CN117402801A - Genetically engineered bacterium for producing 5' -cytidine acid, construction method and application thereof - Google Patents
Genetically engineered bacterium for producing 5' -cytidine acid, construction method and application thereof Download PDFInfo
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- CN117402801A CN117402801A CN202311342307.5A CN202311342307A CN117402801A CN 117402801 A CN117402801 A CN 117402801A CN 202311342307 A CN202311342307 A CN 202311342307A CN 117402801 A CN117402801 A CN 117402801A
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- nucleotide sequence
- cytidine
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Classifications
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
- C12N15/52—Genes encoding for enzymes or proenzymes
-
- 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
- C12P19/305—Pyrimidine nucleotides
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12R—INDEXING SCHEME ASSOCIATED WITH SUBCLASSES C12C - C12Q, RELATING TO MICROORGANISMS
- C12R2001/00—Microorganisms ; Processes using microorganisms
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Abstract
The invention discloses a genetic engineering bacterium for producing 5' -cytidylic acid, and a construction method and application thereof, and belongs to the technical field of genetic engineering. The genetically engineered bacterium takes escherichia coli as a starting bacterium, knocks out genes related to pyrimidine biosynthesis pathways in genome, and comprises the following components: glsA, glsB, argF, pepA, pyrI, nagD, aphA, surE, phoA, yrfG, yjjG, ushA, serB. The invention uses escherichia coli as chassis cells, and uses genetic engineering technology to knock out pyrimidine precursors to compete for biosynthesis genes and negative regulation genes so as to promote biosynthesis of 5 '-cytidine, reduce product metabolism, obviously improve the yield of 5' -cytidine, and has good application prospect.
Description
Technical Field
The invention relates to the technical field of genetic engineering, in particular to a genetic engineering bacterium for producing 5' -cytidine acid, and a construction method and application thereof.
Background
5' -cytidine acid has important physiological functions in organisms as a natural nucleotide. Currently, 5' -cytidine acid is widely used in the fields of foods and medicines. The addition of 5' -cytidine acid to infant milk powder is used for improving infant immunity. In the field of medicine, the method is used for synthesizing citicoline for treating brain injury related diseases; the synthesized cytarabine is used for treating leukemia.
At present, the production routes of 5' -cytidine acid are as follows: first, it is obtained by degradation of RNA, but the degradation product is a mixture of four nucleotides, and separation and purification are difficult, resulting in low yield and high cost, which is not suitable for mass production. The second method is chemical synthesis, but the chemical synthesis has more steps and low yield, and toxic reagents are needed in the production process, so the method has high cost and is not used for industrial production. The third method is enzyme-catalyzed synthesis, which generally uses cytidine as the starting compound, and requires the addition of ATP to provide the phosphate donor, resulting in excessive raw material costs. Therefore, development of a low-cost production method of 5' -cytidine acid still has important economic value.
Microbial fermentation is the use of microbial action and the conversion of useful materials into industrial production or other industrial processes by modern engineering techniques, and because of its sustainability and economic viability, it would be attractive and promising to develop a viable microbial-based cytidine production process.
The metabolic network of cytidine synthesis can be divided into three modules: module I synthesizes precursors from glucose via the Embden-Meyerhof-Parnas (EMP) pathway, pentose Phosphate Pathway (PPP) and tricarboxylic acid (TCA) cycle, wherein the precursors include bicarbonate, glutamine, aspartic acid and 5' -phosphoribosyl pyrophosphate (PRPP); module II synthesizes Uridine Monophosphate (UMP) from the precursor in six steps, which starts with the formation of carbamyl phosphate, which combines with aspartic acid to produce orotate, which is then converted into the common precursor molecule UMP; module III synthesizes cytidine from UMP, which involves a series of biochemical reactions: phosphorylation, amination, and hydrolysis.
Over the past few decades, microbial-based cytidine production has made tremendous progress, and conventional methods for screening high-yield cytidine-producing strains include random mutagenesis and adaptive laboratory evolution to synthesize released cytidine from strict metabolic control. In view of the uncertainties and high strength of these traditional efforts, it has been attractive in recent years to construct a more ideal microbial cell factory for cytidine production based on rational metabolic engineering. Bacillus subtilis is widely used as a chassis cell for pyrimidine nucleoside biosynthesis, where the genes encoding the enzymes required for UMP synthesis are adjacent and constitute the pyrimidine (pyr) operon. Unlike bacillus subtilis, the corresponding genes in escherichia coli are scattered in chromosomes without systematic expression regulation, and escherichia coli is nevertheless proven to be another excellent host for pyrimidine nucleoside biosynthesis and gradually replaces bacillus subtilis due to its unique genetic background and advanced engineering methods. For example Wu et al integrated the modified pyr operon of bacillus subtilis mutant F126 into the escherichia coli genome by CRISPR/Cas9 mediated genome editing techniques (HuyunWu, et al 2018), which could combine the advantages of both candidates.
Therefore, the metabolic pathway of cytidine synthesis is deeply studied, the escherichia coli genome is modified by adopting a plurality of metabolic engineering strategy systems, and the escherichia coli genetic engineering bacteria with high yield of 5' -cytidine acid are constructed so as to realize green economic production, which is a technical problem to be solved by the technicians in the field.
Disclosure of Invention
The invention aims to provide a genetically engineered bacterium for efficiently producing 5 '-cytidine acid, which realizes green and economical industrial production of 5' -cytidine acid.
In order to achieve the above purpose, the invention adopts the following technical scheme:
the invention provides a genetic engineering bacterium for producing 5' -cytidylic acid, which takes escherichia coli as a starting bacterium to knock out genes related to pyrimidine biosynthesis pathway in genome, and comprises the following components: the gene glsA encoding glutaminase A, the gene glsB encoding glutaminase B, the gene argF encoding ornithine carbamoyltransferase, the gene pepA encoding aminopeptidase A, the gene pyrI encoding aspartate aminotransferase, the gene nagD encoding UMP phosphatase, the gene aphA encoding acid phosphatase, the gene survivin encoding nucleotidase, the gene phoA encoding alkaline phosphatase, the gene yrfG encoding purine nucleotidase, the gene yjjG encoding pyrimidine nucleotidase, the gene ushA encoding 5' -nucleotidase, the gene serB encoding phosphoserine phosphatase.
