APPLICATION OF TRANSPORT CARRIER GENE WHICH IMPROVES L-TRYPTOPHAN PRODUCTION EFFICIENCY IN ESCHERICHIA COLI
20220411835 · 2022-12-29
Inventors
- Xixian Xie (Tianjin, CN)
- Bo XIONG (Tianjin, CN)
- Chunguang ZHAO (Ningxia, CN)
- Xiaowei GUO (Ningxia, CN)
- Jiaxuan MEN (Tianjin, CN)
- Aiying WEI (Ningxia, CN)
Cpc classification
C12N2310/20
CHEMISTRY; METALLURGY
C12N9/22
CHEMISTRY; METALLURGY
C12N15/70
CHEMISTRY; METALLURGY
C12N2800/80
CHEMISTRY; METALLURGY
C12N15/11
CHEMISTRY; METALLURGY
International classification
C12P13/22
CHEMISTRY; METALLURGY
C12N15/11
CHEMISTRY; METALLURGY
C12N15/70
CHEMISTRY; METALLURGY
Abstract
A transport protein coding gene, and a method for efficient production of L-tryptophan by a strain containing the gene. Specifically, by heterologous expression of ywkB gene from Bacillus subtilis on the genome of Escherichia coli, L-tryptophan production efficiency of the strain can be improved. Performing shake flask fermentation with the strain can accumulate 15.2 g/L of L-tryptophan within 24 h, which is 35% higher than a control strain.
Claims
1. A genetically engineered bacterial strain for producing L-tryptophan, wherein a bacterial host strain is modified with ywkB gene, and the obtained genetically engineered bacterial strain has the activity of producing a higher yield of L-tryptophan than the bacterial host strain. For example, the ywkB gene is from Bacillus subtilis, and the modification is to modify the yeep pseudogene locus with the ywkB gene. For example, the bacterial host strain is a strain of prokaryotic bacteria, preferably a strain of gram-negative bacteria, more preferably Escherichia coli, most preferably E. coli TRP 03.
2. The genetically engineered bacterial strain according to claim 1, wherein the ywkB gene has a nucleotide sequence encoding the following polypeptide sequence: (A) a protein comprising the amino acid sequence shown in SEQ ID NO: 2 in the sequence listing; (B) a protein which comprises the amino acid sequence obtained by performing deletion, substitution and/or addition of one or more amino acid residues on the amino acid sequence shown in SEQ ID NO: 2 in the sequence listing and still has the ability to improve the production of L-tryptophan and L-tryptophan structural analogs (such as 5-hydroxytryptophan, etc.) by the strain; (C) a protein which has at least 85%, preferably at least 90%, more preferably at least 95%, more preferably at least 96%, 97%, 98%, 99% identity with the amino acid sequence shown in SEQ ID NO: 2, derives from Bacillus subtilis and functions as a metabolite transporter.
3. The genetically engineered bacterial strain according claim 1, wherein the ywkB gene is introduced into the bacterial host strain by means of homologous recombination, expression vector or gene editing, wherein the expression vector is preferably a plasmid, for example, the gene editing means refers to introducing the gene of the amino acid sequence into the chromosome of the bacterial host strain by using the CRISPR/Cas9 method.
4. The genetically engineered bacterial strain according to claim 1, wherein the ywkB gene is under the control of a strong promoter, for example, the strong promoter is a BBa_j23101 promoter or a BBa_j23106 promoter, for example, the amino acid sequence of the BBa_j23106 promoter is shown in SEQ ID NO: 3.
5. A method for constructing a genetically engineered bacterial strain that produces L-tryptophan, wherein ywkB gene is integrated into a bacterial host strain, for example, into E. coli TRP 03 tryptophan-producing bacteria strain as a starting bacteria strain, so as to obtain genetically engineered bacterial strain having the activity of producing a higher yield of L-tryptophan than the bacterial host strain.
6. The method according to claim 5, wherein the integrating step is performed by modifying the yeep pseudogene locus with the ywkB gene, for example, the integrating is performed by means of CRISPR-Cas9 gene editing.
