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Yu H, Hong J, Seok J, Seu YB, Kim IK, Kim KJ. Crystal Structures of 6-Phosphogluconate Dehydrogenase from Corynebacterium glutamicum. J Microbiol Biotechnol 2023; 33:1361-1369. [PMID: 37417004 PMCID: PMC10619557 DOI: 10.4014/jmb.2305.05002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/11/2023] [Accepted: 06/16/2023] [Indexed: 07/08/2023]
Abstract
Corynebacterium glutamicum (C. glutamicum) has been considered a very important and meaningful industrial microorganism for the production of amino acids worldwide. To produce amino acids, cells require nicotinamide adenine dinucleotide phosphate (NADPH), which is a biological reducing agent. The pentose phosphate pathway (PPP) can supply NADPH in cells via the 6-phosphogluconate dehydrogenase (6PGD) enzyme, which is an oxidoreductase that converts 6-phosphogluconate (6PG) to ribulose 5-phosphate (Ru5P), to produce NADPH. In this study, we identified the crystal structure of 6PGD_apo and 6PGD_NADP from C. glutamicum ATCC 13032 (Cg6PGD) and reported our biological research based on this structure. We identified the substrate binding site and co-factor binding site of Cg6PGD, which are crucial for understanding this enzyme. Based on the findings of our research, Cg6PGD is expected to be used as a NADPH resource in the food industry and as a drug target in the pharmaceutical industry.
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Affiliation(s)
- Hyeonjeong Yu
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jiyeon Hong
- KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jihye Seok
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Young-Bae Seu
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
- KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Il-Kwon Kim
- KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
- KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
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2
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Lee S, Kim S, Kim IK, Kim KJ. Structural and Biochemical Studies on Product Inhibition of S-Adenosylmethionine Synthetase from Corynebacterium glutamicum. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:15692-15700. [PMID: 37846083 DOI: 10.1021/acs.jafc.3c05180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
S-Adenosylmethionine (SAM) acts as a methyl donor in living organisms, and S-adenosylmethionine synthetase (MetK) is an essential enzyme for cells, as it synthesizes SAM from methionine and adenosine triphosphate (ATP). This study determined the crystal structures of the apo form and adenosine/triphosphate complex form of MetK from Corynebacterium glutamicum (CgMetK). Results showed that CgMetK has an allosteric inhibitor binding site for the SAM product in the vicinity of the active site and is inhibited by SAM both competitively and noncompetitively. Through structure-guided protein engineering, the CgMetKE68A variant was developed that exhibited an almost complete release of inhibition by SAM with rather enhanced enzyme activity. The crystal structure of the CgMetKE68A variant revealed that the formation of a new hydrogen bond between Tyr66 and Glu102 by the E68A mutation disrupted the allosteric SAM binding site and also improved the protein thermal stability by strengthening the tetramerization of the enzyme.
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Affiliation(s)
- Seunghwan Lee
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Seongmin Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Il-Kwon Kim
- KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
- KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
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Meng G, Zhao W, Liu Q, Zhao C, Zou Y, Zhao N, Liu D, Ying H, Sun W, Chen Y. Strategy for the design of a bioreactor for L-lysine immobilized fermentation using Corynebacterium glutamicum. Appl Microbiol Biotechnol 2022; 106:5449-5458. [PMID: 35902409 DOI: 10.1007/s00253-022-12103-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/08/2022] [Accepted: 07/24/2022] [Indexed: 11/28/2022]
Abstract
Biofilm-immobilized fermentation is a novel strategy that has been utilized in L-lysine fermentation. In this study, we describe a strategy for designing bioreactors for immobilized fermentation. We have constructed steel structures in which the carriers can be sewn, forming several star-like structures with different angles, and changing the ventilation robot to the aeration tray. In a 10-L bioreactor, this structure with 12 angles assisted the immobilized system to remedy the gap between free-cell and immobilized fermentation in the conversion rate. In a 50-L bioreactor, this enlarged structure with 16 angles illustrated a 4.61% higher conversion rate than the free-cell fermentation (67.75%) and increased the production by 28.56%. This successful case is the first step towards to industrial production of biofilm-based immobilized fermentation.Key points• The designed steel structure is useful for L-lysine immobilized fermentation in a 10-L bioreactor.• The conversion rate of immobilized fermentation increased from 13.99 to 60.07% and is 1.03% higher than that of the free-cell fermentation.• The conversion rate of the redesigned 50-L bioreactor is higher than that of free-cell fermentation.
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Affiliation(s)
- Gang Meng
- Ningxia Yipin Biotechnology Co. Ltd, Yinchuan, China
| | - Wei Zhao
- Nanjing Hi-Tech Biological Technology Research Institute Co. Ltd, Nanjing, China
| | - Qingguo Liu
- Nanjing Hi-Tech Biological Technology Research Institute Co. Ltd, Nanjing, China
| | | | - Yanan Zou
- Nanjing Hi-Tech Biological Technology Research Institute Co. Ltd, Nanjing, China
| | - Nan Zhao
- Nanjing Hi-Tech Biological Technology Research Institute Co. Ltd, Nanjing, China
| | - Dong Liu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Hanjie Ying
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Wenjun Sun
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.
| | - Yong Chen
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China.
