encoding a GSHE wherein the polynucleotide has at least 90% sequence identity with the sequence set forth in SEQ ID NO: 1 or the sequence set forth in SEQ ID NO: 4. In another embodiment, the recombinant Trichoderma cell includes a heterologous polynucleotide encoding a GSHE wherein the polynucleotide has the sequence set forth in SEQ ID NO: 1 or the sequence set forth in SEQ ID NO: 4. In a preferred embodiment, the recombinant Trichoderma cell is a T. reesei cell. In certain embodiments of this aspect the heterologous polynucleotide encodes a GSHE that is expressed at a level of greater than 1 g/L.
In a second aspect, the invention provides methods for producing a recombinantly expressed granular starch hydrolyzing enzyme (GSHE) in a filamentous fungal cell which comprises cultivating in a suitable culture medium a filamentous fungal host cell transformed with a DNA construct comprising a promoter having transcriptional activity in the filamentous fungal host cell operably linked to a heterologous polynucleotide encoding a GSHE wherein said GSHE is expressed in the transformed fungal cell, and recovering the expressed GSHE. In some embodiments, the filamentous fungal host cell is selected from the group consisting of Aspergillus, Fusarium, Penicillium and Trichoderma. In further preferred embodiments the fungal host cell is a Trichoderma cell, particularly a T. reesei cell. In other embodiments, the fungal host cell is an Aspergillus cell, particularly an A. awamori, A. niger or A. oryzae cell. In another embodiment, the promoter is derived from a gene of the filamentous fungal host. In a further embodiment, the polynucleotide encoding the GSHE is derived from a strain of Humicola grisea or a strain of Aspergillus awamori. In yet another embodiment, the heterologous GSHE produced by the host fungal cell has at least 80% sequence identity with the polypeptide sequence of SEQ ID NO: 3 or with the polypeptide sequence of SEQ ID NO: 6. In other embodiments, the heterologous GSHE produced by the host fungal cell has at least 95% sequence identity with the polypeptide sequence of SEQ ID NO: 3 or with the polypeptide sequence of SEQ ID NO: 6. In further embodiments, the polynucleotide sequence encoding the GSHE has at least 90% sequence identity with the sequence of SEQ ID NO: 1 or SEQ ID NO: 4. In further embodiments, the recombinantly expressed GSHE is encoded by the polynucleotide of SEQ ID NO: 1 or the polynucleotide SEQ ID NO: 4. In another embodiment, the level of glycosylation of the recombinantly expressed GSHE is different from the level of glycosylation of the corresponding native GSHE. In some embodiments, the level of glycosylation of the recombinantly expressed GSHE is less than the level of glycosylation of the corresponding native GSHE. A further embodiment provides enzymatic compositions comprising the GSHE produced according to the method.
In a third aspect, the invention provides a vector comprising a promoter, a granular starch hydrolyzing enzyme (GSHE) signal sequence, a polynucleotide encoding a mature GSHE and a terminator, wherein the promoter and terminator are each functional in a Trichoderma cell and are derived from a filamentous fungus and the polynucleotide encoding the GSHE is derived from Humicola grisea or Aspergillus awamori. In one embodiment, the vector is the plasmid pTrex3g_N13. In a second embodiment the invention provides a Trichoderma host cell transformed with the vector.
In a fourth aspect, the invention provides a granular starch hydrolyzing enzyme (GSHE) fraction obtained from a substantially pure culture of Trichoderma reesei, wherein the Trichoderma reesei comprises a heterologous polynucleotide encoding a GSHE. In one embodiment, the GSHE enzyme fraction includes a GSHE having at least 80% amino acid sequence identity with SEQ ID NO: 3 or a GSHE having at least 80% amino acid sequence identity with SEQ ID NO: 6.
In a fifth aspect, the invention provides, methods for producing a granular starch hydrolyzing enzyme (GSHE) in a Trichoderma reesei host cell comprising transforming a Trichoderma reesei host cell with a DNA construct, wherein the DNA construct comprises a promoter showing transcriptional activity in Trichoderma reesei and which is operably linked to DNA encoding a heterologous GSHE and culturing the transformed Trichoderma reesei host cell under suitable culture conditions to allow production of the heterologous GSHE. In one embodiment, the DNA encoding the heterologous GSHE has at least 95% sequence identity with SEQ ID NO: 1 and in other embodiment the DNA encoding the heterologous GSHE has at least 95% sequence identity with SEQ ID NO: 4. In a second embodiment, the method further comprises recovering the GSHE enzyme. In another embodiment, the DNA sequence encoding the heterologous GSHE enzyme is derived from Humicola grisea or Aspergillus awamori. In some embodiments, the GSHE produced by the transformed T. reesei host cell has at least 80% amino acid sequence identity with SEQ ID NO: 3, and in other embodiments the GSHE produced by the transformed T. reesei host cell has at least 80% amino acid sequence identity with SEQ ID NO: 6. A further embodiment provides for the Trichoderma obtained according to the method.
In some aspects, the present invention relies on routine techniques and methods used in the field of genetic engineering and molecular biology. The following resources include descriptions of general methodology useful in accordance with the invention: Sambrook et al., M
Unless defined otherwise herein, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Singleton, et al., D
The invention will now be described in detail by way of reference only using the following definitions and examples. All patents and publications, including all sequences disclosed within such patents and publications, referred to herein are expressly incorporated by reference.
Numeric ranges are inclusive of the numbers defining the range.
Unless otherwise indicated, nucleic acids are written left to right in 5′ to 3′ orientation; amino acid sequences are written left to right in amino to carboxy orientation, respectively.
The headings provided herein are not limitations of the various aspects or embodiments of the invention which can be had by reference to the specification as a whole.
The term “glucoamylase” refers to the amyloglucosidase class of enzymes (e.g., EC.3.2.1.3, glucoamylase, 1,4-alpha-D-glucan glucohydrolase). These are exo-acting enzymes which release glucosyl residues from the non-reducing ends of amylose and amylopectin molecules. The enzyme also hydrolyzes alpha-1,6 and alpha-1,3 linkages although at much slower rates than alpha-1,4 linkages.
The term “granular starch hydrolyzing enzyme (GSHE)” as used herein specifically refers to a glucoprotein which has glucoamylase activity and has the ability to hydrolyze starch in granular form. A preferred GSHE is derived from Humicola grisea var. thermoidea. Another preferred GSHE is derived from Aspergillus awamori var. kawachi. In preferred embodiments, the GSHE is expressed in a Trichoderma strain, particularly a T. reesei strain. In particularly preferred embodiments, GSHE is expressed as an extracellular enzyme.
The term “glycosylation” refers to the post-transcriptional modification of a protein by the addition of carbohydrate moieties, wherein the carbohydrate is either N-linked or O-linked resulting in a glucoprotein. An N-linked carbohydrate moiety of a glycoprotein is attached by a glycosidic bond to the β-amide nitrogen of an asparagine residue. An O-linked carbohydrate is attached by a glycosidic bond to a protein through the hydroxy group of a serine or a threonine residue.
The term “recombinant” when used in reference to a cell, nucleic acid, protein or vector, indicates that the cell, nucleic acid, protein or vector, has been modified by the introduction of a heterologous nucleic acid or protein or the alteration of a native nucleic acid or protein, or that the cell is derived from a cell so modified. Thus, for example, recombinant cells express genes that are not found within the native (non-recombinant) form of the cell or express native genes that are otherwise abnormally expressed, under expressed or not expressed at all.
The terms “protein” and “polypeptide” are used interchangeably herein. The conventional one-letter or three-letter code for amino acid residues is used herein.
A “signal sequence” means a sequence of amino acids bound to the N-terminal portion of a protein which facilitates the secretion of the mature form of the protein outside the cell. The definition of a signal sequence is a functional one. The mature form of the extracellular protein lacks the signal sequence which is cleaved off during the secretion process.
The terms “recombinant GSHE”, “recombinantly expressed GSHE” and “recombinantly produced GSHE” refer to a mature GSHE protein sequence that is produced in a host cell from a heterologous polynucleotide. The symbol “r” may be used to denote “recombinant”. The protein sequence of a rGSHE excludes a signal sequence.
