WO2022225320A1 - Nouveau variant de la phosphoglycérate déshydrogénase et procédé de production de xap ou de gmp au moyen de celui-ci - Google Patents

Nouveau variant de la phosphoglycérate déshydrogénase et procédé de production de xap ou de gmp au moyen de celui-ci Download PDF

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WO2022225320A1
WO2022225320A1 PCT/KR2022/005643 KR2022005643W WO2022225320A1 WO 2022225320 A1 WO2022225320 A1 WO 2022225320A1 KR 2022005643 W KR2022005643 W KR 2022005643W WO 2022225320 A1 WO2022225320 A1 WO 2022225320A1
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polypeptide
present application
seq
amino acid
strain
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PCT/KR2022/005643
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Korean (ko)
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심세훈
허란
유혜련
김비나
손성광
이지현
김대영
배현정
김은지
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씨제이제일제당 (주)
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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
    • 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
    • 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
    • C12N15/74—Vectors or expression systems specially adapted for prokaryotic hosts other than E. coli, e.g. Lactobacillus, Micromonospora
    • C12N15/77—Vectors or expression systems specially adapted for prokaryotic hosts other than E. coli, e.g. Lactobacillus, Micromonospora for Corynebacterium; for Brevibacterium
    • 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
    • C12P19/00—Preparation of compounds containing saccharide radicals
    • C12P19/26—Preparation of nitrogen-containing carbohydrates
    • C12P19/28—N-glycosides
    • C12P19/30—Nucleotides
    • C12P19/32—Nucleotides having a condensed ring system containing a six-membered ring having two N-atoms in the same ring, e.g. purine nucleotides, nicotineamide-adenine dinucleotide
    • 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)

Definitions

  • the present application relates to a novel phosphoglyceric acid dehydrogenase variant, a Corynebacterium stationionis strain comprising the variant, and a XMP or GMP production method using the strain.
  • the present inventors provide a novel phosphoglyceric acid dehydrogenase variant that increases XMP or GMP production, Corynebacterium stationis containing the variant, and XMP or GMP production method using the strain and the strain developed and completed this application.
  • One object of the present application is (i) glycine (Glycine), an amino acid corresponding to position 338 of the amino acid sequence of SEQ ID NO: 3, is substituted with aspartic acid, consisting of the amino acid sequence set forth in SEQ ID NO: 5 or (ii) threonine, which is an amino acid corresponding to position 396 of the amino acid sequence of SEQ ID NO: 3, is substituted with isoleucine, consisting of the amino acid sequence set forth in SEQ ID NO: 7, or (iii) SEQ ID NO: 3 Glycine, an amino acid corresponding to the 338th position of the amino acid sequence of To provide phosphoglyceric acid dehydrogenase, which consists of the amino acid sequence described in 1.
  • Another object of the present application is to provide a polynucleotide encoding the variant of the present application.
  • Another object of the present application is to include a variant of the present application or a polynucleotide encoding the variant, and having XMP or GMP production ability, Corynebacterium stationis ( Corynebacterium stationis ) It is to provide a strain.
  • Another object of the present application is to include a variant of the present application or a polynucleotide encoding the variant, and having XMP or GMP production capacity, Corynebacterium stasis strain comprising the step of culturing in a medium , to provide an XMP or GMP production method.
  • One aspect of the present application is (i) glycine (Glycine), an amino acid corresponding to position 338 of the amino acid sequence of SEQ ID NO: 3, is substituted with aspartic acid, consisting of the amino acid sequence set forth in SEQ ID NO: 5 or (ii) threonine, which is an amino acid corresponding to position 396 of the amino acid sequence of SEQ ID NO: 3, is substituted with isoleucine, consisting of the amino acid sequence set forth in SEQ ID NO: 7, or (iii) SEQ ID NO: 3 Glycine, an amino acid corresponding to the 338th position of the amino acid sequence of It provides phosphoglyceric acid dehydrogenase, which consists of the amino acid sequence described in 1.
  • the variant of the present application may have, include, or essentially consist of the amino acid sequence set forth in SEQ ID NO: 1, SEQ ID NO: 5 or SEQ ID NO: 7.
  • the amino acid corresponding to position 338 based on the amino acid sequence of SEQ ID NO: 3 in the amino acid sequence set forth in SEQ ID NO: 1, SEQ ID NO: 5 or SEQ ID NO: 7 is aspartic acid, and/or 396
  • the amino acid corresponding to position No. is isoleucine, and at least 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97 of the amino acid sequence set forth in SEQ ID NO: 1, SEQ ID NO: 5 or SEQ ID NO: 7 %, 98%, 99%, 99.5%, 99.7% or 99.9% or more homology or identity to an amino acid sequence.
  • variants having an amino acid sequence in which some sequences are deleted, modified, substituted, conservatively substituted or added are also included within the scope of the present application. is self-evident
  • sequence additions or deletions naturally occurring mutations, silent mutations or conservation within the N-terminus, C-terminal and/or within the amino acid sequence that do not alter the function of the variants of the present application It is a case of having an enemy substitution.
  • conservative substitution means substituting an amino acid for another amino acid having similar structural and/or chemical properties. Such amino acid substitutions may generally occur based on similarity in the polarity, charge, solubility, hydrophobicity, hydrophilicity and/or amphipathic nature of the residues. Typically, conservative substitutions may have little or no effect on the activity of the protein or polypeptide.