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4
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Li W, Lv J, Dong T, Li X, Li X, Tan Z, Jia S. Effects of Amino Acids and Overexpression of dapA Gene on the Production of ε-Poly-L-lysine by Streptomyces diastatochromogenes Strains. Curr Microbiol 2021; 78:2640-2647. [PMID: 33991200 DOI: 10.1007/s00284-021-02510-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 04/25/2021] [Indexed: 12/15/2022]
Abstract
In this study, the strain Streptomyces diastatochromogenes 6#-7, which efficiently synthesizes ε-Poly-L-lysine, was studied and the effects of 18 amino acids and overexpression of dapA gene on the fermentation efficiency of ε-PL by S. diastatochromogenes were investigated. It was shown that L-proline, L-lysine, L-isoleucine, and L-threonine could promote the production of ε-PL. Moreover, the overexpression of the dihydrodipicolinate synthase gene (dapA) helped improve the fermentation performance of S. diastatochromogenes. The maximum ε-PL yield of the overexpressing strain (S. diastatochromogenes 12#-2) increased by 17.5% compared with the original strain in 500 mL shake flask. When the fermentation was conducted in a 5-L fermenter, the fermentation duration was extended by 48 h, and ε-PL yield reached 30.54 g/L, which was a 19.8% increase compared to the original strain. The results of this study offered a promising approach to augment the production of ε-PL from Streptomyces, thus paving the way to reduce the cost of product ε-PL and enhance the fermentation efficiency of ε-PL production.
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Affiliation(s)
- Wenchao Li
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, 300457, PR China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Junge Lv
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, 300457, PR China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Tianyu Dong
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, 300457, PR China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Xinying Li
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, 300457, PR China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Xiaona Li
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, 300457, PR China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, PR China
| | - Zhilei Tan
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, 300457, PR China.
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, PR China.
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China.
| | - Shiru Jia
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science and Technology, Tianjin, 300457, PR China.
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin, 300457, PR China.
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, PR China.
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Clark JH, Farmer TJ, Ingram IDV, Lie Y, North M. Renewable Self-Blowing Non-Isocyanate Polyurethane Foams from Lysine and Sorbitol. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800665] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- James H. Clark
- Department of Chemistry University of York; Green Chemistry Centre of Excellence; YO10 5DD York UK
| | - Thomas J. Farmer
- Department of Chemistry University of York; Green Chemistry Centre of Excellence; YO10 5DD York UK
| | - Ian D. V. Ingram
- Department of Chemistry University of York; Green Chemistry Centre of Excellence; YO10 5DD York UK
| | - Yann Lie
- Department of Chemistry University of York; Green Chemistry Centre of Excellence; YO10 5DD York UK
| | - Michael North
- Department of Chemistry University of York; Green Chemistry Centre of Excellence; YO10 5DD York UK
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6
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Zhang H, Li Y, Wang C, Wang X. Understanding the high L-valine production in Corynebacterium glutamicum VWB-1 using transcriptomics and proteomics. Sci Rep 2018; 8:3632. [PMID: 29483542 PMCID: PMC5827029 DOI: 10.1038/s41598-018-21926-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/13/2018] [Indexed: 01/27/2023] Open
Abstract
Toward the elucidation of the advanced mechanism of l-valine production by Corynebacterium glutamicum, a highly developed industrial strain VWB-1 was analyzed, employing the combination of transcriptomics and proteomics methods. The transcriptional level of 1155 genes and expression abundance of 96 proteins were changed significantly by the transcriptome and proteome comparison of VWB-1 and ATCC 13869. It was indicated that the key genes involved in the biosynthesis of l-valine, ilvBN, ilvC, ilvD, ilvE were up-regulated in VWB-1, which together made prominent contributions in improving the carbon flow towards l-valine. The l-leucine and l-isoleucine synthesis ability were weakened according to the down-regulation of leuB and ilvA. The up-regulation of the branched chain amino acid transporter genes brnFE promoted the l-valine secretion capability of VWB-1. The NADPH and ATP generation ability of VWB-1 were strengthened through the up-regulation of the genes involved in phosphate pentose pathway and TCA pathway. Pyruvate accumulation was achieved through the weakening of the l-lactate, acetate and l-alanine pathways. The up-regulation of the genes coding for elongation factors and ribosomal proteins were beneficial for l-valine synthesis in C. glutamicum. All information acquired were useful for the genome breeding of better industrial l-valine producing strains.
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Affiliation(s)
- Hailing Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Yanyan Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Chenhui Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China. .,School of Biotechnology, Jiangnan University, Wuxi, 214122, China. .,Synergetic Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, 214122, China.
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7
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Qayyum S, Khan I, Bhatti ZA, Peng C. Cloning and characterization of F3PYC gene encoding pyruvate carboxylase in Aspergillus flavus strain (F3). 3 Biotech 2017; 7:245. [PMID: 28710744 DOI: 10.1007/s13205-017-0806-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/06/2017] [Indexed: 11/24/2022] Open
Abstract
Pyruvate carboxylase is a major enzyme for biosynthesis of organic acids like; citric acid, fumeric acid, and L-malic acid. These organic acids play very important role for biological remediation of heavy metals. In this study, gene walking method was used to clone and characterize pyruvate carboxylase gene (F3PYC) from heavy metal resistant indigenous fungal isolate Aspergillus flavus (F3). 3579 bp of an open reading frame which encodes 1193 amino acid protein (isoelectric point: 6.10) with a calculated molecular weight of 131.2008 kDa was characterized. Deduced protein showed 90-95% similarity to those deduced from PYC gene from different fungal strains including; Aspergillus parasiticus, Neosartorya fischeri, Aspergillus fumigatus, Aspergillus clavatus, and Aspergillus niger. Protein generated from the PYC gene was a homotetramer (α4) and having four potential N-linked glycosylation sites and had no signal peptide. Amongst most possible N-glycosylation sites were -N-S-S-I- at 36 amino acid, -N-G-T-V- at 237 amino acid, N-G-S-S- at 517 amino acid, and N-T-S-R- at 1111 amino acid, with several functions have been proposed for the carbohydrate moiety such as thermal stability, pH, and temperature optima for activity and stabilization of the three-dimensional structure. Hence, cloning of F3PYC gene from A. flavus has important biotechnological applications.
