EP4172310A1 - Verbesserte cystein produzierende stämme - Google Patents

Verbesserte cystein produzierende stämme

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Publication number
EP4172310A1
EP4172310A1 EP20735534.8A EP20735534A EP4172310A1 EP 4172310 A1 EP4172310 A1 EP 4172310A1 EP 20735534 A EP20735534 A EP 20735534A EP 4172310 A1 EP4172310 A1 EP 4172310A1
Authority
EP
European Patent Office
Prior art keywords
gene
ppsa
cysteine
enzyme
microorganism strain
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
EP20735534.8A
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German (de)
English (en)
French (fr)
Inventor
Rupert Pfaller
Johanna Koch
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Wacker Chemie AG
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Wacker Chemie AG
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Filing date
Publication date
Application filed by Wacker Chemie AG filed Critical Wacker Chemie AG
Publication of EP4172310A1 publication Critical patent/EP4172310A1/de
Pending legal-status Critical Current

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    • 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
    • C12N15/70—Vectors or expression systems specially adapted for E. coli
    • 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)
    • C12N9/1294—Phosphotransferases with paired acceptors (2.7.9)
    • 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
    • C12N1/00—Microorganisms, e.g. protozoa; Compositions thereof; Processes of propagating, maintaining or preserving microorganisms or compositions thereof; Processes of preparing or isolating a composition containing a microorganism; Culture media therefor
    • C12N1/20—Bacteria; Culture media therefor
    • 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
    • C12N9/0004—Oxidoreductases (1.)
    • C12N9/0006—Oxidoreductases (1.) acting on CH-OH groups as donors (1.1)
    • 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.)
    • C12N9/1025—Acyltransferases (2.3)
    • C12N9/1029—Acyltransferases (2.3) transferring groups other than amino-acyl groups (2.3.1)
    • 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
    • C12P13/00—Preparation of nitrogen-containing organic compounds
    • C12P13/04—Alpha- or beta- amino acids
    • C12P13/12—Methionine; Cysteine; Cystine
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y207/00—Transferases transferring phosphorus-containing groups (2.7)
    • C12Y207/09—Phosphotransferases with paired acceptors (2.7.9)
    • C12Y207/09002—Pyruvate, water dikinase (2.7.9.2)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12R—INDEXING SCHEME ASSOCIATED WITH SUBCLASSES C12C - C12Q, RELATING TO MICROORGANISMS
    • C12R2001/00—Microorganisms ; Processes using microorganisms
    • C12R2001/01—Bacteria or Actinomycetales ; using bacteria or Actinomycetales
    • C12R2001/185—Escherichia
    • C12R2001/19—Escherichia coli
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y101/00—Oxidoreductases acting on the CH-OH group of donors (1.1)
    • C12Y101/01—Oxidoreductases acting on the CH-OH group of donors (1.1) with NAD+ or NADP+ as acceptor (1.1.1)
    • C12Y101/01095—Phosphoglycerate dehydrogenase (1.1.1.95)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y203/00—Acyltransferases (2.3)
    • C12Y203/01—Acyltransferases (2.3) transferring groups other than amino-acyl groups (2.3.1)
    • C12Y203/0103—Serine O-acetyltransferase (2.3.1.30)

Definitions

  • the invention relates to a microorganism strain which is suitable for the fermentative production of L-cysteine, characterized in that the relative enzyme activity of the enzyme class designated in the KEGG database with the number EC 2.7.9.2 inactivates or based on the specific activity of the wild-type enzyme is reduced, and compared to the microorganism strain with wild-type enzyme activity of the enzyme class designated in the KEGG database with the number EC 2.7.9.2 forms an increased amount of L-cysteine, the gene encoding this enzyme activity is referred to as ppsA.
  • the invention also provides a method for producing L-cysteine using these microorganism cells.
  • Cysteine abbreviated to Cys or C, is an ⁇ -amino acid with the -CH2-SH side chain. Since the naturally occurring enantiomeric form is L-cysteine and only this represents a proteinogenic amino acid, L-cysteine is meant in the context of this invention when the term cysteine is used without a descriptor.
  • L-enantiomer or L-cystine, or (R, R) -3,3'-dithio- bis (2-aminopropionic acid)
  • L-cysteine is a semi-essential amino acid for humans, as it can be formed from the amino acid methionine.
  • Cysteine plays a key role in sulfur metabolism in all organisms and is used in the synthesis of proteins, glutathione, biotin, lipoic acid, thiamine, taurine, methionine and other sulfur-containing metabolites.
  • L-cysteine serves as a precursor for the biosynthesis of coenzyme A.
  • the biosynthesis of cysteine has been studied in detail in bacteria, especially in enterobacteria. A summary of the cysteine biosynthesis can be found in Wada and Takagi, Appl. Microbiol. Biotechnol. (2006) 73: 48-54.
  • the amino acid L-cysteine is of economic importance.
  • a process for the fermentative production of cysteine is also available.
  • the prior art relating to the fermentative production of cysteine with microorganisms is disclosed, for example, in EP 0858510 B1, EP 0885962 B1, EP 1382 684 B1, EP 1220 940 B2, EP 1769 080 B1 and EP 2 138 585 B1.
  • the bacterial host organisms used include strains of the genus Corynebacterium and representatives of the Enterobacteriaceae family, such as B. Escherichia coli or Pantoea ananatis are used.
  • O-Acetyl-L-Serine is formed from L-Serine and Acetyl-CoA.
  • L-serine in sufficient quantities for cysteine production is therefore of great importance.
  • This can be achieved by introducing a serA allele which codes for a 3-phosphoglycerate dehydrogenase with reduced feedback inhibition by L-serine.
  • 3-hydroxypyruvate a biosynthetic precursor of L-serine
  • Examples of such SerA enzymes are described in EP 0620853 B1 and EP 1496 111 B1. But also Bell et al., Eur. J. Biochem. (2002) 269: 4176-4184 disclose changes to the serA gene for deregulating enzyme activity.
  • cysteine yield in fermentation can be increased by weakening or destroying genes which code for cysteine-degrading enzymes, such as the tryptophanase TnaA or the cystathionine ⁇ -lyases MalY or MetC (EP 1571223 Bl).
  • Increasing the transport of cysteine out of the cell is another way of increasing the product yield in the medium. This can be achieved through overexpression of so-called efflux genes. These genes code for membrane-bound proteins that mediate the export of cysteine from the cell.
  • L-cysteine is continuously withdrawn from the intracellular reaction equilibrium, with the result that the level of this amino acid in the cell is kept low and the feedback inhibition of sensitive enzymes by L-cysteine does not occur: (1) L-cysteine (intracellular) L-cysteine (medium)
  • the optimization of the fermentation process ie the way in which the cells are cultivated, also plays an important role in the development of an efficient production process.
  • Various cultivation parameters such as the type and dosage of the carbon and energy source, the temperature, the supply of oxygen (EP 2707 492 B1), the pH value and the composition of the culture medium, the product yield and / or the Influence the product range in the fermentative production of cysteine. Due to continuously increasing raw material and energy costs, there is a constant need to increase the product yield in the cysteine production in order to improve the economic efficiency of the process in this way.
  • the object of the present invention is to provide a microorganism strain for the fermentative production of cysteine with which, compared to known strains from the prior art, higher yields of L-cysteine or L-cystine in fermentation can be achieved.
  • the object is achieved by a microorganism strain that is suitable for the fermentative production of L-cysteine, characterized in that the relative enzyme activity of the enzyme class designated in the KEGG database with the number EC 2. ⁇ .9.2 inactivates or based on the specific activity of the wild-type enzyme is reduced, and compared to the microorganism strain with wild-type enzyme activity of the enzyme class designated in the KEGG database with the number EC 2.7.9.2 forms an increased amount of L-cysteine, this enzyme activity coding gene is referred to as ppsA.
  • the enzyme activity of the enzyme class designated in the KEGG database with the number EC 2. ⁇ .9.2 is defined by the fact that it can produce pyruvate from phosphoenolpyruvate in a reversible reaction according to the formula:
  • AMP adenosine monophosphate
  • ATP adenosine triphosphate
  • This enzyme activity is therefore also referred to as phosphoenolpyruvate synthase (PEP synthase, EC 2.7.9.2) or also synonymously as phosphoenolpyruvate H 2 O dikinase.
  • the gene coding for this protein is abbreviated as ppsA in the context of this invention.
  • Detection of enzyme activity (enzyme assay, PEP synthase assay): The PEP synthase activity of a microorganism strain can be determined by pelleting the cells from the cultivation in a liquid medium, washing them and using a fast prep 24 TM 5G Cell Homogenizer (MP Biomedicals) a cell extract is produced. The protein content of the extract can be determined, for example, using the “ Qubit® Protein Assay Kit” (Thermo Fisher Scientific).
