US10385367B2 - Methods and molecules for yield improvement involving metabolic engineering - Google Patents

Methods and molecules for yield improvement involving metabolic engineering Download PDF

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US10385367B2
US10385367B2 US13/322,383 US201013322383A US10385367B2 US 10385367 B2 US10385367 B2 US 10385367B2 US 201013322383 A US201013322383 A US 201013322383A US 10385367 B2 US10385367 B2 US 10385367B2
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degradation
amino acid
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Jeffrey C. Way
Joseph H. Davis
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Ginkgo Bioworks Inc
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P7/00—Preparation of oxygen-containing organic compounds
    • C12P7/40—Preparation of oxygen-containing organic compounds containing a carboxyl group including Peroxycarboxylic acids
    • C12P7/42—Hydroxy-carboxylic acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/67—General methods for enhancing the expression
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
    • C12N9/12—Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
    • C12N9/1205—Phosphotransferases with an alcohol group as acceptor (2.7.1), e.g. protein kinases
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/95—Fusion polypeptide containing a motif/fusion for degradation (ubiquitin fusions, PEST sequence)

Definitions

  • the invention relates to metabolic engineering of cells for the enhanced production of a cellular product.
  • Metabolic engineering involves the industrial production of chemicals from biological sources. Typically, a microbe such as a bacterium or a single-celled eukaryote is engineered to produce a compound in large amounts that is normally produced in small amounts or not at all. Examples of compounds produced by metabolic engineering include ethanol, butanol, lactic acid, various vitamins and amino acids, and artemisinin. Metabolic engineering generally involves genetic modification of a host organism, such as expression of foreign genes to make enzymes that synthesize compounds that may not be native to the host organism, overexpression of genes using strong promoters, introduction of mutations that alter allosteric regulation, and introduction of mutations that limit the production of alternative products.
  • feedstock the mixture of nutrients used in the medium in which the microbe grows.
  • the feedstock typically includes a carbohydrate source, a source of fixed nitrogen, sources of sulfur, phosphorus, and so on, as well as any specific nutritional requirements.
  • One significant problem in metabolic engineering is that even under conditions of product production, much of the feedstock is channeled into other metabolic pathways that contribute to growth of the organism and production of its biomass.
  • a second problem is the cost of the feedstock itself, especially when the feedstock includes, in addition to a carbohydrate, molecules that fulfill auxotrophic requirements. Therefore, there is a need in the art to limit production of biomass during metabolic engineering and also to reduce the cost of the feedstock.
  • the invention generally provides improved cells, molecules, and methods for synthesis of products by metabolic engineering.
  • the invention provides an engineered cell that synthesizes a product more cost-effectively than current methods by making use of a cell with the following characteristics.
  • the cell contains one or more proteins that include an enzymatic function with an engineered connection to a sequence that can promote degradation of the protein.
  • the cell also includes a regulatory system such that upon addition or withdrawal of a regulatory factor, which may be a chemical, a protein, photons, temperature, or any other factor, the degradation of the protein is enhanced.
  • a regulatory factor which may be a chemical, a protein, photons, temperature, or any other factor
  • the desired product is obtained from the cell or the medium.
  • the enzymatic function may promote growth of the cell during an expansion phase or may allow the culturing and expansion of the cell with less or none of an expensive feedstock component.
  • the invention provides an engineered cell that contains a protein that includes an enzymatic function and a sequence that can promote degradation of the protein, a regulatory system such that upon addition or withdrawal of a regulatory factor, the degradation of the protein is enhanced, synthesis and/or secretion of a desired product is consequently enhanced, and wherein the enzyme is a catabolic enzyme.
  • the invention provides an engineered cell that contains a protein that includes an enzymatic function and a sequence that can promote degradation of the protein, a regulatory system such that upon addition or withdrawal of a regulatory factor, the degradation of the protein is enhanced, synthesis and/or secretion of a desired product is consequently enhanced, and wherein the enzyme is an anabolic enzyme.
  • the invention provides an engineered cell that contains a protein that includes an enzymatic function and a sequence that can promote degradation of the protein, a regulatory system such that upon addition or withdrawal of a regulatory factor, the degradation of the protein is enhanced, synthesis and/or secretion of a desired product is consequently enhanced, and wherein the enzyme is an anabolic enzyme.
  • the invention provides an engineered cell that contains a protein that includes an enzymatic function and a sequence that can promote degradation of the protein, a regulatory system such that upon addition or withdrawal of a regulatory factor, the degradation of the protein is enhanced, synthesis and/or secretion of a desired product is consequently enhanced, and wherein the cell is a bacterial cell.
  • the invention provides an engineered cell that contains a protein that includes an enzymatic function and a sequence that can promote degradation of the protein, a regulatory system such that upon addition or withdrawal of a regulatory factor, the degradation of the protein is enhanced, synthesis and/or secretion of a desired product is consequently enhanced, and wherein the cell is a fungal cell.
  • the invention provides an engineered cell that contains a protein that includes an enzymatic function and a sequence that can promote degradation of the protein, a regulatory system such that upon addition or withdrawal of a regulatory factor, the degradation of the protein is enhanced, synthesis and/or secretion of a desired product is consequently enhanced, and wherein the cell is an insect cell, a plant cell, a protozoan cell, or a mammalian cell.
  • the invention provides an engineered cell that contains a protein that includes an enzymatic function and a sequence that can promote degradation of the protein, a regulatory system such that upon addition or withdrawal of a regulatory factor, the degradation of the protein is enhanced, synthesis and/or secretion of a desired product is consequently enhanced, and wherein the regulatory system controls synthesis of the protein.
  • the invention provides an engineered cell that contains a protein that includes an enzymatic function and a sequence that can promote degradation of the protein, a regulatory system such that upon addition or withdrawal of a regulatory factor, the degradation of the protein is enhanced, synthesis and/or secretion of a desired product is consequently enhanced, and wherein the regulatory system controls synthesis of a second factor that controls the degradation of the protein.
  • the invention provides an engineered cell that contains a protein that includes an enzymatic function and a sequence that can promote degradation of the protein, a regulatory system such that upon addition or withdrawal of a regulatory factor, the degradation of the protein is enhanced, synthesis and/or secretion of a desired product is consequently enhanced, and wherein the sequence that can promote degradation of the protein includes an amino acid sequence that differs from the sequence Ala-Ala-Asn-Asp-Glu-Asn-Tyr-Ala-Leu-Ala-Ala (SEQ ID NO: 1) by at most four amino acid substitutions or deletions.
  • the invention provides an engineered cell that contains a protein that includes an enzymatic function and a sequence that can promote degradation of the protein, a regulatory system such that upon addition or withdrawal of a regulatory factor, the degradation of the protein is enhanced, wherein the enzymatic function in an amino acid biosynthetic function.
  • the invention provides an engineered cell that contains a protein that includes an enzymatic function and a sequence that can promote degradation of the protein, a regulatory system such that upon addition or withdrawal of a regulatory factor, the degradation of the protein is enhanced, wherein the enzymatic function is part of aromatic amino acid synthesis.
  • the invention provides an engineered cell that contains a protein that includes an enzymatic function and a sequence that can promote degradation of the protein, a regulatory system such that upon addition or withdrawal of a regulatory factor, the degradation of the protein is enhanced, wherein the enzymatic function is part of the tricarboxylic acid cycle.