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Affiliation(s)
- Sadia Qayyum
- The Key Lab of Marine Environmental Science and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
- Department of Microbiology, Hazara University, Manshera, 21300, Pakistan
| | - Ibrar Khan
- Department of Microbiology, Hazara University, Manshera, 21300, Pakistan
| | - Zulfiqar Ahmad Bhatti
- Environmental Sciences Department, COMSATS Institute of Information Technology, Abbottabad, 22060, Pakistan
| | - Changsheng Peng
- The Key Lab of Marine Environmental Science and Ecology, Ministry of Education, Ocean University of China, Qingdao, 266100, China.
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
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Wang Y, Li Q, Zheng P, Guo Y, Wang L, Zhang T, Sun J, Ma Y. Evolving the L-lysine high-producing strain of Escherichia coli using a newly developed high-throughput screening method. J Ind Microbiol Biotechnol 2016; 43:1227-35. [PMID: 27369765 PMCID: PMC4983297 DOI: 10.1007/s10295-016-1803-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 06/22/2016] [Indexed: 12/30/2022]
Abstract
This study provided a new method which applied a selected L-lysine-inducible promoter for evolving lysine industrial strains of E. coli. According to the intracellular levels of the enhanced green fluorescent protein (EGFP) whose expression was controlled by the promoter, 186 strains were preliminarily selected using fluorescence-activated cell sorting from a 10-million-mutant library generated from a L-lysine high-producing E. coli strain. By subsequent multiple parameter evaluation of the 186 selected strains according to the concentration and the yield of lysine, the productivity per unit of cell in 96-deep-well blocks, two mutants MU-1 and MU-2 were obtained. They produced 136.51 ± 1.55 and 133.2 9 ± 1.42 g/L of lysine, respectively, in 5-L jars. Compared with the lysine concentration and the yield of the original strain, those of strain MU-1 improved by 21.00 and 9.05 %, respectively, and those of strain MU-2 improved by 18.14 and 10.41 %, respectively. The mutant selection and evaluation system newly established in our study should be useful for continuous improvement of the current E. coli strains in the lysine industry.
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Affiliation(s)
- Yan Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Qinggang Li
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Ping Zheng
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China. .,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China.
| | - Yanmei Guo
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Lixian Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
| | - Tongcun Zhang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, People's Republic of China
| | - Jibin Sun
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China. .,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China.
| | - Yanhe Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, People's Republic of China
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Razak MA, Viswanath B. Comparative studies for the biotechnological production of L-Lysine by immobilized cells of wild-type Corynebacterium glutamicum ATCC 13032 and mutant MH 20-22 B. 3 Biotech 2015; 5:765-774. [PMID: 28324528 PMCID: PMC4569635 DOI: 10.1007/s13205-015-0275-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 01/12/2015] [Indexed: 12/03/2022] Open
Abstract
Establishing a cost and time efficient approach for bioprocess optimization is desired but is challenging. In the present work, we have addressed the effectiveness of using immobilized cells for aerobic processes, behaviour of immobilized cells, optimization and upstream bioprocess analysis for the production of lysine by immobilized cells of Corynebacterium glutamicum ATCC 13032 and MH 20-22 B in stirred tank bioreactor. Optimized operational conditions for maximal yield and productivity were determined with six parameters i.e., pH, temperature, fermentation time, airflow rate, glucose concentration and aeration rate. With the obtained results, it was evident that the optimum values for the upstream parameters viz., fermentation time, pH, temperature, glucose concentration, air flow rate and agitation rate are 96 h, 7.5, 30 °C, 90 g/l, 1.0 vvm and 200 rpm for both immobilized cells of C. glutamicum ATCC 13032 and MH 20-22 B. Immobilized cells of C. glutamicum MH 20-22 B, which is a leucine auxotroph has yielded more L-lysine compare to the immobilized cells of wild type strain C. glutamicum ATCC 13032.
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Affiliation(s)
- Meerza Abdul Razak
- Natco Pharma Limited, Natco House, Road No. 2, Banjara Hills, Hyderabad, 500 034, India
| | - Buddolla Viswanath
- Department of Virology, Sri Venkateswara University, Tirupati, 517502, A. P, India.
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10
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Efflux systems in bacteria and their metabolic engineering applications. Appl Microbiol Biotechnol 2015; 99:9381-93. [PMID: 26363557 DOI: 10.1007/s00253-015-6963-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/20/2015] [Accepted: 08/22/2015] [Indexed: 10/23/2022]
Abstract
The production of valuable chemicals from metabolically engineered microbes can be limited by excretion from the cell. Efflux is often overlooked as a bottleneck in metabolic pathways, despite its impact on alleviating feedback inhibition and product toxicity. In the past, it has been assumed that endogenous efflux pumps and membrane porins can accommodate product efflux rates; however, there are an increasing number of examples wherein overexpressing efflux systems is required to improve metabolite production. In this review, we highlight specific examples from the literature where metabolite export has been studied to identify unknown transporters, increase tolerance to metabolites, and improve the production capabilities of engineered bacteria. The review focuses on the export of a broad spectrum of valuable chemicals including amino acids, sugars, flavins, biofuels, and solvents. The combined set of examples supports the hypothesis that efflux systems can be identified and engineered to confer export capabilities on industrially relevant microbes.
