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Li Y, Guo Y, Niu F, Gao H, Wang Q, Xu M. Regulation of oxidative stress response and antioxidant modification in Corynebacterium glutamicum. World J Microbiol Biotechnol 2024; 40:267. [PMID: 39004689 DOI: 10.1007/s11274-024-04066-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024]
Abstract
As an efficient and safe industrial bacterium, Corynebacterium glutamicum has extensive application in amino acid production. However, it often faces oxidative stress induced by reactive oxygen species (ROS), leading to diminished production efficiency. To enhance the robustness of C. glutamicum, numerous studies have focused on elucidating its regulatory mechanisms under various stress conditions such as heat, acid, and sulfur stress. However, a comprehensive review of its defense mechanisms against oxidative stress is needed. This review offers an in-depth overview of the mechanisms C. glutamicum employs to manage oxidative stress. It covers both enzymatic and non-enzymatic systems, including antioxidant enzymes, regulatory protein families, sigma factors involved in transcription, and physiological redox reduction pathways. This review provides insights for advancing research on the antioxidant mechanisms of C. glutamicum and sheds light on its potential applications in industrial production.
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Affiliation(s)
- Yueshu Li
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Yuanyi Guo
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Fangyuan Niu
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Hui Gao
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Qing Wang
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
| | - Meijuan Xu
- The Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
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Verbeelen T, Fernandez CA, Nguyen TH, Gupta S, Leroy B, Wattiez R, Vlaeminck SE, Leys N, Ganigué R, Mastroleo F. Radiotolerance of N-cycle bacteria and their transcriptomic response to low-dose space-analogue ionizing irradiation. iScience 2024; 27:109596. [PMID: 38638570 PMCID: PMC11024918 DOI: 10.1016/j.isci.2024.109596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/08/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024] Open
Abstract
The advancement of regenerative life support systems (RLSS) is crucial to allow long-distance space travel. Within the Micro-Ecological Life Support System Alternative (MELiSSA), efficient nitrogen recovery from urine and other waste streams is vital to produce liquid fertilizer to feed food and oxygen production in subsequent photoautotrophic processes. This study explores the effects of ionizing radiation on nitrogen cycle bacteria that transform urea to nitrate. In particular, we assess the radiotolerance of Comamonas testosteroni, Nitrosomonas europaea, and Nitrobacter winogradskyi after exposure to acute γ-irradiation. Moreover, a comprehensive whole transcriptome analysis elucidates the effects of spaceflight-analogue low-dose ionizing radiation on the individual axenic strains and on their synthetic community o. This research sheds light on how the spaceflight environment could affect ureolysis and nitrification processes from a transcriptomic perspective.
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Affiliation(s)
- Tom Verbeelen
- Nuclear Medical Applications (NMA), Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400 Mol, Belgium
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Celia Alvarez Fernandez
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Thanh Huy Nguyen
- Department of Proteomics and Microbiology, University of Mons, Av. Du Champs de Mars 6, 7000 Mons, Belgium
| | - Surya Gupta
- Nuclear Medical Applications (NMA), Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400 Mol, Belgium
| | - Baptiste Leroy
- Department of Proteomics and Microbiology, University of Mons, Av. Du Champs de Mars 6, 7000 Mons, Belgium
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, University of Mons, Av. Du Champs de Mars 6, 7000 Mons, Belgium
| | - Siegfried E. Vlaeminck
- Research Group of Sustainable Energy, Air and Water Technology, Department of Bioscience Engineering, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- Centre for Advanced Process Technology for Urban REsource Recovery (CAPTURE), Frieda Saeysstraat 1, 9052 Ghent, Belgium
| | - Natalie Leys
- Nuclear Medical Applications (NMA), Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400 Mol, Belgium
| | - Ramon Ganigué
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000 Ghent, Belgium
- Centre for Advanced Process Technology for Urban REsource Recovery (CAPTURE), Frieda Saeysstraat 1, 9052 Ghent, Belgium
| | - Felice Mastroleo
- Nuclear Medical Applications (NMA), Belgian Nuclear Research Centre (SCK CEN), Boeretang 200, 2400 Mol, Belgium