  • the invention provides an engineered cell that contains a protein that includes an enzymatic function and a sequence that can promote degradation of the protein, wherein the enzymatic function is part of fatty acid synthesis, the oxidative pentose phosphate pathway, or glycolysis.
  • the invention provides an engineered cell that contains a protein that includes an enzymatic function and a sequence that can promote degradation of the protein, wherein the enzymatic function is a kinase, an acetyl-CoA-producing enzyme, an enzyme that joins two carbon-containing reactant molecules into a single, carbon-containing product molecule, and an allosterically regulated enzyme
  • the invention provides an engineered cell that contains a protein that includes an enzymatic function and a sequence that can promote degradation of the protein, wherein enzymatic function is pyruvate kinase, shikimate kinase, pyruvate dehydrogenase, citrate synthase, and DAHP synthase.
  • the invention provides an engineered cell that contains a protein that includes an enzymatic function and a sequence that can promote degradation of the protein, wherein the enzymatic function is hexokinase, glucokinase, glucose-6 phosphatase, glucose-6-phosphate dehydrogenase, glucose phosphate isomerase, phosphofructokinase, fructose bisphosphate aldolase, glyceraldehyde phosphate dehydrogenase, triose phosphate isomerase, phosphoglyceromutase, enolase, phosphoenolpyruvate carboxykinase, pyruvate kinase, pyruvate dehydrogenase, pyruvate decarboxylase, pyruvate-formate lyase, lactate dehydrogenase, pyruvate carboxylase, citrate synthase, aconitate
  • the invention also features nucleic acids encoding proteins, in which the nucleic acid comprises a sequence encoding a protein having any of the above enzymatic activities.
  • the invention provides an engineered cell that contains a protein that includes an enzymatic function and a sequence that can promote degradation of the protein, a regulatory system such that upon addition or withdrawal of a regulatory factor, the degradation of the protein is enhanced, wherein the regulatory system involves expression of an anti-sense RNA.
  • the invention provides an engineered cell that contains a protein that includes an enzymatic function and a sequence that can promote degradation of the protein, a regulatory system such that upon addition or withdrawal of a regulatory factor, the degradation of the protein is enhanced, wherein the regulatory system controls the expression of a protein that promotes degradation of the artificial protein.
  • the invention provides an engineered cell that contains a protein that includes an enzymatic function and a sequence that can promote degradation of the protein, a regulatory system such that upon addition or withdrawal of a regulatory factor, the degradation of the protein is enhanced, wherein the regulatory system controls replication or segregation of a plasmid.
  • the invention also provides nucleic acids encoding proteins, wherein the nucleic acid comprises a sequence encoding an enzyme fused to a sequence that can promote degradation of the protein, wherein the enzyme is an amino acid biosynthetic protein, a protein in the tricarboxylic acid cycle, a glycolytic enzyme, a fatty acid biosynthetic enzyme, or an enzyme of the oxidative pentose phosphate pathway, and wherein the nucleic acid further comprises an engineered operable linkage to a regulatory element.
  • the invention also provides nucleic acids encoding proteins, wherein the nucleic acid comprises a sequence encoding a shikimate kinase enzymatic activity fused to a sequence that can promote degradation of the protein, and wherein the nucleic acid optionally comprises an engineered operable linkage to a regulatory element.
  • the invention also provides methods of production, in which a cell containing a protein that includes an enzymatic function with an engineered connection to a sequence that can promote degradation of the protein is induced to undergo a regulatory switch that promotes degradation of the protein, enhanced synthesis of a desired product results, and the product is obtained from the culture of the cell.
  • the invention also provides methods of production, in which a cell containing a protein that includes an enzymatic function with an engineered connection to a sequence that can promote degradation of the protein is induced to undergo a regulatory switch that promotes degradation of the protein, enhanced synthesis of a desired product results, the product is obtained from the culture of the cell, and the product is purified.
  • the invention provides methods of production of shikimic acid, in which a cell containing a protein that includes an shikimate kinase enzymatic activity with an engineered connection to a sequence that can promote degradation of the protein is induced to undergo a regulatory switch that promotes degradation of the protein, enhanced synthesis of a desired product results, the product is obtained from the culture of the cell, and the product is purified.
  • amino acid biosynthetic function is meant an enzymatic activity corresponding to a point in metabolism at or after a point of feedback inhibition by an amino acid.
  • essential gene of a cell e.g., microbe
  • a gene that is required for growth of the cell for the production of a given product is meant a gene that is required for growth of the cell for the production of a given product.
  • FIGS. 1A and 1B are schematic drawings showing the use of regulated degradation to enhance production by metabolic engineering.
  • FIG. 1A shows a genetic construction ( 1 ) that includes a transcriptional regulatory element ( 2 ), a translational element ( 3 ), a coding sequence for a protein of interest such as an enzyme ( 4 ), fused in-frame to a coding sequence for a peptide or protein element that promotes degradation ( 5 ), the fusion protein product ( 6 ) that includes an enzymatic element (large oval) and a degradation tag that can be recognized by a protein degradation system (small oval), a schematic metabolic pathway in which reactions are represented by arrows ( 7 ), with a particular reaction ( 8 ) catalyzed by the enzymatic element of the fusion protein, leading to production of an undesired product (diamond, 9 ), as well as an alternative pathway leading to production of a desired product (triangle, 10 ).
  • FIG. 1B shows the behavior of the system in response to a regulatory change, in
  • FIG. 2 is a schematic drawing showing an alternative metabolic pathway in which a desired product (triangle) is an intermediate in the production of an undesired product.
  • a desired product triangle
  • the protein that is reduced upon a regulatory switch catalyzes a reaction that converts the desired product into another molecule.
  • the regulatory switch When the regulatory switch is activated, the protein is degraded and the desired product accumulates.
  • FIGS. 3A-3E are schematic drawings showing genetic constructions for regulating the degradation of a protein.
  • FIG. 3A shows a DNA element ( 1 ) that includes a regulated promoter ( 2 ), a coding sequence for an enzyme of interest ( 3 ), and an in-frame coding sequence for a degradation tag ( 4 ).
  • FIG. 3B shows a DNA element similar to that in FIG. 3A , except that it encodes an mRNA whose translation is regulated by a regulatory site within the mRNA ( 5 ).
  • FIG. 1 shows a DNA element that includes a regulated promoter ( 2 ), a coding sequence for an enzyme of interest ( 3 ), and an in-frame coding sequence for a degradation tag ( 4 ).
  • FIG. 3B shows a DNA element similar to that in FIG. 3A , except that it encodes an mRNA whose translation is regulated by a regulatory site within the mRNA ( 5 ).
  • FIG. 1 shows a DNA element that includes a regulated promoter (
  • 3C shows a cellular configuration that includes a gene encoding a protein with a degradation tag, wherein the gene is transcribed, and also includes a second element in which the transcription of an antisense RNA is controlled by a regulated promoter ( 6 ).
  • a regulated promoter 6
  • the antisense RNA is expressed and binds to the mRNA encoding the protein with the degradation tag, blocking its translation and/or inducing its degradation, for example, by nucleases recognizing double-stranded RNA.
  • FIG. 3D shows a cellular configuration that includes a gene encoding a protein with a degradation tag, wherein the gene is transcribed, and also includes a second element in which the transcription of a degradation factor is controlled by a regulated promoter ( 7 ).
