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Rai SN, Dutta T. Role of Yrn2 under oxidative stress in Deinococcus radiodurans. Biochem Biophys Res Commun 2024; 723:150169. [PMID: 38815487 DOI: 10.1016/j.bbrc.2024.150169] [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: 05/15/2024] [Revised: 05/18/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024]
Abstract
Among the two Y RNAs in Deinococcus radiodurans, the functional properties of Yrn2 are still not known. Yrn2 although consists of a long stem-loop for Rsr binding, differs from Yrn1 in the effector binding site. An initial study on Yrn2 delineated it to be a UV-induced noncoding RNA. Apart from that Yrn2 has scarcely been investigated. In the current study, we identified Yrn2 as an γ-radiation induced Y RNA, which is also induced upon H2O2 and mitomycin treatment. Ectopically expressed Yrn2 appeared to be nontoxic to the cell growth. An overabundance of Yrn2 was found to ameliorate cell survival under oxidative stress through the detoxification of intracellular reactive oxygen species with a subsequent decrease in total protein carbonylation. A significant accumulation of intracellular Mn(II) with unaltered Fe(II) and Zn(II) with detected while Yrn2 is overabundant in the cells. This study identified the role of a novel Yrn2 under oxidative stress in D. radiodurans.
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Affiliation(s)
- Shiv Narayan Rai
- RNA Biology Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Tanmay Dutta
- RNA Biology Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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2
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Wang Y, Hao W, Guo Z, Sun Y, Wu Y, Sun Y, Gao T, Luo Y, Jin L, Yang J, Cheng K. Structural and functional investigation of the DHH/DHHA1 family proteins in Deinococcus radiodurans. Nucleic Acids Res 2024; 52:7142-7157. [PMID: 38804263 PMCID: PMC11229311 DOI: 10.1093/nar/gkae451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 04/24/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024] Open
Abstract
DHH/DHHA1 family proteins have been proposed to play critical roles in bacterial resistance to environmental stresses. Members of the most radioresistant bacteria genus, Deinococcus, possess two DHH/DHHA1 family proteins, RecJ and RecJ-like. While the functions of Deinococcus radiodurans RecJ (DrRecJ) in DNA damage resistance have been well characterized, the role and biochemical activities of D. radiodurans RecJ-like (DrRecJ-like) remain unclear. Phenotypic and transcriptomic analyses suggest that, beyond DNA repair, DrRecJ is implicated in cell growth and division. Additionally, DrRecJ-like not only affects stress response, cell growth, and division but also correlates with the folding/stability of intracellular proteins, as well as the formation and stability of cell membranes/walls. DrRecJ-like exhibits a preferred catalytic activity towards short single-stranded RNA/DNA oligos and c-di-AMP. In contrast, DrRecJ shows no activity against RNA and c-di-AMP. Moreover, a crystal structure of DrRecJ-like, with Mg2+ bound in an open conformation at a resolution of 1.97 Å, has been resolved. Subsequent mutational analysis was conducted to pinpoint the crucial residues essential for metal cation and substrate binding, along with the dimerization state, necessary for DrRecJ-like's function. This finding could potentially extend to all NrnA-like proteins, considering their conserved amino acid sequence and comparable dimerization forms.
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Affiliation(s)
- Ying Wang
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Wanshan Hao
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Ziming Guo
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Yiyang Sun
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Yu Wu
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Yukang Sun
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Tianwen Gao
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Yun Luo
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Lizan Jin
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Jieyu Yang
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Kaiying Cheng
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
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Shen L, Hu J, Zhang L, Wu Z, Chen L, Adhikari NP, Ji M, Chen S, Peng F, Liu Y. Genomics-based identification of a cold adapted clade in Deinococcus. BMC Biol 2024; 22:145. [PMID: 38956546 PMCID: PMC11218099 DOI: 10.1186/s12915-024-01944-8] [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: 12/27/2023] [Accepted: 06/25/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Microbes in the cold polar and alpine environments play a critical role in feedbacks that amplify the effects of climate change. Defining the cold adapted ecotype is one of the prerequisites for understanding the response of polar and alpine microbes to climate change. RESULTS Here, we analysed 85 high-quality, de-duplicated genomes of Deinococcus, which can survive in a variety of harsh environments. By leveraging genomic and phenotypic traits with reverse ecology, we defined a cold adapted clade from eight Deinococcus strains isolated from Arctic, Antarctic and high alpine environments. Genome-wide optimization in amino acid composition and regulation and signalling enable the cold adapted clade to produce CO2 from organic matter and boost the bioavailability of mineral nitrogen. CONCLUSIONS Based primarily on in silico genomic analysis, we defined a potential cold adapted clade in Deinococcus and provided an updated view of the genomic traits and metabolic potential of Deinococcus. Our study would facilitate the understanding of microbial processes in the cold polar and alpine environments.
