EP3475437A1 - Verfahren zur herstellung von d-xylonat und coryneformes bakterium - Google Patents

Verfahren zur herstellung von d-xylonat und coryneformes bakterium

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Publication number
EP3475437A1
EP3475437A1 EP17745964.1A EP17745964A EP3475437A1 EP 3475437 A1 EP3475437 A1 EP 3475437A1 EP 17745964 A EP17745964 A EP 17745964A EP 3475437 A1 EP3475437 A1 EP 3475437A1
Authority
EP
European Patent Office
Prior art keywords
gene
corynebacterium
lolr
brevibacterium
xylonate
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.)
Withdrawn
Application number
EP17745964.1A
Other languages
German (de)
English (en)
French (fr)
Inventor
Stephan Noack
Andreas RADEK
Jan Marienhagen
Karin Krumbach
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.)
Forschungszentrum Juelich GmbH
Original Assignee
Forschungszentrum Juelich GmbH
Priority date (The priority date 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 date listed.)
Filing date
Publication date
Application filed by Forschungszentrum Juelich GmbH filed Critical Forschungszentrum Juelich GmbH
Publication of EP3475437A1 publication Critical patent/EP3475437A1/de
Withdrawn legal-status Critical Current

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P7/00—Preparation of oxygen-containing organic compounds
    • C12P7/40—Preparation of oxygen-containing organic compounds containing a carboxyl group including Peroxycarboxylic acids
    • C12P7/58—Aldonic, ketoaldonic or saccharic acids
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/34—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Corynebacterium (G)
    • 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
    • C12N1/36—Adaptation or attenuation of cells