The terms “native GSHE” and “nGSHE” refer to a GSHE that is derived from a microbial host other than the fungal host for which recombinant GSHE expression is desired. In preferred embodiments, a native GSHE is derived from a Humicola grisea strain or an Aspergillus awamori strain.
A “gene” refers to a DNA segment that is involved in producing a polypeptide and includes regions preceding and following the coding regions as well as intervening sequences (introns) between individual coding segments (exons).
The term “nucleic acid” encompasses DNA, RNA, single stranded or double stranded and chemical modifications thereof. The terms “nucleic acid” and “polynucleotide” may be used interchangeably herein. Because the genetic code is degenerate, more than one codon may be used to encode a particular amino acid, and the present invention encompasses polynucleotides which encode a particular amino acid sequence.
A “vector” refers to a polynucleotide sequence designed to introduce nucleic acids into one or more cell types. Vectors include cloning vectors, expression vectors, shuttle vectors, plasmids, phage particles, cassettes and the like.
An “expression vector” as used herein means a DNA construct comprising a DNA sequence which is operably linked to a suitable control sequence capable of effecting expression of the DNA in a suitable host. Such control sequences may include a promoter to effect transcription, an optional operator sequence to control transcription, a sequence encoding suitable ribosome binding sites on the mRNA, enhancers and sequences which control termination of transcription and translation.
A “promoter” is a regulatory sequence that is involved in binding RNA polymerase to initiate transcription of a gene. The promoter may be an inducible promoter or a constitutive promoter. A preferred promoter used in the invention is Trichoderma reesei cbh1, which is an inducible promoter.
“Under transcriptional control” is a term well understood in the art that indicates that transcription of a polynucleotide sequence, usually a DNA sequence, depends on its being operably linked to an element which contributes to the initiation of, or promotes transcription.
“Under translational control” is a term well understood in the art that indicates a regulatory process which occurs after mRNA has been formed.
As used herein when describing proteins and genes that encode them, the term for the gene is not capitalized and is italicized, (e.g., the gene that encodes the Humicola grisea GSHE may be denoted as gla1). The term for the protein is generally not italicized and the first letter is capitalized, (e.g., the protein encoded by the gla1 gene may be denoted as Gla1).
The term “operably linked” refers to juxtaposition wherein the elements are in an arrangement allowing them to be functionally related. For example, a promoter is operably linked to a coding sequence if it controls the transcription of the sequence.
The term “selective marker” refers to a gene capable of expression in a host that allows for ease of selection of those hosts containing an introduced nucleic acid or vector. Examples of selectable markers include but are not limited to antimicrobials (e.g., hygromycin, bleomycin, or chloramphenicol) and/or genes that confer a metabolic advantage, such as a nutritional advantage on the host cell.
The term “derived” encompasses the terms “originated from”, “obtained” or “obtainable from”, and “isolated from”.
“Host strain” or “host cell” means a suitable host for an expression vector or DNA construct comprising a polynucleotide encoding a GSHE according to the invention. Specifically, host strains are preferably filamentous fungal cells. In a preferred embodiment of the invention, “host cell” means both the cells and protoplasts created from the cells of a filamentous fungal strain and particularly a Trichoderma sp. or an Aspergillus sp.
The term “filamentous fungi” refers to all filamentous forms of the subdivision Eumycotina (See, Alexopoulos, C. J. (1962), I
As used herein, the term “Trichoderma” or “Trichoderma sp.” refer to any fungal genus previously or currently classified as Trichoderma.
The term “culturing” refers to growing a population of microbial cells under suitable conditions in a liquid or solid medium.
The term “heterologous” with reference to a polynucleotide or protein refers to a polynucleotide or protein that does not naturally occur in a host cell. In some embodiments, the protein is a commercially important industrial protein. It is intended that the term encompass proteins that are encoded by naturally occurring genes, mutated genes, and/or synthetic genes. The term “homologous” with reference to a polynucleotide or protein refers to a polynucleotide or protein that occurs naturally in the host cell.
The terms “recovered”, “isolated”, and “separated” as used herein refer to a protein, cell, nucleic acid or amino acid that is removed from at least one component with which it is naturally associated.
As used herein, the terms “transformed”, “stably transformed” and “transgenic” used in reference to a cell means the cell has a non-native (e.g., heterologous) nucleic acid sequence integrated into its genome or as an episomal plasmid that is maintained through multiple generations.
As used herein, the term “expression” refers to the process by which a polypeptide is produced based on the nucleic acid sequence of a gene. The process includes both transcription and translation.
The term “introduced” in the context of inserting a nucleic acid sequence into a cell, means “transfection”, or “transformation” or “transduction” and includes reference to the incorporation of a nucleic acid sequence into a eukaryotic or prokaryotic cell wherein the nucleic acid sequence may be incorporated into the genome of the cell (e.g., chromosome, plasmid, plastid, or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (e.g., transfected mRNA).
As used herein the term “specific activity” means an enzyme unit defined as the number of moles of substrate converted to product by an enzyme preparation per unit time under specific conditions. Specific activity is expressed as units (U)/mg of protein.
As used herein the term “enzyme unit” refers to the amount of enzyme that converts 1 micromole of substrate per minute to the substrate product at optimum assay conditions. For example, in one embodiment, the term “glucoamylase activity unit” (GAU) is defined as the amount of enzyme required to produce 1 micromole of glucose per minute under assay conditions of, for example 40° C. and pH 5.0. In another embodiment, a granular starch hydrolyzing enzyme unit (GSHE U) is defined as being the amount of GSHE required to produce 1 g of glucose per minute from granular starch under assay conditions of, for example 25° C. at pH 5.0. In another embodiment a GSHE U is defined as being the amount of GSHE required to produce 1 mg of glucose per minute from granular starch under assay conditions, of 50° C. at pH 4.5.
As used herein the term “starch” refers to any material comprised of the complex polysaccharide carbohydrates of plants, comprised of amylose and amylopectin with the formula (C6H10O5)x, wherein X can be any number. In particular, the term refers to any plant-based material including but not limited to grains, grasses, tubers and roots and more specifically to the plants wheat, barley, corn, rye, rice, sorghum, brans, cassava, millet, potato, sweet potato, and tapioca.
The term “granular starch” refers to raw uncooked starch, e.g., granular starch that has not been subject to gelatinization.
The term “starch-liquefying enzyme” refers to an enzyme that effects the fluidization of granular starch. Exemplary starch liquefying enzymes include alpha amylases (e.g., E.C. 3.2.1.1).
The term “alpha-amylase (e.g., E.C. class 3.2.1.1)” refers to enzymes that catalyze the hydrolysis of alpha-1,4-glucosidic linkages. These enzymes have also been described as those effecting the exo or endohydrolysis of 1,4-α-D-glucosidic linkages in polysaccharides containing 1,4-α-linked D-glucose units. Another term used to describe these enzymes is “glycogenase”. Exemplary enzymes include alpha-1,4-glucan 4-glucanohydrase glucanohydrolase.
“ATCC” refers to American Type Culture Collection located at Manassas, Va. 20108 (ATCC; www.atcc.org).
“NRRL” refers to the Agricultural Research Service Culture Collection, National Center for Agricultural Utilization Research (and previously known as USDA Northern Regional Research Laboratory), Peoria, Ill.
“A”, “an” and “the” include plural references unless the context clearly dictates otherwise.
As used herein the term “comprising” and its cognates are used in their inclusive sense; that is, equivalent to the term “including” and its corresponding cognates.
The present invention provides host cells, which can express a heterologous polynucleotide encoding a GSHE. The host cell is preferably a filamentous fungal cell. In a preferred embodiment, the filamentous fungal host is a strain of Aspergillus sp, Trichoderma sp, Fusarium sp and Penicillium sp. Particularly preferred fungal host cells include A. nidulans, A. awamori, A. oryzae, A. aculeatus, A. niger, A. japonicus, T. reesei, T. viride, F. oxysporum, and F. solani. Aspergillus strains are disclosed in Ward et al. (1993) Appl. Microbiol. Biotechnol. 39:738-743 and Goedegebuur et al., (2002) Curr Gene 41:89-98. In a most preferred embodiment, the host is a strain of Trichoderma and particularly a strain of T. reesei. Strains of T. reesei are known and nonlimiting examples include ATCC No. 13631, ATCC No. 26921, ATCC No. 56764, ATCC No. 56765, ATCC No. 56767 and NRRL 15709. In some preferred embodiments, the host strain is a derivative of RL-P37. RL-P37 is disclosed in Sheir-Neiss et al. (1984) Appl. Microbiol. Biotechnology 20:46-53.