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Affiliation(s)
- Liang Shen
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China.
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, and Auhui Provincial Engineering Research Centre for Molecular Detection and Diagnostics, Anhui Normal University, Wuhu, 241000, China.
| | - Jiayu Hu
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Luyao Zhang
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Zirui Wu
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Liangzhong Chen
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Namita Paudel Adhikari
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China
| | - Mukan Ji
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China
| | - Shaoxing Chen
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Fang Peng
- China Center for Type Culture Collection (CCTCC), College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China.
| | - Yongqin Liu
- State Key Laboratory of Tibetan Plateau Earth System, Environment and Resources (TPESER), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, 100101, China
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou, 730000, China
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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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Sachdeva S, Sarethy IP. Diving into freshwater microbial metabolites: Pioneering research and future prospects. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2024:1-19. [PMID: 38887995 DOI: 10.1080/09603123.2024.2351153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 04/30/2024] [Indexed: 06/20/2024]
Abstract
In practically every facet of life, especially nutrition, agriculture, and healthcare, microorganisms offer a prospective origin for abundant natural substances and products. Among these microorganisms, bacteria also possess the capability to rapidly acclimate to diverse environments, utilize varied resources, and effectively respond to environmental fluctuations, including those influenced by human activities like pollution and climate change. The ever-changing environment of freshwater bodies influences bacterial communities, offering opportunities for improving health and environmental conservation that remain unexplored. Herein, the study discusses the bacterial taxa along with specialised metabolites with antioxidant, antibacterial, and anticancer activity that have been identified from freshwater environments, thus achieving Sustainable Development Goals addressing health and wellbeing (SDG-3), economic growth (SDG-8) along with industrial development (SDG-9). The present review is intended as a compendium for research teams working in the fields of medicinal chemistry, organic chemistry, clinical research, and natural product chemistry.
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Affiliation(s)
- Saloni Sachdeva
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
| | - Indira P Sarethy
- Department of Biotechnology, Jaypee Institute of Information Technology, Noida, India
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Misra HS, Rajpurohit YS. DNA damage response and cell cycle regulation in bacteria: a twist around the paradigm. Front Microbiol 2024; 15:1389074. [PMID: 38605710 PMCID: PMC11007091 DOI: 10.3389/fmicb.2024.1389074] [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: 02/20/2024] [Accepted: 03/13/2024] [Indexed: 04/13/2024] Open
Abstract
The co-protease activity in the RecA-ssDNA complex cleaves the autorepressor LexA, resulting in the derepression of a large number of genes under LexA control. This process is called the SOS response, and genes that are expressed in response to DNA damage are called SOS genes. The proteins encoded by the SOS genes are involved in both DNA repair and maintaining the functions of crucial cell division proteins (e.g., FtsZ) under check until the damaged DNA is presumably repaired. This mechanism of SOS response is the only known mechanism of DNA damage response and cell cycle regulation in bacteria. However, there are bacteria that do not obey this rule of DNA damage response and cell cycle regulation, yet they respond to DNA damage, repair it, and survive. That means such bacteria would have some alternate mechanism(s) of DNA damage response and cell cycle regulation beyond the canonical pathway of the SOS response. In this study, we present the perspectives that bacteria may have other mechanisms of DNA damage response and cell cycle regulation mediated by bacterial eukaryotic type Ser/Thr protein kinases as an alternate to the canonical SOS response and herewith elaborate on them with a well-studied example in the radioresistant bacterium Deinococcus radiodurans.
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Affiliation(s)
- Hari Sharan Misra
- School of Sciences, Gandhi Institute of Technology and Management (GITAM), Visakhapatnam, India
| | - Yogendra Singh Rajpurohit
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India
- Life Sciences, Homi Bhabha National Institute (DAE Deemed to be University), Mumbai, India
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Shen L, Liu Y, Chen L, Lei T, Ren P, Ji M, Song W, Lin H, Su W, Wang S, Rooman M, Pucci F. Genomic basis of environmental adaptation in the widespread poly-extremophilic Exiguobacterium group. THE ISME JOURNAL 2024; 18:wrad020. [PMID: 38365240 PMCID: PMC10837837 DOI: 10.1093/ismejo/wrad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 02/18/2024]
Abstract
Delineating cohesive ecological units and determining the genetic basis for their environmental adaptation are among the most important objectives in microbiology. In the last decade, many studies have been devoted to characterizing the genetic diversity in microbial populations to address these issues. However, the impact of extreme environmental conditions, such as temperature and salinity, on microbial ecology and evolution remains unclear so far. In order to better understand the mechanisms of adaptation, we studied the (pan)genome of Exiguobacterium, a poly-extremophile bacterium able to grow in a wide range of environments, from permafrost to hot springs. To have the genome for all known Exiguobacterium type strains, we first sequenced those that were not yet available. Using a reverse-ecology approach, we showed how the integration of phylogenomic information, genomic features, gene and pathway enrichment data, regulatory element analyses, protein amino acid composition, and protein structure analyses of the entire Exiguobacterium pangenome allows to sharply delineate ecological units consisting of mesophilic, psychrophilic, halophilic-mesophilic, and halophilic-thermophilic ecotypes. This in-depth study clarified the genetic basis of the defined ecotypes and identified some key mechanisms driving the environmental adaptation to extreme environments. Our study points the way to organizing the vast microbial diversity into meaningful ecologically units, which, in turn, provides insight into how microbial communities adapt and respond to different environmental conditions in a changing world.