The E.coli may employ commercial strains commonly used in the art, and may be, but is not limited to, E.coli MG1665.
The invention utilizes the genetic engineering technical means to reform the escherichia coli genome, and realizes the green and economic production of 5' -cytidine acid by knocking out pyrimidine precursors to compete for biosynthesis genes and negative regulation genes. In particular, glutamine and Carbamoyl-P are precursors for biosynthesis of pyrimidine, while they synthesize glutamic acid and citrulline from glsA, glsB and argF, respectively, so knockout of glsA, glsB and argF can increase metabolic flow for pyrimidine synthesis. In the pyrimidine biosynthesis process, pepA and pyrI are negative regulatory genes and are subject to pyrimidine feedback inhibition, so that knocking out pepA and pyrI can release pyrimidine feedback inhibition. nagD, aphA, surE has uridylate phosphatase activity and knockdown of these three genes reduces the decomposition of the 5' -cytidylate precursor uridylate. phoA, yrfG, yjjG, ushA, serB has 5 '-cytidylic acid phosphatase activity in addition to uridylic acid phosphatase activity, so that the knocking-out of the four genes can not only reduce the decomposition of uridylic acid, but also improve the accumulation of 5' -cytidylic acid.
Further, the nucleotide sequence of glsA is shown as SEQ ID NO.1, the nucleotide sequence of glsB is shown as SEQ ID NO.2, the nucleotide sequence of argF is shown as SEQ ID NO.3, the nucleotide sequence of pepA is shown as SEQ ID NO.4, the nucleotide sequence of pyrI is shown as SEQ ID NO.5, the nucleotide sequence of nagD is shown as SEQ ID NO.6, the nucleotide sequence of aphA is shown as SEQ ID NO.7, the nucleotide sequence of survivin is shown as SEQ ID NO.8, the nucleotide sequence of phoA is shown as SEQ ID NO.9, the nucleotide sequence of yffG is shown as SEQ ID NO.10, the nucleotide sequence of yjjG is shown as SEQ ID NO.11, the nucleotide sequence of ushA is shown as SEQ ID NO.12, and the nucleotide sequence of serB is shown as SEQ ID NO. 13.
Furthermore, the genetically engineered bacterium is also knocked out of cytidine phosphatase genes in a genome on the basis of the gene knocked out, and the genetically engineered bacterium comprises: the gene yigL encoding the phosphosugar phosphatase, the gene yfdR encoding the 5 '-deoxynucleotidase, the gene ygdH encoding the nucleotide 5' -monophosphate nucleotidase.
The invention realizes accumulation of the product by blocking the metabolic pathway of 5' -cytidine acid. Specifically, yigL, yfdR, ygdH has 5' -cytidine phosphatase activity, and can catalyze 5' -cytidine to form cytidine, and the conversion of 5' -cytidine to cytidine can be blocked by knocking out yigL, yfdR, ygdH.
Further, the nucleotide sequence of yigL is shown as SEQ ID No.14, the nucleotide sequence of yfdR is shown as SEQ ID No.15, and the nucleotide sequence of ygdH is shown as SEQ ID No. 16.
Furthermore, the genetically engineered bacterium knocks out the encoding cytidylic acid kinase gene cmk in the genome on the basis of the gene knockout. The cmk catalyzes 5 '-cytidine acid to generate cytidine diphosphate, and the knocking out of the gene is beneficial to accumulation of 5' -cytidine acid, so that the yield is improved.
Further, the nucleotide sequence of cmk is shown in SEQ ID NO. 17.
Furthermore, the gene engineering bacteria also overexpress genes related to pyrimidine nucleoside synthesis on the basis of the gene knockout, including a gene prs for encoding ribose phosphate diphosphate kinase, a gene pyrE for encoding orotic acid phosphoribosyl transferase, a gene pyrH for encoding UMP kinase, a gene pyrG for encoding CTP synthetase and a gene nudG for encoding CTP diphosphate enzyme; the nucleotide sequence of prs is shown as SEQ ID NO.18, the nucleotide sequence of pyrE is shown as SEQ ID NO.19, the nucleotide sequence of pyrH is shown as SEQ ID NO.20, the nucleotide sequence of pyrG is shown as SEQ ID NO.21, and the nucleotide sequence of nudG is shown as SEQ ID NO. 22.
The invention promotes the synthesis of 5' -cytidine acid by over-expressing the speed-limiting step gene and the product feedback tolerance gene in the cytidine acid synthesis path. Specifically, prs was feedback inhibited by the product PRPP and prs (N120S-L135I) from Bacillus amyloliquefaciens was feedback tolerant. pyrH, pyrG is feedback inhibited by UTP and CTP, respectively, and pyrH (D93A) and pyrG derived from Corynebacterium glutamicum (D160E-E162A-E168K) are both tolerant to the corresponding products. pyrE, nudG is the rate limiting enzyme in cytidine synthesis, and thus overexpression promotes 5' -cytidine acid synthesis.
The invention also provides a method for constructing the genetically engineered bacterium for producing 5' -cytidine acid, which comprises the following steps: taking escherichia coli as a starting strain, knocking out genes related to pyrimidine biosynthesis pathways in a genome by utilizing a gene editing technology, and obtaining the genetically engineered strain for producing 5' -cytidine acid.
Further, the construction method further comprises: the cytidine phosphatase gene yigL, yfdR, ygdH and the cytidine kinase gene cmk in the genome are knocked out by using a gene editing technology.
