Patent Grant
12123007
The instant application contains a Sequence Listing in ASCII plain text file format as a file named “Seq.txt”, created on Jan. 28, 2021, of 36,864 bytes in size, and which is hereby incorporated by reference in its entirety.
The present disclosure relates to a method for constructing an efficient Bacillus subtilis promoter, and belongs to the technical field of gene engineering.
B. subtilis is a gram positive type strain widely applied to exogenous protein expression, and it is widely applied to the aspect of industrial enzyme preparation production because of the ability to efficiently express exogenous proteins. However, currently-applied B. subtilis promoters, especially natural endogenous B. subtilis promoters (such as P43 promoters) are relatively low in activity and relatively poor in expression stability of exogenous genes, and this defect seriously restricts application of the B. subtilis to the field of efficient expression of the exogenous proteins. In order to overcome this defect, in recent years, on the one hand, people have used the idea of directed evolution to further screen and modify the natural promoters, and on the other hand, they have used the method of gene engineering and the idea of synthetic biology to construct synthetic promoters. Although the activity of the promoters can be greatly improved by modifying the natural promoters, some defects of the natural promoters still cannot be avoided, such as unstable expression and weak incompatibility with other expression regulating and controlling elements. Therefore, the construction of efficient and stable artificial promoters has huge application prospects in the aspect of breaking through the activity bottleneck of the natural promoters and improving the stability and compatibility of promoter elements.
At present, there are mainly two strategies for constructing the artificial promoters, one of the strategies is that the natural promoters are used as basic skeletons, the high-activity natural promoters are screened to be simplified, modified, rearranged and combined, and then new efficient artificial promoters including the natural promoter skeletons are constructed. The other strategy is that random DNA sequences of a certain length are fully artificially synthesized to be cloned to promoter screening vectors, and by virtue of a high-throughput screening device and a high-throughput screening method, the fully artificially synthesized sequences with promoter functions are screened out from the numerous random sequences to be used as promoter elements. Although both of the two strategies have significant disadvantages, the former relies on the high-activity natural promoters, people also need to have a deep understanding of the working principle of the promoters, and as for the series promoters, if the new promoters each include a plurality of repeated sequence fragments, the stability of the promoters and expression vectors will be adversely affected; and although the later does not need to deeply understand the working mechanism of the promoters, target promoters screened from the full random sequences need expensive high-throughput screening apparatuses, and the screening efficiency is low. Therefore, it is of great significance to provide a method for constructing an efficient and stable promoter for the efficient expression of the exogenous proteins.
The first purpose of the present disclosure is to provide an element for regulating and controlling gene expression, which includes an artificial series promoter and a downstream RBS thereof, the artificial series promoter is formed by connecting at least two of promoters PrpoB, PspoVG and PsigW in series and nucleotide sequences of the promoters PrpoB, PspoVG and PsigW are respectively shown as SEQ ID NO:1, SEQ ID NO:7 and SEQ ID NO:11.
In one implementation of the present disclosure, a nucleotide sequence of the artificial series promoter is shown as any one of SEQ ID NO:17-SEQ ID NO:27.
In one implementation of the present disclosure, a nucleotide sequence of the artificial series promoter is shown as any one of SEQ ID NO: 29-SEQ ID NO:59.
In one implementation of the present disclosure, intervening sequences of 60 bp and 75 bp are respectively inserted between core areas of the promoters PrpoB and PspoVG, and new promoters PAW-D60 and PAH-D75 shown as SEQ ID NO:32 and SEQ ID NO:33 are respectively obtained.
In one implementation of the present disclosure, intervening sequences of 45 bp and 75 bp are respectively inserted between core areas of the first two of the promoters PsigW, PrpoB and PspoVG, and new promoters PWAH-D45 and PWAH-D75 shown as SEQ ID NO:43 and SEQ ID NO:45 are respectively obtained.
In one implementation of the present disclosure, intervening sequences of 30 bp and 90 bp are respectively inserted between core areas of the first two of the promoters PrpoB, PsigW and PspoVG, and new promoters PAWH-D30 and PWAH-D90 shown as SEQ ID NO:54 and SEQ ID NO:58 are respectively obtained.
In one implementation of the present disclosure, a nucleotide sequence of the RBS is shown as any one of SEQ ID NO:60-72.