7. The method according to claim 6, wherein the means for CRISPR-Cas9 gene editing comprises the following steps: (1) synthesizing ywkB integrated gene fragment: constructing upstream and downstream homologous arm fragments of the yeep pseudogene, ywkB gene fragment and BBa_j23106 promoter sequence, the ywkB integrated gene fragment comprising the upstream homologous arm of the yeep gene, the downstream homologous arm of the yeep gene, the BBa j23106 promoter fragment and the ywkB gene fragment; (2) expressing the ywkB integrated gene fragment in E. coli TRP 03 using CRISPR/Cas9 technology.
8. The method according to claim 5, wherein the ywkB gene sequence is a nucleotide sequence encoding the following polypeptide sequence: (A) a protein comprising the amino acid sequence shown in SEQ ID NO: 2 in the sequence listing; (B) a protein which comprises the amino acid sequence obtained by performing deletion, substitution and/or addition of one or more amino acid residues on the amino acid sequence shown in SEQ ID NO: 2 in the sequence listing and still has the ability to improve the production of L-tryptophan and L-tryptophan structural analogs (such as 5-hydroxytryptophan, etc.) by the strain; (C) a protein which has at least 85%, preferably at least 90%, more preferably at least 95%, more preferably at least 96%, 97%, 98%, 99% identity with the amino acid sequence shown in SEQ ID NO: 2, derives from Bacillus subtilis and functions as a metabolite transporter.
9. A method for producing L-tryptophan, comprising the step of fermenting the genetically engineered bacterial strain according to claim 1 or the genetically engineered bacterial strain obtained by the method to produce L-tryptophan.
10. The method for producing L-tryptophan according to claim 9, comprising the following steps: 3) fermenting.
11. The method for producing L-tryptophan according to claim 10, further comprising the following steps: 2) preparing a seed solution; step 2) adopts shake flask seed culture: scraping a ring of seeds on the slant with an inoculating loop and inoculating into a 500 mL conical flask containing 30 mL of seed medium, sealing the conical flask with nine layers of gauze, and culturing at 37° C. and 200 rpm for 8-10 h.
12. The method for producing L-tryptophan according to claim 11, further comprising the following steps: 1) activating the bacterial strain; step 1) adopts slant culture: inoculating the bacterial strain preserved at −80° C. onto the activated slant using streak method, culturing at 37° C. for 12 h and passaged once.
13. The method for producing L-tryptophan according to claim 10, wherein step 3) adopts shake flask fermentation culture: inoculating the seed culture at the concentration of 10-15% (v/v) into a 500 mL conical flask containing fermentation medium (final volume: 30 mL), sealing the conical flask with nine layers of gauze, culturing at 37° C. and 200 r/min in a shaking table, during the fermentation, adding ammonia water to maintain pH at 7.0-7.2; adding 60% (m/v) glucose solution to maintain fermentation (with phenol red as indicator, when the color of the fermentation broth no longer changes, it is regarded as lack of glucose, adding 1-2 mL of 60% (m/v) glucose solution to make the glucose concentration in the fermentation broth the initial value of 20-40 g/L); the fermentation period lasting for 22-26 h.
Description
DESCRIPTION OF THE DRAWINGS
[0044] In
[0045]
[0046]
[0047]
DETAILED DESCRIPTION OF THE INVENTION
EXAMPLE 1: Construction of E. coli Strain TRP 05
[0048] 1. Gene Editing Method
[0049] The gene editing method adopted in the present invention refers to literature “Li Y, Lin Z, Huang C, et al. Metabolic engineering of Escherichia coli using CRISPR-Cas9 meditated genome editing. Metabolic engineering, 2015, 31:13-21.” and the maps of the two plasmids used in this method are shown in
[0050] The specific steps of this method:
[0051] 1.1 Construction of pGRB Plasmid
[0052] The purpose of constructing the plasmid pGRB is to transcribe the corresponding gRNA to form a complex with Cas9 protein, and recognize the target site of the target gene through base pairing and PAM to achieve the target DNA double-strand break. The pGRB plasmid was constructed by recombining a DNA fragment containing the target sequence with a linearized vector fragment.
[0053] 1.1.1 Design of Target Sequence
[0054] CRISPR RGEN Tools was used to design the target sequence (PAM: 5′-NGG-3′).