The host strain may be previously manipulated through genetic engineering. In some embodiments, various native genes of the fungal host cell have been inactivated. These genes include, for example genes encoding cellulolytic enzymes, such as endoglucanases (EG) and exocellobiohydrolases (CBH) (e.g. cbh1, cbh2, egl1 and egl3). U.S. Pat. No. 5,650,322 discloses derivative strains of RL-P37 having deletions in the cbh1 gene and the cbh2 gene.
B. Glucoamylases and Granular Starch Hydrolyzing Enzymes
In the context of this invention, a glucoamylase (E.C. 3.2.1.3) is an enzyme that removes successive glucose units from the non-reducing ends of starch. The enzyme can hydrolyze both linear and branched glucosidic linkages of starch, amylose and amylopectin. While glucoamylase may be derived from bacteria, plants and fungi, preferred glucoamylases encompassed by the present invention are derived from fungal strains. Glucoamylases secreted from fungi of the genera Aspergillus, Rhizopus, Humicola and Mucor have been derived from various fungal strains, including Aspergillus niger, Aspergillus awamori, Rhizopus niveus, Rhizopus oryzae, Mucor miehe, Humicola grisea, Aspergillus shirousami and Humicola (Thermomyces) laniginosa (See, Boel et al., (1984) EMBO J. 3:1097-1102; WO 92/00381; WO 00/04136; Chen et al., (1996) Prot. Eng. 9:499-505; Taylor et al., (1978) Carbohydrate Res. 61:301-308 and Jensen et al., (1988) Can. J. Microbiol. 34:218-223).
A particular group of enzymes having glucoamylase activity are known as granular starch hydrolyzing enzyme(s) GSHE (See e.g., Tosi et al., (1993) Can. J. Microbiol. 39:846-855). GSHEs not only have glucoamylase activity, but also are able to hydrolyze granular (raw) starch. GSHEs have been recovered from fungal cells such as Humicola sp., Aspergillus sp. and Rhizopus sp. A Rhizopus oryzae GSHE has been described in Ashikari et al., (1986) Agric. Biol. Chem. 50:957-964 and U.S. Pat. No. 4,863,864. A Humicola grisea GSHE is described by Allison et al., (1992) Curr. Genet. 21:225-229 and European Patent No. 171218. The gene encoding this enzyme is also known in the art as “gla1”. An Aspergillus awamori var. kawachi GSHE is described by Hayashida et al., (1989) Agric. Biol. Chem. 53:923-929. An Aspergillus shirousami GSHE is described by Shibuya et al., (1990) Agric. Biol. Chem. 54:1905-1914.
In one embodiment, a GSHE may be derived from a strain of Humicola grisea, particularly a strain of H. grisea var. thermoidea (See, U.S. Pat. No. 4,618,579).
In some preferred embodiments, the Humicola grisea GSHE is recovered from fungi including ATCC 16453, NRRL (USDA Northern Regional Research Laboratory, Peoria, Ill.) 15219, NRRL 15220, NRRL 15221, NRRL 15222, NRRL 15223, NRRL 15224 and NRRL 15225, as well as genetically altered strains thereof. These species produce enzymatic glucoamylase preparations that are immunologically the same (See, EP 0 171 218).
In one embodiment, a GSHE may be derived from a strain of Aspergillus awamori particularly a strain of A. awamori var. kawachi. (For example see, Hayashida, et al. (1989) Agric. Biol. Chem. 53:923-929).
In another embodiment, GSHEs exhibit a maximum pH activity within a pH range of 4 to 7.5 and also within the pH range of 5 to 7.5 and maximum activity in the temperature range of 50° C. to 60° C.
In another particularly preferred embodiment, the GSHE is a GSHE comprising an amino acid sequence having at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 93%, 95%, 97%, 98% and 99% sequence identity with the amino acid sequence set forth in SEQ ID NO:3. In another embodiment, the GSHE comprises an amino acid sequence having at least 80% sequence identity with SEQ ID NO:3. In a further embodiment, the GSHE comprises an amino acid sequence having at least 90% sequence identity to SEQ ID NO:3. The GSHE may also comprises an amino acid sequence having at least 95% sequence identity with SEQ ID NO:3. In a further embodiment, the GSHE comprises the amino acid sequence of SEQ ID NO:3.
In other embodiments, the GSHE comprising the amino acid sequence of SEQ ID NO:3 or an amino acid sequence having at least 80% sequence identity with SEQ ID NO:3 is encoded by a polynucleotide having at least 70%, 80%, 85%, 90%, 93%, 95%, 97%, 98% and 99% sequence identity to the sequence of SEQ ID NO:1. In a preferred embodiment, the GSHE having an amino acid sequence of SEQ ID NO:3 is encoded by a polynucleotide having at least 70%, 80%, 85%, 90%, 93%, 95%, 97%, 98% and 99% sequence identity with SEQ ID NO:1. In a particularly preferred embodiment, the nucleic acid sequence encoding the GSHE of SEQ ID NO:3 is the nucleic acid sequence of SEQ ID NO:1.
In another particularly preferred embodiment, the GSHE is a GSHE comprising an amino acid sequence having at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 93%, 95%, 97%, 98% and 99% sequence identity with the amino acid sequence set forth in SEQ ID NO:6. In another embodiment, the GSHE comprises an amino acid sequence having at least 80% sequence identity with SEQ ID NO:6. In a further embodiment, the GSHE comprises an amino acid sequence having at least 90% sequence identity with SEQ ID NO:6. The GSHE may also comprises an amino acid sequence having at least 95% sequence identity with SEQ ID NO:6. In a further embodiment, the GSHE comprises the sequence of SEQ ID NO:6.
In other embodiments, the GSHE enzyme comprising the amino acid sequence of SEQ ID NO:6 or an amino acid sequence having at least 80% sequence identity with SEQ ID NO:6 is encoded by a polynucleotide having at least 70%, 80%, 85%, 90%, 93%, 95%, 97%, 98% and 99% sequence identity with the sequence of SEQ ID NO:4. In a preferred embodiment, the GSHE having an amino acid sequence of SEQ ID NO:6 is encoded by a polynucleotide having at least 70%, 80%, 85%, 90%, 93%, 95%, 97%, 98% and 99% sequence identity to SEQ ID NO:3. In a particularly preferred embodiment, the nucleic acid sequence encoding the GSHE of SEQ ID NO:6 is the nucleic acid sequence of SEQ ID NO:4.
A polynucleotide or a polypeptide having a certain percent (e.g. 80%, 85%, 90%, 95%, or 99%) of sequence identity with another sequence means that, when aligned, that percentage of bases or amino acid residues are the same in comparing the two sequences. This alignment and the percent homology or identity can be determined using any suitable software program known in the art, for example those described in C
One skilled in the art will recognize that sequences encompassed by the invention are also defined by the ability to hybridize under stringent hybridization conditions with the exemplified GSHE sequences (e.g., SEQ ID NO:1 or SEQ ID NO:4). A nucleic acid is hybridizable to another nucleic acid sequence when a single stranded form of the nucleic acid can anneal to the other nucleic acid under appropriate conditions of temperature and solution ionic strength. Hybridization and washing conditions are well known in the art (See, e.g., Sambrook (1989) supra, particularly chapters 9 and 11). In some embodiments, stringent conditions correspond to a Tm of 65° C. and 0.1×SSC, 0.1% SDS.
In some embodiments of the present invention, a GSHE is produced as an extracellular enzyme by a filamentous fungal cell and particularly by a Trichoderma host that has been genetically engineered to comprise a heterologous polynucleotide encoding a GSHE derived from a Humicola sp. In preferred embodiments, the GSHE is derived from a strain of Humicola grisea, and in some particularly preferred embodiments, the GSHE is derived from a strain of Humicola grisea var. thermoidea.
