# Patent

## Title
Mutated truncated mt-pfkA gene for the synthesis of active shorter fragment of 6-phosphofructo-1-kinase

## Abstract

The invention deals with mutated truncated mt-pfkA gene encoding shorter fragment of 6-phosphofructo-1-kinase (PFK1), with no need for phosphorylation of the protein molecule for activation, that is not significantly inhibited by citric acid and/or its salts and ATP molecules. Active 49-52 kDa fragment encoded by mt-pfkA gene, retains positive regulatory properties of the native protein and is activated in the presence of specific activators, while citric acid and ATP, important metabolites that function as feed back inhibitors in higher organisms do not reduce its activity. The invention deals with the use of modified shorter fragment in biotechnological processes for fabricating primary and secondary metabolites.

## Background
This application is a national stage application under 35 U.S.C. 371 of international application no. PCT/SI2007/000007 filed 27 Feb. 2007, and claims priority to Slovenian Application No. P-200600107 filed 26 Apr. 2006, the disclosures of which are expressly incorporated herein by reference.
The subject of the invention is mutated truncated mt-pfkA gene encoding the synthesis of an active shorter fragment of 6-phosphofructo-1-kinase (PFK1), with no posttranslational modification needed to induce the activity. The subject of the invention is the use of mutated truncated gene and its protein product for enhancing the rate of cell biomass synthesis and excretion of extracellular enzymes, as well as increasing the productivity of primary and secondary metabolites.
The invention is in the field of microbial biotechnology and biochemistry.
At biotechnological processes a crucial determinant for the final price of the product is the velocity of the product formation. By optimising the processes the final goal is to change micro-organisms, as well as growth conditions to get higher amounts of substrate transformed into the final product per time unit.
In commercial micro-organisms that are capable of excreting specific biotechnological products with increased productivity and yield, anaplerotic reactions are of crucial importance. Such reactions lead to increased concentrations of tricarboxylic cycle (TCA) intermediates in the cells, which are precursors for a number of biosynthetic pathways, since TCA cycle presents the crucial link between catabolic and anabolic reactions in the cells. By increasing the level of TCA cycle intermediates due to increased anaplerotic reactions, the synthesis of the key cellular building blocks, such as lipids, amino acids, porfirins etc. is enhanced, and consequently the rate of synthesis of primary and secondary metabolites of biotechnological value increased.
Several specific metabolic reactions belong to anaplerotic reactions, however uninterrupted metabolic flow through glycolysis seems to be of utmost importance. The enzyme with the key role in regulating glycolysis is 6-phosphofructo-1-kinase (PFK1). In eukaryotic organisms the enzyme is regulated by the feed back mechanism, by citrate and ATP inhibition. In other words its activity decreases when citric acid level, as an important intermediate of TCA cycle and ATP, as the final product of oxidative phosphorylation, increase over a certain level (Voet and Voet, 1995). In fact negative regulation of the enzyme activity diminishes the effectiveness of anapletoric reactions and consequently reduces the rate of synthesis of the final products. A significant increase in the rate of product formation could be achieved by having undisturbed metabolic flow through glycolysis, which could be done by inserting a modified gene encoding PFK1 enzyme that would be resistant to citrate inhibition but sensitive to activation with specific effectors.
In past several attempts were described to increase metabolic flow through glycolysis with the final goal to stimulate the synthesis of the final products, however no success was recorded. In order to enhance the glycolysis, three genes coding for the key regulatory enzymes of the pathway were isolated from the fungus Aspergillus niger including the pfkA gene coding for 6-phosphofructo-1-kinase. The genes were re-introduced into A. niger strain in a higher copy number with the ultimate goal to increase the concentration of the key enzymes and increase the flow of metabolites through the glycolysis. However, the detailed analyses of the transformants have not confirmed the expected results. It was concluded that other complex regulatory mechanisms compensated increased concentration of the key enzymes (Ruijter et al., 1996). In another attempt to improve the properties of PFK1, Aspergillus niger cells were subjected to mutations in order to make the enzyme resistant to citrate inhibition. A mutant was isolated that showed reduced inhibition by citrate, however the enzyme retained only 20% of its maximal velocity when inhibitor was present at slightly increased concentration of 10 mM. A partially increased resistance toward the citrate inhibition had no positive effect on elevating the rate of product formation (Schreferl et al., 1986). In another attempt reduced inhibition by citrate of PFK1 was obtained by cleaving 8 amino acid residues from the C-terminal part of the enzyme, isolated from the rabbit muscle. Modified enzyme has lost its activity only when 10 mM of citrate was present in the system, while the original enzyme was completely inactivated at 2.5 mM of inhibitor (Valaitis et al., 1987).
The PFK1 isolated from Aspergillus niger cells showed more resistance toward the citrate inhibition in comparison to the enzymes from other organisms, yet 10 mM of citrate almost prevented its catalytic activity. Physiological concentration of citric acid in normal cells is in mM values, however in A. niger cells the citrate concentration can reach up to 10 mM (Legi{hacek over (s)}a and Kidri{hacek over (c)}, 1989). PFK1 enzyme isolated from the fungus Aspergillus niger was in past often a subject of investigation (Habison et al., 1979; Habison et al., 1983; Schreferel et al. 1986; Arst et al., 1987), moreover a gene coding for PFK1 has been cloned and sequenced. By analyzing the pfkA gene (EMBL accession number pfkA Z79690) it could be concluded that the protein has a molecular mass of 85 kDa, while by studying enzyme kinetics on a partially purified protein, whose molecular weight was not determined, confirmed that AMP, fructose-2,6-bisphosphate and ammonium ions act as positive effectors (Habison et al., 1983). It was also suggested the ammonium ions decrease the inhibition of PFK1 by citrate to a certain extent (Habison et al., 1983; Arst et al., 1987). In authors lab a shorter form of PFK1 isolated from the Aspergillus niger was described with molecular mass of about 48 kDa, which initially showed no activity, but became active after phopshorylation of the protein molecule. (Legi{hacek over (s)}a and Ben{hacek over (c)}ina, 1994a). C. P. Kubicek, who led investigations of kinetic measurements on the enzyme isolated from A. niger (Habison et al., 1979; Habison et al., 1983; Schreferel et al. 1986; Arst et al., 1987) categorically denied that in his lab a protein of 48 kDa showing the PFK1 activity was ever measured (Legi{hacek over (s)}a and Ben{hacek over (c)}ina, 1994b). In two diploma projects conducted in authors' labs, the procedure for isolation of 48 kDa fragment was described (Smerkolj, 2000) and post-translational modification of the native protein proposed as a mechanism of fragmented enzyme formation (Mesojednik, 2003). Recently the molecular weight of the active shorter fragment was determined to be 49 kDa, as well as post-translational modification and kinetic parameters of the shorter fragment were described (Mesojednik and Legi{hacek over (s)}a, 2005). By an in vitro experiment it has been shown, that the shorter fragment was inactive immediately after the proteolytic cleavage of the native protein and regained its activity only after the phosphorylation of the protein molecule, mediated by cAMP-dependent protein kinase. Measurements of kinetic parameters revealed that the shorter fragment was resistant to citrate inhibition (Mlakar, diploma work), while the negative effect of ATP was suppressed in the presence of fructose-2,6-bisphosphate (Mesojednik and Legi{hacek over (s)}a, 2005). In literature there is no description of any eukaryotic post-translationally modified PFK1 enzyme with retained ability to be up regulated by specific effectors and lost negative regulation. It seems that the shorter fragment of PFK1 enzyme from A. niger cells is the most efficient form of PFK1 enzyme described so far.
In order to avoid complicated posttranslational modification, the shorter PFK1 fragment was prepared from a truncated pfkA gene. A number of genes shortened at 3′ end of the leading strain were prepared and transferred into A. niger cells. After induced phosphorylation, PFK1 activity characteristic for the shorter fragment was detected in homogenate of transformants carrying t-pfkA gene of specific length (Capuder, 2004). Intracellular phosphorylation was induced by the addition of sodium azide, a well known inhibitor of electron transport at cytochrome oxidase aa3 site, which interrupts the synthesis of ATP which decreases the activity of trans-membrane proton pumps (H+-ATPases). Protons that accumulate in cells cause a decrease in intracellular pH value. It is well known that a drop of intracellular pH triggers cAMP synthesis in fungal cells, which induces the activity of cAMP-dependent protein kinase that finally phosphorylates and activates the shorter fragment of PFK1 enzyme.
Although the shorter fragment might be synthesised in vivo from a truncated gene, the enzyme is initially inactive. It is activated only after the phosphorylation of the protein molecule by cAMP-dependent protein kinase that is induced by an increase of cAMP level in the cells. During Aspergillus niger growth cyclic AMP is synthesised after specific changes that spontaneously appear in the medium or it might be triggered artificially by adding specific inhibitors, like azide, to the medium. According to our knowledge spontaneous drop of intracellular pH occurs only in one strain of A. niger (A60), where the shorter fragment could be spontaneously activated as well. In another A. niger strain (A158) more powerful H+-ATPases are present that prevent intracellular acidification and also synthesis of cAMP (Jernejc and Legi{hacek over (s)}a, 2004). In some micro-organisms mechanisms are known, that trigger cAMP formation and activation of kinases that might activate the shorter fragment of PFK1, however such environmental conditions are often contradictory to optimal conditions needed for the synthesis of biotechnological products.
By introducing specific mutations into the truncated t-pfkA gene, the need for phosphorylation of the protein molecule would be omitted.
By literature search some papers were found that describe changed kinetic parameters of PFK1 enzyme after induced changes in nucleotide sequences. However, in those publications authors used site-directed mutagenesis for determination of allosteric binding sites for various effectors. For example a paper of Li et al., 1999, summarises studies of citrate binding sites that were determined on rabbit muscle PFK1 enzyme, while in review paper of Kemp and Gunasekera, 2002 the evolution of allosteric sites on eukaryotic PFK1 enzymes is presented. No mutations were introduced to change phosphorylation sites on PFK1 enzyme so far. Regulation of the enzyme activity was studied more in detail on 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (Kurland et al., 1992; Kurland and Pilkis, 1995), however this enzyme is not directly involved in glycolysis.
No patent could be found that would protect the use of PFK1 enzyme with changed kinetic parameters, by the active form of enzyme synthesised only from a mutated gene.
According to the state-of-art, the problem of the synthesis of an active shorter fragment of PFK1 with improved enzyme characteristics is not sufficiently solved. The aim of the invention is to solve the problem by the procedure that eliminates the need for phosphorylation of the protein molecule for its activation and enables in vivo synthesis of an active protein by inserting modified mt-pfkA gene.
De-regulated glycolytic flux is of utmost importance in commercial micro-organisms for achieving high rates of specific productivity. Such conditions can be accomplished by inserting mutated, truncated mt-pfkA gene, encoding active shorter fragment of PFK1 enzyme that is resistant to citrate inhibition, while other effectors increase its activity to a greater extent in respect to the native enzyme.
According to the invention the task is solved according to independent patent claims.
The present invention addresses the mutated gene, encoding active shorter fragment of 6-phosphofructo-1-kinase, where phosphorylation of the protein molecule is not needed for its activation, whose monomeric molecular mass is between 30 and 55 kDa; whose enzyme activity is not significantly inhibited by citric acid or citrate salts or ATP. The present invention concentrates on the mutated gene encoding shorter fragment of PFK1 that is active immediately after its synthesis and is not inhibited by citric acid, or citrate salts in the range from 0 mM to 10 mM or ATP up to 1.5 ATP in the presence of fructose-2,6-bisphosphate. The invention addresses the modified gene encoding the synthesis of active shorter fragment of PFK1 that can be activated by some metabolites such as fructose-2,6-bisphosphate, ammonium ions and AMP. The shorter fragment originates from the native enzyme with removed N- and/or C-terminal.
The present invention is based on observation that mutated truncated gene, encoding the active fragment of 6-phosphofructo-1-kinase that is resistant to the inhibition by citric acid and/or citrate salts and ATP, increases the rate of primary and secondary metabolite synthesis in the cells.
The invention concentrates on a procedure that includes the use of the mutated gene for the synthesis of the active shorter PFK1 fragment, or insertion of homologous or heterologous gene into the cells for increasing the rate of primary and secondary metabolite synthesis due to increased glycolytic flux.



