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Cai N, Chen J, Gao N, Ni X, Lei Y, Pu W, Wang L, Che B, Fan L, Zhou W, Feng J, Wang Y, Zheng P, Sun J. Engineering of the DNA replication and repair machinery to develop binary mutators for rapid genome evolution of Corynebacterium glutamicum. Nucleic Acids Res 2023; 51:8623-8642. [PMID: 37449409 PMCID: PMC10484736 DOI: 10.1093/nar/gkad602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 06/29/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023] Open
Abstract
Corynebacterium glutamicum is an important industrial workhorse for production of amino acids and chemicals. Although recently developed genome editing technologies have advanced the rational genetic engineering of C. glutamicum, continuous genome evolution based on genetic mutators is still unavailable. To address this issue, the DNA replication and repair machinery of C. glutamicum was targeted in this study. DnaQ, the homolog of ϵ subunit of DNA polymerase III responsible for proofreading in Escherichia coli, was proven irrelevant to DNA replication fidelity in C. glutamicum. However, the histidinol phosphatase (PHP) domain of DnaE1, the α subunit of DNA polymerase III, was characterized as the key proofreading element and certain variants with PHP mutations allowed elevated spontaneous mutagenesis. Repression of the NucS-mediated post-replicative mismatch repair pathway or overexpression of newly screened NucS variants also impaired the DNA replication fidelity. Simultaneous interference with the DNA replication and repair machinery generated a binary genetic mutator capable of increasing the mutation rate by up to 2352-fold. The mutators facilitated rapid evolutionary engineering of C. glutamicum to acquire stress tolerance and protein overproduction phenotypes. This study provides efficient tools for evolutionary engineering of C. glutamicum and could inspire the development of mutagenesis strategy for other microbial hosts.
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Affiliation(s)
- Ningyun Cai
- Tianjin University of Science and Technology, Tianjin 300457, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jiuzhou Chen
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Ning Gao
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaomeng Ni
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yu Lei
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Wei Pu
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Lixian Wang
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Bin Che
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Liwen Fan
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Wenjuan Zhou
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Jinhui Feng
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yu Wang
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Haihe Laboratory of Synthetic Biology, Tianjin 300308, China
| | - Ping Zheng
- Tianjin University of Science and Technology, Tianjin 300457, China
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
| | - Jibin Sun
- Key Laboratory of Engineering Biology for Low-carbon Manufacturing, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
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Liu K, Gao Y, Li ZH, Liu M, Wang FQ, Wei DZ. CRISPR-Cas12a assisted precise genome editing of Mycolicibacterium neoaurum. N Biotechnol 2021; 66:61-69. [PMID: 34653700 DOI: 10.1016/j.nbt.2021.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/09/2021] [Accepted: 10/10/2021] [Indexed: 12/27/2022]
Abstract
Efficient and convenient genetic manipulation of mycobacteria, important microorganisms in human healthcare and the pharmaceutical industry, is limited. In this study, using a model strain Mycolicibacterium neoaurum ATCC 25795, the classical bacterium for the production of valuable steroidal pharmaceuticals, a genome editing system employing CRISPR-Cas12a to achieve efficient and precise genetic manipulation has been developed. Targeted genome mutations could be easily achieved by the CRISPR-Cas12a system without exogenous donor templates, assisted by innate non-homologous end-joining (NHEJ). CRISPR-Cas12a enabled rapid one-step genomic DNA fragment deletions of 1 kb, 5 kb, 10 kb, 15 kb, 20 kb and 24 kb with efficiencies of 70 %, 30 %, 30 %, 20 %, 20 % and 10 %, respectively. Combined with the pNIL/pGOAL system, CRISPR-Cas12a successfully integrated the gene of interest into the targeted genomic site by single crossover and double crossovers with efficiencies of 100 % and 9 %, respectively, using a two-plasmid system. The robust CRISPR systems developed demonstrated strong potential for precise genome editing in M. neoaurum, including targeted deletion of DNA sequences of various lengths and integration of targeted genes into desired sites in the genome.