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Huo Y, Mo J, He Y, Twagirayezu G, Xue L. Transcriptome analysis reveals manganese tolerance mechanisms in a novel native bacterium of Bacillus altitudinis strain HM-12. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 846:157394. [PMID: 35850333 DOI: 10.1016/j.scitotenv.2022.157394] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/11/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Bacillus altitudinis HM-12, isolated from ferromanganese ore tailings, can resist up to 1200 mM Mn(II) when exposed to concentrations from 50 mM to 1400 mM. HM-12 exhibited high Mn(II) removal efficiency (90.6 %). We report the transcriptional profile of HM-12 using RNA-Seq and found 423 upregulated and 536 downregulated differentially expressed genes (DEGs) compared to the control. Gene Ontology analysis showed that DEGs were mainly linked with transporter activity, binding, catalytic activity in molecular function, cellular anatomical entity in cellular component, cellular process, and metabolic process. Kyoto Encyclopedia of Genes and Genomes analysis showed that DEGs were mostly mapped to membrane transport, signal transduction, carbohydrate and amino acid metabolism, energy metabolism, and cellular community pathways. Transport analysis showed that two manganese importer systems, mntH and mntABC, were significantly downregulated. The manganese efflux genes (mneS, yceF and ykoY) exhibited significant upregulation. Manganese homeostasis seems to be subtly regulated by manganese uptake and efflux genes. Moreover, it was found that copA as a Mn(II) oxidase gene and a copper chaperone gene copZ were considerably upregulated by signal transduction analysis. csoR encoding a transcriptional repressor which can regulate the copZA operon was upregulated. The strong Mn(II) oxidizing activity of HM-12 was also confirmed by physicochemical characterization. In metabolism and environmental information processing, yjqC encoding manganese catalase was significantly upregulated, while katE and katX encoding heme catalases were significantly downregulated. The antioxidant gene pcaC was significantly upregulated, but ykuU encoding alkyl hydroperoxide reductase, yojM encoding superoxide dismutase, and perR encoding redox-sensing transcriptional repressor were downregulated. These results highlight the oxidative activity of HM-12 by regulating the transcription of oxidase, catalase, peroxidase, and superoxide dismutase to sense the cellular redox status and prevent Mn(II) intoxication. This study provides relevant information on the biological tolerance and oxidation mechanisms in response to Mn(II) stress.
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Affiliation(s)
- Yanli Huo
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Lanzhou 730070, China
| | - Jiarun Mo
- School of Life Sciences, Lanzhou University, Lanzhou 730070, China
| | - Yuanyuan He
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Lanzhou 730070, China
| | - Gratien Twagirayezu
- School of Environmental and Municipal Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China
| | - Lingui Xue
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou 730070, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering of Gansu Province, Lanzhou 730070, China.
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Lira-Parada PA, Tuveri A, Seibold GM, Bar N. Comparison of noninvasive, in-situ and external monitoring of microbial growth in fed-batch cultivations in Corynebacterium glutamicum. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.107989] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Chen C, Cui Z, Zhao J, Li S, Ren X, Chen T, Wang Z. Improving diacetyl production in Corynebacterium glutamicum via modifying respiratory chain. J Biotechnol 2021; 332:20-28. [PMID: 33771625 DOI: 10.1016/j.jbiotec.2021.03.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 03/03/2021] [Accepted: 03/16/2021] [Indexed: 12/11/2022]
Abstract
To explore the suitability of Corynebacterium glutamicum as a chassis for diacetyl production from glucose, diacetyl metabolic pathway and the respiratory chain were linked to achieve redox balance. The carbon flux was redirected from pyruvate to diacetyl by overexpressing the α-acetolactate synthase, in combination with disruption the biosynthetic pathways of lactate, acetoin, 2,3-butanediol and acetate in C. glutamicum ATCC 13032. These modifications resulted in a sharp increase of the NADH/NAD+ ratio from 0.53 to 1.10, and produced 0.58 g/L diacetyl under aerobic conditions, representing a 58-fold increase over the wild type. Although the modification of the by-product pathways is an effective strategy, these disruption led to intracellular cofactor imbalance. NADH re-oxidization was further successfully solved by overexpressing of cytochrome bd oxidase. We constructed an efficient respiration-dependent cell factory by modification of the respiratory chain, improving diacetyl titer to 1.29 g/L in CGC11, decreased NADH/NAD+ ratio to 0.45, increased the ATP concentration from 8.51 to 10.64 μM/gDCW. To our best knowledge, this is the first report of diacetyl synthesis in C. glutamicum. Intracellular cofactor imbalance can be reduced by modification of the respiratory chain for production of diacetyl as well as other bio-based products with cofactor imbalance in C. glutamicum.