  • variant means that one or more amino acids are conservatively substituted and/or modified so that they differ from the amino acid sequence before the mutation of the variant, but have functions or properties. refers to a polypeptide that is maintained. Such variants can generally be identified by modifying one or more amino acids in the amino acid sequence of the polypeptide and evaluating the properties of the modified polypeptide. That is, the ability of the variant may be increased, unchanged, or decreased compared to the polypeptide before the mutation. In addition, some variants may include variants in which one or more portions, such as an N-terminal leader sequence or a transmembrane domain, have been removed.
  • variants may include variants in which a portion is removed from the N- and/or C-terminus of the mature protein.
  • variant may be used interchangeably with terms such as mutant, modified, mutant polypeptide, mutated protein, mutant and mutant (in English, modified, modified polypeptide, modified protein, mutant, mutein, divergent, etc.) and, as long as it is a term used in a mutated sense, it is not limited thereto.
  • the variant is a glycine corresponding to position 338 of the amino acid sequence of SEQ ID NO: 3 is substituted with aspartic acid, and/or threonine, an amino acid corresponding to position 396, is substituted with isoleucine, It may be a polypeptide comprising the amino acid sequence set forth in SEQ ID NO: 1, SEQ ID NO: 5 or SEQ ID NO: 7.
  • variants may include deletions or additions of amino acids that have minimal effect on the properties and secondary structure of the polypeptide.
  • a signal (or leader) sequence involved in protein translocation may be conjugated to the N-terminus of the mutant, either co-translationally or post-translationally.
  • the variants may also be conjugated with other sequences or linkers for identification, purification, or synthesis.
  • the term 'homology' or 'identity' refers to the degree of similarity between two given amino acid sequences or nucleotide sequences and may be expressed as a percentage.
  • the terms homology and identity can often be used interchangeably.
  • Sequence homology or identity of a conserved polynucleotide or polypeptide is determined by standard alignment algorithms, with default gap penalties established by the program used may be used. Substantially homologous or identical sequences are generally capable of hybridizing with all or part of a sequence under moderate or high stringent conditions. It is apparent that hybridization also includes hybridization with polynucleotides containing common codons or codons taking codon degeneracy into account in the polynucleotide.
  • a GAP program can be defined as the total number of symbols in the shorter of the two sequences divided by the number of similarly aligned symbols (ie, nucleotides or amino acids).
  • Default parameters for the GAP program are: (1) a binary comparison matrix (containing values of 1 for identity and 0 for non-identity) and Schwartz and Dayhoff, eds., Atlas Of Protein Sequence And Structure, National Biomedical Research Foundation , pp. 353-358 (1979), Gribskov et al (1986) Nucl. Acids Res. 14: weighted comparison matrix of 6745 (or EDNAFULL (EMBOSS version of NCBI NUC4.4) substitution matrix); (2) a penalty of 3.0 for each gap and an additional 0.10 penalty for each symbol in each gap (or a gap open penalty of 10, a gap extension penalty of 0.5); and (3) no penalty for end gaps.
  • the variant of the present application may have phosphoglyceric acid dehydrogenase activity.
  • the variant of the present application may have an activity to increase XMP or GMP production capacity compared to the wild-type polypeptide having phosphoglyceric acid dehydrogenase activity.
  • the term "Phosphoglycerate dehydrogenase” catalyzes the conversion of 3-phosphoglycerite to 3-phosphohydroxypyruvate.
  • the phosphoglyceric acid dehydrogenase of the present application may be used in combination with SerA.
  • the phosphoglyceric acid dehydrogenase sequence can be obtained from GenBank of NCBI, which is a known database. Specifically, it may be a polypeptide having phosphoglyceric acid dehydrogenase activity encoded by serA , but is not limited thereto.
  • corresponding to refers to an amino acid residue at a listed position in a polypeptide, or to an amino acid residue that is similar, identical or homologous to a listed residue in a polypeptide. Identifying an amino acid at a corresponding position may be determining a specific amino acid in a sequence that refers to a specific sequence.
  • corresponding region generally refers to a similar or corresponding position in a related protein or reference protein.
  • any amino acid sequence is aligned with SEQ ID NO: 3, and based on this, each amino acid residue of the amino acid sequence can be numbered with reference to the numerical position of the amino acid residue corresponding to the amino acid residue of SEQ ID NO: 3 .
  • a sequence alignment algorithm such as that described in this application can identify the position of an amino acid, or a position at which modifications, such as substitutions, insertions, or deletions, occur compared to a query sequence (also referred to as a "reference sequence").
  • Such alignments include, for example, the Needleman-Wunsch algorithm (Needleman and Wunsch, 1970, J. Mol. Biol. 48: 443-453), the Needleman program in the EMBOSS package (EMBOSS: The European Molecular Biology Open Software Suite, Rice et al. , 2000), Trends Genet. 16: 276-277), etc., but is not limited thereto, and a sequence alignment program known in the art, a pairwise sequence comparison algorithm, etc. may be appropriately used.
  • Another aspect of the present application is to provide a polynucleotide encoding the variant of the present application.
  • polynucleotide refers to a DNA or RNA strand of a certain length or longer as a polymer of nucleotides in which nucleotide monomers are linked in a long chain by covalent bonds, and more specifically, encoding the variant. polynucleotide fragments.
  • the polynucleotide encoding the variant of the present application may include a nucleotide sequence encoding the amino acid sequence set forth in SEQ ID NO: 1, SEQ ID NO: 5 or SEQ ID NO: 7.