  • FIG. 3E shows a plasmid containing a gene encoding a protein with a degradation tag, and also containing an origin of replication that functions in a conditional manner ( 8 ).
  • FIG. 4 is a schematic drawing showing a bacterial cell for production of L-Valine.
  • the cell contains a plasmid encoding constitutive promoters ( 1 , 5 ) driving transcription of ilvE ( 3 ) and panB ( 6 ) fused to ssrA degradation tags variants ( 4 , 7 ).
  • the protein product from each gene is translated using the encoded ribosome binding site ( 2 ).
  • This plasmid contains a conditionally-replicated origin ( 8 ), allowing for facile curing of the plasmid (by a temperature shift, for example).
  • the bacterial chromosome ( 9 ) contains mutations rendering the endogenous copies of ilvE ( 10 ) and panB ( 11 ) inactive.
  • FIGS. 5A and 5B are schematic drawings showing a bacterial cell for production of L-Valine.
  • a conditionally-replicated plasmid ( 3 ) is maintained by a cell bearing loss-of-function chromosomal mutations ( 4 ) in specific metabolic enzymes.
  • the plasmid encodes for the production of ssrA-tagged metabolic enzymes ( 1 , 2 ) which complement the chromosomal mutants.
  • production of these enzymes outpaces degradation resulting in a steady state pool of the protein products.
  • FIG. 5B Upon shifting to the restrictive conditions ( FIG. 5B ), the plasmid is lost from the cell, essentially terminating synthesis. Under these conditions, an energy-dependent protease ( 5 ) degrades the remaining ssrA-tagged protein products.
  • a central aspect of the invention is the insight that it is useful and feasible to essentially harness the power of directed proteolysis to eliminate essential proteins during the production phase of metabolic engineering. To illustrate this insight, the generalized principles are described and exemplary schemes provided.
  • the methods of the invention control either the production, using regulated promoters, or degradation, using fused peptide segments which promote proteolysis (termed ‘degradation tags’), of one or more important or essential proteins.
  • a microbe carrying such a construction When a microbe carrying such a construction is to be grown to a large scale, conditions are created in which the rate of production of the protein of interest exceeds the combined rates of degradation and dilution (via cell growth and division) of said protein. Such ‘growth conditions’ produce sufficient steady-state concentrations of the protein of interest to allow for growth and replication of the microbe.
  • the fermentation conditions are perturbed such that production is slowed and/or degradation is hastened resulting in depletion of the protein of interest.
  • the protein of interest is an enzyme that controls a major competing metabolic flux that does not contribute to the particular product. Depletion of such an enzyme results in increased flux through the desired metabolic pathway thereby enhancing the production efficiency of the product of interest.
  • the protein of interest is fused to a degradation tag and its production is placed under the control of a regulated promoter.
  • a regulated promoter Under ‘growth conditions’, the promoter is induced such that production outpaces the basal levels of degradation.
  • the regulated promoter Upon switching to ‘production conditions’, the regulated promoter is repressed, thereby largely or completely terminating synthesis. Targeted protein degradation continues unabated until the protein of interest is essentially completely removed from the cell.
  • the gene of interest may reside on a conditionally-replicated plasmid vector (bearing a temperature-sensitive origin, for example). Under the permissive conditions, the plasmid is maintained by the cell, allowing for robust synthesis of the protein of interest. Upon moving to non-permissive conditions, the plasmid is lost from the cell, essentially terminating synthesis of the protein of interest and, through the aforementioned degradation pathways, resulting in removal of this protein from the cell.
  • microbial protein degradation systems or components thereof (e.g., adaptors, unfoldases, or proteases), are not essential, so an alternative configuration is to express a component of a protein degradation system from a regulated promoter and to express the protein of interest, fused to a degradation tag, from its native promoter or a weak, foreign promoter. In this configuration, the production of the protease component is repressed during the growth phase and induced during the production phase.
  • a cell When a cell is configured to express an inducible degradation factor with a protein of interest fused to a degradation tag and expressed from a distinctly regulated promoter, under some circumstances the degradation of the protein of interest is inadequate due to continued expression. In such circumstances, it is often useful to express an anti-sense RNA that can inhibit translation of the protein of interest, for example from the same inducible promoter that regulates the degradation factor.
  • proteolysis inhibitors or activators may be regulated, either using inducible promoters or conditionally-replicated plasmids, such that targeted degradation is inhibited during the ‘growth phase’ and permitted during the ‘production phase’.
  • inducible promoters or conditionally-replicated plasmids such that targeted degradation is inhibited during the ‘growth phase’ and permitted during the ‘production phase’.
  • growth-phase-dependent promoters may be utilized.
  • the E. coli promoter, osmY is known to be strongly induced during stationary phase.
  • the use of this, or a similarly regulated promoter, to drive production of a degradation component would allow for minimal degradation during culture growth (exponential phase) and efficient degradation once the culture had been saturated (stationary phase).
  • the gene of interest could be present during growth of the culture and later depleted allowing for efficient production of the small molecule of interest.
  • an exponential-phase promoter may be used to drive production of the protein of interest.
  • production would outpace degradation, allowing for sufficient steady-state levels of this protein to support growth.
  • this promoter Upon entering stationary phase, this promoter would be down-regulated, slowing production and allowing for degradation to remove the protein from the cell, thereby terminating growth and improving the production efficiency of the molecule of interest.
  • the principles of the invention may also be applied in a eukaryotic system.
  • yeasts are often used in the production of ethanol from a carbohydrate.
  • ethanol formation is promoted by pyruvate decarboxylase, while use of carbon for biomass production is promoted by the pyruvate dehydrogenase complex.
  • pyruvate dehydrogenase is manipulated as follows. A chromosome gene encoding a subunit of the pyruvate dehydrogenase complex (PDH) is knocked out according to standard procedures.
  • PDH pyruvate dehydrogenase complex
  • the corresponding gene is placed under control of a regulated promoter, such as a GAL1 promoter, GAL7 promoter or GAL10 promoter, which are inducible by galactose, or the CUP1 promoter, which is inducible by copper, zinc and other metal ions.
  • a regulated promoter such as a GAL1 promoter, GAL7 promoter or GAL10 promoter, which are inducible by galactose, or the CUP1 promoter, which is inducible by copper, zinc and other metal ions.
  • the coding sequence for the subunit of the pyruvate dehydrogenase complex is also fused to a sequence encoding a protein segment that promotes ubiquitination.
  • an F box protein segment is used as a fusion partner to promote degradation of the subunit of the PDH. Zhou et al.
  • Molecular Cell [2000] 6:751-756 describe how to construct an F box fusion to a second protein and express the protein in yeast and also in mammalian cells.
  • a CUP1(promoter)-Fbox-PDH subunit genetic construction is placed in a yeast cell with a knockout of the corresponding chromosomal gene encoding the PDH subunit, the yeast cell is grown in the presence of an inducing metal ion, the inducing metal ion is withdrawn, and enhanced ethanol production results.
  • carbohydrate sources such as glucose, sucrose, molasses, high-fructose corn syrup, depolymerized cellulosic biomass, or glycerol
  • carbohydrate sources such as glucose, sucrose, molasses, high-fructose corn syrup, depolymerized cellulosic biomass, or glycerol
  • pyruvate and acetyl-CoA Much of the carbon flux from such carbon sources goes through pyruvate and acetyl-CoA.