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Affiliation(s)
- Ke Liu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Yang Gao
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Zhen-Hai Li
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Min Liu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Feng-Qing Wang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
| | - Dong-Zhi Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China.
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3
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Gao L, Wu X, Zhu C, Jin Z, Wang W, Xia X. Metabolic engineering to improve the biomanufacturing efficiency of acetic acid bacteria: advances and prospects. Crit Rev Biotechnol 2020; 40:522-538. [DOI: 10.1080/07388551.2020.1743231] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ling Gao
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, PR China
- State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology Shandong Academy of Sciences, Jinan, PR China
| | - Xiaodan Wu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education School of Biotechnology, Jiangnan University, Wuxi, PR China
| | - Cailin Zhu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education School of Biotechnology, Jiangnan University, Wuxi, PR China
| | - Zhengyu Jin
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, PR China
| | - Wu Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education School of Biotechnology, Jiangnan University, Wuxi, PR China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education School of Biotechnology, Jiangnan University, Wuxi, PR China
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4
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Ma Q, Mo X, Zhang Q, Hou Z, Tan M, Xia L, Sun Q, Xie X, Chen N. Comparative metabolomic analysis reveals different evolutionary mechanisms for branched-chain amino acids production. Bioprocess Biosyst Eng 2019; 43:85-95. [DOI: 10.1007/s00449-019-02207-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 08/09/2019] [Accepted: 08/10/2019] [Indexed: 12/21/2022]
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Sandberg TE, Salazar MJ, Weng LL, Palsson BO, Feist AM. The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology. Metab Eng 2019; 56:1-16. [PMID: 31401242 DOI: 10.1016/j.ymben.2019.08.004] [Citation(s) in RCA: 254] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/01/2019] [Accepted: 08/05/2019] [Indexed: 12/21/2022]
Abstract
Harnessing the process of natural selection to obtain and understand new microbial phenotypes has become increasingly possible due to advances in culturing techniques, DNA sequencing, bioinformatics, and genetic engineering. Accordingly, Adaptive Laboratory Evolution (ALE) experiments represent a powerful approach both to investigate the evolutionary forces influencing strain phenotypes, performance, and stability, and to acquire production strains that contain beneficial mutations. In this review, we summarize and categorize the applications of ALE to various aspects of microbial physiology pertinent to industrial bioproduction by collecting case studies that highlight the multitude of ways in which evolution can facilitate the strain construction process. Further, we discuss principles that inform experimental design, complementary approaches such as computational modeling that help maximize utility, and the future of ALE as an efficient strain design and build tool driven by growing adoption and improvements in automation.
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Affiliation(s)
- Troy E Sandberg
- Department of Bioengineering, University of California, San Diego, CA, 92093, USA
| | - Michael J Salazar
- Department of Bioengineering, University of California, San Diego, CA, 92093, USA
| | - Liam L Weng
- Department of Bioengineering, University of California, San Diego, CA, 92093, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, CA, 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Adam M Feist
- Department of Bioengineering, University of California, San Diego, CA, 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark.