Definitions

  • the invention relates to a process for the preparation of D-xylonate and a coryneform bacterium.
  • D-xylonic acid (C5H10O6) is an organic acid which, as described by Toivari et al. in Appl Microbiol Biotechnol, 2012, 96 (1): 1-8, can serve as a precursor for polyamides, polyesters, and 1, 2,4-butanetriol, and thus has broad application potential in the pharmaceutical, food, and pharmaceutical industries chemical industry up.
  • the following explanations refer to D-xylonate, the salt of D-xylonic acid.
  • D-xylonate is among the top 30 most potentially high-quality, second-generation renewable resources, e.g. Pentose-containing hemicellulose-based, precursor chemicals.
  • D-xylonate is similar to D-gluconate (C6H1 107), which has a global market of 80 kt / yr.
  • D-xylonate is naturally produced in some bacteria via a two-step reaction.
  • D-xylose is oxidized to D-xylonolactone, where specific dehydrogenases are catalytically active depending on the organism.
  • the D-xylonolactone can then be converted to D-xylonate either by specific lactonases or spontaneously, without enzyme catalyst.
  • D-xylonate production strains e.g., yeast of the species Saccharomyces cerevisiae, bacteria of the species Escherichia coli and fungi of the species Aspergillus niger
  • yeast of the species Saccharomyces cerevisiae bacteria of the species Escherichia coli and fungi of the species Aspergillus niger
  • D-xylose dehydrogenases e.g. From Caulobacter crescentus, as described by (Liu et al., Bioresour Technol, 2012, 1 15: 244-248, Richard et al., 2012, US20120005788 A1 (US 13 / 256,559), Toivari et al., Metab Eng, 2012, 14 (4): 427-436).
  • D-xylonate can be electrochemically (Jokic et al., Journal of Applied Electrochemistry, 21 (4): 321-326), enzymatically (Pezzotti et al., Carbohydr Res, 2006, 341 (13): 2290-2292 ) or by chemical oxidation (Isbell et al., Bureau of
  • organic acids or their salts can be prepared by fermentation of strains of coryneform bacteria, in particular Corynebacterium glutamicum.
  • Non-natural D-xylonate producers are genetically modified organisms within the meaning of the Genetic Engineering Act (GenTG) ⁇ 3, according to which an organism is genetically modified if it is capable of heterologous expression or for this organism contains foreign genes, that is, recombinantly altered, among others different yeasts, mushrooms and bacteria. This creates a disadvantage for use in certain industrial areas, such. B. Food and pharmaceutical industry as a result of complex approval procedures.
  • a microorganism and a method which can be used in industrial applications, in particular in the food industry, the pharmaceutical and chemical industries and readily meet the conditions of approval for use in the food and pharmaceutical and chemical industries .
  • the disadvantages associated with genetically modified organisms within the meaning of the law governing genetic engineering ⁇ 3, in particular recombinantly modified organisms, should preferably be avoided.
  • simple and inexpensive media for cultivation should be used, which are inexpensive and easy to use.
  • the microorganisms used should have high growth rates on defined media, achieve high biomass yields and simplify subsequent product processing.
  • the object is achieved according to the invention in the characterizing part of the claims specified characteristics.
  • the microorganism according to the invention With the microorganism according to the invention, its genome and the preparation process according to the invention, it is now possible to produce D-xylonate in a high yield, for example> 0.5 g of D-xylonate / g D-xylose, with an enantiomeric purity of 100%.
  • the microorganisms according to the invention are well suited for industrial use and, in a preferred embodiment, overcome the approval criteria for use in the food industry and the pharmaceutical and chemical industries; in particular, they are regarded as non-recombinantly modified according to the Genetic Engineering Act.
  • the microorganisms according to the invention achieve high growth rates and high biomass yields on defined media and enable simple product workup.
  • the disadvantages of the prior art are overcome.
  • the defined media are cheaper and less expensive to use.
  • the growth of production organisms is more reproducible than with undefined media.
  • the complexity of the media is low and thus reduces the number of necessary process steps for product processing.
  • the invention therefore relates to a coryneform bacterium in which the activity of the lolR gene against wild-type or a wild-type mutant, preferably a non-recombinant mutant containing this gene, diminished or completely eliminated or in which the lolR gene is at least partially deleted and a process for the production of D-xylonate with a coryneform bacterium, in which the lolR gene is reduced in its activity or completely eliminated or in which the lolR gene is at least partially deleted.
  • the coryneform bacteria modified according to the invention can be derived from the wild form or from a genetically modified form which is preferably not recombinantly modified in comparison to the wild form.
  • the wild-type strains are particularly preferred for the pharmaceutical and food industries because they are particularly easy to produce.
  • the wild form contains as starting strain of the method according to the invention a natural lolR gene.
  • the genetically modified strains also contain a natural lolR gene in their initial form.
  • a genetically modified strain is to be understood as meaning, for example, a strain which is genetically modified in such a way that targets or target genes of the regulator IOR are increasingly expressed.
  • all or part of the genes relevant in myo-inositol metabolism which code for the enzymes of myo-inositol metabolism, can be overexpressed.