  • the PEP synthase enzyme activity can be measured by the stoichiometric production of phosphate from the reaction of pyruvate and ATP, according to equation (4), for example with the aid of the "Malachite Green Phosphate Assay Kit” (SigmaAldrich).
  • the stoichiometric production of AMP or phosphoenolpyruvate or the stoichiometric consumption of pyruvate or ATP can be determined (cf. equation 4).
  • a test for determining the PEP synthase enzyme activity via the ATP-dependent consumption of pyruvate is described, for example, in Berman and Cohn, J. Biol. Chem. (1970) 245: 5309-5318.
  • a test for the ATP-dependent formation of phosphoenolpyruvate is also described in Berman and Cohn, J. Biol. Chem. (1970) 245: 5309-5318.
  • the specific enzyme activity is calculated by relating the enzyme activity to 1 mg total protein of the cell extract that has not been further purified or treated (U / mg protein). It must be taken into account that the cell extract must be produced in the same way in order to compare different PEP synthase enzymes. As already described, the cell extract can e.g. be produced with the help of a FastPrep-24 TM 5G cell homogenizer (MP Biomedicals).
  • the specific activity can also be related to 1 mg of the enzymes purified in the same way in each case (U / mg purified protein).
  • a method for purifying PEP synthase and for determining the specific activity of the purified protein is described, for example, in Berman and Cohn, J. Biol. Chem. (1970) 245: 5309-5338.
  • the relative enzyme activity can be determined by setting the specific enzyme activity, determined in the PEP synthase assay, of the microorganism strain that carries the Wt allele in relation to the gene encoding the PEP synthase. The value measured in the PEP synthase assay for the specific enzyme activity of a sample is given as a percentage in relation to this strain with Wt enzyme.
  • the area of the DNA or RNA which begins with a start codon and ends with a stop codon and codes for the amino acid sequence of a protein is referred to as the open reading frame (ORF, synonymous with cds, coding sequence).
  • ORF is also known as the coding region or structural gene.
  • the gene is the segment of DNA that contains all the basic information required to produce a biologically active RNA.
  • a gene contains the DNA segment from which a single-stranded RNA copy is produced by transcription and the expression signals that are involved in the regulation of this copying process.
  • the expression signals include, for example, at least one promoter, a transcription start, a translation start and a ribosome binding site.
  • a terminator and one or more operators are also possible as expression signals.
  • proteins such as PpsA begin with a capital letter, while the sequences (cds) encoding these proteins are designated with a lower case letter (e.g. ppsA).
  • E. coli ppsA designates the cds of the ppsA gene from E. coli indicated in SEQ ID NO: 1 of nucleotide 333-2711.
  • E. coli PpsA denotes the protein encoded by this cds (E. coli ppsA), given in SEQ ID NO: 2.
  • the protein is a phosphoenolpyruvate synthase.
  • P. ananatis ppsA refers to the cds of the ppsA gene from P. ananatis indicated in SEQ ID NO: 3 from nucleotide 417-2801.
  • P. ananatis PpsA denotes the protein encoded by this cds (P. ananatis ppsA), given in SEQ ID NO: 4.
  • WT Wt
  • the wild-type gene is the form of the gene that emerged naturally through evolution and is present in the wild-type genome.
  • the DNA sequence of Wt genes is publicly accessible in databases such as NCBI.
  • Alleles are defined as the states of a gene that can be converted into one another by mutation, i.e. by changing the nucleotide sequence of the DNA.
  • the gene naturally occurring in a microorganism is called the wild-type allele and the variants derived from it are called mutated alleles of the gene.
  • homologous genes or homologous sequences are to be understood as meaning that the DNA sequences of these genes or DNA segments are at least 80%, preferably at least 90% and particularly preferably at least 95% identical.
  • the degree of DNA identity is determined by the program "nucleotide blast", to be found on the page http: //blast.ncbi.nlm,nih.gov/, which is based on the blastn algorithm.
  • the preset parameters were used for an alignment of two or more nucleotide sequences.
  • the program “protein blast” on the website http://blast.ncbi.nlm.nih.gov/ is used to compare protein sequences. This program uses the blastp algorithm.
  • the preset parameters were used for algorithm parameters for aligning two or more protein sequences.
  • the relative enzyme activity of the enzyme class designated in the KEGG database with the number EC 2.7.9.2 is inactivated or, based on the specific activity of the wild-type enzyme, preferably by at least 10%, particularly preferably by at least 25% , especially preferably by at least 60% and especially preferably by at least 70%.
  • An enzyme activity of the enzyme encoded by the ppsA gene reduced by at least 10% (or 25% / 60% / 70%) is also referred to as a residual activity of at most 90% (or 75% / 40% / 30%).
  • the microorganism strain is characterized in that it no longer contains any enzyme activity of the enzyme class designated in the KEGG database with the number EC 2.7.9.2, ie the relative enzyme activity in the KEGG database
  • the enzyme class designated with the number EC 2.7.9.2 is reduced by 100% based on the specific activity of the wild-type enzyme.
  • Compared with / compared to / based on the (corresponding) wild-type enzyme” means in the context of this invention compared to the activity of the protein which is encoded by the non-mutated form of the gene from a microorganism, ie of the gene that was created naturally through evolution and that is present in the wild-type genome of this microorganism.
  • the microorganism strains suitable for the fermentative production of L-cysteine include all microorganisms that contain a deregulated biosynthetic metabolic pathway (homologous or heterologous) that leads to the synthesis of cysteine, cystine or derivatives derived therefrom. Such strains are disclosed, for example, in EP 0885962 B1, EP 1382684 B1, EP 1 220 940 B2, EP 1769080 B1 and EP 2138585 B1.
  • the microorganisms suitable for fermentative production of L-cysteine are preferably characterized in that they have one of the following changes: a) The microorganism strains are characterized by a modified 3-phosphoglycerate dehydrogenase (serA) with a compared to the corresponding Wild-type enzyme reduced feedback inhibition by L-serine by at least a factor of two (as described, for example, in EP 1950287 B1). Particularly preferred variants of 3-phosphoglycerate dehydrogenase (serA) have, compared to the corresponding wild-type enzyme, a feedback factor that is at least a factor of 5, particularly preferably at least a factor of 10 and, in a further preferred embodiment, a factor of at least 50. Inhibition by L-serine. b) The microorganism strains contain a serine-O-acetyl-
  • Transferase which, compared to the corresponding wild-type enzyme, has feedback inhibition by at least a factor of two (as described, for example, in EP 0858 510 B1 or Nakamori et al., Appl. Env. Microbiol. (1998) 64 : 1607-1611).
  • Particularly preferred variants of the serine O-acetyl transferase have, compared to the corresponding wild-type enzyme, a by at least a factor of 5, in particular preferably by at least a factor of 10 and in a further preferred embodiment by at least the Factor 50 decreased feedback inhibition by cysteine.
  • the microorganism strains have an increased by at least a factor of two due to overexpression of an efflux gene Cysteine export from the cell compared to the corresponding wild-type cell.
  • an efflux gene leads, compared to a wild-type cell, preferably to a cysteine export from the cell which is increased by at least a factor of 5, particularly preferably by at least a factor 10, particularly preferably by at least a factor of 20.
  • the efflux gene preferably comes from the group ydeD (see EP 0885 962 Bl), yfiK (see EP 1382684 Bl), cydDC (see WO 2004/113373 A1), bcr (see US 2005-221453 AA) and emrAB (see US 2005- 221453 AA) from E. coli or the corresponding homologous gene from another microorganism.
  • strains are known, for example, from EP 0858510 B1 and EP 0 885 962 B1.
  • the microorganism strains suitable for the fermentative production of L-cysteine are furthermore preferably characterized in that at least one cysteine-degrading enzyme is weakened to such an extent that in the cell only a maximum of 50% of this enzyme activity compared to a wild-type cell is present.
  • the cysteine-degrading enzyme preferably comes from the group tryptophanase (TnaA) and cystathionine-ß-lyase (MalY, MetC).
  • microorganism strains described in the previous sections that are suitable for the fermentative production of L-cysteine are deregulated in their cysteine metabolism in such a way that they have wild-type enzyme activity in the KEGG compared to the microorganism strain not deregulated in the cysteine metabolism -Database with the number EC 2.7.9.2 designated enzyme class form an increased amount of L-cysteine. Since in the cells of a microorganism strain not deregulated in cysteine metabolism with wild-type enzyme activity of the enzyme class designated in the KEGG database with the number EC 2.7.9.2, the amount of L-cysteine in the culture mixture is approximately 0 g / 1 (cf. Tab. 2), increased amount means any amount that is 0.05 g / 1 L-cysteine measured in the culture after 24 hours of cultivation.
