WO2024130898A1 - Engineered strain for producing 2'-fucosyllactose, constructing method, and use - Google Patents
Engineered strain for producing 2'-fucosyllactose, constructing method, and use Download PDFInfo
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- WO2024130898A1 WO2024130898A1 PCT/CN2023/087183 CN2023087183W WO2024130898A1 WO 2024130898 A1 WO2024130898 A1 WO 2024130898A1 CN 2023087183 W CN2023087183 W CN 2023087183W WO 2024130898 A1 WO2024130898 A1 WO 2024130898A1
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Definitions
- the invention belongs to the technical field of genetic engineering, and specifically relates to an engineering strain producing 2'-fucosyllactose, a construction method and an application thereof.
- HMOs Human milk oligosaccharides
- Such oligosaccharides have many beneficial effects on the health of newborns, and therefore have received sustained and extensive attention.
- host strains produced by fermentation methods are easy to obtain, highly safe, and low in cost. Therefore, the industry has used engineered microorganisms to study the large-scale production methods of various human milk oligosaccharides.
- the development of molecular biology technology and metabolic engineering has also promoted the progress of human milk oligosaccharide production technology.
- 2'-fucosyllactose (2'-FL), 3-fucosyllactose, lacto-N-tetraose, lacto-N-neotetraose, 3'-sialyllactose, 6'-sialyllactose and some complex fucosylated human milk oligosaccharides have been fermented by engineered bacteria. Among them, the fermentation of 2'-fucosyllactose has been the most extensively studied.
- Lu et al. (Lu M, et al. Engineered Microbial Routes for Human Milk Oligosaccharides Synthesis [J]. ACS Synthetic Biology, 2021.) reviewed in detail the latest progress in the research on human milk oligosaccharides, especially 2'-fucosyllactose fermentation technology and strain construction in recent years, and summarized the key enzymes and regulatory factors such as the de novo synthesis pathway and salvage pathway involved in the biosynthesis of 2'-fucosyllactose.
- Sugar efflux transporters are beneficial to reduce the intracellular 2'-fucosyllactose concentration and promote product efflux.
- Transcriptional regulatory factor genes rcsA and rcsB can positively regulate manA, manB, manC, wcaG, gmd, etc.
- GDP-L-fucose is a key precursor for the synthesis of fucosylated human milk oligosaccharides and can be synthesized through the de novo synthesis pathway and the salvage pathway.
- the de novo pathway is generally used as the preferred pathway for the synthesis of GDP-L-fucose.
- Inactivation of the lon and/or wcaj genes involved in the biosynthesis of colanic acid, and/or overexpression of the transcriptional regulatory factor gene rcsA, can increase the supply of GDP-L-fucose in cells (Drouillard S, et al.
- chromosomal genes wcaJ, nudD and nudK involved in the degradation of precursors GDP-L-fucose and GDP-mannose were deleted. It was found that rcsA and rcsB were more conducive to the formation of GDP-L-fucose, thereby promoting the production of 2'-fucosyllactose.
- the present invention adopts gene editing technology to edit the gene of Escherichia coli transcriptional regulatory factor, etc., and obtains an engineered Escherichia coli bacteria that can increase 2'-fucosyllactose.
- One of the technical solutions of the present invention provides an engineered strain for producing 2'-fucosyllactose, wherein the starting strain of the engineered strain is Escherichia coli.
- the engineered strain overexpresses the transcriptional regulatory factor genes rcsA and rcsB on the plasmid to increase the fermentation yield of 2'-fucosyllactose.
- the sugar efflux transporter A encoding gene setA and/or the methionine aminopeptidase encoding gene map of the engineered strain can also be edited so that the engineered strain overexpresses the sugar efflux transporter A encoding gene setA and/or expresses a methionine aminopeptidase mutant.
- the amino acid sequence of the methionine aminopeptidase mutant corresponds to the 44th amino acid position of the wild-type methionine aminopeptidase (Map) amino acid sequence shown in SEQ ID NO: 24, and has a mutation: I>S, and the homology of the methionine aminopeptidase mutant to the wild-type methionine aminopeptidase amino acid sequence shown in SEQ ID NO: 24 is >90%.
- the engineered strain overexpresses the sugar efflux transporter A encoding gene setA, and expresses the aforementioned methionine aminopeptidase mutant;
- the methionine aminopeptidase mutant amino acid sequence corresponds to the 44th amino acid position of the wild-type methionine aminopeptidase (Map) amino acid sequence shown in SEQ ID NO: 24, and has a mutation: I>S, and the methionine aminopeptidase mutant has a homology of >90% with the wild-type methionine aminopeptidase amino acid sequence shown in SEQ ID NO: 24.
- the engineered strain in situ overexpresses the sugar efflux transporter A encoding gene setA, and expresses the aforementioned methionine aminopeptidase mutant;
- the methionine aminopeptidase mutant amino acid sequence corresponds to the 44th amino acid position of the wild-type methionine aminopeptidase (Map) amino acid sequence shown in SEQ ID NO: 24, and has a mutation: I>S, and the methionine aminopeptidase mutant has a homology of >90% with the wild-type methionine aminopeptidase amino acid sequence shown in SEQ ID NO: 24.
- plasmid overexpression is gene overexpression on plasmids, that is, using expression control elements with different transcription or translation strengths, constructing a plasmid library ex situ, and transforming the plasmid into microbial cells.
- expression of the target gene can be quickly achieved.
- In situ overexpression or chromosome in situ overexpression is a commonly used term in the art, which refers to overexpression in situ, that is, by molecular biological means, such as promoters, ribosome binding sites and transcriptional regulatory factors, or codon optimization, etc., the target gene located in the chromosome in situ is regulated to improve the level of gene transcription and translation.
- the additionally inserted promoter for gene overexpression can be a constitutive promoter and/or an inducible promoter.
- constitutive promoter and inducible promoter described herein refer to promoters suitable for prokaryotic expression systems, especially promoters suitable for Escherichia coli expression systems, including natural promoters and artificially constructed promoters.
- Constitutive promoters such as P J23102 , P J23104 , P J23105 , P J23108 , P J23100 , P J23110 , P J23111, P J23113 , P J23116 , P J23119 , P 637 , P 699 , etc., have been used in the field of Escherichia coli gene editing. These constitutive promoters and inducible promoters can be used for overexpression of rcsA, rcsB, and setA .
- the in situ expression level of the chromosome of setA can be increased by inserting an additional promoter, and the in situ expression level can be increased by other methods that are easy for a person skilled in the art to think of, such as modifying the promoter activity of the small molecule regulatory RNA gene sgrS in front of the setA gene, or inserting an additional promoter in front of the sgrS gene.
- a constitutive promoter is inserted in front of setA for in situ overexpression and/or a promoter of a chloramphenicol resistance gene is inserted for in situ overexpression.
- the nucleotide sequence of the promoter of the chloramphenicol resistance gene is as shown in SEQ ID NO: 23.
- the constitutive promoter used is selected from any one of PJ23108 , PJ23110 , PJ23116 , and PJ23119 .
- PJ23108 , PJ23110 , PJ23116 , and PJ23119 can also be used for overexpression of rcsA and rcsB.
- the amino acid sequence of the methionine aminopeptidase mutant is shown in SEQ ID NO: 15.
- the methionine aminopeptidase mutant shown in SEQ ID NO: 15 has only the 44th amino acid position mutated from isoleucine to serine relative to the aforementioned wild-type methionine aminopeptidase. It has been verified that the methionine aminopeptidase mutant shown in SEQ ID NO: 15 is beneficial to improving the fermentation yield of 2'-fucosyllactose.
- the present invention further provides a gene encoding a methionine aminopeptidase mutant shown in SEQ ID NO: 15 that can be expressed in cells, wherein the gene encoding at least comprises a nucleotide fragment shown in SEQ ID NO: 22.
- the target gene can be introduced into the genetically engineered bacterium by a plasmid transformation method or the like. Therefore, the genome of the aforementioned engineered strain can contain a nucleotide fragment shown in SEQ ID NO: 22 or a nucleotide sequence fragment encoding the same amino acid sequence, so as to express the methionine aminopeptidase mutant shown in SEQ ID NO: 15.
- nucleotide sequence of the aforementioned rcsA is shown as SEQ ID NO: 20; the nucleotide sequence of the aforementioned rcsB is shown as SEQ ID NO: 21; and the nucleotide sequence of the aforementioned setA is shown as SEQ ID NO: 14.
- the starting strain is selected from any one of Escherichia coli K12 MG1655, Escherichia coli BL21 (DE3), Escherichia coli JM109, Escherichia coli W3110, and Escherichia coli BW25113.
- Escherichia coli K12 MG1655 (Escherichia colistrain K12 MG1655) is one of the most famous and well-studied organisms in biology.
- E. coli K12 MG1655 has been deposited in the American Type Culture Collection (deposit number ATCC53103, ATCC 47076, ATCC 700926); E.
- coli BL21 (DE3) has been deposited in BCCM genecorner (deposit number LMBP 1455); E. coli JM109 has been deposited in the American Type Culture Collection (deposit number ATCC68635, ATCC68868); E. coli W3110 has been deposited in the Coli Genetics Stock Center (deposit number CGSC#:4474) and E. coli BW25113 has been deposited in the Coli Genetics Stock Center (deposit number CGSC#7636).
- the starting strains commonly used by technicians in the field those skilled in the art are capable of knowing the sources and purchase channels of the above strains.
- gene editing can also be performed on the de novo synthesis pathway of 2'-fucosyllactose in the engineered strain, the coding genes of enzymes and transporters related to the salvage synthesis pathway, the lactose lac operon sequence, etc.
- At least one of the following genes on the Escherichia coli genome can be knocked out: knock out at least one of the following genes on the Escherichia coli genome: ⁇ -galactosidase encoding gene lacZ, UDP-glucose lipid carrier transferase encoding gene wcaj, GDP-mannose hydrolase encoding gene nudd, regulatory gene lacI in the lactose lac operon sequence, L-fucose isomerase encoding gene fucI, L-fucokinase encoding gene fuc K, L-fucose-1-phosphate aldolase encoding gene fucA; and/or overexpression or insertion of at least one of the following genes: GDP-fucose synthase encoding gene wcaG, GDP-mannose-4,6-dehydratase encoding gene gmd,
- the engineered strain and the genetically engineered bacteria include the following gene editing: knocking out the ⁇ -galactosidase encoding gene lacZ on the Escherichia coli genome;
- the mannose-1-phosphate guanylyltransferase encoding gene manC was overexpressed on the plasmid.
- nucleotide sequence of the aforementioned lacZ is shown in SEQ ID NO: 3; the nucleotide sequence of the aforementioned wcaG is shown in SEQ ID NO: 5; the nucleotide sequence of the aforementioned gmd is shown in SEQ ID NO: 6; the nucleotide sequence of the aforementioned lacY is shown in SEQ ID NO: 7; the nucleotide sequence of the aforementioned manA is shown in SEQ ID NO: 9; the nucleotide sequence of the aforementioned manB is shown in SEQ ID NO: 10; the nucleotide sequence of the aforementioned wcaj is shown in SEQ ID NO: 11; the nucleotide sequence of the aforementioned nudd is shown in SEQ ID NO: 13; the nucleotide sequence of the aforementioned futC is shown in SEQ ID NO: 16; and the nucleotide sequence of the aforementioned manC is shown in SEQ ID NO: 17.
- the aforementioned wcaG, gmd, manA, manB, lacY, futC and manC are overexpressed using the Ptrc promoter (an inducible promoter);
- the plasmid is selected from any one of pTrc99a, pSB4K5, pET28a or pET22b; the nucleotide sequence of the Ptrc promoter is shown in SEQ ID NO: 4.
- the second technical solution of the present invention provides a construction method of the aforementioned engineering strain, using Escherichia coli K12MG1655 as the starting strain, and the construction method comprises the following steps (in no particular order):
- the P lac promoter sequence and the regulatory gene lacI and the ⁇ -galactosidase encoding gene lac Z in the lactose lac operon sequence of the starting strain were knocked out, and the GDP-fucose synthase encoding gene wcaG, the GDP-mannose-4,6-dehydratase encoding gene gmd and the ⁇ -galactosidase permease encoding gene lac Y were overexpressed with the P trc promoter behind the original ⁇ -galactosidase encoding gene lac Z site;
- the phosphomannose isomerase encoding gene manA and the phosphomannose mutase encoding gene manB were overexpressed by using the P trc promoter at the alcohol dehydrogenase encoding gene adhe site of the starting strain;
- the methionine aminopeptidase encoding gene mab of the starting strain is point mutated into the encoding gene as shown in SEQ ID NO: 22; a plasmid overexpressing the mannose-1-phosphate guanine transferase encoding gene manC and the 2'-fucosyllactose synthase encoding gene futC is introduced into the starting strain; preferably, a recombinant strain is constructed by constructing a plasmid containing the two genes in series and then introducing it into the starting strain.
- the third technical solution of the present invention provides the use of the aforementioned engineered strain in the fermentation production of 2'-fucosyllactose.
- the carbon source of the fermentation medium of the engineered strain is selected from at least one of glycerol and lactose;
- the organic nitrogen source of the fermentation medium of the strain is selected from at least one of yeast powder, tryptone and beef extract; the fermentation temperature is 36° C. to 40° C.; and the pH of the fermentation is 6.8 to 7.8.
- the inventors of the present invention have conducted a series of gene editing and improvement studies on Escherichia coli and found that overexpression of transcriptional regulatory factor genes rcsA and rcsB on the Escherichia coli plasmid is beneficial to improving the fermentation yield of 2'-fucosyllactose.
- overexpression of transcriptional regulatory factor genes rcsA and rcsB on the Escherichia coli plasmid is beneficial to improving the fermentation yield of 2'-fucosyllactose.
- setA of Escherichia coli is further overexpressed in situ and the methionine aminopeptidase encoding gene map is point mutated, the fermentation yield of 2'-fucosyllactose can be further improved.
- Escherichia coli W2 is constructed with Escherichia coli K12 MG1655 as the starting strain, the P lac promoter sequence and the regulatory genes lacI and lacZ in the lactose lac operon sequence of the starting strain are knocked out, and wcaG, gmd and lacY are overexpressed with the P trc promoter after the original lacZ site to obtain the W1 strain, and then ManA and ManB are overexpressed with the P trc promoter at the adhe site of the alcohol dehydrogenase encoding gene to obtain the W2 strain.
- the nucleotide sequence of the Plac promoter involved in the construction of Escherichia coli W2 is shown in SEQ ID NO: 1; the nucleotide sequence of lacI is shown in SEQ ID NO: 2; the nucleotide sequence of lacZ is shown in SEQ ID NO: 3; the nucleotide sequence of the Ptrc promoter is shown in SEQ ID NO: 4; the nucleotide sequence of wcaG is shown in SEQ ID NO: 5; the nucleotide sequence of gmd is shown in SEQ ID NO:
- the nucleotide sequence of lacY is shown in SEQ ID NO: 6; the nucleotide sequence of adhE is shown in SEQ ID NO: 8; the nucleotide sequence of manA is shown in SEQ ID NO: 9; and the nucleotide sequence of manB is shown in SEQ ID NO: 10.
- CRISPR/Cas9 technology was used to knock out wcaj (nucleotide sequence is shown in SEQ ID NO: 11).
- the CRISPR/Cas9 technology used in the experiment refers to the previous research report [Zhao D, et al. CRISPR/Cas9-assisted gRNA-free one-step genome editing with no sequence limitations and improved targeting efficiency. Sci Rep 7, 16624].