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Zhang J, Zhou X, Wang D, Zhou X, Yun F, Tan S. A Comprehensive Study of Extraction of L-Lysine withSec-Octylphenoxy Acetic Acid in Sulfonated Kerosene. SEP SCI TECHNOL 2014. [DOI: 10.1080/01496395.2013.876047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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12
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Pátek M, Holátko J, Busche T, Kalinowski J, Nešvera J. Corynebacterium glutamicum promoters: a practical approach. Microb Biotechnol 2013; 6:103-17. [PMID: 23305350 PMCID: PMC3917453 DOI: 10.1111/1751-7915.12019] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 11/05/2012] [Accepted: 11/08/2012] [Indexed: 11/27/2022] Open
Abstract
Transcription initiation is the key step in gene expression in bacteria, and it is therefore studied for both theoretical and practical reasons. Promoters, the traffic lights of transcription initiation, are used as construction elements in biotechnological efforts to coordinate ‘green waves’ in the metabolic pathways leading to the desired metabolites. Detailed analyses of Corynebacterium glutamicum promoters have already provided large amounts of data on their structures, regulatory mechanisms and practical capabilities in metabolic engineering. In this minireview the main aspects of promoter studies, the methods developed for their analysis and their practical use in C. glutamicum are discussed. These include definitions of the consensus sequences of the distinct promoter classes, promoter localization and characterization, activity measurements, the functions of transcriptional regulators and examples of practical uses of constitutive, inducible and modified promoters in biotechnology. The implications of the introduction of novel techniques, such as in vitro transcription and RNA sequencing, to C. glutamicum promoter studies are outlined.
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Affiliation(s)
- Miroslav Pátek
- Institute of Microbiology AS CR, vvi, Prague 4, Czech Republic.
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13
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Fazius F, Shelest E, Gebhardt P, Brock M. The fungal α-aminoadipate pathway for lysine biosynthesis requires two enzymes of the aconitase family for the isomerization of homocitrate to homoisocitrate. Mol Microbiol 2012; 86:1508-30. [PMID: 23106124 PMCID: PMC3556520 DOI: 10.1111/mmi.12076] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2012] [Indexed: 11/30/2022]
Abstract
Fungi produce α-aminoadipate, a precursor for penicillin and lysine via the α-aminoadipate pathway. Despite the biotechnological importance of this pathway, the essential isomerization of homocitrate via homoaconitate to homoisocitrate has hardly been studied. Therefore, we analysed the role of homoaconitases and aconitases in this isomerization. Although we confirmed an essential contribution of homoaconitases from Saccharomyces cerevisiae and Aspergillus fumigatus, these enzymes only catalysed the interconversion between homoaconitate and homoisocitrate. In contrast, aconitases from fungi and the thermophilic bacterium Thermus thermophilus converted homocitrate to homoaconitate. Additionally, a single aconitase appears essential for energy metabolism, glutamate and lysine biosynthesis in respirating filamentous fungi, but not in the fermenting yeast S. cerevisiae that possesses two contributing aconitases. While yeast Aco1p is essential for the citric acid cycle and, thus, for glutamate synthesis, Aco2p specifically and exclusively contributes to lysine biosynthesis. In contrast, Aco2p homologues present in filamentous fungi were transcribed, but enzymatically inactive, revealed no altered phenotype when deleted and did not complement yeast aconitase mutants. From these results we conclude that the essential requirement of filamentous fungi for respiration versus the preference of yeasts for fermentation may have directed the evolution of aconitases contributing to energy metabolism and lysine biosynthesis.
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Affiliation(s)
- Felicitas Fazius
- Microbial Biochemistry and Physiology, Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knoell-Institute, Beutenbergstr. 11a, 07745 Jena, Germany
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Reductive whole-cell biotransformation with Corynebacterium glutamicum: improvement of NADPH generation from glucose by a cyclized pentose phosphate pathway using pfkA and gapA deletion mutants. Appl Microbiol Biotechnol 2012; 97:143-52. [PMID: 22851018 PMCID: PMC3536970 DOI: 10.1007/s00253-012-4314-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 07/16/2012] [Accepted: 07/16/2012] [Indexed: 11/02/2022]
Abstract
In this study, the potential of Corynebacterium glutamicum for reductive whole-cell biotransformation is shown. The NADPH-dependent reduction of the prochiral methyl acetoacetate (MAA) to the chiral (R)-methyl 3-hydroxybutyrate (MHB) by an alcohol dehydrogenase from Lactobacillus brevis (Lbadh) was used as model reaction and glucose served as substrate for the regeneration of NADPH. Since NADPH is mainly formed in the oxidative branch of the pentose phosphate pathway (PPP), C. glutamicum was engineered to redirect carbon flux towards the PPP. Mutants lacking the genes for 6-phosphofructokinase (pfkA) or glyceraldehyde 3-phosphate dehydrogenase (gapA) were constructed and analyzed with respect to growth, enzyme activities, and biotransformation performance. Both mutants showed strong growth defects in glucose minimal medium. For biotransformation of MAA to MHB using glucose as reductant, strains were transformed with an Lbadh expression plasmid. The wild type showed a specific MHB production rate of 3.1 mmol(MHB) h(-1) g (cdw) (-1) and a yield of 2.7 mol(MHB) mol (glucose) (-1) . The ∆pfkA mutant showed a similar MHB production rate, but reached a yield of 4.8 mol(MHB) mol (glucose) (-1) , approaching the maximal value of 6 mol(NADPH) mol (glucose) (-1) expected for a partially cyclized PPP. The specific biotransformation rate of the ΔgapA mutant was decreased by 62 % compared to the other strains, but the yield was increased to 7.9 mol(MHB) mol (glucose) (-1) , which to our knowledge is the highest one reported so far for this mode of NADPH regeneration. As one fourth of the glucose was converted to glycerol, the experimental yield was close to the theoretically maximal yield of 9 mol(NADPH) mol (glucose) (-1) .