  • the microorganism strain is preferably characterized in that the microorganism strain is a strain from the Enterobacteriaceae or Corynebacteriaceae family, particularly preferably a strain from the Enterobacteriaceae family.
  • Such strains can be purchased, for example, from the DSMZ German Collection of Microorganisms and Cell Cultures GmbH (Braunschweig).
  • the microorganism strain is preferably selected from the group consisting of Escherichia coli, Pantoea ananatis and Corynehacterium glutamicum, particularly preferably from the group consisting of Escherichia coli and Pantoea ananatis.
  • the microorganism strain is particularly preferably a strain of the species Escherichia coli.
  • the E. coli strain is particularly preferably selected from E. coli K12, particularly preferably E. coli K12 W3110. Such strains are available, inter alia, from the DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (Braunschweig), including E. coli K12 W3110 DSM 5911 (id. ATCC 27325) and Pantoea ananatis DSM 30070 (id. ATCC 11530).
  • PpsA is preferably PpsA from E. coli with SEQ ID NO: 2 or PpsA from P. ananatis with SEQ ID NO: 4.
  • the microorganism strain is preferably characterized in that it contains at least one mutation in the ppsA gene. At the same time, in this preferred embodiment, too, the strain forms an increased amount of L-cysteine compared to wild-type cells.
  • the genetic change in the ppsA gene preferably leads to the protein expressed by this gene having no or reduced relative enzyme activity of the enzyme class designated in the KEGG database with the number EC 2.7.9.2 based on the specific activity of the wild-type enzyme owns.
  • the production strain according to the invention can be optimized even further in order to further improve the cysteine production.
  • the optimization can, for example, take place genetically by additional expression of one or more genes that are suitable for improving the production properties.
  • genes can be expressed in a manner known per se as their own gene constructs or, however, also combined as an expression unit (as a so-called operon) in the production strain.
  • the production strain can also be optimized by inactivating other genes in addition to the ppsA gene, the gene products of which have a negative effect on cysteine production.
  • genetic changes in the ppsA gene are defined such that a) the coding sequence of the ppsA gene is partially or completely deleted, b) the coding sequence of the ppsA gene by one or more insertions or 5'- , or 3'-elongations is changed, c) the ppsA structural gene contains one or more mutations, in particular point mutations, with the result that the expressed phosphoenolpyruvate synthase has a weakened enzyme activity or is completely inactive, d) the ppsA Structural gene contains one or more mutations, in particular point mutations, with the result that ppsA expression is greatly weakened or completely suppressed, or the stability of the mRNA is reduced, or e) due to genetic changes in the 5 'or 3' not encoding ppsA sequences (promoter, 5'-UTR, Shine-Dalgarno sequence or terminator) expression of the ppsA gene or the translation of the ppsA
  • any combination of the genetic changes listed in a) to e) in the ppsA gene is also possible.
  • the change in the ppsA gene in the strain according to the invention is preferably based on complete or partial deletion of the ppsA structural gene, mutation of the ppsA structural gene in a manner that leads to a weakening of the enzyme activity or inactivation of the enzyme, or mutation of the ppsA structural gene and / or its expression-regulating 5'- and 3'-flanking non-transcribed or non-translated gene regions in such a way that the expression or translation of the ppsA gene is weakened or completely is suppressed, or the stability of the ppsA-mRNA is reduced.
  • the inactivation of the ppsA gene in the strain according to the invention as a result of complete or partial deletion of the ppsA cds (ie for the ppsA cds of E. coli nucleotide 333-2711 of SEQ ID NO: 1, or for the ppsA cds. cds of P. ananatis nucleotide 417-2801 of SEQ ID NO: 3) or the mutation of the ppsA structural gene in a manner that leads to Weakening of the enzyme activity or inactivation of the enzyme or reduction of the stability of the mRNA.
  • the microorganism strain is characterized in that the mutated gene is selected from the group consisting of the ppsA gene from Escherichia coli, the ppsA gene from Pantoea ananatis and a gene homologous to these genes.
  • the ppsA Gene from E. coli is disclosed in the entry in the NCBI gene database with the gene ID 946209
  • the ppsA gene from P. ananatis is disclosed in the entry in the NCBI gene database with the gene ID 11796889.
  • the definition given above applies to the mological gene.
  • the mutated ppsA gene is particularly preferably the ppsA gene from Escherichia coli.
  • the cds of the ppsA gene from E. coli which is disclosed in SEQ ID NO: 1 nucleotide 333-2711 (coding for a protein with SEQ ID NO: 2), or the cds of the ppsA gene from Pantoea ananatis, which is disclosed in SEQ ID NO: 3 nucleotide 417-2801 (coding for a protein with SEQ ID NO: 4).
  • the microorganism strain is characterized in that the coding DNA sequence of the ppsA gene is SEQ ID NO: 5 or a sequence which is homogeneous thereto, particularly preferably SEQ ID NO: 5.
  • SEQ ID NO: 5 or a sequence which is homogeneous thereto, particularly preferably SEQ ID NO: 5.
  • the definition given above applies to the term homologous sequence.
  • the mutations of the DNA sequence given in SEQ ID NO: 1 lead to the mutation of the three amino acids of the WT protein sequence given in SEQ ID NO: 2, namely valine at position 126 mutated to methionine (V126M), arginine Position 427 mutates to histidine (R427H) and valine at position 434 mutates to isoleucine (V434I), corresponding to a ppsA-MHI gene with the DNA sequence as in SEQ ID NO: 5, coding for a ppsA-MHI protein with the Amino acid sequence as disclosed in SEQ ID NO: 6.
  • Various methods are known to the person skilled in the art for inactivating and mutating the ppsA gene.
  • the starting strain can be subjected to mutagenesis in a known manner (for example chemically by mutagenic chemicals such as N-methyl-N'-nitro-N-nitrosoguanidine or physically by UV radiation), with random mutations in the genomic DNA are generated and the desired ppsA mutant is then selected from the multitude of mutants generated, for example, in each case after the mutants have been isolated, due to the lack of a color reaction based on the enzyme activity or genetically by detection of a defective ppsA gene.
  • mutagenic chemicals such as N-methyl-N'-nitro-N-nitrosoguanidine or physically by UV radiation
  • the ppsA gene can be specifically inactivated in a simpler manner, for example by the known mechanism of homologous recombination.
  • Cloning systems for targeted gene inactivation by means of homologous recombination are known to the person skilled in the art and are commercially available, for example disclosed in the user manual of the “Quick and Easy E. coli Gene Deletion Kit”, based on the Red® / ET® technology from the company. Gene Bridges GmbH (see "Technical Protocol, Quick & Easy E. coli Gene Deletion Kit, by Red ® / ET ® Recombination, Cat. No.
  • the ppsA gene or a part of the gene can be isolated and a foreign DNA cloned into the ppsA gene, whereby the open reading frame of the ppsA gene that defines the protein is interrupted.
  • a DNA construct suitable for the targeted inactivation of the ppsA gene can therefore consist of a 5 'DNA segment that is homologous to the genomic ppsA gene, followed by a gene segment comprising the foreign DNA and connected to it 3 'DNA segment, which in turn is homologous to the genomic ppsA gene, exist.
  • the region of the ppsA gene that is suitable for homologous recombination can therefore not only include the region coding for phosphoenolpyruvate synthase.
  • the in The area in question can also include DNA sequences flanking the ppsA gene, namely in the 5 'area before the beginning of the coding area (promoter of gene transcription, e.g. nucleotide 1 - 332 in SEQ ID NO: 1, or nucleotide 1 - 416 in SEQ ID NO:
  • the foreign DNA is preferably a selection marker expression cassette.
  • This consists of a gene transcription promoter which is functionally linked to the actual selection marker gene and optionally followed by a gene transcription terminator.
  • the selection marker also contains 5 'and 3' flanking homologous sequences of the ppsA gene.
  • the selection marker preferably contains 5 'and 3' flanking homologous sequences of the ppsA gene each at least 30 nucleotides in length, particularly preferably each at least 50 nucleotides in length.
  • the DNA construct for inactivating the ppsA gene can therefore, starting from the 5 'end, consist of a sequence homologous to the ppsA gene, followed by the expression cassette of the selection marker, for example selected from the class of antibiotic resistance genes and followed by another sequence homologous to the ppsA gene.