DESCRIPTION OF FIGURES
FIG. 1: Specific activities of PFK1 enzymes measured in homogenates of parental strain of Aspergillus niger (A645, which is a derivative of A158 strain) and two transformants (T12 and T14) with integrated t-pfkA gene, before and after the induction of phosphorylation by azide.
FIG. 2: Specific activities of PFK1 enzymes measured in homogenates of parental strain of Aspergillus niger (A645, which is a derivative of A158 strain), T12 transformant with integrated t-pfkA gene and An-TEGI-23 transformant with integrated mutated truncated mt-pfkA gene. No azide was added to the medium.
FIG. 3: Citric acid accumulation in the medium by Aspergillus niger strains transformed with truncated t-pfkA gene. FIG. 3a: transformants originating from A645 strain (derivative of A158 strain). FIG. 3b: transformants originating from A60 strain.
FIG. 4: Citric acid accumulation in the medium by Aspergillus niger transformants with integrated mutated truncated mt-pfkA gene. As a parental strain A645 strain, derivative of A158 strain has been taken.
FIG. 5: Excretion of α-amylases by growing A. niger (A158 strain) and An-TEGI-23 transformant on the medium with starch as a sole carbon source. After three days of growth the remaining starch was stained by iodine solution. A clearing zone with no starch can be observed around the colony of An-TEGI-23. No clearing zone appeared around the colony of the parental strain.
FIG. 6: Activities of extracellular α-amylases excreted by parental strain of A. niger (A158) and An-TEGI-23 transformant detected in the filtrate of the medium with starch as a sole carbon source.
FIG. 7: Itaconic acid accumulation in the medium by transformants of Aspergillus terreus with integrated mutated truncated mt-pfkA gene (AT-TEGI1), integrated truncated t-pfkA gene (AT-44) and parental strain A156.