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Kick-starting evolution efficiency with an autonomous evolution mutation system. Metab Eng 2019; 54:127-136. [DOI: 10.1016/j.ymben.2019.03.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/19/2019] [Accepted: 03/30/2019] [Indexed: 01/25/2023]
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Fernández‐Cabezón L, Cros A, Nikel PI. Evolutionary Approaches for Engineering Industrially Relevant Phenotypes in Bacterial Cell Factories. Biotechnol J 2019; 14:e1800439. [DOI: 10.1002/biot.201800439] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/08/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Lorena Fernández‐Cabezón
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark 2800 Kongens Lyngby Denmark
| | - Antonin Cros
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark 2800 Kongens Lyngby Denmark
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of Denmark 2800 Kongens Lyngby Denmark
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Otoupal PB, Chatterjee A. CRISPR Gene Perturbations Provide Insights for Improving Bacterial Biofuel Tolerance. Front Bioeng Biotechnol 2018; 6:122. [PMID: 30234107 PMCID: PMC6131188 DOI: 10.3389/fbioe.2018.00122] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/14/2018] [Indexed: 11/13/2022] Open
Abstract
Economically-viable biofuel production is often limited by low levels of microbial tolerance to high biofuel concentrations. Here we demonstrate the first application of deactivated CRISPR perturbations of gene expression to improve Escherichia coli biofuel tolerance. We construct a library of 31 unique CRISPR inhibitions and activations of gene expression in E. coli and explore their impacts on growth during 10 days of exposure to n-butanol and n-hexane. We show that perturbation of metabolism and membrane-related genes induces the greatest impacts on growth in n-butanol, as does perturbation of redox-related genes in n-hexanes. We identify uncharacterized genes yjjZ and yehS with strong potential for improving tolerance to both biofuels. Perturbations demonstrated significant temporal dependencies, suggesting that rationally designing time-sensitive gene circuits can optimize tolerance. We also introduce a sgRNA-specific hyper-mutator phenotype (~2,600-fold increase) into our perturbation strains using error-prone Pol1. We show that despite this change, strains exhibited similar growth phenotypes in n-butanol as before, demonstrating the robustness of CRISPR perturbations during prolonged use. Collectively, these results demonstrate the potential of CRISPR manipulation of gene expression for improving biofuel tolerance and provide constructive starting points for optimization of biofuel producing microorganisms.
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Affiliation(s)
- Peter B Otoupal
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO, United States
| | - Anushree Chatterjee
- Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO, United States.,BioFrontiers Institute, University of Colorado at Boulder, Boulder, CO, United States
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9
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Gong Z, Nielsen J, Zhou YJ. Engineering Robustness of Microbial Cell Factories. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201700014] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 08/13/2017] [Indexed: 12/25/2022]
Affiliation(s)
- Zhiwei Gong
- Division of BiotechnologyDalian Institute of Chemical PhysicsCAS457 Zhongshan RoadDalian 116023P.R. China
- College of Chemistry and Chemical EngineeringWuhan University of Science and Technology947 Heping RoadWuhan 430081P.R. China
| | - Jens Nielsen
- Department of Biology and Biological EngineeringChalmers University of TechnologyKemivägen 10 Gothenburg SE‐41296Sweden
| | - Yongjin J. Zhou
- Division of BiotechnologyDalian Institute of Chemical PhysicsCAS457 Zhongshan RoadDalian 116023P.R. China
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Rosenberg J, Ischebeck T, Commichau FM. Vitamin B6 metabolism in microbes and approaches for fermentative production. Biotechnol Adv 2016; 35:31-40. [PMID: 27890703 DOI: 10.1016/j.biotechadv.2016.11.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 11/21/2016] [Accepted: 11/21/2016] [Indexed: 12/20/2022]
Abstract
Vitamin B6 is a designation for the six vitamers pyridoxal, pyridoxine, pyridoxamine, pyridoxal 5'-phosphate (PLP), pyridoxine 5'-phosphate, and pyridoxamine. PLP, being the most important B6 vitamer, serves as a cofactor for many proteins and enzymes. In contrast to other organisms, animals and humans have to ingest vitamin B6 with their food. Several disorders are associated with vitamin B6 deficiency. Moreover, pharmaceuticals interfere with metabolism of the cofactor, which also results in vitamin B6 deficiency. Therefore, vitamin B6 is a valuable compound for the pharmaceutical and the food industry. Although vitamin B6 is currently chemically synthesized, there is considerable interest on the industrial side to shift from chemical processes to sustainable fermentation technologies. Here, we review recent findings regarding biosynthesis and homeostasis of vitamin B6 and describe the approaches that have been made in the past to develop microbial production processes. Moreover, we will describe novel routes for vitamin B6 biosynthesis and discuss their potential for engineering bacteria that overproduce the commercially valuable substance. We also highlight bottlenecks of the vitamin B6 biosynthetic pathways and propose strategies to circumvent these limitations.