  • the latter molecule is the starting point for both the citric acid cycle (also known as the TCA cycle or the Krebs cycle), as well as fatty acid synthesis.
  • the process for converting pyruvate to acetyl-CoA is an essential process for growth of typical organisms used in metabolic engineering such as yeast or E. coli.
  • the goal when the goal is to produce a lactic acid, it is useful to eliminate the competing reaction of the conversion of pyruvate to acetyl-CoA. It is generally not useful to simply mutate the gene or genes involved in this process, as they are often important or essential during the organism's growth phase.
  • E. coli two major systems exist for converting pyruvate to acetyl-CoA: pyruvate dehydrogenase and pyruvate-formate lyase. Mutational inactivation of both of these systems prevents growth on glucose as a sole carbon source.
  • one of these systems such as pyruvate-formate lyase (which functions under anaerobic conditions) is mutated, and pyruvate dehydrogenase is engineered to be active under conditions of growth, but is then post-translationally inactivated.
  • Two specific methods of inactivation are provided by the invention, degradation by proteolysis and enzyme-mediated chemical modification such as phosphorylation.
  • These forms of post-translational modification are optionally inducible and are preferably induced when switching from growth conditions to production conditions. It is also generally useful to turn off transcription of the relevant genes upon switching to production conditions.
  • the proteolysis method may be employed as follows. Many bacteria, including E. coli , possess compartmentalized, energy-dependent proteases that recognize their substrates via short, fused peptide tags. Experiments in vitro and in vivo have shown that incorporation of such tags into foreign proteins is sufficient to direct efficient proteolysis of the targeted protein.
  • the best characterized tag, ssrA is derived from a system for degrading incorrectly translated proteins. Said system involves the ssrA tag sequence (Ala-Ala-Asn-Asp-Glu-Asn-Tyr-Ala-Leu-Ala-Ala in E.
  • coli coli ; SEQ ID NO: 1), an adaptor protein encoded by sspB that recognizes the ssrA-encoded peptide, and a series of downstream-functioning proteins (ClpX, ClpA, and ClpP) that unfold and degrade the tagged protein (Sauer et al., Cell 119:9-18 [2004]; Flynn et al., PNAS 98:10584-10589 [2001]).
  • this ssrA tag sequence is incorporated into partially translated proteins where the ribosome has stalled due to a truncated or otherwise defective mRNA.
  • this sequence or a variation thereof is incorporated into a protein of interest such as pyruvate dehydrogenase at the C-terminus.
  • the DNA sequence encoding the pyruvate dehydrogenase-ssrA fusion protein is expressed from an inducible/repressible promoter, and is repressed upon switching engineered bacteria from growth conditions to production conditions.
  • the pyruvate dehydrogenase-ssrA fusion protein is degraded at a constant rate, and when the transcription of the gene is halted, the mRNA naturally decays and the protein also decays due to the ssrA tag.
  • the user may choose from a wild-type tag or various mutant tags, depending on the desired efficacy of binding between the protease and the substrate. Since the degradation rate of a protein-ssrA fusion will vary somewhat as a function of the protein sequence and the intracellular substrate concentration, some routine experimentation is required to identify an optimal ssrA degradation tag.
  • an alternative configuration is the regulated expression of SspB in a strain in which the chromosomal copy of pyruvate dehydrogenase has been fused to the mutated ssrA tag. In this way, the native control elements of pyruvate dehydrogenase remain unperturbed.
  • adaptors from other bacteria C. crescentus CC_2101, for example have been identified which bind their cognate ssrA tags (AANDNFAEEFAVAA in C. crescentus ; SEQ ID NO: 3) and are capable of delivering bound substrates to E. coli ClpXP for degradation (Chien et al., Structure 15(10):1296-1305; Griffith et al., Mol Microbiol 70(4):1012-1025; Chowdhury et al., Protein Science 19(2):242-254).
  • variants of these foreign tags are not bound by the E. coli SspB variant allowing for control of suitably tagged substrates via the foreign adaptor.
  • the chromosomal copy of pyruvate dehydrogenase is fused to such a degradation tag.
  • the cognate adaptor is then introduced on a plasmid vector under the control of a regulated promoter. Pyruvate dehydrogenase is targeted for degradation only under conditions in which the foreign adaptor is produced. In this manner, both the endogenous protease system and control elements of pyruvate dehydrogenase remain unperturbed.
  • Fusion of endoprotease recognition sites which, when cleaved give rise to one of these N-end rule residues, may also be used to target proteins for degradation via the N-terminus (Wang et al., Genes Dev 21(4):403-408).
  • the following discussion will focus on a single implementation in which the protein of interest is targeted for degradation via fusion to an unmodified E. coli ssrA tag. Any other tag or degradation system may also be utilized.
  • Sample degradation tags include those listed in Table 1.
  • crescentus AANDNFAEEFAVAA ssrA tag (SEQ ID NO: 3) ccSsra Specificity A D NDNFAEEFA D
  • S Mutant 1 (SEQ ID NO: 11) ⁇ O tag (N-terminal tag) MTNTAKILNFGRAS (SEQ ID NO: 12)
  • the mutant tags allow for a reduced rate of intracellular degradation relative to the wild-type tag.
  • the result is that after switching to a medium that represses synthesis of the pyruvate dehydrogenase-ssrA protein, this protein is degraded over a period of 2-60 minutes depending on the needs of the user, and metabolic flux of carbon into acetyl-CoA from pyruvate essentially ceases. As a result, flux through lactate dehydrogenase is increased.
  • the method of the invention may be employed in combination with other engineering steps that enhance production of lactic acid, such as overproduction of lactate dehydrogenase, mutation of the zwf gene, growth in anaerobic conditions, and so on.
  • Metabolic engineering techniques to improve the biological production of amino acids have been applied with great success to the microbes B. subtilis, C. glutamicum , and E. coli .
  • genes encoding enzymes that catalyze off-pathway reactions have been removed from the production strain allowing for increased metabolic flux through the pathway of interest.
  • random mutagenesis and selected breeding approaches have resulted in strains that overproduce the amino acid of interest (Park et al. PNAS [2007] 104(19):7797-7802). Mapping of said mutant strains often reveals that genes catalyzing off-target reactions have been inactivated confirming the efficacy of this approach.
  • the off-target pathways catalyze the production of alternative amino acids and thus inactivation of these genes results in strains auxotrophic for a variety of amino acids.
  • pantothenate In E. coli and the industrially relevant microbe C. glutamicum , production of the branched amino acids, L-Leucine, L-Valine and the coenzyme A precursor, pantothenate all utilize the metabolic intermediate, 2-ketoisovalerate. This intermediate is channeled to L-Leucine through the enzyme leuA, to L-Valine through ilvE and to panthonate through panB. According to the invention, when overproduction of L-Leucine is desired, ilvE and panB are targeted for degradation as follows.