  • the polynucleotide of the present application may have or include the sequence of SEQ ID NO: 2, SEQ ID NO: 6, or SEQ ID NO: 8.
  • the polynucleotide of the present application may consist of, or consist essentially of, the sequence of SEQ ID NO: 2, SEQ ID NO: 6, or SEQ ID NO: 8.
  • the polynucleotides of the present application are various in the coding region within the range that does not change the amino acid sequence of the variants of the present application. Deformation can be made.
  • the polynucleotide of the present application has 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% homology or identity to the sequence of SEQ ID NO: 2, SEQ ID NO: 6 or SEQ ID NO: 8 or more, 96% or more, 97% or more, 98% or more, and less than 100% of the base sequence, or the homology or identity with the sequence of SEQ ID NO: 2, SEQ ID NO: 6, or SEQ ID NO: 8 is 70% or more; 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 96% or more, 97% or more, 98% or more, and less than 100% of the nucleotide sequence may consist of, or consist essentially of, but is not limited thereto.
  • the codon encoding the amino acid corresponding to the 338th position of SEQ ID NO: 1 or SEQ ID NO: 5 may be one of the codons encoding aspartic acid, SEQ ID NO: 1 or
  • the codon encoding the amino acid corresponding to position 396 of SEQ ID NO: 7 may be one of the codons encoding isoleucine.
  • polynucleotide of the present application may be included without limitation as long as it can hybridize under stringent conditions with a probe that can be prepared from a known gene sequence, for example, a sequence complementary to all or part of the polynucleotide sequence of the present application.
  • stringent condition means a condition that enables specific hybridization between polynucleotides. These conditions are described in J. Sambrook et al., Molecular Cloning, A Laboratory Manual, 2nd Edition, Cold Spring Harbor Laboratory press, Cold Spring Harbor, New York, 1989; F.M. Ausubel et al., Current Protocols in Molecular Biology, John Wiley & Sons, Inc., New York, 9.50-9.51, 11.7-11.8).
  • polynucleotides with high homology or identity 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 95% or more, 96% or more, 97% or more, 98% or more, or a condition in which polynucleotides having 99% or more homology or identity hybridize with each other and polynucleotides with lower homology or identity do not hybridize, or a washing condition of conventional Southern hybridization at 60°C, 1 ⁇ SSC, 0.1% SDS, specifically 60°C, 0.1 ⁇ SSC, 0.1% SDS, more specifically 68°C, 0.1 ⁇ SSC, 0.1% SDS at a salt concentration and temperature equivalent to once, specifically twice The conditions for washing to 3 times can be enumerated.
  • Hybridization requires that two nucleic acids have complementary sequences, although mismatch between bases is possible depending on the stringency of hybridization.
  • complementary is used to describe the relationship between nucleotide bases capable of hybridizing to each other.
  • adenine is complementary to thymine
  • cytosine is complementary to guanine.
  • the polynucleotides of the present application may also include substantially similar nucleic acid sequences as well as isolated nucleic acid fragments complementary to the overall sequence.
  • a polynucleotide having homology or identity to the polynucleotide of the present application can be detected using the hybridization conditions including a hybridization step at a Tm value of 55° C. and using the above-described conditions.
  • the Tm value may be 60° C., 63° C. or 65° C., but is not limited thereto and may be appropriately adjusted by those skilled in the art according to the purpose.
  • the appropriate stringency for hybridizing the polynucleotides depends on the length of the polynucleotides and the degree of complementarity, and the parameters are well known in the art (eg, J. Sambrook et al., supra).
  • Another aspect of the present application is to provide a vector comprising the polynucleotide of the present application.
  • the vector may be an expression vector for expressing the polynucleotide in a host cell, but is not limited thereto.
  • the term "vector” refers to a DNA preparation comprising the base sequence of a polynucleotide encoding the target polypeptide operably linked to a suitable expression control region (or expression control sequence) so that the target polypeptide can be expressed in a suitable host.
  • the expression control region may include a promoter capable of initiating transcription, an optional operator sequence for regulating such transcription, a sequence encoding a suitable mRNA ribosome binding site, and a sequence regulating the termination of transcription and translation.
  • the vector After transformation into an appropriate host cell, the vector can replicate or function independently of the host genome, and can be integrated into the genome itself.
  • the vector used in the present application is not particularly limited, and any vector known in the art may be used.
  • Examples of commonly used vectors include plasmids, cosmids, viruses and bacteriophages in a natural or recombinant state.
  • pWE15, M13, MBL3, MBL4, IXII, ASHII, APII, t10, t11, Charon4A, and Charon21A may be used as phage vectors or cosmid vectors, and pDZ-based, pBR-based, and pUC-based plasmid vectors may be used.
  • pBluescript II-based pGEM-based, pTZ-based, pCL-based, pET-based and the like
  • pDZ pDC, pDCM2, pACYC177, pACYC184, pCL, pECCG117, pUC19, pBR322, pMW118, pCC1BAC vectors and the like
  • pC1BAC vectors and the like can be used.
  • a polynucleotide encoding a target polypeptide may be inserted into a chromosome through a vector for intracellular chromosome insertion.
  • the insertion of the polynucleotide into the chromosome may be performed by any method known in the art, for example, homologous recombination, but is not limited thereto.
  • It may further include a selection marker (selection marker) for confirming whether the chromosome is inserted.