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Affiliation(s)
- Liang Shen
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, and Anhui Provincial Engineering Research Centre for Molecular Detection and Diagnostics, Anhui Normal University, Wuhu 241000, China
| | - Yongqin Liu
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Liangzhong Chen
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Tingting Lei
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Ping Ren
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Mukan Ji
- Center for the Pan-Third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Weizhi Song
- Centre for Marine Bio-Innovation, University of New South Wales, Sydney, NSW 2052, Australia
| | - Hao Lin
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Wei Su
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Sheng Wang
- Shanghai Zelixir Biotech Company Ltd., Shanghai 200030, China
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels 1050, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Brussels 1050, Belgium
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Brussels 1050, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Brussels 1050, Belgium
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Mishra S, Tewari H, Chaudhary R, S Misra H, Kota S. Differential cellular localization of DNA gyrase and topoisomerase IB in response to DNA damage in Deinococcus radiodurans. Extremophiles 2023; 28:7. [PMID: 38062175 DOI: 10.1007/s00792-023-01323-1] [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: 05/16/2023] [Accepted: 11/02/2023] [Indexed: 12/18/2023]
Abstract
Topoisomerases are crucial enzymes in genome maintenance that modulate the topological changes during DNA metabolism. Deinococcus radiodurans, a Gram-positive bacterium is characterized by its resistance to many abiotic stresses including gamma radiation. Its multipartite genome encodes both type I and type II topoisomerases. Time-lapse studies using fluorescently tagged topoisomerase IB (drTopoIB-RFP) and DNA gyrase (GyrA-RFP) were performed to check the dynamics and localization with respect to DNA repair and cell division under normal and post-irradiation growth conditions. Results suggested that TopoIB and DNA gyrase are mostly found on nucleoid, highly dynamic, and show growth phase-dependent subcellular localization. The drTopoIB-RFP was also present at peripheral and septum regions but does not co-localize with the cell division protein, drFtsZ. On the other hand, DNA gyrase co-localizes with PprA a pleiotropic protein involved in radioresistance, on the nucleoid during the post-irradiation recovery (PIR). The topoIB mutant was found to be sensitive to hydroxyurea treatment, and showed more accumulation of single-stranded DNA during the PIR, compared to the wild type suggesting its role in DNA replication stress. Together, these results suggest differential localization of drTopoIB-RFP and GyrA-RFP in D. radiodurans and their interaction with PprA protein, emphasizing the functional significance and role in radioresistance.
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Affiliation(s)
- Shruti Mishra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
- Homi Bhabha National Institute, Mumbai, 400094, India
| | - Himani Tewari
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
- Homi Bhabha National Institute, Mumbai, 400094, India
| | - Reema Chaudhary
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
- National Centre for Microbial Resource, National Centre for Cell Science, Sai Trinity Complex, Sus Road, Pashan, Pune, 411021, India
| | - Hari S Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
- Homi Bhabha National Institute, Mumbai, 400094, India
- Centre of Multidisciplinary Unit of Research On Translational Initiatives and School of Science, GITAM (Deemed to Be University), Gandhinagar, Rushikonda, Visakhapatnam, 530045, India
| | - Swathi Kota
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India.
- Homi Bhabha National Institute, Mumbai, 400094, India.
