1
|
Yang Y, Wang T, Yu Q, Liu H, Xun L, Xia Y. The pathway of recombining short homologous ends in Escherichia coli revealed by the genetic study. Mol Microbiol 2021; 115:1309-1322. [PMID: 33372330 DOI: 10.1111/mmi.14677] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/17/2020] [Accepted: 12/23/2020] [Indexed: 11/30/2022]
Abstract
The recombination of short homologous ends in Escherichia coli has been known for 30 years, and it is often used for both site-directed mutagenesis and in vivo cloning. For cloning, a plasmid and target DNA fragments were converted into linear DNA fragments with short homologous ends, which are joined via recombination inside E. coli after transformation. Here this mechanism of joining homologous ends in E. coli was determined by a linearized plasmid with short homologous ends. Two 3'-5' exonucleases ExoIII and ExoX with nonprocessive activity digested linear dsDNA to generate 5' single-strand overhangs, which annealed with each other. The polymerase activity of DNA polymerase I (Pol I) was exclusively employed to fill in the gaps. The strand displacement activity and the 5'-3' exonuclease activity of Pol I were also required, likely to generate 5' phosphate termini for subsequent ligation. Ligase A (LigA) joined the nicks to finish the process. The model involving 5' single-stranded overhangs is different from established recombination pathways that all generate 3' single-stranded overhangs. This recombination is likely common in bacteria since the involved enzymes are ubiquitous.
Collapse
Affiliation(s)
- Yuqing Yang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China.,Institute of Marine Science and Technology, Shandong University, Qingdao, People's Republic of China
| | - Tianqi Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Qiaoli Yu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Huaiwei Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Luying Xun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China.,School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Yongzhen Xia
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| |
Collapse
|
2
|
The effects of kanamycin concentration on gene transcription levels in Escherichia coli. 3 Biotech 2020; 10:93. [PMID: 32099734 DOI: 10.1007/s13205-020-2100-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 01/24/2020] [Indexed: 10/25/2022] Open
Abstract
In the area of microbial production of valuable chemicals, plasmids have been widely applied for overexpressing rate-limiting enzymes with high yields. However, the effect of antibiotic concentrations on the transcription of target genes in E. coli is less involved in previous reports. In this study, we constructed E. coli strains expressing the reporter gene and the kanamycin resistant gene in an operon, and analyzed the transcription levels of the reporter gene and the fluorescent intensity of the recombinant E. coli under different kanamycin concentrations. We found that the growth and gene transcription of the recombinant strain were affected obviously by the concentration of kanamycin, indicating the importance of fine-tuning of antibiotic concentrations in microbial fermentation.
Collapse
|
3
|
Zhuang Q, Qi Q. Engineering the pathway in Escherichia coli for the synthesis of medium-chain-length polyhydroxyalkanoates consisting of both even- and odd-chain monomers. Microb Cell Fact 2019; 18:135. [PMID: 31409350 PMCID: PMC6693092 DOI: 10.1186/s12934-019-1186-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 08/03/2019] [Indexed: 12/19/2022] Open
Abstract
Background Medium-chain-length polyhydroxyalkanoates (mcl-PHAs) containing various chain length monomers from C6 to C14 have more applications besides sustainable and environmental-friendly biomaterials owing to their superior physical and mechanical properties. We engineered a reversed fatty acid β-oxidation pathway in Escherichia coli that can synthesize mcl-PHA directly from glucose and achieved high yield. However, there were only even-chain monomers in the biosynthetic polymers. The need for mcl-PHA harboring both even- and odd-chain monomers with better and wider utility impels us to develop the biosynthetic routes for the production of the novel and unnatural mcl-PHA through rewiring the basic metabolism. Results In the present study, a propionate assimilation and metabolic route was integrated into the reversed fatty acid β-oxidation in order to produce mcl-PHA consisting of both even- and odd-numbered monomers. The content of odd-numbered monomers in mcl-PHA was improved with the increased propionate addition. After further deletion of pyruvate oxidase (PoxB) and pyruvate formate-lyase (PflB), the metabolically engineered chassis E. coli LZ08 harboring pQQ05 and pZQ06 (overexpression of prpP and prpE genes from Ralstonia eutropha H16) innovatively accumulated 6.23 wt% mcl-PHA containing odd-chain monomers ranging from 7 to 13 carbon atoms about 20.03 mol%. Conclusions This is the first successful report on production of mcl-PHA harboring both even- and odd-chain monomers (C6–C14) synthesized from glucose and propionate in recombinant E. coli. This present study achieved the highest yield of de novo production of mcl-PHA containing odd-numbered monomers in E. coli at shake-flask fermentation level. Continued engineering of host strains and pathway enzymes will ultimately lead to more economical production of odd-chain monomers based on market demand. The synthetic pathway can provide a promising platform for production of other value-added chemicals and biomaterials that use acetyl-CoA and propionyl-CoA as versatile precursors and can be extended to other microorganisms as intelligent cell factories. Electronic supplementary material The online version of this article (10.1186/s12934-019-1186-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Qianqian Zhuang
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, People's Republic of China. .,Shandong Provincial Key Laboratory of Microbial Engineering, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, People's Republic of China.