DEFINITIONS
Abbreviation PFK1 stands for the enzyme 6-phosphofructo-1-kinase (EC 2.7.1.11).
Term “shorter fragment” stands for the protein which number of amino acid residues is smaller than that of the native protein.
Term “shorter PFK1 fragment” stands for the PFK1 protein which number of amino acid residues is smaller than that of the native 6-phosphofructo-1-kinase that is normally present in genetically unmodified cells.
Abbreviation “pfkA” stands for the gene encoding 6-phosphofructo-1-kinase.
Abbreviation “t-pfkA” stands for truncated pfkA gene, which number of nucleotides is lower than that of the native pfkA gene, encoding the synthesis of shorter PFK1 fragment, which number of amino acid residues is lower than that of the native PFK1 enzyme.
Term “mutation” stands for permanent change in nucleotide sequence of a specific gene.
Term “mutated pfkA gene” stands for a permanent change of one or more nucleotides anywhere in the sequence of pfkA gene encoding PFK1 enzyme with change of one or more amino acid residues anywhere in the protein.
Term “mutated mt-pfkA gene” stands for permanent change of one or more nucleotides anywhere in the sequence of truncated t-pfkA gene encoding shorter PFK1 fragment with change of one or more amino acid residues anywhere in the protein.
Term “6-phosphofructo-1-kinase” stands for the enzyme, that converts fructose-6-phosphate to fructose-1,6-bisphosphate on expense of ATP in the presence of Mg2+ ions and is an enzyme in the process of glycolysis.
Term “inhibition by citric acid” stands for negative action of citric acid or its salts, such as citrates, on the enzyme activity of 6-phosphofructo-1-kinase.
Term “inhibition by ATP” stands for negative action of ATP on the enzyme activity of 6-phosphofructo-1-kinase.
Term “activation” stands for increasing the activity of the enzyme above the basic level in the presence of activating components such as: cellular metabolites, for instance fructose-2,6-bisphosphate and ammonium ions and AMP.
Term “N- and/or C-terminal part” of the protein stands for the part of the protein from the NH2— group or beginning of the protein toward the central part of the protein and from the central part of the protein toward the COOH— group or the terminal part of the protein.
Term “post-translational modification” stands for a change in amino acid sequence of the protein by cleaving the protein by proteases or by attaching other bio-chemically functional groups to amino acid sequence, such as the addition of phosphate group by a process of phosphorylation catalysed by protein kinase. Post-translational modifications are described in the scientific literature.
Term “metabolites” stands for the products of cellular metabolism.
Term “anaplerotic reaction” stands for the process of replenishment of tricarboxylic acid cycle intermediates.
Term “originating or the native enzyme or the gene” stands for the enzyme of 6-phosphofructo-1-kinase and the gene encoding the enzyme, that is present in the cells of the wild type strain, which is the strain present in nature.
Term “recombinant origin” stands for the gene or protein that is modified by the laboratory techniques known to the experts from the field.
Term “synthetic origin” stands for the synthetically made gene or protein that is prepared by the techniques known to the experts from the field. Synthetic protein could be represented by the combination of animal and microbial protein.
Term “restriction at 5′ and/or 3′ part of the native gene” stands for the removal of the gene from 5′ part toward the central part and/or removal from the central part toward the 3′ part of the gene. Removal is conducted by techniques known to the experts from the field and can be done by specific endonucleases, unspecific cleavage or by multiplying the gene by the method of Polymerase Chain Reaction by the use of oligo-nucleotide primers, that are complementary to the gene at 5′ and 3′ end.
Term “mutated homologous recombinant gene” stands for the mutated gene encoding shorter fragment, prepared by the recombinant techniques and is introduced into the cells of the same species as the native gene comes from.
Term “mutated heterologous recombinant gene” stands for the mutated gene encoding shorter fragment, prepared by the recombinant techniques and is introduced into the cells of other species as the native gene comes from.
The invention deals with the gene encoding the shorter, genetically modified fragment of 6-phosphofructo-1-kinase that is active immediately after the synthesis, therefore no phosphorylation of protein molecule is needed for its activation; and in the presence of citric acid and/or citric acid salts up to concentration of 15 mM and ATP up to concentration 1.5 mM its activity is reduced for less than 30%; and can be activated by fructose-2,6-bisphosphate, ammonium ions and AMP; and is encoding a protein that differs for at least one amino acid residue of the original amino acid sequence of shorter fragments and which genes are present in the genomes of microbial, animal or plant origin, preferably fungi, preferably from the species Aspergillus, Trichoderma, Penicillium, Pichia, Saccharomyces, Schizosaccharomyces, Candida, Kluyveromyces, Neurospora, preferably Aspergillus niger. The gene encodes a shorter, genetically modified fragment of PFK1 with molecular mass higher than 30 kDa and lower than 55 kDa, which has no N- and/or C-terminal part of the native 6-phosphofructo-1-kinase.
The invention concentrates on the gene encoding the shorter, genetically modified fragment of PFK1 that is active immediately after the synthesis, therefore no phosphorylation of protein molecule is needed for its activation; and in the presence of citric acid and/or citric acid salts up to concentration of 15 mM and ATP up to concentration 1.5 mM its activity is reduced for less than 30%; and can be activated by fructose-2,6-bisphosphate, ammonium ions and AMP; and is encoding a protein with amino acid residue sequence SEQ ID NO: 1 or SEQ ID NO:2, that differs for at least one amino acid residue from amino acid sequence of the shorter PFK1 fragment of the sequence SEQ ID NO:3, which gene sequence SEQ ID NO:4 is present in the genome of Aspergillus niger; and encodes a protein with molecular mass higher than 30 kDa and lower than 55 kDa, which has no N- and/or C-terminal part of the native 6-phosphofructo-1-kinase.
The invention deals with an expression vector that carries the above mentioned gene functionally connected to controlling sequences, promoter, and other relevant DNA sequences enabling protein synthesis, which is coded by the gene and expression vector that enables expression of the gene in eukaryotic host cells or prokaryotic host cells, preferably animal tissue cultures, plant tissue cultures, filamentous fungi, yeasts, bacteria, preferably filamentous fungi, preferably from the genus Aspergillus, Trichoderma, Penicillium, and preferably yeasts, preferably from the genus Pichia, Saccharomyces, Schizosaccharomyces, and preferably bacteria, preferably from the genus Acetobacter, Escherichia, Bacillus, Streptomyces, Zymomonas, preferably in filamentous fungi of the genus Aspergillus, preferably Aspergillus niger, Aspergillus terreus, Aspergillus oryzae. 
The invention deals with the organisms that contain above mentioned gene and/or above mentioned expression vector and that the above mentioned expression vector that corresponds to a specific organism, is inserted into above mentioned organism by the laboratory techniques known to the experts from the field in a way that enables expression of the above mentioned gene and the organisms are of microbial origin, preferably filamentous fungi, preferably from the genus Aspergillus, Trichoderma, Penicillium, and yeasts preferably from the gene Pichia, Saccharomyces, Schizosaccharomyces, or filamentous fungi from the genus Aspergillus, preferably Aspergillus niger, Aspergillus terreus, Aspergillus oryzae, or bacteria preferably from the genus Acetobacter, Escherichia, Bacillus, Streptomyces, Zymomonas and of plant and animal origin, preferably tissue cultures of plant and animal origin.
