WO2011157573A2 - Enzyme permettant de produire du méthylmalonate-semi-aldéhyde - Google Patents

Enzyme permettant de produire du méthylmalonate-semi-aldéhyde Download PDF

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Publication number
WO2011157573A2
WO2011157573A2 PCT/EP2011/059178 EP2011059178W WO2011157573A2 WO 2011157573 A2 WO2011157573 A2 WO 2011157573A2 EP 2011059178 W EP2011059178 W EP 2011059178W WO 2011157573 A2 WO2011157573 A2 WO 2011157573A2
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amino acid
seq
acid sequence
group
coenzyme
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PCT/EP2011/059178
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German (de)
English (en)
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WO2011157573A3 (fr
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Markus PÖTTER
Achim Marx
Steffen Schaffer
Liv Reinecke
Thomas Haas
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Evonik Röhm Gmbh
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Publication of WO2011157573A2 publication Critical patent/WO2011157573A2/fr
Publication of WO2011157573A3 publication Critical patent/WO2011157573A3/fr

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P7/00—Preparation of oxygen-containing organic compounds
    • C12P7/62—Carboxylic acid esters
    • 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.)
    • C12N9/001—Oxidoreductases (1.) acting on the CH-CH group of donors (1.3)

Definitions

  • the invention relates to an enzyme for the production of methylmalonate semialdehyde or malonate semialdehyde, nucleic acids containing coding sequences for this enzyme, cells which have been transformed with these nucleic acids, as well as the use of this enzyme.
  • DE102006025821 describes an enzyme from Sulfolobus tokodaii which is capable of producing S- or R-methylmalonyl-coenzyme A and malonyl-coenzyme A to the corresponding ones
  • This enzyme is used in processes for the preparation of (S) - or (R) - methylmalonate semialdehyde, (S) - or (R) -3-hydroxyisobutyric acid or (S) - or (R) -3-hydroxyisobutyric acid based polyhydroxyalkanoates and in processes for the preparation of malonate semialdehyde, of 3-hydroxypropionic acid or of
  • Hydroxypropionic acid based polyhydroxyalkanoates used. These process products are commercially valuable starting materials for chemical syntheses. This justifies, as in the present invention, the industrial applicability.
  • a disadvantage of the enzyme described lies in the relatively low activity of the enzyme, in particular with regard to the substrates S- and R-methylmalonyl-coenzyme A.
  • the object of the invention was to provide enzymes which have a greater specific activity in the reactions described above and thus in a shorter time more (S) - or (R) -Methylmalonatsemialdehyd or Malonatsemialdehyd from S- or R-methylmalonyl coenzyme A or Malonyl coenzyme A, in particular more (S) - or (R) -
  • Methylmalonatsemialdehyd from S- or R-methylmalonyl coenzyme A assets to make.
  • nucleic acids comprising nucleic acids encoding the polypeptides of the invention as well as cells containing the
  • the invention relates to the use of the substances according to the invention for the preparation of (S) - or (R) -methylmalonate semialdehyde, of (S) - or (R) -3-hydroxyisobutyric acid, of (S) - or (R) -3-hydroxyisobutyric acid-based Polyhydroxyalkanoates, malonate semialdehyde, 3-hydroxypropionic acid and 3-hydroxypropionic acid based polyhydroxyalkanoates.
  • polypeptides according to the invention are, in addition to the described activities, also the very high stability.
  • the increased stability leads to a long availability of the polypeptides according to the invention
  • Another advantage is that bioprocesses are made possible, which can be carried out at elevated temperatures and thus require less cooling.
  • SEQ. ID. NO. 2 SEQ. ID. NO. 4, SEQ. ID. NO. 6, SEQ.ID.NO. 8, SEQ.ID.NO. 10, SEQ. ID. NO. 12, SEQ ID NO. 14, SEQ. ID. NO. 16 and SEQ ID NO. 18, in particular SEQ.-ID-No. 2,
  • Amino acid sequence is capable of producing S- or R-methylmalonyl coenzyme A and malonyl