  • a plasmid bearing a temperature-sensitive origin as well as ssrA-tagged variants of ilvE and panB driven by a constitutive promoter is transformed into a host strain in which ilvE and panB have been knocked out of the chromosome. Under growth conditions, the plasmid is maintained and production outpaces degradation. Upon conversion to production conditions, the plasmid is cured from the cell, thereby effectively terminating synthesis and allowing for degradation to remove these enzymes from the cell. As such, metabolic flux is diverted toward the production of L-Leucine. Alternatively, when L-Valine production is desired, leuA and panB are targeted for degradation as described above.
  • Shikimic acid is an intermediate in aromatic amino acid synthesis, and is also used in the chemical synthesis of the drug Tamiflu® as well as in combinatorial chemical libraries.
  • the pathway for aromatic amino acid synthesis is illustrated below.
  • phosphoenolpyruvate and erythrose-4-phosphate both from central metabolism, are condensed to a single 7-carbon intermediate that is processed through a series of intermediates that ultimately diverge into separate pathways for phenylalanine, tryptophan, and tyrosine.
  • Shikimic acid is produced by the aroE gene product, and is then converted to shikimate phosphate by shikimate kinase, which in E. coli is produced independently by two genes, aroL and aroK.
  • Current methods for producing shikimic acid involve the null mutation of both aroL and aroK, blocking shikimate phosphate production and leading to accumulation of shikimic acid.
  • the aroK aroL double mutant is auxotrophic for tryptophan, tyrosine, and phenylalanine, each of which is an expensive molecule that must be added to the feedstock when shikimic acid is produced by metabolic engineering.
  • a shikimic acid-producing strain may be engineered as follows.
  • One of the shikimate kinase genes e.g., aroL
  • the other e.g., aroK
  • ssrA peptide fused to its C-terminus is expressed from a regulated promoter, such as the lac promoter, a quorum-sensing promoter, a promoter that is repressed in low-fixed nitrogen, a promoter that is induced by growth on glucose and repressed by growth on glycerol, or any other promoter that works well in the chosen conditions for switching from a growth mode to a production mode.
  • a regulated promoter such as the lac promoter, a quorum-sensing promoter, a promoter that is repressed in low-fixed nitrogen, a promoter that is induced by growth on glucose and repressed by growth on glycerol, or any other promoter that works well in the chosen conditions for switching from a growth mode to
  • shikimate kinase levels can be coupled to other strategies to enhance shikimic acid production, some of which are known in the art of metabolic engineering.
  • transport of glucose or most other carbohydrates normally involves transfer of a phosphate from phosphoenolpyruvate onto glucose.
  • a gene such as the glf gene from Zymomonas mobilis is often used.
  • One common method is to knock out the endogenous ptsI gene and instead express the glf gene.
  • an alternative method is to express a ptsI-ssrA fusion protein from a regulated promoter, and to also constitutively express the glf gene.
  • a pyruvate kinase-ssrA fusion protein is expressed from a regulated promoter and the wild-type pyruvate kinase gene is inactivated. The result is accumulation of PEP, which is then used by the engineered bacteria to produce shikimic acid.
  • an E. coli strain that is otherwise wild-type for example, MG1655 or W3110, may be engineered to have the following alterations:
  • the strain is grown in a minimal medium such as M9 medium with glucose, sucrose, or molasses as a carbon source, and in the absence of tryptophan, tyrosine, or phenylalanine.
  • a minimal medium such as M9 medium with glucose, sucrose, or molasses as a carbon source
  • tryptophan, tyrosine, or phenylalanine When the lambda P R system is used, the strain is grown at 42° C.
  • the temperature is lowered to 30° C., whereupon shikimic acid is produced.
  • shikimate kinase, pyruvate kinase, and the phosphotransferase I protein are repressed, and the corresponding proteins are degraded and not replaced, since mRNAs in E.
  • coli are generally unstable and have a half-life of only a few minutes.
  • the cessation of aromatic amino acid synthesis leads to an up-regulation of the initial steps of this pathway, such as the genes aroF, aroG, and aroH, which encode DAHP synthases.
  • the loss of pyruvate kinase activity leads to an accumulation of phosphoenolpyruvate (PEP), one of the substrates of DAHP synthase.
  • PEP phosphoenolpyruvate
  • the loss of the phosphotransferase I protein leads to a cessation of glucose transport by the phosphotransferase system, further assisting in PEP accumulation.
  • the loss of shikimate kinase activity results in accumulation of shikimic acid, which is collected by standard procedures.
  • the E. coli strain described above optionally includes other modifications described by Kraemer et al. (op. cit.), including but not limited to deletion of the shikimate transporter shiA, and use of an AroD/E-homologous protein from N. tabacum to reduce production of quinic acid.
  • the starting point for fatty acid synthesis is acetyl-CoA, which is also the starting point for the tricarboxylic acid cycle.
  • Such a construction has the effect of preventing entry into the TCA cycle, with the result that acetyl-CoA is preferentially directed into fatty acid synthesis.
  • production of ethanol may be enhanced.
  • DAHP synthase-ssrA fusion protein is expressed from a regulated promoter, and the promoter is turned off when production of a fatty acid product or related product is desired.
  • three isotypes of DAHP synthase are encoded by the genes aroF, aroG, and aroH.
  • coli it is generally useful to inactivate the chromosomal copies of these genes by mutation, then construct a fusion of one of genes to DNA encoding the ssrA peptide, which is then placed under the control of a regulated promoter.
  • dodecanoic acid (lauric acid; C12 fatty acid; CH 3 (CH 2 ) 10 COOH).
  • Voelker and Davies J. Bact. [1994] 176[23]7320-7327
  • the C12 thioesterase has the effect of releasing lauric acid from acyl carrier protein during fatty acid synthesis, and the fadD encodes a fatty acid degradation enzyme that recycles the carbon in fatty acids that cannot be incorporated into membranes.
  • the C12 thioesterase-expressing fadD knockout strain synthesizes lauric acid at a high level. However, it is noteworthy that this strain grows and divides (FIG. 5 of Voelker and Davies), evidently converting much of the input carbon into biomass even though the C12 thioesterase is expressed constitutively at a high level.
  • a C12 thioesterase-expressing fadD knockout strain when a C12 thioesterase-expressing fadD knockout strain is also engineered to express a DAHP synthase-ssrA fusion protein from a regulated promoter, and the promoter is turned off, the DAHP synthase-ssrA fusion protein is degraded and not replaced, protein synthesis essentially ceases, and production of lauric acid is enhanced relative to the C12 thioesterase-expressing fadD knockout strain.
  • a strain expressing valine synthesis genes, 2-ketoacid decarboxylase, and alcohol dehydrogenase is also engineered to express a DAHP synthase-ssrA fusion protein from a regulated promoter, and the promoter is turned off, the DAHP synthase-ssrA fusion protein is degraded and not replaced, protein synthesis essentially ceases, and production of isobutanol is enhanced relative to the parental isobutanol-secreting strain.
  • Atsumi et al. described the production of a variety of alpha-keto carboxylic acids such as 2-ketobutyrate, 2-ketoisovalerate, 2-ketovalerate, 2-keto-3-methyl-valerate, 2-keto-4-methyl-valerate, and phenylpyruvate, which can be decarboxylated to create an aldehyde and then reduced by the serial actions of 2-ketoacid decarboxylase, and alcohol dehydrogenase, to create a series of useful alcohols.