- the pCAGO plasmid contains the recombinase gene, as well as cas9 and gRNA genes [Zhao D, et al. CRISPR/Cas9-assisted gRNA-free one-step genome editing with no sequence limitations and improved targeting efficiency. Sci Rep 7, 16624].
- the first step homologous recombination strain was inoculated into a medium containing 100 mg/L ampicillin, 0.1 mM IPTG and 2g/L arabinose in LB liquid medium, cultured at 30°C for more than 6h, and single colonies were separated by streaking on plates, and clones that could grow on LB plates containing 100mg/L ampicillin but could not grow on LB plates containing 25mg/L chloramphenicol were screened. Sequencing confirmed the correct clone that underwent the second homologous recombination, and further cultured it at 37°C to lose the pCAGO plasmid, thereby obtaining strain W2 ⁇ wcaj.
- the nudd gene on the genome was knocked out using the same method as the above CRISPR/Cas9 technology (nucleotide sequence as shown in SEQ ID NO: 13), and the strain W2 ⁇ wcaj ⁇ nudd was constructed and named ZKYW1.
- the specific method is described in detail below:
- Second step of homologous recombination The steps of the second step of homologous recombination were the same as those for knocking out the wcaj gene.
- the correct clone that underwent the second homologous recombination was obtained by sequencing and further cultured at 37°C to lose the pCAGO plasmid, thereby obtaining the strain W2 ⁇ wcaj ⁇ nudd, which was named TKYW1.
- the constitutive promoter P J23110 http://parts.igem.org/Part:BBa_J23100 was inserted in front of the sugar efflux transporter setA gene (nucleotide sequence as shown in SEQ ID NO: 14) using the same method as the above-mentioned CRISPR/Cas9 technology.
- the sequence of the promoter P J23110 is: TTTACGGCTAGCTCAGTCCTAGGTACAATGCTAGC; at the same time, when CRISPR/Cas9 was used for the second recombination, the promoter of the chloramphenicol resistance gene (nucleotide sequence as shown in SEQ ID NO: 23) was retained to achieve in situ overexpression of setA by dual promoters.
- the resulting strain was named TKYW2-2.
- the first step is to construct the homologous recombination fragment.
- the primer pairs Sup-1 and Sup-2 and the primer pairs Sdown-1 and Sdown-2 in Table 3 were used as primers to PCR amplify the upstream and downstream homologous arms of homologous recombination.
- the primers Scm-1 and Scm-2 in Table 3 were used for PCR amplification to obtain a fragment with the cat gene sequence.
- PCR amplification was performed without using a template to obtain a gene fragment with the P J23110 promoter.
- Sup-1 and Sdown-2 as primers, the upstream homologous arm obtained by the above PCR amplification, the fragment with the cat gene sequence, the gene fragment with the P J23110 promoter, and the downstream homologous arm, a total of 4 fragments were used as templates for overlapping PCR amplification to obtain the fragments for the first step of homologous recombination.
- the pCAGO plasmid was transformed into the strain TKYW1 using a conventional plasmid transformation method to obtain the strain TKYW1 (pCAGO).
- the TKYW1 (pCAGO) competent state was prepared using LB medium containing 1% glucose and 0.1 mM IPTG, and the above-mentioned fragments for the first homologous recombination were introduced respectively using the electroporation method.
- the transformed bacterial liquid was spread on LB plates containing 100 mg/L ampicillin and 25 mg/L chloramphenicol, as well as 1% glucose, and cultured at 30°C. The transformants were picked for colony PCR identification to obtain the correct first step homologous recombination strain.
- Second step of homologous recombination The steps of the second step of homologous recombination were the same as those for knocking out the wcaj gene.
- the correct clone that underwent the second homologous recombination was obtained by sequencing and further cultured at 37°C to lose the pCAGO plasmid, thereby obtaining a strain with the P J23110 promoter, named TKYW2-2.
- the amino acid sequence of the wild-type methionine aminopeptidase of Escherichia coli K12 MG1655 is shown in SEQ ID NO: 24.
- the methionine aminopeptidase gene map on the genome was subjected to point mutation using the same method as the above-mentioned CRISPR/Cas9 technology, and the 44th isoleucine of its translated protein was mutated to serine (Map Ile44Ser , the amino acid sequence is shown in SEQ ID NO: 15), and the constructed strain was named TKYW3.
- a mutant strain of MG1655map T131G (map T131G nucleotide sequence is shown in SEQ ID NO: 22) with a point mutation in the map gene preserved in the laboratory was used as a template, and the primer pair Mup-1 and Mup-2, and the primer pair Mdown-1 and Mdown-2 in Table 4 were used as primers to PCR amplify the upstream and downstream homologous arms of homologous recombination.
- the fragment with the cat-N20 sequence obtained by PCR when constructing strain W2 ⁇ wcaj was used as a template, and PCR amplification was performed using primers Mcat-1 and Mcat20-2 to obtain a new fragment with the cat-N20 sequence.
- the upper and downstream homologous arms, the new fragment with the cat-N20 sequence, and these three fragments were used as templates, and overlapping PCR was performed using primers Mup-1 and Mdown-2 to obtain the first homologous recombination fragment, which contains a point mutation in the map gene, that is, the 131st base of the wild-type map gene changes from T to For G.
- the pCAGO plasmid was transformed into the strain TKYW2-2 using a conventional plasmid transformation method to obtain the strain TKYW2-2 (pCAGO).
- the TKYW2-2 (pCAGO) competent state was prepared using LB medium containing 1% glucose and 0.1 mM IPTG, and the first homologous recombination fragment was introduced using an electroporation method.
- the transformed bacterial solution was spread on an LB plate containing 100 mg/L ampicillin and 25 mg/L chloramphenicol, as well as 1% glucose, and cultured at 30°C. The transformants were picked for colony PCR identification to obtain the correct first step homologous recombination strain.
- the steps of the second homologous recombination were the same as those for knocking out the wcaj gene.
- the correct clone that underwent the second homologous recombination was obtained by sequencing and further cultured at 37°C to lose the pCAGO plasmid, thereby obtaining the strain TKYW2-2map T131G , which was named TKYW3.
- the plasmid pTrc99a-futC-manC described in patent document CN112501106A was used as a template (the nucleotide sequence of the P trc promoter involved in the construction of the plasmid pTrc99a-futC-manC is shown in SEQ ID NO: 4; the nucleotide sequence of the arabinose-inducible promoter P ara promoter is shown in SEQ ID NO: 18; the nucleotide sequence of the mannose-1-phosphate guanine transferase encoding gene manC is shown in SEQ ID NO: 17; the nucleotide sequence of the 2'-fucosyllactose synthase encoding gene futC is shown in SEQ ID NO: 16), and PCR amplification was performed using Darac-F and Darac-R in Table 5 as primers.
- the seamless cloning enzyme pEASY-Uni Seamless Cloning and Assembly Kit, Beijing Quanshijin Biotechnology Co., Ltd.
- Escherichia coli JM109 competent cells cultured on LB plates containing 100 mg/L ampicillin, and the transformants were picked for sequencing verification to obtain the correct recombinant plasmid, named plasmid pTrc99a-P trc -futC-manC, whose nucleotide sequence is shown in SEQ ID NO: 19.
- the plasmid pTrc99a-P trc -futC-manC in Example 4 was constructed by overexpressing the transcriptional regulatory factor genes rcsA (nucleotide sequence as shown in SEQ ID NO: 20) and rcsB (nucleotide sequence as shown in SEQ ID NO: 21) of Escherichia coli MG1655 using the constitutive promoter P J23116 .
- the sequence of the promoter P J23116 is: GTTGACAGCTAGCTCAGTCCTAGGGACTATGCTAGCTAC (http://parts.igem.org/Part:BBa_J23100).
- Plasmid construction process Using plasmid pTrc99a-P trc -futC-manC as a template, PCR amplification was performed using amp-f and trc-r in Table 6 as primers to obtain linear vector fragments containing futC and manC genes. Using the genome of Escherichia coli MG1655 (GeneBank accession NO. NC_000913) as a template, PCR amplification was performed using csAB-F and csA-R as primers, and csB-F and csAB-R as primers to obtain fragments containing the transcriptional regulatory factor rcsA gene and fragments containing the transcriptional regulatory factor rcsB gene, respectively.
- the above three PCR products namely, the vector fragments containing futC and manC, the fragment with rcsA, and the fragment with rcsB, were purified and recovered, connected using seamless cloning enzyme, transformed into E. coli JM109 competent cells, cultured on LB plates containing 100 mg/L ampicillin, and the transformants were picked for sequencing verification to obtain the correct recombinant plasmid pTrc99a-P trc -futC-manC-P J23116 -rcsA-rcsB.
- the plasmid pTrc99a-P trc -futC-manC was introduced into TKYW1 by electroporation to construct 2'-fucosylated lactone
- the sugar-producing strain TKYW1 (pTrc99a-P trc -futC-manC); the plasmids pTrc99a-P trc -futC-manC and pTrc99a-P trc -futC-manC-P J23116 -rcsA-rcsB were introduced into TKYW2-2 and TKYW3, respectively, to construct the 2'-fucosyllactose-producing strains TKYW2-2 (pTrc99a-P trc -futC-manC) and TKYW3 (pTrc99a-P trc -futC-manC), TKYW2-2 (pTr
- the fermentation production level of the above strains was tested using the following culture medium: LB culture medium: NaCl 10 g/L, yeast powder 5 g/L, peptone 10 g/L, pH 7.0. Fermentation medium: KH2PO4 3g /L, yeast powder 8g/L, ( NH4 ) 2SO4 4g /L, citric acid 1.7g/L, MgSO4 ⁇ 7H2O 2g/L, thiamine 10mg/L, glycerol 10g/L, lactose 5g/L, 1ml/L trace elements ( FeCl3 ⁇ 6H2O 25g/L, MnCl2 ⁇ 4H2O 9.8g/ L , CoCl2 ⁇ 6H2O 1.6g/L, CuCl2 ⁇ H2O 1g /L, H3BO3 1.9g/L, ZnCl2 2.6g/L, Na2MoO4 ⁇ 2H2O 1.1g/ L , Na2Se
- the fermentation test process is:
- strain TKYW2-2 (pTrc99a-P trc -futC-manC) overexpressing setA can improve the yield compared with TKYW1 (pTrc99a-P trc -futC-manC).
- strain TKYW2-2 (pTrc99a-P trc -futC-manC) as the control
- strain TKYW2-2 (pTrc99a-P trc -futC-manC-P J23116 -rcsA-rcsB) with overexpression of rcsA and rcsB
- TKYW3 (pTrc99a-P trc -futC-manC) with the introduction of Map Ile44Ser point mutation has a better effect on improving the strain level, with an increase of 48.03%
- the strain TKYW3 (pTrc99a-P trc -futC-manC-P J23116 -rcsA-rcsB) with overexpression of
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Abstract
Provided are an engineered strain for producing 2'-fucosyllactose, a construction method, and use. By means of multi-copying and over-expression of transcription regulatory factor coding genes rcsA and rcsB on plasmids, plus the in-situ over-expression of a coding gene setA of a sugar efflux transporter A and/or a point mutation of a coding gene map of methionine aminopeptidase, the provided engineered strain is beneficial to improving the fermentation yield of 2'-fucosyllactose. Further, wcaG, gmd, lacY, manA, and manB of the genetically engineered strain are subjected to genome overexpression, lacZ, wcaj, and nudd are knocked out, and futC and manC genes are multi-copied and over-expressed on plasmids, which further promote the fermentation yield of 2'-fucosyllactose.
Description
本发明属于基因工程技术领域,具体涉及一种产2'-岩藻糖基乳糖的工程菌株及构建方法和应用。The invention belongs to the technical field of genetic engineering, and specifically relates to an engineering strain producing 2'-fucosyllactose, a construction method and an application thereof.
母乳寡糖(Human milk oligosaccharides,HMOs)是母乳中的重要成分之一。此类寡糖对新生儿健康有诸多有益作用,因而受到持续且广泛地关注。相对于化学合成法和酶法而言,发酵法生产的宿主菌株易于获得、安全性高,且成本低。因此,业内已经使用工程微生物研究了多种母乳寡糖的大规模生产方法。此外,分子生物学技术和代谢工程的发展也促进了母乳寡糖生产技术的进步。2'-岩藻糖基乳糖(2'-fucosyllactose,2'-FL)、3-岩藻糖基乳糖、乳-N-四糖、乳-N-新四糖、3'-唾液乳糖、6'-唾液乳糖和一些结构复杂的岩藻糖基化母乳寡糖已经通过工程菌进行了发酵生产。其中对2'-岩藻糖基乳糖的发酵研究最为广泛。Human milk oligosaccharides (HMOs) are one of the important components of breast milk. Such oligosaccharides have many beneficial effects on the health of newborns, and therefore have received sustained and extensive attention. Compared with chemical synthesis and enzymatic methods, host strains produced by fermentation methods are easy to obtain, highly safe, and low in cost. Therefore, the industry has used engineered microorganisms to study the large-scale production methods of various human milk oligosaccharides. In addition, the development of molecular biology technology and metabolic engineering has also promoted the progress of human milk oligosaccharide production technology. 2'-fucosyllactose (2'-FL), 3-fucosyllactose, lacto-N-tetraose, lacto-N-neotetraose, 3'-sialyllactose, 6'-sialyllactose and some complex fucosylated human milk oligosaccharides have been fermented by engineered bacteria. Among them, the fermentation of 2'-fucosyllactose has been the most extensively studied.
Lu等(Lu M,et al.Engineered Microbial Routes for Human Milk Oligosaccharides Synthesis[J].ACS Synthetic Biology,2021.)对近年来母乳寡糖尤其是2'-岩藻糖基乳糖发酵工艺及菌株构建相关研究的最新进展进行了详细综述,并对2'-岩藻糖基乳糖生物合成涉及的从头合成途径和补救途径等关键酶和调节因素进行了汇总。2'-岩藻糖基乳糖生物合成中,GDP-岩藻糖合成酶编码基因wcaG、GDP-甘露糖-4,6-脱水酶编码基因gmd、β-半乳糖苷透性酶编码基因lacY、磷酸甘露糖异构酶编码基因manA、磷酸甘露糖变位酶编码基因manB、UDP-葡萄糖脂质载体转移酶编码基因wcaj、2'-岩藻糖基乳糖合成酶编码基因futC、甘露糖-1-磷酸鸟嘌呤转移酶编码基因manC等在酶促步骤中的作用极为关键。糖外排转运体则有利于降低胞内2'-岩藻糖基乳糖浓度,促进产物外排。转录调控因子基因rcsA和rcsB可对manA、manB、manC、wcaG、gmd等进行正调控。Lu et al. (Lu M, et al. Engineered Microbial Routes for Human Milk Oligosaccharides Synthesis [J]. ACS Synthetic Biology, 2021.) reviewed in detail the latest progress in the research on human milk oligosaccharides, especially 2'-fucosyllactose fermentation technology and strain construction in recent years, and summarized the key enzymes and regulatory factors such as the de novo synthesis pathway and salvage pathway involved in the biosynthesis of 2'-fucosyllactose. In the biosynthesis of 2'-fucosyllactose, the GDP-fucosyllactase encoding gene wcaG, GDP-mannose-4,6-dehydratase encoding gene gmd, β-galactosidase encoding gene lacY, phosphomannose isomerase encoding gene manA, phosphomannose mutase encoding gene manB, UDP-glucose lipid carrier transferase encoding gene wcaj, 2'-fucosyllactose synthase encoding gene futC, mannose-1-phosphate guanine transferase encoding gene manC, etc. play a critical role in the enzymatic step. Sugar efflux transporters are beneficial to reduce the intracellular 2'-fucosyllactose concentration and promote product efflux. Transcriptional regulatory factor genes rcsA and rcsB can positively regulate manA, manB, manC, wcaG, gmd, etc.