In one embodiment encompassed by the invention, the GSHE produced by the Trichoderma host (rGSHE) has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 93%, 95%, 97%, 98% or 99% sequence identity with the amino acid sequence set forth in SEQ ID NO:3. In another embodiment, a Trichoderma host, is transformed with a heterologous polynucleotide encoding a GSHE having at least 80% sequence identity with SEQ ID NO:3. In a further embodiment, a Trichoderma host, is transformed with a heterologous polynucleotide encoding a GSHE having at least 90% sequence identity with SEQ ID NO:3. In another embodiment, a Trichoderma host, is transformed with a heterologous polynucleotide encoding a GSHE having at least 95% sequence identity to SEQ ID NO:3. In other embodiments, the polynucleotide encoding the GSHE has at least 80% sequence identity with SEQ ID NO:1 and preferably at least 95% sequence identity with SEQ ID NO:1. In a particularly preferred embodiment, the rGSHE is expressed in a Trichoderma reesei strain and has at least 80% sequence identity with the amino acid sequence of SEQ ID NO:3.
In another preferred embodiment of the invention, the GSHE is produced as an extracellular enzyme by a filamentous fungal cell and particularly by a Trichoderma host that has been genetically engineered to comprise a polynucleotide encoding a GSHE derived from Aspergillus sp. In some embodiments, the GSHE derived from a strain of Aspergillus awamori, and in some particularly preferred embodiments, the GSHE is derived from a strain of Aspergillus awamori var. kawachi.
In one embodiment, the GSHE produced by the Trichoderma host (rGSHE) has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 93%, 95%, 97%, 98% or 99% sequence identity with the amino acid sequence set forth in SEQ ID NO:6. In another embodiment, a Trichoderma host is transformed with a heterologous polynucleotide encoding a GSHE having at least 80% sequence identity with SEQ ID NO:6. In a further embodiment, a Trichoderma host is transformed with a heterologous polynucleotide encoding a GSHE having at least 90% sequence identity to SEQ ID NO:6. In another embodiment, a Trichoderma host is be transformed with a heterologous polynucleotide encoding a GSHE having at least 95% sequence identity with SEQ ID NO:6. In other embodiments, the polynucleotide encoding the GSHE will have at least 90% sequence identity with SEQ ID NO:4 and preferably at least 95% sequence identity with SEQ ID NO:4. In a particularly preferred embodiment, the GSHE is expressed in a Trichoderma reesei strain and has at least 80% sequence identity with the sequence of SEQ ID NO:6.
In some embodiments, the level of glycosylation of a recombinantly expressed GSHE is different than the level of glycosylation of the corresponding native GSHE (e.g., GSHE which was originally derived from Humicola grisea or Aspergillus awamori has a different level of glycosylation than the level of glycosylation of the produced recombinant GSHE). In one embodiment, the level of glycosylation is different even if the rGSHE has at least 80% amino acid sequence identity to the native GSHE derived from Humicola grisea or Aspergillus awamori. More specifically, in some embodiments, a rGSHE expressed in Trichoderma and particularly a strain of T. reesei has a different level of glycosylation than the level of glycosylation from the corresponding nGSHE. In other embodiments, the level of glycosylation is higher, while in other embodiments the level of glycosylation is lower.
In one embodiment, the level of glycosylation of the recombinantly expressed GSHE is lower than the level of a corresponding native GSHE. For example, the level of glycosylation for rGSHE may be at least 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45% 50%, 55%, 60%, or 65% less than the level of glycosylation of the corresponding nGSHE. In some embodiments, the level of glycosylation in a rGSHE according to the invention is at least 25% less than the level of glycosylation of a corresponding nGSHE. In other embodiments, the level of glycosylation of rGSHE expressed by a host may be at least 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40% 50%, 60% 70%, 80%, 100%, 125%, 150%, 175%, 200%, 225% or 250% greater than the level of a corresponding native form of GSHE. In some embodiments, the level of glycosylation of rGSHE expressed by a host is at least 100% greater that the level of nGSHE.
In another embodiment, the recombinantly produced GSHE encompassed by the invention has greater stability at lower pH levels than a corresponding native GSHE at optimum temperature levels. More specifically, in some embodiments, a rGSHE expressed in Trichoderma, which was originally derived from Humicola grisea var. thermoidea, has greater stability at pH levels of 3.5 to 4.0 compared to a corresponding native GSHE at temperatures of 45-55° C. For example, in one embodiment, at a pH level about 3.5 the stability of rGSHE, and particularly Humicola grisea var. thermoidea GSHE expressed in Trichoderma reesei, is more than double the level of stability of nGSHE from Humicola grisea var. thermoidea.
C. Vectors
According to the invention, a DNA construct comprising nucleic acid encoding a GSHE encompassed by the invention is constructed to transfer GSHE into a host cell. Thus, GSHE which can be expressed in enzyme form may be introduced into a host cell using a vector, particularly an expression vector which comprises regulatory sequences operably linked to a GSHE coding sequence.
The vector may be any vector which when introduced into a fungal host cell is integrated into the host cell genome and is replicated. Reference is made to the Fungal Genetics Stock Center Catalogue of Strains (FGSC, <www.fgsc.net>) for a list of vectors. Additional examples of suitable expression and/or integration vectors are provided in Sambrook et al., (1989) supra, and Ausubel (1987) supra, and van den Hondel et al. (1991) in Bennett and Lasure (Eds.) M
In preferred embodiments, nucleic acid encoding a GSHE encompassed by the invention is operably linked to a suitable promoter, which shows transcriptional activity in the fungal host cell. The promoter may be derived from genes encoding proteins either homologous or heterologous to the host cell. Preferably, the promoter is useful in a Trichoderma host. Suitable nonlimiting examples of promoters include cbh1, cbh2, egl1, egl2. In one embodiment, the promoter is one that is native to the host cell. For example, when T. reesei is the host, the promoter is a native T. reesei promoter. In a preferred embodiment, the promoter is T. reesei cbh1, which is an inducible promoter and has been deposited in GenBank under Accession No. D86235. An “inducible promoter” is a promoter that is active under environmental or developmental regulation. In another embodiment, the promoter is one that is heterologous to the fungal host cell. Other examples of useful promoters include promoters from A. awamori and A. niger glucoamylase genes (See, Nunberg et al., (1984) Mol. Cell. Biol. 4:2306-2315 and Boel et al., (1984) EMBO J. 3:1581-1585). Also, the promoters of the T. reesei xln1 gene and the cellobiohydrolase 1 gene may be useful (EPA 137280A1).
In some preferred embodiments, the GSHE coding sequence is operably linked to a signal sequence. The DNA encoding the signal sequence is preferably that which is naturally associated with the GSHE gene to be expressed. Preferably, the signal sequence is en coded by a Humicola grisea or Aspergillus awamori gene which encodes a GSHE. More preferably the signal sequence has at least 90%, at least 95%, at least 97%, and at least 99% sequence identity to the signal sequence of depicted in
In some embodiments, the expression vector also includes a termination sequence. In one embodiment, the termination sequence and the promoter sequence are derived from the same source. In another embodiment, the termination sequence is homologous to the host cell. A particularly suitable terminator sequence is cbh1 derived from a Trichoderma strain and particularly T. reesei. Other useful fungal terminators include the terminator from A. niger or A. awamori glucoamylase gene (Nunberg et al. (1984) supra, and Boel et al., (1984) supra).
In some embodiments, an expression vector includes a selectable marker. Examples of preferred selectable markers include ones which confer antimicrobial resistance (e.g., hygromycin and phleomycin). Nutritional selective markers also find use in the present invention including those markers known in the art as amdS argB and pyr4. Markers useful in vector systems for transformation of Trichoderma are known in the art (See, e.g., Finkelstein, chapter 6 in B
An expression vector comprising a DNA construct with a polynucleotide encoding a GSHE may be any vector which is capable of replicating autonomously in a given fungal host organism or of integrating into the DNA of the host. In some embodiments, the expression vector is a plasmid. In preferred embodiments, two types of expression vectors for obtaining expression of genes are contemplated.