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Affiliation(s)
- Jonathan Rosenberg
- Department of General Microbiology, Georg-August-University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Till Ischebeck
- Department of Plant Biochemistry, Georg-August-University of Göttingen, Justus-von-Liebig-Weg 11, D-37077 Göttingen, Germany
| | - Fabian M Commichau
- Department of General Microbiology, Georg-August-University of Göttingen, Grisebachstr. 8, D-37077 Göttingen, Germany.
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11
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A CRISPR-Cas9 Assisted Non-Homologous End-Joining Strategy for One-step Engineering of Bacterial Genome. Sci Rep 2016; 6:37895. [PMID: 27883076 PMCID: PMC5121644 DOI: 10.1038/srep37895] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 11/01/2016] [Indexed: 11/08/2022] Open
Abstract
Homologous recombination-mediated genome engineering has been broadly applied in prokaryotes with high efficiency and accuracy. However, this method is limited in realizing larger-scale genome editing with numerous genes or large DNA fragments because of the relatively complicated procedure for DNA editing template construction. Here, we describe a CRISPR-Cas9 assisted non-homologous end-joining (CA-NHEJ) strategy for the rapid and efficient inactivation of bacterial gene (s) in a homologous recombination-independent manner and without the use of selective marker. Our study show that CA-NHEJ can be used to delete large chromosomal DNA fragments in a single step that does not require homologous DNA template. It is thus a novel and powerful tool for bacterial genomes reducing and possesses the potential for accelerating the genome evolution.
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12
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Isolation and characterization of butanol-tolerant Staphylococcus aureus. Biotechnol Lett 2016; 38:1929-1934. [DOI: 10.1007/s10529-016-2180-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 07/19/2016] [Indexed: 01/09/2023]
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13
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Wang JL, Wu B, Qin H, You Y, Liu S, Shui ZX, Tan FR, Wang YW, Zhu QL, Li YB, Ruan ZY, Ma KD, Dai LC, Hu GQ, He MX. Engineered Zymomonas mobilis for salt tolerance using EZ-Tn5-based transposon insertion mutagenesis system. Microb Cell Fact 2016; 15:101. [PMID: 27287016 PMCID: PMC4901475 DOI: 10.1186/s12934-016-0503-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 06/01/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The cell growth and ethanol yield of Zymomonas mobilis may be detrimentally affected by salt stress frequently present in some biomass-based fermentation systems, leading to a decrease in the rate of sugar conversion to ethanol or other bioproducts. To address this problem, improving the salt tolerance of Z. mobilis is a desirable way. However, limited progress has been made in development of Z. mobilis with higher salt tolerance for some technical challenges in the past decades. Recently, transposon insertion mutant system has been widely used as a novel genetic tool in many organisms to develop mutant strains. In this study, Tn5-based transposon insertion mutagenesis system firstly used for construction of higher salt tolerance strain in Z. mobilis. RESULTS Approximately 200 Z. mobilis ZM4 mutants were generated by using Tn5-based transposon mutagenesis system. The mutant strain ZMT2 with improved salt tolerance phenotype was obtained by screening on RM agar plates with additional 1 % NaCl. Strain ZMT2 was confirmed to exhibit better fermentation performance under NaCl stress than wild type of strain ZM4. The transposon insertion was located in ZMO1122 (himA) by genome walking. Discruption of himA gene showed that himA may play an important role in response to salt tolerance in Z. mobils. CONCLUSIONS The mutant strain ZMT2 with a transposon insertion in himA gene of the genome showed obviously higher sugar conversion rate to ethonal under up to 2 % NaCl stress than did the wild ZM4 strain. Besides, ZMT2 exhibited shared fermentative capabilities with wild ZM4 strain under no or low NaCl stress. This report firstly showed that himA played a role in responding to NaCl stress. Furthermore, the result indicated that Tn5-based transposon mutagenesis system was a feasible tool not only for genetic engineering in Z. mobilis strain improvement, but also in tapping resistent genes.