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Affiliation(s)
- Cong Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China
| | - Zhenzhen Cui
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China
| | - Juntao Zhao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China
| | - Shuting Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China
| | - Xiaoting Ren
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China
| | - Tao Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China
| | - Zhiwen Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China.
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The osnR gene of Corynebacterium glutamicum plays a negative regulatory role in oxidative stress responses. ACTA ACUST UNITED AC 2019; 46:241-248. [DOI: 10.1007/s10295-018-02126-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 12/20/2018] [Indexed: 11/26/2022]
Abstract
Abstract
Among the Corynebacterium glutamicum ORFs that have been implicated in stress responses, we chose ORF cg3230, designated osnR, and analyzed it further. Unlike the osnR-deleted strain (ΔosnR), the osnR-overexpressing strain (P180-osnR) developed growth defects and increased sensitivity to various oxidants including H2O2. Transcription in the P180-osnR strain of genes such as sodA (superoxide dismutase), ftn (ferritin biosynthesis), and ahpD (alkyl hydroperoxide reductase; cg2674), which are involved in the detoxification of reactive oxygen species, was only 40% that of the wild type. However, transcription of katA, encoding H2O2-detoxifying catalase, was unchanged in this strain. Genes such as trxB (thioredoxin reductase) and mtr (mycothiol disulfide reductase), which play roles in redox homeostasis, also showed decreased transcription in the strain. 2D-PAGE analysis indicated that genes involved in redox reactions were considerably affected by osnR overexpression. The NADPH/NADP+ ratio of the P180-osnR strain (1.35) was higher than that of the wild-type stain (0.78). Collectively, the phenotypes of the ΔosnR and P180-osnR strains suggest a global regulatory role as well as a negative role for the gene in stress responses, particularly in katA-independent oxidative stress responses.
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Hong EJ, Jeong H, Lee DS, Kim Y, Lee HS. TheahpDgene ofCorynebacterium glutamicumplays an important role in hydrogen peroxide-induced oxidative stress response. J Biochem 2018; 165:197-204. [DOI: 10.1093/jb/mvy097] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 11/14/2018] [Indexed: 12/17/2022] Open
Affiliation(s)
- Eun-Ji Hong
- Department of Biotechnology and Bioinformatics, Korea University, 2511 Sejong-ro, Sejong-si, Korea
| | - Haeri Jeong
- Department of Biotechnology and Bioinformatics, Korea University, 2511 Sejong-ro, Sejong-si, Korea
| | - Dong-Seok Lee
- Department of Biotechnology and Bioinformatics, Korea University, 2511 Sejong-ro, Sejong-si, Korea
| | - Younhee Kim
- Department of Korean Medicine, Semyung University, 65 Semyeong-ro, Jecheon-si, Chungbuk, Korea
| | - Heung-Shick Lee
- Department of Biotechnology and Bioinformatics, Korea University, 2511 Sejong-ro, Sejong-si, Korea
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Kim HA, Kim HJ, Park J, Choi AR, Heo K, Jeong H, Jung KH, Seok YJ, Kim P, Lee SJ. An evolutionary optimization of a rhodopsin-based phototrophic metabolism in Escherichia coli. Microb Cell Fact 2017; 16:111. [PMID: 28619035 PMCID: PMC5472908 DOI: 10.1186/s12934-017-0725-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/12/2017] [Indexed: 02/02/2023] Open
Abstract
Background The expression of the Gloeobacter rhodopsin (GR) in a chemotrophic Escherichia coli enables the light-driven phototrophic energy generation. Adaptive laboratory evolution has been used for acquiring desired phenotype of microbial cells and for the elucidation of basic mechanism of molecular evolution. To develop an optimized strain for the artificially acquired phototrophic metabolism, an ancestral E. coli expressing GR was adaptively evolved in a chemostat reactor with constant illumination and limited glucose conditions. This study was emphasized at an unexpected genomic mutation contributed to the improvement of microbial performance. Results During the chemostat