  • genes can be integrated into the genome, which code for these enzymes and allow an increased expression of these genes.
  • the genes can also be introduced chromosomally.
  • coryneform bacteria of the species Corynebacterium, Brevibacterium, in particular Corynebacterium glutamicum, Corynebacterium acetoglutamicum, Corynebacterium thermoaminogenes, Brevibacterium flavum, Brevibacterium lactofermentum or Brevibacterium divaricatum can be used.
  • coryneform bacteria which, according to the invention, are altered starting from the wild form, for example the wild forms
  • Brevibacterium divaricatum ATCC 14020 used. The list is not limiting, but exemplary.
  • Corynebacterium glutamicum as a production organism offers special advantages, because i) it is a "Generally Recognized As Safe” (GRAS) organism that can be used in all industrial sectors;
  • This preferred embodiment has the advantage that it does not undergo any authorization restrictions in the chemical, pharmaceutical or food production as wild species changed according to the invention.
  • the lolR gene is completely switched off.
  • Complete inactivation of the lolR gene can also be carried out by other measures known to the person skilled in the art.
  • the appropriate culture guide e.g. by the use of myo-inositol as substrate / inducer of loIR, insertion of another DNA sequence into the gene region of the lolR gene, in particular the lolR gene cg0196.
  • a gene region is to be understood as a region in which the change still has an influence on the activity of the lolR gene. This region may be located before, after or in the open reading frame of the lolR gene.
  • Complete inactivation can also be achieved by completely eliminating the gene expression of loIR by genetically altering (mutating) the signal structures of gene expression.
  • Signaling structures of gene expression include repressor genes, activator genes, operators, promoters, attenuators, ribosome binding sites, the start codon, and terminators. Information on this is the expert z.
  • Knippers Knippers "Molekulare Genetik", 8th Edition, 2001, Georg Thieme Verlag, Stuttgart, Germany) or reviews (Pokala et al., J Struct Biol, 2001, 134 (2-3): 269-281, Jaenicke et al., Angew Chem Int Ed Engl, 2003, 42 (2): 140-142, Lily, EMBO Rep, 2003, 4 (4): 346 -351, Pei et al., Proc Natl Acad Sci USA, 2003, 100 (20): 1 1361-1 1366, Dokholyan, Proteins, 2004, 54 (4): 622-628, Tramontano, Angew Chem Int Ed Engl, 2004, 43 (25): 3222-3223).
  • the corneiform bacteria produced in this way have no lolR gene activity and lead to a high yield of enantiomerically pure D-xylonate. It is the best embodiment of the invention, in particular the complete deletion is preferred.
  • the activity of the lolR gene is reduced.
  • Partial inactivation of the lolR gene may also be accomplished by other means known to those skilled in the art.
  • the appropriate culture guide e.g. by the use of myo-inositol as substrate / inducer of loIR, insertion of another DNA sequence into the gene region of the lolR gene, in particular the lolR gene cg0196.
  • a gene region is to be understood as a region in which the change still has an influence on the activity of the lolR gene. This region may be located before, after or in the open reading frame of the lolR gene.
  • Partial inactivation can also be achieved by partially eliminating the gene expression of loIR by genetically altering (mutating) the signal structures of gene expression.
  • Signal structures of gene expression are, for example, repressor genes, activator genes, operators, promoters, attenuators, ribosome binding sites, the start codon and terminators. In principle, the same procedures can be used as for the complete deletion.
  • Mutations that lead to a change in the functional properties of loIR, in particular to an altered substrate specificity, can also lead to a partial elimination of the activity of the lolR gene. Mutations include transitions, transversions, insertions and deletions, as well as directed evolutionary methods. Again, the above methods can be used.
  • the lolR gene cg0196 is given in Sequence Listing No. 1.
  • a lolR gene of an open reading frame coryneform bacterium ATCC13032 is shown in Sequence No. 2.
  • the organisms of coryneform bacteria modified according to the invention produce D-xylonate or D-xylonic acid 100% enantiopure with a high yield.
  • the genome of the invention produced in this way enables coryneform bacteria to produce D-xylonate or D-xylonic acid with a high yield and an enantiomeric purity of 100%.
  • D-xylonate with the coryneform bacteria according to the invention can be carried out with known fermentative processes customary in laboratories or in production.
  • the microorganisms produced according to the invention can be cultivated continuously or discontinuously in batch process (batch cultivation) or in fed-batch (feed process) or repeated-fed batch (repetitive feed process) for the purpose of D-xylonate production.
  • batch cultivation or in fed-batch (feed process) or repeated-fed batch (repetitive feed process) for the purpose of D-xylonate production.
  • Storhas Bioreactors and Peripheral Facilities (Vieweg Verlag, Braunschweig / Wiesbaden, 1994)
  • the culture medium to be used must suitably satisfy the requirements of the respective microorganisms. Descriptions of culture media of various microorganisms are contained in the Manual of Methods for General Bacteriology of the American Society for Bacteriology (Washington DC, USA, 1981).
  • sugars and carbohydrates such as e.g. Glucose, sucrose, lactose, fructose, maltose, molasses, starch and cellulose, oils and fats such as e.g. As soybean oil, sunflower oil, peanut oil and coconut oil, fatty acids such. As palmitic acid, stearic acid and linoleic acid, alcohols such. As glycerol and ethanol and organic acids such. As acetic acid can be used. These substances can be used individually or as a mixture.