The invention concentrates on the use of the above mentioned gene and/or expression vectors and/or the above mentioned organisms for the rise of metabolic flux through glycolysis to enhance anaplerotic reaction during the process of bioproducts formation, preferably cell biomass; homologous and heterologous proteins; primary metabolites, such as ethanol, acetate, lactate, organic acids, amino acids, polyols; secondary metabolites, such as antibiotics, ergot alkaloids, statins, vitamins, immuno-modulators, citostatics, insecticides, herbicides.
The invention concentrates on the process for bio-products formation that include the use of the above mentioned gene that is inserted in the above mentioned expression vectors that is introduced into the above mentioned organisms and that the above mentioned organism is cultivated in a way to synthesise the bio-product.
The description of methods in the following text is merely of informative nature and serves for explanation of the invention. For the procedures other relevant materials and methods can be used known to the experts from the field.
1. DESIGNING AND TESTING MUTATED TRUNCATED GENE mt-pfkA
1.1.1. Growth of Fungus Aspergillus niger 
Spores of the fungus Aspergillus niger, strain A60 (MZKI, Microbiological Collection of the National Institute of Chemistry, Ljubljana, Slovenia), that developed on the wort agar slant after 7 days of incubation at 30° C. were suspended in 25 ml of sterile Tween 80 solution (0.1%, w/v). Final concentration of spores was about 107 spores per ml.
For rapid growth of biomass, complex medium was inoculated by spores that contained in 1 litre: 2 g glucose, 0.5 g yeast extract, 0.2 g casein acid hydrolysate, 6 g NaNO3, 1.5 g KH2PO4, 0.5 g MgSO4×7H2O, 0.5 g KCl, 10 ml trace metal solution (Vishniac and Santer, 1957), pH=6.0.
For enzyme kinetic determination the mycelium of parental strain and transformants was grown in the medium that contained in 1 litre: 20 g glucose, 5 g NH4(SO4)2, 5 g KH2PO4, 1 g MgSO4×7H2O, 0.5 g NaCl, 10 mg MnCl2, 10 mg peptone, pH=6.0.
All media (100 ml) in 500 ml baffled Erlenmeyer flasks were inoculated by 5 ml of spore inoculum and incubated on a rotary shaker at 100 rpm and 30° C.
1.1.2. Preparing pyrG− Auxotrophic Mutants
Single auxotrophic mutants of Aspergillus niger suitable for homologous transformation were prepared after the disruption of the pyrG gene in A158 strain (MZKI, Microbiological Collection of the National Institute of Chemistry, Ljubljana, Slovenia) by one step replacement method as described previously (Rothstein, 1983). Plasmid pGWII that was used for silencing of pryG gene, was prepared from pGW635 plasmid (Goosen et al., 1987) carrying pyrG gene of A. niger and pBluescript II KS+ (Stratagene, La Jolla, Calif.). From a 3.9 kbp long KpnI/XbaI digest of pGW635 a 0.8 kbp BglII/BamHI fragment of the pyrG gene was excised, while the remaining flanking regions (KpnI/BglII of 1.3 kbp and BamHI/XbaI of 1.8 kbp) were ligated and inserted into pBS vector. After transformation with pGWII plasmid, protoplasts were regenerated on the minimal medium in the presence of uridine (5 mM) and 5-fluoro-orotic acid (1 mg/ml). Recovered colonies were checked for auxotrophy. Auxotrophic pyrG− mutant prepared from A158 strain was designated as A645.
1.1.3. Preparing pMOJ004 Plasmid
Expression vector pMOJ004 originates from pBluescript II KS+plasmid (Stratagene, La Jolla, Calif.) with integrated promoter region of gene encoding for glyceraldehyde-3-phosphate dehydrogenase (gpdA) and termination region of the gene encoding for glutamine amido transferase (trpC) of the fungus Aspergillus nidulans. Promoter gpdA (Z32524) was amplified by the PCR method by using pAN7-1 vector (Z32698) as a template and gpdA specific oligonucleotide primers: 5′-GAGCTCGTGACCGGTGACTCTTTC-3′ (SEQ ID No: 5) and 5′-TCTAGATGCATATGGGTGATGTCTGCTCAAGC-3′ (SEQ ID No: 6), that simultaneously enabled the insertion of SstI and XbaI-NdeI restriction sites at the 5′ end. Similarly trpC terminator region (X023390) was amplified by using the following oligonucleotide primers: 5′-CCATGGGTCTAGACGGATCCTAGTGATTTAATAGCTCCATGTC-3′ (SEQ ID No: 7) and 5′-GAATTCAAGCTTCCGCGGCCGGGTATTGGGTG-3′ (SEQ ID No: 8) that simultaneously enabled the insertion of XbaI/BamHI and XhoI restriction sites at the 5′ end. For preparing gpdA promoter PCR products were cut by SstI and XbaI enzymes, while for trpC terminator region the restriction was made by XbaI and XhoI enzyme. By using QIAquick GEL Extraction Kit (Qiagen) 0.9 and 1.5 kbp long fragments were isolated from the agarose gel. Finally PCR products were ligated into opened pBluescript II KS+ by the aid of T4DNA polymerase (New England Biolabs, Promega) and the newly formed plasmid was designated as pMOJ004 expression vector.
1.1.4. Construction of Truncated t-pfkA Gene
NdeI/ApaI-ATT-BamHI fragments of A. niger pfkA gene (EMBL Accession No. pfkA Z79690) was amplified by PCR reaction by using following primers: 5′-CCG CGG ATG CAT ATG GCT CCC CCC CAA GC-3′ (SEQ ID No: 9) and 5′-TGG ATC CTT ACC CGG GAT CAT AGT GCC GGC ACA GAC C-3′ (SEQ ID No: 10) and subcloned into EcoRV digest of pBluescript II KS+ (pBS) (Stratagene, La Jolla, Calif.). After amplification of the pBS-t-pfkA plasmid in E. coli DH5α and the isolation of the plasmid by GeneElute Plasmid Mini Prep kit (Sigma), the t-pfkA sequence was determined by MWG-Biotech AG (Ebersberg, Germany) in positively oriented plasmids to exclude the appearance of any mutations. NdeI/BamHI digest of pBS-t-pfkA was finally ligated into pET3a plasmid for expression in bacteria and/or pMOJ004 for expression in filamentous fungi.
Truncated t-pfkA gene encoded a protein of 452 amino acids with molecular mass of 49.8 kDa. Protein has retained identical amino acid sequence of the N-terminal part of the native protein, however amino acid residues at position 451 and 452 were added to match the appropriate restriction site. After verifying the nucleotide sequence, the truncated t-pfkA gene was inserted into Aspergillus niger auxotrophic strain (pyrG−).
1.2.1. Introducing Site Directed Mutations into t-pfkA Gene
By studying three dimensional structure of PFK1 enzyme and by predicting phosphorylation sites of the amino acid residues of the enzyme using NetPhos 2.0 computer programme, the threonine residue at site 89 of the N-terminal part of the enzyme seemed to be the most likely candidate for phosphorylation and activation of the shorter PFK1 fragment. By site directed mutagenesis nucleotide triplets were changed on t-pfkA gene to substitute specific amino acid residues with analogous residues found on PFK1 enzyme of E. coli. Mutagenesis was conducted by QuikChange II XL Site-Directed Mutagenesis Kit (Stratagene, La Jolla, Calif.) by using the following oligonucleotide primers: for changing T89E, 5′-CC GCC CGC TGC ATG GAG TTC CGT GAG CGC CC-3′ (SEQ ID No: 11) and 5′-GG GCG CTC ACG GAA CTC CAT GCA GCG GGC GG-3′ (SEQ ID No: 12); for changing G951, 5′-C CGC TGC ATG GAG TTC CGT GAG CGC CCC ATC CGT CTG CGG G-3′ (SEQ ID No: 13) and 5′-C CCG CAG ACG GAT GGG GCG CTC ACG GAA CTC CAT GCA GCG G-3′ (SEQ ID No: 14). After amplification of pET3a plasmid carrying mutated t-pfkA gene, the sequence of mutated t-pfkA gene has been verified (MWG-Biotech, Eberberg, Germany), in order to confirm the accuracy of the genetic change. Mutated t-pfkA gene was designated as mt-pfkA gene.
By using QuikChange II XL Site-Directed Mutagenesis Kit (Stratagene, La Jolla, Calif.) nucleotides of two codons were changed that enable replacement of two amino acid residues: threonine (T) at site 89 with glutamic acid (E) and glycin (G) at site 95 with isoleucine (I). After verifying the sequence of mutated truncated gene the construct was inserted into A. niger cells.
1.2.2. Insertion of Additional Mutations into mt-pfkA Gene. Construction of Mt-pfkA Gene
Additional mutations were inserted into mt-pfkA gene encoding modified shorter PFK1 fragment of fungus Aspergillus niger to give a protein with 14 amino acid residues around the initial phosphorylation site of A. niger protein to be identical to E. coli protein. Nucleotide triplets for the synthesis of five more amino acid residues had to be changed as shown in Table 1.