Further, the construction method further comprises: and integrating copies of coding genes of prs (N120S-L135I), pyrH (D93A), pyrG (D160E-E162A-E168K), pyrE and nudG in a genome by utilizing a gene editing technology, or introducing recombinant expression plasmids containing the coding genes to obtain the genetically engineered bacterium for producing the 5' -cytidine acid.
The invention also provides application of the genetically engineered bacterium for producing 5 '-cytidine acid in preparation of 5' -cytidine acid.
Specifically, the application includes: and (3) amplifying and culturing the genetically engineered bacteria for producing the 5 '-cytidine acid, inoculating the genetically engineered bacteria into a fermentation medium, and separating from a fermentation product after fermentation culture to obtain the 5' -cytidine acid.
Further, the application includes: after the genetically engineered bacterium for producing 5' -cytidine acid is subjected to amplification culture, inoculating the genetically engineered bacterium into a fermentation culture medium, controlling the pH of the culture medium to be neutral in the fermentation process, controlling the fermentation temperature to be 30-37 ℃, and controlling dissolved oxygen by feeding glucose to keep the final concentration to be 0.1 percent>25%, separating and obtaining a product 5' -cytidine acid from fermentation liquor after fermentation is finished; wherein the components of the fermentation medium include: glucose 10g/L, KH 2 PO 4 1.35g/L, yeast extract powder 10g/L, ammonium sulfate 2.5g/L, mgSO 4 1g/L, 1.1g/L of citric acid, and inorganic salt components in a culture medium: feSO 4 ·7H 2 O 150mg/L，MnSO 4 ·7H 2 O15 mg/L, cobalt chloride 3.5mg/L and zinc sulfate 3.5mg/L.
The invention has the beneficial effects that:
the invention provides a recombinant genetic engineering bacterium for high yield of 5' -cytidine acid, which takes escherichia coli as chassis cells, and utilizes genetic engineering technology to knock out pyrimidine precursors to compete for biosynthesis genes and negative regulation genes so as to promote biosynthesis of the 5' -cytidine acid, reduce product metabolism, remarkably improve the yield of the 5' -cytidine acid and has good application prospect.
Detailed Description
The invention will be further illustrated with reference to specific examples. The following examples are only for illustrating the present invention and are not intended to limit the scope of the present invention. Modifications and substitutions to methods, procedures, or conditions of the present invention without departing from the spirit and nature of the invention are intended to be within the scope of the present invention.
The test methods used in the following examples are conventional methods unless otherwise specified; the materials, reagents and the like used, unless otherwise specified, are those commercially available.
The nucleotide sequence is 5 'to 3' from left to right.
Example 1: knockout of glsA in E.coli MG1665 (Escherichia coli str. K-12 substre. MG1655)
Gene knockout was performed using the method of the literature (Yu Jiang, et al, multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system, appl Environ Microbiol.2015,81 (7): 2506-14).
Amplifying an upstream homologous fragment by using a primer glsAF1 and glsAR 1; amplifying the downstream homologous fragment of glsAF2 and glsAR 2; the primers glsAF1 and glsAR2 amplify homologous fragments for upstream and downstream fusion of gene knockout by using the upstream and downstream homologous fragments as templates. The primer glsA20F, glsA R amplified the gRNA plasmid. The resulting knockout strain was numbered ZH1. The sequences of the primers are respectively:
glsAF1:GATCAGCTGTTCTGCACT；
glsAR1:ACTGTTGCCATCTTCGTCTGTAAGCCTGATCCACTG；
glsAF2:CAGTGGATCAGGCTTACAGACGAAGATGGCAACAGT；
glsAR2:CATGGTTGCTTAAGGAGT；
glsA20F:GTTATCGCCTTAGAGTTGCAGTTTTAGAGCTAGAAATAGC；
glsA20R:TGCAACTCTAAGGCGATAACACTAGTATTATACCTAGGAC。
example 2: knockout of glsB in E.coli ZH1
Gene knockout was performed using the method of the literature (Yu Jiang, et al, multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system, appl Environ Microbiol.2015,81 (7): 2506-14).
Amplifying an upstream homologous fragment by using a primer glsBF1 and glsBR 1; amplifying the downstream homologous fragment by glsBF2 and glsBR 2; the homologous fragments of the upstream and downstream fusion are used as templates, and the primers glsBF1 and glsBR2 amplify the homologous fragments of the upstream and downstream fusion for gene knockout. The primer glsB20F, glsB R amplified the gRNA plasmid. The resulting knockout strain was numbered ZH2. The sequences of the primers are respectively:
glsBF1:CAGAAATGACCGCGTTTC；
glsBR1:CGTCAATTGTTCAAGAACTTTACCCTGACCAATGAG；
glsBF2:CTCATTGGTCAGGGTAAAGTTCTTGAACAATTGACG；
glsBR2:GAACCAAGATAGCATGTT；
glsB20F:TTCCTTAGTGCAACTGGAAAGTTTTAGAGCTAGAAATAGC；
glsB20R:TTTCCAGTTGCACTAAGGAAACTAGTATTATACCTAGGAC。
example 3: knocking out pepA in E.coli ZH2
Gene knockout was performed using the method of the literature (Yu Jiang, et al, multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system, appl Environ Microbiol.2015,81 (7): 2506-14).
Primers pepF1, pepR1 amplified the upstream homologous fragment; pepF2, pepR2 amplified downstream homologous fragment; the primers pepF1 and pepR2 are used as templates to amplify homologous fragments for upstream and downstream fusion of gene knockout. Primer pep20F, pep R amplified the gRNA plasmid. The resulting knockout strain was numbered ZH3. The sequences of the primers are respectively:
pepF1:cacgaagtcatcgcaaca；
pepR1:agttgttcctgatactcgtgacgcactttccagtag；
pepF2:ctactggaaagtgcgtcacgagtatcaggaacaact；
pepR2:cttcacaggcgatgagca；
pep20F:gagatgaagtacgatatgtggttttagagctagaaatagc；
pep20R:cacatatcgtacttcatctcactagtattatacctaggac。
example 4: knocking out argF in E.coli ZH3
Gene knockout was performed using the method of the literature (Yu Jiang, et al, multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system, appl Environ Microbiol.2015,81 (7): 2506-14).