  • the selection marker is used to select cells transformed with the vector, that is, to determine whether a target nucleic acid molecule is inserted, and selectable phenotypes such as drug resistance, auxotrophy, resistance to cytotoxic agents, or surface polypeptide expression. Markers to be given can be used. In an environment treated with a selective agent, only the cells expressing the selectable marker survive or exhibit other expression traits, so that the transformed cells can be selected.
  • the term "transformation” refers to introducing a vector including a polynucleotide encoding a target polypeptide into a host cell or microorganism so that the polypeptide encoded by the polynucleotide can be expressed in the host cell.
  • the transformed polynucleotide may include all of them regardless of whether they are inserted into the chromosome of the host cell or located outside the chromosome, as long as they can be expressed in the host cell.
  • the polynucleotide includes DNA and/or RNA encoding a target polypeptide.
  • the polynucleotide may be introduced in any form as long as it can be introduced and expressed into a host cell.
  • the polynucleotide may be introduced into a host cell in the form of an expression cassette, which is a gene construct including all elements necessary for self-expression.
  • the expression cassette may include a promoter operably linked to the polynucleotide, a transcription termination signal, a ribosome binding site, and a translation termination signal.
  • the expression cassette may be in the form of an expression vector capable of self-replication.
  • the polynucleotide may be introduced into a host cell in its own form and operably linked to a sequence required for expression in the host cell, but is not limited thereto.
  • operably linked means that a promoter sequence that initiates and mediates transcription of a polynucleotide encoding the target variant of the present application and the polynucleotide sequence are functionally linked.
  • Another aspect of the present application is to provide a strain of Corynebacterium stationis ( Corynebacterium stationis ) comprising a variant of the present application or a polynucleotide of the present application.
  • the strain of the present application may include a vector comprising the mutant polypeptide of the present application, a polynucleotide encoding the polypeptide, or the polynucleotide of the present application.
  • strain or microorganism
  • strain includes both wild-type microorganisms and microorganisms in which genetic modification has occurred naturally or artificially.
  • a specific mechanism is weakened or enhanced as a microorganism, and may be a microorganism including genetic modification for the production of a desired polypeptide, protein or product.
  • the strain of the present application includes a strain comprising any one or more of a mutant of the present application, a polynucleotide of the present application, and a vector including the polynucleotide of the present application; a strain modified to express a variant of the present application or a polynucleotide of the present application; a variant of the present application, or a strain expressing the polynucleotide of the present application (eg, a recombinant strain); Or it may be a strain having the mutant activity of the present application (eg, a recombinant strain), but is not limited thereto.
  • the strain of the present application may be a strain having the ability to produce 5'-xanthosine monophosphate (XMP) or 5'-guanosine monophosphate (GMP).
  • XMP 5'-xanthosine monophosphate
  • GMP 5'-guanosine monophosphate
  • the strain of the present application is a microorganism having a phosphoglyceric acid dehydrogenase or XMP or GMP production ability naturally, or a mutant or It may be a microorganism into which a polynucleotide encoding the same (or a vector including the polynucleotide) is introduced and/or XMP or GMP production ability is imparted, but is not limited thereto.
  • the strain of the present application is transformed with a vector containing the polynucleotide of the present application or a polynucleotide encoding the variant of the present application, and expresses the variant of the present application as a cell or microorganism
  • the strains of the application may include all microorganisms capable of producing XMP or GMP, including the variants of the present application.
  • the strain of the present application is a natural wild-type microorganism, or a phosphoglyceric acid dehydrogenase variant is expressed by introducing a polynucleotide encoding the variant of the present application into a microorganism producing XMP or GMP, XMP or It may be a recombinant strain with increased GMP production capacity.
  • the recombinant strain with increased XMP or GMP production capacity compared to the natural wild-type microorganism or phosphoglyceric acid dehydrogenase unmodified microorganism (that is, a microorganism expressing wild-type phosphoglyceric acid dehydrogenase), XMP or GMP It may be a microorganism with increased productivity, but is not limited thereto.
  • the strain with increased XMP or GMP production capacity of the present application may be a microorganism with increased XMP or GMP production capacity compared to Corynebacterium stasis comprising the polypeptide of SEQ ID NO: 3 or a polynucleotide encoding the same.
  • the target strain to compare whether the increase in XMP or GMP production capacity, phosphoglyceric acid dehydrogenase unmodified microorganism may be ATCC6872 or CJX1664 strain (KR 10-1950141 B1), but is not limited thereto .
  • the recombinant strain with increased production capacity is about 1% or more, about 2.5% or more, about 5% or more, about 6% or more, about 7% or more compared to the XMP or GMP production capacity of the parent strain or unmodified microorganism before mutation.
  • the upper limit is not particularly limited, and may be, for example, about 10 times or less, about 5 times or less, about 3 times or less, or about 2 times or less) may be increased, but is not limited thereto.
  • the term "about” is a range including all of ⁇ 0.5, ⁇ 0.4, ⁇ 0.3, ⁇ 0.2, ⁇ 0.1, etc., including all numerical values in a range equal to or similar to the numerical value following the term about, but not limited
  • the term "unmodified microorganism” does not exclude a strain containing a mutation that can occur naturally in a microorganism, it is a wild-type strain or a natural-type strain itself, or a genetic variation caused by natural or artificial factors. It may mean the strain before being changed.
  • the unmodified microorganism may refer to a strain in which the phosphoglyceric acid dehydrogenase variant described herein is not introduced or before it is introduced.