TABLE 1







Additional changes introduced into genetically modified PFK1


fragment, encoded by Mt-pfkA gene.











Changed amino acid residue in a


Amino acid residue in
Site at N-
protein encoded by


PFK1 protein of A. niger
terminal part
Mt-pfKA gene





Cysteine
87
Phenilalanine


Methionine
88
Proline


Glutaminic acid
92
Aspartic acid


Arginine
93
Glutamic acid


Proline
94
Asparagine









Additional mutations in mt-pfkA gene were conducted by PCR method of two overlapping fragments with 297 and 1128 bases that formed 23 complementary bases. For amplification of both fragments, pMOJ004-mt-pfkA has been taken as a template. To enable insertion of MT-pfkA gene into pALTER-Ex1 plasmid (Promega), BamHI restriction site had to be replaced with XbaI restriction site at the 3′ end of Mt-pfkA gene. Mt-pfkA gene was finally constructed by PCR ligation of both fragments. The oligonucleotide primers used are shown in Table 2.







TABLE 2





Oligonucleotide primers used for the construction of Mt-pfkA gene.
















Amplification and mutagenesis of 297 bases long fragment



5′-CCATCGCACGCATATGGCTCC-3′


(SEQ ID No: 15)


 


5′-ATGTTCTCGTCACGGAACTCGGGGAAGCGGGCGGAACCGATCAAG-3′


(SEQ ID No: 16)


 


Amplification and mutagenesis of 1128 bases long fragment


5′-CCCGAGTTCCGTGACGAGAACATCCGTCTGCGGGCTGCC-3′


(SEQ ID No: 17)


 


5′-TAGGCGTTTATCGCTGCTTCTAGAGGATCCTTACCCGGGATCATAG-3′


(SEQ ID No: 18)


 


PCR ligation of both fragments


5′-CCATCGCACGCATATGGCTCC-3′


(SEQ ID No: 19)


 


5′-TAGGCGTTTATCGCTGCTTCTAGAGGATCCTTACCCGGGATCATAG-3′


(SEQ ID No: 20)









Mt-pfkA gene was ligated into the pALTER-Ex1 plasmid under the control of tac promoter. After cloning the sequence of Mt-pfkA gene inserted into the pALTER-Ex1 vector was checked (MWG-Biotech, Edberg, Germany).
1.3.1. Transformation of A. niger Cells with pMOJ004-t-pfkA and pMOJ004-mt-pfkA Plasmid
Mycelium of A. niger was harvested after 16-18 hours of submerged growth in a complex medium. Protoplast formation and transformation was conducted as reported previously (Kusters-van Someren et al., 1991), only that lytic enzyme Caylase-4 (Cayla, Toulouse, France) was used instead of Novozyme 234. As a selection marker pyrA gene located on pGW635 plasmid was used. Co-transformation of A645 auxotrophic strain was performed with 1 μg of pGW635 and 15 μg of pMOJ004-t-pfkA or pMOJ004-mt-pfkA carrying truncated or mutated truncated gene for the synthesis of modified shorter PFK1 fragment. Transformants were isolated after re-inoculation on medium without uridine.
1.3.1.1. Southern Analysis
Chromosomal DNA (3 μg) of transformants was degraded overnight by 30 U of BamHI restriction enzyme in a final volume of 200 μl. DNA molecules were separated on 0.5% agarose gel (1× Tris-acetate-EDTA buffer with 2 μl/ml of etidium bromide) and blotted on nylon membrane (HybondTM-N+, Amersham). Single stranded DNA was cross-linked to membrane by UV light (Biometra Ti3, Biometra, Goetingen, Germany). DNA probe was prepared from NdeI/BamHI cut of the pRCR-pfkA plasmid and labeled with BioPrime DNA Labeling System (Life Technologies) according to the instructions. Chemiluminescence detection with CDP-Star (Roche Applied Science) was done by exposure of membranes to X-Omat AR Film (Kodak).
Seventeen transformants with integrated truncated genes enabling the synthesis of the PFK1 fragment were isolated. Southern analysis showed different number of integrated plasmids in eleven transformants. Estimated number of integrated gene copies is presented in Table 3.







TABLE 3







Estimated number of truncated t-pfkA gene copies as detected


after Southern analysis in total DNA isolated from various


transformants.













Estimated



Parental strain (uridine
Plasmids taken for
number of


Strain
auxotroph)
co-transformation
copies













ANPM 3
A158 (A645)
pGW635,
10




pMOJ004-t-pfkA


ANPM 4
A158 (A645)
pGW635,
9




pMOJ004-t-pfkA


ANPM 5
A158 (A645)
pGW635,
6




pMOJ004-t-pfkA


ANPM 9
A158 (A645)
pGW635,
12




pMOJ004-t-pfkA


ANPM 14
A158 (A645)
pGW635,
1




pMOJ004-t-pfkA


ANPM 16
A158 (A645)
pGW635,
1




pMOJ004-t-pfkA


ANPM 29
A158 (A645)
pGW635,
3




pMOJ004-t-pfkA


ANPM 30
A158 (A645)
pGW635,
5




pMOJ004-t-pfkA


ANPM 31
A158 (A645)
pGW635,
12




pMOJ004-t-pfkA


ANPM 32
A158 (A645)
pGW635,
10




pMOJ004-t-pfkA


ANPM 34
A158 (A645)
pGW635,
10




pMOJ004-t-pfkA









After co-transformation of mutated truncated mt-pfkA gene into the auxotrophic strain of Aspergillus niger, different numbers of integrated copies were detected by Southern analysis. Estimated numbers of copies are presented in Table 4.







TABLE 4







Estimated number of mutated truncated mt-pfkA gene copies as


detected by Southern analysis in total DNA isolated from various


transformants.











Parental strain





(Uridine
Plasmids taken for
Estimated


Strain
auxotroph)
co-transformation
number of copies





An-TEGI1
A158 (A645)
pGW635,
1




pMOJ004-mt-pfkA


An-TEGI4
A158 (A645)
pGW635,
2




pMOJ004-mt-pfkA


An-TEGI5
A158 (A645)
pGW635,
2




pMOJ004-mt-pfkA


An-TEGI6
A158 (A645)
pGW635,
1




pMOJ004-mt-pfkA


An-TEGI12
A158 (A645)
pGW635,
1




pMOJ004-mt-pfkA


An-TEGI22
A158 (A645)
pGW635,
5




pMOJ004-mt-pfkA


An-TEGI23
A158 (A645)
pGW635,
5




pMOJ004-mt-pfkA









1.3.2. Transformation of Aspergillus terreus with pMOJ004-mt-pfkA Plasmid
Mycelium of A. terreus was harvested after 16-18 hours of submerged growth in a complex medium. Protoplast formation and transformation was conducted as reported previously (Kusters-van Someren et al., 1991), only that lytic enzyme Caylase-4 (Cayla, Toulouse, France) was used instead of Novozyme 234. A. terreus transformants with integrated mt-pfkA genes were isolated after protoplasts were co-transformed with pMOJ004-mt-pfkA plasmid and pUT720 plasmid, carrying gene for phleomycin resistance.
1.3.2.1. Southern Analysis
In five strains the presence of mt-pfkA was confirmed by PCR method. Southern analysis revealed different number of integrated genes in individual transformants as presented in Table 5.







TABLE 5







Estimated number of mutated truncated mt-pfkA gene copies as


detected by Southern analysis in total DNA isolated from various


transformants of Aspergillus terreus.











