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Singhvi N, Talwar C, Nagar S, Verma H, Kaur J, Mahato NK, Ahmad N, Mondal K, Gupta V, Lal R. Insights into the radiation and oxidative stress mechanisms in genus Deinococcus. Comput Biol Chem 2024; 112:108161. [PMID: 39116702 DOI: 10.1016/j.compbiolchem.2024.108161] [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: 05/24/2024] [Revised: 07/04/2024] [Accepted: 07/24/2024] [Indexed: 08/10/2024]
Abstract
Deinococcus species, noted for their exceptional resistance to DNA-damaging environmental stresses, have piqued scientists' interest for decades. This study dives into the complex mechanisms underpinning radiation resistance in the Deinococcus genus. We have examined the genomes of 82 Deinococcus species and classified radiation-resistance proteins manually into five unique curated categories: DNA repair, oxidative stress defense, Ddr and Ppr proteins, regulatory proteins, and miscellaneous resistance components. This classification reveals important information about the various molecular mechanisms used by these extremophiles which have been less explored so far. We also investigated the presence or lack of these proteins in the context of phylogenetic relationships, core, and pan-genomes, which offered light on the evolutionary dynamics of radiation resistance. This comprehensive study provides a deeper understanding of the genetic underpinnings of radiation resistance in the Deinococcus genus, with potential implications for understanding similar mechanisms in other organisms using an interactomics approach. Finally, this study reveals the complexities of radiation resistance mechanisms, providing a comprehensive understanding of the genetic components that allow Deinococcus species to flourish under harsh environments. The findings add to our understanding of the larger spectrum of stress adaption techniques in bacteria and may have applications in sectors ranging from biotechnology to environmental research.
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Affiliation(s)
- Nirjara Singhvi
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun 248007, India
| | - Chandni Talwar
- Department of Pathology and Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Shekhar Nagar
- Department of Zoology, Deshbandhu College, University of Delhi, New Delhi 110019, India
| | - Helianthous Verma
- Department of Zoology, Ramjas College, University of Delhi, Delhi 110007, India
| | - Jasvinder Kaur
- Department of Zoology, Gargi College, University of Delhi, New Delhi 110049, India
| | - Nitish Kumar Mahato
- University Department of Zoology, Kolhan University, Chaibasa, Jharkhand, India
| | - Nabeel Ahmad
- School of Allied Sciences, Dev Bhoomi Uttarakhand University, Dehradun 248007, India
| | - Krishnendu Mondal
- Ministry of Environment, Forest and Climate Change, Integrated Regional Office, Dehradun 248001, India
| | - Vipin Gupta
- Ministry of Environment, Forest and Climate Change, Integrated Regional Office, Dehradun 248001, India.
| | - Rup Lal
- Acharya Narendra Dev College, University of Delhi, New Delhi 110019, India.
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Gouveia AG, Salgueiro BA, Ranmar DO, Antunes WDT, Kirchweger P, Golani O, Wolf SG, Elbaum M, Matias PM, Romão CV. Unraveling the multifaceted resilience of arsenic resistant bacterium Deinococcus indicus. Front Microbiol 2023; 14:1240798. [PMID: 37692390 PMCID: PMC10483234 DOI: 10.3389/fmicb.2023.1240798] [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: 06/15/2023] [Accepted: 08/09/2023] [Indexed: 09/12/2023] Open
Abstract
Arsenic (As) is a toxic heavy metal widely found in the environment that severely undermines the integrity of water resources. Bioremediation of toxic compounds is an appellative sustainable technology with a balanced cost-effective setup. To pave the way for the potential use of Deinococcus indicus, an arsenic resistant bacterium, as a platform for arsenic bioremediation, an extensive characterization of its resistance to cellular insults is paramount. A comparative analysis of D. indicus cells grown in two rich nutrient media conditions (M53 and TGY) revealed distinct resistance patterns when cells are subjected to stress via UV-C and methyl viologen (MV). Cells grown in M53 demonstrated higher resistance to both UV-C and MV. Moreover, cells grow to higher density upon exposure to 25 mM As(V) in M53 in comparison with TGY. This analysis is pivotal for the culture of microbial species in batch culture bioreactors for bioremediation purposes. We also demonstrate for the first time the presence of polyphosphate granules in D. indicus which are also found in a few Deinococcus species. To extend our analysis, we also characterized DiArsC2 (arsenate reductase) involved in arsenic detoxification and structurally determined different states, revealing the structural evidence for a catalytic cysteine triple redox system. These results contribute for our understanding into the D. indicus resistance mechanism against stress conditions.