  • V16T preferably V16T, L149K, L149M, L149R, Y203L, T207P, T207S, I330A, I330C and I330W.
  • Polypeptides having the polypeptide sequences of group A and the said amino acids having the polypeptide sequences of group A and the said amino acids
  • Amino acid exchanges are capable of forming S- or R-methylmalonyl coenzyme A to the corresponding semialdehyde ((S) - or (R) -methylmalonate semialdehyde) with preferably at least 1 10%, more preferably at least 150%, especially at least 200%, completely especially to convert at least 300% of the specific activity of the respective polypeptide with the polypeptide sequence of group A without said amino acid substitutions.
  • Preferred polypeptides according to the invention have at least one combination of
  • Amino acid substitution selected from the group consisting of A07S Y203F, V16T K38R, K38R L149M, K38R L149R, K38R T207P, K38R I208V, L149I T207P, L149M Y203M, L149M T207P, L149M R315K, L149M K317E and L149Q T207P, especially L149M T207P
  • preferred polypeptides have at least one combination of
  • Amino acid substitution selected from the group consisting of
  • nucleotide identity or "amino acid identity” is determined in the context of the present invention by known methods. In general, special computer programs are used with algorithms taking into account special requirements.
  • Determination of identity include, but are not limited to, the GCG program package, including GAP (Deveroy, J. et al., Nucleic Acid Research 12 (1984), page 387, Genetics Computer Group University of Wisconsin, Medicine (Wi), and BLASTP, BLASTN and FASTA (Altschul, S. et al., Journal of Molecular Biology 215 (1990), pages 403-410
  • the BLAST program can be obtained from the National Center for Biotechnology Information (NCBI) and from other sources (BLAST Handbook, Altschul S. et al., NCBI NLM NIH Bethesda ND 22894; Altschul S. et al., Supra).
  • the well-known Smith-Waterman algorithm can also be used to determine nucleotide identity.
  • the above parameters are the default parameters in nucleotide sequence comparison.
  • the GAP program is also suitable for use with the above parameters.
  • Preferred parameters for the determination of "amino acid identity” are when using the BLASTP program (Altschul, S. et al., Journal of Molecular Biology 215 (1990), pages 403-410:
  • compositional adjustments Conditional compositional score matrix adjustment
  • the above parameters are the default parameters in the amino acid sequence comparison.
  • the GAP program is also suitable for use with the above parameters.
  • the nomenclature for the amino acid substitutions defined above is well known to those skilled in the art.
  • V16T describes that the amino acid valine at position 16 has been replaced by a threonine.
  • the numbering of the amino acid position always refers to the corresponding position in the considered amino acid sequence with SEQ. ID. NO. 2 for reference.
  • the sequence to be considered with SEQ. ID no. 2 matched using the BlastP program using the above parameters; the numerical position indicated in the amino acid substitution is then found in the amino acid sequence under consideration in accordance with SEQ.ID.No. 2 assigned again.
  • amino acid sequence under consideration at the indicated numerical position has a different amino acid than in the first place given in the amino acid exchange, this other amino acid is the last in the amino acid exchange
  • Polypeptide sequence that do not lead to any significant changes in the properties and function of the given polypeptide are known in the art.
  • so-called conserved amino acids can be exchanged for each other;
  • suitable amino acid substitutions are: Ala versus Ser; Arg against Lys; Asn versus Gin or His; Asp against Glu; Cys versus Ser; Gin vs Asn; Glu vs Asp; Gly vs Pro; His against Asn or Gin; against Leu or Val; Leu vs Met or Val; Lys versus Arg or Gin or Glu; Mead against Leu or hell; Phe versus Met or Leu or Tyr; Ser against Thr; Thr against Ser; Trp against Tyr; Tyr against Trp or Phe; Val against hell or leu.
