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Jeong S, Singh H, Jung JH, Jung KW, Ryu S, Lim S. Comparative genomics of Deinococcus radiodurans: unveiling genetic discrepancies between ATCC 13939K and BAA-816 strains. Front Microbiol 2024; 15:1410024. [PMID: 38962131 PMCID: PMC11219805 DOI: 10.3389/fmicb.2024.1410024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 06/04/2024] [Indexed: 07/05/2024] Open
Abstract
The Deinococcus genus is renowned for its remarkable resilience against environmental stresses, including ionizing radiation, desiccation, and oxidative damage. This resilience is attributed to its sophisticated DNA repair mechanisms and robust defense systems, enabling it to recover from extensive damage and thrive under extreme conditions. Central to Deinococcus research, the D. radiodurans strains ATCC BAA-816 and ATCC 13939 facilitate extensive studies into this remarkably resilient genus. This study focused on delineating genetic discrepancies between these strains by sequencing our laboratory's ATCC 13939 specimen (ATCC 13939K) and juxtaposing it with ATCC BAA-816. We uncovered 436 DNA sequence differences within ATCC 13939K, including 100 single nucleotide variations, 278 insertions, and 58 deletions, which could induce frameshifts altering protein-coding genes. Gene annotation revisions accounting for gene fusions and the reconciliation of gene lengths uncovered novel protein-coding genes and refined the functional categorizations of established ones. Additionally, the analysis pointed out genome structural variations due to insertion sequence (IS) elements, underscoring the D. radiodurans genome's plasticity. Notably, ATCC 13939K exhibited a loss of six ISDra2 elements relative to BAA-816, restoring genes fragmented by ISDra2, such as those encoding for α/β hydrolase and serine protease, and revealing new open reading frames, including genes imperative for acetoin decomposition. This comparative genomic study offers vital insights into the metabolic capabilities and resilience strategies of D. radiodurans.
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Affiliation(s)
- Soyoung Jeong
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Harinder Singh
- Department of Biological Sciences, Sunandan Divatia School of Science, NMIMS Deemed to be University, Mumbai, India
| | - Jong-Hyun Jung
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Kwang-Woo Jung
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Sangyong Lim
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup, Republic of Korea
- Department of Radiation Science, University of Science and Technology, Daejeon, Republic of Korea
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Meng W, Ma C, Xu P, Gao C. Biotechnological production of chiral acetoin. Trends Biotechnol 2022; 40:958-973. [DOI: 10.1016/j.tibtech.2022.01.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 11/28/2022]
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Cui Z, Wang Z, Zheng M, Chen T. Advances in biological production of acetoin: a comprehensive overview. Crit Rev Biotechnol 2021; 42:1135-1156. [PMID: 34806505 DOI: 10.1080/07388551.2021.1995319] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Acetoin, a high-value-added bio-based platform chemical, is widely used in foods, cosmetics, agriculture, and the chemical industry. It is an important precursor for the synthesis of: 2,3-butanediol, liquid hydrocarbon fuels and heterocyclic compounds. Since the fossil resources are becoming increasingly scarce, biological production of acetoin has received increasing attention as an alternative to chemical synthesis. Although there are excellent reviews on the: application, catabolism and fermentative production of acetoin, little attention has been paid to acetoin production via: electrode-assisted fermentation, whole-cell biocatalysis, and in vitro/cell-free biocatalysis. In this review, acetoin biosynthesis pathways and relevant key enzymes are firstly reviewed. In addition, various strategies for biological acetoin production are summarized including: cell-free biocatalysis, whole-cell biocatalysis, microbial fermentation, and electrode-assisted fermentation. The advantages and disadvantages of the different approaches are discussed and weighed, illustrating the increasing progress toward economical, green and efficient production of acetoin. Additionally, recent advances in acetoin extraction and recovery in downstream processing are also briefly reviewed. Moreover, the current issues and future prospects of diverse strategies for biological acetoin production are discussed, with the hope of realizing the promises of industrial acetoin biomanufacturing in the near future.
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Affiliation(s)
- Zhenzhen Cui
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
| | - Zhiwen Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
| | - Meiyu Zheng
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
| | - Tao Chen
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, China
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Xie NZ, Li JX, Huang RB. Biological Production of (S)-acetoin: A State-of-the-Art Review. Curr Top Med Chem 2019; 19:2348-2356. [PMID: 31648637 DOI: 10.2174/1568026619666191018111424] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 08/28/2019] [Accepted: 09/02/2019] [Indexed: 12/24/2022]
Abstract
Acetoin is an important four-carbon compound that has many applications in foods, chemical synthesis, cosmetics, cigarettes, soaps, and detergents. Its stereoisomer (S)-acetoin, a high-value chiral compound, can also be used to synthesize optically active drugs, which could enhance targeting properties and reduce side effects. Recently, considerable progress has been made in the development of biotechnological routes for (S)-acetoin production. In this review, various strategies for biological (S)- acetoin production are summarized, and their constraints and possible solutions are described. Furthermore, future prospects of biological production of (S)-acetoin are discussed.