Parental
Plasmids taken for co-
Estimated


Strain
strain
transformation
number of copies













At-TEGI1
A156
pUN720
6




pMOJ004-PFK10EI


At-TEGI2
A156
pUN720
10




pMOJ004-PFK10EI 


At-TEGI3
A156
pUN720
10




pMOJ004-PFK10EI


At-TEGI4
A156
pUN720
3




pMOJ004-PFK10EI


At-TEGI5
A156
pUN720
3




pMOJ004-PFK10EI









1.3.3. Transformation of Bacterium E. coli Strain DF 1010 with pALTER-Ex1 Plasmid Carrying Mt-pfkA Gene
Plasmid pAlter-Ex1 carrying Mt-pfkA gene was inserted into E. coli strain DF 1010, with deleted bacterial pfkA and pfkB genes. Effectiveness of transformation was tested by growth of bacteria on selective medium. Plasmid pALTER-Ex1 contains a gene for expression of tetracycline resistance in bacterial cells.
1.4.1. Detecting the Activity of Shorter Fragment Synthesised from t-pfkA Gene
Transformant with integrated t-pfkA gene were grown on minimal medium for 14 hours as described under 1.1.1. Sodium azide was added to the medium in final concentration of 1 mM and culture incubated for additional 15 minutes. Azide, a well known inhibitor of electron transport over cytochromes, causes protons to accumulate in the cells, which results in a drop of intracellular pH. Cells respond by the synthesis of a signalling molecule cyclic AMP to the slight acidification. CyclicAMP activates cAMP-dependent protein kinase that ultimately phosphorylates shorter fragment of PFK1 encoded by t-pfkA gene. Different PFK1 kinetic parameters were detected in cell-free extracts of transformants after phosphorylation was induced, while no change in kinetics could be observed in parental strain in spite of induced phosphorylation.
1.4.2. Detecting the Activity of Shorter Fragment Encoded by mt-pfkA Gene.
Transformants with integrated mt-pfkA gene that enabled synthesis of modified shorter PFK1 fragment were grown for 14 hours on a minimal medium as described under 1.1.1. No sodium azide was added to the medium prior to measuring PFK1 kinetics in cell free extracts. The presence of active shorter fragment of PFK1 has been confirmed by detection of PFK1 kinetics characteristic for the shorter fragment.
1.5.1. Enzyme Tests
1.5.1.1 Homogenate Preparation
Mycelium was collected by suction filtration and washed with cold 50 mM phosphate buffer containing 0.5 mM dithioerithritol (DTE) and 1 mM EDTA.
Approximately 50 g of wet weight of mycelium was frozen under the liquid nitrogen and disrupted for 1 minute in a glass bead disintegrator (Braun, Melsungen). After thawing the crushed cells were extracted with 5 ml of cold 50 mM phosphate buffer, pH=7,8, containing 0.5 mM DTE and 10 μl of protease inhibitor cocktail (Sigma). Finally the extract was centrifuged for 15 minutes at 15,000 rpm. Protein concentration in supernatant exceeded 5 mg/ml.
1.5.1.2. Measuring Enzyme Kinetics
PFK1 activity was measured spectrophotometrically at 340 nm according to slightly modified procedure of Legi{hacek over (s)}a and Mattey, 1988, using a coupled reaction system. The reaction was carried out in the final volume of 1 ml and in the presence of: 50 mM Tris-HCl buffer, pH=7.8, 0.5 mM DTE, 200 mM KCl, 5 mM MgCl2, 0.2 mM NADH, 20 μl of homogenate, various concentrations of fructose-6-phosphate, 0.9 U/ml aldolase (Roche Molecular Biochemicals, Indianapolis, Ind.), 2.4 U/ml triosephosphate isomerase and glycerol-3-phosphate dehydrogenase (Sigma), 4.5 U/ml aldolase (Sigma).
In order to remove ammonium ions the auxiliary enzymes were dialysed against 50 mM Tris-HCl buffer pH=7.8, 0.5 mM DTE, 30% glycerol, overnight at 4° C. with one change of buffer after 8 hours. The auxiliary enzymes remained active for several weeks when stored in refrigerator.
When kinetic parameters of the shorter fragment were determined, all measurements were conducted in a buffer containing 5 mg/ml of albumine, which was added to the system just before the measurements.
To differentiate between kinetics of the native enzyme and the shorter fragment, the measurements have started with adding fructose-6-phosphate and 0.1 mM ATP to the system, followed by increasing the concentration of ATP to 1 mM and finally in the presence of 4 μM of fructose-2,6-bisphosphate.
1.5.2. Demonstrating the Synthesis of the Shorter Fragment from t-pfkA Gene
Since no active shorter fragment can be synthesised from t-pfkA gene, due to the need for phosphorylation of the protein molecule, intracellular phosphorylation must have been induced by an external stimulus. It has been achieved by adding sodium azide to the medium. Azide inhibits electron transport over cytochromes, which causes proton accumulation. Slight acidification is sensed as a stress in the cells that respond by the formation of signal molecule cAMP. Increased level of cAMP activates cAMP-dependent protein kinase that phosphorylates shorter PFK1 fragment, encoded by t-pfkA gene. In cell homogenates containing inactive shorter PFK1 fragment, changed enzyme kinetics was detected after induced phosphorylation (FIG. 1) that was characteristic for the shorter fragment. No alternation in enzyme kinetics could be observed in homogenate of parental strains, in spite of induced phosphorylation by azide. A series of other truncated pfkA genes were tested that coded for proteins shortened at C-terminal part, with molecular masses between 40 to 52 kDa and that differed for 8 amino acid residues. However, none of the other genes inserted into A. niger cells enabled synthesis of an active PFK1 enzyme with modified kinetics.
1.5.3. Demonstrating the Synthesis of Active Shorter PFK1 Fragment from mt-pfkA Gene
For testing mt-pfkA gene intracellular phosphorylation was not induced by adding sodium azide to the medium before mycelium was homogenised and PFK1 activity measured. Parental strain, transformants with t-pfkA gene inserted and cells with mt-pfkA gene were tested for changed PFK1 activity. Enzyme kinetics characteristic for shorter PFK1 fragment were detected only in extracts from transformants carrying mt-pfkA gene, while normal PFK1 activity was observed in the parental strain and t-pfkA transformants.
1.5.4. Determining α-Amylolytic Activity in Filtrate
Alpha-amylolytic activity was measured in the medium filtrate as described under the Example 2.2., by using commercial Kit for evaluation of α-amylolytic activity according to the Ceralpha method (Megazyme, Bray, Ireland).
2. EXAMPLES
2.1. Testing Aspergillus niger Transformants for Increased Citric Acid Productivity
For testing citric acid accumulation by Aspergillus niger strains the fungus was grown in a medium that contained the following ingredients in 1 litre: 150 g sucrose, 2.5 g (NH4)2SO4, 1.5 g KH2PO4, 0.5 g MgSO4×7H2O, 6.5 mg FeSO4, 1.3 mg ZnSO4.7H2O with pH value adjusted to 2.5.
The amount of citric acid in the medium filtrate was determined as reported previously (Legi{hacek over (s)}a and Jernejc, 2002). Data are means of five independent experiments inoculated with individual strain/transformant.
All transformants with inserted un-mutated truncated t-pfkA gene excreted citric acid more slowly and accumulated less acid in respect to the parental strain A158 (FIG. 3a). In Aspergillus niger strain A158 potent H+-ATPases were described (Jernejc and Legi{hacek over (s)}a, 2004) that can maintain pH homeostasis (Hesse et al., 2002). Lack of a slight intracellular acidification prevents triggering of cAMP synthesis and activation of cAMP-dependent protein kinase, therefore no phosphorylation and activation of inactive shorter PFK1 fragment can take place. In contrast to A158 strain, transformants of A60 strain with inserted t-pfkA gene showed increased citric acid production in respect to their parental strain (FIG. 3b). Less active H+-ATPases were described in A60 strain (Jernejc and Legi{hacek over (s)}a, 2002) that cause a drop of intracellular pH value during the growth in citric acid yielding medium, which finally induces cAMP synthesis and phosphorylation of the shorter PFK1 fragment.
On the other hand the majority of transformants with inserted mutated truncated mt-pfkA genes accumulated citric acid more efficiently in respect to A158 strain. With some strains more than 50% increased productivity was recorded, as well as product yields at the end of fermentation were increased, in comparison to the parental strain (FIG. 4). Some strains with inserted mt-pfkA genes indeed produced less citric acid, however it should be noted that during transformation plasmids might induce mutations during the insertion into the chromosome. In some transformants one plasmid copy might be inserted at a site that causes negative mutation in sense of good citric acid production.
2.2. Testing Aspergillus niger Transformants for Increased α-Amylase Productivity
For testing α-amylase production the medium of the following composition was used that contained in 1 liter: 20 g starch, 6.0 g NaNO3, 1.5 g KH2PO4, 0.5 g MgSO4.7H2O, 0.5 g KCl, 0.1 g EDTA, 44 mg ZnSO4, 10 mg MnCl2.4H2O, 3.2 mg CoCl2.6 H2O, 3.2 mg CuSO4.5 H2O, 2.2 mg (NH4)6Mo7O24.4 H2O, 14.7 mg CaCl2.2H2O, 10 mg FeSO4.7H2O, agar 1.5% (m/v). Agar plates containing the medium were inoculated with 5 μl of spore suspension of both A. niger strain A158 and transformant An-TEGI23. After three days of incubation at 30° C. the plates were poured with iodine solution (J20.4M/KJ 0.4M) and the clearing zones measured around the colonies (FIG. 5).
Transformant with integrated mt-pfkA genes grew faster and the colony diameter reached 26 mm, while the parental strain diameter was smaller—22 mm. After staining with the iodine solution a clearing zone could be observed around the colony of transformant, while no starch was degraded around the colony but only beneath the mycelium of the parental strain.
Alpha-amylolytic activity of the parental A. niger strain (A158) and transformant with integrated mt-pfkA genes (An-TEGI23) was detected during the submerged growth in the medium as described above, without agar added. The activity was determined in the filtrate of fermentation broths according to Ceralpha method. Data are means of three independent experiments and are shown in FIG. 6.
2.3. Testing Aspergillus terreus Transformants for Increased Itaconic Acid Productivity
For testing itaconic acid excretion, the strains of Aspergillus terreus were grown in productive medium as described previously (Riscaldati et al., 2000) and contained in 1 litre: 150 g glucose, 2.36 g (NH4)2SO4, 0.11 g KH2PO4, 208 mg MgSO4×7H2O, 130 mg KCl, 74 mg NaCl, 0.2 mg CuSO4.5H2O, 5.5 mg FeSO4.7H2O, 0.7 mg MnCl2.4H2O, 1.3 mg ZnSO4.7H2O, pH adjusted to 3.4.
The amount of itaconic acid was determined by ionic chromatography by using CIM discs (Bia, Ljubljana, SI) and itaconate (Sigma) as a standard. The data are means of five independent experiments inoculated with the same strain/transformant. FIG. 6 shows the amount of accumulated itaconate by parental strain and transformant At-TEGI-1. In transformant carrying higher number of integrated mt-pfkA genes, the yields of itaconic acid were increased up to 40%.
2.4. Testing Transformants of Bacterium E. coli (DF 1020) for Growth on Specific Substrates
Parental strains and double transformants of the bacterium E. coli were grown on minimal medium in the presence of the following carbon-hydrates as sole carbon sources: glucose, fructose, mannose and manitol. IPTG was added to the medium that promoted constitutive expression of Mt-pfkA gene. Apart from E. coli DE 1020 strain carrying Mt-pfkA gene the following E. coli strains were tested. BL21 strain, DF 1020 strain, DF 1020 strain with integrated native pfkA gene of Aspergillus niger, DF 1020 strain with integrated t-pfkA gene. After the incubation at 37° C. for several days, growth of individual colonies was observed. Growth rates of colonies have been evaluated and are shown in Table 6.