GDP-L-岩藻糖是合成岩藻糖基化母乳寡糖的关键前体,可通过从头合成途径和补救途径合成。从头途径通常被用作GDP-L-岩藻糖合成的首选途径。参与可拉酸生物合成的lon和/或wcaj基因的失活,和/或转录调控因子基因rcsA的过表达,可以增加细胞内GDP-L-岩藻糖的供应(Drouillard S,et al.Large-scale synthesis of H-antigen oligosaccharides by expressingHelicobacter pylorialpha1,2-fucosyltransferase in metabolically engineeredEscherichia colicells[J].Angewandte Chemie,2010,118(11):1778-1780.)。Ni等(Ni ZJ,et al.Multi-Path
Optimization for Efficient Production of 2′-Fucosyllactosein an EngineeredEscherichia coliC41(DE3)Derivative[J].Frontiers inBioengineering and Biotechnology,2020,8.)使用lacZ突变体大肠杆菌C41(DE3)构建了2'-岩藻糖基乳糖生产用菌株,删除了参与前体GDP-L-岩藻糖和GDP-甘露糖降解的染色体基因wcaJ、nudD和nudK,发现rcsA和rcsB更有利于GDP-L-岩藻糖的形成,从而促进2'-岩藻糖基乳糖的产生。GDP-L-fucose is a key precursor for the synthesis of fucosylated human milk oligosaccharides and can be synthesized through the de novo synthesis pathway and the salvage pathway. The de novo pathway is generally used as the preferred pathway for the synthesis of GDP-L-fucose. Inactivation of the lon and/or wcaj genes involved in the biosynthesis of colanic acid, and/or overexpression of the transcriptional regulatory factor gene rcsA, can increase the supply of GDP-L-fucose in cells (Drouillard S, et al. Large-scale synthesis of H-antigen oligosaccharides by expressing Helicobacter pylorialpha1,2-fucosyltransferase in metabolically engineered Escherichia coli cells [J]. Angewandte Chemie, 2010, 118 (11): 1778-1780.). Ni et al. (Ni ZJ, et al. Multi-Path Optimization for Efficient Production of 2′-Fucosyllactose in an Engineered Escherichia coli C41 (DE3) Derivative [J]. Frontiers in Bioengineering and Biotechnology, 2020, 8.) A strain for producing 2'-fucosyllactose was constructed using the lacZ mutant Escherichia coli C41 (DE3). The chromosomal genes wcaJ, nudD and nudK involved in the degradation of precursors GDP-L-fucose and GDP-mannose were deleted. It was found that rcsA and rcsB were more conducive to the formation of GDP-L-fucose, thereby promoting the production of 2'-fucosyllactose.
然而,由于代谢模式和调控路径的复杂性和不确定性,对不同酶或转运体编码基因的编辑尤其是对多种酶或转运体编码基因的组合编辑,对2'-岩藻糖基乳糖产率可能造成的影响是难以预期的。因此,仍需要创造性劳动,对工程菌进行不断改良,以提高2'-岩藻糖基乳糖的发酵产率。However, due to the complexity and uncertainty of metabolic patterns and regulatory pathways, the editing of genes encoding different enzymes or transporters, especially the combined editing of multiple enzyme or transporter encoding genes, may have an unpredictable effect on the yield of 2'-fucosyllactose. Therefore, creative work is still needed to continuously improve the engineered bacteria to increase the fermentation yield of 2'-fucosyllactose.
发明内容Summary of the invention
为了解决上述技术问题,本发明采用基因编辑技术,对大肠杆菌转录调控因子基因等进行基因编辑,获得了一种可提高2'-岩藻糖基乳糖的大肠杆菌工程菌。In order to solve the above technical problems, the present invention adopts gene editing technology to edit the gene of Escherichia coli transcriptional regulatory factor, etc., and obtains an engineered Escherichia coli bacteria that can increase 2'-fucosyllactose.
本发明的技术方案之一,提供了一种生产2'-岩藻糖基乳糖的工程菌株,该工程菌株的出发菌株为大肠杆菌。该工程菌株在质粒上过表达转录调控因子基因rcsA和rcsB以提高2'-岩藻糖基乳糖发酵产率。为进一步提高2'-岩藻糖基乳糖发酵产率,还可以对该工程菌株的糖外排转运体A编码基因setA和/或甲硫氨酸氨肽酶编码基因map进行编辑,使工程菌株过表达糖外排转运体A编码基因setA和/或表达一种甲硫氨酸氨肽酶突变体。其中,所述甲硫氨酸氨肽酶突变体氨基酸序列对应于SEQ ID NO:24所示的野生型甲硫氨酸氨肽酶(Map)氨基酸序列的第44位氨基酸位点具有突变:I>S,且所述甲硫氨酸氨肽酶突变体与SEQ ID NO:24所示的野生型甲硫氨酸氨肽酶氨基酸序列的同源性>90%。One of the technical solutions of the present invention provides an engineered strain for producing 2'-fucosyllactose, wherein the starting strain of the engineered strain is Escherichia coli. The engineered strain overexpresses the transcriptional regulatory factor genes rcsA and rcsB on the plasmid to increase the fermentation yield of 2'-fucosyllactose. In order to further increase the fermentation yield of 2'-fucosyllactose, the sugar efflux transporter A encoding gene setA and/or the methionine aminopeptidase encoding gene map of the engineered strain can also be edited so that the engineered strain overexpresses the sugar efflux transporter A encoding gene setA and/or expresses a methionine aminopeptidase mutant. Wherein, the amino acid sequence of the methionine aminopeptidase mutant corresponds to the 44th amino acid position of the wild-type methionine aminopeptidase (Map) amino acid sequence shown in SEQ ID NO: 24, and has a mutation: I>S, and the homology of the methionine aminopeptidase mutant to the wild-type methionine aminopeptidase amino acid sequence shown in SEQ ID NO: 24 is >90%.
进一步地,所述工程菌株过表达糖外排转运体A编码基因setA,且表达前述甲硫氨酸氨肽酶突变体;所述甲硫氨酸氨肽酶突变体氨基酸序列对应于SEQ ID NO:24所示的野生型甲硫氨酸氨肽酶(Map)氨基酸序列的第44位氨基酸位点具有突变:I>S,且所述甲硫氨酸氨肽酶突变体与SEQ ID NO:24所示的野生型甲硫氨酸氨肽酶氨基酸序列的同源性>90%。Furthermore, the engineered strain overexpresses the sugar efflux transporter A encoding gene setA, and expresses the aforementioned methionine aminopeptidase mutant; the methionine aminopeptidase mutant amino acid sequence corresponds to the 44th amino acid position of the wild-type methionine aminopeptidase (Map) amino acid sequence shown in SEQ ID NO: 24, and has a mutation: I>S, and the methionine aminopeptidase mutant has a homology of >90% with the wild-type methionine aminopeptidase amino acid sequence shown in SEQ ID NO: 24.
再进一步地,所述工程菌株原位过表达糖外排转运体A编码基因setA,且表达前述甲硫氨酸氨肽酶突变体;所述甲硫氨酸氨肽酶突变体氨基酸序列对应于SEQ ID NO:24所示的野生型甲硫氨酸氨肽酶(Map)氨基酸序列的第44位氨基酸位点具有突变:I>S,且所述甲硫氨酸氨肽酶突变体与SEQ ID NO:24所示的野生型甲硫氨酸氨肽酶氨基酸序列的同源性>90%。Furthermore, the engineered strain in situ overexpresses the sugar efflux transporter A encoding gene setA, and expresses the aforementioned methionine aminopeptidase mutant; the methionine aminopeptidase mutant amino acid sequence corresponds to the 44th amino acid position of the wild-type methionine aminopeptidase (Map) amino acid sequence shown in SEQ ID NO: 24, and has a mutation: I>S, and the methionine aminopeptidase mutant has a homology of >90% with the wild-type methionine aminopeptidase amino acid sequence shown in SEQ ID NO: 24.
在利用原核细胞等细胞体系发酵生产特定物质时,出于提高目的物质产率的目的,往
往需要利用基因工程技术对相关基因的表达水平进行上调。使目的基因表达量明显提高的技术,称为基因过表达,包括原位过表达、质粒过表达等。其中质粒过表达是在质粒上进行基因过表达,即使用具有不同转录或翻译强度的表达调控元件,离位(ex situ)构建质粒文库,并将质粒转化进入微生物细胞内。伴随质粒在细胞质内的自我复制,可快速实现目的基因的表达。而原位过表达或称为染色体原位过表达,是本领域约定俗称的术语,是指在原位(in situ)进行过表达,即通过分子生物学手段,比如启动子、核糖体结合位点及转录调控因子改造或密码子优化等,对位于染色体原位(in situ)的目的基因进行调控,提高基因转录翻译水平。When using prokaryotic cells or other cell systems to ferment and produce specific substances, in order to increase the yield of the target substance, In the past, it was necessary to use genetic engineering technology to increase the expression level of related genes. The technology that significantly improves the expression amount of the target gene is called gene overexpression, including in situ overexpression, plasmid overexpression, etc. Among them, plasmid overexpression is gene overexpression on plasmids, that is, using expression control elements with different transcription or translation strengths, constructing a plasmid library ex situ, and transforming the plasmid into microbial cells. Accompanying the self-replication of the plasmid in the cytoplasm, the expression of the target gene can be quickly achieved. In situ overexpression or chromosome in situ overexpression is a commonly used term in the art, which refers to overexpression in situ, that is, by molecular biological means, such as promoters, ribosome binding sites and transcriptional regulatory factors, or codon optimization, etc., the target gene located in the chromosome in situ is regulated to improve the level of gene transcription and translation.
用于基因过表达(包括原位过表达、质粒过表达)的额外插入的启动子可以是组成型启动子和/或诱导型启动子。毫无疑问,此处所述的组成型启动子、诱导型启动子是指适用于原核表达系统的启动子,尤其是适用于大肠杆菌表达系统的启动子,包括天然启动子及人工构建的启动子。组成型启动子,例如PJ23102、PJ23104、PJ23105、PJ23108、PJ23100、PJ23110、PJ23111、PJ23113、PJ23116、PJ23119、P637、P699等已在大肠杆菌基因编辑领域得到应用。这些组成型启动子及诱导型启动子均可用于rcsA、rcsB、setA的过表达。The additionally inserted promoter for gene overexpression (including in situ overexpression and plasmid overexpression) can be a constitutive promoter and/or an inducible promoter. Undoubtedly, the constitutive promoter and inducible promoter described herein refer to promoters suitable for prokaryotic expression systems, especially promoters suitable for Escherichia coli expression systems, including natural promoters and artificially constructed promoters. Constitutive promoters, such as P J23102 , P J23104 , P J23105 , P J23108 , P J23100 , P J23110 , P J23111, P J23113 , P J23116 , P J23119 , P 637 , P 699 , etc., have been used in the field of Escherichia coli gene editing. These constitutive promoters and inducible promoters can be used for overexpression of rcsA, rcsB, and setA .
对于setA的原位过表达,可通过插入额外的启动子提高setA的染色体原位表达水平,通过本领域技术人员比较容易想到的其它方式提高原位表达水平,比如改造setA基因前面的小分子调控RNA基因sgrS的启动子活性,或者在sgrS基因前插入额外的启动子。优选地,所述setA前面插入组成型启动子进行原位过表达和/或插入氯霉素抗性基因的启动子进行原位过表达。进一步优选地,所述氯霉素抗性基因的启动子的核苷酸序列如SEQ ID NO:23所示。For in situ overexpression of setA, the in situ expression level of the chromosome of setA can be increased by inserting an additional promoter, and the in situ expression level can be increased by other methods that are easy for a person skilled in the art to think of, such as modifying the promoter activity of the small molecule regulatory RNA gene sgrS in front of the setA gene, or inserting an additional promoter in front of the sgrS gene. Preferably, a constitutive promoter is inserted in front of setA for in situ overexpression and/or a promoter of a chloramphenicol resistance gene is inserted for in situ overexpression. Further preferably, the nucleotide sequence of the promoter of the chloramphenicol resistance gene is as shown in SEQ ID NO: 23.
进一步优选地,所用的组成型启动子选自PJ23108、PJ23110、PJ23116、PJ23119中的任一种。PJ23108、PJ23110、PJ23116、PJ23119也可用于rcsA、rcsB的过表达。More preferably, the constitutive promoter used is selected from any one of PJ23108 , PJ23110 , PJ23116 , and PJ23119 . PJ23108 , PJ23110 , PJ23116 , and PJ23119 can also be used for overexpression of rcsA and rcsB.
进一步优选地,所述甲硫氨酸氨肽酶突变体的氨基酸序列如SEQ ID NO:15所示。SEQ ID NO:15所示的甲硫氨酸氨肽酶突变体相对于前述野生型甲硫氨酸氨肽酶仅第44位氨基酸位点由异亮氨酸突变为丝氨酸。经验证,SEQ ID NO:15所示的甲硫氨酸氨肽酶突变体有利于提高2'-岩藻糖基乳糖的发酵产率。Further preferably, the amino acid sequence of the methionine aminopeptidase mutant is shown in SEQ ID NO: 15. The methionine aminopeptidase mutant shown in SEQ ID NO: 15 has only the 44th amino acid position mutated from isoleucine to serine relative to the aforementioned wild-type methionine aminopeptidase. It has been verified that the methionine aminopeptidase mutant shown in SEQ ID NO: 15 is beneficial to improving the fermentation yield of 2'-fucosyllactose.
由于密码子的兼并性,一种氨基酸序列可以被无限多种不同的核酸序列翻译表达出来。鉴于此,本发明进一步提供了一种可在细胞内表达SEQ ID NO:15所示的甲硫氨酸氨肽酶突变体的编码基因,所述编码基因至少包含SEQID NO:22所示的核苷酸片段。可通过对前述
野生型甲硫氨酸氨肽酶编码基因的定点突变,并将突变的编码基因导入基因工程菌内,使基因工程菌可表达SEQ ID NO:15所示的甲硫氨酸氨肽酶突变体。可采用质粒转化法等方法将目的基因导入基因工程菌。因此,前述工程菌株的基因组可以包含SEQID NO:22所示的核苷酸片段或编码相同氨基酸序列的核苷酸序列片段,以表达SEQ ID NO:15所示的甲硫氨酸氨肽酶突变体。Due to the compatibility of codons, an amino acid sequence can be translated and expressed by an infinite number of different nucleic acid sequences. In view of this, the present invention further provides a gene encoding a methionine aminopeptidase mutant shown in SEQ ID NO: 15 that can be expressed in cells, wherein the gene encoding at least comprises a nucleotide fragment shown in SEQ ID NO: 22. Site-directed mutagenesis of a wild-type methionine aminopeptidase encoding gene, and introducing the mutated encoding gene into a genetically engineered bacterium, so that the genetically engineered bacterium can express the methionine aminopeptidase mutant shown in SEQ ID NO: 15. The target gene can be introduced into the genetically engineered bacterium by a plasmid transformation method or the like. Therefore, the genome of the aforementioned engineered strain can contain a nucleotide fragment shown in SEQ ID NO: 22 or a nucleotide sequence fragment encoding the same amino acid sequence, so as to express the methionine aminopeptidase mutant shown in SEQ ID NO: 15.
对于rcsA和rcsB,二者均可采用多拷贝过表达。For rcsA and rcsB, multiple copies of both can be overexpressed.