  • the CGXII medium (Unthan et al., Biotechnol Bioeng, 2014, 11 (1) (2): 359-371) with D-xylose and D-glucose as carbon and energy sources. This makes it possible to achieve high specific growth rates for Corynebacte with glutamicum ATCC13032 of up to 0.61 h -1 . Moreover, the use of the CGXII medium ensures simple removal of the target product D-xylonate from the culture supernatant, for example by ethanol precipitation followed by vacuum drying (Liu et al., Bioresource Technology, 2012, 1 15: 244-248) The simple medium is part of the task to be solved.
  • the nitrogen source there may be used organic nitrogen-containing compounds such as peptones, yeast extract, meat extract, malt extract, corn steep liquor, soybean meal and urea, or inorganic compounds such as ammonium sulfate, ammonium chloride, ammonium phosphate, ammonium carbonate and ammonium nitrate.
  • organic nitrogen-containing compounds such as peptones, yeast extract, meat extract, malt extract, corn steep liquor, soybean meal and urea
  • inorganic compounds such as ammonium sulfate, ammonium chloride, ammonium phosphate, ammonium carbonate and ammonium nitrate.
  • the nitrogen sources can be used singly or as a mixture.
  • potassium dihydrogen phosphate or dipotassium hydrogen phosphate or the corresponding sodium-containing salts can be used as the phosphorus source.
  • the culture medium should contain salts of metals, e.g. Magnesium sulfate or iron sulfate necessary for growth.
  • salts of metals e.g. Magnesium sulfate or iron sulfate necessary for growth.
  • essential growth substances such as amino acids and vitamins can be used in addition to the above-mentioned substances.
  • the said starting materials can be added to the culture in the form of a one-time batch or fed in during the cultivation in a suitable manner.
  • basic compounds such as sodium hydroxide, potassium hydroxide, ammonia or acidic compounds such as hydrochloric acid, phosphoric acid g or sulfuric acid are used in a suitable manner.
  • a preferred pH range for cell growth is between 6 and 8.
  • antifoams such as e.g. Fatty acid polyglycol esters.
  • oxygen or oxygen-containing gas mixtures e.g. Air entered into the culture.
  • the temperature of the culture is usually 20 ° C to 45 ° C, and preferably 25 ° C to 40 ° C.
  • the culture is preferably continued until a maximum of D-xylonate has formed. This goal is usually reached within 10 hours to 160 hours.
  • Fig.2 GC-ToF-MS spectrum of a purified precipitate
  • FIG. 1 shows the culturing processes for the strain Corynebacterium glutamicum AloIR in subfigures A) and B).
  • the abscissas of the graphics in all subfigures are the time in hours h.
  • the ordinates of the first row indicate the amount of D-xylose and D-glucose in millimolar [mM].
  • the ordinates of the second row mean the biomass in grams per liter [g / L] and the ordinates of the third row mean the amount of D-xylonate in millimolar [mM].
  • Part 1 B shows the cultivation process for the strain C. glutamicum AloIR in the fed-batch process. A final titer of D-xylonate of 20.0 ⁇ 1.0 g / L was achieved.
  • Figure 2 shows the spectrum of the purified precipitate, which was generated by GC-ToF-MS analysis (Paczia et al., Microbial Cell Factories, 2012, 11). The relative peak intensity in the ordinate is plotted against the chromatographic transit time as the abscissa.
  • the gene "loIR” was deleted in-frame ("in-frame") so as not to affect the expression of downstream genes as far as possible.
  • a cross-over PCR was performed. In two first PCRs, two 400 bp downstream and upstream flanking DNA regions of the gene to be deleted were separately amplified.
  • the olive gonukleotide used for this purpose (iolR_DF1_for CCCAAGCTTGAGGTACTTGCCGAAAGATTG (HindIII), i- olR_DF1_rev CTCGATTACTTGGCCGGAGGGCTACTTGGAAGTAGAGG, iolR_DF2_for TCCGGCCAAGTAATCGAG, iolR_DF2_rev CGGGATCCATCGCGTTGGCATTCTTC (Bam Hl)) was modified so that the resulting PCR fragments at the 5 'end of long, each with a 18 nucleotide homologous sequence that was complementary to each other in the fragments.
  • the products of the first PCRs were used as a DNA template, with annealing taking place over the complementary region during the reaction.
  • the deletion construct was generated, which was cloned into the vector pK19mobsacB.
  • clones were isolated in which the plasmid was integrated into the chromosome by homologous recombination.
  • glutamicum was carried out via the PCR with which were complementary to an area outside the gene (K_DiolR_for GCACGTTATGACCTGCAAACTC, K_DiolR_rev TACGGTCTGGCTATCTACATCC).
  • the strain C. glutamicum AloIR produced in this way was cultivated in a batch and fed-batch process in 1.5 l bioreactors (DASGIP AG, Juelich, Germany) at 30 ° C. and a constant gassing rate of 1 vvm. Throughout aerobic conditions (> 30% dissolved oxygen) were achieved via the oxygen input with adjustment of the stirrer speed (400 - 1200 rpm). The pH in the culture medium was constantly adjusted to pH 7.1 with 5 MH 3 PO4 and 5 M NH 4 OH.
  • the batch process was performed in two independent reactors from an overnight preculture on CGXII medium (Unthan et al., Biotechnol Bioeng, 2014, 11 (2): 359-371) with 40 g / L D-glucose to an OD of 1 in CGXII medium without urea and inoculated with 10 g / L D-glucose and 30 g / L D-xylose.
  • the fed-batch process was carried out in two independent reactors from an overnight preculture on CGXII medium with 40 g / L D-glucose to an OD of 1 in CGXII medium without urea and with 20 g / L D-glucose and 40 g / L D-xylose inoculated.
  • a continuous feed was started with 100 g / L D-glucose and a rate of 2.5 ml / h (reactor 1) or 5 mUh (reactor 2). All cultivations were sampled at regular intervals, the samples were centrifuged, and the resulting cell-free supernatant was used for substrate and product analysis.