In one implementation of the present disclosure, an expression host of a target gene includes B. subtilis.
In one implementation of the present disclosure, the expression host of the target gene includes B. subtilis 168, B. subtilis WB400, B. subtilis WB600 or B. subtilis WB800.
In one implementation of the present disclosure, the target gene includes an exogenous gene or an endogenous gene.
In one implementation of the present disclosure, the target gene includes an enzyme gene or a non-enzyme gene.
The second purpose of the present disclosure is to provide a vector containing the above element.
The third purpose of the present disclosure is to provide a genetic engineering bacterium for expressing the above vector.
The fourth purpose of the present disclosure is to provide a method for regulating and controlling expression of a target gene in B. subtilis, and the above regulating and controlling element is co-expressed with the target gene.
In one implementation of the present disclosure, a target protein includes an enzyme.
In one implementation of the present disclosure, the B. subtilis includes B. subtilis 168, B. subtilis WB400, B. subtilis WB600 or B. subtilis WB800.
The fifth purpose of the present disclosure is to provide application of the above regulating and controlling element or genetic engineering bacterium to preparation of the target protein.
The sixth purpose of the present disclosure is to provide application of the above regulating and controlling element or genetic engineering bacterium to a field of food, pharmaceuticals or chemical engineering.
The present disclosure has the beneficial effects: the promoters identified by different sigma subunits are screened and characterized firstly in the present disclosure, promoters (recombinant plasmids containing different regulating and controlling elements are transformed into the B. subtilis, and the expression quantity of the target gene and the activity of the regulating and controlling elements are characterized by the fluorescence intensity of a culture solution cultured by recombinant bacteria) having the highest activity and identified by the subunits of sigA, sigH and sigW are selected therefrom, and through double series connection and triple series connection of the core areas, intervening sequence optimization of the core areas, RBS redesign and other modes, the regulating and controlling element with the activity being further improved is obtained.
The fluorescence intensities of PAW-D60 and PAH-D75 are respectively 0.94 time and 1.03 times higher than the fluorescence intensity of PAW (with the fluorescence intensity of 20262 a.u/OD600) before modification; the fluorescence intensities (18245 a.u/OD600) of PWAH-D45 and PWAH-D75 are respectively 0.87 time and 0.96 time higher than the fluorescence intensity of PWAH (with the fluorescence intensity of 10261 a.u/OD600) before modification; and the fluorescence intensities of PAWH-D30 and PWAH-D90 are respectively 0.78 time and 0.78 time higher than the fluorescence intensity of PAWH (with the fluorescence intensity of 16879 a.u/OD600) before modification.
When PAH-D75 is combined with RBS11 (SEQ ID NO:70), the fluorescence intensity can reach 76216 a.u/OD600 and is 0.85 time higher than that of PAH-D75; when PWAH-D75 is combined with RBS13 (SEQ ID NO:72), the fluorescence intensity can reach 77751 a.u/OD600 and is 1.17 times higher than that of PWAH-D75; and when PAWH-D30 is combined with RBS13 (SEQ ID NO:72), the fluorescence intensity can reach 73781 a.u/OD600 and is 1.45 times higher than that of PAWH-D30.
Through the method provided by the present disclosure, people can obtain the promoters with the higher activity and stronger designability and compatibility through simple and convenient promoter design and modification methods. The method is simple and easy to implement and has wide application prospects in the construction of an exogenous protein efficient expression system and synthetic biology research.
1. A cloning method of a promoter: A primer including a promoter sequence is designed. An Escherichia coli-B. subtilis shuttle vector pB-sfGFP (i.e., pBSG03, a construction method is shown in Guan C, Cui W, Cheng J, et al. Construction and development of an auto-regulatory gene expression system in Bacillus subtilis [J]. Microbial Cell Factories, 2015, 14 (1): 150) with an sfGFP report gene (Genbank ID: AVR55189.1) is taken as a template. PrimeSTAR MAX DNA polymerase (purchased from Takara with an article number of R045Q) is used for full plasmid PCR. PCR procedures are: pre-denaturation at 98° C. for 1 min, circulation including denaturation at 98° C. for 30 s, annealing at 50° C. for 30 s, and extending at 72° C. for 1 min for a total of 30 times, and final extending at 72° C. for 10 min. Then, a plasmid template is digested and removed with a restriction enzyme DpnI to purify a PCR product. Then, fragments are cyclized through an Infusion reassembling method to be transformed into E. coli JM109 competent cells.