  • alpha-keto carboxylic acids such as 2-ketobutyrate, 2-ketoisovalerate, 2-ketovalerate, 2-keto-3-methyl-valerate, 2-keto-4-methyl-valerate, and phenylpyruvate, which can be decarboxylated to create an aldehyde and then reduced by the serial actions of 2-ketoacid decarboxylase, and alcohol dehydrogenase, to create a series of useful alcohol
  • strains when such strains are also engineered to express a DAHP synthase-ssrA fusion protein from a regulated promoter, and the promoter is turned off, the DAHP synthase-ssrA fusion protein is degraded and not replaced, protein synthesis essentially ceases, and production of the desired alcohols is enhanced relative to the parental alcohol-producing strains.
  • Shikimate kinase (AroK)-ssrA (SEQ ID NO: 14) MAEKRNIFLVGPMGAGKSTIGRQLAQQLNMEFYDSDQEIEKRTGADVG WVFDLEGEEGFRDREEKVINELTEKQGIVLATGGGSVKSRETRNRLSA RGVVVYLETTIEKQLARTQRDKKRPLLHVETPPREVLEALANERNPLY EEIADVTIRTDDQSAKVVANQIIHMLESNAANDENYALAA Shikimate kinase-linker-ssrA (SEQ ID NO: 15) MAEKRNIFLVGPMGAGKSTIGRQLAQQLNMEFYDSDQEIEKRTGADVG WVFDLEGEEGFRDREEKVINELTEKQGIVLATGGGSVKSRETRNRLSA RGVVVYLETTIEKQLARTQRDKKRPLLHVETPPREVLEALANERNPLY EEIADVTIRTDDQS
  • An E. coli strain capable of being grown in the absence of aromatic amino acids and producing shikimic acid was engineered as follows.
  • the strain was engineered to express a shikimate kinase isoform, the product of the aroK gene, from a plasmid, while the chromosomal genes encoding shikimate kinase were non-functional.
  • the plasmid-borne shikimate kinase isoform was engineered to have a degradation tag at its C-terminus. In this case and throughout the invention, it was and is useful to inspect the three-dimensional structure of a protein to verify that a chosen terminus is compatible with addition of a degradation tag.
  • the solved structure of the aroK product, PDB file 1KAG was inspected and the steric availability of the C-terminus was verified.
  • Plasmid vectors were generated which allow for conditional expression of E. coli shikimate kinase I, aroK. Using standard plasmid construction techniques, the coding sequence for aroK was fused to each of the four degradation tags, AANDENYALAA (SEQ ID NO: 1), AANDENYALVA (SEQ ID NO: 8), AANDENYADAS (SEQ ID NO: 2), and AANDENYALDD (SEQ ID NO: 13). This fusion construct was inserted downstream of either the IPTG-inducible lac promoter (SEQ ID NO: 33) or the HSL-inducible LuxR-derived promoter, F2620 (SEQ ID NO: 32).
  • Each construct contained the ribosome binding site (SEQ ID NO: 34) and resided on the plasmid backbone, pSB3C5 (SEQ ID NO: 31), a chloramphenicol-resistant low-copy plasmid bearing a p15a origin of replication. Nucleotide sequences for each component are listed below, as well as a sample assembled sequence for the construct F2620-B0032-AroK-LVA (SEQ ID NO: 41) as present in pSB3C5.
  • PCR1-LAA was then incubated with restriction enzymes XbaI and PstI in NEB Buffer #2 supplemented with BSA for 2 hours at 37° C.; PCR2-F2620 was incubated with restriction enzymes EcoRI and SpeI under identical conditions. Successful PCR amplification and restriction digestion was analyzed by gel electrophoresis. After removing heat-denatured restriction enzymes using a Qiagen PCR purification kit, digested PCR1-LAA and PCR2-F2620 were mixed in a stoichiometric ratio with plasmid backbone pSB3C5 which had been treated with EcoRI and PstI.
  • the 3-component mixture was incubated with T4 DNA ligase for 2 hours at room temperature. Chemically competent E. coli NEB 10 ⁇ cells were then transformed with this ligation product and plated on LB/chloramphenicol. Individual colonies were picked and grown in liquid culture overnight.
  • GBW181, GBW182, and GBW183 were engineered as follows. The relevant features were that GBW181, GWB182, and GWB183 contained a version of aroK with a C-terminal “AANDENYADAS” (SEQ ID NO: 2), “AANDENYALVA” (SEQ ID NO: 8), and “AANDENYALDD” (SEQ ID NO: 13), variants of the AANDENYALAA (SEQ ID NO: 1) degradation tag (see table above). Of these, the AANDENYALVA (SEQ ID NO: 8) tag triggered the greatest degradation, while the AANDENYALDD (SEQ ID NO: 13) did not cause degradation and served as a negative control.
  • AANDENYADAS SEQ ID NO: 2
  • AANDENYALVA SEQ ID NO: 8
  • AANDENYALDD SEQ ID NO: 13
  • the aroK-tag genes were regulated by a strong promoter that was induced by homoserine lactone.
  • the aroK gene was expressed from the element F2620 (SEQ ID NO: 32), which encodes a luxR transcriptional regulatory protein that is activated by homoserine lactone (HSL), a LuxR-regulated promoter directing transcription of the E. coli aroK gene fused to a DNA segment encoding AANDENYALVA (SEQ ID NO: 8), and a p15a origin of replication.
  • HSL homoserine lactone
  • SEQ ID NO: 8 a DNA segment encoding AANDENYALVA
  • the chromosomal copies of aroK and aroL were mutated by conventional procedures.
  • the supernatants were tested for levels of shikimic acid by a bioassay as follows, based on the ability of shikimic acid to support growth of an aroE mutant of E. coli .
  • Each supernatant was diluted 2-fold into fresh medium containing about 10 4 of an aroK mutant strain of E. coli , JW3242-1 (Coli Genetic Stock Center, New Haven, Conn.).
  • serial dilutions of shikimic acid were added to similar cultures. The cultures were grown for 24 hours and optical densities compared. Based on this analysis, the shikimic acid level in the culture lacking homoserine lactone was about 10 ⁇ g/ml. The culture with 10 nM homoserine lactone produced no detectable shikimic acid.
  • shikimic acid was also observed in a culture of strain 182 grown in the absence of amino acid supplements.
  • a culture is grown in the presence of homoserine lactone in, for example, M9 medium containing glucose, sucrose, glycerol, molasses, or treated cellulosic biomass, is grown to a late logarithmic stage, the homoserine lactone is removed, and shikimic acid is produced by the cells as the aroK product is degraded and not replaced. The resulting shikimic acid is purified from the supernatant.
  • strain 182 is engineered to express the glf gene from Zymomonas mobilis.
  • Example 2 Production of Shikimic Acid from a Microbial Strain in Which Shikimate Kinase is Fused to a Degradation Tag and Expressed from an Episome with Conditional Replication
  • an E. coli strain that could be grown in the absence of aromatic amino acids and produce shikimic acid was engineered as follows.
  • Four variants were constructed from a plasmid derivative of the low-copy vector pSC101, in which the origin of the plasmid was temperature-sensitive for replication.
  • the plasmid encoded the E. coli aroK gene expressed from its endogenous promoter.