The first expression vector comprises DNA sequences in which the promoter, GSHE-coding region, and terminator all originate from the gene to be expressed. In some embodiments, gene truncation is obtained by deleting undesired DNA sequences (e.g., DNA encoding unwanted domains) to leave the domain to be expressed under control of its own transcriptional and translational regulatory sequences.
The second type of expression vector is preassembled and contains sequences required for high-level transcription and a selectable marker. In some embodiments, the coding region for a GSHE gene or part thereof is inserted into this general-purpose expression vector such that it is under the transcriptional control of the expression construct promoter and terminator sequences. In some embodiments, genes or part thereof are inserted downstream of a strong promoter, such as the strong cbh1 promoter.
Methods used to ligate the DNA construct comprising a polynucleotide encoding a GSHE, a promoter, a terminator and other sequences and to insert them into a suitable vector are well known in the art. Linking is generally accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide linkers are used in accordance with conventional practice. (See, Sambrook (1989) supra, and Bennett and Lasure, M
Where it is desired to obtain a fungal host cell having one or more inactivated genes known methods may be used (e.g. methods disclosed in U.S. Pat. No. 5,246,853, U.S. Pat. No. 5,475,101 and WO92/06209). Gene inactivation may be accomplished by complete or partial deletion, by insertional inactivation or by any other means which renders a gene nonfunctional for its intended purpose (such that the gene is prevented from expression of a functional protein). Any gene from a Trichoderma sp or other filamentous fungal host, which has been cloned can be deleted, for example cbh1, cbh2, egl1 and egl2 genes. In some embodiments, gene deletion may be accomplished by inserting a form of the desired gene to be inactivated into a plasmid by methods known in the art. The deletion plasmid is then cut at an appropriate restriction enzyme site(s), internal to the desired gene coding region, and the gene coding sequence or part thereof is replaced with a selectable marker. Flanking DNA sequences from the locus of the gene to be deleted (preferably between about 0.5 to 2.0 kb) remain on either side of the marker gene. An appropriate deletion plasmid will generally have unique restriction enzyme sites present therein to enable the fragment containing the deleted gene, including the flanking DNA sequences and the selectable markers gene to be removed as a single linear piece.
D. Transformation of Host Cells
Introduction of a DNA construct or vector into a host cell includes techniques such as transformation; electroporation; nuclear microinjection; transduction; transfection, (e.g., lipofection mediated and DEAE-Dextrin mediated transfection); incubation with calcium phosphate DNA precipitate; high velocity bombardment with DNA-coated microprojectiles; and protoplast fusion. General transformation techniques are known in the art (See, e.g., Ausubel et al., (1987), supra, chapter 9; and Sambrook (1989) supra, and Campbell et al., (1989) Curr. Genet. 16:53-56). The expression of heterologous protein in Trichoderma is described in U.S. Pat. No. 6,022,725; U.S. Pat. No. 6,268,328; Harkki et al. (1991); Enzyme Microb. Technol. 13:227-233; Harkki et al., (1989) Bio Technol. 7:596-603; EP 244,234; EP 215,594; and Nevalainen et al., “The Molecular Biology of Trichoderma and its Application to the Expression of Both Homologous and Heterologous Genes”, in M
Preferably, genetically stable transformants are constructed with vector systems whereby the nucleic acid encoding GSHE is stably integrated into a host strain chromosome. Transformants are then purified by known techniques.
In one nonlimiting example, stable transformants including an amdS marker are distinguished from unstable transformants by their faster growth rate and the formation of circular colonies with a smooth, rather than ragged outline on solid culture medium containing acetamide. Additionally, in some cases a further test of stability is conducted by growing the transformants on solid non-selective medium (i.e., medium that lacks acetamide), harvesting spores from this culture medium and determining the percentage of these spores which subsequently germinate and grow on selective medium containing acetamide. Alternatively, other methods known in the art may be used to select transformants.
In one specific embodiment, the preparation of Trichoderma sp. for transformation involves the preparation of protoplasts from fungal mycelia. (See, Campbell et al., (1989) Curr. Genet. 16:53-56). In some embodiments, the mycelia are obtained from germinated vegetative spores. The mycelia are treated with an enzyme that digests the cell wall resulting in protoplasts. The protoplasts are then protected by the presence of an osmotic stabilizer in the suspending medium. These stabilizers include sorbitol, mannitol, potassium chloride, magnesium sulfate and the like. Usually the concentration of these stabilizers varies between 0.8 M and 1.2 M. It is preferable to use about a 1.2 M solution of sorbitol in the suspension medium.
Uptake of DNA into the host Trichoderma sp. strain is dependent upon the calcium ion concentration. Generally, between about 10 mM CaCl2 and 50 mM CaCl2 is used in an uptake solution. Besides the need for the calcium ion in the uptake solution, other compounds generally included are a buffering system such as TE buffer (10 Mm Tris, pH 7.4; 1 mM EDTA) or 10 mM MOPS, pH 6.0 buffer (morpholinepropanesulfonic acid) and polyethylene glycol (PEG). It is believed that the polyethylene glycol acts to fuse the cell membranes, thus permitting the contents of the medium to be delivered into the cytoplasm of the Trichoderma sp. strain and the plasmid DNA is transferred to the nucleus. This fusion frequently leaves multiple copies of the plasmid DNA integrated into the host chromosome.
Usually a suspension containing the Trichoderma sp. protoplasts or cells that have been subjected to a permeability treatment at a density of 105 to 107/mL, preferably 2×106/mL are used in transformation. A volume of 100 μL of these protoplasts or cells in an appropriate solution (e.g., 1.2 M sorbitol; 50 mM CaCl2) are mixed with the desired DNA. Generally a high concentration of PEG is added to the uptake solution. From 0.1 to 1 volume of 25% PEG 4000 can be added to the protoplast suspension. However, it is preferable to add about 0.25 volumes to the protoplast suspension. Additives such as dimethyl sulfoxide, heparin, spermidine, potassium chloride and the like may also be added to the uptake solution and aid in transformation. Similar procedures are available for other fungal host cells. (See, e.g., U.S. Pat. Nos. 6,022,725 and 6,268,328, both of which are incorporated by reference).
Generally, the mixture is then incubated at approximately 0° C. for a period of between 10 to 30 minutes. Additional PEG is then added to the mixture to further enhance the uptake of the desired gene or DNA sequence. The 25% PEG 4000 is generally added in volumes of 5 to 15 times the volume of the transformation mixture; however, greater and lesser volumes may be suitable. The 25% PEG 4000 is preferably about 10 times the volume of the transformation mixture. After the PEG is added, the transformation mixture is then incubated either at room temperature or on ice before the addition of a sorbitol and CaCl2 solution. The protoplast suspension is then further added to molten aliquots of a growth medium. This growth medium permits the growth of transformants only.
E. Cell Culture
Generally, cells are cultured in a standard medium containing physiological salts and nutrients (See, e.g., Pourquie, J. et al., B
Culture conditions are also standard, (e.g., cultures are incubated at approximately 28° C. in appropriate medium in shake cultures or fermenters until desired levels of GSHE expression are achieved). Preferred culture conditions for a given filamentous fungus are known in the art and may be found in the scientific literature and/or from the source of the fungi such as the American Type Culture Collection and Fungal Genetics Stock Center.
After fungal growth has been established, the cells are exposed to conditions effective to cause or permit the expression of a GSHE and particularly a GSHE as defined herein. In cases where a GSHE coding sequence is under the control of an inducible promoter, the inducing agent (e.g., a sugar, metal salt or antimicrobial), is added to the medium at a concentration effective to induce GSHE expression.
F. Identification of GSHE Activity
In some embodiments, in order to evaluate the expression of a GSHE by a cell line that has been transformed with a heterologous polynucleotide encoding a GSHE encompassed by the invention, assays are carried out at the protein level, the RNA level and/or by use of functional bioassays particular to glucoamylase activity and/or production.