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Daly MJ. The scientific revolution that unraveled the astonishing DNA repair capacity of the Deinococcaceae: 40 years on. Can J Microbiol 2023; 69:369-386. [PMID: 37267626 DOI: 10.1139/cjm-2023-0059] [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] [Indexed: 06/04/2023]
Abstract
The family Deinococcaceae exhibits exceptional radiation resistance and possesses all the necessary traits for surviving in radiation-exposed environments. Their survival strategy involves the coupling of metabolic and DNA repair functions, resulting in an extraordinarily efficient homologous repair of DNA double-strand breaks (DSBs) caused by radiation or desiccation. The keys to their survival lie in the hyperaccumulation of manganous (Mn2+)-metabolite antioxidants that protect their DNA repair proteins under extreme oxidative stress and the persistent structural linkage by Holliday junctions of their multiple genome copies per cell that facilitates DSB repair. This coupling of metabolic and DNA repair functions has made polyploid Deinococcus bacteria a useful tool in environmental biotechnology, radiobiology, aging, and planetary protection. The review highlights the groundbreaking contributions of the late Robert G.E. Murray to the field of Deinococcus research and the emergent paradigm-shifting discoveries that revolutionized our understanding of radiation survivability and oxidative stress defense, demonstrating that the proteome, rather than the genome, is the primary target responsible for survivability. These discoveries have led to the commercial development of irradiated vaccines using Deinococcus Mn-peptide antioxidants and have significant implications for various fields.
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Affiliation(s)
- Michael J Daly
- Uniformed Services University of the Health Sciences (USUHS), School of Medicine, Department of Pathology, Bethesda, MD 20814-4799, USA
- Committee on Planetary Protection (CoPP), National Academies of Sciences, Washington, DC 20001, USA
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Fernandes A, Williamson A, Matias PM, Moe E. Structure/function studies of the NAD +-dependent DNA ligase from the poly-extremophile Deinococcus radiodurans reveal importance of the BRCT domain for DNA binding. Extremophiles 2023; 27:26. [PMID: 37712998 PMCID: PMC10504179 DOI: 10.1007/s00792-023-01309-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: 04/04/2023] [Accepted: 08/21/2023] [Indexed: 09/16/2023]
Abstract
Bacterial NAD+-dependent DNA ligases (LigAs) are enzymes involved in replication, recombination, and DNA-repair processes by catalyzing the formation of phosphodiester bonds in the backbone of DNA. These multidomain proteins exhibit four modular domains, that are highly conserved across species, with the BRCT (breast cancer type 1 C-terminus) domain on the C-terminus of the enzyme. In this study, we expressed and purified both recombinant full-length and a C-terminally truncated LigA from Deinococcus radiodurans (DrLigA and DrLigA∆BRCT) and characterized them using biochemical and X-ray crystallography techniques. Using seeds of DrLigA spherulites, we obtained ≤ 100 µm plate crystals of DrLigA∆BRCT. The crystal structure of the truncated protein was obtained at 3.4 Å resolution, revealing DrLigA∆BRCT in a non-adenylated state. Using molecular beacon-based activity assays, we demonstrated that DNA ligation via nick sealing remains unaffected in the truncated DrLigA∆BRCT. However, DNA-binding assays revealed a reduction in the affinity of DrLigA∆BRCT for dsDNA. Thus, we conclude that the flexible BRCT domain, while not critical for DNA nick-joining, plays a role in the DNA binding process, which may be a conserved function of the BRCT domain in LigA-type DNA ligases.
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Affiliation(s)
- Andreia Fernandes
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Adele Williamson
- Department of Chemistry, UiT-The Arctic University of Norway, Tromsø, Norway
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Pedro M Matias
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
- Institute of Experimental and Technological Biology (IBET), Oeiras, Portugal
| | - Elin Moe
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal.
- Department of Chemistry, UiT-The Arctic University of Norway, Tromsø, Norway.
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Rollo F, Martins GD, Gouveia AG, Ithurbide S, Servant P, Romão CV, Moe E. Insights into the role of three Endonuclease III enzymes for oxidative stress resistance in the extremely radiation resistant bacterium Deinococcus radiodurans. Front Microbiol 2023; 14:1266785. [PMID: 37771704 PMCID: PMC10523315 DOI: 10.3389/fmicb.2023.1266785] [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: 07/25/2023] [Accepted: 08/29/2023] [Indexed: 09/30/2023] Open
Abstract
The extremely radiation and desiccation resistant bacterium Deinococcus radiodurans possesses three genes encoding Endonuclease III-like enzymes (DrEndoIII1, DrEndoIII2, DrEndoIII3). In vitro enzymatic activity measurements revealed that DrEndoIII2 is the main Endonuclease III in this organism, while DrEndoIII1 and 3 possess unusual and, so far, no detectable EndoIII activity, respectively. In order to understand the role of these enzymes at a cellular level, DrEndoIII knockout mutants were constructed and subjected to various oxidative stress related conditions. The results showed that the mutants are as resistant to ionizing and UV-C radiation as well as H2O2 exposure as the wild type. However, upon exposure to oxidative stress induced by methyl viologen, the knockout strains were more resistant than the wild type. The difference in resistance may be attributed to the observed upregulation of the EndoIII homologs gene expression upon addition of methyl viologen. In conclusion, our data suggest that all three EndoIII homologs are crucial for cell survival in stress conditions, since the knockout of one of the genes tend to be compensated for by overexpression of the genes encoding the other two.