进一步地,前述rcsA的核苷酸序列如SEQ ID NO:20所示;前述rcsB的核苷酸序列如SEQ ID NO:21所示;前述setA的核苷酸序列如SEQ ID NO:14所示。Furthermore, the nucleotide sequence of the aforementioned rcsA is shown as SEQ ID NO: 20; the nucleotide sequence of the aforementioned rcsB is shown as SEQ ID NO: 21; and the nucleotide sequence of the aforementioned setA is shown as SEQ ID NO: 14.
进一步地,前述出发菌株选自大肠杆菌K12 MG1655、大肠杆菌BL21(DE3)、大肠杆菌JM109、大肠杆菌W3110、大肠杆菌BW25113中的任一种。上述菌株已得到大量应用,大肠杆菌K12MG1655(Escherichia colistrain K12 MG1655)是生物学中最著名和研究最充分的生物体之一。其中大肠杆菌K12 MG1655在美国模式培养集存库已有保藏(保藏编号ATCC53103、ATCC 47076、ATCC 700926);大肠杆菌BL21(DE3)在BCCM genecorner已有保藏(保藏编号LMBP 1455);大肠杆菌JM109在美国模式培养集存库已有保藏(保藏编号ATCC68635、ATCC68868);大肠杆菌W3110大肠杆菌遗传学库存中心(Coli Genetics Stock Center)已有保藏(保藏编号CGSC#:4474)大肠杆菌BW25113在大肠杆菌遗传学库存中心(Coli GeneticsStock Center)已有保藏(保藏编号CGSC#7636)。作为本领域技术人员常用的出发菌株,本领域技术人员有能力获知上述菌株的来源和购买渠道。Furthermore, the starting strain is selected from any one of Escherichia coli K12 MG1655, Escherichia coli BL21 (DE3), Escherichia coli JM109, Escherichia coli W3110, and Escherichia coli BW25113. The above strains have been widely used, and Escherichia coli K12 MG1655 (Escherichia colistrain K12 MG1655) is one of the most famous and well-studied organisms in biology. Among them, E. coli K12 MG1655 has been deposited in the American Type Culture Collection (deposit number ATCC53103, ATCC 47076, ATCC 700926); E. coli BL21 (DE3) has been deposited in BCCM genecorner (deposit number LMBP 1455); E. coli JM109 has been deposited in the American Type Culture Collection (deposit number ATCC68635, ATCC68868); E. coli W3110 has been deposited in the Coli Genetics Stock Center (deposit number CGSC#:4474) and E. coli BW25113 has been deposited in the Coli Genetics Stock Center (deposit number CGSC#7636). As the starting strains commonly used by technicians in the field, those skilled in the art are capable of knowing the sources and purchase channels of the above strains.
为进一步提高2'-岩藻糖基乳糖发酵产率,还可以对工程菌株2'-岩藻糖基乳糖从头合成途径、补救合成途径相关酶及转运体的编码基因、乳糖lac操纵子序列等进行基因编辑。优选地,为进一步提高2'-岩藻糖基乳糖发酵产率,可以敲除大肠杆菌基因组上以下基因的至少一种:敲除大肠杆菌基因组上以下基因的至少一种:β-半乳糖苷酶编码基因lacZ、UDP-葡萄糖脂质载体转移酶编码基因wcaj、GDP-甘露糖水解酶编码基因nudd、乳糖lac操纵子序列中的调节基因lacI、L-岩藻糖异构酶编码基因fucI、L-墨角藻糖激酶编码基因fucK、L-墨角藻糖-1-磷酸醛缩酶编码基因fucA;和/或过表达或插入以下基因的至少一种:GDP-岩藻糖合成酶编码基因wcaG、GDP-甘露糖-4,6-脱水酶编码基因gmd、β-半乳糖苷透性酶编码基因lacY、磷酸甘露糖异构酶编码基因manA、磷酸甘露糖变位酶编码基因manB、甘露糖-1-磷酸鸟嘌呤转移酶编码基因manC、D-阿拉伯糖异构酶编码基因ara A、L-鼠李糖异构酶编码基因rhaA、2'-岩藻糖基乳糖合成酶编码基因futC、L-岩藻糖激酶/GDP-L-岩藻糖焦磷酸化
酶编码基因fkp。In order to further improve the fermentation yield of 2'-fucosyllactose, gene editing can also be performed on the de novo synthesis pathway of 2'-fucosyllactose in the engineered strain, the coding genes of enzymes and transporters related to the salvage synthesis pathway, the lactose lac operon sequence, etc. Preferably, in order to further improve the fermentation yield of 2'-fucosyllactose, at least one of the following genes on the Escherichia coli genome can be knocked out: knock out at least one of the following genes on the Escherichia coli genome: β-galactosidase encoding gene lacZ, UDP-glucose lipid carrier transferase encoding gene wcaj, GDP-mannose hydrolase encoding gene nudd, regulatory gene lacI in the lactose lac operon sequence, L-fucose isomerase encoding gene fucI, L-fucokinase encoding gene fuc K, L-fucose-1-phosphate aldolase encoding gene fucA; and/or overexpression or insertion of at least one of the following genes: GDP-fucose synthase encoding gene wcaG, GDP-mannose-4,6-dehydratase encoding gene gmd, β-galactosidase encoding gene lacY, phosphomannose isomerase encoding gene manA, phosphomannose mutase encoding gene manB, mannose-1-phosphate guanyl transferase encoding gene manC, D-arabinose isomerase encoding gene ara A, L-rhamnose isomerase encoding gene rhaA, 2'-fucosyllactose synthase encoding gene futC, L-fucokinase/GDP-L-fucose pyrophosphorylation gene Enzyme encoding gene fkp.
具体而言,在一个优选的方案中,所述工程菌株所述基因工程菌包括下述基因编辑:敲除大肠杆菌基因组上的β-半乳糖苷酶编码基因lacZ;Specifically, in a preferred embodiment, the engineered strain and the genetically engineered bacteria include the following gene editing: knocking out the β-galactosidase encoding gene lacZ on the Escherichia coli genome;
在大肠杆菌基因组上插入GDP-岩藻糖合成酶编码基因wcaG;Insert the GDP-fucose synthase encoding gene wcaG into the E. coli genome;
在大肠杆菌基因组上插入GDP-甘露糖-4,6-脱水酶编码基因gmd;Insert the GDP-mannose-4,6-dehydratase encoding gene gmd into the Escherichia coli genome;
原位过表达β-半乳糖苷透性酶编码基因lacY;In situ overexpression of β-galactoside permease encoding gene lacY;
在大肠杆菌基因组上插入磷酸甘露糖异构酶编码基因manA;Insert the phosphomannose isomerase encoding gene manA into the Escherichia coli genome;
在大肠杆菌基因组上插入磷酸甘露糖变位酶编码基因manB;Inserting the phosphomannose mutase encoding gene manB into the Escherichia coli genome;
敲除大肠杆菌基因组上的UDP-葡萄糖脂质载体转移酶编码基因wcaj;Knock out the UDP-glucose lipid carrier transferase encoding gene wcaj in the Escherichia coli genome;
敲除大肠杆菌基因组上的GDP-甘露糖水解酶编码基因nudd;Knock out the GDP-mannose hydrolase encoding gene nudd in the Escherichia coli genome;
在质粒上过表达2'-岩藻糖基乳糖合成酶编码基因futC;The 2'-fucosyllactose synthase encoding gene futC was overexpressed on a plasmid;
在质粒上过表达甘露糖-1-磷酸鸟嘌呤转移酶编码基因manC。The mannose-1-phosphate guanylyltransferase encoding gene manC was overexpressed on the plasmid.
进一步地,前述lacZ的核苷酸序列如SEQ ID NO:3所示;前述wcaG的核苷酸序列如SEQ ID NO:5所示;前述gmd的核苷酸序列如SEQ ID NO:6所示;前述lacY的核苷酸序列如SEQ ID NO:7所示;前述manA的核苷酸序列如SEQ ID NO:9所示;前述manB的核苷酸序列如SEQ ID NO:10所示;前述wcaj的核苷酸序列如SEQ ID NO:11所示;前述nudd的核苷酸序列如SEQ ID NO:13所示;前述futC的核苷酸序列如SEQ ID NO:16所示;前述manC的核苷酸序列如SEQ ID NO:17所示。Further, the nucleotide sequence of the aforementioned lacZ is shown in SEQ ID NO: 3; the nucleotide sequence of the aforementioned wcaG is shown in SEQ ID NO: 5; the nucleotide sequence of the aforementioned gmd is shown in SEQ ID NO: 6; the nucleotide sequence of the aforementioned lacY is shown in SEQ ID NO: 7; the nucleotide sequence of the aforementioned manA is shown in SEQ ID NO: 9; the nucleotide sequence of the aforementioned manB is shown in SEQ ID NO: 10; the nucleotide sequence of the aforementioned wcaj is shown in SEQ ID NO: 11; the nucleotide sequence of the aforementioned nudd is shown in SEQ ID NO: 13; the nucleotide sequence of the aforementioned futC is shown in SEQ ID NO: 16; and the nucleotide sequence of the aforementioned manC is shown in SEQ ID NO: 17.
进一步地,前述wcaG、gmd、manA、manB、lacY、futC和manC使用Ptrc启动子(属于诱导型启动子)过表达;所述质粒选自pTrc99a、pSB4K5、pET28a或pET22b中的任一种;所述Ptrc启动子的核苷酸序列如SEQ ID NO:4所示。Furthermore, the aforementioned wcaG, gmd, manA, manB, lacY, futC and manC are overexpressed using the Ptrc promoter (an inducible promoter); the plasmid is selected from any one of pTrc99a, pSB4K5, pET28a or pET22b; the nucleotide sequence of the Ptrc promoter is shown in SEQ ID NO: 4.
本发明的技术方案之二,提供了前述工程菌株的构一种构建方法,以大肠杆菌K12MG1655为出发菌株,构建方法包括以下步骤(不分先后):The second technical solution of the present invention provides a construction method of the aforementioned engineering strain, using Escherichia coli K12MG1655 as the starting strain, and the construction method comprises the following steps (in no particular order):
敲除出发菌株的乳糖lac操纵子序列中的Plac启动子序列及调节基因lacI和β-半乳糖苷酶编码基因lac Z,在原β-半乳糖苷酶编码基因lac Z位点之后以Ptrc启动子过表达GDP-岩藻糖合成酶编码基因wcaG、GDP-甘露糖-4,6-脱水酶编码基因gmd和β-半乳糖苷透性酶编码基因lac Y;The P lac promoter sequence and the regulatory gene lacI and the β-galactosidase encoding gene lac Z in the lactose lac operon sequence of the starting strain were knocked out, and the GDP-fucose synthase encoding gene wcaG, the GDP-mannose-4,6-dehydratase encoding gene gmd and the β-galactosidase permease encoding gene lac Y were overexpressed with the P trc promoter behind the original β-galactosidase encoding gene lac Z site;
在出发菌株的乙醇脱氢酶编码基因adhe位点上以Ptrc启动子过表达磷酸甘露糖异构酶编码基因manA和磷酸甘露糖变位酶编码基因manB;
The phosphomannose isomerase encoding gene manA and the phosphomannose mutase encoding gene manB were overexpressed by using the P trc promoter at the alcohol dehydrogenase encoding gene adhe site of the starting strain;
敲除出发菌株的UDP-葡萄糖脂质载体转移酶编码基因wcaj和GDP-甘露糖水解酶编码基因nudd;Knock out the UDP-glucose lipid carrier transferase encoding gene wcaj and the GDP-mannose hydrolase encoding gene nudd of the starting strain;
在出发菌株的setA前面插入组成型启动子,并插入氯霉素抗性基因的启动子;Insert a constitutive promoter in front of setA of the starting strain, and insert the promoter of the chloramphenicol resistance gene;
将出发菌株的甲硫氨酸氨肽酶编码基因mab点突变为如SEQ ID NO:22所示的编码基因;在出发菌株中导入过表达甘露糖-1-磷酸鸟嘌呤转移酶编码基因manC和2'-岩藻糖基乳糖合成酶编码基因futC的质粒;优选地,通过构建含有该两基因串联的质粒,再导入出发菌株中构建重组菌株。The methionine aminopeptidase encoding gene mab of the starting strain is point mutated into the encoding gene as shown in SEQ ID NO: 22; a plasmid overexpressing the mannose-1-phosphate guanine transferase encoding gene manC and the 2'-fucosyllactose synthase encoding gene futC is introduced into the starting strain; preferably, a recombinant strain is constructed by constructing a plasmid containing the two genes in series and then introducing it into the starting strain.
前述工程菌株、突变体、编码基因及其构建涉及的基因编辑技术以及实现前述基因的原位过表达或质粒过表达常用的额外插入的启动子(如组成型启动子P406、P479、P535等;诱导表达型启动子Ptac等)是本领域技公知的,可参见彭秀玲等编著的《基因工程实验技术》(长沙:湖南科学技术出版社1998年第2版)、袁婺洲编著的《基因工程》(北京:化学工业出版社,2019年第2版)韦宇拓编著的《基因工程原理与技术》(北京:北京大学出版社,2017年第1版)、曹卫军编著的《微生物工程》(科学出版社2007年第2版)等。在此前公开的技术文献中,也有充分的公开和报道,例如但不限于以下文献:The aforementioned engineering strains, mutants, coding genes and gene editing technologies involved in their construction, as well as additionally inserted promoters commonly used to achieve in situ overexpression or plasmid overexpression of the aforementioned genes (such as constitutive promoters P406, P479, P535, etc.; inducible expression promoters Ptac, etc.) are well known in the art, and can be found in "Gene Engineering Experimental Technology" edited by Peng Xiuling et al. (Changsha: Hunan Science and Technology Press, 2nd edition, 1998), "Gene Engineering" edited by Yuan Wuzhou (Beijing: Chemical Industry Press, 2nd edition, 2019), "Principles and Techniques of Genetic Engineering" edited by Wei Yutuo (Beijing: Peking University Press, 1st edition, 2017), "Microbial Engineering" edited by Cao Weijun (Science Press, 2nd edition, 2007), etc. In the previously disclosed technical literature, there are also sufficient disclosures and reports, such as but not limited to the following documents:
(1)Chen D,et al.Development of a DNA double-strand break-free base editing tool inCorynebacterium glutamicumfor genome editing and metabolic engineering-ScienceDirect.Metabolic Engineering Communications,2020,11,e00135.(1) Chen D, et al. Development of a DNA double-strand break-free base editing tool in Corynebacterium glutamicum for genome editing and metabolic engineering - Science Direct. Metabolic Engineering Communications, 2020, 11, e00135.
(2)刘洋,等.微生物细胞工厂的代谢调控.生物工程学报,2021,37(5):1541-1563.(2) Liu Yang, et al. Metabolic regulation of microbial cell factories. Chinese Journal of Biotechnology, 2021, 37(5): 1541-1563.
(3)Liang ST,et al.Activities of constitutive promoters inEscherichia coli.Journal of Molecular Biology,1999,292(1):19-37.(3) Liang ST, et al. Activities of constitutive promoters in Escherichia coli. Journal of Molecular Biology, 1999, 292(1): 19-37.
(4)Zhou L,et al.Chromosome engineering ofEscherichia colifor constitutive production of salvianic acid A.Microbial Cell Factories,2017,16(1):84.(4) Zhou L, et al. Chromosome engineering of Escherichia coli for constitutive production of salvianic acid A. Microbial Cell Factories, 2017, 16(1): 84.