  • Example 3 To determine the specific activity of the protein under consideration with respect to the ability to convert S- or R-methylmalonyl-coenzyme A or malonyl-coenzyme A to the corresponding semialdehydes, the method described in Example 3 with correspondingly known enzyme concentrations can be used.
  • the polypeptide according to the invention is an enzyme which comprises both the conversion of (S) - or (R) -methylmalonyl-coenzyme A to (S) - or (R) - Methylmalonatsemialdehyd and the conversion of malonyl coenzyme A to Malonatsemialdehyd to catalyze.
  • a polypeptide can be synthesized, for example, starting from the DNA sequence of SEQ. ID. NO. 01, SEQ ID NO. 03, SEQ ID NO. 05, SEQ ID NO. 07, SEQ ID NO. 09, SEQ ID NO. 1 1, SEQ.ID.NO. 13, SEQ ID NO. 15 or SEQ ID NO. 17, or by transformation of a suitable cell with a
  • suitable vector comprising the abovementioned nucleic acid sequences, expression of the protein encoded by these nucleic acid sequences in the cell, lysis of the cell to obtain a cell extract and subsequent purification of the enzyme by means of purification techniques known to those skilled in the art, for example by HPLC or others
  • Purification of the polypeptide from cell extracts can also take advantage of the fact that the polypeptide of the invention is heat stable up to a temperature of at least 75 ° C. Therefore, one can heat the cell extract to a temperature of, for example, 75 ° C, thereby causing coagulation and thus precipitation of the non-heat stable
  • Polypeptides in the cell extract comes.
  • the polypeptide according to the invention remains in undenatured form in the cell extract.
  • nucleic acids in particular isolated nucleic acids encoding polypetide according to the invention.
  • coding for is meant here the genetic code having a codon usage, as found for example in E. coli, but also constellations are conceivable in which an unconventional codon usage is used, as in Tetrahymena, for example.
  • Plasmodium, Mycobacterium pneumoniae or Candida tropicalis can lead to polypeptides according to the invention. These nucleic acids are also considered to be "coding for
  • the invention further comprises the nucleotide sequences described
  • a vector preferably an expression vector, comprising a nucleic acid according to the invention, as defined above.
  • Suitable vectors are all vectors known to the person skilled in the art
  • Preferred vectors are selected from the group comprising plasmids, such as the E. coli plasmids pTrc99A, pBR345 and pBR322, viruses such as bacteriophages, adenoviruses, vaccinia viruses, baculoviruses, measles viruses and retroviruses, cosmids or YACs, with plasmids being vectors most are preferred.
  • plasmids such as the E. coli plasmids pTrc99A, pBR345 and pBR322
  • viruses such as bacteriophages, adenoviruses, vaccinia viruses, baculoviruses, measles viruses and retroviruses, cosmids or YACs, with plasmids being vectors most are preferred.
  • the nucleic acid according to the invention is under the control of a regulatable promoter which is used to express the polypeptide encoded by these DNA sequences in the cell of a
  • a microorganism preferably a bacterial, yeast or pilin cell, more preferably a bacterial cell, most preferably one pound. co // cell, is suitable.
  • promoters are, for example, the trp promoter or the tac promoter.
  • the vector according to the invention should, in addition to a promoter, preferably a
  • Ribosome binding site and a terminator include. It is particularly preferred that the DNA according to the invention is incorporated into an expression cassette of the vector comprising the promoter, the ribosome binding site and the terminator.
  • the vector may further comprise selection genes known to those skilled in the art.
  • Transformation cell obtained with this vector obtained with this vector.
  • the cells which can be transformed with the vector according to the invention can be any suitable transformation cell obtained with this vector.
  • Be prokaryotes or eukaryotes These may be mammalian cells (such as human cells), plant cells, or microorganisms such as yeasts, fungi or bacteria, with microorganisms being most preferred and bacteria and yeasts being most preferred.