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Affiliation(s)
- Filipe Rollo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Guilherme D. Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - André G. Gouveia
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Solenne Ithurbide
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif sur Yvette, France
| | - Pascale Servant
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif sur Yvette, France
| | - Célia V. Romão
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
| | - Elin Moe
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Oeiras, Portugal
- Department of Chemistry, UiT - The Arctic University of Norway, Tromsø, Norway
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12
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Sadowska-Bartosz I, Bartosz G. Antioxidant defense of Deinococcus radiodurans: how does it contribute to extreme radiation resistance? Int J Radiat Biol 2023; 99:1803-1829. [PMID: 37498212 DOI: 10.1080/09553002.2023.2241895] [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: 01/09/2023] [Revised: 06/28/2023] [Accepted: 07/08/2023] [Indexed: 07/28/2023]
Abstract
PURPOSE Deinococcus radiodurans is an extremely radioresistant bacterium characterized by D10 of 10 kGy, and able to grow luxuriantly under chronic ionizing radiation of 60 Gy/h. The aim of this article is to review the antioxidant system of D. radiodurans and its possible role in the unusual resistance of this bacterium to ionizing radiation. CONCLUSIONS The unusual radiation resistance of D. radiodurans has apparently evolved as a side effect of the adaptation of this extremophile to other damaging environmental factors, especially desiccation. The antioxidant proteins and low-molecular antioxidants (especially low-molecular weight Mn2+ complexes and carotenoids, in particular, deinoxanthin), as well as protein and non-protein regulators, are important for the antioxidant defense of this species. Antioxidant protection of proteins from radiation inactivation enables the repair of DNA damage caused by ionizing radiation.
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Affiliation(s)
- Izabela Sadowska-Bartosz
- Laboratory of Analytical Biochemistry, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
| | - Grzegorz Bartosz
- Department of Bioenergetics, Food Analysis and Microbiology, Institute of Food Technology and Nutrition, College of Natural Sciences, University of Rzeszow, Rzeszow, Poland
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13
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Yuan D, Wang L, Wang H, Miao R, Wang Y, Jin H, Tan L, Wei C, Hu Q, Gong Y. Application of microalgae Scenedesmus acuminatus enhances water quality in rice-crayfish culture. Front Bioeng Biotechnol 2023; 11:1143622. [PMID: 37214297 PMCID: PMC10192885 DOI: 10.3389/fbioe.2023.1143622] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
Improper management of aquatic environments substantially restricts the development of the aquaculture industry. The industrialisation of the crayfish Procambarus clarkii, for example, is currently being limited by poor water quality. Research suggests that microalgal biotechnology has a great potential for water quality regulation. However, the ecological effects of microalgal applications on aquatic communities in aquaculture systems remain largely unknown. In the present study, 5 L Scenedesmus acuminatus GT-2 culture (biomass 120 g L-1) was added to an approximately 1,000 m2 rice-crayfish culture to examine the response of aquatic ecosystems to microalgal application. The total nitrogen content decreased significantly as a result of microalgal addition. Moreover, the microalgal addition changed the bacterial community structure directionally and produced more nitrate reducing and aerobic bacteria. The effect of microalgal addition on plankton community structure was not obvious, except for a significant difference in Spirogyra growth which was inhibited by 81.0% under microalgal addition. Furthermore, the network of microorganisms in culture systems with the added microalga had higher interconnectivity and was more complex, which indicating microalgal application enhance the stability of aquaculture systems. The application of microalgae was found to have the greatest effect on the 6th day of the experiment, as supported by both environmental and biological evidence. These findings can provide valuable guidance for the practical application of microalgae in aquaculture systems.