  • the "unmodified microorganism” may be used interchangeably with "strain before modification", “microbe before modification”, “unmodified strain”, “unmodified strain”, “unmodified microorganism” or "reference microorganism”.
  • the microorganism of the present application is Corynebacterium stationis ( Corynebacterium stationis ), Corynebacterium crudilactis ( Corynebacterium crudilactis ), Corynebacterium deserti ( Corynebacterium deserti ), Cory Nebacterium efficiens ( Corynebacterium efficiens ), Corynebacterium callunae ), Corynebacterium glutamicum ( Corynebacterium glutamicum ), Corynebacterium singulare ( Corynebacterium singulare ), Corynebacterium halo Tolerans ( Corynebacterium halotolerans ), Corynebacterium striatum ( Corynebacterium striatum ), Corynebacterium ammoniagenes ( Corynebacterium ammoniagenes ), Corynebacterium pollutisoli ( Corynebacterium pollutisoli ), Corynebacterium polluti
  • the term "weakening" of a polypeptide is a concept that includes both reduced or no activity compared to intrinsic activity.
  • the attenuation may be used interchangeably with terms such as inactivation, deficiency, down-regulation, decrease, reduce, attenuation, and the like.
  • the attenuation is when the activity of the polypeptide itself is reduced or eliminated compared to the activity of the polypeptide possessed by the original microorganism due to mutation of the polynucleotide encoding the polypeptide, etc.
  • the overall polypeptide activity level and/or concentration (expression amount) in the cell is lower than that of the native strain due to (translation) inhibition, etc., when the expression of the polynucleotide is not made at all, and/or when the expression of the polynucleotide is Even if there is no activity of the polypeptide, it may also be included.
  • the "intrinsic activity” refers to the activity of a specific polypeptide originally possessed by the parent strain, wild-type or unmodified microorganism before transformation when the trait is changed due to genetic mutation caused by natural or artificial factors. This may be used interchangeably with “activity before modification”. "Inactivation, deficiency, reduction, downregulation, reduction, attenuation” of the activity of the polypeptide compared to the intrinsic activity means that the activity of the specific polypeptide originally possessed by the parent strain or unmodified microorganism before transformation is lowered.
  • Attenuation of the activity of such a polypeptide may be performed by any method known in the art, but is not limited thereto, and may be achieved by application of various methods well known in the art (eg, Nakashima N et al., Bacterial cellular engineering by genome editing and gene silencing. Int J Mol Sci. 2014;15(2):2773-2793, Sambrook et al. Molecular Cloning 2012, etc.).
  • the attenuation of the polypeptide activity of the present application is
  • an antisense oligonucleotide eg, antisense RNA
  • an antisense oligonucleotide that complementarily binds to the transcript of said gene encoding the polypeptide
  • deletion of a part or all of the gene encoding the polypeptide may be the removal of the entire polynucleotide encoding the endogenous target polypeptide in the chromosome, replacement with a polynucleotide in which some nucleotides are deleted, or replacement with a marker gene.
  • the expression control region includes, but is not limited to, a promoter, an operator sequence, a sequence encoding a ribosome binding site, and a sequence regulating the termination of transcription and translation.
  • the base sequence modification encoding the start codon or 5'-UTR region of the gene transcript encoding the polypeptide is, for example, a base encoding another start codon having a lower expression rate of the polypeptide compared to the intrinsic start codon It may be substituted with a sequence, but is not limited thereto.
  • the modification of the amino acid sequence or polynucleotide sequence of 3) and 4) above deletes, inserts, non-conservative or conservative substitution of the amino acid sequence of the polypeptide or the polynucleotide sequence encoding the polypeptide so as to weaken the activity of the polypeptide.
  • a combination thereof may result in a mutation in sequence, or replacement with an amino acid sequence or polynucleotide sequence improved to have weaker activity or an amino acid sequence or polynucleotide sequence improved to have no activity, but is not limited thereto.
  • the expression of a gene may be inhibited or attenuated, but is not limited thereto.
  • antisense oligonucleotide eg, antisense RNA
  • antisense RNA an antisense oligonucleotide that complementarily binds to the transcript of the gene encoding the polypeptide
  • Weintraub, H. et al. Antisense-RNA as a molecular tool. for genetic analysis, Reviews - Trends in Genetics, Vol. 1(1) 1986].
  • RTE reverse transcription engineering
  • the term "enhancement" of a polypeptide activity means that the activity of the polypeptide is increased compared to the intrinsic activity.
  • the reinforcement may be used interchangeably with terms such as activation, up-regulation, overexpression, and increase.
  • activation, enhancement, up-regulation, overexpression, and increase may include all of those exhibiting an activity that was not originally possessed, or exhibiting an improved activity compared to an intrinsic activity or an activity prior to modification.
  • intrinsic activity refers to the activity of a specific polypeptide originally possessed by the parent strain or unmodified microorganism before transformation when the trait is changed due to genetic mutation caused by natural or artificial factors.
  • Enhance, "up-regulation”, “overexpression” or “increase” in the activity of a polypeptide compared to its intrinsic activity means the activity of a specific polypeptide originally possessed by the parent strain or unmodified microorganism before transformation. And / or concentration (expression amount) means improved compared to.
  • the enrichment can be achieved by introducing an exogenous polypeptide, or by enhancing the activity and/or concentration (expression amount) of the endogenous polypeptide. Whether or not the activity of the polypeptide is enhanced can be confirmed from the increase in the level of activity, expression level, or the amount of product excreted from the polypeptide.