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Affiliation(s)
- Jing-Li Wang
- Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Nanlu, Chengdu, 610041, People's Republic of China
| | - Bo Wu
- Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Nanlu, Chengdu, 610041, People's Republic of China
| | - Han Qin
- Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Nanlu, Chengdu, 610041, People's Republic of China
| | - Yang You
- Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Nanlu, Chengdu, 610041, People's Republic of China
| | - Song Liu
- Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Nanlu, Chengdu, 610041, People's Republic of China
| | - Zong-Xia Shui
- Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Nanlu, Chengdu, 610041, People's Republic of China
| | - Fu-Rong Tan
- Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Nanlu, Chengdu, 610041, People's Republic of China
| | - Yan-Wei Wang
- Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Nanlu, Chengdu, 610041, People's Republic of China
| | - Qi-Li Zhu
- Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Nanlu, Chengdu, 610041, People's Republic of China
| | - Yan-Bin Li
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources, College of Life Sciences, Tarim University, Tarim Basin, Alaer City, 843300, People's Republic of China
| | - Zhi-Yong Ruan
- Key Laboratory of Microbial Resources (Ministry of Agriculture, China), Institute of Agricultural Resources and Regional Planning, CAAS, Beijing, 100081, People's Republic of China
| | - Ke-Dong Ma
- College of Environmental and Chemical Engineering, Dalian University, Dalian, 116622, People's Republic of China
| | - Li-Chun Dai
- Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Nanlu, Chengdu, 610041, People's Republic of China
| | - Guo-Quan Hu
- Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Nanlu, Chengdu, 610041, People's Republic of China
| | - Ming-Xiong He
- Key Laboratory of Development and Application of Rural Renewable Energy (Ministry of Agriculture), Biomass Energy Technology Research Centre, Biogas Institute of Ministry of Agriculture, Section 4-13, Renmin Nanlu, Chengdu, 610041, People's Republic of China.
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Production of carbon-13-labeled cadaverine by engineered Corynebacterium glutamicum using carbon-13-labeled methanol as co-substrate. Appl Microbiol Biotechnol 2015; 99:10163-76. [PMID: 26276544 DOI: 10.1007/s00253-015-6906-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 07/30/2015] [Accepted: 07/31/2015] [Indexed: 10/23/2022]
Abstract
Methanol, a one-carbon compound, can be utilized by a variety of bacteria and other organisms as carbon and energy source and is regarded as a promising substrate for biotechnological production. In this study, a strain of non-methylotrophic Corynebacterium glutamicum, which was able to produce the polyamide building block cadaverine as non-native product, was engineered for co-utilization of methanol. Expression of the gene encoding NAD+-dependent methanol dehydrogenase (Mdh) from the natural methylotroph Bacillus methanolicus increased methanol oxidation. Deletion of the endogenous aldehyde dehydrogenase genes ald and fadH prevented methanol oxidation to carbon dioxide and formaldehyde detoxification via the linear formaldehyde dissimilation pathway. Heterologous expression of genes for the key enzymes hexulose-6-phosphate synthase and 6-phospho-3-hexuloisomerase of the ribulose monophosphate (RuMP) pathway in this strain restored growth in the presence of methanol or formaldehyde, which suggested efficient formaldehyde detoxification involving RuMP key enzymes. While growth with methanol as sole carbon source was not observed, the fate of 13C-methanol added as co-substrate to sugars was followed and the isotopologue distribution indicated incorporation into central metabolites and in vivo activity of the RuMP pathway. In addition, 13C-label from methanol was traced to the secreted product cadaverine. Thus, this synthetic biology approach led to a C. glutamicum strain that converted the non-natural carbon substrate methanol at least partially to the non-native product cadaverine.
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