(5)Zhao,D,et al.CRISPR/Cas9-assisted gRNA-free one-step genome editing with no sequence limitations and improved targeting efficiency.Scientific Reports,2017,7(1):16624.(5) Zhao, D, et al. CRISPR/Cas9-assisted gRNA-free one-step genome editing with no sequence limitations and improved targeting efficiency. Scientific Reports, 2017, 7(1): 16624.
(6)Guo,M,et al.Using the promoters of MerR family proteins as"rheostats"to engineer whole-cell heavy metal biosensors withadjustable sensitivity[J].Journal of BiologicalEngineering,2019,13(1):1-9(PMID:31452678).(6) Guo, M, et al. Using the promoters of MerR family proteins as "rheostats" to engineer whole-cell heavy metal biosensors with adjustable sensitivity[J]. Journal of Biological Engineering, 2019, 13(1): 1-9 (PMID: 31452678).
本发明的技术方案之三,提供了前述工程菌株在发酵生产2'-岩藻糖基乳糖中的应用。The third technical solution of the present invention provides the use of the aforementioned engineered strain in the fermentation production of 2'-fucosyllactose.
优选地,所述工程菌株的发酵培养基碳源选自甘油、乳糖中的至少一种;所述工程菌
株的发酵培养基有机氮源选自酵母粉、胰蛋白胨、牛肉膏中的至少一种;发酵培养的温度为36℃~40℃;发酵培养的pH为6.8~7.8。Preferably, the carbon source of the fermentation medium of the engineered strain is selected from at least one of glycerol and lactose; The organic nitrogen source of the fermentation medium of the strain is selected from at least one of yeast powder, tryptone and beef extract; the fermentation temperature is 36° C. to 40° C.; and the pH of the fermentation is 6.8 to 7.8.
本发明的有益效果:Beneficial effects of the present invention:
本发明的发明人对大肠杆菌进行了一系列的基因编辑改良研究,发现大肠杆菌质粒上过表达转录调控因子基因rcsA和rcsB有利于提高2'-岩藻糖基乳糖的发酵产率。当进一步对大肠杆菌的setA进行原位过表达,对甲硫氨酸氨肽酶编码基因map进行点突变时2'-岩藻糖基乳糖的发酵产率可进一步提高。当在此基础上,进一步对2'-岩藻糖基乳糖的从头合成途径和补救途径以及乳糖lac操纵子序列、2'-岩藻糖基乳糖合成前体降解相关酶的编码基因进行有益基因编辑时,可达到更高的2'-岩藻糖基乳糖产率。The inventors of the present invention have conducted a series of gene editing and improvement studies on Escherichia coli and found that overexpression of transcriptional regulatory factor genes rcsA and rcsB on the Escherichia coli plasmid is beneficial to improving the fermentation yield of 2'-fucosyllactose. When setA of Escherichia coli is further overexpressed in situ and the methionine aminopeptidase encoding gene map is point mutated, the fermentation yield of 2'-fucosyllactose can be further improved. On this basis, when beneficial gene editing is further performed on the de novo synthesis pathway and salvage pathway of 2'-fucosyllactose, the lactose lac operon sequence, and the encoding genes of the enzymes related to the degradation of 2'-fucosyllactose synthesis precursors, a higher 2'-fucosyllactose yield can be achieved.
下面通过具体的实施方案叙述本发明。除非特别说明,本发明中所用的技术手段均为本领域技术人员所公知的方法。另外,实施方案应理解为说明性的,而非限制本发明的范围,本发明的实质和范围仅由权利要求书所限定。对于本领域技术人员而言,在不背离本发明实质和范围的前提下,对这些实施方案中的物料成分和用量进行的各种改变或改动也属于本发明的保护范围。The present invention is described below by specific embodiments. Unless otherwise specified, the technical means used in the present invention are methods known to those skilled in the art. In addition, the embodiments should be understood as illustrative rather than limiting the scope of the present invention, and the essence and scope of the present invention are limited only by the claims. For those skilled in the art, various changes or modifications to the material composition and dosage in these embodiments, without departing from the essence and scope of the present invention, also belong to the protection scope of the present invention.
以下实施例中引物序列的书写顺序均为5’端至3’端。The primer sequences in the following examples are written from 5' to 3' end.
实施例1构建菌株TKYW2-2Example 1 Construction of strain TKYW2-2
在专利文献CN112501106A中所述大肠杆菌W2(E.coliK12MG1655△lacIZ::Ptrc-wcaG-gmd-lacy,△adhE::Ptrc-manB-manA)的基础上,敲除基因组上的UDP-葡萄糖脂质载体转移酶编码基因wcaj和GDP-甘露糖水解酶编码基因nudd,进一步在基因组原位过表达糖流出转运蛋白基因setA,构建出菌株TKYW2-2。Based on the Escherichia coli W2 (E. coli K12MG1655△lacIZ::P trc -wcaG-gmd-lacy,△adhE::P trc -manB-manA) described in patent document CN112501106A, the UDP-glucose lipid carrier transferase encoding gene wcaj and the GDP-mannose hydrolase encoding gene nudd on the genome were knocked out, and the sugar efflux transporter gene setA was further overexpressed in situ in the genome to construct strain TKYW2-2.
在此基于专利文献CN112501106A的内容对大肠杆菌W2的构建进行简要描述,将其构建方法引入本实施例。其中CN112501106A中大肠杆菌W2是以大肠杆菌K12 MG1655为出发菌株构建,敲除出发菌株的乳糖lac操纵子序列中的Plac启动子序列及调节基因lacI和lacZ,在原lacZ位点之后以Ptrc启动子过表达wcaG、gmd和lacY得到W1菌株,进而在乙醇脱氢酶编码基因adhe位点上以Ptrc启动子过表达ManA和ManB得到W2菌株。大肠杆菌W2构建涉及的Plac启动子的核苷酸序列如SEQ ID NO:1所示;lacI的核苷酸序列如SEQ ID NO:2所示;lacZ的核苷酸序列如SEQ ID NO:3所示;Ptrc启动子的核苷酸序列如SEQ ID NO:4所示;wcaG的核苷酸序列如SEQ ID NO:5所示;gmd的核苷酸序列如SEQ ID
NO:6所示;lacY的核苷酸序列如SEQ ID NO:7所示;adhE的核苷酸序列如SEQ ID NO:8所示;manA的核苷酸序列如SEQ ID NO:9所示;manB的核苷酸序列如SEQ ID NO:10所示。Here, the construction of Escherichia coli W2 is briefly described based on the content of patent document CN112501106A, and its construction method is introduced into this embodiment. In CN112501106A, Escherichia coli W2 is constructed with Escherichia coli K12 MG1655 as the starting strain, the P lac promoter sequence and the regulatory genes lacI and lacZ in the lactose lac operon sequence of the starting strain are knocked out, and wcaG, gmd and lacY are overexpressed with the P trc promoter after the original lacZ site to obtain the W1 strain, and then ManA and ManB are overexpressed with the P trc promoter at the adhe site of the alcohol dehydrogenase encoding gene to obtain the W2 strain. The nucleotide sequence of the Plac promoter involved in the construction of Escherichia coli W2 is shown in SEQ ID NO: 1; the nucleotide sequence of lacI is shown in SEQ ID NO: 2; the nucleotide sequence of lacZ is shown in SEQ ID NO: 3; the nucleotide sequence of the Ptrc promoter is shown in SEQ ID NO: 4; the nucleotide sequence of wcaG is shown in SEQ ID NO: 5; the nucleotide sequence of gmd is shown in SEQ ID NO: The nucleotide sequence of lacY is shown in SEQ ID NO: 6; the nucleotide sequence of adhE is shown in SEQ ID NO: 8; the nucleotide sequence of manA is shown in SEQ ID NO: 9; and the nucleotide sequence of manB is shown in SEQ ID NO: 10.
构建菌株W2△wcajConstruction of strain W2Δwcaj
使用菌株W2作为出发菌株,利用CRISPR/Cas9技术敲除wcaj(核苷酸序列如SEQ ID NO:11所示)。实验中所用的CRISPR/Cas9技术参考前期的研究报道【Zhao D,et al.CRISPR/Cas9-assisted gRNA-free one-step genome editing with no sequence limitations and improved targetingefficiency.Sci Rep 7,16624】。首先,构建第一步同源重组片段,包含上下游同源臂、氯霉素抗性基因cat和通用的N20+NGG序列(TAGTCCATCGAACCGAAGTAAGG),将第一步同源重组片段通过电转化导入含有pCAGO质粒的W2菌株中,进行第一步重组,pCAGO质粒含有重组酶基因,以及cas9和gRNA基因等【Zhao D,et al.CRISPR/Cas9-assisted gRNA-free one-step genome editing with no sequencelimitations and improved targeting efficiency.Sci Rep 7,16624】。挑选正确克隆,进行第二次同源重组。挑取第二次同源重组后的正确克隆,传代丢失pCAGO质粒,从而获得敲除wcaj基因的W2△wcaj菌株。Using strain W2 as the starting strain, CRISPR/Cas9 technology was used to knock out wcaj (nucleotide sequence is shown in SEQ ID NO: 11). The CRISPR/Cas9 technology used in the experiment refers to the previous research report [Zhao D, et al. CRISPR/Cas9-assisted gRNA-free one-step genome editing with no sequence limitations and improved targeting efficiency. Sci Rep 7, 16624]. First, construct the first homologous recombination fragment, including the upstream and downstream homologous arms, the chloramphenicol resistance gene cat and the universal N20+NGG sequence (TAGTCCATCGAACCGAAGTAAGG), and introduce the first homologous recombination fragment into the W2 strain containing the pCAGO plasmid by electroporation for the first step of recombination. The pCAGO plasmid contains the recombinase gene, as well as cas9 and gRNA genes [Zhao D, et al. CRISPR/Cas9-assisted gRNA-free one-step genome editing with no sequence limitations and improved targeting efficiency. Sci Rep 7, 16624]. Select the correct clone and perform the second homologous recombination. Pick the correct clone after the second homologous recombination, pass down the pCAGO plasmid to obtain the W2△wcaj strain with the wcaj gene knocked out.
以下详细描述具体方法:The following describes the specific method in detail:
(1)第一步同源重组片段的构建。以大肠杆菌菌株E.coliK12 MG1655基因组(GeneBank accession NO.NC_000913)为模板,分别利用表1中的引物up-1和up-2,以及引物down-1和down-2,PCR扩增得到同源重组的上、下游同源臂。以实验室保存的一株带有氯霉素抗性基因cat(SEQ ID NO:12,SEQ ID NO:12为cat基因及其启动子序列)的菌株基因组为模板,利用引物cat-1和cat20-2进行PCR扩增,获得带有cat-N20序列的片段。以上、下游同源臂,带有cat-N20序列的片段,这3个片段为模板,利用引物up-1和down-2进行重叠PCR扩增,得到第一步同源重组片段。(1) Construction of the first step homologous recombination fragment. Using the genome of E. coli strain E. coli K12 MG1655 (GeneBank accession NO. NC_000913) as a template, primers up-1 and up-2, and primers down-1 and down-2 in Table 1 were used to PCR amplify the upstream and downstream homologous arms of homologous recombination. Using the genome of a strain carrying the chloramphenicol resistance gene cat (SEQ ID NO: 12, SEQ ID NO: 12 is the cat gene and its promoter sequence) preserved in the laboratory as a template, primers cat-1 and cat20-2 were used for PCR amplification to obtain a fragment with the cat-N20 sequence. Using the upper and downstream homologous arms, the fragment with the cat-N20 sequence, and these three fragments as templates, primers up-1 and down-2 were used for overlapping PCR amplification to obtain the first step homologous recombination fragment.
(2)第一步同源重组。利用常规的质粒转化法将pCAGO质粒转化到菌株W2中,获得菌株W2(pCAGO)。利用含有1%葡萄糖以及浓度为0.1mM的IPTG的LB培养基制备W2(pCAGO)感受态,利用电转化方法导入第一次同源重组片段,转化后的菌液涂布于含100mg/L氨苄青霉素和25mg/L氯霉素,以及1%葡萄糖的LB平板上,30℃培养。挑取转化子进行菌落PCR鉴定,获得正确的第一步同源重组菌株。(2) First step homologous recombination. The pCAGO plasmid was transformed into strain W2 using conventional plasmid transformation methods to obtain strain W2 (pCAGO). W2 (pCAGO) competent cells were prepared using LB medium containing 1% glucose and 0.1 mM IPTG, and the first homologous recombination fragment was introduced using electroporation. The transformed bacterial solution was spread on an LB plate containing 100 mg/L ampicillin and 25 mg/L chloramphenicol, as well as 1% glucose, and cultured at 30°C. Transformants were picked for colony PCR identification to obtain the correct first step homologous recombination strain.
(3)第二步同源重组。将第一步同源重组菌株接种到含有100mg/L氨苄青霉素、0.1
mM的IPTG以及2g/L阿拉伯糖的LB液体培养基中,在30℃培养6h以上,平板划线分离单菌落,筛选出能够在含有100mg/L氨苄青霉素的LB平板上生长,但是在含有25mg/L氯霉素的LB平板上不能够生长的克隆。测序验证发生第二次同源重组的正确克隆,进一步将其在37℃条件下培养,丢失其中的pCAGO质粒,从而获得菌株W2△wcaj。(3) Second step homologous recombination. The first step homologous recombination strain was inoculated into a medium containing 100 mg/L ampicillin, 0.1 mM IPTG and 2g/L arabinose in LB liquid medium, cultured at 30°C for more than 6h, and single colonies were separated by streaking on plates, and clones that could grow on LB plates containing 100mg/L ampicillin but could not grow on LB plates containing 25mg/L chloramphenicol were screened. Sequencing confirmed the correct clone that underwent the second homologous recombination, and further cultured it at 37°C to lose the pCAGO plasmid, thereby obtaining strain W2△wcaj.
表1敲除wcaj基因所用引物
Table 1 Primers used to knock out the wcaj gene
Table 1 Primers used to knock out the wcaj gene
2.构建菌株W2△wcaj△nudd2. Construction of strain W2△wcaj△nudd
在大肠杆菌菌株W2△wcaj的基础上,利用与上述CRISPR/Cas9技术同样的方法,敲除基因组上的nudd基因(核苷酸序列如SEQ ID NO:13所示),构建出菌株W2△wcaj△nudd,命名为ZKYW1。以下详细描述具体方法:Based on the E. coli strain W2△wcaj, the nudd gene on the genome was knocked out using the same method as the above CRISPR/Cas9 technology (nucleotide sequence as shown in SEQ ID NO: 13), and the strain W2△wcaj△nudd was constructed and named ZKYW1. The specific method is described in detail below:
(1)第一步同源重组片段的构建。以菌株E.coliK12 MG1655基因组为模板,分别利用表2中的引物对Nup-1和Nup-2,引物对Ndown-1和Ndown-2,PCR扩增得到同源重组的上、下游同源臂。以构建菌株W2△wcaj时获得的带有cat-N20序列的片段为模板,利用表2中的引物Ncat-1和Ncat20-2进行PCR扩增,获得新的带有cat-N20序列的片段。以上、下游同源臂,新的带有cat-N20序列的片段,这3个片段为模板,利用引物Nup-1和Ndown-2进行重叠PCR扩增,得到第一步同源重组片段。(1) Construction of the first step homologous recombination fragment. Using the genome of strain E. coli K12 MG1655 as a template, the primer pairs Nup-1 and Nup-2 and the primer pairs Ndown-1 and Ndown-2 in Table 2 were used to PCR amplify the upstream and downstream homologous arms of homologous recombination. Using the fragment with the cat-N20 sequence obtained when constructing strain W2△wcaj as a template, the primers Ncat-1 and Ncat20-2 in Table 2 were used for PCR amplification to obtain a new fragment with the cat-N20 sequence. Using the upper and downstream homologous arms and the new fragment with the cat-N20 sequence, these three fragments were used as templates, and overlapping PCR amplification was performed using primers Nup-1 and Ndown-2 to obtain the first step homologous recombination fragment.