  • the enhancement of the activity of the polypeptide can be applied by various methods well known in the art, and is not limited as long as it can enhance the activity of the target polypeptide compared to the microorganism before modification. Specifically, it may be one using genetic engineering and/or protein engineering well known to those skilled in the art, which is a routine method of molecular biology, but is not limited thereto (eg, Sitnicka et al. Functional Analysis of Genes. Advances in Cell). Biology 2010, Vol. 2. 1-16, Sambrook et al. Molecular Cloning 2012, etc.).
  • modification of the polynucleotide sequence encoding the polypeptide to enhance the polypeptide activity eg, modification of the polynucleotide sequence of the polypeptide gene to encode a polypeptide modified to enhance the activity of the polypeptide
  • the increase in the intracellular copy number of the polynucleotide encoding the polypeptide is achieved by introduction into the host cell of a vector to which the polynucleotide encoding the polypeptide is operably linked, which can replicate and function independently of the host it may be Alternatively, the polynucleotide encoding the polypeptide may be achieved by introducing one copy or two or more copies into a chromosome in a host cell.
  • the introduction into the chromosome may be performed by introducing a vector capable of inserting the polynucleotide into the chromosome in the host cell into the host cell, but is not limited thereto.
  • the vector is the same as described above.
  • Replacing the gene expression control region (or expression control sequence) on the chromosome encoding the polypeptide with a sequence with strong activity is, for example, deletion, insertion, non-conservative or Conservative substitution or a combination thereof may result in a mutation in the sequence, or replacement with a sequence having a stronger activity.
  • the expression control region is not particularly limited thereto, but may include a promoter, an operator sequence, a sequence encoding a ribosome binding site, and a sequence controlling the termination of transcription and translation.
  • the original promoter may be replaced with a strong promoter, but is not limited thereto.
  • Examples of known strong promoters include CJ1 to CJ7 promoters (US 7662943 B2), lac promoter, trp promoter, trc promoter, tac promoter, lambda phage PR promoter, PL promoter, tet promoter, gapA promoter, SPL7 promoter, SPL13 (sm3) promoter (US Patent US 10584338 B2), O2 promoter (US Patent US 10273491 B2), tkt promoter, yccA promoter, etc., but is not limited thereto.
  • Modification of the nucleotide sequence encoding the start codon or 5'-UTR region of the gene transcript encoding the polypeptide is, for example, a nucleotide sequence encoding another start codon having a higher expression rate of the polypeptide compared to the intrinsic start codon. It may be a substitution, but is not limited thereto.
  • the modification of the amino acid sequence or polynucleotide sequence of 4) and 5) above may include deletion, insertion, non-conservative or conservative substitution of the amino acid sequence of the polypeptide or the polynucleotide sequence encoding the polypeptide to enhance the activity of the polypeptide;
  • a combination thereof may result in sequence mutation, or replacement with an amino acid sequence or polynucleotide sequence improved to have stronger activity or an amino acid sequence or polynucleotide sequence improved to increase activity, but is not limited thereto.
  • the replacement may be specifically performed by inserting a polynucleotide into a chromosome by homologous recombination, but is not limited thereto.
  • the vector used may further include a selection marker for confirming whether or not the chromosome is inserted.
  • the selection marker is the same as described above.
  • the introduction of the foreign polynucleotide exhibiting the activity of the polypeptide may be the introduction of the foreign polynucleotide encoding the polypeptide exhibiting the same/similar activity as the polypeptide into a host cell.
  • the foreign polynucleotide is not limited in its origin or sequence as long as it exhibits the same/similar activity as the polypeptide.
  • the method used for the introduction can be performed by appropriately selecting a known transformation method by those skilled in the art, and the introduced polynucleotide is expressed in a host cell to generate a polypeptide and increase its activity.
  • Codon optimization of the polynucleotide encoding the polypeptide is codon-optimized so that the transcription or translation of the endogenous polynucleotide is increased in the host cell, or the transcription and translation of the foreign polynucleotide is optimized in the host cell. It may be that its codons are optimized so that the
  • Selecting an exposed site by analyzing the tertiary structure of the polypeptide and modifying or chemically modifying it is, for example, by comparing the sequence information of the polypeptide to be analyzed with a database in which sequence information of known proteins is stored to determine the degree of sequence similarity. Accordingly, it may be to determine a template protein candidate, check the structure based on this, and select an exposed site to be modified or chemically modified and modified or modified.
  • Such enhancement of polypeptide activity is to increase the activity or concentration of the corresponding polypeptide relative to the activity or concentration of the polypeptide expressed in the wild-type or pre-modified microbial strain, or increase the amount of product produced from the polypeptide.
  • the present invention is not limited thereto.
  • Modification of part or all of the polynucleotide in the microorganism of the present application is (a) homologous recombination using a vector for chromosome insertion in the microorganism or genome correction using engineered nuclease (e.g., CRISPR-Cas9) and/or (b) It may be induced by light and/or chemical treatments such as, but not limited to, ultraviolet and radiation.
  • the method for modifying part or all of the gene may include a method by DNA recombination technology.
  • a part or all of the gene may be deleted.
  • the injected nucleotide sequence or vector may include a dominant selection marker, but is not limited thereto.
  • Another aspect of the present application provides a method for producing XMP or GMP, comprising the step of culturing a Corynebacterium stationionis strain comprising a variant of the present application or a polynucleotide of the present application in a medium.