In general, assays employed to analyze the expression of a GSHE include Northern blotting, dot blotting (DNA or RNA analysis), RT-PCR (reverse transcriptase polymerase chain reaction), or in situ hybridization, using an appropriately labeled probe (based on the nucleic acid coding sequence) and conventional Southern blotting and autoradiography.
In addition, the production and/or expression of a GSHE may be measured in a sample directly, for example, by assays directly measuring reducing sugars such as glucose in the culture medium and by assays for measuring glucoamylase activity, expression and/or production. Substrates useful for assaying GSHE activity include granular starch substrates, including but not limited to corn, wheat, rice, barley, tapioca, potato, and cassava. For example, in some embodiments, glucose concentration is determined by any convenient method such as by using glucose reagent kit No 15-UV (Sigma Chemical Co.) or an instrument such as Technicon Autoanalyzer. In addition glucose oxidase kits and glucose hexose kits are commercially available from Instrumentation Lab. (Lexington, Mass.). Glucoamylase activity may be assayed by the 3,5-dinitrosalicylic acid (DNS) method (See, Goto et al., (1994) Biosci. Biotechnol. Biochem. 58:49-54). In one nonlimiting example, a rGSHE has the ability to hydrolyze granular starch in a 15% starch solids suspension in water to a solution of saccharides of at least 90%, 95% and/or 97% wt glucose on a dry substance basis.
In some embodiments of the invention, the GSHE expressed by a recombinant Trichoderma host is greater than 0.5 gram protein per liter (g/L) of culture medium. In some embodiments, the amount of GSHE expressed by a recombinant Trichoderma host is greater than 1 g/L of culture media. In some embodiments, the amount of GSHE expressed by a recombinant Trichoderma host is greater than 2 g/L of culture media. In other embodiments, the amount of GSHE expressed by a recombinant Trichoderma host is greater than 5 g/L of culture media. Yet in other embodiments, the amount of GSHE expressed by a recombinant Trichoderma host is greater than 10 g/L of culture medium. The amount of expressed GSHE in some instances is greater than 20 g/L, greater than 25 g/L, greater than 30 g/L and greater than 50 g/L of culture media.
In additional embodiments, protein expression, is evaluated by immunological methods, such as immunohistochemical staining of cells, tissue sections or immunoassay of tissue culture medium, (e.g., by Western blot or ELISA). Such immunoassays can be used to qualitatively and quantitatively evaluate expression of a GSHE. The details of such methods are known to those of skill in the art and many reagents for practicing such methods are commercially available. Exemplary assays include ELISA, competitive immunoassays, radioimmunoassays, Western blot, immunofluorescent assays and the like. In general, commercially available antibodies and/or kits may be used for the quantitative immunoassay of the expression level of a GSHE.
G. Methods for Purifying GSHE
In general, a GSHE produced in cell culture is secreted into the medium and may be purified or isolated, (e.g., by removing unwanted components from the cell culture medium). In some cases, a GSHE is produced in a cellular form, necessitating recovery from a cell lysate. In such cases, the enzyme is purified from the cells in which it was produced using techniques routinely employed by those of skill in the art. Examples of these techniques include, but are not limited to, affinity chromatography (Tilbeurgh et al., (1984) FEBS Lett. 16:215), ion-exchange chromatographic methods (Goyal et al., (1991) Biores. Technol. 36:37; Fliess et al., (1983) Eur. J. Appl. Microbiol. Biotechnol. 17:314; Bhikhabhai et al., (1984) J. Appl. Biochem. 6:336; and Ellouz et al., (1987) Chromatography 396:307), including ion-exchange using materials with high resolution power (Medve et al., (1998) J. Chromatography A 808:153), hydrophobic interaction chromatography (See, Tomaz and Queiroz, (1999) J. Chromatography A 865:123; two-phase partitioning (See, Brumbauer, et al., (1999) Bioseparation 7:287); ethanol precipitation; reverse phase HPLC, chromatography on silica or on a cation-exchange resin such as DEAE, chromatofocusing, SDS-PAGE, ammonium sulfate precipitation, and gel filtration (e.g., Sephadex G-75). The degree of purification desired will vary depending on the use of the GSHE. In some embodiments of the present invention, purification will not be necessary.
H. Industrial Uses of the rGSHE—Fermentations
In some embodiments of the present invention, fungal cells expressing a heterologous GSHE are grown under batch or continuous fermentation conditions. A classical batch fermentation is a closed system, wherein the composition of the medium is set at the beginning of the fermentation and is not subject to artificial alterations during the fermentation. Thus, at the beginning of the fermentation the medium is inoculated with the desired organism(s). In this method, fermentation is permitted to occur without the addition of any components to the system. Typically, a batch fermentation qualifies as a “batch” with respect to the addition of the carbon source and attempts are often made at controlling factors such as pH and oxygen concentration. The metabolite and biomass compositions of the batch system change constantly up to the time the fermentation is stopped. Within batch cultures, cells progress through a static lag phase to a high growth log phase and finally to a stationary phase where growth rate is diminished or halted. If untreated, cells in the stationary phase eventually die. In general, cells in log phase are responsible for the bulk of production of end product.
A variation on the standard batch system is the “fed-batch fermentation” system, which also finds use with the present invention. In this variation of a typical batch system, the substrate is added in increments as the fermentation progresses. Fed-batch systems are useful when catabolite repression is apt to inhibit the metabolism of the cells and where it is desirable to have limited amounts of substrate in the medium. Measurement of the actual substrate concentration in fed-batch systems is difficult and is therefore estimated on the basis of the changes of measurable factors such as pH, dissolved oxygen and the partial pressure of waste gases such as CO2. Batch and fed-batch fermentations are common and well known in the art.
Continuous fermentation is an open system where a defined fermentation medium is added continuously to a bioreactor and an equal amount of conditioned medium is removed simultaneously for processing. Continuous fermentation generally maintains the cultures at a constant high density where cells are primarily in log phase growth.
Continuous fermentation allows for the modulation of one factor or any number of factors that affect cell growth and/or end product concentration. For example, in one embodiment, a limiting nutrient such as the carbon source or nitrogen source is maintained at a fixed rate an all other parameters are allowed to moderate. In other systems, a number of factors affecting growth can be altered continuously while the cell concentration, measured by media turbidity, is kept constant. Continuous systems strive to maintain steady state growth conditions. Thus, cell loss due to medium being drawn off must be balanced against the cell growth rate in the fermentation. Methods of modulating nutrients and growth factors for continuous fermentation processes as well as techniques for maximizing the rate of product formation are well known in the art of industrial microbiology.
There are a wide variety of industrial uses for the recombinant GSHE produced according to the invention. The GSHE is most useful in applications requiring granular starch hydrolysis to sugars, for example in the manufacture of glucose syrups and for grain processing in ethanol production.
The following examples are provided in order to demonstrate and further illustrate certain preferred embodiments and aspects of the present invention and are not to be construed as limiting the scope thereof. Indeed, it is contemplated that these teachings will find use in further optimizing the process systems described herein.
In the disclosure and experimental section which follows, the following abbreviations apply: wt % (weight percent); ° C. (degrees Centigrade); rpm (revolutions per minute); H2O (water); dH2O (deionized water); aa (amino acid); bp (base pair); kb (kilobase pair); kD (kilodaltons); g (grams); μg (micrograms); mg (milligrams); μL (microliters); ml and mL (milliliters); mm (millimeters); μm (micrometer); M (molar); mM (millimolar); μM (micromolar); U (units); V (volts); MW (molecular weight); sec (seconds); min(s) (minute/minutes); hr(s) (hour/hours); PAGE (polyacrylamide gel electrophoresis); DO (dissolved oxygen); phthalate buffer (sodium phthalate in water, 20 mM, pH 5.0); PBS (phosphate buffered saline [150 mM NaCl, 10 mM sodium phosphate buffer, pH 7.2]); SDS (sodium dodecyl sulfate); Tris (tris(hydroxymethyl)aminomethane); w/v (weight to volume); w/w (weight to weight); v/v (volume to volume); Genencor (Genencor International, Inc., Palo Alto, Calif.); and Shin Nihon (Shin Nihon, Japan).
