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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] [MESH Headings] [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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Sakai M, Shimosaka T, Katsumata K, Yohda M, Narumi I. Developing a new host-vector system for Deinococcus grandis. Front Microbiol 2024; 15:1387296. [PMID: 38863757 PMCID: PMC11165121 DOI: 10.3389/fmicb.2024.1387296] [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: 02/17/2024] [Accepted: 04/26/2024] [Indexed: 06/13/2024] Open
Abstract
Deinococcus spp. are known for their radiation resistance, toxic compound removal, and production of valuable substances. Therefore, developing gene expression systems for Deinococcus spp. is crucial in advancing genetic engineering applications. To date, plasmid vectors that express foreign genes in D. radiodurans and D. geothermalis have been limited to plasmid pI3 and its derivatives. In contrast, plasmid vectors that express foreign genes in D. grandis include plasmid pZT23 and its derivatives. In this study, we developed a new system for the stable introduction and retention of expression plasmids for D. grandis. Two cryptic plasmids were removed from the wild-type strain to generate the TY3 strain. We then constructed a shuttle vector plasmid, pGRC5, containing the replication initiation region of the smallest cryptic plasmid, pDEGR-3, replication initiation region of the E. coli vector, pACYC184, and an antibiotic resistance gene. We introduced pGRC5, pZT23-derived plasmid pZT29H, and pI3-derived plasmid pRADN8 into strain TY3, and found their coexistence in D. grandis cells. The quantitative PCR assay results found that pGRC5, pZT29H, and pRADN8 had relative copy numbers of 11, 26, and 5 per genome, respectively. Furthermore, we developed a new plasmid in which the luciferase gene was controlled by the promoter region, which contained radiation-desiccation response operator sequences for D. grandis DdrO, a stress response regulon repressor in D. grandis, hence inducing gene expression via ultraviolet-C light irradiation. These plasmids are expected to facilitate the removal and production of toxic and valuable substances, in D. grandis, respectively, particularly of those involving multiple genes.
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Affiliation(s)
- Miyabi Sakai
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Taichi Shimosaka
- Department of Life Sciences, Faculty of Life Sciences, Toyo University, Asaka, Japan
| | | | - Masafumi Yohda
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Issay Narumi
- Department of Life Sciences, Faculty of Life Sciences, Toyo University, Asaka, Japan
- Graduate School of Life Sciences, Toyo University, Asaka, Japan
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Liu L, Liang Z, Ma S, Li L, Liu X. Radioprotective countermeasures for radiation injury (Review). Mol Med Rep 2023; 27:66. [PMID: 36799170 PMCID: PMC9926870 DOI: 10.3892/mmr.2023.12953] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 01/10/2023] [Indexed: 02/09/2023] Open
Abstract
A series of physiological and pathological changes occur after radiotherapy and accidental exposure to ionizing radiation (IR). These changes cause serious damage to human tissues and can lead to death. Radioprotective countermeasures are radioprotective agents that prevent and reduce IR injury or have therapeutic effects. Based on a good understanding of radiobiology, a number of protective agents have achieved positive results in early clinical trials. The present review grouped known radioprotective agents according to biochemical categories and potential clinical use, and reviewed radiation countermeasures, i.e., radioprotectors, radiation mitigators and radiotherapeutic agents, with an emphasis on their current status and research progress. The aim of the present review is to facilitate the selection and application of suitable radioprotectors for clinicians and researchers, to prevent or reduce IR injury.
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Affiliation(s)
- Lianchang Liu
- National Health Commission Key Laboratory of Radiobiology, School of Public Health of Jilin University, Jilin, Changchun 130021, P.R. China,School of Public Health and Management, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China,Department of Intervention, The Second Affiliated Hospital of Jilin University, Changchun, Jilin 130041, P.R. China
| | - Zhenzhen Liang
- School of Public Health, Xinxiang Medical University, Xinxiang 453003, P.R. China
| | - Shumei Ma
- School of Public Health and Management, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China,Key Laboratory of Watershed Science and Health of Zhejiang Province, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou, Zhejiang 325035, P.R. China
| | - Lan Li
- School of Public Health and Management, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China,Key Laboratory of Watershed Science and Health of Zhejiang Province, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou, Zhejiang 325035, P.R. China,Correspondence to: Professor Lan Li, School of Public Health and Management, Wenzhou Medical University, 1 North Zhongxin Road, Chashan, Wenzhou, Zhejiang 325035, P.R. China, E-mail:
| | - Xiaodong Liu
- National Health Commission Key Laboratory of Radiobiology, School of Public Health of Jilin University, Jilin, Changchun 130021, P.R. China,School of Public Health and Management, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China,Key Laboratory of Watershed Science and Health of Zhejiang Province, Wenzhou Medical University, Wenzhou, Zhejiang 325035, P.R. China,South Zhejiang Institute of Radiation Medicine and Nuclear Technology, Wenzhou, Zhejiang 325035, P.R. China,Professor Xiaodong Liu, National Health Commission Key Laboratory of Radiobiology, School of Public Health of Jilin University, 1163 Xinmin Road, Changchun, Jilin 130021, P.R. China, E-mail:
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Coexistence of SOS-Dependent and SOS-Independent Regulation of DNA Repair Genes in Radiation-Resistant Deinococcus Bacteria. Cells 2021; 10:cells10040924. [PMID: 33923690 PMCID: PMC8072749 DOI: 10.3390/cells10040924] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 11/28/2022] Open
Abstract
Deinococcus bacteria are extremely resistant to radiation and able to repair a shattered genome in an essentially error-free manner after exposure to high doses of radiation or prolonged desiccation. An efficient, SOS-independent response mechanism to induce various DNA repair genes such as recA is essential for radiation resistance. This pathway, called radiation/desiccation response, is controlled by metallopeptidase IrrE and repressor DdrO that are highly conserved in Deinococcus. Among various Deinococcus species, Deinococcus radiodurans has been studied most extensively. Its genome encodes classical DNA repair proteins for error-free repair but no error-prone translesion DNA polymerases, which may suggest that absence of mutagenic lesion bypass is crucial for error-free repair of massive DNA damage. However, many other radiation-resistant Deinococcus species do possess translesion polymerases, and radiation-induced mutagenesis has been demonstrated. At least dozens of Deinococcus species contain a mutagenesis cassette, and some even two cassettes, encoding error-prone translesion polymerase DnaE2 and two other proteins, ImuY and ImuB-C, that are probable accessory factors required for DnaE2 activity. Expression of this mutagenesis cassette is under control of the SOS regulators RecA and LexA. In this paper, we review both the RecA/LexA-controlled mutagenesis and the IrrE/DdrO-controlled radiation/desiccation response in Deinococcus.
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