  • XMP or GMP of the present application may include the step of culturing a Corynebacterium stationionis strain comprising the variant of the present application or the polynucleotide of the present application or the vector of the present application in a medium.
  • the term "cultivation” means growing the Corynebacterium stasis strain of the present application under moderately controlled environmental conditions.
  • the culture process of the present application may be performed according to a suitable medium and culture conditions known in the art. Such a culture process can be easily adjusted and used by those skilled in the art according to the selected strain.
  • the culture may be a batch, continuous and/or fed-batch, but is not limited thereto.
  • the term "medium” refers to a material in which nutrients required for culturing the Corynebacterium stasis strain of the present application are mixed as a main component, and nutrients including water essential for survival and development and growth factors.
  • any medium and other culture conditions used for culturing the Corynebacterium stasis strain of the present application may be used without particular limitation as long as it is a medium used for culturing conventional microorganisms, but the Corynebacterium of the present application Rium stasis strains can be cultured while controlling temperature, pH, etc. under aerobic conditions in a conventional medium containing an appropriate carbon source, nitrogen source, phosphorus, inorganic compound, amino acid and/or vitamin.
  • the culture medium for the Corynebacterium sp. strain can be found in the literature ["Manual of Methods for General Bacteriology” by the American Society for Bacteriology (Washington D.C., USA, 1981)].
  • the carbon source includes carbohydrates such as glucose, saccharose, lactose, fructose, sucrose, maltose, and the like; sugar alcohols such as mannitol and sorbitol; organic acids such as pyruvic acid, lactic acid, citric acid and the like; amino acids such as glutamic acid, methionine, lysine, and the like may be included.
  • natural organic nutrient sources such as starch hydrolyzate, molasses, blackstrap molasses, rice winter, cassava, sugar cane offal and corn steep liquor can be used, specifically glucose and sterilized pre-treated molasses (i.e., converted to reducing sugar). molasses) may be used, and other appropriate amounts of carbon sources may be variously used without limitation. These carbon sources may be used alone or in combination of two or more, but is not limited thereto.
  • nitrogen source examples include inorganic nitrogen sources such as ammonia, ammonium sulfate, ammonium chloride, ammonium acetate, ammonium phosphate, anmonium carbonate, and ammonium nitrate; Amino acids such as glutamic acid, methionine, glutamine, and organic nitrogen sources such as peptone, NZ-amine, meat extract, yeast extract, malt extract, corn steep liquor, casein hydrolyzate, fish or degradation products thereof, defatted soybean cake or degradation products thereof, etc. can be used These nitrogen sources may be used alone or in combination of two or more, but is not limited thereto.
  • inorganic nitrogen sources such as ammonia, ammonium sulfate, ammonium chloride, ammonium acetate, ammonium phosphate, anmonium carbonate, and ammonium nitrate
  • Amino acids such as glutamic acid, methionine, glutamine
  • organic nitrogen sources such as peptone, NZ-amine, meat extract, yeast extract
  • the phosphorus may include potassium first potassium phosphate, second potassium phosphate, or a sodium-containing salt corresponding thereto.
  • potassium first potassium phosphate potassium phosphate
  • second potassium phosphate or a sodium-containing salt corresponding thereto.
  • sodium chloride, calcium chloride, iron chloride, magnesium sulfate, iron sulfate, manganese sulfate, calcium carbonate, etc. may be used, and in addition, amino acids, vitamins and/or suitable precursors may be included. These components or precursors may be added to the medium either batchwise or continuously. However, the present invention is not limited thereto.
  • the pH of the medium may be adjusted.
  • an antifoaming agent such as fatty acid polyglycol ester may be used to suppress bubble formation.
  • oxygen or oxygen-containing gas may be injected into the medium, or nitrogen, hydrogen or carbon dioxide gas may be injected without or without gas to maintain anaerobic and microaerobic conditions, it is not
  • the culture temperature may be maintained at 20 to 45° C., specifically, 25 to 40° C., and may be cultured for about 10 to 160 hours, but is not limited thereto.
  • XMP or GMP produced by the culture of the present application may be secreted into the medium or remain in the cells.
  • preparing the Corynebacterium stasis strain of the present application may further include.
  • the XMP or GMP production method of the present application may further include recovering the XMP or GMP from the culture medium (the culture medium) or the Corynebacterium stationionis strain of the present application.
  • the recovering step may be further included after the culturing step.
  • the recovery may be to collect the desired XMP or GMP using a suitable method known in the art according to the culture method of the microorganism of the present application, for example, a batch, continuous or fed-batch culture method, etc. .
  • a suitable method known in the art for example, centrifugation, filtration, treatment with a crystallized protein precipitating agent (salting out method), extraction, ultrasonic disruption, ultrafiltration, dialysis, molecular sieve chromatography (gel filtration), adsorption chromatography, ion exchange chromatography, affinity
  • Various chromatography such as island chromatography, HPLC, or a combination thereof may be used, and the desired XMP or GMP may be recovered from the medium or microorganism using a suitable method known in the art.
  • the XMP or GMP production method of the present application may include an additional purification step.
  • the purification may be performed using a suitable method known in the art.
  • the recovery step and the purification step are performed continuously or discontinuously regardless of the order, or are integrated into one step or simultaneously may be performed, but is not limited thereto.
  • the GMP production method of the present application may further include the step of converting the XMP to GMP.