  • the four plasmid variant coding sequences for the degradation tags AANDENYALAA (SEQ ID NO: 1), AANDENYALVA (SEQ ID NO: 8), AANDENYADAS (SEQ ID NO: 2) and the non-degrading control variant AANDENYALDD (SEQ ID NO: 13) were fused to the 3′ end of the aroK coding sequence. These vectors also encoded a chloramphenicol-resistance marker. Expression of shikimate kinase from the E. coli chromosome was defective.
  • the four strains were inoculated into the M9 glucose thiamin tryptophan-dropout medium described in Example 1 and incubated with aeration at 30° C. for 16 hours.
  • the strains encoding shikimate kinase with the AANDENYADAS (SEQ ID NO: 2) and AANDENYALDD (SEQ ID NO: 13) tags reached near-saturation while the strains encoding shikimate kinase with the AANDENYALAA (SEQ ID NO: 1) and AANDENYALVA (SEQ ID NO: 8) tags showed no detectable growth.
  • the strain encoding the shikimate kinase-AANDENYADAS (SEQ ID NO: 2) fusion protein was pelleted in a centrifuge and resuspended in fresh medium for a net 2-fold dilution, and then incubated at 37° C. for about 5.5 hours with aeration.
  • the cells were pelleted in a centrifuge, and the supernatant was withdrawn, filter-sterilized, and tested for shikimic acid levels in the bioassay essentially as described in Example 1. Based on the results of this bioassay, the shikimic acid in the filter-sterilized supernatant of the culture was about 0.05 micrograms/ml.
  • shikimic acid was produced by the following mechanism.
  • the culture bearing plasmid with the shikimate kinase-AANDENYADAS (SEQ ID NO: 2) expression construction and the temperature-sensitive origin of replication was transferred to 37° C.
  • replication of the plasmid largely or completely stopped, and the plasmid was lost from many cells during cell division.
  • the remaining shikimate kinase-AANDENYADAS (SEQ ID NO: 2) protein was degraded and not replaced, leaving the cell without shikimate kinase enzyme activity.
  • Such cells produced shikimic acid and secreted this molecule into the medium.

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Cited By (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11193149B2 (en) 2017-02-21 2021-12-07 Duke University Compositions and methods for robust dynamic metabolic control of alanine production
US20230088135A1 (en) * 2020-05-20 2023-03-23 Cj Cheiljedang Corporation Novel polypeptide and method for producing l-leucine using same
US20240101977A1 (en) * 2020-12-11 2024-03-28 Cj Cheiljedang Corporation Novel branched-chain amino acid aminotransferase variant and method for producing isoleucine using the same

Families Citing this family (36)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8647642B2 (en) 2008-09-18 2014-02-11 Aviex Technologies, Llc Live bacterial vaccines resistant to carbon dioxide (CO2), acidic PH and/or osmolarity for viral infection prophylaxis or treatment
WO2010077806A1 (fr) 2008-12-15 2010-07-08 Greenlight Biosciences, Inc. Procédés de commande de flux dans des voies métaboliques
US10385367B2 (en) 2009-06-01 2019-08-20 Ginkgo Bioworks, Inc. Methods and molecules for yield improvement involving metabolic engineering
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US9540652B2 (en) * 2011-09-02 2017-01-10 The Regents Of The University Of California Metabolic engineering of the shikimate pathway
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MY172692A (en) 2012-07-13 2019-12-10 Calysta Inc Biorefinery system, methods and compositions thereof
WO2014074886A1 (fr) 2012-11-09 2014-05-15 Calysta Energy, Inc. Compositions et procédés de production biologique de dérivés d'acides gras
US9611487B2 (en) 2012-12-21 2017-04-04 Greenlight Biosciences, Inc. Cell-free system for converting methane into fuel and chemical compounds
WO2014160059A1 (fr) 2013-03-13 2014-10-02 Gen9, Inc. Compositions et procédés pour la synthèse d'oligonucléotides à fidélité élevée
EP3030671B1 (fr) 2013-08-05 2018-10-03 Greenlight Biosciences, Inc. Protéines produites par génie génétique avec site de clivage par les protéases
MY203868A (en) 2014-06-11 2024-07-22 Univ Duke Compositions and methods for rapid and dynamic flux control using synthetic metabolic valves
WO2016160936A1 (fr) 2015-03-30 2016-10-06 Greenlight Biosciences, Inc. Production acellulaire d'acide ribonucléique
US10676723B2 (en) 2015-05-11 2020-06-09 David Gordon Bermudes Chimeric protein toxins for expression by therapeutic bacteria
US11208649B2 (en) 2015-12-07 2021-12-28 Zymergen Inc. HTP genomic engineering platform
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US9988624B2 (en) 2015-12-07 2018-06-05 Zymergen Inc. Microbial strain improvement by a HTP genomic engineering platform
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JP2019519241A (ja) 2016-06-30 2019-07-11 ザイマージェン インコーポレイテッド グルコース透過酵素ライブラリーを生成するための方法およびその使用
US11129906B1 (en) 2016-12-07 2021-09-28 David Gordon Bermudes Chimeric protein toxins for expression by therapeutic bacteria
US11180535B1 (en) 2016-12-07 2021-11-23 David Gordon Bermudes Saccharide binding, tumor penetration, and cytotoxic antitumor chimeric peptides from therapeutic bacteria
WO2018112014A2 (fr) * 2016-12-15 2018-06-21 The Government Of The United States Of America, As Represented By The Secretary Of The Navy Cascades d'enzymes fixées à des nanoparticules pour biocatalyse multi-étapes accélérée
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WO2020056343A1 (fr) 2018-09-13 2020-03-19 Northwestern University Systèmes et procédés de promoteur de rétroaction commutable riborégulé
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PL439032A1 (pl) * 2021-09-24 2023-03-27 Uniwersytet Warszawski Konstrukty peptydowe do celowanej degradacji białek

Citations (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2003089614A2 (fr) * 2002-04-18 2003-10-30 Genencor International, Inc. Production d'anticorps fonctionnels dans des champignons filamenteux
US20060073577A1 (en) * 2004-09-17 2006-04-06 San Ka-Yiu High succinate producing bacteria
US20070118916A1 (en) 2005-10-14 2007-05-24 Metanomics Gmbh Process for the production of fine chemicals
US20080038779A1 (en) 1992-11-05 2008-02-14 Danisco Sweeteners Oy Manufacture of Five-Carbon Sugars and Sugar Alcohols
US20090000047A1 (en) 2006-12-28 2009-01-01 Nobuhiro Mashiko Toothbrush
US20090137010A1 (en) * 2007-09-27 2009-05-28 Rustem Saidovich Shakulov Method for producing amino acids using bacterium of the enterobacteriaceae family
WO2009065777A1 (fr) * 2007-11-20 2009-05-28 Dsm Ip Assets B.V. Production d'acide dicarboxylique dans un champignon filamenteux
WO2010141468A1 (fr) 2009-06-01 2010-12-09 Way Jeffrey C Procédés et molécules permettant une amélioration du rendement faisant appel à l'ingénierie métabolique

Family Cites Families (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN104212844A (zh) * 2007-06-01 2014-12-17 索拉兹米公司 在微生物中生产油

Patent Citations (8)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20080038779A1 (en) 1992-11-05 2008-02-14 Danisco Sweeteners Oy Manufacture of Five-Carbon Sugars and Sugar Alcohols
WO2003089614A2 (fr) * 2002-04-18 2003-10-30 Genencor International, Inc. Production d'anticorps fonctionnels dans des champignons filamenteux
US20060073577A1 (en) * 2004-09-17 2006-04-06 San Ka-Yiu High succinate producing bacteria
US20070118916A1 (en) 2005-10-14 2007-05-24 Metanomics Gmbh Process for the production of fine chemicals
US20090000047A1 (en) 2006-12-28 2009-01-01 Nobuhiro Mashiko Toothbrush
US20090137010A1 (en) * 2007-09-27 2009-05-28 Rustem Saidovich Shakulov Method for producing amino acids using bacterium of the enterobacteriaceae family
WO2009065777A1 (fr) * 2007-11-20 2009-05-28 Dsm Ip Assets B.V. Production d'acide dicarboxylique dans un champignon filamenteux
WO2010141468A1 (fr) 2009-06-01 2010-12-09 Way Jeffrey C Procédés et molécules permettant une amélioration du rendement faisant appel à l'ingénierie métabolique

Non-Patent Citations (41)

* Cited by examiner, † Cited by third party
Title
Andexer et al., Emerging Enzymes for ATP Regeneration in Biocatlytic Processes., ChemBioChem (2015), vol. 16, pp. 380-386. *
Atsumi et al., "Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels." Nature. 451: (2008). 86-90.