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Affiliation(s)
- Danni Yuan
- School of Environmental Ecology and Biological Engineering, Wuhan Institute of Technology, Wuhan, China
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Lan Wang
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Hongxia Wang
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Rongli Miao
- Hydrobiological Data Analysis Center, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yulu Wang
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Hu Jin
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Lu Tan
- Systems Ecology and Watershed Ecology Center for Freshwater Ecology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Chaojun Wei
- Hydrobiological Data Analysis Center, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Qiang Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yingchun Gong
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
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14
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The radioresistant and survival mechanisms of Deinococcus radiodurans. RADIATION MEDICINE AND PROTECTION 2023. [DOI: 10.1016/j.radmp.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
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15
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Yang J, Sun Y, Wang Y, Hao W, Cheng K. Structural and DNA end resection study of the bacterial NurA-HerA complex. BMC Biol 2023; 21:42. [PMID: 36829173 PMCID: PMC9960219 DOI: 10.1186/s12915-023-01542-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 02/10/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND The nuclease NurA and the ATPase/translocase HerA play a vital role in repair of double-strand breaks (DSB) during the homologous recombination in archaea. A NurA-HerA complex is known to mediate DSB DNA end resection, leading to formation of a free 3' end used to search for the homologous sequence. Despite the structures of individual archaeal types of NurA and HerA having been reported, there is limited information regarding the molecular mechanisms underlying this process. Some bacteria also possess homologs of NurA and HerA; however, the bacterial type of this complex, as well as the detailed mechanisms underlying the joining of NurA-HerA in DSB DNA end resection, remains unclear. RESULTS We report for the first time the crystal structures of Deinococcus radiodurans HerA (drHerA) in the nucleotide-free and ADP-binding modes. A D. radiodurans NurA-HerA complex structure was constructed according to a low-resolution cryo-electron microscopy map. We performed site-directed mutagenesis to map the drNurA-HerA interaction sites, suggesting that their interaction is mainly mediated by ionic links, in contrast to previously characterized archaeal NurA-HerA interactions. The key residues responsible for the DNA translocation activity, DNA unwinding activity, and catalytic activities of the drNurA-HerA complex were identified. A HerA/FtsK-specific translocation-related motif (TR motif) that guarantees the processivity of double-stranded DNA (dsDNA) translocation was identified. Moreover, a mechanism for the translocation-regulated resection of the 5' tail of broken dsDNA and the corresponding generation of a recombinogenic 3' single-stranded DNA tail by the drNurA-HerA complex was elucidated. CONCLUSIONS Our work provides new insights into the mechanism underlying bacterial NurA-HerA-mediated DSB DNA end resection, and the way this complex digests the 5' tail of a DNA duplex and provides long 3' free end for strand invasion in the bacterial homologous recombination process.
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Affiliation(s)
- Jieyu Yang
- grid.410595.c0000 0001 2230 9154Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121 China
| | - Yiyang Sun
- grid.410595.c0000 0001 2230 9154Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121 China
| | - Ying Wang
- grid.410595.c0000 0001 2230 9154Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121 China
| | - Wanshan Hao
- grid.410595.c0000 0001 2230 9154Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121 China
| | - Kaiying Cheng
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China. .,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China.
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16
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A Novel Glycoside Hydrolase DogH Utilizing Soluble Starch to Maltose Improve Osmotic Tolerance in Deinococcus radiodurans. Int J Mol Sci 2023; 24:ijms24043437. [PMID: 36834856 PMCID: PMC9967864 DOI: 10.3390/ijms24043437] [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: 12/26/2022] [Revised: 01/25/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023] Open
Abstract
Deinococcus radiodurans is a microorganism that can adjust, survive or thrive in hostile conditions and has been described as "the strongest microorganism in the world". The underlying mechanism behind the exceptional resistance of this robust bacterium still remains unclear. Osmotic stress, caused by abiotic stresses such as desiccation, salt stress, high temperatures and freezing, is one of the main stresses suffered by microorganisms, and it is also the basic response pathway by which organisms cope with environmental stress. In this study, a unique trehalose synthesis-related gene, dogH (Deinococcus radiodurans orphan glycosyl hydrolase-like family 10), which encodes a novel glycoside hydrolase, was excavated using a multi-omics combination method. The content accumulation of trehalose and its precursors under hypertonic conditions was quantified by HPLC-MS. Ours results showed that the dogH gene was strongly induced by sorbitol and desiccation stress in D. radiodurans. DogH glycoside hydrolase hydrolyzes α-1,4-glycosidic bonds by releasing maltose from starch in the regulation of soluble sugars, thereby increasing the concentration of TreS (trehalose synthase) pathway precursors and trehalose biomass. The maltose and alginate content in D. radiodurans amounted to 48 μg mg protein-1 and 45 μg mg protein-1, respectively, which were 9 and 28 times higher than those in E. coli, respectively. The accumulation of greater intracellular concentrations of osmoprotectants may be the true reason for the higher osmotic stress tolerance of D. radiodurans.
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17
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MoaE Is Involved in Response to Oxidative Stress in Deinococcus radiodurans. Int J Mol Sci 2023; 24:ijms24032441. [PMID: 36768763 PMCID: PMC9916421 DOI: 10.3390/ijms24032441] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/19/2023] [Accepted: 01/22/2023] [Indexed: 01/28/2023] Open
Abstract
Molybdenum ions are covalently bound to molybdenum pterin (MPT) to produce molybdenum cofactor (Moco), a compound essential for the catalytic activity of molybdenum enzymes, which is involved in a variety of biological functions. MoaE is the large subunit of MPT synthase and plays a key role in Moco synthesis. Here, we investigated the function of MoaE in Deinococcus radiodurans (DrMoaE) in vitro and in vivo, demonstrating that the protein contributed to the extreme resistance of D. radiodurans. The crystal structure of DrMoaE was determined by 1.9 Å resolution. DrMoaE was shown to be a dimer and the dimerization disappeared after Arg110 had been mutated. The deletion of drmoaE resulted in sensitivity to DNA damage stress and a slower growth rate in D. radiodurans. The increase in drmoaE transcript levels the and accumulation of intracellular reactive oxygen species levels under oxidative stress suggested that it was involved in the antioxidant process in D. radiodurans. In addition, treatment with the base analog 6-hydroxyaminopurine decreased survival and increased intracellular mutation rates in drmoaE deletion mutant strains. Our results reveal that MoaE plays a role in response to external stress mainly through oxidative stress resistance mechanisms in D. radiodurans.