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Affiliation(s)
- André G. Gouveia
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Universidade Nova de Lisboa, Oeiras, Portugal
| | - Bruno A. Salgueiro
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Universidade Nova de Lisboa, Oeiras, Portugal
| | - Dean O. Ranmar
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Wilson D. T. Antunes
- Instituto Universitário Militar, Centro de Investigação da Academia Militar (CINAMIL), Unidade Militar Laboratorial de Defesa Biológica e Química (UMLDBQ), Lisbon, Portugal
| | - Peter Kirchweger
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Ofra Golani
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Sharon G. Wolf
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Michael Elbaum
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Pedro M. Matias
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Universidade Nova de Lisboa, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal
| | - Célia V. Romão
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Universidade Nova de Lisboa, Oeiras, Portugal
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Yang SK, Jeong S, Baek I, Choi JI, Lim S, Jung JH. Deionococcus proteotlycius Genomic Library Exploration Enhances Oxidative Stress Resistance and Poly-3-hydroxybutyrate Production in Recombinant Escherichia coli. Microorganisms 2023; 11:2135. [PMID: 37763980 PMCID: PMC10538107 DOI: 10.3390/microorganisms11092135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/18/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023] Open
Abstract
Cell growth is inhibited by abiotic stresses during industrial processes, which is a limitation of microbial cell factories. Microbes with robust phenotypes are critical for its maximizing the yield of the target products in industrial biotechnology. Currently, there are several reports on the enhanced production of industrial metabolite through the introduction of Deinococcal genes into host cells, which confers cellular robustness. Deinococcus is known for its unique genetic function thriving in extreme environments such as radiation, UV, and oxidants. In this study, we established that Deinococcus proteolyticus showed greater resistance to oxidation and UV-C than commonly used D. radiodurans. By screening the genomic library of D. proteolyticus, we isolated a gene (deipr_0871) encoding a response regulator, which not only enhanced oxidative stress, but also promoted the growth of the recombinant E. coli strain. The transcription analysis indicated that the heterologous expression of deipr_0871 upregulated oxidative-stress-related genes such as ahpC and sodA, and acetyl-CoA-accumulation-associated genes via soxS regulon. Deipr_0871 was applied to improve the production of the valuable metabolite, poly-3-hydroxybutyrate (PHB), in the synthetic E. coli strain, which lead to the remarkably higher PHB than the control strain. Therefore, the stress tolerance gene from D. proteolyticus should be used in the modification of E. coli for the production of PHB and other biomaterials.
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Affiliation(s)
- Seul-Ki Yang
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea (S.L.)
- Graduate School of Biotechnology and Institute of Life Science and Resources, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Soyoung Jeong
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea (S.L.)
- Department of Food and Animal Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Inwoo Baek
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea (S.L.)
| | - Jong-il Choi
- Department of Biotechnology and Bioengineering, Chonnam National University, Gwangju 61186, Republic of Korea;
| | - Sangyong Lim
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea (S.L.)
- Department of Radiation Science and Technology, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Jong-Hyun Jung
- Radiation Biotechnology Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea (S.L.)
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Park AM, Khadka S, Sato F, Omura S, Fujita M, Hashiwaki K, Tsunoda I. Bacterial and fungal isolation from face masks under the COVID-19 pandemic. Sci Rep 2022; 12:11361. [PMID: 35851044 PMCID: PMC9293923 DOI: 10.1038/s41598-022-15409-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/23/2022] [Indexed: 02/08/2023] Open
Abstract
The COVID-19 pandemic has led people to wear face masks daily in public. Although the effectiveness of face masks against viral transmission has been extensively studied, there have been few reports on potential hygiene issues due to bacteria and fungi attached to the face masks. We aimed to (1) quantify and identify the bacteria and fungi attaching to the masks, and (2) investigate whether the mask-attached microbes could be associated with the types and usage of the masks and individual lifestyles. We surveyed 109 volunteers on their mask usage and lifestyles, and cultured bacteria and fungi from either the face-side or outer-side of their masks. The bacterial colony numbers were greater on the face-side than the outer-side; the fungal colony numbers were fewer on the face-side than the outer-side. A longer mask usage significantly increased the fungal colony numbers but not the bacterial colony numbers. Although most identified microbes were non-pathogenic in humans; Staphylococcus epidermidis, Staphylococcus aureus, and Cladosporium, we found several pathogenic microbes; Bacillus cereus, Staphylococcus saprophyticus, Aspergillus, and Microsporum. We also found no associations of mask-attached microbes with the transportation methods or gargling. We propose that immunocompromised people should avoid repeated use of masks to prevent microbial infection.