Amplifying an upstream homologous fragment by using a primer argF1 and argR 1; amplifying the downstream homologous fragment by argF2 and argR 2; the upstream and downstream homologous fragments are used as templates, and primers argF1 and argR2 amplify homologous fragments for upstream and downstream fusion of gene knockout. The primer arg20F, arg20R amplified the gRNA plasmid. Strain No. ZH4 after the argF knockout. The sequences of the primers are respectively:
argF1:gtggagcagcatgacaaag；
argR1:gtcggtatagataaagtcagcagagaagtgaactgt；
argF2:acagttcacttctctgctgactttatctataccgac；
argR2:gaggatctgcaacgcacg；
arg20F:tatgacggcattcagtatcggttttagagctagaaatagc；
arg20R:cgatactgaatgccgtcataactagtattatacctaggac。
example 5: knock-out pyrI in E.coli ZH4
Gene knockout was performed using the method of the literature (Yu Jiang, et al, multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system, appl Environ Microbiol.2015,81 (7): 2506-14).
Primers pyrIF1, pyrIR1 amplifying the upstream homologous fragment; amplifying the downstream homologous fragment by pyrIF2 and pyrIR 2; the primers pyrIF1 and pyrIR2 amplify homologous fragments for upstream and downstream fusion for gene knockout by using the upstream and downstream homologous fragments as templates. The primer pyrI20F, pyrI R amplified the gRNA plasmid. Strain No. ZH5 after knocking out pyrI. The sequences of the primers are respectively:
pyrIF1:GCTGGACTTATTCACTATTC；
pyrIR1:ATTATAGGGAGCCAGACTTATCGTGTGTCATCTCTA；
pyrIF2:TAGAGATGACACACGATAAGTCTGGCTCCCTATAAT；
pyrIR2:CATGATAGCCCGGATTTC；
pyrI20F:CTGTATCAGCCATGCCGAACGTTTTAGAGCTAGAAATAGC；
pyrI20R:GTTCGGCATGGCTGATACAGACTAGTATTATACCTAGGAC。
example 6: knockout of nagD in E.coli ZH5
Gene knockout was performed using the method of the literature (Yu Jiang, et al, multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system, appl Environ Microbiol.2015,81 (7): 2506-14).
Amplifying an upstream homologous fragment by using a primer nagDF1 and nagDR 1; amplifying the downstream homologous fragment by nagDF2 and nagDR 2; the homologous fragments at the upstream and downstream are used as templates, and primers nagDF1 and nagDR2 amplify homologous fragments for upstream and downstream fusion of gene knockout. The primer nagD20F, nagD R amplified the gRNA plasmid. Strain number ZH6 after nagD knockout. The sequences of the primers are respectively:
nagDF1:GTAATTTGCGATATCGACGG；
nagDR1:ATTGGTGGCGATAAAACGTGCAGGGTTCACATCGGTAATA；
nagDF2:CACGTTTTATCGCCACCAAT；
nagDR2:CAGATAACGTCGATTTCAGC；
nagD20F:GCGAAACGCGTTCCTACAACGTTTTAGAGCTAGAAATAGC；
nagD20R:GTTGTAGGAACGCGTTTCGCACTAGTATTATACCTAGGAC。
example 7: knockout of aphA in E.coli ZH6
Gene knockout was performed using the method of the literature (Yu Jiang, et al, multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system, appl Environ Microbiol.2015,81 (7): 2506-14).
Amplifying the upstream homologous fragment by the primer aphaF1 and aphaR 1; amplifying the downstream homologous fragment of aphaF2 and aphaR 2; the primers aphAF1 and aphAR2 are used as templates to amplify homologous fragments for upstream and downstream fusion of gene knockout. The primer aphA20F, aphA R amplified the gRNA plasmid. Strain No. ZH7 after aphA was knocked out. The sequences of the primers are respectively:
aphAF1:GTGCATCTAGCTCAACAGG；
aphAR1:AACAGCATTCGGGAGAGCATCTGTGTGATCTTGCGCAT；
aphAF2:ATGCGCAAGATCACACAGATGCTCTCCCGAATGCTGTT；
aphAR2:CCTTGTAGTGTCGCGATGATG；
aphA20F:ATTGATATGCATGTACGCCGGTTTTAGAGCTAGAAATAGC；
aphA20R:CGGCGTACATGCATATCAATACTAGTATTATACCTAGGAC。
example 8: knocking out survivin in E.coli ZH7
Gene knockout was performed using the method of the literature (Yu Jiang, et al, multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system, appl Environ Microbiol.2015,81 (7): 2506-14).
Primers surEF1 and survivin 1 amplify upstream homologous fragments; amplifying the downstream homologous fragment by survivin 2 and survivin 2; the homologous fragments of the upstream and downstream fusion are amplified by using the primers survivin 1 and survivin 2 as templates, and the homologous fragments of the upstream and downstream fusion are used for gene knockout. The primer surE20F, surE R amplified the gRNA plasmid. Strain number ZH8 after knocking out surviving. The sequences of the primers are respectively:
surEF1:TTGCTGAGTAATGATGACGG；
surER1:GCAAAATTGAACAGGTTACGAATAAATAACATCATCCCCCA；
surEF2:GTAACCTGTTCAATTTTGC；
surER2:ACTCCCACGCTGTTTAACCA；
surE20F:AGGCCGTCATTTAGGTTTTCGTTTTAGAGCTAGAAATAGC；
surE20R:GAAAACCTAAATGACGGCCTACTAGTATTATACCTAGGAC。
example 9: knockout of phoA in E.coli ZH8
Gene knockout was performed using the method of the literature (Yu Jiang, et al, multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system, appl Environ Microbiol.2015,81 (7): 2506-14).