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Brunet R, Guillén-Gosálbez G, Pérez-Correa JR, Caballero JA, Jiménez L. Hybrid simulation-optimization based approach for the optimal design of single-product biotechnological processes. Comput Chem Eng 2012. [DOI: 10.1016/j.compchemeng.2011.07.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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16
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Kuhn D, Blank LM, Schmid A, Bühler B. Systems biotechnology - Rational whole-cell biocatalyst and bioprocess design. Eng Life Sci 2010. [DOI: 10.1002/elsc.201000009] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Overexpression of wild-type aspartokinase increases L-lysine production in the thermotolerant methylotrophic bacterium Bacillus methanolicus. Appl Environ Microbiol 2008; 75:652-61. [PMID: 19060158 DOI: 10.1128/aem.01176-08] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aspartokinase (AK) controls the carbon flow into the aspartate pathway for the biosynthesis of the amino acids l-methionine, l-threonine, l-isoleucine, and l-lysine. We report here the cloning of four genes (asd, encoding aspartate semialdehyde dehydrogenase; dapA, encoding dihydrodipicolinate synthase; dapG, encoding AKI; and yclM, encoding AKIII) of the aspartate pathway in Bacillus methanolicus MGA3. Together with the known AKII gene lysC, dapG and yclM form a set of three AK genes in this organism. Overexpression of dapG, lysC, and yclM increased l-lysine production in wild-type B. methanolicus strain MGA3 2-, 10-, and 60-fold (corresponding to 11 g/liter), respectively, without negatively affecting the specific growth rate. The production levels of l-methionine (less than 0.5 g/liter) and l-threonine (less than 0.1 g/liter) were low in all recombinant strains. The AK proteins were purified, and biochemical analyses demonstrated that they have similar V(max) values (between 47 and 58 micromol/min/mg protein) and K(m) values for l-aspartate (between 1.9 and 5.0 mM). AKI and AKII were allosterically inhibited by meso-diaminopimelate (50% inhibitory concentration [IC(50)], 0.1 mM) and by l-lysine (IC(50), 0.3 mM), respectively. AKIII was inhibited by l-threonine (IC(50), 4 mM) and by l-lysine (IC(50), 5 mM), and this enzyme was synergistically inhibited in the presence of both of these amino acids at low concentrations. The correlation between the impact on l-lysine production in vivo and the biochemical properties in vitro of the individual AK proteins is discussed. This is the first example of improving l-lysine production by metabolic engineering of B. methanolicus and also the first documentation of considerably increasing l-lysine production by overexpression of a wild-type AK.
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Developments and achievements in microbial production of amino acids at the institute of microbiology—BAS. J Biotechnol 2008. [DOI: 10.1016/j.jbiotec.2008.07.624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Sanchez S, Demain AL. Metabolic regulation and overproduction of primary metabolites. Microb Biotechnol 2008; 1:283-319. [PMID: 21261849 PMCID: PMC3815394 DOI: 10.1111/j.1751-7915.2007.00015.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Revised: 10/04/2007] [Accepted: 10/23/2007] [Indexed: 12/01/2022] Open
Abstract
Overproduction of microbial metabolites is related to developmental phases of microorganisms. Inducers, effectors, inhibitors and various signal molecules play a role in different types of overproduction. Biosynthesis of enzymes catalysing metabolic reactions in microbial cells is controlled by well-known positive and negative mechanisms, e.g. induction, nutritional regulation (carbon or nitrogen source regulation), feedback regulation, etc. The microbial production of primary metabolites contributes significantly to the quality of life. Fermentative production of these compounds is still an important goal of modern biotechnology. Through fermentation, microorganisms growing on inexpensive carbon and nitrogen sources produce valuable products such as amino acids, nucleotides, organic acids and vitamins which can be added to food to enhance its flavour, or increase its nutritive values. The contribution of microorganisms goes well beyond the food and health industries with the renewed interest in solvent fermentations. Microorganisms have the potential to provide many petroleum-derived products as well as the ethanol necessary for liquid fuel. Additional applications of primary metabolites lie in their impact as precursors of many pharmaceutical compounds. The roles of primary metabolites and the microbes which produce them will certainly increase in importance as time goes on. In the early years of fermentation processes, development of producing strains initially depended on classical strain breeding involving repeated random mutations, each followed by screening or selection. More recently, methods of molecular genetics have been used for the overproduction of primary metabolic products. The development of modern tools of molecular biology enabled more rational approaches for strain improvement. Techniques of transcriptome, proteome and metabolome analysis, as well as metabolic flux analysis. have recently been introduced in order to identify new and important target genes and to quantify metabolic activities necessary for further strain improvement.
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Affiliation(s)
- Sergio Sanchez
- Departamento de Biologia Molecular y Biotecnologia, Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de Mexico (UNAM), Mexico City, Mexico
| | - Arnold L. Demain
- Research Institute for Scientists Emeriti (RISE), Drew University, Madison, NJ 07940, USA
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Gayen K, Venkatesh KV. A phenomenological model to represent the kinetics of growth by Corynebacterium glutamicum for lysine production. J Ind Microbiol Biotechnol 2007; 34:363-72. [PMID: 17256152 DOI: 10.1007/s10295-007-0205-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2006] [Accepted: 12/29/2006] [Indexed: 11/29/2022]
Abstract
Corynebacterium glutamicum is commonly used for lysine production. In the last decade, several metabolic engineering approaches have been successfully applied to C. glutamicum. However, only few studies have been focused on the kinetics of growth and lysine production. Here, we present a phenomenological model that captures the growth and lysine production during different phases of fermentation at various initial dextrose concentrations. The model invokes control coefficients to capture the dynamics of lysine and trehalose synthesis. The analysis indicated that maximum lysine productivity can be obtained using 72 g/L of initial dextrose concentration in the media, while growth was optimum at 27 g/L of dextrose concentration. The predictive capability was demonstrated through a two-stage fermentation strategy to enhance the productivity of lysine by 1.5 times of the maximum obtained in the batch fermentation. Two-stage fermentation indicated that the kinetic model could be further extended to predict the optimal feeding strategy for fed-batch fermentation.