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Affiliation(s)
- Ah-Mee Park
- Department of Microbiology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan.
| | - Sundar Khadka
- Department of Microbiology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
| | - Fumitaka Sato
- Department of Microbiology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
| | - Seiichi Omura
- Department of Microbiology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
| | - Mitsugu Fujita
- Department of Microbiology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
| | - Kazuki Hashiwaki
- Department of Microbiology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
| | - Ikuo Tsunoda
- Department of Microbiology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
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5
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Thiol Reductases in Deinococcus Bacteria and Roles in Stress Tolerance. Antioxidants (Basel) 2022; 11:antiox11030561. [PMID: 35326211 PMCID: PMC8945050 DOI: 10.3390/antiox11030561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/11/2022] [Accepted: 03/13/2022] [Indexed: 12/10/2022] Open
Abstract
Deinococcus species possess remarkable tolerance to extreme environmental conditions that generate oxidative damage to macromolecules. Among enzymes fulfilling key functions in metabolism regulation and stress responses, thiol reductases (TRs) harbour catalytic cysteines modulating the redox status of Cys and Met in partner proteins. We present here a detailed description of Deinococcus TRs regarding gene occurrence, sequence features, and physiological functions that remain poorly characterised in this genus. Two NADPH-dependent thiol-based systems are present in Deinococcus. One involves thioredoxins, disulfide reductases providing electrons to protein partners involved notably in peroxide scavenging or in preserving protein redox status. The other is based on bacillithiol, a low-molecular-weight redox molecule, and bacilliredoxin, which together protect Cys residues against overoxidation. Deinococcus species possess various types of thiol peroxidases whose electron supply depends either on NADPH via thioredoxins or on NADH via lipoylated proteins. Recent data gained on deletion mutants confirmed the importance of TRs in Deinococcus tolerance to oxidative treatments, but additional investigations are needed to delineate the redox network in which they operate, and their precise physiological roles. The large palette of Deinococcus TR representatives very likely constitutes an asset for the maintenance of redox homeostasis in harsh stress conditions.
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6
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Chen Z, Tang Y, Hua Y, Zhao Y. Structural features and functional implications of proteins enabling the robustness of Deinococcus radiodurans. Comput Struct Biotechnol J 2020; 18:2810-2817. [PMID: 33133422 PMCID: PMC7575645 DOI: 10.1016/j.csbj.2020.09.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 12/21/2022] Open
Abstract
Deinococcus radiodurans can survive under extreme conditions, including high doses of DNA damaging agents and ionizing radiation, desiccation, and oxidative stress. Both the efficient cellular DNA repair machinery and antioxidation systems contribute to the extreme resistance of this bacterium, making it an ideal organism for studying the cellular mechanisms of environmental adaptation. The number of stress-related proteins identified in this bacterium has mushroomed in the past two decades. The newly identified proteins reveal both commonalities and diversity of structure, mechanism, and function, which impact a wide range of cellular functions. Here, we review the unique and general structural features of these proteins and discuss how these studies improve our understanding of the environmental stress adaptation mechanisms of D. radiodurans.