  • the DNA construct for inactivating the ppsA gene starting from the 5 'end, consists of a sequence homologous to the ppsA gene of at least 30 nucleotides in length, particularly preferably at least 50 nucleotides in length, followed by the expression cassette of the selection marker , selected from the class of antibiotic resistance genes as well as followed by a further sequence from which is homologous to the ppsA gene at least 30 nucleotides in length, particularly preferably at least 50 nucleotides in length.
  • the selection marker genes are generally genes whose gene product enables the parent strain to grow under selective conditions under which the original parent strain cannot grow.
  • Preferred selection marker genes are selected from the group of antibiotic resistance genes such as the ampicillin resistance gene, the tetracycline resistance gene, the kanamycin resistance gene, the chloramphenicol resistance gene or also the neomycin resistance gene.
  • Other preferred selection marker genes enable parent strains with a metabolic defect (e.g. amino acid auotrophies) to grow under selective conditions by their expression correcting the metabolic defect.
  • selection marker genes are also possible, the gene product of which chemically changes and thus inactivates a compound that is toxic to the parent strain (eg the gene for the enzyme acetamidase, which converts the compound acetamide, which is toxic to many microorganisms, into the non-toxic products acetate and ammonia) splits).
  • selection marker genes are the ampicillin resistance gene, the tetracycline resistance gene, the kamycin resistance gene and the chloramphenicol resistance gene.
  • the tetracycline resistance gene and the kamycin resistance gene are particularly preferred.
  • strains according to the invention with inactivated ppsA gene are the strains E. coli W3110-AppsA and P. ananatis- ⁇ ppsA :: kan disclosed in the examples. Both strains are characterized in that their ppsA gene was inactivated by homologous recombination.
  • Example 3 Another such system for targeted gene inactivation based on homologous recombination is a method known to the person skilled in the art and described in Example 3 for gene inactivation or genetic modification, based on a combination of lambda red recombination with a counter-selection - ons screening. This system is described, for example, in Sun et al., Appl. Env. Microbiol. (2008) 74: 4241-4245.
  • a DNA construct is used to inactivate, for example, the ppsA gene, starting from the 5 'end, consisting of a sequence homologous to the ppsA gene, followed by two expression cassettes in any order, consisting of a) an expression cassette of the selection marker , selected from the class of antibiotic resistance genes and b) an expression cassette of the sacB gene, coding for the enzyme levansucrase and finally followed by a further sequence homologous to the ppsA gene.
  • the DNA construct is transformed into the production strain and antibiotic-resistant clones are isolated.
  • the clones obtained are distinguished by the fact that they cannot grow on sucrose as a result of the included sacB gene.
  • the two marker genes can be removed by replacing the two marker genes with homologous recombination in a second step using a suitable DNA fragment.
  • the clones obtained in this step can then grow again on sucrose and are then again sensitive to the antibiotic.
  • This method is used in Example 3 to replace the ppsA-WT gene from E. coli (SEQ ID NO: 1) by the triple mutant ppsA-MHI (SEQ ID NO: 5) described below.
  • the E. coli strain W3110-ppsA-MHI contains the cds of the PpsA triple mutant PpsA-V126M-R427H-V434I (ppsA-MHI).
  • the cds of the mutated gene of ppsA-MHI corresponds to the DNA sequence SEQ ID NO: 5 and codes for a PpsA protein with the sequence SEQ ID NO: 6.
  • PpsA-MHI is characterized in that the protein with the sequence SEQ ID NO: 6 contains the following changes in the amino acid sequence compared to the WT sequence given in SEQ ID NO: 2: Valine at position 126 is mutated to methionine (V126M), arginine at position 427 is mutated to histidine (R427H) and valine at position 434 is mutated to isoleucine (V434I).
  • the PpsA-MHI protein only had a relative enzyme activity of 26.8% compared to the specific wild-type enzyme activity (see Example 5, Tab. 1).
  • At least one of the mutations in the CD leads to at least one of the following changes in the amino acid sequence in SEQ ID NO:
  • valine at position 126 leads: valine at position 126, arginine at position 427 and / or valine at position 434, each of the three amino acids being able to be exchanged for any other amino acid.
  • the mutations in the ppsA-MHI gene according to the invention are introduced into the ppsA WT gene in a manner known per se, for example by so-called “site-directed” mutagenesis using a commercially available cloning kit, such as, for example, in the user manual for “QuickChange II Site-Directed Mutagenesis Kit "from Agilent disclosed.
  • the ppsA-MHI gene according to the invention can also be produced in a known manner by DNA synthesis.
  • the strain according to the invention characterized by mutating the ppsA structural gene in a way that leads to a weakening of the enzyme activity, such as the E.
  • coli ppsA-MHI triple mutant can be produced by using the combination of lambda-red recombination with a previously described Counter-selection screening for genetic modification (see, for example, Sun et al., Appl. Env. Microbiol. (2008) 74:
  • E. coli W3110 AppsA (described in Example 1) and E. coli W3110 ppsA-MHI (described in Example 3) are particularly preferred as strains.
  • the invention also relates to a fermentative process for the production of L-cysteine, characterized in that the microorganism cells according to the invention are used.
  • L-cysteine is formed as the primary product of the process according to the invention, from which the compounds L-cystine and thiazolidine can be formed.
  • L-cystine and thiazolidine arise during fermentation and accumulate in both the culture supernatant and the precipitate.
  • Thiazolidine is 2-methyl-2,4-thiazolidinedicarboxylic acid, an adduct of cysteine and pyruvate, which can be formed as a by-product of cysteine production (EP 0885962 B1).
  • the total cysteine yield is defined in the context of this invention as the sum of the cysteine, cystine and thiazolidine produced. This is determined from the entire culture batch, as described in Example 7. For example, you can use the colorimetric test of Gaitonde (Gaitonde, M.
  • the prior art does not disclose any processes or production strains in which, by attenuating or inactivating the Phosphoenolpyruvate synthase enzyme activity can improve the production of an amino acid, particularly cysteine.
  • the weakening or inactivation of the ppsA enzyme activity in a microorganism strain suitable for cysteine production is suitable for the yields of total cysteine, ie the sum of the cysteine, cystine and thiazolidine produced, in a fermentative process to increase significantly. According to the prior art, this was completely unexpected.
  • the attenuation or inactivation of the phosphoenolpyruvate synthase activity thus represents a new useful measure for improving the cysteine production in other cysteine-producing strains as well.
  • Example 7 shows that a strain capable of cysteine production encoding the ppsA mutant ppsA-MHI with reduced PpsA enzyme activity instead of the Wt enzyme achieves significantly higher cysteine yields in the fermentation than a strain containing a ppsA WT gene.
  • biomass of the production strain according to the invention and, on the other hand, cysteine and its oxidation product cystine are formed.
  • the formation of biomass and cysteine can correlate with time or be decoupled from one another in time.
  • Cultivation takes place in a manner familiar to the person skilled in the art. For this purpose, cultivation can take place in shake flasks (laboratory scale) or by fermentation (production scale).
  • a process on a production scale by fermentation with a fermentation volume of greater than 1 L is preferred, the production scale of greater than 10 L being preferred, greater than 1000 L being particularly preferred and a fermentation volume greater than 10,000 L being particularly preferred.
  • Culture media are familiar to the person skilled in the art from the practice of microbial cultivation. They typically consist of a carbon source (C source), a nitrogen source (N source) and additives such as vitamins, salts and trace elements as well as a sulfur source (S source), through which cell growth and cysteine production be optimized.
  • C source carbon source
  • N source nitrogen source
  • S source sulfur source
  • C sources are those that can be used by the production strain for cysteine product formation. This includes all forms of monosaccharides, including C6 sugars (hexoses) such as B. glucose, mannose, fructose or galactose as well as C5 sugars (pentosene) such as xylose, arabinose or ribose.
  • C6 sugars hexoses
  • pentosene pentosene
  • the production process according to the invention also includes all carbon sources in the form of disaccharides, in particular sucrose, lactose, maltose or cellobiose.
  • the production process according to the invention also includes all carbon sources in the form of higher saccharides, glycosides or carbohydrates with more than two sugar units such as. B. maltodextrin, starch, cellulose, hemicellulose, pectin or monomers or oligomers released from them by hydrolysis (enzymatically or chemically).
  • the hydrolysis of the higher carbon sources can take place upstream of the production process according to the invention or else take place in situ during the production process according to the invention.
  • carbon sources other than sugars or carbohydrates are acetic acid (or acetate salts derived therefrom), ethanol, glycerine, citric acid (and its salts) or pyruvate (and its salts).
  • gaseous C sources such as carbon dioxide or carbon monoxide are also conceivable.
  • the C sources affected by the production process according to the invention include both the isolated pure substances or, to increase profitability, mixtures of the individual C sources that have not been further purified, such as hydrolyzates through chemical or enzymatic digestion of the vegetable raw materials can be won.