culture, increase of cell size was observed, which were distinguished from that of the typical rod-shaped ancestral cells. A descendant ET5 strain was randomly isolated from the chemostat culture at 88-days. The phototrophic growth and the light-induced proton pumping of the ET5 strain were twofold and eightfold greater, respectively, than those of the ancestral E. coli strain. Single point mutation of C1082A at dgcQ gene (encoding diguanylate cyclase, also known as the yedQ gene) in the chromosome of ET5 strain was identified from whole genome sequencing analysis. An ancestral E. coli complemented with the same dgcQ mutation from the ET5 was repeated the subsequently enhancements of light-driven phototrophic growth and proton pumping. Intracellular c-di-GMP, the product of the diguanylate cyclase (dgcQ), of the descendant ET5 strain was suddenly increased while that of the ancestral strain was negligible. Conclusions Newly acquired phototrophic metabolism of E. coli was further improved via adaptive laboratory evolution by the rise of a point mutation on a transmembrane cell signaling protein followed by increase of signal molecule that eventually led an increase proton pumping and phototrophic growth. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0725-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hyun Aaron Kim
- Hana Academy Seoul, Seoul, Republic of Korea.,Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hyun Ju Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Gyeonggi, Republic of Korea
| | - Jihoon Park
- Department of Biotechnology, The Catholic University of Korea, Bucheon, Gyeonggi, Republic of Korea
| | - Ah Reum Choi
- Department of Life Sciences, Sogang University, Seoul, Republic of Korea
| | - Kyoo Heo
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Haeyoung Jeong
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Kwang-Hwan Jung
- Department of Life Sciences, Sogang University, Seoul, Republic of Korea
| | - Yeong-Jae Seok
- Department of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Pil Kim
- Department of Biotechnology, The Catholic University of Korea, Bucheon, Gyeonggi, Republic of Korea.
| | - Sang Jun Lee
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Gyeonggi, Republic of Korea.
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Park SH, Singh H, Appukuttan D, Jeong S, Choi YJ, Jung JH, Narumi I, Lim S. PprM, a Cold Shock Domain-Containing Protein from Deinococcus radiodurans, Confers Oxidative Stress Tolerance to Escherichia coli. Front Microbiol 2017; 7:2124. [PMID: 28119668 PMCID: PMC5222802 DOI: 10.3389/fmicb.2016.02124] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 12/15/2016] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli is a representative microorganism that is frequently used for industrial biotechnology; thus its cellular robustness should be enhanced for the widespread application of E. coli in biotechnology. Stress response genes from the extremely radioresistant bacterium Deinococcus radiodurans have been used to enhance the stress tolerance of E. coli. In the present study, we introduced the cold shock domain-containing protein PprM from D. radiodurans into E. coli and observed that the tolerance to hydrogen peroxide (H2O2) was significantly increased in recombinant strains (Ec-PprM). The overexpression of PprM in E. coli elevated the expression of some OxyR-dependent genes, which play important roles in oxidative stress tolerance. Particularly, mntH (manganese transporter) was activated by 9-fold in Ec-PprM, even in the absence of H2O2 stress, which induced a more than 2-fold increase in the Mn/Fe ratio compared with wild type. The reduced production of highly reactive hydroxyl radicals (·OH) and low protein carbonylation levels (a marker of oxidative damage) in Ec-PprM indicate that the increase in the Mn/Fe ratio contributes to the protection of cells from H2O2 stress. PprM also conferred H2O2 tolerance to E. coli in the absence of OxyR. We confirmed that the H2O2 tolerance of oxyR mutants reflected the activation of the ycgZ-ymgABC operon, whose expression is activated by H2O2 in an OxyR-independent manner. Thus, the results of the present study showed that PprM could be exploited to improve the robustness of E. coli.