Primers phoAF1, phoAR1 amplifying the upstream homologous fragment; amplifying the downstream homologous fragments by phoAF2 and phoAR 2; the primers phoAF1 and phoAR2 are used as templates to amplify homologous fragments for upstream and downstream fusion of gene knockout. The primer phoA20F, phoA20R amplified the gRNA plasmid. Strain No. ZH9 after phoA knockout. The sequences of the primers are respectively:
phoAF1:GAGAAACGTTTCGCTGGT；
phoAR1:TGGCTTTGTCGGTCATCTACAGTAACGGTAAGAGTGC；
phoAF2:GCACTCTTACCGTTACTGTAGATGACCGACAAAGCCA；
phoAR2:CCGAAAAGCAAGGTAACCAG；
phoA20F:CGTTTCTACCGCAGAGTTGCGTTTTAGAGCTAGAAATA；
phoA20R:GCAACTCTGCGGTAGAAACGACTAGTATTATACCTAGGA。
example 10: knockout of yrfG in E.coli ZH9
Gene knockout was performed using the method of the literature (Yu Jiang, et al, multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system, appl Environ Microbiol.2015,81 (7): 2506-14).
Amplifying an upstream homologous fragment by using a primer yrfGF1 and a primer yrfGR 1; amplifying the downstream homologous fragment by using the yrfGF2 and the yrfGR 2; the homologous fragments of the upstream and downstream fusion are amplified by using the primers yrfGF1 and yrfGR2 as templates, and the homologous fragments of the upstream and downstream fusion are used for gene knockout. The primer yrfG20F, yrfG R amplified the gRNA plasmid. Strain number ZH10 after knockout of yffg. The sequences of the primers are respectively:
yrfGF1:GATTTTGTTGATCAGCCC；
yrfGR1:GTCATTCAGTGACGGATGTCCATATCCAGCAGAACG；
yrfGF2:CGTTCTGCTGGATATGGACATCCGTCACTGAATGA；
yrfGR2:GTCATGTTGCGGCATAATCA；
yrfG20F:TTACTTTCCACCCACACATTGTTTTAGAGCTAGAAATAG；
yrfG20R:AATGTGTGGGTGGAAAGTAAACTAGTATTATACCTAGGAC。
example 11: knock-out of yjjG in E.coli ZH10
Gene knockout was performed using the method of the literature (Yu Jiang, et al, multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system, appl Environ Microbiol.2015,81 (7): 2506-14).
Primers yjjGF1, yjjGR1 amplifying the upstream homologous fragment; amplifying the downstream homologous fragments by yjGF 2 and yjGR 2; the primers yjjGF1 and yjjGR2 are used as templates to amplify homologous fragments for upstream and downstream fusion of gene knockout. The primer yjjG20F, yjjG20R amplified the gRNA plasmid. Strain No. ZH11 after yjjG was knocked out. The sequences of the primers are respectively:
yjjGF1:CTATCACTGGAAGGCGCTCA；
yjjGR1:AGGCAATCAGTGTTTACAAATGAGTCAAAGGTAAACA；
yjjGF2:TGTTTACCTTTGACTCATTTGTAAACACTGATTGCCT；
yjjGR2:CTTCATCGAGCAGCTCCATC；
yjjG20F:ACTTCATTACAGCTTCAGCAGTTTTAGAGCTAGAAATAGC；
yjjG20R:TGCTGAAGCTGTAATGAAGTACTAGTATTATACCTAGGAC。
example 12: knocking out ushA in E.coli ZH11
Gene knockout was performed using the method of the literature (Yu Jiang, et al, multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system, appl Environ Microbiol.2015,81 (7): 2506-14).
Amplifying an upstream homologous fragment by using a primer ushAF1 and ushAR 1; amplifying the downstream homologous fragment by ushAF2 and ushAR 2; the primers ushAF1 and ushAR2 are used as templates to amplify homologous fragments for upstream and downstream fusion of gene knockout. The primer ushA20F, ushA R amplified the gRNA plasmid. Strain No. ZH12 after knockout of ushA. The sequences of the primers are respectively:
ushAF1:GGATCATGTCGTTCAGCAG；
ushAR1:GAGATCATTTGCTGGTTTTCTTGGTATGCAGAACTGTAA；
ushAF2:TTACAGTTCTGCATACCAAGAAAACCAGCAAATGATCTC；
ushAR2:CTTTCAGCACTTCGGCATCA；
ushA20F:CATTACGATAATGGTGAGCAGTTTTAGAGCTAGAAATAGC；
ushA20R:TGCTCACCATTATCGTAATGACTAGTATTATACCTAGGAC。
example 13: knocking out serB in E.coli ZH12
Gene knockout was performed using the method of the literature (Yu Jiang, et al, multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system, appl Environ Microbiol.2015,81 (7): 2506-14).
Amplifying an upstream homologous fragment by a primer serBF1 and serBR 1; amplifying a downstream homologous fragment by serBF2 and serBR 2; the upstream and downstream homologous fragments are used as templates, and primers serBF1 and serBR2 amplify homologous fragments for upstream and downstream fusion of gene knockout. The primer serB20F, serB R amplified the gRNA plasmid. Strain No. ZH13 after knockout of serB. The sequences of the primers are respectively:
serBF1:CCAGAACGTGCGATAAGAT；
serBR1:TGAGAGGATGCAGAATACATCACTTCATCACCACTT；
serBF2:AAGTGGTGATGAAGTGATGTATTCTGCATCCTCTCA；
serBR2:ACAGCGTTTTCATCTGCT；
serB20F:TGACGCCAATATTCTGCAACGTTTTAGAGCTAGAAATAGC；
serB20R:GTTGCAGAATATTGGCGTCAACTAGTATTATACCTAGGAC。
example 14: knockout of yigL in e.coli ZH13
Gene knockout was performed using the method of the literature (Yu Jiang, et al, multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system, appl Environ Microbiol.2015,81 (7): 2506-14).