2. A detection method of an sfGFP fluorescence intensity: A sample is centrifuged at 12000×g for 2 min, and bacteria are collected, washed with PBS 3 times, and then diluted with PBS to a certain concentration to obtain a bacterium suspension. 200 μL of the bacterium suspension is taken to a 96-well ELISA plate, and the 96-well ELISA plate is placed into a Synergy™ H4 fluorescence microplate reader for fluorescence detection. Fluorescence is detected with excitation light of 485 nm and absorbed light of 528 nm.
3. A medium: LB medium (g·L−1): 10 of Tryptone, 10 of NaCl, 5 of a yeast extract, pH 7.0, and 20 of agar powder added when a solid medium is prepared.
4. A transformation method of B. subtilis 168: Single colonies of the B. subtilis 168 are picked to be inoculated into a 2 mL SPI medium and subjected to shaking culture at 37° C. for 12-14 h. 100 μL of a culture is taken to be inoculated into a 5 mL SPI medium and subjected to shaking culture at 37° C. for 4-5 h, and then, OD600 starts to be detected. When OD600 is about 1.0, 200 μL of a bacterium solution is pipetted to be transferred into a 2 mL SPII medium and subjected to shaking incubation at 37° C. and 100 r·min−1 for 1.5 h. 20 μL of a 100×EGTA solution is added into a tube to be cultured in a shaking table at 37° C. and 100 r·min−1 for 10 min, and then each centrifuge tube of 1.5 mL is filled with 500 L of a mixture. A proper quantity of plasmids verified to be correct by sequencing are added into the tubes, and subjected to blowing-suction uniform mixing to be placed into the shaking table at 37° C. and 100 r·min−1 for 2 h. Culture is completed, and about 200 μL of a bacterium solution is sucked to be uniformly smeared on a corresponding selective plate to be cultured at 37° C. for 12-14 h.
Promoters (with nucleotide sequences respectively shown as SEQ ID NO:1-SEQ ID NO:6) identified by six SigA subunits of PrpoB, PsucA, PmtnK, PylbP, PylxM and PyydE, promoters (with nucleotide sequences respectively shown as SEQ ID NO: 7-SEQ ID NO: 10) identified by four SigH subunits of PspoVG, PpspoVS, Pspo0m and PminC and promoters (with nucleotide sequences respectively shown as SEQ ID NO: 11-SEQ ID NO: 16) identified by six SigW subunits of PsigW, PydbS, PyobJ, PyqeZ, PythP and PyuaF are selected for testing. Core areas of the cloned promoters include −10 areas, −35 areas and transcriptional start sites (TSS) of the above promoters, with a total of 70 bp. To-be-screened-and-identified promoter sequences are designed on primers (shown in Table 2). The promoter sequences are introduced into a vector skeleton pB-sfGFP through a full plasmid PCR method, and then, through DpnI digestion, purification and assembly, cloned sfGFP expression plasmids containing the single promoters are transformed and constructed. The sfGFP expression plasmids for expressing the single promoters are transformed into strains of B. subtilis 168, and recombinant B. subtilis is constructed. The obtained recombinant B. subtilis is cultured in an LB medium at 37° C. and 200 rpm for 24 h, the expression level of sfGFP in bacteria is detected, and the degree of the activity of the promoters is judged through the intensity of an sfGFP fluorescence signal. The results are shown in
Series design is performed on PrpoB, PspoVG and PsigW. Full plasmid PCR is conducted by adopting primers in Table 5 and taking three plasmids constructed in Example 1 with promoters PrpoB, PspoVG and PsigW as templates. Plasmids containing the series promoters and expressing sfGFP are constructed. The series promoters are named according to the type and order of series core areas, and double-series promoters PAH, PAW, PHA, PHW, PAW, PWA and PWH (with nucleotide sequences respectively shown as SEQ ID NO:17-SEQ ID NO:22) and triple-series promoters PAHW, PAWH, PHAW, PHWA, PWAH and PWHA (with nucleotide sequences respectively shown as SEQ ID NO:23-SEQ ID NO:28) are obtained. The constructed recombinant plasmids are transformed into B. subtilis 168, and recombinant B. subtilis is obtained. The obtained recombinant B. subtilis is cultured in an LB medium at 37° C. and 200 rpm, after 6 h, 12 h and 24 h, a fluorescence signal is detected, and the degree of the activity of the promoters is judged through the intensity of the sfGFP fluorescence signal.