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Affiliation(s)
- Sun-Ha Park
- Research Division for Biotechnology, Korea Atomic Energy Research Institute Jeongeup, South Korea
| | - Harinder Singh
- Research Division for Biotechnology, Korea Atomic Energy Research Institute Jeongeup, South Korea
| | - Deepti Appukuttan
- Research Division for Biotechnology, Korea Atomic Energy Research Institute Jeongeup, South Korea
| | - Sunwook Jeong
- Research Division for Biotechnology, Korea Atomic Energy Research Institute Jeongeup, South Korea
| | - Yong Jun Choi
- Research Division for Biotechnology, Korea Atomic Energy Research Institute Jeongeup, South Korea
| | - Jong-Hyun Jung
- Research Division for Biotechnology, Korea Atomic Energy Research Institute Jeongeup, South Korea
| | - Issay Narumi
- Radiation Microbiology Laboratory, Department of Life Sciences, Faculty of Life Sciences, Toyo University Gunma, Japan
| | - Sangyong Lim
- Research Division for Biotechnology, Korea Atomic Energy Research Institute Jeongeup, South Korea
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Jeong H, Lee SJ, Kim P. Procedure for Adaptive Laboratory Evolution of Microorganisms Using a Chemostat. J Vis Exp 2016. [PMID: 27684991 DOI: 10.3791/54446] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Natural evolution involves genetic diversity such as environmental change and a selection between small populations. Adaptive laboratory evolution (ALE) refers to the experimental situation in which evolution is observed using living organisms under controlled conditions and stressors; organisms are thereby artificially forced to make evolutionary changes. Microorganisms are subject to a variety of stressors in the environment and are capable of regulating certain stress-inducible proteins to increase their chances of survival. Naturally occurring spontaneous mutations bring about changes in a microorganism's genome that affect its chances of survival. Long-term exposure to chemostat culture provokes an accumulation of spontaneous mutations and renders the most adaptable strain dominant. Compared to the colony transfer and serial transfer methods, chemostat culture entails the highest number of cell divisions and, therefore, the highest number of diverse populations. Although chemostat culture for ALE requires more complicated culture devices, it is less labor intensive once the operation begins. Comparative genomic and transcriptome analyses of the adapted strain provide evolutionary clues as to how the stressors contribute to mutations that overcome the stress. The goal of the current paper is to bring about accelerated evolution of microorganisms under controlled laboratory conditions.
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Affiliation(s)
- Haeyoung Jeong
- Super-Bacteria Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)
| | - Sang J Lee
- Microbiomics and Immunity Research Center, Korea Research Institute of Bioscience and Bioengineering (KRIBB)
| | - Pil Kim
- Department of Biotechnology, The Catholic University of Korea;
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Agu CV, Ujor V, Gopalan V, Ezeji TC. Use of Cupriavidus basilensis-aided bioabatement to enhance fermentation of acid-pretreated biomass hydrolysates by Clostridium beijerinckii. J Ind Microbiol Biotechnol 2016; 43:1215-26. [PMID: 27400988 DOI: 10.1007/s10295-016-1798-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 06/16/2016] [Indexed: 10/21/2022]
Abstract
Lignocellulose-derived microbial inhibitors (LDMICs) prevent efficient fermentation of Miscanthus giganteus (MG) hydrolysates to fuels and chemicals. To address this problem, we explored detoxification of pretreated MG biomass by Cupriavidus basilensis ATCC(®)BAA-699 prior to enzymatic saccharification. We document three key findings from our test of this strategy to alleviate LDMIC-mediated toxicity on Clostridium beijerinckii NCIMB 8052 during fermentation of MG hydrolysates. First, we demonstrate that growth of C. basilensis is possible on furfural, 5-hydroxymethyfurfural, cinnamaldehyde, 4-hydroxybenzaldehyde, syringaldehyde, vanillin, and ferulic, p-coumaric, syringic and vanillic acid, as sole carbon sources. Second, we report that C. basilensis detoxified and metabolized ~98 % LDMICs present in dilute acid-pretreated MG hydrolysates. Last, this bioabatement resulted in significant payoffs during acetone-butanol-ethanol (ABE) fermentation by C. beijerinckii: 70, 50 and 73 % improvement in ABE concentration, yield and productivity, respectively. Together, our results show that biological detoxification of acid-pretreated MG hydrolysates prior to fermentation is feasible and beneficial.
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Affiliation(s)
- Chidozie Victor Agu
- Department of Animal Sciences, Ohio State Agricultural Research and Development Center (OARDC), The Ohio State University, 305 Gerlaugh Hall, 1680 Madison Avenue, Wooster, OH, 44691, USA
| | - Victor Ujor
- Renewable Energy Program, Agricultural Technical Institute, The Ohio State University, 1328 Dover Road, Wooster, OH, 44691, USA
| | - Venkat Gopalan
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, 484 West 12th Avenue, Columbus, OH, 43210, USA
| | - Thaddeus Chukwuemeka Ezeji
- Department of Animal Sciences, Ohio State Agricultural Research and Development Center (OARDC), The Ohio State University, 305 Gerlaugh Hall, 1680 Madison Avenue, Wooster, OH, 44691, USA.