  • hydrolysates of starch monosaccharide glucose
  • sugar beet monosaccharide glucose, fructose and arabinose
  • sugar cane disaccharide sucrose
  • pectin monosaccharide galacturonic acid
  • lignocellulose monosaccharide glucose
  • waste products from the digestion of vegetable raw materials can also serve as C sources, e.g. molasses (sugar beet) or bagasse (sugar cane).
  • Preferred carbon sources for growing the production strains are glucose, fructose, sucrose, mannose, xylose, arabinose and vegetable hydrolysates which can be obtained from starch, lignocellulose, sugar cane or sugar beet.
  • Particularly preferred carbon sources are glucose and sucrose, either in isolated form or as a component of a vegetable hydrolyzate.
  • a particularly preferred carbon source is glucose.
  • N-sources are those that can be used by the production strain to form biomass. This includes ammonia, gaseous or in aqueous solution as NH 4 OH or its salts such as. B. ammonium sulfate, ammonium chloride, ammonium phosphate, ammonium acetate or ammonium nitrate. Furthermore, the known nitrate salts such as. B. KNO 3 , NaNCb, ammonium nitrate, Ca (NO 3) 2 , Mg (NO 3 ) 2 and other N sources such as urea.
  • the N sources also include complex amino acid mixtures such as yeast extract, proteose peptone, malt extract, soy peptone, casamino acids, corn steep liquor (corn steep liquor, liquid or also dried as so-called CSD) as well as NZ amines and yeast nitrogen Base.
  • complex amino acid mixtures such as yeast extract, proteose peptone, malt extract, soy peptone, casamino acids, corn steep liquor (corn steep liquor, liquid or also dried as so-called CSD) as well as NZ amines and yeast nitrogen Base.
  • the addition of a sulfur source is necessary for the efficient production of cysteine and cysteine derivatives.
  • the continuous metering can take place as a pure feed solution or as a mixture with another feed component such as glucose.
  • Suitable sulfur sources are salts of sulfates, sulfites, dithionites, thiosulfates or sulfides, the use of the respective acids also being conceivable given a given stability.
  • Preferred sulfur sources are salts of sulfates, sulfites, thiosulfates and sulfides.
  • Particularly preferred sources of sulfur are salts of sulfates and thiosulfates.
  • Salts of thiosulfate such as, for example, sodium thiosulfate and ammonium thiosulfate, are particularly preferred.
  • the cultivation can take place in the so-called batch mode, whereby the cultivation medium is inoculated with a starter culture of the production strain and then the cells grow without further feeding of nutrient sources.
  • the cultivation can also take place in the so-called fed-batch mode, with additional nutrient sources being fed in after an initial phase of growth in the batch mode (feed) in order to compensate for their consumption.
  • the feed can consist of the C source, the N source, the sulfur source, one or more vitamins or trace elements that are important for production, or a combination of the above.
  • the feed components can be metered in together as a mixture or else separately in individual feed sections.
  • other media components and additives that specifically increase cysteine production can also be added to the feed.
  • the feed can be fed in continuously or in portions (discontinuously), or else in a combination of continuous and discontinuous feed. Cultivation according to the fed-batch mode is preferred.
  • Preferred C sources in the feed are glucose, sucrose, and plant hydrolysates containing glucose or sucrose, and mixtures of the preferred C sources in any mixing ratio.
  • a particularly preferred carbon source in the feed is glucose.
  • the carbon source is preferably metered into the culture in such a way that the content of the carbon source in the fermenter does not exceed 10 g / L during the production phase.
  • a maximum concentration of 2 g / L, particularly preferably 0.5 g / L, particularly preferably 0.1 g / L is preferred.
  • Preferred N sources in the feed are ammonia, in gaseous form or in aqueous solution as NH 4 OH and its salts ammonium sulfate, ammonium phosphate, ammonium acetate and ammonium chloride, furthermore Urea, KNO 3 , NaNO 3 and ammonium nitrate, yeast extract, proteose peptone, malt extract, soy peptone, casamino acids, corn steep liquor as well as NZ amines and yeast nitrogen base.
  • N sources in the feed are ammonia or ammonium salts, urea, yeast extract, soy peptone, malt extract or corn steep liquor (liquid or in dried form).
  • Preferred sulfur sources in the feed are salts of sulfates, sulfites, thiosulfates and sulfides.
  • Particularly preferred sulfur sources in the feed are salts of sulfates and thiosulfates.
  • Salts of thiosulphate such as sodium thiosulphate and ammonium thiosulphate, are particularly preferred as the source of sulfur in the feed.
  • Salts of the elements phosphorus, chlorine, sodium, magnesium, nitrogen, potassium, calcium, iron and in traces (ie in mM concentrations) salts of the elements molybdenum, boron, cobalt, manganese, zinc, copper and nickel can be added as additional media additives will.
  • organic acids e.g. acetate, citrate
  • amino acids e.g. isoleucine
  • vitamins e.g. vitamin B1, vitamin B6
  • the cultivation takes place under pH and temperature conditions, which favor the growth and the cysteine production of the production strain.
  • the useful pH range extends from pH 5 to pH 9.
  • a pH range from pH 5.5 to pH 8 is preferred.
  • a pH range from pH 6.0 to pH 7.5 is particularly preferred.
  • the preferred temperature range for the growth of the production stem is 20 ° C to 40 ° C.
  • the temperature range from 25 ° C. to 37 ° C. and particularly preferably from 28 ° C. to 34 ° C. is particularly preferred.
  • the production strain can optionally grow without oxygen supply (anaerobic cultivation) or with oxygen supply (aerobic cultivation). Aerobic cultivation with oxygen is preferred.
  • the regulation of the oxygen saturation in the culture takes place automatically in accordance with the state of the art via a combination of gas supply and stirring speed.
  • the oxygen supply is ensured by the introduction of compressed air or pure oxygen. Aerobic cultivation through the introduction of compressed air is preferred.
  • the useful range of the compressed air supply in aerobic cultivation is 0.05 vvm to 10 vvm (vvm: entry of compressed air into the fermentation batch given in liters of compressed air per liter of fermentation volume per minute).
  • a compressed air entry of 0.2 vvm to 8 vvm is preferred, particularly preferred from 0.4 to 6 vvm and especially preferred from 0.8 to 5 vvm.
  • the maximum stirring speed is 2500 rpm, preferably 2000 rpm and particularly preferably 1800 rpm.
  • the cultivation time is between 10 h and 200 h.
  • a cultivation time of 20 h to 120 h is preferred.
  • a cultivation time of 30 h to 100 h is particularly preferred.
  • Cultivation batches that are obtained by the method described above contain the cysteine either dissolved in the culture supernatant or, oxidized as cystine, in precipitated form.
  • the cysteine or cystine contained in the cultivation batches can either be used directly without further processing or else isolated from the cultivation batch.
  • the method is preferably characterized in that the cysteine formed is isolated.
  • Process steps known per se are available for isolating the cysteine and cystine, including centrifugation, decanting, dissolving the crude product with a mineral acid, filtration, extraction, chromatography or crystallization or precipitation. These process steps can be combined in any form in order to isolate the cysteine in the desired purity. The desired degree of purity depends on the further use.
  • the cystine obtained during processing can be reduced to cysteine for further use.
  • a method for reducing L-cystine to L-cysteine in an electrochemical process is disclosed in EP 0235908.
  • the invention can also be used to produce improved microorganism strains for the fermentative production of compounds whose biosynthesis starts from 3-phosphoglycerate and leads to L-cysteine and L-cystine via L-serine.
  • This also includes strains of microorganisms for the fermentative production of derivatives of L-serine and L-cysteine, including phosphoserine, O-acetylserine, N-acetylserine and thiazolidine, a condensation product of L-cysteine and pyruvate.
  • FIG. 1 shows the 3.4 kb vector pKD13 used in Example 1 and Example 2.
  • FIG. 2 shows the 6.3 kb vector pKD46 used in Example 1 and Example 3.
  • Example 4 shows the 4.2 kb vector pACYC184 used in Example 4.
  • Example 1 Production of a ppsA deletion mutant in Escherichia coli
  • Escherichia coli K12 W3110 was used as the starting strain for gene isolation and for strain development (available for purchase under the strain number DSM 5911 from the DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH).
  • the aim of the gene inactivation was the coding sequence of the ppsA gene from E. coli.
  • the DNA sequence of the ppsA gene from E. coli K12 (Genbank GenelD: 946209) is disclosed in SEQ ID NO: 1.
  • Nucleotides 333-2711 (designated E. coli ppsA) code for a phosphoenolpyruvate synthase protein with the in SEQ ID NO: 2 disclosed amino acid sequence (E. coli PpsA).