Primers yignf 1, yignr 1 amplifying the upstream homologous fragment; amplifying downstream homologous fragments by yigff 2 and yigfr 2; the primers yigff 1 and yigfr 2 amplify homologous fragments for upstream and downstream fusion of gene knockout by using the upstream and downstream homologous fragments as templates. The primer yigL20F, yigL R amplified the gRNA plasmid. Strain number ZH14 after knockout of yigL. The sequences of the primers are respectively:
yigLF1:CGTGATTCGTATGCCGTC；
yigLR1:AGAGTTTACGCAGATAATGACGTGCCATCTAAATCAG；
yigLF2:CTGATTTAGATGGCACGTCATTATCTGCGTAAACTCT；
yigLR2:CAAGCCAGTCCAGAAATG；
yigL20F:GTTTATGAATCGCCATCGCCGTTTTAGAGCTAGAAATAGC；
yigL20R:GGCGATGGCGATTCATAAACACTAGTATTATACCTAGGAC。
example 15: knock-out ygdH in E.coli ZH14
Gene knockout was performed using the method of the literature (Yu Jiang, et al, multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system, appl Environ Microbiol.2015,81 (7): 2506-14).
Amplifying an upstream homologous fragment by using a primer ygdHF1 and ygdHR 1; amplifying downstream homologous fragments by ygdHF2 and ygdHR 2; the homologous fragments of the upstream and downstream are used as templates, and the primers ygdHF1 and ygdHR2 amplify homologous fragments of the upstream and downstream fusion for gene knockout. The primer ygdH20F, ygdH20R amplified the gRNA plasmid. Strain number ZH15 after knockout of ygdH. The sequences of the primers are respectively:
ygdHF1:GACCACAAGACTGGTTCG；
ygdHR1:AGCCATATTCTCGTGAGATGCAAAGCGCGAATAATT；
ygdHF2:AATTATTCGCGCTTTGCATCTCACGAGAATATGGCT；
ygdHR2:GAAACGTTTGCGTTGCAA；
ygdH20F:AGCAAATAGAGCAACTCTTCACTAGTATTATACCTAGGAC；
ygdH20R:GAAGAGTTGCTCTATTTGCTGTTTTAGAGCTAGAAATAGC。
example 16: knock-out of yfdR in E.coli ZH15
Gene knockout was performed using the method of the literature (Yu Jiang, et al, multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system, appl Environ Microbiol.2015,81 (7): 2506-14).
Primers yfdff 1, yfdfrr 1 amplified upstream homologous fragments; yfdff 2, yfdfrr 2 amplified downstream homologous fragments; the primers yfdff 1 and yfdfrr 2 are used as templates to amplify homologous fragments for upstream and downstream fusion of gene knockout. Primer yfdR20F, yfdR R amplified the gRNA plasmid. Strain number ZH16 after knockout of yfdR. The sequences of the primers are respectively:
yfdRF1:CTGATTTTGAAGATAATG；
yfdRR1:ATGCGCATTTGCGTAACTTTAATCACGATGTCGTCT；
yfdRF2:AGACGACATCGTGATTAAAGTTACGCAAATGCGCAT；
yfdRR2:CTCTACTTCCAGAGATAC；
yfdR20F:TGCAACAGAAGCGTATTGCCGTTTTAGAGCTAGAAATAGC；
yfdR20R:GGCAATACGCTTCTGTTGCAACTAGTATTATACCTAGGAC。
example 17: knockout of cmk in E.coli ZH16
Gene knockout was performed using the method of the literature (Yu Jiang, et al, multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system, appl Environ Microbiol.2015,81 (7): 2506-14).
Amplifying an upstream homologous fragment by using a primer cmkF1 and a cmkR 1; amplifying the downstream homologous fragment by using cmkF2 and cmkR 2; the upstream and downstream homologous fragments are used as templates, and the primers cmkF1 and cmkR2 amplify homologous fragments for upstream and downstream fusion of gene knockout. The primer cmk20F, cmk R amplified the gRNA plasmid. Strain number ZH17 after knockout of cmk. The sequences of the primers are respectively:
cmkF1:CAATAAATCCCCATCTGA；
cmkR1:ATTTTCACTGGTGCATCAGGATGCCATTGCAACGCTT；
cmkF2:AAGCGTTGCAATGGCATCCTGATGCACCAGTGAAAAT；
cmkR2:GTCATGTTTAATCTTCAG；
cmk20F:ATCTGGAAGTGATCCTCGAAGTTTTAGAGCTAGAAATAGC；
cmk20R:TTCGAGGATCACTTCCAGATACTAGTATTATACCTAGGAC。
example 18: gene prs (N120S-L135I), pyrH (D93A), pyrG (D160E-E162A-E168K), pyrE and nudG cloned into pET-30a (+
prs (see SEQ ID NO. 18) was synthesized by Nanjing Jinsri Biotech and cloned into the NdeI and BglII cleavage sites of pET-30a (+). The cloned plasmid was designated pET30prs.
After amplification of pyrE with primers pyrEF, pyrER, the plasmid was cloned into the BglII site of pET30prs using the cloning kit from Tuber biosciences, inc., and the cloned plasmid was designated pET30prs-pyrE.
After PCR amplification of pyrH (see SEQ ID NO. 20), the plasmid was cloned into the EcoRV site of pET30-pyrE using the cloning recombination kit from Tuber biosciences, inc., and the cloned plasmid was designated pET30prs-pyrE-pyrH.
pyrG (see SEQ ID NO. 21) was synthesized by Nanjin St Biotech and cloned into the EcoRV and BamHI cleavage sites of pET-30a (+) and then enzymatically cleaved to clone into the EcoRV and BamHI cleavage sites of pET30prs-pyrE-pyrH, the cloned plasmid designated pET30prs-pyrE-pyrH-pyrG.
nudG was amplified using primers nudGF, nudGR, and cloned into the SacI site of pET30prs-pyrE-pyrH-pyrG using a cloning kit from Tuber biosciences, inc., and the cloned plasmid was designated pET30prs-pyrE-pyrH-pyrG-nudG.