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Affiliation(s)
- Kalyan Gayen
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Lai H, Kraszewski JL, Purwantini E, Mukhopadhyay B. Identification of pyruvate carboxylase genes in Pseudomonas aeruginosa PAO1 and development of a P. aeruginosa-based overexpression system for alpha4- and alpha4beta4-type pyruvate carboxylases. Appl Environ Microbiol 2006; 72:7785-92. [PMID: 16997990 PMCID: PMC1694264 DOI: 10.1128/aem.01564-06] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pyruvate carboxylase (PYC) is an ecologically, medically, and industrially important enzyme. It is widespread in all three domains of life, the archaea, bacteria, and eukarya. PYC catalyzes ATP-dependent carboxylation of pyruvate to oxaloacetate. Detailed structure-function studies of this enzyme have been hampered due to the unavailability of a facile recombinant overexpression system. Except for the alpha4 enzyme from a thermophilic Bacillus species, Escherichia coli has been unsuitable for overexpression of PYCs. We show that a Pseudomonas aeruginosa strain carrying the T7 polymerase gene can serve as a host for the overexpression of Mycobacterium smegmatis alpha4 PYC and Pseudomonas aeruginosa alpha4beta4 PYC under the control of the T7 promoter from a broad-host-range conjugative plasmid. Overexpression occurred both in aerobic (LB medium) and nitrate-respiring anaerobic (LB medium plus glucose and nitrate) cultures. The latter system presented a simpler option because it involved room temperature cultures in stationary screw-cap bottles. We also developed a P. aeruginosa Deltapyc strain that allowed the expression of recombinant PYCs in the absence of the native enzyme. Since P. aeruginosa can be transformed genetically and lysed for cell extract preparation rather easily, our system will facilitate site-directed mutagenesis, kinetics, X-ray crystallographic, and nuclear magnetic resonance-based structure-function analysis of PYCs. During this work we also determined that, contrary to a previous report (C. K. Stover et al., Nature 406:959-964, 2000), the open reading frame (ORF) PA1400 does not encode a PYC in P. aeruginosa. The alpha4beta4 PYC of this organism was encoded by the ORFs PA5436 and PA5435.
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Affiliation(s)
- Huafang Lai
- Virginia Bioinformatics Institute, Department of Biochemistry, Virginia Polytechnic Institute and State University, Washington Street, MC 0477, Blacksburg, VA 24061, USA
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Oldiges M, Noack S, Wahl A, Qeli E, Freisleben B, Wiechert W. From Enzyme Kinetics to Metabolic Network Modeling – Visualization Tool for Enhanced Kinetic Analysis of Biochemical Network Models. Eng Life Sci 2006. [DOI: 10.1002/elsc.200620911] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Usuda Y, Kurahashi O. Effects of deregulation of methionine biosynthesis on methionine excretion in Escherichia coli. Appl Environ Microbiol 2005; 71:3228-34. [PMID: 15933025 PMCID: PMC1151843 DOI: 10.1128/aem.71.6.3228-3234.2005] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several regulators of methionine biosynthesis have been reported in Escherichia coli, which might represent barriers to the production of excess l-methionine (Met). In order to examine the effects of these factors on Met biosynthesis and metabolism, deletion mutations of the methionine repressor (metJ) and threonine biosynthetic (thrBC) genes were introduced into the W3110 wild-type strain of E. coli. Mutations of the metK gene encoding S-adenosylmethionine synthetase, which is involved in Met metabolism, were detected in 12 norleucine-resistant mutants. Three of the mutations in the metK structural gene were then introduced into metJ and thrBC double-mutant strains; one of the resultant strains was found to accumulate 0.13 g/liter Met. Mutations of the metA gene encoding homoserine succinyltransferase were detected in alpha-methylmethionine-resistant mutants, and these mutations were found to encode feedback-resistant enzymes in a 14C-labeled homoserine assay. Three metA mutations were introduced, using expression plasmids, into an E. coli strain that was shown to accumulate 0.24 g/liter Met. Combining mutations that affect the deregulation of Met biosynthesis and metabolism is therefore an effective approach for the production of Met-excreting strains.
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Affiliation(s)
- Yoshihiro Usuda
- Fermentation & Biotechnology Laboratories, Institute of Life Sciences, Ajinomoto Co. Inc., 1-1 Suzuki-cho, Kawasaki-ku, Kawasaki-shi 210-8681, Japan.