TABLE 6







Growth of E. coli transformants on the minimal medium with


various carbon sources. More pulses indicate higher specific growth


rate. Negative sign represents no growth.














E. coli
E. coli


Sole carbon
E. coli
E. coli
DF1020 + n-
DF 1020 +


source
BL21
DF1020
n-pfkA
Mt-pfkA





Glucose
++
+
++
++


Fructose
++
+++
+++
+++


Mannose
++
−
++
+++


Manitol
++
−
++
+++









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## Claims

1. A nucleic acid sequence encoding a mutated and truncated 6-phosphofructo-1-kinase (PFK1) fragment of a wild type fungal PFK1 enzyme, wherein the nucleic acid includes at least one mutation selected from the group consisting of
an encoded amino acid substitution at an amino acid that aligns with threonine 89 of SEQ ID NO: 3, and an encoded amino acid substitution at an amino acid that aligns with glycine 95 of SEQ ID NO: 3;
wherein the mutation allows the PFK1 fragment to exhibit greater enzyme activity without phosphorylation than the wild type PFK1 without phosphorylation;
wherein the truncated PFK1 fragment has less than 785 amino acids and is truncated at the C-terminus relative to the wild type PFK1; and
wherein the PFK1 fragment has a molecular weight of about 30 kDa to about 55 kDa as determined by SDS-PAGE.

2. The nucleic acid of claim 1, wherein the PFK1 fragment loses less than 30% of its enzyme activity in the presence of citric acid and/or salts of citric acid in concentration up to 15 mM.

3. The nucleic acid of claim 1, wherein the PFK1 fragment loses less than 30% of its enzyme activity in the presence of ATP in concentration up to 1.5 mM.

4. The nucleic acid of claim 1, wherein the PFK1 fragment loses less than 30% of its enzyme activity in the presence of citric acid and/or salts of citric acid in concentration up to 15 mM and ATP in concentration up to 1.5 mM.

5. The nucleic acid of claim 1, wherein the substituted amino acid at an amino acid that aligns with amino acid 89 of SEQ ID NO: 3 is a glutamic acid.

6. The nucleic acid of claim 1, wherein the mutation includes the encoded amino acid substitution at an amino acid that aligns with amino acid 89 of SEQ ID NO: 3 and the encoded amino acid substitution at an amino acid that aligns with glycine 95 of SEQ ID NO: 3.

7. The nucleic acid of claim 1, wherein the substituted amino acid at an amino acid that aligns with amino acid 95 of SEQ ID NO: 3 is an isoleucine.

8. The nucleic acid of claim 1, wherein the truncated PFK1 fragment includes a mutation corresponding to a deletion of at least one amino acid from the N-terminus of the wild type PFK1.

9. The nucleic acid of claim 1, wherein the truncated PFK1 fragment includes a mutation corresponding to a deletion of at least two amino acids from the C-terminus of the wild type PFK1.

10. The nucleic acid of claim 1, wherein the PFK1 fragment includes a polypeptide comprising the amino acid sequence of SEQ ID NO: 1 or SEQ ID NO: 2.

11. The nucleic acid of claim 1, wherein the PFK1 fragment is from a genus of filamentous fungi.

12. A nucleic acid sequence that encodes a mutated and truncated PFK1 fragment of a wild type Aspergillus PFK1, wherein the truncated PFK1 fragment exhibits greater enzyme activity without phosphorylation than the wild type PFK1 without phosphorylation, wherein the nucleic acid sequence includes at least one mutation selected from the group consisting of
an encoded amino acid substitution at an amino acid that aligns with threonine 89 of SEQ ID NO: 3, and
an encoded amino acid substitution at an amino acid that aligns with glycine 95 of SEQ ID NO: 3, and
wherein the truncated PFK1 fragment has less than 785 amino acids, has a molecular weight of about 30 kDa to about 55 kDa as determined by SDS-PAGE, and is truncated at the C-terminus relative to the wild type PFK1.