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, People's Republic of China
| |
Collapse
|
4
|
Production of succinate by recombinant Escherichia coli using acetate as the sole carbon source. 3 Biotech 2018; 8:421. [PMID: 30305992 DOI: 10.1007/s13205-018-1456-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 09/24/2018] [Indexed: 10/28/2022] Open
Abstract
Acetate is a potential low-cost carbon source that can be generated by biological and chemical processes. In this study, deletion of sdhAB encoding succinate dehydrogenase, iclR encoding the isocitrate lyase regulator, and maeB encoding the malic enzyme, and overexpression of acs encoding acetyl-CoA synthetase, gltA encoding citrate synthase, and acnB encoding aconitate hydratase in the wild-type Escherichia coli MG1655 strain yielded the recombinant E. coli strain WCY-7, which could synthesize succinate from acetate. After 48 h batch fermentation, this strain accumulated 11.23 mM succinate from 50 mM sodium acetate. This work indicates that microbial fermentation using acetate as the sole carbon source may be a suitable route to produce high yields of the valuable chemicals.
Collapse
|
5
|
Wang Q, Xu J, Sun Z, Luan Y, Li Y, Wang J, Liang Q, Qi Q. Engineering an in vivo EP-bifido pathway in Escherichia coli for high-yield acetyl-CoA generation with low CO 2 emission. Metab Eng 2018; 51:79-87. [PMID: 30102971 DOI: 10.1016/j.ymben.2018.08.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 07/25/2018] [Accepted: 08/09/2018] [Indexed: 11/20/2022]
Abstract
The low carbon yield from native metabolic machinery produces unfavorable process economics during the biological conversion of substrates to desirable bioproducts. To obtain higher carbon yields, we constructed a carbon conservation pathway named EP-bifido pathway in Escherichia coli by combining Embden-Meyerhof-Parnas Pathway, Pentose Phosphate Pathway and "bifid shunt", to generate high yield acetyl-CoA from glucose. 13C-Metabolic flux analysis confirmed the successful and appropriate employment of the EP-bifido pathway. The CO2 release during fermentation significantly reduced compared with the control strains. Then we demonstrated the in vivo effectiveness of the EP-bifido pathway using poly-β-hydroxybutyrate (PHB), mevalonate and fatty acids as example products. The engineered EP-bifido strains showed greatly improved PHB yield (from 26.0 mol% to 63.7 mol%), fatty acid yield (from 9.17% to 14.36%), and the highest mevalonate yield yet reported (64.3 mol% without considering the substrates used for cell mass formation). The synthetic pathway can be employed in the production of chemicals that use acetyl-CoA as a precursor and can be extended to other microorganisms.
Collapse
Affiliation(s)
- Qian Wang
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
| | - Jiasheng Xu
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
| | - Zhijie Sun
- Marine Biology Institute, Shantou University, Shantou 515063, PR China
| | - Yaqi Luan
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
| | - Ying Li
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
| | - Junshu Wang
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
| | - Quanfeng Liang
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, National Glycoengineering Research Center, Shandong University, Jinan 250100, PR China; CAS Key Lab of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, PR China.
| |
Collapse
|
6
|
Gu P, Su T, Wang Q, Liang Q, Qi Q. Tunable switch mediated shikimate biosynthesis in an engineered non-auxotrophic Escherichia coli. Sci Rep 2016; 6:29745. [PMID: 27406890 PMCID: PMC4942831 DOI: 10.1038/srep29745] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/23/2016] [Indexed: 12/28/2022] Open
Abstract
Shikimate is a key intermediate in the synthesis of neuraminidase inhibitors. Compared with traditional methods, microbial production of shikimate has the advantages of environmental friendliness, low cost, feed stock renewability, and product selectivity and diversity. Despite these advantages, shikimate kinase I and II respectively encoded by aroK and aroL are inactivated in most shikimate microbial producers, thus requiring the addition of aromatic compounds during the fermentation process. To overcome this problem, we constructed a non-auxotrophic, shikimate-synthesising strain of Escherichia coli. By inactivation of repressor proteins, blocking of competitive pathways and overexpression of key enzymes, we increased the shikimate production of wild-type E. coli BW25113 to 1.73 g/L. We then designed a tunable switch that can conditionally decrease gene expression and substituted it for the original aroK promoters. Expression of aroK in the resulting P-9 strain was maintained at a high level during the growth phase and then reduced at a suitable time by addition of an optimal concentration of inducer. In 5-L fed-batch fermentation, strain P-9 produced 13.15 g/L shikimate without the addition of any aromatic compounds. The tunable switch developed in this study is an efficient tool for regulating indispensable genes involved in critical metabolic pathways.