The primer sequences were as follows:
pyrEF:CTACCTGTTCAGCTGAAAAGGAGGATATACATATGAAACCATATCAGCGCCA；
pyrER:TCGTCGTCGTCGGTACTTAAACGCCAAACTCTTC；
nudGF:ACTGAGAGTGCATCCATAAAAAGGAGGATATACATATGAAAATGATTGAAG TT；
nudGR:CCGCAAGCTTGTCGACCTAATCCGCTGGTCTGGC。
example 19: construction of recombinant genetically engineered bacteria
pET30prs-pyrE-pyrH-pyrG-nudG of example 18 was transformed into strain ZH13 of example 13 and strain ZH17 of example 17, respectively, with the transformed strain numbers: ZH13 (pET 30 prs-pyrE-pyrH-pyrG-nudG), ZH17 (pET 30 prs-pyrE-pyrH-pyrG-nudG).
Example 20: cytidine acid production of ZH8, ZH13, ZH16
The present example explores the cytidine acid yield of genetically engineered bacteria obtained in example 8, example 13 and example 16 after shake flask fermentation, and the specific method is as follows:
1. shaking flask fermentation of genetically engineered bacteria
A single colony was picked up and inoculated into a tube containing LB medium, to which kanamycin sulfate was added at a final concentration of 50. Mu.g/mL, and cultured overnight at 30℃and 220 rpm. Then, the mixture was inoculated into a shaking flask containing 20mL of the fermentation broth at an inoculum size of 1%, and after four hours of cultivation at 37℃and 220rpm, IPTG was added to a final concentration of 50. Mu.g/mL, and the shaking flask was placed at 37℃and fermentation cultivation was performed at 220 rpm. The composition of the LB culture solution is: yeast extract powder 0.5%, tryptone 1.0% and sodium chloride 1.0%. The fermentation medium comprises the following components: tryptone 2.0%, yeast extraction 2.4%, glycerol 0.4%, KH 2 PO 4 0.23％，K 2 HPO 4 1.254％，pH 7.0。
2. HPLC detection of cytidine acid in fermentation broth
After fermentation for 24 hours, 1mL of the fermentation broth was centrifuged at 12000rpm for 10 minutes, and the supernatant was filtered. The filtrate was subjected to HPLC detection. The detection method comprises the following steps: mobile phase: 50mM potassium dihydrogen phosphate: methanol=95: 5, detecting wavelength 260nm,Waters XBridge Amide C18 (250 mm multiplied by 460 mm) column temperature 30 ℃, flow rate 1mL/min, detecting time 15min and sample injection quantity 10 mu L.
3. Cytidine acid yield
The detection result shows that Cytidine Monophosphate (CMP) and cytidine are not detected in the metabolite of the escherichia coli MG1665, after glsA, glsB, argF, pepA, pyrI, nagD, aphA, surE is knocked out in the genome, the yield of the cytidine is 8.8MG/L, after phoA, yrfG, yjjG, ushA, serB is knocked out further, the yield of the cytidine is 96.7MG/L, the yield of the cytidine is 47.6MG/L, yigL, yfdR, ygdH is knocked out further, the yield of the CMP is 161.3MG/L, and the yield of the cytidine is 43.3MG/L.
Example 21: cytidine acid production by ZH13 (pET 30 prs-pyrE-pyrH-pyrG-nudG), ZH17 (pET 30 prs-pyrE-pyrH-pyrG-nudG)
The embodiment explores the cytidine acid yield of the genetically engineered bacterium obtained in the embodiment 19 after shaking flask fermentation, and the specific method is as follows:
1. shaking flask fermentation of genetically engineered bacteria
A single colony was picked up and inoculated into a tube containing LB medium, to which kanamycin sulfate was added at a final concentration of 50. Mu.g/ml, and cultured overnight at 30℃and 220 rpm. Then, the mixture was inoculated into a shaking flask containing 20ml of the fermentation broth at an inoculum size of 1%, and after four hours of cultivation at 37℃and 220rpm, IPTG was added to a final concentration of 50. Mu.g/ml, and the shaking flask was left to stand at 37℃and 220rpm for fermentation cultivation. The composition of the LB culture solution is: yeast extract powder 0.5%, tryptone 1.0% and sodium chloride 1.0%. The fermentation medium comprises the following components: tryptone 2.0%, yeast extraction 2.4%, glycerol 0.4%, KH 2 PO 4 0.23％，K 2 HPO 4 1.254％，pH 7.0。
2. The HPLC detection of cytidine acid in the fermentation broth was performed in the same manner as in example 20.
3. Cytidine acid yield
The results show that the yield of cytidine acids in the fermentation product of ZH13 (pET 30 prs-pyrE-pyrH-pyrG-nudG): 570.6mg/L, cytidine acid yield in fermentation product of ZH17 (pET 30 prs-pyrE-pyrH-pyrG-nudG): 1066.4mg/L.