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Affiliation(s)
- Zijing Chen
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuyue Tang
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuejin Hua
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ye Zhao
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
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7
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Lim S, Jung JH, Blanchard L, de Groot A. Conservation and diversity of radiation and oxidative stress resistance mechanisms in Deinococcus species. FEMS Microbiol Rev 2019; 43:19-52. [PMID: 30339218 PMCID: PMC6300522 DOI: 10.1093/femsre/fuy037] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 10/17/2018] [Indexed: 12/17/2022] Open
Abstract
Deinococcus bacteria are famous for their extreme resistance to ionising radiation and other DNA damage- and oxidative stress-generating agents. More than a hundred genes have been reported to contribute to resistance to radiation, desiccation and/or oxidative stress in Deinococcus radiodurans. These encode proteins involved in DNA repair, oxidative stress defence, regulation and proteins of yet unknown function or with an extracytoplasmic location. Here, we analysed the conservation of radiation resistance-associated proteins in other radiation-resistant Deinococcus species. Strikingly, homologues of dozens of these proteins are absent in one or more Deinococcus species. For example, only a few Deinococcus-specific proteins and radiation resistance-associated regulatory proteins are present in each Deinococcus, notably the metallopeptidase/repressor pair IrrE/DdrO that controls the radiation/desiccation response regulon. Inversely, some Deinococcus species possess proteins that D. radiodurans lacks, including DNA repair proteins consisting of novel domain combinations, translesion polymerases, additional metalloregulators, redox-sensitive regulator SoxR and manganese-containing catalase. Moreover, the comparisons improved the characterisation of several proteins regarding important conserved residues, cellular location and possible protein–protein interactions. This comprehensive analysis indicates not only conservation but also large diversity in the molecular mechanisms involved in radiation resistance even within the Deinococcus genus.
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Affiliation(s)
- Sangyong Lim
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
| | - Jong-Hyun Jung
- Biotechnology Research Division, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
| | | | - Arjan de Groot
- Aix Marseille Univ, CEA, CNRS, BIAM, Saint Paul-Lez-Durance, France
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8
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Aguileta G, Badouin H, Hood ME, Møller AP, Le Prieur S, Snirc A, Siguenza S, Mousseau TA, Shykoff JA, Cuomo CA, Giraud T. Lower prevalence but similar fitness in a parasitic fungus at higher radiation levels near Chernobyl. Mol Ecol 2016; 25:3370-83. [PMID: 27136128 DOI: 10.1111/mec.13675] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 04/04/2016] [Accepted: 04/15/2016] [Indexed: 12/24/2022]
Abstract
Nuclear disasters at Chernobyl and Fukushima provide examples of effects of acute ionizing radiation on mutations that can affect the fitness and distribution of species. Here, we investigated the prevalence of Microbotryum lychnidis-dioicae, a pollinator-transmitted fungal pathogen of plants causing anther-smut disease in Chernobyl, its viability, fertility and karyotype variation, and the accumulation of nonsynonymous mutations in its genome. We collected diseased flowers of Silene latifolia from locations ranging by more than two orders of magnitude in background radiation, from 0.05 to 21.03 μGy/h. Disease prevalence decreased significantly with increasing radiation level, possibly due to lower pollinator abundance and altered pollinator behaviour. Viability and fertility, measured as the budding rate of haploid sporidia following meiosis from the diploid teliospores, did not vary with increasing radiation levels and neither did karyotype overall structure and level of chromosomal size heterozygosity. We sequenced the genomes of twelve samples from Chernobyl and of four samples collected from uncontaminated areas and analysed alignments of 6068 predicted genes, corresponding to 1.04 × 10(7) base pairs. We found no dose-dependent differences in substitution rates (neither dN, dS, nor dN/dS). Thus, we found no significant evidence of increased deleterious mutation rates at higher levels of background radiation in this plant pathogen. We even found lower levels of nonsynonymous substitution rates in contaminated areas compared to control regions, suggesting that purifying selection was stronger in contaminated than uncontaminated areas. We briefly discuss the possibilities for a mechanistic basis of radio resistance in this nonmelanized fungus.