  • the E. coli ppsA gene was inactivated with the Red ® / ET ® technology from Gene Bridges GmbH as detailed below (described in the user manual of the "Quick and Easy E. coli Gene Deletion Kit", see “Technical Protocol, Quick & Easy E. coli Gene Deletion Kit, by Red ® / ET ® Recombination, Cat.
  • the 3.4 kb plasmid pKD13 (FIG. 1) is disclosed in the “GenBank” gene database under the accession number
  • the 6.3 kb plasmid pKD46 (FIG. 2) is disclosed in the “GenBank” gene database under the accession number
  • the 9.4 kb plasmid pCP20 is disclosed in Cherepanov and Wackernagel, Gene 158 (1995): 9-14.
  • E. coli W3110 was transformed with the plasmid pKD46 (so-called “Red Recombinase” plasmid, FIG. 2) and an ampicillin-resistant clone was isolated (designated as W3110 ⁇ pKD46).
  • a ppsA-specific DNA fragment suitable for its inactivation was in a PCR reaction (“Phusion TM High-Fidelity” DNA polymerase, Thermo Scientific TM) with DNA from plasmid pKD13 (FIG. 1) and the primers pps-5f (SEQ ID NO:
  • Primer pps-5f contained 30 nucleotides (nt) from the 5 'region of the ppsA gene (nt 333-362 in SEQ ID NO: 1) and, connected to it, 20 nt specific for the plasmid pKD13 (referred to as “pr-1 "in Fig. 1).
  • Primer pps-6r contained 30 nt from the 3 'region of the ppsA gene (nt 2682-2711 in SEQ ID NO: 1, in reverse complementary form) and connected to it 20 nt specific for the plasmid pKD13 (designated as “pr -2 "in Fig. 1).
  • DNA of the plasmid pKD13 was used to prepare a 1.4 kb PCR product with the primers pps-5f and pps-6r, which contained a DNA segment of 30 nt at the 5 'and at the 3' end, the was specific for the ppsA gene from E. coli W3110.
  • the PCR product contained the expression cassette of the kanamycin resistance gene contained in pKD13 and, flanking the 5 'and 3' end of the kanamycin expression cassette, so-called “FRT direct repeats” (referred to as “FRT1” and “FRT2 "in FIG. 1), short DNA segments which were used in a later work step to remove the antibiotic marker kanamycin as the recognition sequence for the" FLP recombinase "(contained on the plasmid pCP20).
  • FRT direct repeats referred to as “FRT1” and “FRT2 "in FIG. 1
  • the 1.4 kb PCR product was isolated and treated with the methylated DNA-cutting restriction endonuclease Dpn I, which is familiar to the person skilled in the art, in order to remove residual pKD13 plasmid DNA. Non-methylated DNA from the PCR reaction is not degraded.
  • LBkan plates contained LB medium (10 g / L tryptone, 5 g / L yeast extract, 5 g / L NaCl), 1.5% agar and 15 mg / L kamenycin.
  • Ten of the kanamycin-resistant clones obtained were purified on LBkan plates (ie isolation of a clone by singulation) and checked in a PCR reaction whether the kamycin-resistance cassette had been correctly integrated into the ppsA gene.
  • the genomic DNA used for the PCR reaction (“Phusion TM High-Fidelity” DNA Polymerase, Thermo Scientific TM) was isolated with a DNA isolation kit (Qiagen) from cells of the cultivation of kanamycin-resistant clones of E. coli W3110 in LBkan medium (10 g / L tryptone, 5 g / L yeast extract, 5 g / L NaCl, 15 mg / L kanamycin) isolated using genomic DNA of the E. coli W3110 wild type strain as control
  • Primers used were pps-7f (SEQ ID NO: 9) and pps-8r (SEQ ID NO: 10).
  • Primer pps-7f contained nt 167-188 from SEQ ID NO: 1, primer pps-8r from nt 2779-2800 SEQ ID NO:
  • E. coli W3110 wild type DNA resulted in a DNA fragment of 2630 bp in the PCR reaction, as expected for the intact gene.
  • a kanamycin-resistant clone examined resulted in a DNA fragment of approx. 1660 bp in the PCR reaction, as expected in the event that the 1.4 kb PCR product was linked to the primers pps-5f and pps-6r defined sites in the ppsA gene had been integrated. This result showed that the kanamycin resistance gene could be successfully integrated at the gene location of the ppsA gene and thus the ppsA gene had been inactivated.
  • the clone with inactivated ppsA gene was selected and was given the designation W3110-AppsA :: kan.
  • W3110-AppsA :: kan was transformed with the plasmid pCP20 and transformants were selected at 30.degree.
  • the 9.4 kb vector pCP20 is disclosed in Cherepanov and Wackernagel (1995), Gene 158: 9-14.
  • the gene for the FLP recombinase is contained in the vector pCP20.
  • the FLP recombinase recognizes the FRT sequences which flank the expression cassette of the kanamycin resistance gene and removes the kamycin expression cassette.
  • the clones obtained at 30.degree. C. were incubated at 37.degree. Under these conditions, on the one hand, the expression of the FLP recombinase was induced and, on the other hand, the replication of the pCP20 vector was prevented.
  • W3110-AppsA kan was kanamycin-sensitive again after treatment with the pCP20 plasmid, which was checked as follows:
  • genomic DNA was isolated from the kanamycin-sensitive clones (Qiagen DNA isolation kit) and in a PCR reaction (“Phusion TM High-Fidelity” DNA polymerase, Thermo Scientific TM) with the primers pps-7f (SEQ ID NO: 9 ) and pps-8r (SEQ ID NO: 10) E. coli W3110 wild-type DNA resulted in a DNA fragment of about 2630 bp in the PCR reaction, as expected for the intact ppsA gene.
  • the kamycin-sensitive clone on the other hand, the PCR reaction resulted in a DNA fragment of approx.
  • the strain isolated from this step was named E. coli W3110- ⁇ ppsA. This strain is distinguished by the fact that it contained an inactivated ppsA gene and that this strain was again sensitive to the antibiotic kamenycin.
  • Pantoea ananatis was used as the starting strain for gene isolation and strain development (available for purchase under the strain number DSM 30070 from the DSMZ Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH).
  • the aim of the gene inactivation was the ppsA gene from Pantoea ananatis.
  • the DNA sequence of the ppsA gene from P. ananatis (Genbank GelD: 31510655) is disclosed in SEQ ID NO: 3.
  • Nucleotides 417-2801 (designated P. ananatis ppsA) also code for a phosphoenolpyruvate synthase protein the amino acid sequence disclosed in SEQ ID NO: 4 (P. ananatis PpsA).
  • the P. ananatis ppsA gene has been with the Red ® / ET ® technology the company. Gene Bridges GmbH as listed below in detail inactivated fourth (described in the user manual for the "Quick and Easy E. coli Gene Deletion Kit", see “Technical Protocol , Quick & Easy E. coli Gene deletion Kit, by Red ® / ET ® recombination. Cat. No. K006, version 2.3, June 2012 and literature cited therein, for example Datsenko and Wanner, Proc. Natl. Acad Sci. USA 97 (2000): 6640-6645) using the plasmids pKD13 and pRedET.
  • the 3.4 kb plasmid pKD13 (FIG. 1) is disclosed in the “GenBank” gene database under the accession number
  • P. ananatis was transformed with the plasmid pRedET (so-called “Red Recombinase” plasmid) and a tetracycline-resistant clone was isolated (referred to as P. ananatis x pRedET).
  • a ppsA-specific DNA fragment suitable for its inactivation was in a PCR reaction (“Phusion TM High-Fidelity” DNA polymerase, Thermo Scientific TM) with DNA from plasmid pKD13 (FIG. 1) and the primers ppsapa-3f (SEQ ID NO: 11) and pps-4r (SEQ ID NO: 12).
  • Primer ppsapa-3f contained 49 nt from the 5 'region of the ppsA gene (nt 417-465 in SEQ ID NO: 3) and, connected thereto, 20 nt specific for the plasmid pKD13 (designated as “pr-1” in FIG. 1 ).
  • Primer ppsapa-4r contained 49 nt from the 3 'region of the ppsA gene (nt 2753-2801 in SEQ ID NO: 3, in reverse complementary form) and, connected to it, 20 nt specific for the plasmid pKD13 (designated as “pr -2 "in Fig. 1).
  • DNA of the plasmid pKD13 was used to prepare a 1.4 kb PCR product with the primers ppsapa-3f and pps-4r, which contained a DNA segment of 49 nt at the 5 'and 3' ends was specific for the ppsA gene from P. ananatis.