  • yeasts or fungi especially those bacteria, yeasts or fungi are suitable, which in the German Collection of Microorganisms and Cell Cultures GmbH (DSMZ), Braunschweig, Germany, as bacterial, yeast or fungal strains are deposited.
  • DSMZ German Collection of Microorganisms and Cell Cultures GmbH
  • Bacteria suitable according to the invention belong to the genera under
  • Yeasts which are suitable according to the invention belong to those genera which are listed under http://www.dsmz.de/species/yeasts.htm
  • Particularly preferred cells according to the invention are those of the genera
  • Yarrowia lipolytica Methylobacterium extorquens, Ralstonia eutropha and Pichia pastoris are particularly preferred.
  • these are acetogenic microorganisms, such as, for example, species of the genus Acetobacterium, such as A. woodii and Clostridium aceticum.
  • the acetogenic cells are selected from the group comprising, in particular consisting of, Acetoanaerobium notera, Acetobacterium woodii, Archaeoglobus fulgidus, Butyribacterium methylotrophicum, Butyribacterium methyltrophicum, Carboxydibrachium pacificus, Carboxydocella sporoproducens, Carboxydocella
  • thermoautotrophica Carboxydothermus hydrogenoformans, Citrobacter sp. Y19, Clostridium aceticum, Clostridium acetobutylicum, Clostridium autoethanogenum, Clostridium
  • Desulfotomaculum kuznetsovii Desulfotomaculum thermobenzoicum subsp.
  • thermosyntrophicum Eubacterium limosum, Methanosarcina acetivorans C2A, Methanosarcina barkeri, Methanothermobacter thermoautotrophicus, Moorella AMP, Moorella thermoacetica, Moorella thermoautotrophica, Oxobacter pfennigii, Peptostreptococcus productus,
  • Rhodopseudomonas palustris P4 Rhodospirillum rubrum, Rubrivivax gelatinosus, Thermincola carboxydiphila, Thermincola ferriacetica, Thermococcus AM4, Thermolithobacter carboxydivorans and Thermoanaerobacter kivui.
  • a particularly suitable cell in this context is Clostridium carboxidivorans, in particular such strains as “P7” and "P1 1". Such cells are described, for example, in US 2007/0275447 and US 2008/0057554.
  • Another particularly suitable cell in this context is Clostridium ljungdahlii, in particular strains selected from the group comprising, in particular consisting of, Clostridium ljungdahlii PETC, Clostridium ljungdahlii ERI2, Clostridium IjungdahlW C0I and Clostridium ljungdahlii 0-52; these are described in WO 98/00558 and WO 00/68407.
  • polypeptides, nucleic acids, vectors and cells according to the invention can be advantageously used for the preparation of (S) - or (R) -methylmalonate semialdehyde, of (S) - or (R) -3-hydroxyisobutyric acid, of (S) - or (R) 3-hydroxyisobutyric acid based
  • Embodiments should be limited.
  • the Sulfolobus tokodaii mcr gene was isolated from the plasmid pTrc99A-mcr (Alber B et al., J. Bacteriol, 188: 8551-8559) with the two primers mcr_fwd_Ncol (5 ').
  • the pET-28a (+) - mcr expression construct was transformed into competent cells of the E. coli expression strain Rosetta TM 2 (DE3) (Merck KGaA, Darmstadt, Germany).
  • SeSaM mutant library was prepared by the SeSaM method described in EP1670914 and labeled with the primers SEQ.ID.NO. 19 and 20 cloned.
  • SDM mutant libraries were prepared using the Phusion TM site-directed mutagenesis kit (Finnzymes Oy, Espoo, Finland) according to the manufacturer's instructions in the pET-28a (+) - mcr plasmid.
  • Proteins were heat-precipitated by incubation for 15 min at 75 ° C and 15 min on ice. The denatured proteins and cell debris were spun down for 20 min at 16,000 g and 4 ° C. The clear supernatant was used in the MCR activity detection.
  • the proof of activity is based on the decrease of NADPH and is determined by measuring the
  • NADPH 0.3mM X-CoA.
  • the decrease in absorbance at 340 nm is monitored for 8 min in the cuvette heated to 55 ° C.
  • Amino acid mutation has a significant increase in specific activity on the substrate methylmalonyl-CoA found in such enzymes with amino acid substitutions of: Y203L, A07S Y203F, L149M, L149R, L149K, V16T, V16T, T207P, T207S, I330A, I330C and I330W.
  • Amino acid exchange was set to 100%.