(2)第一步同源重组。利用常规的质粒转化法将pCAGO质粒转化到菌株W2△wcaj中,获得菌株W2△wcaj(pCAGO)。利用含有1%葡萄糖以及浓度为0.1mM的IPTG(异丙基-β-D-硫代半乳糖苷)的LB培养基制备W2△wcaj(pCAGO)感受态,利用电转化方法导入第一次同源重组片段,转化后的菌液涂布于含100mg/L氨苄青霉素和25mg/L氯霉素,以及1%葡萄糖的LB平板上,30℃培养。挑取转化子进行菌落PCR鉴定,获得正确的第一步同源重组菌株。
(2) First step of homologous recombination. The pCAGO plasmid was transformed into strain W2△wcaj using conventional plasmid transformation methods to obtain strain W2△wcaj (pCAGO). W2△wcaj (pCAGO) competent cells were prepared using LB medium containing 1% glucose and 0.1 mM IPTG (isopropyl-β-D-thiogalactoside), and the first homologous recombination fragment was introduced using electroporation. The transformed bacterial solution was spread on an LB plate containing 100 mg/L ampicillin and 25 mg/L chloramphenicol, as well as 1% glucose, and cultured at 30°C. Transformants were picked for colony PCR identification to obtain the correct first step homologous recombination strain.
(3)第二步同源重组。与上述敲除wcaj基因时第二部同源重组的步骤相同。测序验证获得发生第二次同源重组的正确克隆,进一步将其在37℃条件下培养,丢失其中的pCAGO质粒,从而获得菌株W2△wcaj△nudd,命名为TKYW1。(3) Second step of homologous recombination. The steps of the second step of homologous recombination were the same as those for knocking out the wcaj gene. The correct clone that underwent the second homologous recombination was obtained by sequencing and further cultured at 37°C to lose the pCAGO plasmid, thereby obtaining the strain W2△wcaj△nudd, which was named TKYW1.
表2敲除nudd基因所用引物
Table 2 Primers used to knock out the nudd gene
Table 2 Primers used to knock out the nudd gene
3.构建菌株TKYW2-23. Construction of strain TKYW2-2
在菌株TKYW1的基础上,利用与上述CRISPR/Cas9技术同样的方法,在糖流出转运蛋白setA基因(核苷酸序列如SEQ ID NO:14所示)前面插入组成型启动子PJ23110(http://parts.igem.org/Part:BBa_J23100),启动子PJ23110序列为:TTTACGGCTAGCTCAGTCCTAGGTACAATGCTAGC;同时,在利用CRISPR/Cas9进行第二次重组时,保留了氯霉素抗性基因的启动子(核苷酸序列如SEQ ID NO:23所示),以实现双启动子对setA进行原位过表达,所获菌株命名为TKYW2-2。Based on strain TKYW1, the constitutive promoter P J23110 (http://parts.igem.org/Part:BBa_J23100) was inserted in front of the sugar efflux transporter setA gene (nucleotide sequence as shown in SEQ ID NO: 14) using the same method as the above-mentioned CRISPR/Cas9 technology. The sequence of the promoter P J23110 is: TTTACGGCTAGCTCAGTCCTAGGTACAATGCTAGC; at the same time, when CRISPR/Cas9 was used for the second recombination, the promoter of the chloramphenicol resistance gene (nucleotide sequence as shown in SEQ ID NO: 23) was retained to achieve in situ overexpression of setA by dual promoters. The resulting strain was named TKYW2-2.
(1)第一步同源重组片段的构建。以菌株E.coliK12 MG1655基因组为模板,分别利用表3中的引物对Sup-1和Sup-2,引物对Sdown-1和Sdown-2为引物,分别PCR扩增得到同源重组的上、下游同源臂。以构建菌株W2△wcaj时获得的带有cat-N20序列的片段为模板,利用表3中的引物Scm-1和Scm-2进行PCR扩增,获得带有cat基因序列的片段。以N20-1为上游引物,以110-2为下游引物,不使用模板,进行PCR扩增,获得带有PJ23110启动子的基因片段。以Sup-1和Sdown-2为引物,利用上述PCR扩增得到的上游同源臂、带有cat基因序列的片段、带有PJ23110启动子的基因片段、以及下游同源臂,共4个片段为模板,进行重叠PCR扩增,得到第一步同源重组用的片段。(1) The first step is to construct the homologous recombination fragment. Using the genome of strain E. coli K12 MG1655 as a template, the primer pairs Sup-1 and Sup-2 and the primer pairs Sdown-1 and Sdown-2 in Table 3 were used as primers to PCR amplify the upstream and downstream homologous arms of homologous recombination. Using the fragment with the cat-N20 sequence obtained when constructing strain W2△wcaj as a template, the primers Scm-1 and Scm-2 in Table 3 were used for PCR amplification to obtain a fragment with the cat gene sequence. Using N20-1 as the upstream primer and 110-2 as the downstream primer, PCR amplification was performed without using a template to obtain a gene fragment with the P J23110 promoter. Using Sup-1 and Sdown-2 as primers, the upstream homologous arm obtained by the above PCR amplification, the fragment with the cat gene sequence, the gene fragment with the P J23110 promoter, and the downstream homologous arm, a total of 4 fragments were used as templates for overlapping PCR amplification to obtain the fragments for the first step of homologous recombination.
表3构建在基因组上过表达setA基因的菌株所用引物
Table 3 Primers used to construct strains overexpressing the setA gene in the genome
Table 3 Primers used to construct strains overexpressing the setA gene in the genome
(2)第一步同源重组。利用常规的质粒转化法将pCAGO质粒转化到菌株TKYW1中,获得菌株TKYW1(pCAGO)。利用含有1%葡萄糖和浓度为0.1mM的IPTG的LB培养基制备TKYW1(pCAGO)感受态,利用电转化方法分别导入上述第一次同源重组用的片段,转化后的菌液分别涂布于含100mg/L氨苄青霉素和25mg/L氯霉素,以及1%葡萄糖的LB平板上,30℃培养。挑取转化子进行菌落PCR鉴定,获得正确的第一步同源重组的菌株。(2) First step of homologous recombination. The pCAGO plasmid was transformed into the strain TKYW1 using a conventional plasmid transformation method to obtain the strain TKYW1 (pCAGO). The TKYW1 (pCAGO) competent state was prepared using LB medium containing 1% glucose and 0.1 mM IPTG, and the above-mentioned fragments for the first homologous recombination were introduced respectively using the electroporation method. The transformed bacterial liquid was spread on LB plates containing 100 mg/L ampicillin and 25 mg/L chloramphenicol, as well as 1% glucose, and cultured at 30°C. The transformants were picked for colony PCR identification to obtain the correct first step homologous recombination strain.
(3)第二步同源重组。与上述敲除wcaj基因时第二部同源重组的步骤相同。测序验证获得发生第二次同源重组的正确克隆,进一步将其在37℃条件下培养,丢失其中的pCAGO质粒,从而获得带有PJ23110启动子的菌株,命名为TKYW2-2。(3) Second step of homologous recombination. The steps of the second step of homologous recombination were the same as those for knocking out the wcaj gene. The correct clone that underwent the second homologous recombination was obtained by sequencing and further cultured at 37°C to lose the pCAGO plasmid, thereby obtaining a strain with the P J23110 promoter, named TKYW2-2.
实施例2构建菌株TKYW3Example 2 Construction of strain TKYW3
大肠杆菌K12 MG1655的野生型甲硫氨酸氨肽酶氨基酸序列如SEQ ID NO:24所示。在菌株TKYW2-2的基础上,利用与上述CRISPR/Cas9技术同样的方法,对基因组上的甲硫氨酸氨肽酶基因map进行点突变,将其翻译蛋白的第44位异亮氨酸突变为丝氨酸(MapIle44Ser,氨基酸序列如SEQ ID NO:15所示),构建出的菌株命名为TKYW3。The amino acid sequence of the wild-type methionine aminopeptidase of Escherichia coli K12 MG1655 is shown in SEQ ID NO: 24. Based on the strain TKYW2-2, the methionine aminopeptidase gene map on the genome was subjected to point mutation using the same method as the above-mentioned CRISPR/Cas9 technology, and the 44th isoleucine of its translated protein was mutated to serine (Map Ile44Ser , the amino acid sequence is shown in SEQ ID NO: 15), and the constructed strain was named TKYW3.
1.第一步同源重组片段的构建1. Construction of the first homologous recombination fragment
以实验室保存的一株带有map基因点突变的MG1655突变株MG1655mapT131G(mapT131G核苷酸序列如SEQ ID NO:22所示)为模板,分别利用表4中的引物对Mup-1和Mup-2,引物对Mdown-1和Mdown-2为引物,PCR扩增得到同源重组的上、下游同源臂。以构建菌株W2△wcaj时PCR获得的带有cat-N20序列的片段为模板,利用引物Mcat-1和Mcat20-2进行PCR扩增,获得新的带有cat-N20序列的片段。以上、下游同源臂,新的带有cat-N20序列的片段,这3个片段为模板,利用引物Mup-1和Mdown-2进行重叠PCR,得到第一次同源重组片段,该片段含有map基因的点突变,即野生型map基因的第131位碱基由T变
为G。A mutant strain of MG1655map T131G (map T131G nucleotide sequence is shown in SEQ ID NO: 22) with a point mutation in the map gene preserved in the laboratory was used as a template, and the primer pair Mup-1 and Mup-2, and the primer pair Mdown-1 and Mdown-2 in Table 4 were used as primers to PCR amplify the upstream and downstream homologous arms of homologous recombination. The fragment with the cat-N20 sequence obtained by PCR when constructing strain W2△wcaj was used as a template, and PCR amplification was performed using primers Mcat-1 and Mcat20-2 to obtain a new fragment with the cat-N20 sequence. The upper and downstream homologous arms, the new fragment with the cat-N20 sequence, and these three fragments were used as templates, and overlapping PCR was performed using primers Mup-1 and Mdown-2 to obtain the first homologous recombination fragment, which contains a point mutation in the map gene, that is, the 131st base of the wild-type map gene changes from T to For G.
2.第一步同源重组2. First step: homologous recombination
利用常规的质粒转化法将pCAGO质粒转化到菌株TKYW2-2中,获得菌株TKYW2-2(pCAGO)。利用含有1%葡萄糖和浓度为0.1mM的IPTG的LB培养基制备TKYW2-2(pCAGO)感受态,利用电转化方法导入第一次同源重组片段,转化后的菌液涂布于含100mg/L氨苄青霉素和25mg/L氯霉素,以及1%葡萄糖的LB平板上,30℃培养。挑取转化子进行菌落PCR鉴定,获得正确的第一步同源重组菌株。The pCAGO plasmid was transformed into the strain TKYW2-2 using a conventional plasmid transformation method to obtain the strain TKYW2-2 (pCAGO). The TKYW2-2 (pCAGO) competent state was prepared using LB medium containing 1% glucose and 0.1 mM IPTG, and the first homologous recombination fragment was introduced using an electroporation method. The transformed bacterial solution was spread on an LB plate containing 100 mg/L ampicillin and 25 mg/L chloramphenicol, as well as 1% glucose, and cultured at 30°C. The transformants were picked for colony PCR identification to obtain the correct first step homologous recombination strain.
3.第二步同源重组3. Second step homologous recombination
与上述敲除wcaj基因时第二部同源重组的步骤相同。测序验证获得发生第二次同源重组的正确克隆,进一步将其在37℃条件下培养,丢失其中的pCAGO质粒,从而获得菌株TKYW2-2mapT131G,命名为TKYW3。The steps of the second homologous recombination were the same as those for knocking out the wcaj gene. The correct clone that underwent the second homologous recombination was obtained by sequencing and further cultured at 37°C to lose the pCAGO plasmid, thereby obtaining the strain TKYW2-2map T131G , which was named TKYW3.
表4构建map基因点突变菌株所用引物
Table 4 Primers used to construct map gene point mutation strains
Table 4 Primers used to construct map gene point mutation strains
实施例3构建质粒pTrc99a-Ptrc-futC-manCExample 3 Construction of plasmid pTrc99a-P trc -futC-manC
以专利文献CN112501106A中所述质粒pTrc99a-futC-manC为模板(质粒pTrc99a-futC-manC构建涉及的Ptrc启动子的核苷酸序列如SEQ ID NO:4所示;阿拉伯糖诱导型启动子Para启动子的核苷酸序列如SEQ ID NO:18所示;甘露糖-1-磷酸鸟嘌呤转移酶编码基因manC的核苷酸序列如SEQ ID NO:17所示;2'-岩藻糖基乳糖合成酶编码基因futC的核苷酸序列如SEQ ID NO:16所示),以表5中的Darac-F和Darac-R为引物进行PCR扩增,将PCR产物进行纯化和回收后,使用无缝克隆酶(pEASY-Uni SeamlessCloning and Assembly Kit,北京全式金生物技术有限公司)自接,转化到大肠杆菌E.coliJM109感受态细胞中,在含有100mg/L氨苄青霉素的LB平板上培养,挑取转化子测序验证,获得正确的重组质粒,命名为质粒pTrc99a-Ptrc-futC-manC,其核苷酸序列如SEQ ID NO:19所示。
The plasmid pTrc99a-futC-manC described in patent document CN112501106A was used as a template (the nucleotide sequence of the P trc promoter involved in the construction of the plasmid pTrc99a-futC-manC is shown in SEQ ID NO: 4; the nucleotide sequence of the arabinose-inducible promoter P ara promoter is shown in SEQ ID NO: 18; the nucleotide sequence of the mannose-1-phosphate guanine transferase encoding gene manC is shown in SEQ ID NO: 17; the nucleotide sequence of the 2'-fucosyllactose synthase encoding gene futC is shown in SEQ ID NO: 16), and PCR amplification was performed using Darac-F and Darac-R in Table 5 as primers. After the PCR product was purified and recovered, the seamless cloning enzyme (pEASY-Uni Seamless Cloning and Assembly Kit, Beijing Quanshijin Biotechnology Co., Ltd.), transformed into Escherichia coli JM109 competent cells, cultured on LB plates containing 100 mg/L ampicillin, and the transformants were picked for sequencing verification to obtain the correct recombinant plasmid, named plasmid pTrc99a-P trc -futC-manC, whose nucleotide sequence is shown in SEQ ID NO: 19.
表5构建质粒pTrc99a-Ptrc-futC-manC所用引物
Table 5 Primers used to construct plasmid pTrc99a-P trc -futC-manC
Table 5 Primers used to construct plasmid pTrc99a-P trc -futC-manC
实施例4质粒pTrc99a-Ptrc-futC-manC-PJ23116-rcsA-rcsB构建Example 4 Construction of plasmid pTrc99a-P trc -futC -manC -P J23116 -rcsA-rcsB
在实施例4的质粒pTrc99a-Ptrc-futC-manC上,利用组成型启动子PJ23116过表达大肠杆菌MG1655的转录调控因子基因rcsA(核苷酸序列如SEQ ID NO:20所示)和rcsB(核苷酸序列如SEQ ID NO:21)所示,构建出质粒pTrc99a-Ptrc-futC-manC-PJ23116-rcsA-rcsB。启动子PJ23116的序列为:GTTGACAGCTAGCTCAGTCCTAGGGACTATGCTAGCTAC(http://parts.igem.org/Part:BBa_J23100)。The plasmid pTrc99a-P trc -futC-manC in Example 4 was constructed by overexpressing the transcriptional regulatory factor genes rcsA (nucleotide sequence as shown in SEQ ID NO: 20) and rcsB (nucleotide sequence as shown in SEQ ID NO: 21) of Escherichia coli MG1655 using the constitutive promoter P J23116 . The sequence of the promoter P J23116 is: GTTGACAGCTAGCTCAGTCCTAGGGACTATGCTAGCTAC (http://parts.igem.org/Part:BBa_J23100).