  • the converting step may be further included after the culturing step or the recovering step.
  • the converting step can be carried out using a suitable method known in the art.
  • the conversion may be performed using a coryneform microorganism, Escherichia coli, or 5'-xanthyl acid aminase (KR 10-0655902 B1), but is not limited thereto.
  • variants, polynucleotides, vectors, strains, XMP and GMP, etc. are as described in the other aspects above.
  • Another aspect of the present application provides a variant of the present application, a polynucleotide encoding the variant, a vector including the polynucleotide or a Corynebacterium stasis strain comprising the polynucleotide of the present application; the culture medium; Or to provide a composition for XMP or GMP production comprising a combination of two or more of them.
  • composition of the present application may further include any suitable excipients commonly used in compositions for XMP or GMP production, and these excipients include, for example, preservatives, wetting agents, dispersing agents, suspending agents, buffering agents, stabilizing agents or isotonic agents. and the like, but is not limited thereto.
  • composition of the present application variants, polynucleotides, vectors, strains, XMPs and GMPs are the same as those described in the other aspects above.
  • Example 1 Construction of a vector for the expression of phosphoglyceric acid dehydrogenase variants in microorganisms
  • Glycine at position 338 of the phosphoglyceric acid dehydrogenase amino acid sequence (SEQ ID NO: 3) is substituted with aspartic acid (G338D; SEQ ID NO: 5), or threonine at position 396 is substituted with isoleucine (T396I; SEQ ID NO: 7) ), a mutant (G338D+T396I; SEQ ID NO: 1) in which glycine at position 338 is substituted with aspartic acid and threonine at position 396 is substituted with isoleucine (G338D+T396I; SEQ ID NO: 1) to determine the effect on XMP production.
  • the plasmid pDCM2 (Korea Publication No. 10-2020-0136813) for the insertion and replacement of genes in the Nebacterium chromosome was used as follows.
  • PCR was performed using a primer pair of sequences of SEQ ID NOs: 9 and 10 and a pair of primers of sequences of SEQ ID NOs: 11 and 12 using gDNA (genomic DNA) of wild-type Corynebacterium stasis ATCC6872 as a template, respectively.
  • gDNA genomic DNA
  • overlapping PCR was performed again using the primer pair of SEQ ID NO: 9 and SEQ ID NO: 12 to obtain a fragment.
  • PCR was repeated 30 times at 94°C for 30 seconds, at 55°C for 30 seconds, and at 72°C for 1 minute and 30 seconds, and then at 72°C for 5 minutes.
  • the pDCM2 vector was treated with SmaI and the PCR product obtained above was fusion cloned. Fusion cloning was performed using the In-Fusion® HD cloning kit (Clontech). The resulting plasmid was named pDCM2-serA (G338D).
  • PCR was performed using a pair of primers of sequences of SEQ ID NOs: 9 and 15 and a pair of primers of sequences of SEQ ID NOs: 16 and 12 using gDNA (genomic DNA) of wild-type Corynebacterium stasis ATCC6872 as a template, respectively.
  • gDNA genomic DNA
  • overlapping PCR was performed again using the primer pair of SEQ ID NO: 9 and SEQ ID NO: 12 to obtain a fragment.
  • PCR was repeated 30 times at 94°C for 30 seconds, at 55°C for 30 seconds, and at 72°C for 1 minute and 30 seconds, and then at 72°C for 5 minutes.
  • the pDCM2 vector was treated with SmaI and the PCR product obtained above was fusion cloned. Fusion cloning was performed using the In-Fusion® HD cloning kit (Clontech). The resulting plasmid was named pDCM2-serA(T396I).
  • Example 2 Evaluation of XMP-producing ability of microorganisms expressing phosphoglyceric acid dehydrogenase variants
  • the vector prepared in Example 1 was transformed into Corynebacterium stasis CJX1664 strain (KR 10-1950141 B1).
  • each selected strain was named CJX1664_serA_G338D and CJX1664_serA_T396I, and the strain introduced with both mutations was named CJX1664_serA_G338D+T396I.
  • XMP production capacity was analyzed by evaluating the flask fermentation titer of the strain prepared in Example 2-1 and the control parent strain.
  • each strain was inoculated into a test tube with a diameter of 18 mm containing 2 ml of the seed medium, and cultured with shaking at 30 ° C. for 24 hours was used as a seed culture medium.
  • 0.7 ml of the seed culture solution was inoculated into a 250 ml corner-baffle flask containing 32 ml of the following production medium (24 ml of the main medium + 8 ml of a separate sterilization medium) and cultured at 30° C. for 75 hours at 170 rmp.
  • the production capacity of XMP was measured by HPLC.
  • the XMP concentration and the concentration increase rate in the culture medium for each strain tested are shown in Table 1 below.

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Abstract

La présente invention concerne un nouveau variant de la phosphoglycérate déshydrogénase, une souche de Corynebacterium stationis comprenant ce variant et un procédé de production de XMP ou de GMP au moyen de cette souche.
PCT/KR2022/005643 2021-04-20 2022-04-20 Nouveau variant de la phosphoglycérate déshydrogénase et procédé de production de xap ou de gmp au moyen de celui-ci WO2022225320A1 (fr)

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KR102273638B1 (ko) * 2021-04-20 2021-07-06 씨제이제일제당 주식회사 신규한 포스포글리세린산 디하이드로게나제 변이체 및 이를 이용한 xmp 또는 gmp 생산 방법

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