Burton et al., "Nucleotide-dependent substrate recognition by the AAA+ HsIUV protease," Nat. Struct. Mol. Bio. 12(3): 245-251 (2005).
Chien et al., "Structure and Substrate Specificity of an SspB Ortholog: Design Implications for AAA+ Adaptors," Structure. 15(10):1296-1305 (2007).
Chowdhury et al., "Versatile modes of peptide recognition by the CIpX N domain mediate alternative adaptor-binding specificities in different bacterial species," Protein Science 19(2): 242-254 (2010).
Definition of metabolic-pathway (last viewed on Jul. 14, 2017). *
Dosselaere et al., A Metabolic Node in Action: Chorismate-Utilizing Enzymes in Microorganisms, Critical Reviews in Microbiology (2001), vol. 27, No. 2 , pp. 75-131. *
Flynn et al., "Overlapping recognition determinants within the ssrA degradation tag allow modulation of proteolysis," PNAS 98:10584-10589 (2001).
Flynn et al., "Proteomic Discovery of Cellular Substrates of the ClpXP Protease Reveals Five Classes of ClpXP-Recognition Signals," Mol. Cell 11(3): 671-683 (2003).
glycolysis-10-steps-explained (last viewed on Aug. 2, 2016). *
Gottesman, Proteolysis in Bacterial Regulatory Circuits, Annual Review of Cell and Developmental Biology (2003), vol. 19, pp. 565-587. *
Griffith et al., "Inducible protein degradation in Bacillus subtilis using heterologous peptide tags and adaptor proteins to target substrates to the protease ClpXP," Mol. Microbiol. 70(4): 1012-1025 (2008).
Grilly et al., "A synthetic gene network for tuning protein degradation in Saccharomyces cerevisiae," Mol. Syst. Biol. 3 (127): 1-5 (2007).
Gur et al., "Biological Sciences-Biochemistry," PNAS. 105(42): 16113-16118 (2008).
Gur et al., "Degrons in protein substrates program the speed and operating efficiency of the AAA+ Lon proteolytic machine," PNAS. 106(44): 18503-18508 (2009).
Gur et al., "Biological Sciences—Biochemistry," PNAS. 105(42): 16113-16118 (2008).
Hersch et al., SspB delivery of substrates for ClpXP proteolysis probed by the design of improved degradation tags., PNAS (2004), vol. 101, pp. 12136-12141. *
International Search Report for International Patent Application No. PCT/US2010/36902 dated Oct. 28, 2010.
Janssen et al., "Metabolic pathways and energetics of the acetone-oxidizing, sulfate-reducing bacterium, Desulfobacteriumcetonicum," March. Microbiol. 163(3): 188-194 (1995).
Kang et al. Functional Proteolytic Complexes of the Human Mitochondrial ATP-dependent Protease, hClpXP., The Journal of Biological Chemistry (2002), vol. 277, pp. 21095-21102. *
Kinoshita et al. Regulation of CMV promoter-driven exogenous gene expression with doxorubicin in genetically modified cells. J Pharm Pharmacol. (2008), vol. 60(12), pp. 1659-1665. *
Kramer et al., "Metabolic engineering for microbial production of shikimic acid,"Metabolic Engineering. 5:277-283 (2003).
McGinness et al.,"Engineering Controllable Protein Degradation," Mol. Cell. 22(5): 701-707 (2006).
Meada et al., The Shikimate Pathway and Aromatic Amino acid Biosynthesis in Plants., Annu. Rev. Plant Biol. (2012), vol. 63, pp. 73-105. *
metK_BACSU (last viewed on Feb. 1, 2016). *
Park and Lee. "Fermentative production of branched chain amino acids: a focus on metabolic engineering," Appl. Micribiol. Biotechnol. 85:491-596 (2010).
Park et al., "Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation," PNAS. 104(19):7797-7802 (2007).
pcDNA3 Invitrogen (last viewed on Jul. 13, 2017). *
Pedrido et al Spo0A links de novo fatty acid synthesis to sporulation and biofilm development in Bacillus subtilis., Molecular Microbiology (2013), vol. 87(2), pp. 348-367. *
pGEM vector system Promega (last viewed on Jul. 17, 2017). *
Sauer et al., "Sculpting the Proteome with AAA+ Proteases and Disassembly Machines," Cell. 119(1): 9-18 (2004).
Smith et al. ATP Binding to PAN or the 26S ATPases Causes Association with the 20S Proteasome, Gate Opening, and Translocation of Unfolded Proteins., Molecular Cell (2005), vol. 20, Issue 5, pp. 687-698. *
SSPB_ECOLI (last viewed on Feb. 1, 2016). *
Stack et al. A ubiquitin-based tagging system for controlled modulation of protein stability., Nature Biotechnology (2000), vol. 18, pp. 1298-1302. *
Voelker and Davies. "Alteration of the specificity and regulation of fatty acid synthesis of Escherichia coli by expression of a plant medium-chain acyl-acyl carrier protein thioesterase," J. Bact. 176 (23): 7320-7327 (1994).
Whitten et al., The Structure of the KinA-Sda Complex Suggests an Allosteric Mechanism of Histidine Kinase Inhibition., The Journal of Molecular Biology (2007), vol. 368, Issue 2, pp. 407-420. *
Wiegert et al., SsrA-Mediated Tagging in Bacillus subtilis., Journal of Bacteriology (2001), vol. 183, pp. 3885-3889. *
Written Opinion for PCT/US2010/036902, 6 pages dated (Oct. 28, 2010).
Yuan et al., "Molecular basis for the accumulation of acidic isozymes of triosephosphate isomerase on aging," Mech. Ageing Dev. 17(2): 151-162 (1981).
Zhang et al. The inhibition of CMV promoter by heat shock factor 4b is regulated by Daxx., The International Journal of Biochemistry & Cell Biology (2010), vol. 42, Issue 10, pp. 1698-1707. *
Zhou et al., "Harnessing the Ubiquitination Machinery to Target the Degradation of Specific Cellular Proteins," Molecular Cell. 6(3): 751-756 (2000).

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