质粒构建过程:以质粒pTrc99a-Ptrc-futC-manC为模板,以表6中的amp-f和trc-r为引物进行PCR扩增,得到含有futC和manC基因的线性载体片段。以大肠杆菌MG1655基因组(GeneBank accession NO.NC_000913)为模板,分别以csAB-F和csA-R为引物、以csB-F和csAB-R为引物,进行PCR扩增,获得分别带有转录调控因子rcsA基因的片段、带有转录调控因子rcsB基因的片段。将上述3种PCR产物,即:含有futC和manC载体片段、带有rcsA的片段、带有rcsB的片段,进行纯化和回收后,使用无缝克隆酶连接,转化到E.coliJM109感受态细胞中,在含有100mg/L氨苄青霉素的LB平板上培养,挑取转化子测序验证,获得正确的重组质粒pTrc99a-Ptrc-futC-manC-PJ23116-rcsA-rcsB。Plasmid construction process: Using plasmid pTrc99a-P trc -futC-manC as a template, PCR amplification was performed using amp-f and trc-r in Table 6 as primers to obtain linear vector fragments containing futC and manC genes. Using the genome of Escherichia coli MG1655 (GeneBank accession NO. NC_000913) as a template, PCR amplification was performed using csAB-F and csA-R as primers, and csB-F and csAB-R as primers to obtain fragments containing the transcriptional regulatory factor rcsA gene and fragments containing the transcriptional regulatory factor rcsB gene, respectively. The above three PCR products, namely, the vector fragments containing futC and manC, the fragment with rcsA, and the fragment with rcsB, were purified and recovered, connected using seamless cloning enzyme, transformed into E. coli JM109 competent cells, cultured on LB plates containing 100 mg/L ampicillin, and the transformants were picked for sequencing verification to obtain the correct recombinant plasmid pTrc99a-P trc -futC-manC-P J23116 -rcsA-rcsB.
表6构建质粒pTrc99a-Ptrc-futC-manC-PJ23116-rcsA-rcsB所用引物
Table 6 Primers used to construct plasmid pTrc99a-P trc -futC -manC -P J23116 -rcsA-rcsB
Table 6 Primers used to construct plasmid pTrc99a-P trc -futC -manC -P J23116 -rcsA-rcsB
实施例5 2'-岩藻糖基乳糖生产菌种的构建和发酵测试Example 5 Construction and fermentation test of 2'-fucosyllactose producing strain
利用电转化的方法,将质粒pTrc99a-Ptrc-futC-manC导入TKYW1,构建出2'-岩藻糖基乳
糖生产菌株TKYW1(pTrc99a-Ptrc-futC-manC);将质粒pTrc99a-Ptrc-futC-manC和pTrc99a-Ptrc-futC-manC-PJ23116-rcsA-rcsB分别导入TKYW2-2和TKYW3,分别构建出2'-岩藻糖基乳糖生产菌株TKYW2-2(pTrc99a-Ptrc-futC-manC)和TKYW3(pTrc99a-Ptrc-futC-manC),TKYW2-2(pTrc99a-Ptrc-futC-manC-PJ23116-rcsA-rcsB)和TKYW3(pTrc99a-Ptrc-futC-manC-PJ23116-rcsA-rcsB)。测试上述菌株发酵生产水平,所用培养基为:LB培养基:NaCl 10g/L,酵母粉5g/L,蛋白胨10g/L,pH为7.0。发酵培养基:KH2PO43g/L,酵母粉8g/L,(NH4)2SO44g/L,柠檬酸1.7g/L,MgSO4·7H2O 2g/L,硫胺素10mg/L,甘油10g/L,乳糖5g/L,1ml/L微量元素(FeCl3·6H2O 25g/L,MnCl2·4H2O 9.8g/L,CoCl2·6H2O 1.6g/L,CuCl2·H2O 1g/L,H3BO31.9g/L,ZnCl22.6g/L,Na2MoO4·2H2O 1.1g/L,Na2SeO31.5g/L,NiSO4·6H2O 1.5g/l),利用氨水调pH为7.2。The plasmid pTrc99a-P trc -futC-manC was introduced into TKYW1 by electroporation to construct 2'-fucosylated lactone The sugar-producing strain TKYW1 (pTrc99a-P trc -futC-manC); the plasmids pTrc99a-P trc -futC-manC and pTrc99a-P trc -futC-manC-P J23116 -rcsA-rcsB were introduced into TKYW2-2 and TKYW3, respectively, to construct the 2'-fucosyllactose-producing strains TKYW2-2 (pTrc99a-P trc -futC-manC) and TKYW3 (pTrc99a-P trc -futC-manC), TKYW2-2 (pTrc99a-P trc -futC-manC-P J23116 -rcsA-rcsB), and TKYW3 (pTrc99a-P trc -futC-manC ) -rcsA-rcsB). The fermentation production level of the above strains was tested using the following culture medium: LB culture medium: NaCl 10 g/L, yeast powder 5 g/L, peptone 10 g/L, pH 7.0. Fermentation medium: KH2PO4 3g /L, yeast powder 8g/L, ( NH4 ) 2SO4 4g /L, citric acid 1.7g/L, MgSO4·7H2O 2g/L, thiamine 10mg/L, glycerol 10g/L, lactose 5g/L, 1ml/L trace elements ( FeCl3 · 6H2O 25g/L, MnCl2·4H2O 9.8g/ L , CoCl2·6H2O 1.6g/L, CuCl2·H2O 1g /L, H3BO3 1.9g/L, ZnCl2 2.6g/L, Na2MoO4 · 2H2O 1.1g/ L , Na2SeO3 1.5g / L , NiSO4 ·6H2O 25g / L , MnCl2 ·4H2O 9.8g/L, CoCl2 · 6H2O 1.6g/L, CuCl2 · H2O 1g /L, H3BO3 1.9g /L, ZnCl2 2.6g /L 2 O 1.5 g/l), and the pH was adjusted to 7.2 with aqueous ammonia.
发酵测试过程为:The fermentation test process is:
挑取2'-岩藻糖基乳糖生产菌株单菌落,转接到含有50mg/L氨苄青霉素的LB液体培养基中,进行摇瓶培养,摇床温度为37℃、转速为220转/min,培养过夜。取10微升培养液作为种子,转接到每个孔中含有1mL发酵培养基的24深孔板中,发酵培养基中含有50mg/L氨苄青霉素以及0.1mM的IPTG,在孔板震荡培养箱中培养,温度为37℃,转速为800转/min。每个菌株平行培养3个样品。培养48h后取样0.5ml,利用超声破碎仪破碎细胞,离心收集上清,煮沸十分钟,加入等体积的乙腈,再次离心收集上清,然后利用0.22μm滤膜过滤。利用HPLC检测2'-岩藻糖基乳糖的浓度,HPLC分析所用色谱柱为Carbohydrate ES 5u 250mm×4.6mm,检测器为蒸发光检测器,流动相为70%乙腈(乙腈:水),流速为0.8mL/min,柱温设定为30℃,进样量为5μL。利用2'-岩藻糖基乳糖标准品对样品浓度进行定量。2'-岩藻糖基乳糖产量见表7。Pick a single colony of the 2'-fucosyllactose production strain, transfer it to LB liquid medium containing 50mg/L ampicillin, and culture it in a shake flask. The shaker temperature is 37°C and the speed is 220 rpm. Culture overnight. Take 10 microliters of culture solution as a seed and transfer it to a 24-deep well plate containing 1mL of fermentation medium in each well. The fermentation medium contains 50mg/L ampicillin and 0.1mM IPTG. Culture it in a well plate shaking incubator at 37°C and 800 rpm. Culture 3 samples in parallel for each strain. After 48 hours of culture, take a sample of 0.5ml, use an ultrasonic disruptor to break the cells, collect the supernatant by centrifugation, boil for ten minutes, add an equal volume of acetonitrile, collect the supernatant by centrifugation again, and then filter it with a 0.22μm filter membrane. The concentration of 2'-fucosyllactose was detected by HPLC. The column used for HPLC analysis was Carbohydrate ES 5u 250mm×4.6mm, the detector was an evaporative light detector, the mobile phase was 70% acetonitrile (acetonitrile: water), the flow rate was 0.8mL/min, the column temperature was set at 30℃, and the injection volume was 5μL. The sample concentration was quantified using 2'-fucosyllactose standards. The yield of 2'-fucosyllactose is shown in Table 7.
表7 2'-岩藻糖基乳糖生产菌株发酵测试结果
Table 7 Fermentation test results of 2'-fucosyllactose producing strains
Table 7 Fermentation test results of 2'-fucosyllactose producing strains
可以看出,与TKYW1(pTrc99a-Ptrc-futC-manC)相比,过表达setA的菌株TKYW2-2(pTrc99a-Ptrc-futC-manC)能够提高产量。以菌株TKYW2-2(pTrc99a-Ptrc-futC-manC)的2'-岩藻糖基乳糖产量作为对照,rcsA和rcsB过表达的菌株TKYW2-2(pTrc99a-Ptrc-futC-manC-PJ23116-rcsA-rcsB)能够进一步提高菌株生产2'-岩藻糖基乳糖水平,提高幅度为11.47%;引入MapIle44Ser点突变的TKYW3(pTrc99a-Ptrc-futC-manC)提高菌种水平的效果更好,提高幅度为48.03%;我们经过大量的实验发现,rcsA和rcsB过表达结合MapIle44Se突变的菌株TKYW3(pTrc99a-Ptrc-futC-manC-PJ23116-rcsA-rcsB)能够起到意想不到的效果,菌种产2'-岩藻糖基乳糖水平大幅提高,提高幅度达到121.51%,比rcsA和rcsB过表达,或MapIle44Se突变单独作用的效果,以及这两者效果简单相加(59.50%)的结果明显具有优势。It can be seen that the strain TKYW2-2 (pTrc99a-P trc -futC-manC) overexpressing setA can improve the yield compared with TKYW1 (pTrc99a-P trc -futC-manC). Taking the 2'-fucosyllactose production of strain TKYW2-2 (pTrc99a-P trc -futC-manC) as the control, the strain TKYW2-2 (pTrc99a-P trc -futC-manC-P J23116 -rcsA-rcsB) with overexpression of rcsA and rcsB can further improve the strain's 2'-fucosyllactose production level by 11.47%; TKYW3 (pTrc99a-P trc -futC-manC) with the introduction of Map Ile44Ser point mutation has a better effect on improving the strain level, with an increase of 48.03%; after a large number of experiments, we found that the strain TKYW3 (pTrc99a-P trc -futC-manC-P J23116 -rcsA-rcsB) with overexpression of rcsA and rcsB combined with Map Ile44Ser mutation -rcsA-rcsB) can have an unexpected effect, and the level of 2'-fucosyllactose produced by the strain is greatly increased, with an increase of 121.51%, which is significantly better than the effect of rcsA and rcsB overexpression, or Map Ile44Se mutation alone, and the result of the simple addition of the two effects (59.50%).
以上所述仅为本发明的较佳实施例而已,并不用以限制本发明,凡在本发明的精神和原则之内,所作的任何修改、等同替换、改进等,均应包含在本发明的保护范围之内。
The above description is only a preferred embodiment of the present invention and is not intended to limit the present invention. Any modifications, equivalent substitutions, improvements, etc. made within the spirit and principle of the present invention should be included in the protection scope of the present invention.
Claims (17)
- 一种产2'-岩藻糖基乳糖的工程菌株,所述工程菌株的出发菌株为大肠杆菌,其特征在于,所述工程菌株的基因编辑包括:在质粒上过表达转录调控因子基因rcsA和rcsB,过表达糖外排转运体A编码基因setA和/或表达一种甲硫氨酸氨肽酶突变体,所述甲硫氨酸氨肽酶突变体的氨基酸序列对应于SEQ ID NO:24所示的野生型甲硫氨酸氨肽酶氨基酸序列的第44位氨基酸位点具有突变:I>S,所述甲硫氨酸氨肽酶突变体与SEQ ID NO:24所示的野生型甲硫氨酸氨肽酶氨基酸序列的同源性>90%;且所述出发菌株为在体内能够合成2'-岩藻糖基乳糖的大肠杆菌。A 2'-fucosyllactose-producing engineered strain, wherein the starting strain of the engineered strain is Escherichia coli, and the gene editing of the engineered strain comprises: overexpressing transcriptional regulatory factor genes rcsA and rcsB on a plasmid, overexpressing the sugar efflux transporter A encoding gene setA and/or expressing a methionine aminopeptidase mutant, the amino acid sequence of the methionine aminopeptidase mutant corresponds to the 44th amino acid position of the wild-type methionine aminopeptidase amino acid sequence shown in SEQ ID NO: 24, and has a mutation: I>S, and the homology between the methionine aminopeptidase mutant and the wild-type methionine aminopeptidase amino acid sequence shown in SEQ ID NO: 24 is >90%; and the starting strain is Escherichia coli capable of synthesizing 2'-fucosyllactose in vivo.
- 根据权利要求1所述的工程菌株,其特征在于,所述工程菌株过表达糖外排转运体A编码基因setA,且表达一种甲硫氨酸氨肽酶突变体;所述甲硫氨酸氨肽酶突变体的氨基酸序列对应于SEQ ID NO:24所示的野生型甲硫氨酸氨肽酶氨基酸序列的第44位氨基酸位点具有突变:I>S,所述甲硫氨酸氨肽酶突变体与SEQ ID NO:24所示的野生型甲硫氨酸氨肽酶氨基酸序列的同源性>90%。The engineered strain according to claim 1 is characterized in that the engineered strain overexpresses the sugar efflux transporter A encoding gene setA and expresses a methionine aminopeptidase mutant; the amino acid sequence of the methionine aminopeptidase mutant corresponds to the 44th amino acid position of the wild-type methionine aminopeptidase amino acid sequence shown in SEQ ID NO: 24, and has a mutation: I>S, and the methionine aminopeptidase mutant has a homology of >90% with the wild-type methionine aminopeptidase amino acid sequence shown in SEQ ID NO: 24.
- 根据权利要求2所述的工程菌株,其特征在于,所述工程菌株原位过表达糖外排转运体A编码基因setA,所述糖外排转运体A编码基因setA前面插入组成型启动子进行原位过表达和/或插入氯霉素抗性基因的启动子进行原位过表达。The engineered strain according to claim 2 is characterized in that the engineered strain in situ overexpresses the sugar efflux transporter A encoding gene setA, and a constitutive promoter is inserted in front of the sugar efflux transporter A encoding gene setA for in situ overexpression and/or a promoter of a chloramphenicol resistance gene is inserted in front of the sugar efflux transporter A encoding gene setA for in situ overexpression.
- 根据权利要求3所述的工程菌株,其特征在于,所述氯霉素抗性基因的启动子的核苷酸序列如SEQ ID NO:23所示。The engineered strain according to claim 3 is characterized in that the nucleotide sequence of the promoter of the chloramphenicol resistance gene is as shown in SEQ ID NO: 23.