[0055] 1.1.2 Preparation of DNA Fragment Containing Target Sequence
[0056] The primer 5′-linearized vector end sequence (15 bp)-restriction site-target sequence (without PAM sequence)-linearized vector end sequence (15 bp)-3′ and its reverse complementary primer were designed, and a DNA fragment containing the target sequence was prepared by annealing of a single-stranded DNA. Reaction conditions: pre-denaturation at 95° C. for 5 min; annealing at 30-50° C. for 1 min. The annealing system was as follows:
TABLE-US-00001 Annealing system Reaction system Volume (20 μL) Primer 10 μL Reverse complementary primer 10 μL
[0057] 1.1.3 Preparation of Linearized Vector
[0058] The linearization of the vector adopted the method of inverse PCR amplification.
[0059] 1.1.4 Recombination Reaction
[0060] The recombination system is shown in the following table. The recombinases used were all enzymes of the ClonExpress®II One Step Cloning Kit series. Recombination conditions: 37° C., 30 min.
TABLE-US-00002 Recombination system Reaction system Volume (10 μL) 5 × CE II Buffer 2 μL Linearized clone vector 0.5 μL.sup. Inserted fragment clone vector 0.5 μL.sup. Exnase ® II 1 μL ddH.sub.2O 6 μL
[0061] 1.1.5 Transformation of Plasmid
[0062] Ten μL of the reaction solution were added to 100 mL of DH5α competent cells and mixed gently. The resulting mixture was cooled in an ice bath for 20 min, heated shock at 42° C. for 45-90 s, cooled immediately in an ice bath for 2-3 min, added with 900 μL of SOC, and recovered at 37° C. for 1 h. The mixture was centrifuged at 8,000 rpm for 2 min, part of the supernatant was discarded and the remaining 200 μL of the supernatant was used to resuspend the cells. The cells were then spread onto a plate containing 100 mg/L ampicillin, and the plate was placed upside down and cultured at 37° C. overnight. After single colonies were grown on the plate, positive recombinants were identified and picked by colony PCR.
[0063] 1.1.6 Identification of Clones
[0064] The PCR-positive colonies were inoculated into LB medium containing 100 mg/L ampicillin for overnight culture, and the bacteria were preserved. The plasmids were extracted and identified by enzyme digestion.
[0065] 1.2 Preparation of Recombinant DNA Fragment
[0066] The recombinant fragment for knockout consists of the upstream and downstream homologous arms of the gene to be knocked out (upstream homologous arm-downstream homologous arm); the recombinant fragment for integration consists of the upstream and downstream homologous arms of the integration site and the gene fragment to be integrated (upstream homologous arm-target gene-downstream homologous arm). Using the primer design software primer5, the upstream and downstream sequences of the gene to be knocked out or the site to be integrated were used as the template to design the primers for the amplification of the upstream and downstream homologous arms (amplification product length: about 400-500 bp); the gene to be integrated was used as the template to design the primers for the amplification of the integrated gene. After amplifying the upstream and downstream homologous arms and the target gene fragment by PCR, respectively, the recombinant fragment was prepared by overlap PCR. The DNA polymerases used in PCR were purchased from TaKaRa, including high-fidelity PrimeSTAR HS DNA Polymerase and Ex.taq DNA Polymerase for generating sticky-end PCR products. The PCR systems and methods are shown in the following tables:
TABLE-US-00003 PCR amplification system with HS enzyme Component Volume (50 μL) DNA template 1 μL Forward primer (10 μmol/L) 2 μL Reverse primer (10 μmol/L) 2 μL dNTP mixture (10 mmol/L) 4 μL 5 × Buffer 10 μL HS enzyme (5 U/μL) 0.5 μL.sup. ddH.sub.2O 30.5 μL
[0067] The colony PCR system is shown in the following table:
TABLE-US-00004 PCR amplification system with Ex. taq enzyme Component Volume (15 μL) DNA template .sup. 1 μL Forward primer (10 μmol/L) 0.5 μL Reverse primer (10 μmol/L) 0.5 μL 2 × Rapid Taq Master Mix 7.5 μL ddH.sub.2O 6.5 μL DNA template .sup. 1 μL
[0068] The overlap PCR system is shown in the following table:
TABLE-US-00005 Overlap PCR amplification system with HS enzyme Component Volume (50 μL) Template 1 μL Forward primer for the upstream 2 μL homologous arm (10 μmol/L) Reverse primer for the downstream 2 μL homologous arm (10 μmol/L) dNTP mixture (10 mmol/L) 4 μL 5 × Buffer 10 μL HS enzyme (5 U/μL) 0.5 μL.sup. ddH.sub.2O 30.5 μL
[0069] Note: The template was composed of equal moles of amplified fragments of the upstream homologous arm and the downstream homologous arm and the target gene, and the total amount was less than 10 ng.