  • the PCR product contained the expression cassette of the kanamycin resistance gene contained in pKD13 and, flanking the 5 'and 3' end of the kanamycin expression cassette, so-called “FRT direct repeats” (referred to as “FRT1” and “FRT2 "in Fig. 1), short DNA segments which, if necessary, enable the antibiotic marker kanamycin in ppsA deletion mutants to be removed.
  • the 1.4 kb PCR product was isolated and treated with the methylated DNA-cutting restriction endonuclease Dpn I, which is familiar to the person skilled in the art, to remove residual pKD13 Remove plasmid DNA. Non-methylated DNA from the PCR reaction is not degraded.
  • the 1.4 kb PCR product specific for the ppsA gene and containing an expression cassette for the kanamycin resistance gene was transformed into P. ananatis x pRedET and isolated on LBkan plates at 30.degree. C. kanamycin-resistant clones.
  • LBkan plates contained LB medium (10 g / L tryptone, 5 g / L yeast extract, 5 g / L NaCl), 1.5% agar and 15 mg / L kamenycin.
  • a kanamycin-resistant clone was purified on LBkan plates (ie a clone was isolated by singulation) and it was checked in a PCR reaction whether the kanamycin-resistance cassette had been correctly integrated into the ppsA gene.
  • the genomic DNA used for the PCR reaction (“Phusion TM High-Fidelity” DNA Polymerase, Thermo Scientific TM) was isolated from cells of the kanamycin-resistant clone of P. ananatis in LBkan using a DNA isolation kit (Qiagen) -Medium (10 g / L tryptone, 5 g / L yeast extract, 5 g / L NaCl, 15 mg / L Kanamycin) isolated. Genomic DNA of the P. anatis wild-type strain served as control.
  • the PCR - Primers used in the reaction were ppsapa-lf (SEQ ID NO: 13) and ppsapa-2r (SEQ ID NO: 14). Primer ppsapa-lf contained nt 281-302 in SEQ ID NO: 3, primer ppsapa-2r nt 2901- 2922 in SEQ ID NO: 3, in reverse complementary form).
  • P. ananatis wild type DNA resulted in a DNA fragment of 2640 bp in the PCR reaction, as expected for the intact gene.
  • a kanamycin-resistant clone examined resulted in a DNA fragment of approx. 1670 bp in the PCR reaction, as expected in the event that the 1.4 kb PCR product was linked to the primer ppsapa-3f (SEQ ID NO : 11) and ppsapa-4r (SEQ ID NO: 12) defined sites in the ppsA gene had been integrated.
  • ppsapa-3f SEQ ID NO : 11
  • ppsapa-4r SEQ ID NO: 12
  • E. coli W3110-ppsA-MHI characterized by mutations of the ppsA structural gene in a manner which lead to a weakening of the enzyme activity, was produced by using the combination of lambda-red recombination and counter-selection screening for genetic modification, which is known to the person skilled in the art (see e.g. Sun et al., Appl. Env. Microbiol. (2008) 74: 4241-
  • ppsA-MHI The DNA sequence of the ppsA-MHI gene is disclosed in SEQ ID NO: 5 (ppsA-MHI), coding for a protein with the sequence as given in SEQ ID NO: 6 (PpsA-MHI).
  • ppsA-MHI was obtained from the ppsA WT gene by successively introducing the mutations into the ppsA WT gene by “site-directed” mutagenesis. This was done using the commercially available cloning kit, “QuickChange II Site-Directed Mutagenesis Kit "from Agilent according to the information in the user manual.
  • the 3.2 kb Kan-sacB cassette was first removed from the plasmid pKan-SacB (FIG. 3) by PCR with the primers pps-9f (SEQ ID NO: 15) and pps-10r (SEQ ID NO: 16) isolated.
  • the plasmid pKan-sacB contains expression cassettes both for the kanamycin (Kan) resistance gene and for the sacB gene, coding for the enzyme levansucrase.
  • the primer pps-9f contained 30 nt starting from the start ATG of the ppsA gene (nt 333-362 in SEQ ID NO: 1) and, connected to it, 20 nt specific for the plasmid pKan-SacB (referred to as “pr-f "in Fig. 3).
  • the primer pps-10r contained 30 nt starting from the stop codon of the ppsA gene (nt 2682-2711 in SEQ ID NO: 1, in reverse complementary form) and connected to it 21 nt specific for the plasmid pKan-SacB (designated as "Pr-r” in Fig. 3).
  • E. coli W3110 x pKD46 (production see Example 1) was transformed with the ppsA-specific 3.2 kb PCR product and kanamycin-resistant clones were isolated.
  • the clones were inoculated onto LBSC plates (10 g / L tryptone, 5 g / L yeast extract, 7% sucrose, 1.5% agar and 15 mg / L kanamycin).
  • Clones with an integrated sacB gene produced toxic levan from the saccharose, which led to growth inhibition. Such clones were selected and checked in a PCR reaction whether the Kan-sacB cassette had been correctly integrated into the ppsA gene.
  • the genomic DNA used for the PCR reaction (“Phusion TM High-Fidelity” DNA Polymerase, Thermo Scientific TM) was previously grown with a DNA isolation kit (Qiagen) from cells of kanamycin-resistant clones of E. coli W3110 in LBkan medium (10 g / L tryptone, 5 g / L yeast extract, 5 g / L NaCl, 15 mg / L kanamycin) using genomic DNA of the E. coli W3110 wild type strain as a control.
  • the primers used for the PCR reaction were pps-7f (SEQ ID NO: 9) and pps-8r (SEQ ID NO: 10).
  • E. coli W3110 wild-type DNA produced a DNA fragment of 2630 nt in the PCR reaction, as expected for the intact gene.
  • Kamycin-resistant clones produced a DNA fragment of approx. 3400 nt in the PCR reaction, as expected in the event that the 3.2 kb PCR product is linked to the primer pps-9f (SEQ ID NO: 15) and pps-10r (SEQ ID NO: 16) defined sites in the ppsA gene had been integrated. This result showed that successful at the locus of the ppsA gene the Kan-sacB cassette could be integrated and thus the ppsA gene was inactivated.
  • a clone with an integrated Kan-sacB cassette was selected and was given the designation W3110- ⁇ ppsA :: kan-sacB x pKD46.
  • the Kan-sacB cassette was exchanged for the ppsA-MHI gene.
  • the ppsA-MHI DNA fragment from step 2 was used in a PCR reaction ("Phusion TM High-Fidelity" DNA polymerase, Thermo Scientific TM) with the primers pps-llf (SEQ ID NO: 17) and pps-12r ( SEQ ID NO: 18) a 2.5 kb DNA fragment was amplified, primer pps-llf contained nt 300-319 in SEQ ID NO: 1, primer pps-12r nt 2743-2763 in SEQ ID NO: 1, in reverse complementary shape.
  • the 2.5 kb ppsA-MHI gene was transformed into E. coli W3110-AppsA :: kan-sacB x pKD46 and clones on LBS plates (10 g / L tryptone, 5 g / L yeast extract, 7% sucrose, 1.5% agar) selected without kanamycin. Only clones which no longer contained an active sacB gene could grow on LBS plates.
  • Genomic DNA was obtained from cells grown in LB medium (10 g / L tryptone, 5 g / L yeast extract, 5 g / L NaCl) using a DNA isolation kit (Qiagen). Genomic DNA of the E. coli W3110 wild type strain was used as a control.
  • the primers used for the PCR reaction were pps-7f (SEQ ID NO: 9) and pps-8r (SEQ ID NO: 10).
  • PCR products of the expected size of 2630 nt were analyzed by DNA sequencing (Eurofins Genomics). Clones with correctly integrated ppsA-MHI gene gave the DNA sequence as disclosed in SEQ ID NO: 5, coding for a protein corresponding to the sequence from SEQ ID NO: 6. A clone with the correct ppsA-MHI gene, containing the mutations V126M, R427H and V434I, was selected and was given the designation E. coli W3110-ppsA-MHI.
  • pACYC184-cysEX-GAPDH-ORF306-serA317 derived from the starting vector pACYC184 (FIG. 4) was used as the cysteine-specific production plasmid.
  • pACYCl84-cysEX-GAPDH-ORF306-serA317 is a derivative of the plasmid pACYC184-cysEX-GAPDH-ORF306 disclosed in EP 0885962 B1.
  • the plasmid pACYC184-cysEX-GAPDH-ORF306 contains, in addition to the origin of replication and a tetracycline resistance gene (starting vector pACYC184), the cysEX allele, which codes for a serine O-acetyl transferase with reduced feedback inhibition by cysteine ydeDlux gene (ORF306), the expression of which is controlled by the constitutive GAPDH promoter.