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Hong EJ, Kim P, Kim ES, Kim Y, Lee HS. Involvement of the osrR gene in the hydrogen peroxide-mediated stress response of Corynebacterium glutamicum. Res Microbiol 2015; 167:20-8. [PMID: 26433092 DOI: 10.1016/j.resmic.2015.09.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 06/30/2015] [Accepted: 09/22/2015] [Indexed: 01/19/2023]
Abstract
A transcriptional profile of the H2O2-adapted Corynebacterium glutamicum HA strain reveals a list of upregulated regulatory genes. Among them, we selected ORF NCgl2298, designated osrR and analyzed its role in H2O2 adaptation. The osrR-deleted (ΔosrR) mutant had defective growth in minimal medium, which was even more pronounced in an osrR deletion mutant of an HA strain. The ΔosrR strain displayed increased sensitivity to H2O2. In addition to H2O2 sensitivity, the ΔosrR strain was found to be temperature-sensitive at 37 °C. 2D-PAGE analysis of the ΔosrR mutant found that MetE and several other proteins involved in redox metabolism were affected by the mutation. Accordingly, the NADPH/NADP(+) ratio of the ΔosrR strain (0.85) was much lower than that of the wild-type strain (2.01). In contrast, the NADH/NAD(+) ratio of the mutant (0.54) was considerably higher than that of the wild-type (0.21). Based on these findings, we propose that H2O2-detoxifying metabolic systems, excluding those involving catalase, are present in C. glutamicum and are regulated, in part, by osrR.
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Affiliation(s)
- Eun-Ji Hong
- Department of Biotechnology and Bioinformatics, Korea University, 2511 Sejong-ro, Sejong-si 339-700, Republic of Korea.
| | - Pil Kim
- Department of Biotechnology, The Catholic University of Korea, Bucheon, Gyeonggi 420-743, Republic of Korea.
| | - Eung-Soo Kim
- Department of Biological Engineering, Inha University, Incheon 402-751, Republic of Korea.
| | - Younhee Kim
- Department of Korean Medicine, Semyung University, 65 Semyeong-ro, Jecheon-si, Chungbuk 390-711, Republic of Korea.
| | - Heung-Shick Lee
- Department of Biotechnology and Bioinformatics, Korea University, 2511 Sejong-ro, Sejong-si 339-700, Republic of Korea.
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Growth retardation of Escherichia coli by artificial increase of intracellular ATP. J Ind Microbiol Biotechnol 2015; 42:915-24. [PMID: 25838237 DOI: 10.1007/s10295-015-1609-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 03/19/2015] [Indexed: 12/27/2022]
Abstract
Overexpression of phosphoenolpyruvate carboxykinase (PCK) was reported to cause the harboring of higher intracellular ATP concentration in Escherichia coli, accompanied with a slower growth rate. For systematic determination of the relationship between the artificial increase of ATP and growth retardation, PCKWT enzyme was directly evolved in vitro and further overexpressed. The evolved PCK67 showed a 60% greater catalytic efficiency than that of PCKWT. Consequently, the PCK67-overexpressing E. coli showed the highest ATP concentration at the log phase of 1.45 μmol/gcell, with the slowest growth rate of 0.66 h(-1), while the PCKWT-overexpressing cells displayed 1.00 μmol/gcell ATP concentration with the growth rate of 0.84 h(-1) and the control had 0.28 μmol/gcell with 1.03 h(-1). To find a plausible reason, PCK-overexpressing cells in a steady state during chemostat growth were applied to monitor intracellular reactive oxygen species (ROS). Higher amount of intracellular ROS were observed as the ATP levels increased. To confirm the hypothesis of slower growth rate without perturbation of the carbon flux by PCK-overexpression, phototrophic Gloeobacter rhodopsin (GR) was expressed. The GR-expressing strain under illumination harbored 81% more ATP concentration along with 82% higher ROS, with a 54% slower maximum growth rate than the control, while both the GR-expressing strain under dark and dicarboxylate transporter (a control membrane protein)-expressing strain showed a lower ATP and increased ROS, and slower growth rate. Regardless of carbon flux changes, the artificial ATP increase was related to the ROS increase and it was reciprocally correlated to the maximum growth rate. To verify that the accumulated intracellular ROS were responsible for the growth retardation, glutathione was added to the medium to reduce the ROS. As a result, the growth retardation was restored by the addition of 0.1 mM glutathione. Anaerobic culture even enabled the artificial ATP-increased E. coli to grow faster than control. Collectively, it was concluded that artificial ATP increases inhibit the growth of E. coli due to the overproduction of ROS.
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