TABLE-US-00006 Overlap PCR amplification system with Ex. taq enzyme Component Volume (50 μL) Template 2 μL Forward primer for the upstream 1 μL homologous arm (10 μmol/L) Reverse primer for the downstream 1 μL homologous arm (10 μmol/L) dNTP mixture (10 mmol/L) 4 μL 10 × Buffer 5 μL Ex. taq enzyme (5 U/μL) 0.25 μL ddH.sub.2O 36.75 μL
[0070] Note: The template was composed of equal moles of amplified fragments of the upstream homologous arm and the downstream homologous arm and the target gene, and the total amount was less than 10 ng.
[0071] PCR reaction conditions: pre-denaturation. at 95° C. for 5 min; 30 cycles of denaturation at 98° C. for 10 s, annealing at (Tm-3/5) ° C. for 15 s, extension at 72° C. (enzyme activity: about 1 minute per kb); and a final extension at 72° C. for 10 min; hold at 4° C.
[0072] 1.3 Transformation of Plasmid and Recombinant DNA Fragment
[0073] 1.3.1 Transformation of pREDCas9
[0074] The pREDCas9 plasmid was electro-transformed into the electro-transformation competent cells of W3110 by electro-transformation. The cells were recovered and cultured and spread on LB plates containing spectinomycin, and cultured at 32° C. overnight. Single colonies grown on the plates with the antibiotic were subjected to colony PCR with identification primers to screen positive recombinants.
[0075] 1.3.2 Preparation of Electro-Transformation Competent Cells of the Target Strain Containing pREDCas9
[0076] The strain was cultured at 32° C. until the culture reached an OD600 of from 0.1 to 0.2, and then 0.1 M IPTG was added (to a final concentration of 0.1 mM). The culture was continued until OD600 value reached from 0.6 to 0.7. The obtained cells were used for the preparation of competent cells. The purpose of adding IPTG is to induce the expression of the recombinase on the pREDCas9 plasmid. The medium and preparation process required for the preparation of the competent cells refer to conventional standard operations.
[0077] 1.3.3 Transformation of pGRB and Recombinant DNA Fragment
[0078] The pGRB plasmid and the donor DNA fragment were simultaneously electro-transformed into the electro-transformation competent cells containing pREDCas9. After electro-transformation, the cells were recovered and cultured and spread on LB plates containing ampicillin and spectinomycin, and cultured at 32° C. overnight. Colony PCR verification was performed by using the forward primer for the upstream homologous arm and the reverse primer for the downstream homologous arm, or by using specifically designed primers for identification, to screen positive recombinants and the recombinant bacteria were preserved.
[0079] 1.4 Elimination of Plasmid
[0080] 1.4.1 Elimination of Plasmid pGRB
[0081] The positive recombinants were cultured overnight in LB medium containing 0.2% arabinose, and after appropriate dilution, they were spread on LB plates containing spectinomycin, and cultured at 32° C. overnight. The recombinants were then inoculated into LB plates containing ampicillin and spectinomycin, respectively, and single colonies that did not grow on the plate containing ampicillin but grew on the plate containing spectinomycin were picked and preserved.
[0082] 1.4.2 Elimination of Plasmid pREDCas9
[0083] The positive recombinants were transferred to LB liquid medium without antibiotics, cultured overnight at 42° C., and spread on LB plates without antibiotics after appropriate dilution, and cultured at 37° C. overnight. The recombinants were then inoculated into LB plates containing spectinomycin and without antibiotics, respectively, single colonies that did not grow on the plate with spectinomycin but grew on the LB plate without antibiotics were picked and preserved.
[0084] 2. Construction of Engineered L-Tryptophan-Producing E. coli Strain TRP 05
[0085] 2.1 Synthesis of ywkB Gene
[0086] (1) Using E. coli W3110 genome as the template, PCR was performed with the primers for the upstream homologous arm (yeep-up-S, yeep-up-A) and the primers for the downstream homologous arm (yeep-down-S, yeep-down-A) designed at both ends of the yeep pseudogene to amplify the upstream and downstream homologous arms of the yeep pseudogene.