  • pACYC184-cysEX-GAPDH-ORF306-serA317 also contains, cloned behind the ydeD (ORF306) efflux gene, the serA317 gene fragment, coding for the N-terminal 317 amino acids of the SerA protein (total length 410 amino acids).
  • the E. coli serA gene is disclosed in the “GenBank” gene database with the Gene ID 945258.
  • serA317 is disclosed in Bell et al., Eur. J. Biochem. (2002) 269: 4176-4184, therein referred to as “NSD: 317 "and codes for a serine feedback-resistant variant of 3-phosphoglycerate dehydrogenase.
  • the expression of serA317 is controlled by the serA promoter.
  • Plasmid-carrying transformants were selected on LBtet agar plates (10 g / L tryptone, 5 g / L yeast extract, 5 g / L NaCl, 1.5% agar, 15 mg / L tetracycline). Selected Transformants were checked for the transformed pCYS plasmid by plasmid isolation using the QIAprep Spin Plasmid Kit (Qiagen) and restriction analysis. Transformants with correctly incorporated plasmid pCYS were used in the cultivation to check the ppsA enzyme activity (example 5) and to determine the cysteine production (example 6 and example 7).
  • the ppsA enzyme activity of the E. coli strains W3110, W3110-AppsA, W3110-ppsA-MHI, each transformed with the production plasmid pCYS was determined.
  • Cells from the shake flask culture in 50 ml of SMI medium (composition see example 6) of the three strains were pelleted by centrifugation for 10 min and washed once with 10 ml of 0.9% (w / v) NaCl.
  • the cell pellets were taken up in 10 ml test buffer (100 mM Tris-HCl, pH 8.0; 10 mM MgCl 2 ) and a cell extract was prepared.
  • the FastPrep-24 TM 5G cell homogenizer from MP Biomedicals was used.
  • 2 x 1 ml cell suspension was disrupted in 1.5 ml tubes with glass beads ("Lysing Matrix B") prefabricated by the manufacturer (3 x 20 sec at a shaking frequency of 6000 rpm with a 30 sec pause between each inter- vallen)
  • the resulting homogenate was centrifuged and the supernatant used as a cell extract for the determination of the activity.
  • the protein content of the extract was determined with a Qubit 3.0 fluorometer from Thermo Fisher Scientific using the “ Qubit® Protein Assay Kit” according to the manufacturer's instructions.
  • the phosphate detection kit “Malachite Green Phosphate Assay Kit” from SigmaAldrich (catalog number MAK307) was used in accordance with the manufacturer's instructions. This is based on the fact that in the equilibrium reaction (4) by the ppsA enzyme activity Pyruvate is converted with ATP to phosphoenolpyruvate. This creates phosphate in stoichimetric amounts, which is used to determine the activity.
  • test batches contained 100 ⁇ g cell extract, 4 mM Na pyruvate and 4 mM ATP in 1 ml test buffer (100 mM Tris-HCl, pH 8.0; 10 mM MgCl 2).
  • the specific ppsA enzyme activity was calculated by relating the ppsA enzyme activity to 1 mg total protein of the cell extract (U / mg protein).
  • Composition of the SMl medium 12 g / LK 2 HPO 4 , 3 g / L KH 2 PO 4 , 5 g / L (NH 4 ) 2 SO 4 , 0.3 g / L MgSO 4 x 7 H 2 0, 0.015 g / L CaCl 2 x 2 H 2 O, 0.002 g / L FeSO 4 x 7 H 2 0, 1 g / L Na 3 citrate x 2 H 2 O, 0.1 g / L NaCl;
  • composition of the trace element solution 0.15 g / L Na 2 MoO 4 x 2 H 2 0, 2.5 g / LH 3 BO 3 , 0.7 g / L COCI 2 x 6 H 2 O, 0.25 g / L CuSO 4 x 5 H 2 O, 1.6 g / L MnCl 2 x 4 H 2 O, 0.3 g / L ZnSO 4 x 7 H 2 O.
  • the main culture was inoculated with preculture so much that an initial cell density OÜ 6 oo / ml (optical density of the main culture, as measured at 600 nm) of 0.025 / ml was adjusted. Starting from this, the entire 30 ml mixture was incubated for 24 h at 30 ° C. and 135 rpm.
  • Table 2 Cell density and total cysteine content after a culture time of 24 h in the shake flask
  • Table 3 Cell density and total cysteine content after a culture time of 24 h in the shake flask
  • the preculture 1 was then completely transferred into 100 ml of SM1 medium supplemented with 5 g / L glucose, 5 mg / L vitamin B1 and 15 mg / L tetracycline (composition of SM1 medium see Example 6).
  • the cultures were shaken in Erlenmeyer flasks (1 L volume) at 30 ° C. for 17 h at 150 rpm (Infors chest shaker). After this incubation, the cell density OD 600 / ml was between 3 and 5.
  • the fermentation was carried out in a fermenter of type Pendorf "® DASGIP In parallel Bioreactor Systems for microbiology" from Epstein. There were used volume culture vessels with 1.81 total.
  • the fermentation medium (900 ml) containing 15 g / L Glucose, 10 g / L tryptone (Difco), 5 g / L yeast extract (Difco), 5 g / L (NH 4 ) 2 SO 4 , 1.5 g / L KH 2 PO 4 , 0.5 g / L NaCl , 0.3 g / L MgSO 4 x 7 H 2 O, 0.015 g / L CaCl 2 x 2 H 2 O, 0.075 g / L FeSO 4 x 7 H 2 O, 1 g / L Na3 citrate x 2 H 2 O and 1 ml trace element solution (see Example 6), 0.005 g / L vitamin B1 and 15 mg / L tetracycline.
  • the pH in the fermenter was initially adjusted to 6.5 by pumping in a 25% NH 4 OH solution. During the fermentation, the pH was kept at a value of 6.5 by automatic correction with 25% NH 4 OH.
  • 100 ml of preculture 2 were pumped into the fermenter vessel. The initial volume was thus about 1 L.
  • the cultures were initially stirred at 400 rpm and gassed with a ventilation rate of 2 vvm (volume of air per volume of culture medium per minute) of compressed air disinfected via a sterile filter. Under these starting conditions, the oxygen probe was calibrated to 100% saturation before the inoculation.
  • the target value for the O 2 saturation during the fermentation was set to 30%. After the level of the 0 2 saturation below the desired value a regulatory cascade was started again introduce to the target value by the 0 2 saturation.
  • the gas supply was initially increased continuously (to a maximum of 5 vvm) and then the stirring speed was increased continuously (to a maximum of 1,500 rpm).
  • the fermentation was carried out at a temperature of 30 ° C. After a fermentation time of 2 h, the feed was added a sulfur source in the form of a sterile 60% (w / v) stock solution of sodium thiosulfate x 5 H 2 O at a rate of 1.5 ml per hour.
  • the fermentation time was 48 hours. Samples were then taken from the fermentation batch and the content of L-cysteine and the derivatives derived from it in the culture supernatant (especially L-cysteine and thiazolidine) and in the precipitate (L-cystine) were determined separately from one another.
  • the colorimetric test of Gaitonde was used in each case (Gaitonde, M.K. (1967), Biochem. J. 104, 627-633).
  • the L-cystine in the precipitate first had to be dissolved in 8% (v / v) hydrochloric acid before it could be quantified in the same way. Finally, the total amount of cysteine was determined as the sum of the cysteine in the pellet and in the supernatant.
  • the cell density OD 600 / ml of the strains examined was comparable, albeit somewhat higher for the control strain W3110 x pCYS.
  • the cysteine volume production (in g / L) was significantly higher (approx. Factor 3) in both W3110-ppsA-MHI x pCYS and in W3110-AppsA x pCYS than in the control strain W3110 x pCYS with the wild-type ppsA gene.
  • bla gene that confers resistance to ampicillin ( ⁇ -lactamase)
  • rrnB term rrnB terminator for transcription
  • kanR gene that confers resistance to kanamycin
  • FRT1 recognition sequence 1 for FLP recombinase
  • FRT2 recognition sequence 2 for FLP recombinase araC: araC gene (repressor gene)
  • P araC promoter of the araC gene
  • P araB promoter of the araB gene
  • Bet lambda phage Bet recombination gene
  • RepA gene for the plasmid replication protein
  • a sacB levansucrase gene pr-f: binding site f for primer (forward)
  • pr-r binding site r for primer (reverse)
  • IHF binding site for DNS binding protein IHF ("Integration Host Factor")
  • CamR gene that confers resistance to chloramphenicol TetR: gene that confers resistance to tetracycline P15A ORI: origin of replication

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