- 根据权利要求1所述的工程菌株,其特征在于,所述甲硫氨酸氨肽酶突变体的氨基酸序列如SEQ ID NO:15所示。The engineered strain according to claim 1 is characterized in that the amino acid sequence of the methionine aminopeptidase mutant is as shown in SEQ ID NO: 15.
- 根据权利要求5所述的工程菌株,其特征在于,所述工程菌株基因组的至少包含SEQ ID NO:22所示的核苷酸片段或编码相同氨基酸序列的核苷酸序列片段。The engineered strain according to claim 5 is characterized in that the genome of the engineered strain contains at least the nucleotide fragment shown in SEQ ID NO: 22 or a nucleotide sequence fragment encoding the same amino acid sequence.
- 根据权利要求1所述的工程菌株,其特征在于,所述rcsA和rcsB为多拷贝过表达。The engineered strain according to claim 1, characterized in that the rcsA and rcsB are overexpressed in multiple copies.
- 根据权利要求1所述的工程菌株,其特征在于,所述rcsA、rcsB、糖外排转运体A编码基setA采用组成型启动子进行过表达。The engineered strain according to claim 1 is characterized in that the rcsA, rcsB, and sugar efflux transporter A coding gene setA are overexpressed using a constitutive promoter.
- 根据权利要求8所述的工程菌株,其特征在于,所述组成型启动子选自PJ23102、PJ23104、PJ23105、PJ23108、PJ23100、PJ23110、PJ23111、PJ23113、PJ23116、PJ23119、P637、P699中的任一种。The engineered strain according to claim 8, characterized in that the constitutive promoter is selected from any one of P J23102 , P J23104 , P J23105 , P J23108 , P J23100 , P J23110 , P J23111 , P J23113 , P J23116 , P J23119 , P 637 , and P 699 .
- 根据权利要求1所述的工程菌株,其特征在于,所述rcsA的核苷酸序列如SEQ ID NO:20所示;所述rcsB的核苷酸序列如SEQ ID NO:21所示;所述糖外排转运体A编码基setA的核苷酸序列如SEQ ID NO:14所示。 The engineered strain according to claim 1, characterized in that the nucleotide sequence of rcsA is shown in SEQ ID NO: 20; the nucleotide sequence of rcsB is shown in SEQ ID NO: 21; and the nucleotide sequence of the sugar efflux transporter A encoding gene setA is shown in SEQ ID NO: 14.
- 根据权利要求1所述的工程菌株,其特征在于,所述出发菌株选自大肠杆菌K12 MG1655、大肠杆菌BL21(DE3)、大肠杆菌JM109、大肠杆菌W3110、大肠杆菌BW25113中的任一种。The engineered strain according to claim 1 is characterized in that the starting strain is selected from any one of Escherichia coli K12 MG1655, Escherichia coli BL21 (DE3), Escherichia coli JM109, Escherichia coli W3110, and Escherichia coli BW25113.
- 根据权利要求1所述的工程菌株,其特征在于,所述工程菌株进一步包括对2'-岩藻糖基乳糖合成途径相关酶或转运体的编码基因的基因编辑;The engineered strain according to claim 1, characterized in that the engineered strain further comprises gene editing of genes encoding enzymes or transporters related to the 2'-fucosyllactose synthesis pathway;优选地,其包括敲除大肠杆菌基因组上以下基因的至少一种:敲除大肠杆菌基因组上以下基因的至少一种:β-半乳糖苷酶编码基因lacZ、UDP-葡萄糖脂质载体转移酶编码基因wcaj、GDP-甘露糖水解酶编码基因nudd、乳糖lac操纵子序列中的调节基因lacI、L-岩藻糖异构酶编码基因fucI、L-墨角藻糖激酶编码基因fucK、L-墨角藻糖-1-磷酸醛缩酶编码基因fucA、D-阿拉伯糖异构酶编码基因ara A、L-鼠李糖异构酶编码基因rhaA;和/或其包括过表达或插入以下基因的至少一种:GDP-岩藻糖合成酶编码基因wcaG、GDP-甘露糖-4,6-脱水酶编码基因gmd、β-半乳糖苷透性酶编码基因lacY、磷酸甘露糖异构酶编码基因manA、磷酸甘露糖变位酶编码基因manB、甘露糖-1-磷酸鸟嘌呤转移酶编码基因manC、2'-岩藻糖基乳糖合成酶编码基因futC、L-岩藻糖激酶/GDP-L-岩藻糖焦磷酸化酶编码基因fkp;Preferably, it includes knocking out at least one of the following genes on the Escherichia coli genome: knocking out at least one of the following genes on the Escherichia coli genome: β-galactosidase encoding gene lacZ, UDP-glucose lipid carrier transferase encoding gene wcaj, GDP-mannose hydrolase encoding gene nudd, the regulatory gene lacI in the lactose lac operon sequence, L-fucose isomerase encoding gene fucI, L-fucokinase encoding gene fucK, L-fucose-1-phosphate aldolase encoding gene fucA, D-arabinose isomerase encoding gene ara A, L- Rhamnose isomerase encoding gene rhaA; and/or it includes overexpression or insertion of at least one of the following genes: GDP-fucose synthase encoding gene wcaG, GDP-mannose-4,6-dehydratase encoding gene gmd, β-galactosidase encoding gene lacY, phosphomannose isomerase encoding gene manA, phosphomannose mutase encoding gene manB, mannose-1-phosphate guanine transferase encoding gene manC, 2'-fucosyllactose synthase encoding gene futC, L-fucokinase/GDP-L-fucose pyrophosphorylase encoding gene fkp;更有选地,所述基因工程菌包括下述基因编辑:More preferably, the genetically engineered bacteria include the following gene editing:敲除大肠杆菌基因组上的β-半乳糖苷酶编码基因lacZ;Knock out the β-galactosidase encoding gene lacZ in the Escherichia coli genome;在大肠杆菌基因组上插入GDP-岩藻糖合成酶编码基因wcaG;Insert the GDP-fucose synthase encoding gene wcaG into the E. coli genome;在大肠杆菌基因组上插入GDP-甘露糖-4,6-脱水酶编码基因gmd;Insert the GDP-mannose-4,6-dehydratase encoding gene gmd into the Escherichia coli genome;原位过表达β-半乳糖苷透性酶编码基因lacY;In situ overexpression of β-galactoside permease encoding gene lacY;在大肠杆菌基因组上插入磷酸甘露糖异构酶编码基因manA;Insert the phosphomannose isomerase encoding gene manA into the Escherichia coli genome;在大肠杆菌基因组上插入磷酸甘露糖变位酶编码基因manB;Inserting the phosphomannose mutase encoding gene manB into the Escherichia coli genome;敲除大肠杆菌基因组上的UDP-葡萄糖脂质载体转移酶编码基因wcaj;Knock out the UDP-glucose lipid carrier transferase encoding gene wcaj in the Escherichia coli genome;敲除大肠杆菌基因组上的GDP-甘露糖水解酶编码基因nudd;Knock out the GDP-mannose hydrolase encoding gene nudd in the Escherichia coli genome;在质粒上过表达2'-岩藻糖基乳糖合成酶编码基因futC;The 2'-fucosyllactose synthase encoding gene futC was overexpressed on a plasmid;在质粒上过表达甘露糖-1-磷酸鸟嘌呤转移酶编码基因manC。The mannose-1-phosphate guanylyltransferase encoding gene manC was overexpressed on the plasmid.
- 根据权利要求12所述的工程菌株,其特征在于,所述GDP-岩藻糖合成酶编码基因wcaG、GDP-甘露糖-4,6-脱水酶编码基因gmd、磷酸甘露糖异构酶编码基因manA、磷酸甘露糖变位酶编码基因manB为单拷贝插入基因组过表达;所述甘露糖-1-磷酸鸟嘌呤转移酶编码基因manC、2'-岩藻糖基乳糖合成酶编码基因futC为多拷贝过表达。 The engineered strain according to claim 12 is characterized in that the GDP-fucose synthase encoding gene wcaG, the GDP-mannose-4,6-dehydratase encoding gene gmd, the phosphomannose isomerase encoding gene manA, and the phosphomannose mutase encoding gene manB are single-copy inserted into the genome for overexpression; the mannose-1-phosphate guanine transferase encoding gene manC and the 2'-fucosyllactose synthase encoding gene futC are multi-copy overexpression.
- 根据权利要求12所述的工程菌株,其特征在于,所述GDP-岩藻糖合成酶编码基因wcaG、GDP-甘露糖-4,6-脱水酶编码基因gmd、磷酸甘露糖异构酶编码基因manA、磷酸甘露糖变位酶编码基因manB、β-半乳糖苷透性酶编码基因lacY、2'-岩藻糖基乳糖合成酶编码基因futC和甘露糖-1-磷酸鸟嘌呤转移酶编码基因manC使用Ptrc启动子过表达;所述质粒选自pTrc99a、pSB4K5、pET28a或pET22b中的任一种;所述Ptrc启动子的核苷酸序列如SEQ ID NO:4所示。The engineering strain according to claim 12 is characterized in that the GDP-fucose synthase encoding gene wcaG, GDP-mannose-4,6-dehydratase encoding gene gmd, phosphomannose isomerase encoding gene manA, phosphomannose mutase encoding gene manB, β-galactoside permease encoding gene lacY, 2'-fucosyllactose synthase encoding gene futC and mannose-1-phosphate guanine transferase encoding gene manC are overexpressed using the Ptrc promoter; the plasmid is selected from any one of pTrc99a, pSB4K5, pET28a or pET22b; the nucleotide sequence of the Ptrc promoter is shown in SEQ ID NO: 4.
- 根据权利要12所述的工程菌株,其特征在于,所述β-半乳糖苷酶编码基因lacZ的核苷酸序列如SEQ ID NO:3所示;所述GDP-岩藻糖合成酶编码基因wcaG的核苷酸序列如SEQ ID NO:5所示;所述GDP-甘露糖-4,6-脱水酶编码基因gmd的核苷酸序列如SEQ ID NO:6所示;所述β-半乳糖苷透性酶编码基因lacY的核苷酸序列如SEQ ID NO:7所示;所述磷酸甘露糖异构酶编码基因manA的核苷酸序列如SEQ ID NO:9所示;所述磷酸甘露糖变位酶编码基因manB的核苷酸序列如SEQ ID NO:10所示;所述UDP-葡萄糖脂质载体转移酶编码基因wcaj的核苷酸序列如SEQ ID NO:11所示;所述GDP-甘露糖水解酶编码基因nudd的核苷酸序列如SEQ ID NO:13所示;所述2'-岩藻糖基乳糖合成酶编码基因futC的核苷酸序列如SEQ ID NO:16所示;所述甘露糖-1-磷酸鸟嘌呤转移酶编码基因manC的核苷酸序列如SEQ ID NO:17所示。The engineered strain according to claim 12 is characterized in that the nucleotide sequence of the β-galactosidase encoding gene lacZ is as shown in SEQ ID NO: 3; the nucleotide sequence of the GDP-fucose synthase encoding gene wcaG is as shown in SEQ ID NO: 5; the nucleotide sequence of the GDP-mannose-4,6-dehydratase encoding gene gmd is as shown in SEQ ID NO: 6; the nucleotide sequence of the β-galactoside permease encoding gene lacY is as shown in SEQ ID NO: 7; the nucleotide sequence of the phosphomannose isomerase encoding gene manA is as shown in SEQ ID NO: 9 as shown; the nucleotide sequence of the phosphomannose mutase encoding gene manB is as shown in SEQ ID NO: 10; the nucleotide sequence of the UDP-glucose lipid carrier transferase encoding gene wcaj is as shown in SEQ ID NO: 11; the nucleotide sequence of the GDP-mannose hydrolase encoding gene nudd is as shown in SEQ ID NO: 13; the nucleotide sequence of the 2'-fucosyllactose synthase encoding gene futC is as shown in SEQ ID NO: 16; the nucleotide sequence of the mannose-1-phosphate guanine transferase encoding gene manC is as shown in SEQ ID NO: 17.
- 权利要求12至15任一项所述工程菌株的构建方法,其特征在于,所述出发菌株选自大肠杆菌K12 MG1655,所述构建方法包括不分先后的以下步骤:The method for constructing an engineered strain according to any one of claims 12 to 15, characterized in that the starting strain is selected from Escherichia coli K12 MG1655, and the construction method comprises the following steps in no particular order:敲除出发菌株的乳糖lac操纵子序列中的Plac启动子序列及调节基因lacI和β-半乳糖苷酶编码基因lacZ,在原β-半乳糖苷酶编码基因lac Z位点之后以Ptrc启动子过表达GDP-岩藻糖合成酶编码基因wcaG、GDP-甘露糖-4,6-脱水酶编码基因gmd和β-半乳糖苷透性酶编码基因lac Y;The P lac promoter sequence and the regulatory gene lacI and the β-galactosidase encoding gene lacZ in the lactose lac operon sequence of the starting strain were knocked out, and the GDP-fucose synthase encoding gene wcaG, the GDP-mannose-4,6-dehydratase encoding gene gmd and the β-galactosidase permease encoding gene lac Y were overexpressed with the P trc promoter behind the original β-galactosidase encoding gene lac Z site;在出发菌株的乙醇脱氢酶编码基因adhe位点上以Ptrc启动子过表达磷酸甘露糖异构酶编码基因manA和磷酸甘露糖变位酶编码基因manB;The phosphomannose isomerase encoding gene manA and the phosphomannose mutase encoding gene manB were overexpressed by using the P trc promoter at the alcohol dehydrogenase encoding gene adhe site of the starting strain;敲除出发菌株的UDP-葡萄糖脂质载体转移酶编码基因wcaj和GDP-甘露糖水解酶编码基因nudd;Knock out the UDP-glucose lipid carrier transferase encoding gene wcaj and the GDP-mannose hydrolase encoding gene nudd of the starting strain;在出发菌株的setA前面插入组成型启动子,并插入氯霉素抗性基因的启动子;Insert a constitutive promoter in front of setA of the starting strain, and insert the promoter of the chloramphenicol resistance gene;将出发菌株的甲硫氨酸氨肽酶编码基因mab点突变为如SEQ ID NO:22所示的编码基因;在出发菌株中导入过表达甘露糖-1-磷酸鸟嘌呤转移酶编码基因manC和2'-岩藻糖基乳糖 合成酶编码基因futC的质粒;优选地,通过构建含有该两基因串联的质粒,再导入出发菌株中构建重组菌株。The methionine aminopeptidase encoding gene mab of the starting strain was point mutated into the encoding gene as shown in SEQ ID NO: 22; the overexpressed mannose-1-phosphate guanine transferase encoding gene manC and 2'-fucosyllactose were introduced into the starting strain. Preferably, the recombinant strain is constructed by constructing a plasmid containing the two genes in tandem and then introducing the plasmid into the starting strain.
- 权利要求1至15任一项所述的工程菌株或权利要求16所构建的工程菌株在发酵生产2'-岩藻糖基乳糖中的应用;优选地,所述工程菌株的发酵培养基碳源选自甘油、乳糖中的至少一种;所述工程菌株的发酵培养基有机氮源选自酵母粉、胰蛋白胨、牛肉膏中的至少一种;发酵培养的温度为36℃~40℃;发酵培养的pH为6.8~7.8。 Use of the engineered strain according to any one of claims 1 to 15 or the engineered strain constructed according to claim 16 in the fermentation production of 2'-fucosyllactose; preferably, the carbon source of the fermentation medium of the engineered strain is selected from at least one of glycerol and lactose; the organic nitrogen source of the fermentation medium of the engineered strain is selected from at least one of yeast powder, trypsin, and beef extract; the fermentation culture temperature is 36°C to 40°C; the fermentation culture pH is 6.8 to 7.8.
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