Genomic DNA (SEQ ID NO:1) was extracted from frozen Scytalidium thermophilum (ATCC 16453, anamorph, H. grisea var. thermoidea) mycelia. The frozen mycelia were ground with dry ice in a coffee grinder and the DNA was extracted by the EasyDNA protocol (Invitrogen). An extra chloroform/phenol/isoamyl alcohol extraction was added to the standard protocol. PCR primers were designed, based on the NCBI database accession #M89475 sequence. The forward primer contained a motif for directional cloning into the pENTR/D vector (Invitrogen).
The sequence of the RSH003f primer was CAACATGCATACCTTCTCCAAGCTCCTC (SEQ ID NO. 7) and the sequence of the RSH004r primer was TTAACGCCACGAATCATTCA CCGTC (SEQ ID NO. 8).
The PCR product was cloned into pENTR/D, according to the Invitrogen Gateway system protocol. The vector was then transformed into chemically competent Top10 E. coli (Invitrogen) with kanamycin selection. Plasmid DNA from several clones was restriction digested to confirm the correct size insert. The gla1 insert was sequenced (Sequetech, Mountain View, Calif.) from several clones. Plasmid DNA from one clone, pENTR/D_N13, was added to the LR clonase reaction (Invitrogen Gateway system) with pTrex3g/amdS destination vector DNA. Recombination, in the LR clonase reaction, replaced the CmR and ccdB genes of the destination vector with the H. grisea gla1 from the pENTR/D vector. This recombination directionally inserted gla1 between the cbhI promoter and terminator of the destination vector. Recombination site sequences of 48 and 50 bp remained upstream and downstream, respectively, of gla1. An aliquot of the LR clonase reaction was transformed into chemically competent Top10 E. coli and grown overnight with carbenicillin selection. Plasmid DNA, from several clones, was digested with appropriate restriction enzymes to confirm the correct insert size. Plasmid DNA from clone, pTrex3g_N13 (see
The cassette was sequenced by Sequetech, Mountain View, Calif. and the DNA for GSHE is illustrated in
Approximately 2 cm2 of a plate of sporulated mycelia (grown on a PDA plate for 5 days at 30° C.) was inoculated into 50 ml of YEG (5 g/L yeast extract plus 20 g/L glucose) broth in a 250 ml, 4-baffle shake flask and incubated at 37° C. for 16-20 hours at 200 rpm. The mycelia were recovered by transferring the liquid volume into 50 ml conical tubes and spinning at 2500 rpm for 10 minutes. The supernatant was decanted. The mycelial pellet was transferred into a 250 ml, 0.22 micron CA Corning filter bottle containing 40 ml of filtered β-D-glucanase solution and incubated at 30° C., 200 rpm for 2 hrs to generate protoplasts for transformation.
Protoplasts were harvested by filtration through sterile miracloth into a 50 ml conical tube. They were pelleted by spinning at 2000 rpm for 5 minutes and aspirated. The protoplast pellet was washed once with 50 ml of 1.2 M sorbitol, spun down, aspirated, and washed with 25 ml of sorbitol/CaCl2. Protoplasts were counted and then pelleted at 2000 rpm for 5 min, the supernate was decanted, and the protoplast pellet was resuspended in an amount of sorbitol/CaCl2 sufficient to generate a protoplast concentration of 1.25×108 protoplasts per ml, generating a protoplast solution.
Aliquots of up to 20 μg of expression vector DNA (in a volume no greater than 20 μl) were placed into 15 ml conical tubes and the tubes were put on ice. Then 200 μl of the protoplast suspension was added along with 50 μl PEG solution to each transformation aliquot. The tubes were mixed gently and incubated on ice for 20 min. PEG solution (2 ml) was added to the transformation aliquot tubes, and these were incubated at room temperature for 5 minutes. Sorbitol/CaCl2 (4 ml) solution was added to the tubes (generating a total volume of 6.2 ml). The transformation mixture was divided into 3 aliquots each containing about 2 ml. An overlay mixture was created by adding each of these three aliquots to three tubes of melted top agar (kept molten by holding at 50° C.) and this overlay mixture was poured onto a transformation plate. The transformation plates were then incubated at 30° C. for four to seven days.
The transformation was performed with amdS selection. Acetamide/sorbitol plates and top agar were used for the transformation. Top agar was prepared by the same Sorbitol/acetamide agar recipe as the plates, except that low melting agarose was used in place of Noble agar. Transformants were purified by transfer of isolated colonies to fresh selective media containing acetamide (i.e., Sorbitol/acetamide agar, without sorbitol).
With reference to the examples the solutions were prepared as follows.
1) 40 ml β-D-glucanase solution was made up in 1.2M sorbitol and included 600 mg β-D-glucanase (InterSpex Products Inc., San Mateo, Calif.) and 400 mg MgSO4.7H2O.
2) 200 ml PEG mix contained 50 g PEG 4000 (BDH Laboratory Supplies Poole, England) and 1.47 g CaCl2.2H2O made up in dH2O.
3) Sorbitol/CaCl2 contained 1.2M sorbitol and 50 mM CaCl2.
4) Acetamide/sorbitol agar:
Part II—20 g Noble agar and 218 g sorbitol brought to volume (700 mls) with dH2O and autoclaved.
Part II was added to part I for a final volume of 1 L.
5) 1000× Salts—5 g FeSO4.7H2O, 1.6 g MnSO4.H2O, 1.4 g ZnSO4.7H2O, 1 g CoCl2.6H2O were combined and the volume was brought to 1 L with dH2O. The solution was filter sterilized.
In general, the fermentation protocol as described in Foreman et al. (Foreman et al. (2003) J. Biol. Chem. 278:31988-31997) was followed. More specifically, duplicate fermentations were run for each of the strains displayed in
Sample supernatants were run of 4-12% BIS-TRIS SDS-PAGE gels, under reducing conditions with MOPS (morpholinepropanesulfonic acid) SDS running buffer and LDS sample buffer. The results are provided in
Enzyme Activity
GSHE activity was determined as milligrams (mg) of reducing sugars released (measured as glucose equivalent) per minute (min) during an incubation of 5 ml of 10% granular cornstarch in a 0.1 M acetate buffer, pH 4.5, 50° C. with an aliquot of the enzyme preparation. One unit of GSHE is defined as 1.0 mg of reducing sugar released per min under the assay conditions.
Native GSHE (nGSHE) from Humicola grisea var. thermoidea and recombinant GSHE produced from T. reesei were purified by standard techniques using hydrophobic interaction chromatography using phenyl-sepharose (Amersham Biosciences, Piscataway, N.J.) followed by ion exchange chromatography using SP-sepharose (Amersham Biosciences, Piscataway, N.J.). The recombinant GSHE initially expressed by T. reesei clones included two protein peak fractions in about equal concentrations. These peaks were labeled rGSHE1 and rGSHE2. The two peaks differed in mass by 1500 D and by 0.3 pH units as measured by matrix assisted laser desorption and ionization (MALDI-TOF) on a voyageur mass spectrometer (Applied Biosystems, Foster City, Calif.) and an isoelectric focusing gel (SERVA Electrophoresis, GmbH, Heidelberg, Germany) according to manufacturer directions. Both rGSHE1 and rGSHE2 have the same specific activity as measured by the raw starch hydrolyzing assay and protein measurements using a MicroBCA protein assay kit (Pierce, Rockford, Ill.) and the percent solution extinction coefficient (A280 0.1%=1.963). After a period of time, measured at approximately 72 hours after initial rGSHE expression, only one form of rGSHE is represented (rGSHE3). (See Table 1).
The % carbohydrate (CHO) of the GSHEs was determined by acid hydrolysis using 4N trifluoroacetic acid at 100° C. for 5 hrs and measurements were made of the released reducing sugars using parahydroxybenzoic acid hydrazide.
When initially expressed, the glycosylation of rGSHE1 and rGSHE2 was 2.70% of the total carbohydrate. However, after 72 hours, the level of glycosylation of rGSHE3 found in the medium was 0.57% total CHO. The level of glycosylation of native GSHE was 1.12%.