[0087] (2) The PCR primers (ywkB-S, ywkB-A) were designed according to the gene sequence of the putative metabolite transporter ywkB of Bacillus subtilis (Bacillus subtilis subsp. subtilis str. 168) published in GENBANK, and the sequence of BBa j23106 promoter was designed in the forward primer for the ywkB gene and its fragment was amplified with HS enzyme.
[0088] (3) The amplified fragment obtained in steps (1) and (2) were used as the templates to obtain the integrated fragment of the BBa j23106-ywkB gene by overlap PCR, and the fragment was composed of the upstream homologous arm of the yeep gene, the downstream homologous arm of the yeep gene, the BBa j23106 promoter fragment and the ywkB gene fragment.
[0089] 2.2 Integration of the ywkB Gene
[0090] (1) Construction of pGRB-yeep: plasmid pGRB containing the target sequence was prepared according to the method described in section 1.1, specifically, primers, pGRB-yeep-S and pGRB-yeep-A, were designed according to the method of section 1.1 and then the DNA fragment containing the target sequence was obtained by annealing; the plasmid pGRB was linearized according to the method of section 1.1.3, and then plasmid pGRB-yeep containing the target sequence was prepared according to the method of section 1.1.4;
[0091] (2) preparation of competent cells of E. coli TRP 03;
[0092] (3) Acquisition of E. coli strain TRP 05: according to the method described in section 1.3, positive clones were screened after the pREDCas9 plasmid was transformed into E. coli TRP 03, and then the competent cells of E. coli TRP 03 containing the pREDCas9 plasmid was prepared, electro-transformed with the plasmid pGRB-yeep and the recombinant DNA fragments prepared in step (3) in section 2.1; colony PCR verification was performed after 12-16 hours of plate culture, positive recombinants were screened and preserved; according to the method described in section 1.4, plasmid pGRB-yeep and plasmid pREDCas9 were eliminated, respectively, and finally the E. coli strain TRP 05 was screened through PCR identification and stored at −80° C.
[0093] The electropherogram of the construction of the BBa_j23106 ywkB gene integration fragment and the PCR verification of the positive strain are shown in
[0094] 3. The primers used in the strain improvement are shown in the following table:
TABLE-US-00007 SEQ ID Primer Sequence (5′-3′) NO: yeep-up-S GGTCAGGAGGTAAC 4 TTATCAGCG yeep-up-A CTGCTAGCACTATA 5 CCTAGGACTGAGCT AGCCGTAAAATGGC AGGGCTCCGTTTT ywkB-S AGGTATAGTGCTAG 6 CAGGAAACAGACCT TGAGCATCTTAGAT ATCTTAATCCTCC ywkB-A AAATCCAGTTCAGC 7 AAAAAGCTCCCTT AAAGGG yeep- TTTTTGCTGAACTG 8 down-S GATTTTCTTC TGAACCTGT yeep- ACGATGTCAGCAG 9 down-A CCAGCA pGRB- AGTCCTAGGTATA 10 yeep-S ATACTAGTACAGA ATATTCGCGAAAA AAGTTTTAG AGCTAGAA pGRB- TTCTAGCTCTAAA 11 yeep-A ACTTTTTTCGCGA A TATTCTGTACT AGTATTATACCTA GGACT
EXAMPLE 2: Shake Flask Fermentation of Genetically Engineered Escherichia coli For the Production of L-Tryptophan
[0095] A specific operation of using genetically engineered Escherichia coli to produce L-tryptophan by shake flask fermentation was as follows: [0096] slant culture: inoculating the bacterial strain preserved at −80° C. onto an activated slant using streak method, culturing at 37° C. for 12 h and passaged once; [0097] shake flask seed culture: scraping a ring of seeds on the slant with an inoculating loop and inoculating into a 500 mL conical flask containing 30 mL of seed medium, sealing the conical flask with nine layers of gauze, and culturing at 37° C. and 200 rpm for 8-10 h; [0098] shake flask fermentation culture: inoculating the seed culture at the concentration of 10-15% (v/v) into a 500 mL conical flask containing fermentation medium (final volume: 30 mL), sealing the conical flask with nine layers of gauze, culturing at 37° C. and 200 r/min in a shaking table, during the fermentation, adding ammonia water to maintain pH at 7.0-7.2; adding 60% (m/v) glucose solution to maintain fermentation (with phenol red as indicator, when the color of the fermentation broth no longer changes, it is regarded as lack of glucose, adding 1-2 mL of 60% (m/v) glucose solution to make the glucose concentration in the fermentation broth the initial value of 20-40 g/L); the fermentation period lasting for 22-26 h.