The fluorescence intensity of the recombinant bacteria with the sfGFP expression plasmids containing the double-series and triple-series promoters after culture for 6, 12 and 24 h is shown in
Intervening sequences (
The results show that for example, the fluorescence intensities of PAW-D60 and PAH-D75 are respectively 0.94 time and 1.03 times higher than the fluorescence intensity of PAW (with the fluorescence intensity of 20262 a.u/OD600) before modification; the fluorescence intensities (18245 a.u/OD600) of PWAH-D45 and PWAH-D75 are respectively 0.87 time and 0.96 time higher than the fluorescence intensity of PWAH (with the fluorescence intensity of 10261 a.u/OD600) before modification; and the fluorescence intensities of PAWH-D30 and PWAH-D90 are respectively 0.78 time and 0.78 time higher than the fluorescence intensity of PAWH (with the fluorescence intensity of 16879 a.u/OD600) before modification.
(
The promoters PrpoB, PspoVG, PsigW, PAH-D75, PWAH-D75 and PAWH-D30 in Example 1 and Example 3 are respectively combined with 13 RBSs. RBS1-13 sequences (with nucleotide sequences respectively shown as SEQ ID NO:60-SEQ ID NO:72) are respectively cloned onto a vector containing series promoters. Then, recombinant plasmids are transformed into B. subtilis 168. After the obtained recombinant B. subtilis is cultured in an LB medium at 37° C. and 200 rpm for 24 h, a fluorescence signal is detected, and the degree of the activity of the promoters is judged through the intensity of the fluorescence signal of sfGFP. Then, correlation analysis is performed on RBS theoretical intensities of different combinations and actually-measured fluorescence values, and correlations are evaluated through r values. The result is shown in
As shown in Table 8, when PAH-D75 is combined with RBS11 (SEQ ID NO:70), the fluorescence intensity can reach 76216 a.u/OD600 and is 0.85 time higher than that of PAH-D75; when PWAH-D75 is combined with RBS13 (SEQ ID NO:72), the fluorescence intensity can reach 77751 a.u/OD600 and is 1.17 times higher than that of PWAH-D75; and when PAWH-D30 is combined with RBS13 (SEQ ID NO:72), the fluorescence intensity can reach 73781 a.u/OD600 and is 1.45 times higher than that of PAWH-D30. It shows that the expression of a target gene can be further enhanced through the design of the RBSs by the series promoters.
Although the present disclosure has been disclosed as above as exemplary examples, it is not intended to limit the present disclosure. Any of those skilled in the art may make various alterations and modifications without departing from the spirit and scope of the present disclosure. Therefore, the protection scope of the present disclosure shall be as defined in the claims.
| Number | Date | Country | Kind |
|---|---|---|---|
| 201811542085.0 | Dec 2018 | CN | national |
| Number | Name | Date | Kind |
|---|---|---|---|
| 5593860 | Fischer | Jan 1997 | A |
| Number | Date | Country |
|---|---|---|
| 105505931 | Apr 2016 | CN |
| 105779444 | Jul 2016 | CN |
| Entry |
|---|
| McAllister (Journal of Biological Chemistry 263.24 (1988): 11743-11749) (Year: 1988). |
| Zuber (Cold Spring Harbor symposia on quantitative biology. vol. 50. Cold Spring Harbor Laboratory Press, 1985) (Year: 1985). |
| Chunlei GE et. al., “Efficient overexpression of recombinant Nattokinase in Bacillus subtilis by tandem promoters” Modern Food Science and Technology, 2016, v32 No. 11. |
| M.C. Magno-perez-bryan, et. al. “Comparative genomics within the Bacillus genus reveal the singularities of two robust Bacillus amyloliquefaciens biocontrol strains” Mol Plant Microbe Interact, Oct. 31, 2015, vol. 10 No. 28, p. 1102-1116. |
| Number | Date | Country | |
|---|---|---|---|
| 20210163962 A1 | Jun 2021 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | PCT/CN2019/078816 | Mar 2019 | WO |
| Child | 17160561 | US |