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Abstract

La présente invention concerne une enzyme permettant de produire du méthylmalonate-semi-aldéhyde ou du malonate-semi-aldéhyde, des acides nucléiques contenant des séquences codantes de cette enzyme, des cellules qui ont été transformées avec ces acides nucléiques, ainsi que l'utilisation de cette enzyme.
PCT/EP2011/059178 2010-06-14 2011-06-03 Enzyme permettant de produire du méthylmalonate-semi-aldéhyde WO2011157573A2 (fr)

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DE102010023748.5 2010-06-14

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Cited By (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8980594B2 (en) 2009-11-11 2015-03-17 Evonik Roehm Gmbh Use of a protein homologous to a MeaB protein for increasing the enzymatic activity of a 3-hydroxycarboxylic acid-CoA mutase
US9249435B2 (en) 2011-12-22 2016-02-02 Evonik Degussa Gmbh Process for the improved separation of a hydrophobic organic solution from an aqueous culture medium
US9315443B2 (en) 2011-02-16 2016-04-19 Evonik Degussa Gmbh Liquid cation exchanger
US9765370B2 (en) 2012-04-02 2017-09-19 Evonik Degussa Gmbh Method for aerobically producing alanine or a compound produced using alanine
US10787688B2 (en) 2012-05-11 2020-09-29 Evonik Operations Gmbh Multi-stage synthesis method with synthesis gas
DE102016212497B4 (de) 2015-07-13 2024-04-25 Sk Innovation Co., Ltd. Mutanter Mikroorganismus, der ein Gen umfasst, das Methylmalonyl-CoA-Reductase codiert, und seine Verwendung

Citations (6)

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WO1998000558A1 (fr) 1994-11-30 1998-01-08 Bioengineering Resources, Inc. Production biologique d'acide acetique a partir de gaz residuaires
WO2000068407A1 (fr) 1999-05-07 2000-11-16 Bioengineering Resources, Inc. Souches de clostridium produisant de l'ethanol a partir de gaz de combustion
EP1670914A1 (fr) 2003-10-02 2006-06-21 Basf Aktiengesellschaft Procédé pour la mutagenèse de saturation de séquence (sesam)
US20070275447A1 (en) 2006-05-25 2007-11-29 Lewis Randy S Indirect or direct fermentation of biomass to fuel alcohol
DE102006025821A1 (de) 2006-06-02 2007-12-06 Degussa Gmbh Ein Enzym zur Herstellung von Mehylmalonatsemialdehyd oder Malonatsemialdehyd
US20080057554A1 (en) 2006-08-31 2008-03-06 Huhnke Raymond L Isolation and characterization of novel clostridial species

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DE102007015583A1 (de) * 2007-03-29 2008-10-02 Albert-Ludwigs-Universität Freiburg Ein Enzym zur Herstellung von Methylmalonyl-Coenzym A oder Ethylmalonyl-Coenzym A sowie dessen Verwendung

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WO1998000558A1 (fr) 1994-11-30 1998-01-08 Bioengineering Resources, Inc. Production biologique d'acide acetique a partir de gaz residuaires
WO2000068407A1 (fr) 1999-05-07 2000-11-16 Bioengineering Resources, Inc. Souches de clostridium produisant de l'ethanol a partir de gaz de combustion
EP1670914A1 (fr) 2003-10-02 2006-06-21 Basf Aktiengesellschaft Procédé pour la mutagenèse de saturation de séquence (sesam)
US20070275447A1 (en) 2006-05-25 2007-11-29 Lewis Randy S Indirect or direct fermentation of biomass to fuel alcohol
DE102006025821A1 (de) 2006-06-02 2007-12-06 Degussa Gmbh Ein Enzym zur Herstellung von Mehylmalonatsemialdehyd oder Malonatsemialdehyd
US20080057554A1 (en) 2006-08-31 2008-03-06 Huhnke Raymond L Isolation and characterization of novel clostridial species

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Cited By (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8980594B2 (en) 2009-11-11 2015-03-17 Evonik Roehm Gmbh Use of a protein homologous to a MeaB protein for increasing the enzymatic activity of a 3-hydroxycarboxylic acid-CoA mutase
US9315443B2 (en) 2011-02-16 2016-04-19 Evonik Degussa Gmbh Liquid cation exchanger
US10071951B2 (en) 2011-02-16 2018-09-11 Evonik Degussa Gmbh Liquid cation exchanger
US9249435B2 (en) 2011-12-22 2016-02-02 Evonik Degussa Gmbh Process for the improved separation of a hydrophobic organic solution from an aqueous culture medium
US9765370B2 (en) 2012-04-02 2017-09-19 Evonik Degussa Gmbh Method for aerobically producing alanine or a compound produced using alanine
US10787688B2 (en) 2012-05-11 2020-09-29 Evonik Operations Gmbh Multi-stage synthesis method with synthesis gas
DE102016212497B4 (de) 2015-07-13 2024-04-25 Sk Innovation Co., Ltd. Mutanter Mikroorganismus, der ein Gen umfasst, das Methylmalonyl-CoA-Reductase codiert, und seine Verwendung

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