Collapse
Affiliation(s)
- Pengfei Gu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
| | - Tianyuan Su
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
| | - Qian Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
| | - Quanfeng Liang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
| |
Collapse
|
7
|
Evolution of a chimeric aspartate kinase for L-lysine production using a synthetic RNA device. Appl Microbiol Biotechnol 2015; 99:8527-36. [DOI: 10.1007/s00253-015-6615-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 03/20/2015] [Accepted: 04/15/2015] [Indexed: 10/23/2022]
|
8
|
Gu P, Yang F, Su T, Li F, Li Y, Qi Q. Construction of an L-serine producing Escherichia coli via metabolic engineering. J Ind Microbiol Biotechnol 2014; 41:1443-50. [PMID: 24997624 DOI: 10.1007/s10295-014-1476-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 06/16/2014] [Indexed: 12/14/2022]
Abstract
L-Serine is a nonessential amino acid, but plays a crucial role as a building block for cell growth. Currently, L-serine production is mainly dependent on enzymatic or cellular conversion. In this study, we constructed a recombinant Escherichia coli that can fermentatively produce L-serine from glucose. To accumulate L-serine, sdaA encoding the L-serine dehydratase, iclR encoding the isocitrate lyase regulator, and arcA encoding the aerobic respiration control protein were deleted in turn. In batch fermentation, the engineered E. coli strain YF-5 exhibited obvious L-serine accumulation but poor cell growth. To restore cell growth, aceB encoding the malate synthase was knocked out, and the engineered strain was then transformed with plasmid that overexpressed serA (FR) , serB, and serC genes. The resulting strain YF-7 produced 4.5 g/L L-serine in batch cultivation and 8.34 g/L L-serine in fed-batch cultivation.
Collapse
Affiliation(s)
- Pengfei Gu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, People's Republic of China
| | | | | | | | | | | |
Collapse
|
9
|
Wang Q, Liu X, Qi Q. Biosynthesis of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) from glucose with elevated 3-hydroxyvalerate fraction via combined citramalate and threonine pathway in Escherichia coli. Appl Microbiol Biotechnol 2014; 98:3923-31. [PMID: 24425304 DOI: 10.1007/s00253-013-5494-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 12/20/2013] [Accepted: 12/22/2013] [Indexed: 11/25/2022]
Abstract
The biosynthesis of polyhydroxyalkanoate copolymers in Escherichia coli from unrelated carbon sources becomes attractive nowadays. We previously developed a poly(hydroxybutyrate-co-hydroxyvalerte) (PHBV) biosynthetic pathway from an unrelated carbon source via threonine metabolic route in E. coli (Chen et al., Appl Environ Microbiol 77:4886-4893, 2011). In our study, a citramalate pathway was introduced in recombinant E. coli by cloning a cimA gene from Leptospira interrogans. By blocking the pyruvate and the propionyl-CoA catabolism and replacing the β-ketothiolase gene, the PHBV with 11.5 mol% 3HV fraction was synthesized. Further, the combination of citramalate pathway with the threonine biosynthesis pathway improved the 3HV fraction in PHBV copolymer to 25.4 mol% in recombinant E. coli.
Collapse
Affiliation(s)
- Qian Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, People's Republic of China
| | | | | |
Collapse
|
10
|
Li Y, Li M, Zhang X, Yang P, Liang Q, Qi Q. A novel whole-phase succinate fermentation strategy with high volumetric productivity in engineered Escherichia coli. BIORESOURCE TECHNOLOGY 2013; 149:333-40. [PMID: 24125798 DOI: 10.1016/j.biortech.2013.09.077] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 09/14/2013] [Accepted: 09/18/2013] [Indexed: 05/22/2023]
Abstract
The strategic design of this study aims at fermentative succinate production with high volumetric productivity in engineered Escherichia coli. An E. coli YL106/pSCsfcA was engineered to produce succinate under aerobic, microaerobic and anaerobic conditions by derepressing the inhibition of low dissolved oxygen, eliminating the NADH competitive pathways, modulating the redistribution of metabolic flux, and increasing the transport rate of the sole carbon source glucose. Based on this strain, a novel "whole-phase" succinate production strategy was further developed, in which the engineered strain was first cultivated aerobically, then shifted to microaerobic phase at the end of exponential growth, and finally kept in anaerobic phase until the end of fermentation. Employing this strategy, the engineered E. coli YL106/pSCsfcA was able to produce 85.30 g l(-1) succinate with an overall volumetric productivity of 2.13 g l(-1)h(-1). This process offers an efficiently fermentative method for industrial succinate production in metabolically engineered E. coli.
Collapse
Affiliation(s)
- Yikui Li
- State Key Laboratory of Microbial Technology, Shandong University, 27 Shanda Nanlu, Jinan 250100, People's Republic of China
| | | | | | | | | | | |
Collapse
|