[0099] Determination of L-tryptophan concentration in fermentation mL of fermentation broth was collected, centrifuged at 13,000 rpm for 1 min, and the supernatant was collected; the collected supernatant was diluted (to 0.1-0.5 g/L,) with deionized water, filtered through a 0.22 μm micropore, and the L-tryptophan concentration was determined by liquid chromatography; the chromatographic conditions were as follows: chromatographic column: Kromasil C18 column (250 mm×460 mm, 5 μm), mobile phase: 10% acetonitrile solution, flow rate: 1.0 mL/min, column temperature: 40° C., detection wavelength: 278 nm, injection volume: 20 μL, and the appearance time of the main peak was about 3.5 min; the concentration of L-tryptophan in the fermentation broth was calculated from its peak area according to a standard curve; [0100] Plotting a standard curve of L-tryptophan: solutions with L-tryptophan concentrations of 0.1 g/L, 0.3 g/L, 0.5 g/L, 0.6 g/L and 1 g/L were subjected to the above liquid chromatography to obtain the peak areas corresponding to the L-tryptophan concentrations and the peak area was plotted against the concentration of L-tryptophan to generate the standard curve, as shown in FIG. 3.
[0101] Components of activated slant medium: 1-3 g/L glucose, 5-10 g/L tryptone, 5-10 g/L beef extract, 2-5 g/L yeast extract, 2-5 g/L NaCl, 15-30 g/L agar, the residual is water, pH 7.0-7.2, sterilized in an autoclave at 121° C. for 20 min
[0102] Components of seed medium: 20-40 g/L glucose, 1-5 g/L (NH.sub.4).sub.2SO.sub.4, 1-5 g/L KH.sub.2PO.sub.4, 0.5-2 g/L MgSO.sub.4.7H.sub.2O, 2-5 g/L yeast extract, 1-3 mg/L FeSO.sub.4.7H.sub.2O, 1-3 mg/L MnSO.sub.4.H.sub.2O, 0.1-0.5 mg/L V.sub.H; 0.5-1.0 mg/L V.sub.B1, 1-3 ml/L trace element mixture, 15-30 g/L phenol red, the residual is water, pH 7.0-7.2, sterilized in an autoclave at 115° C. for 15 min.
[0103] Components of fermentation medium: 20-40 g/L glucose, 2-6 g/L (NH.sub.4).sub.2SO.sub.4, 1-5 g/L KH.sub.2PO.sub.4, 0.5-2 g/L MgSO.sub.4.7H.sub.2O, 1-5 g/L yeast extract, 30-60 mg/L FeSO.sub.4.7H.sub.2O, 1-5 mg/L MnSO.sub.4.7H.sub.2O, 0.1-0.5 mg/L V.sub.H, 0.5-1.0 mg/L V.sub.B1, 1-3 ml/L trace element mixture, 15-30 g/L phenol red, the residual is water, pH 7.0-7.2, sterilized in an autoclave at 115° C. for 15 min.
[0104] Components of the trace element mixture: 2.5 g/L Na.sub.2MoO.sub.4.2H.sub.2O, 2.5 g/L AlCl.sub.3.6H.sub.2O, 2.5 g/L NiSO.sub.4.6H.sub.2O, 1.75 g/L CoCl.sub.2.6H.sub.2O, 10 g/L CaCl.sub.2.2H.sub.2O, 0.5 g/L ZnSO.sub.4.7H.sub.2O, 0.25 g/L CuCl.sub.2.2H.sub.2O, 0.125 g/L, H.sub.3BO.sub.3.
[0105] The engineered L-tryptophan-producing E. coil strain TRP 05 constructed above was used for shake flask fermentation, and the engineered L-tryptophan-producing E. coli strain TRP 03 preserved in the Metabolic Engineering Laboratory of Tianjin University of Science and Technology was used as a control for the same shake flask fermentation. The experimental results are shown in