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18
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Karavaeva V, Sousa FL. Modular structure of complex II: An evolutionary perspective. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148916. [PMID: 36084748 DOI: 10.1016/j.bbabio.2022.148916] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/21/2022] [Accepted: 09/02/2022] [Indexed: 11/25/2022]
Abstract
Succinate dehydrogenases (SDHs) and fumarate reductases (FRDs) catalyse the interconversion of succinate and fumarate, a reaction highly conserved in all domains of life. The current classification of SDH/FRDs is based on the structure of the membrane anchor subunits and their cofactors. It is, however, unknown whether this classification would hold in the context of evolution. In this work, a large-scale comparative genomic analysis of complex II addresses the questions of its taxonomic distribution and phylogeny. Our findings report that for types C, D, and F, structural classification and phylogeny go hand in hand, while for types A, B and E the situation is more complex, highlighting the possibility for their classification into subgroups. Based on these findings, we proposed a revised version of the evolutionary scenario for these enzymes in which a primordial soluble module, corresponding to the cytoplasmatic subunits, would give rise to the current diversity via several independent membrane anchor attachment events.
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Affiliation(s)
- Val Karavaeva
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria
| | - Filipa L Sousa
- Department of Functional and Evolutionary Ecology, University of Vienna, Djerassiplatz 1, 1030 Wien, Austria.
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19
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Characterization of DNA Processing Protein A (DprA) of the Radiation-Resistant Bacterium Deinococcus radiodurans. Microbiol Spectr 2022; 10:e0347022. [PMID: 36453941 PMCID: PMC9769556 DOI: 10.1128/spectrum.03470-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Environmental DNA uptake by certain bacteria and its integration into their genome create genetic diversity and new phenotypes. DNA processing protein A (DprA) is part of a multiprotein complex and facilitates the natural transformation (NT) phenotype in most bacteria. Deinococcus radiodurans, an extremely radioresistant bacterium, is efficient in NT, and its genome encodes nearly all of the components of the natural competence complex. Here, we have characterized the DprA protein of this bacterium (DrDprA) for the known characteristics of DprA proteins of other bacteria and the mechanisms underlying the DNA-RecA interaction. DrDprA has three domains. In vitro studies showed that purified recombinant DrDprA binds to both single-strand DNA (ssDNA) and double-strand DNA (dsDNA) and is able to protect ssDNA from nucleolytic degradation. DrDprA showed a strong interaction with DrRecA and facilitated RecA-catalyzed functions in vivo. Mutational studies identified DrDprA amino acid residues crucial for oligomerization, the interaction with DrRecA, and DNA binding. Furthermore, we showed that both oligomerization and DNA binding properties of DrDprA are integral to its support of the DrRecA-catalyzed strand exchange reaction (SER) in vitro. Together, these data suggested that DrDprA is largely structurally conserved with other DprA homologs but shows some unique structure-function features like the existence of an additional C-terminal Drosophila melanogaster Miasto-like protein 1 (DML1) domain, equal affinities for ssDNA and dsDNA, and the collective roles of oligomerization and DNA binding properties in supporting DrRecA functions. IMPORTANCE Bacteria can take up extracellular DNA (eDNA) by natural transformation (NT). Many bacteria, including Deinococcus radiodurans, have constitutive competence systems and can take up eDNA throughout their growth phase. DprA (DNA processing protein A) is a transformation-specific recombination mediator protein (RMP) that plays a role in bacterial NT, and the absence of this gene significantly reduces the transformation efficiencies of both chromosomal and plasmid DNA. NT helps bacteria survive under adverse conditions and contributes to genetic diversity in bacteria. The present work describes the characterization of DprA from D. radiodurans and will add to the existing knowledge of DprA biology.