13. The nucleic acid of claim 12, wherein the PFK1 fragment loses less than 30% of enzyme activity in the presence of citric acid and/or salts of citric acid in concentration up to 15 mM.

14. The nucleic acid of claim 12, wherein the PFK1 fragment loses less than 30% of its enzyme activity in the presence of ATP in concentration up to 1.5 mM.

15. The nucleic acid of claim 12, wherein the PFK1 fragment loses less than 30% of its enzyme activity in the presence of citric acid and/or salts of citric acid in concentration up to 15 mM and ATP in concentration up to 1.5 mM.

16. The nucleic acid of claim 12, wherein the substituted amino acid that aligns with the amino acid 89 of SEQ ID NO: 3 is a glutamic acid.

17. The nucleic acid of claim 12, wherein the mutation includes the encoded amino acid substitution at an amino acid that aligns with amino acid 89 of SEQ ID NO: 3 and the encoded amino acid substitution at an amino acid that aligns with glycine 95 of SEQ ID NO: 3.

18. The nucleic acid of claim 12, wherein the substituted amino acid that aligns with the amino acid 95 of SEQ ID NO: 3 is an isoleucine.

19. An isolated nucleic acid comprising a sequence that encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 1 or SEQ ID NO: 2.

20. An isolated nucleic acid comprising a sequence that encodes the amino acid sequence of SEQ ID NO: 1 or SEQ ID NO: 2.

21. An isolated nucleic acid comprising a sequence that encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 1 with 0-6 amino acid substitutions, wherein the polypeptide exhibits greater enzyme activity without phosphorylation than the polypeptide of SEQ ID NO: 3 without phosphorylation.

22. A polypeptide comprising a mutated and truncated PFK1 fragment of a wild type fungal PFK1, wherein the PFK1 fragment exhibits greater enzyme activity without phosphorylation than the wild type PFK1 without phosphorylation; and wherein the truncated PFK1 fragment includes at least one mutation selected from the group consisting of an amino acid substitution at an amino acid that aligns with threonine 89 of SEQ ID NO: 3, and an amino acid substitution at an amino acid that aligns with glycine 95 of SEQ ID NO: 3, and
wherein the PFK1 fragment has less than 785 amino acids, has a molecular weight of about 30 kDa to about 55 kDa as determined by SDS-PAGE, and is truncated at the C-terminus relative to the wild type PFK1.

23. The polypeptide of claim 22, wherein the PFK1 fragment loses less than 30% of enzyme activity in the presence of citric acid and/or salts of citric acid in concentration up to 15 mM.

24. The polypeptide of claim 22, wherein the PFK1 fragment loses less than 30% of enzyme activity in the presence of ATP in concentration up to 1.5 mM.

25. The polypeptide of claim 22, wherein the PFK1 fragment loses less than 30% of enzyme activity in the presence of citric acid and/or salts of citric acid in concentration up to 15 mM and ATP in concentration up to 1.5 mM.

26. The polypeptide of claim 22, wherein the substituted amino acid that aligns with amino acid 89 of SEQ ID NO: 3 is a glutamic acid.

27. The polypeptide of claim 22, wherein the substituted amino acid that aligns with amino acid 95 of SEQ ID NO: 3 is an isoleucine.

28. The polypeptide of claim 22, wherein the PFK1 fragment includes the amino acid substitution at an amino acid that aligns with amino acid 89 of SEQ ID NO: 3 and the amino acid substitution at an amino acid that aligns with amino acid 95 of SEQ ID NO: 3.

29. The polypeptide of claim 28, wherein the amino acid that aligns with amino acid 95 of SEQ ID NO: 3 is an isoleucine and the amino acid that aligns with amino acid 89 of SEQ ID NO: 3 is a glutamic acid.

30. The polypeptide of claim 22, wherein the PFK1 fragment includes a polypeptide comprising the amino acid sequence of SEQ ID NO: 1 or SEQ ID NO:2.

31. The polypeptide of claim 22, wherein the PFK1 fragment includes a polypeptide comprising the amino acid sequence of SEQ ID NO: 1 with 0 to 5 amino acid substitutions, deletions, and/or additions.

32. An isolated polypeptide comprising the amino acid sequence of SEQ ID NO: 1 or SEQ ID NO: 2.

33. A DNA including a first sequence which encodes a mutated and truncated PFK1 fragment of a wild type fungal PFK1, wherein the mutation allows the truncated PFK1 fragment to exhibit greater enzyme activity without phosphorylation than the wild type PFK1 without phosphorylation, and includes at least one mutation selected from the group consisting of an encoded amino acid substitution, addition, and/or deletion at an amino acid that aligns with threonine 89 of SEQ ID NO: 3, and an encoded amino acid substitution at an amino acid that aligns with glycine 95 of SEQ ID NO: 3, and
wherein the truncated PFK1 fragment has less than 785 amino acids, has a molecular weight of about 30 kDa to about 55 kDa as determined by SDS-PAGE, and is truncated at the C-terminus relative to the wild type PFK1; and wherein the first segment is fused in frame to a heterologous coding sequence.

34. An expression vector comprising a nucleic acid sequence encoding a mutated and truncated PFK1 fragment of a wild type fungal PFK1 origin having a molecular weight of about 30 kDa to about 55 kDa as determined by SDS-PAGE,
wherein the truncated PFK1 fragment exhibits greater enzyme activity without phosphorylation than the wild type PFK1 without phosphorylation,
wherein the truncated PFK1 fragment includes at least one mutation selected from the group consisting of an encoded amino acid substitution at an amino acid that aligns with threonine 89 of SEQ ID NO: 3, and an encoded amino acid substitution at an amino acid that aligns with glycine 95 of SEQ ID NO: 3; and
wherein the nucleic acid sequence is fused in frame to an expression control sequence.

35. A cultured cell comprising the vector of claim 34.

36. A filamentous fungi comprising the vector of claim 34.

37. A yeast comprising the vector of claim 34.

38. A bacteria comprising the vector of claim 34.

39. A method of producing bio-products, the method comprising:
obtaining an organism capable of producing bio-products;
inserting an expression vector into the organism, wherein the expression vector comprises a nucleic acid segment encoding a mutated and truncated PFK1 fragment of a wild type fungal PFK1,
wherein the truncated PFK1 fragment exhibits greater enzyme activity without phosphorylation than the wild type PFK1 without phosphorylation, and has a molecular weight of about 30 kDa to about 55 kDa as determined by SDS-PAGE,
wherein the nucleic acid segment is fused in frame to an expression control sequence,
wherein the nucleic acid segment includes at least one mutation selected from the group consisting of an encoded amino acid substitution at an amino acid that aligns with threonine 89 of SEQ ID NO: 3, and an encoded amino acid substitution at an amino acid that aligns with glycine 95 of SEQ ID NO: 3; and growing the organism.

40. The method of claim 39, wherein the expression vector enhances anaplerotic reaction during organism growth, thereby increasing bio-product production.

41. The method of claim 39, wherein bio-products are selected from cell biomass, homologous proteins, heterologous proteins, primary metabolites, and secondary metabolites.

42. The method of claim 39, wherein the nucleic acid segment is of filamentous fungal origin.

43. The method of claim 42, wherein the filamentous fungi is of a genera selected from the group consisting of Aspergillus, Trichoderma, and Penicillium.

44. The method of claim 39, wherein the organism is selected from the group consisting of a yeast, a filamentous fungi, and a bacterium.

45. The method of claim 44, wherein the yeast is of a genus selected from the group consisting of Pichia and Saccharomyces, 
the filamentous fungi is of a genus selected from the group consisting of Aspergillus, Trichoderma, and Penicillium, and
the bacteria is of a genus selected from the group consisting of Acetobacter, Escherichia, Bacillus, Streptomyces, and Zymomonas.