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Tryfona T, Bustard MT. Fermentative production of lysine by Corynebacterium glutamicum: transmembrane transport and metabolic flux analysis. Process Biochem 2005. [DOI: 10.1016/j.procbio.2004.01.037] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Kim YH, Park JS, Cho JY, Cho K, Park YH, Lee J. Proteomic response analysis of a threonine-overproducing mutant of Escherichia coli. Biochem J 2004; 381:823-9. [PMID: 15104539 PMCID: PMC1133892 DOI: 10.1042/bj20031763] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2003] [Revised: 04/21/2004] [Accepted: 04/23/2004] [Indexed: 11/17/2022]
Abstract
The proteomic response of a threonine-overproducing mutant of Escherichia coli was quantitatively analysed by two-dimensional electrophoresis. Evidently, 12 metabolic enzymes that are involved in threonine biosynthesis showed a significant difference in intracellular protein level between the mutant and native strain. The level of malate dehydrogenase was more than 30-fold higher in the mutant strain, whereas the synthesis of citrate synthase seemed to be severely inhibited in the mutant. Therefore, in the mutant, it is probable that the conversion of oxaloacetate into citrate was severely inhibited, but the oxidation of malate to oxaloacetate was significantly up-regulated. Accumulation of oxaloacetate may direct the metabolic flow towards the biosynthetic route of aspartate, a key metabolic precursor of threonine. Synthesis of aspartase (aspartate ammonia-lyase) was significantly inhibited in the mutant strain, which might lead to the enhanced synthesis of threonine by avoiding unfavourable degradation of aspartate to fumarate and ammonia. Synthesis of threonine dehydrogenase (catalysing the degradation of threonine finally back to pyruvate) was also significantly down-regulated in the mutant. The far lower level of cystathionine beta-lyase synthesis in the mutant seems to result in the accumulation of homoserine, another key precursor of threonine. In the present study, we report that the accumulation of important threonine precursors, such as oxaloacetate, aspartate and homoserine, and the inhibition of the threonine degradation pathway played a critical role in increasing the threonine biosynthesis in the E. coli mutant.
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Affiliation(s)
- Yang-Hoon Kim
- *Department of Chemical and Biological Engineering, Korea University, Anam-Dong 5-1, Sungbuk-Ku, Seoul 136-701, South Korea
| | - Jin-Seung Park
- *Department of Chemical and Biological Engineering, Korea University, Anam-Dong 5-1, Sungbuk-Ku, Seoul 136-701, South Korea
| | - Jae-Yong Cho
- †Department of Bioindustry and Technology, Sangji University, 660 Wonju-Si, Kangwon-Do 220-702, South Korea
| | - Kwang Myung Cho
- ‡R&D Center for Bioproducts, Institute of Science and Technology, CJ Corporation, Ichon-Si, Kyongggi-Do 467-810, South Korea
| | - Young-Hoon Park
- ‡R&D Center for Bioproducts, Institute of Science and Technology, CJ Corporation, Ichon-Si, Kyongggi-Do 467-810, South Korea
- Correspondence may be addressed to either author (e-mail )
| | - Jeewon Lee
- *Department of Chemical and Biological Engineering, Korea University, Anam-Dong 5-1, Sungbuk-Ku, Seoul 136-701, South Korea
- Correspondence may be addressed to either author (e-mail )
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Netzer R, Peters-Wendisch P, Eggeling L, Sahm H. Cometabolism of a nongrowth substrate: L-serine utilization by Corynebacterium glutamicum. Appl Environ Microbiol 2004; 70:7148-55. [PMID: 15574911 PMCID: PMC535176 DOI: 10.1128/aem.70.12.7148-7155.2004] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2004] [Accepted: 07/31/2004] [Indexed: 11/20/2022] Open
Abstract
Despite its key position in central metabolism, L-serine does not support the growth of Corynebacterium glutamicum. Nevertheless, during growth on glucose, L-serine is consumed at rates up to 19.4 +/- 4.0 nmol min(-1) (mg [dry weight])(-1), resulting in the complete consumption of 100 mM L-serine in the presence of 100 mM glucose and an increased growth yield of about 20%. Use of 13C-labeled L-serine and analysis of cellularly derived metabolites by nuclear magnetic resonance spectroscopy revealed that the carbon skeleton of L-serine is mainly converted to pyruvate-derived metabolites such as L-alanine. The sdaA gene was identified in the genome of C. glutamicum, and overexpression of sdaA resulted in (i) functional L-serine dehydratase (L-SerDH) activity, and therefore conversion of L-serine to pyruvate, and (ii) growth of the recombinant strain on L-serine as the single substrate. In contrast, deletion of sdaA decreased the L-serine cometabolism rate with glucose by 47% but still resulted in degradation of L-serine to pyruvate. Cystathionine beta-lyase was additionally found to convert L-serine to pyruvate, and the respective metC gene was induced 2.4-fold under high internal L-serine concentrations. Upon sdaA overexpression, the growth rate on glucose is reduced 36% from that of the wild type, illustrating that even with glucose as a single substrate, intracellular L-serine conversion to pyruvate might occur, although probably the weak affinity of L-SerDH (apparent Km, 11 mM) prevents substantial L-serine degradation.
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Affiliation(s)
- Roman Netzer
- Institut für Biotechnologie, Forschungszentrum Jülich GmbH, Jülich, Germany
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Danchin A. The bag or the spindle: the cell factory at the time of systems' biology. Microb Cell Fact 2004; 3:13. [PMID: 15537427 PMCID: PMC534799 DOI: 10.1186/1475-2859-3-13] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2004] [Accepted: 11/10/2004] [Indexed: 11/10/2022] Open
Abstract
Genome programs changed our view of bacteria as cell factories, by making them amenable to systematic rational improvement. As a first step, isolated genes (including those of the metagenome), or small gene clusters are improved and expressed in a variety of hosts. New techniques derived from functional genomics (transcriptome, proteome and metabolome studies) now allow users to shift from this single-gene approach to a more integrated view of the cell, where it is more and more considered as a factory. One can expect in the near future that bacteria will be entirely reprogrammed, and perhaps even created de novo from bits and pieces, to constitute man-made cell factories. This will require exploration of the landscape made of neighbourhoods of all the genes in the cell. Present work is already paving the way for that futuristic view of bacteria in industry.