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Affiliation(s)
- Neng-Zhong Xie
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China
| | - Jian-Xiu Li
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China
| | - Ri-Bo Huang
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Key Laboratory of Bio-refinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning, 530007, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China
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Li JX, Huang YY, Chen XR, Du QS, Meng JZ, Xie NZ, Huang RB. Enhanced production of optical ( S)-acetoin by a recombinant Escherichia coli whole-cell biocatalyst with NADH regeneration. RSC Adv 2018; 8:30512-30519. [PMID: 35546830 PMCID: PMC9085422 DOI: 10.1039/c8ra06260a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 08/21/2018] [Indexed: 12/19/2022] Open
Abstract
Acetoin is an important platform chemical with a variety of applications in foods, cosmetics, chemical synthesis, and especially in the asymmetric synthesis of optically active pharmaceuticals. It is also a useful breath biomarker for early lung cancer diagnosis. In order to enhance production of optical (S)-acetoin and facilitate this building block for a series of chiral pharmaceuticals derivatives, we have developed a systematic approach using in situ-NADH regeneration systems and promising diacetyl reductase. Under optimal conditions, we have obtained 52.9 g L-1 of (S)-acetoin with an enantiomeric purity of 99.5% and a productivity of 6.2 g (L h)-1. The results reported in this study demonstrated that the production of (S)-acetoin could be effectively improved through the engineering of cofactor regeneration with promising diacetyl reductase. The systematic approach developed in this study could also be applied to synthesize other optically active α-hydroxy ketones, which may provide valuable benefits for the study of drug development.
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Affiliation(s)
- Jian-Xiu Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Life Science and Biotechnology College, Guangxi University 100 Daxue Road Nanning 530004 China
- State Key Laboratory of No-Food Biomass and Enzyme Technology, National Engineering Research Center for No-Food Biorefinery, Guangxi Key Laboratory of Biorefinery, Guangxi Academy of Sciences 98 Daling Road Nanning 530007 China
| | - Yan-Yan Huang
- State Key Laboratory of No-Food Biomass and Enzyme Technology, National Engineering Research Center for No-Food Biorefinery, Guangxi Key Laboratory of Biorefinery, Guangxi Academy of Sciences 98 Daling Road Nanning 530007 China
| | - Xian-Rui Chen
- State Key Laboratory of No-Food Biomass and Enzyme Technology, National Engineering Research Center for No-Food Biorefinery, Guangxi Key Laboratory of Biorefinery, Guangxi Academy of Sciences 98 Daling Road Nanning 530007 China
| | - Qi-Shi Du
- State Key Laboratory of No-Food Biomass and Enzyme Technology, National Engineering Research Center for No-Food Biorefinery, Guangxi Key Laboratory of Biorefinery, Guangxi Academy of Sciences 98 Daling Road Nanning 530007 China
| | - Jian-Zong Meng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Life Science and Biotechnology College, Guangxi University 100 Daxue Road Nanning 530004 China
| | - Neng-Zhong Xie
- State Key Laboratory of No-Food Biomass and Enzyme Technology, National Engineering Research Center for No-Food Biorefinery, Guangxi Key Laboratory of Biorefinery, Guangxi Academy of Sciences 98 Daling Road Nanning 530007 China
| | - Ri-Bo Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Life Science and Biotechnology College, Guangxi University 100 Daxue Road Nanning 530004 China
- State Key Laboratory of No-Food Biomass and Enzyme Technology, National Engineering Research Center for No-Food Biorefinery, Guangxi Key Laboratory of Biorefinery, Guangxi Academy of Sciences 98 Daling Road Nanning 530007 China
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Takeda M, Matsumura AT, Kurosaki K, Chhetri RT, Motomatsu S, Suzuki I, Sahabi DM. An enantioselective NADP+-dependent alcohol dehydrogenase responsible for cooxidative production of (3S)-5-hydroxy-3-methyl-pentanoic acid. Biosci Biotechnol Biochem 2016; 80:1155-63. [DOI: 10.1080/09168451.2016.1148578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Abstract
A soil bacterium, Mycobacterium sp. B-009, is able to grow on racemic 1,2-propanediol (PD). The strain was revealed to oxidize 3-methyl-1,5-pentanediol (MPD) to 5-hydroxy-3-methyl-pentanoic acid (HMPA) during growth on PD. MPD was converted into an almost equimolar amount of the S-form of HMPA (S-HMPA) at 72%ee, suggesting the presence of an enantioselective MPD dehydrogenase (MPD-DH). As expected, an NADP+-dependent alcohol dehydrogenase, which catalyzes the initial step of MPD oxidation, was detected and purified from the cell-free extract. This enzyme was suggested to be a homodimeric medium-chain alcohol dehydrogenase/reductase (MDR). The catalytic and kinetic parameters indicated that MPD is the most suitable substrate for the enzyme. The enzyme was encoded by a 1047-bp gene (mpd1) and several mycobacterial strains were found to have putative MDR genes similar to mpd1. In a phylogenetic tree, MPD-DH formed an independent clade together with the putative MDR of Mycobacterium neoaurum, which produces opportunistic infections.
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Affiliation(s)
- Minoru Takeda
- Graduate School of Engineering, Yokohama National University, Yokohama, Japan
| | | | - Kaishi Kurosaki
- Graduate School of Engineering, Yokohama National University, Yokohama, Japan
| | - Rajan Thapa Chhetri
- Graduate School of Engineering, Yokohama National University, Yokohama, Japan
| | - Shigekazu Motomatsu
- Graduate School of Engineering, Yokohama National University, Yokohama, Japan
| | - Ichiro Suzuki
- Graduate School of Engineering, Yokohama National University, Yokohama, Japan
| | - Danladi Mahuta Sahabi
- Graduate School of Engineering, Yokohama National University, Yokohama, Japan
- Department of Biochemistry, Usmanu Danfodiyo University, Sokoto, Nigeria
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