A. pH Stability was Determined from pH 3 to 7
The collected samples of recombinantly produced GSHE as described above in example 3 and samples of native GSHE were diluted to equal protein concentrations with 20 mM acetate buffer at pH 4.5. Reactions were then run in 100 mM citrate/NaOH buffers at 50° C. for 30 minutes at pH levels 3 to 7.
1.0 ml of the reaction was then added to 5 ml of 10% corn starch (Cargill Foods, Minneapolis, Minn.) in 100 mM acetate, pH 4.5 in sample tubes. The tubes were shaken at 50° C. for 20 minutes. Then 0.5 ml 2.0% NaOH was added. Tubes were spun and 0.5 ml of the supernatant was assayed for reducing sugars using the Dinitro Salicylic acid (DNS) assay (Goto et al., (1994) supra).
The results of the assay are depicted in
Stability was also measured at pH 7.5 to 10.5 using the methods as described above. However, the buffer was 100 mM boric acid/NaOH buffer. As exhibited in
B. Profile of Activity as a Function of Temperature
Temperature stability was determined at pH 5.75. Using essentially the same procedures as described above for the pH stability studies, enzyme samples were diluted to equal protein concentrations in a 100 mM acetate buffer and then 1.0 ml of the diluted enzymes was exposed to a water bath temperature of 40° C., 50° C., 60° C. and 70° C. for 10 minutes and assayed as described above in the pH stability studies. The results are presented in Table 2.
The profile of activity as a function of temperature of the recombinantly produced GSHE is similar to that of the corresponding native GSHE.
c. Hydrolysis of Granular Corn Starch by nGSHE And rGSHE
Both Native GSHE from H. Grisea Var. Thermoidea (nGSHE) and recombinantly expressed H. grisea var. thermoidea (rGSHE) in Trichoderma reesei were diluted to equal protein concentrations in pH 4.5 acetate buffer. One ml of the dilution was added to a 10% corn starch (Cargill Foods, Minneapolis, Minn.) slurry in 20 mM pH 4.5 acetate buffer and shaken at 350 rpm at 50° C. At designated time intervals 100 μL of slurry was removed and added to 10 μL of 2% NaOH. The sample was spun and the supernatant was assayed for glucose (mg glucose/mg protein) using the glucose oxidase reagent in a Monarch clinical analyzer (Instrumentation Laboratory, Lexington, Mass.). As shown in
Genomic DNA was extracted from frozen mycelia of a strain of A. awamori var. kawachi according to the methods described in Example 1. The PCR primer sequences were designed based on the published sequence of the A. awamori var. kawachi glucoamylase GAI (Hayashida, et al. (1989) Agric. Biol. Chem. 53:923-929). This GAI is a GSHE. The following primers were used: the RSH10f primer having the sequence, CAC CAT GTC GTT CCG ATC TCT TCT C (SEQ ID NO:9), which includes the Gateway (Invitrogen) directional cloning motif CACC and the RSH11r primer having the sequence, CTA CCG CCA GGT GTC GGT CAC (SEQ ID NO:10).
The DNA sequence is provided in
The 2.16 kb PCR product was gel-purified (Gel Purification kit, Qiagen) and cloned into pENTR/D (Invitrogen), according to the Gateway system protocol. The vector was then transformed into chemically competent Top10 E. coli (Invitrogen) with kanamycin selection. Plasmid DNA from several clones was restriction digested to confirm the correct size insert. The GAI gene insert was sequenced (Sequetech, Mountain View, Calif.) from several clones (SEQ ID NO:4). Plasmid DNA from one clone, pENTR/D_Ak33xx#1, was added to the LR clonase reaction (Invitrogen Gateway system) with the pTrex3g/amdS destination vector DNA. Recombination, in the LR clonase reaction, replaced the CmR and ccdB genes of the destination vector with the A. kawachi GAI from the pENTR/D vector. This recombination directionally inserted GAI between the cbhI promoter and terminator of the destination vector. AttB recombination site sequences of 48 and 50 bp remained upstream and downstream, respectively, of the glucoamylase. Reference is made to
A Trichoderma reesei spore suspension was spread onto the center ˜6 cm diameter of an MABA transformation plate (150 μl of a 5×107-5×108 spore/ml suspension). The plate was then air dried in a biological hood. Stopping screens (BioRad 165-2336) and macrocarrier holders (BioRad 1652322) were soaked in 70% ethanol and air dried. DriRite desiccant was placed in small Petri dishes (6 cm Pyrex) and overlaid with Whatman filter paper. The macrocarrier holder containing the macrocarrier (BioRad 165-2335) was placed flatly on top of filter paper and the Petri dish lid replaced.
A tungsten particle suspension was prepared by adding 60 mg tungsten M-10 particles (microcarrier, 0.7 micron, Biorad #1652266) to an Eppendorf tube. One ml ethanol (100%) was added. The tungsten was vortexed in the ethanol solution and allowed to soak for 15 minutes. The Eppendorf tube was microfuged briefly at maximum speed to pellet the tungsten. The ethanol was decanted and washed three times with sterile distilled water. After the water wash was decanted the third time, the tungsten was resuspended in 1 ml of sterile 50% glycerol. The tungsten was prepared fresh every two weeks.
The transformation reaction was prepared by adding 25 μl of suspended tungsten to a 1.5 ml Eppendorf tube for each transformation. Subsequent additions were made in order, 0.5-5 μl DNA (0.2-1 μg/μl), 25 μl 2.5M CaCl2, 10 μl 0.1 M spermidine. The reaction was vortexed continuously for 5-10 minutes, keeping the tungsten suspended. The Eppendorf tube was then microfuged briefly and decanted. The tungsten pellet was washed with 200 μl of 70% ethanol, microfuged briefly to pellet and decanted. The pellet was washed with 200 μl of 100% ethanol, microfuged briefly to pellet, and decanted. The tungsten pellet was resuspended, by pipetting, in 24 μl 100% ethanol. The Eppendorf tube was placed in an ultrasonic water bath for 15 seconds and 8 μl aliquots were transferred onto the center of the desiccated macrocarriers. The macrocarriers were left to dry in the desiccated Petri dishes.
A He tank was turned on to 1500 psi. 1100 psi rupture discs (BioRad 165-2329) were used in the Model PDS-1000/He Biolistic Particle Delivery System (BioRad). When the tungsten solution was dry, a stopping screen and the macrocarrier holder were inserted into the PDS-1000. An MABA plate, containing the target T. reesei spores, was placed 6 cm below the stopping screen. A vacuum of 29 inches Hg was pulled on the chamber and held. The He Biolistic Particle Delivery System was fired. The chamber was vented and the MABA plate removed for incubation, 28° C. for 5-7 days.
With reference to Example 7 the were prepared as follows.
5 g
1 g
Expression of rGSHE (A. awamori var. kawachi GSHE expressed in T. reesei) was determined as described above for expression of H. grisea var. thermoidea in Examples 3 and 4. The level of expression was determined to be greater than 1 g/L (data not shown).
The present application is a divisional of U.S. patent application Ser. No. 11/960,259, filed Dec. 19, 2007, which is a divisional of U.S. patent application Ser. No. 11/633,309, filed Dec. 4, 2006, now U.S. Pat. No. 7,335,503, which is a Continuation of U.S. patent application Ser. No. 10/992,187, filed Nov. 18, 2004, now U.S. Pat. No. 7,262,041, which claims priority to U.S. Provisional Patent Appln. Ser. No. 60/524,279, filed Nov. 21, 2003; U.S. Provisional Patent Appln. No. 60/531,953, filed Dec. 22, 2003; and U.S. Provisional Patent Appln. No. 60/566,358, filed Apr. 28, 2004.
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| Number | Date | Country | |
|---|---|---|---|
| 20140179007 A1 | Jun 2014 | US |
| Number | Date | Country | |
|---|---|---|---|
| 60566358 | Apr 2004 | US | |
| 60531953 | Dec 2003 | US | |
| 60524279 | Nov 2003 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 11960259 | Dec 2007 | US |
| Child | 14097168 | US | |
| Parent | 11633309 | Dec 2006 | US |
| Child | 11960259 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 10992187 | Nov 2004 | US |
| Child | 11633309 | US |