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Affiliation(s)
- Antoine Danchin
- Genetics of Bacterial Genomes, Institut Pasteur, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
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Hermann T. Using functional genomics to improve productivity in the manufacture of industrial biochemicals. Curr Opin Biotechnol 2004; 15:444-8. [PMID: 15464376 DOI: 10.1016/j.copbio.2004.07.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent developments in the field of functional genomics have been used to increase productivity in the manufacture of industrial biochemicals. Technologies like transcriptomics and proteomics have profited from the increasing number of genome sequencing projects. Meanwhile functional genomics has evolved from several isolated technologies, such as DNA chip technology and proteomics, to combined approaches that can help us to understand why organisms produce a certain product. The combination of expression studies and kinetic studies, such as carbon flux determination or metabolite measurements, has significantly improved productivity in production processes.
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Affiliation(s)
- Thomas Hermann
- Degussa AG, Feed Additives, Research and Development, Kantstrasse 2, 33790 Halle/Westfalen, Germany.
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Barrett E, Stanton C, Zelder O, Fitzgerald G, Ross RP. Heterologous expression of lactose- and galactose-utilizing pathways from lactic acid bacteria in Corynebacterium glutamicum for production of lysine in whey. Appl Environ Microbiol 2004; 70:2861-6. [PMID: 15128544 PMCID: PMC404391 DOI: 10.1128/aem.70.5.2861-2866.2004] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genetic determinants for lactose utilization from Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 and galactose utilization from Lactococcus lactis subsp. cremoris MG 1363 were heterologously expressed in the lysine-overproducing strain Corynebacterium glutamicum ATCC 21253. The C. glutamicum strains expressing the lactose permease and beta-galactosidase genes of L. delbrueckii subsp. bulgaricus exhibited beta-galactosidase activity in excess of 1000 Miller units/ml of cells and were able to grow in medium in which lactose was the sole carbon source. Similarly, C. glutamicum strains containing the lactococcal aldose-1-epimerase, galactokinase, UDP-glucose-1-P-uridylyltransferase, and UDP-galactose-4-epimerase genes in association with the lactose permease and beta-galactosidase genes exhibited beta-galactosidase levels in excess of 730 Miller units/ml of cells and were able to grow in medium in which galactose was the sole carbon source. When grown in whey-based medium, the engineered C. glutamicum strain produced lysine at concentrations of up to 2 mg/ml, which represented a 10-fold increase over the results obtained with the lactose- and galactose-negative control, C. glutamicum 21253. Despite their increased catabolic flexibility, however, the modified corynebacteria exhibited slower growth rates and plasmid instability.
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Affiliation(s)
- Eoin Barrett
- Dairy Products Research Centre, Teagasc, Moorepark, Fermoy, Ireland
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Brett D, Droege M, Weber-Lehmann J. Optimization of industrial bacterial strains via mutation analysis: a high-throughput DNA sequencing and bioinformatic approach. IEEE ENGINEERING IN MEDICINE AND BIOLOGY MAGAZINE : THE QUARTERLY MAGAZINE OF THE ENGINEERING IN MEDICINE & BIOLOGY SOCIETY 2004; 23:74-6. [PMID: 15508388 DOI: 10.1109/memb.2004.1337953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
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Marx A, Hans S, Möckel B, Bathe B, de Graaf AA, McCormack AC, Stapleton C, Burke K, O'Donohue M, Dunican LK. Metabolic phenotype of phosphoglucose isomerase mutants of Corynebacterium glutamicum. J Biotechnol 2003; 104:185-97. [PMID: 12948638 DOI: 10.1016/s0168-1656(03)00153-6] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A series of experiments reported in the literature using fluxomics as an efficient functional genomics tool revealed that the L-lysine production of the Corynebacterium glutamicum strain MH20-22B correlates with the extent of intracellular NADPH supply. Some alternative metabolic engineering strategies to increase intracellular NADPH supply in the C. glutamicum strain DSM5715 were considered and finally the redirection of carbon flux through the pentose phosphate pathway with two NADPH generating enzymatic reactions was favored. Elsewhere, the construction of a phosphoglucose isomerase (Pgi) null mutant of the C. glutamicum strain DSM5715 has been described by utilizing genetic engineering as well as some aspects of its metabolic phenotype. Most interestingly, it was shown that not only could the L-lysine formation be increased by 1.7-fold but the by-product concentration for the null mutant strain was also able to be drastically reduced. In this publication we discuss this metabolic phenotype in detail and present additional data on by-product formation as well as yield considerations. Results from isotope based metabolic flux analysis in combination with considerations on NADPH metabolism clearly exclude the existence of Pgi isoenzymes in C. glutamicum strain DSM5715. The genome region containing the pgi gene was analyzed. It cannot be excluded that polar effects might have been caused by the disruption of the pgi gene and might have contributed to the observed metabolic phenotype of C. glutamicum Pgi mutants. We illustrate growth characteristics of a Pgi mutant of an industrial L-lysine production strain. A reduced growth rate and a biphasic growth behavior was observed. The importance of NADPH reoxidation for well balanced growth in Pgi mutants is discussed. Another phosphoglucose isomerase mutant of C. glutamicum has been described in literature with which an increase in L-lysine yield from 42 to 52% was observed. This finding highlights the general potential of metabolic flux redirection towards the pentose phosphate pathway, which could be used for metabolic engineering of the biotechnological synthesis of (1) aromatic amino acids and (2) chemicals whose synthesis depends on intracellular NADPH supply.
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Affiliation(s)
- Achim Marx
- Degussa AG, Feed Additives, R&D Biotechnology, Kantstr. 2, D-33790 Halle, Westf., Germany.
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Enhancement of heterologous protein expression in Escherichia coli by co-expression of nonspecific DNA-binding stress protein, Dps. Enzyme Microb Technol 2003. [DOI: 10.1016/s0141-0229(03)00148-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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