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EP17745964.1A 2016-06-25 2017-05-19 Verfahren zur herstellung von d-xylonat und coryneformes bakterium Withdrawn EP3475437A1 (de)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
DE102016007810.3A DE102016007810B4 (de) 2016-06-25 2016-06-25 Verfahren zur Herstellung von D-Xylonat
PCT/DE2017/000138 WO2017220059A1 (de) 2016-06-25 2017-05-19 Verfahren zur herstellung von d-xylonat und coryneformes bakterium

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EP3475437A1 true EP3475437A1 (de) 2019-05-01

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US (1) US10760104B2 (zh)
EP (1) EP3475437A1 (zh)
JP (1) JP7061577B2 (zh)
CN (1) CN109415743B (zh)
DE (1) DE102016007810B4 (zh)
WO (1) WO2017220059A1 (zh)

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WO2020011294A1 (de) 2018-07-11 2020-01-16 Forschungszentrum Jülich GmbH D-xylose-dehydrogenase aus coryneformen bakterien und verfahren zur herstellung von d-xylonat
CN113906044B (zh) * 2021-04-07 2022-05-31 Cj第一制糖株式会社 转录调节因子变体及使用其生产l-缬氨酸的方法
KR102306008B1 (ko) * 2021-04-07 2021-09-27 씨제이제일제당 (주) 신규한 전사 조절자 변이체 및 이를 이용한 l-발린 생산 방법
CN116555135A (zh) * 2022-01-29 2023-08-08 廊坊梅花生物技术开发有限公司 高产苏氨酸基因工程菌的构建方法

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DE4440118C1 (de) 1994-11-11 1995-11-09 Forschungszentrum Juelich Gmbh Die Genexpression in coryneformen Bakterien regulierende DNA
AU2005320486B2 (en) * 2004-12-28 2009-08-13 Ajinomoto Co., Inc. L-glutamic acid-producing microorganism and a method for producing L-glutamic acid
FI20095278A0 (fi) 2009-03-18 2009-03-18 Valtion Teknillinen Ksylonihapon valmistus
WO2013069634A1 (ja) 2011-11-11 2013-05-16 味の素株式会社 発酵法による目的物質の製造法
WO2013159710A1 (zh) * 2012-04-25 2013-10-31 中国科学院上海生命科学研究院 一种提高拜氏梭菌木糖消耗率的方法
JP6221478B2 (ja) 2013-08-02 2017-11-01 三菱ケミカル株式会社 ペントース資化能を有する微生物を用いた有機化合物の製造方法

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US10760104B2 (en) 2020-09-01
JP2019518453A (ja) 2019-07-04
WO2017220059A1 (de) 2017-12-28
US20190203236A1 (en) 2019-07-04
DE102016007810A1 (de) 2017-12-28
CN109415743B (zh) 2023-01-03
CN109415743A (zh) 2019-03-01
JP7061577B2 (ja) 2022-04-28
DE102016007810B4 (de) 2023-12-07

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