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Affiliation(s)
- Gabriela Aguileta
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Helene Badouin
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Michael E Hood
- Biology Department, Amherst College, Amherst, MA 01002, USA
| | - Anders P Møller
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Stephanie Le Prieur
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Alodie Snirc
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Sophie Siguenza
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, F-31326, France.,CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, F-31326, France
| | - Timothy A Mousseau
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Jacqui A Shykoff
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | | | - Tatiana Giraud
- Ecologie Systématique Evolution, CNRS, Univ. Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
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9
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Gerber E, Bernard R, Castang S, Chabot N, Coze F, Dreux-Zigha A, Hauser E, Hivin P, Joseph P, Lazarelli C, Letellier G, Olive J, Leonetti JP. Deinococcus as new chassis for industrial biotechnology: biology, physiology and tools. J Appl Microbiol 2015; 119:1-10. [PMID: 25809882 PMCID: PMC4682472 DOI: 10.1111/jam.12808] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/20/2015] [Accepted: 03/03/2015] [Indexed: 11/28/2022]
Abstract
Deinococcus spp are among the most radiation-resistant micro-organisms that have been discovered. They show remarkable resistance to a range of damage caused by ionizing radiation, desiccation, UV radiation and oxidizing agents. Traditionally, Escherichia coli and Saccharomyces cerevisiae have been the two platforms of choice for engineering micro-organisms for biotechnological applications, because they are well understood and easy to work with. However, in recent years, researchers have begun using Deinococcus spp in biotechnologies and bioremediation due to their specific ability to grow and express novel engineered functions. More recently, the sequencing of several Deinococcus spp and comparative genomic analysis have provided new insight into the potential of this genus. Features such as the accumulation of genes encoding cell cleaning systems that eliminate organic and inorganic cell toxic components are widespread among Deinococcus spp. Other features such as the ability to degrade and metabolize sugars and polymeric sugars make Deinococcus spp. an attractive alternative for use in industrial biotechnology.
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Affiliation(s)
- E Gerber
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
| | - R Bernard
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
| | - S Castang
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
| | - N Chabot
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
| | - F Coze
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
| | - A Dreux-Zigha
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
| | - E Hauser
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
| | - P Hivin
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
| | - P Joseph
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
| | - C Lazarelli
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
| | - G Letellier
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
| | - J Olive
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
| | - J-P Leonetti
- Deinove, Cap Sigma/ZAC Euromédecine IIGrabels, France
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10
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Dai J, Dai W, Qiu C, Yang Z, Zhang Y, Zhou M, Zhang L, Fang C, Gao Q, Yang Q, Li X, Wang Z, Wang Z, Jia Z, Chen X. Unraveling adaptation of Pontibacter korlensis to radiation and infertility in desert through complete genome and comparative transcriptomic analysis. Sci Rep 2015; 5:10929. [PMID: 26057562 PMCID: PMC4460873 DOI: 10.1038/srep10929] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 04/27/2015] [Indexed: 11/10/2022] Open
Abstract
The desert is a harsh habitat for flora and microbial life due to its aridness and strong radiation. In this study, we constructed the first complete and deeply annotated genome of the genus Pontibacter (Pontibacter korlensis X14-1T = CCTCC AB 206081T, X14-1). Reconstruction of the sugar metabolism process indicated that strain X14-1 can utilize diverse sugars, including cellulose, starch and sucrose; this result is consistent with previous experiments. Strain X14-1 is also able to resist desiccation and radiation in the desert through well-armed systems related to DNA repair, radical oxygen species (ROS) detoxification and the OstAB and TreYZ pathways for trehalose synthesis. A comparative transcriptomic analysis under gamma radiation revealed that strain X14-1 presents high-efficacy operating responses to radiation, including the robust expression of catalase and the manganese transport protein. Evaluation of 73 novel genes that are differentially expressed showed that some of these genes may contribute to the strain’s adaptation to radiation and desiccation through ferric transport and preservation.
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Affiliation(s)
- Jun Dai
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan 430068, China
| | | | | | | | - Yi Zhang
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan 430068, China
| | - Mengzhou Zhou
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan 430068, China
| | - Lei Zhang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chengxiang Fang
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Qiang Gao
- BGI Shenzhen, Shenzhen 518083, China
| | - Qiao Yang
- East China Sea fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China
| | - Xin Li
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan 430068, China
| | - Zhi Wang
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan 430068, China
| | | | - Zhenhua Jia
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan 430068, China
| | - Xiong Chen
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, College of Bioengineering, Hubei University of Technology, Wuhan 430068, China
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11
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Recent progress in understanding the molecular mechanisms of radioresistance in Deinococcus bacteria. Extremophiles 2015; 19:707-19. [DOI: 10.1007/s00792-015-0759-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 05/17/2015] [Indexed: 12/17/2022]
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12
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There are more small amino acids and fewer aromatic rings in proteins of ionizing radiation-resistant bacteria. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0612-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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