Example 22: fermentation in genetically engineered bacteria fermenter
The genetically engineered bacterium ZH17 (pET 30 prs-pyrE-pyrH-pyrG-nudG) obtained in example 19 was picked up as a single colony and inoculated into LB seed medium, and cultured at 30℃for 15 hours at 250rpm to obtain a seed solution. Then 1L of seed solution is sucked into the fermentation culture medium according to the inoculation amount of 10 percent, and the total volume of the culture medium after inoculation is 10L. The formula (g/L) of the culture medium for fermentation culture is as follows: glucose 10, KH 2 PO 4 1.35 Yeast extract powder 10, ammonium sulfate 2.5, mgSO 4 1, citric acid 1.1; other inorganic salt components (mg/L) in the medium: feSO 4 ·7H 2 O 150，MnSO 4 ·7H 2 O15, cobalt chloride 3.5 and zinc sulfate 3.5, and 50mg/L of the kananamycin is added into the culture medium. In the fermentation process, the pH of the culture medium is regulated and controlled to 7.0 by ammonia water, the fermentation temperature is 37 ℃, IPTG is added to the final concentration of 50 mug/ml in the 3 rd fermentation time, glucose is fed in to keep the final concentration of about 0.1%, and dissolved oxygen is controlled>25%, fermentation period 50h.
And detecting the fermentation liquor by HPLC, wherein the final cytidine acid yield reaches 15g/L.
Claims (10)
1. A genetically engineered bacterium for producing 5' -cytidylic acid, wherein the genetically engineered bacterium uses escherichia coli as a starting bacterium, knocks out genes related to pyrimidine biosynthesis pathway in a genome, and comprises: the gene glsA encoding glutaminase A, the gene glsB encoding glutaminase B, the gene argF encoding ornithine carbamoyltransferase, the gene pepA encoding aminopeptidase A, the gene pyrI encoding aspartate aminotransferase, the gene nagD encoding UMP phosphatase, the gene aphA encoding acid phosphatase, the gene survivin encoding nucleotidase, the gene phoA encoding alkaline phosphatase, the gene yrfG encoding purine nucleotidase, the gene yjjG encoding pyrimidine nucleotidase, the gene ushA encoding 5' -nucleotidase, the gene serB encoding phosphoserine phosphatase.
2. The genetically engineered bacterium for producing 5' -cytidine acid according to claim 1, wherein the nucleotide sequence of glsA is shown in SEQ ID No.1, the nucleotide sequence of glsB is shown in SEQ ID No.2, the nucleotide sequence of argF is shown in SEQ ID No.3, the nucleotide sequence of pepA is shown in SEQ ID No.4, the nucleotide sequence of pyrI is shown in SEQ ID No.5, the nucleotide sequence of nagD is shown in SEQ ID No.6, the nucleotide sequence of aphA is shown in SEQ ID No.7, the nucleotide sequence of survivin is shown in SEQ ID No.8, the nucleotide sequence of phoA is shown in SEQ ID No.9, the nucleotide sequence of yrfG is shown in SEQ ID No.10, the nucleotide sequence of yjg is shown in SEQ ID No.11, the nucleotide sequence of ushA is shown in SEQ ID No.12, and the nucleotide sequence of serB is shown in SEQ ID No. 13.
3. The genetically engineered strain for producing 5' -cytidine acid according to claim 1, wherein the cytidine phosphatase gene in the genome is further knocked out, comprising: the gene yigL encoding the phosphosugar phosphatase, the gene yfdR encoding the 5 '-deoxynucleotidase, the gene ygdH encoding the nucleotide 5' -monophosphate nucleotidase.
4. The genetically engineered strain for producing 5' -cytidine acid as defined in claim 3, wherein the nucleotide sequence of yigL is shown in SEQ ID No.14, the nucleotide sequence of yfdR is shown in SEQ ID No.15, and the nucleotide sequence of ygdH is shown in SEQ ID No. 16.
5. The genetically engineered strain for the production of 5' -cytidine acid as recited in claim 3, wherein the gene cmk encoding cytidine kinase in the genome is further knocked out.
6. The genetically engineered bacterium for the production of 5' -cytidine acid as recited in claim 5, wherein the nucleotide sequence of cmk is set forth in SEQ ID No. 17.
7. Genetically engineered bacterium that produces 5' -cytidine acids according to any one of claims 1-6, further overexpressing genes related to pyrimidine nucleoside synthesis, including gene prs encoding ribophosphodiphosphate kinase, gene pyrE encoding orotate phosphoribosyl transferase, gene pyrH encoding UMP kinase, gene pyrG encoding CTP synthase, gene nudG encoding CTP diphosphate; the nucleotide sequence of prs is shown as SEQ ID NO.18, the nucleotide sequence of pyrE is shown as SEQ ID NO.19, the nucleotide sequence of pyrH is shown as SEQ ID NO.20, the nucleotide sequence of pyrG is shown as SEQ ID NO.21, and the nucleotide sequence of nudG is shown as SEQ ID NO. 22.
8. The method for constructing a genetically engineered bacterium for producing 5' -cytidine acid as recited in any one of claims 1 to 7, comprising: taking escherichia coli as a starting strain, knocking out genes related to pyrimidine biosynthesis pathways in a genome by utilizing a gene editing technology, and obtaining the genetically engineered strain for producing 5' -cytidine acid.
9. Use of the genetically engineered bacterium for producing 5 '-cytidine acid as defined in any one of claims 1 to 7 in the preparation of 5' -cytidine acid.
10. The use according to claim 9, comprising: after the genetically engineered bacterium for producing 5' -cytidine acid is subjected to amplification culture, inoculating the genetically engineered bacterium into a fermentation culture medium, controlling the pH of the culture medium to be neutral in the fermentation process, controlling the fermentation temperature to be 30-37 ℃, and controlling dissolved oxygen by feeding glucose to keep the final concentration to be 0.1 percent>25%, separating and obtaining a product 5' -cytidine acid from fermentation liquor after fermentation is finished; wherein the components of the fermentation medium include: glucose 10g/L, KH 2 PO 4 1.35g/L, yeast extract powder 10g/L, ammonium sulfate 2.5g/L, mgSO 4 1g/L, 1.1g/L of citric acid, and inorganic salt components in a culture medium: feSO 4 ·7H 2 O 150mg/L，MnSO 4 ·7H 2 O15 mg/L, cobalt chloride 3.5mg/L and zinc sulfate 3.5mg/L.
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