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20
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FtsK, a DNA Motor Protein, Coordinates the Genome Segregation and Early Cell Division Processes in Deinococcus radiodurans. mBio 2022; 13:e0174222. [PMID: 36300930 PMCID: PMC9764985 DOI: 10.1128/mbio.01742-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Filament temperature-sensitive mutant K (FtsK)/SpoIIIE family proteins are DNA translocases known as the fastest DNA motor proteins that use ATP for their movement on DNA. Most of the studies in single chromosome-containing bacteria have established the role of FtsK in chromosome dimer resolution (CDR), connecting the bacterial chromosome segregation process with cell division. Only limited reports, however, are available on the interdependent regulation of genome segregation and cell division in multipartite genome harboring (MGH) bacteria. In this study, for the first time, we report the characterization of FtsK from the radioresistant MGH bacterium Deinococcus radiodurans R1 (drFtsK). drFtsK shows the activity characteristics of a typical FtsK/SpoIIIE/Tra family. It stimulates the site-specific recombination catalyzed by Escherichia coli tyrosine recombinases. drFtsK interacts with various cell division and genome segregation proteins of D. radiodurans. Microscopic examination of different domain deletion mutants of this protein reveals alterations in cellular membrane architecture and nucleoid morphology. In vivo localization studies of drFtsK-RFP show that it forms multiple foci on nucleoid as well as on the membrane with maximum density on the septum. drFtsK coordinates its movement with nucleoid separation. The alignment of its foci shifts from old to new septum indicating its cellular dynamics with the FtsZ ring during the cell division process. Nearly, similar positional dynamicity of FtsK was observed in cells recovering from gamma radiation exposure. These results suggest that FtsK forms a part of chromosome segregation, cell envelope, and cell division machinery in D. radiodurans. IMPORTANCE Deinococcus radiodurans show extraordinary resistance to gamma radiation. It is polyploid and harbors a multipartite genome comprised of 2 chromosomes and 2 plasmids, packaged in a doughnut-shaped toroidal nucleoid. Very little is known about how the tightly packed genome is accurately segregated and the next divisional plane is determined. Filament temperature-sensitive mutant K (FtsK), a multifunctional protein, helps in pumping the septum-trapped DNA in several bacteria. Here, we characterized FtsK of D. radiodurans R1 (drFtsK) for the first time and showed it to be an active protein. The absence of drFtsK causes many defects in morphology at both cellular and nucleoid levels. The compact packaging of the deinococcal genome and cell membrane formation is hindered in ftsK mutants. In vivo drFtsK is dynamic, forms foci on both nucleoid and septum, and coordinates with FtsZ for the next cell division. Thus, drFtsK role in maintaining the normal genome phenotype and cell division in D. radiodurans is suggested.
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21
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Ren CY, Xu QJ, Mathieu J, Alvarez PJJ, Zhu L, Zhao HP. A Carotenoid- and Nuclease-Producing Bacterium Can Mitigate Enterococcus faecalis Transformation by Antibiotic Resistance Genes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:15167-15178. [PMID: 35862635 DOI: 10.1021/acs.est.2c03919] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Dissemination of antibiotic resistance genes (ARGs) through natural transformation is facilitated by factors that stabilize extracellular DNA (eDNA) and that induce reactive oxygen species (ROS) that permeabilize receptor cells and upregulate transformation competence genes. In this study, we demonstrate that Deinococcus radiodurans can mitigate this ARG dissemination pathway by removing both eDNA and ROS that make recipient cells more vulnerable to transformation. We used plasmid RP4 as source of extracellular ARGs (tetA, aphA, and blaTEM-2) and the opportunistic pathogen Enterococcus faecalis as receptor. The presence of D. radiodurans significantly reduced the transformation frequency from 2.5 ± 0.7 × 10-6 to 7.4 ± 1.4 × 10-7 (p < 0.05). Based on quantification of intracellular ROS accumulation and superoxide dismutase (SOD) activity, and quantitative polymerase chain reaction (qPCR) and transcriptomic analyses, we propose two mechanisms by which D. radiodurans mitigates E. faecalis transformation by ARGs: (a) residual antibiotics induce D. radiodurans to synthesize liposoluble carotenoids that scavenge ROS and thus mitigate the susceptibility of E. faecalis for eDNA uptake, and (b) eDNA induces D. radiodurans to synthesize extracellular nucleases that degrade eARGs. This mechanistic insight informs biological strategies (including bioaugmentation) to curtail the spread of ARGs through transformation.
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Affiliation(s)
- Chong-Yang Ren
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China, 310058
| | - Qiu-Jin Xu
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China, 310058
| | - Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
| | - Lizhong Zhu
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China, 310058
| | - He-Ping Zhao
- MOE Key Lab of Environmental Remediation and Ecosystem Health, College of Environmental and Resource Science, Zhejiang University, Hangzhou, China, 310058
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22
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Disentangling Unusual Catalytic Properties and the Role of the [4Fe-4S] Cluster of Three Endonuclease III from the Extremophile D. radiodurans. Molecules 2022; 27:molecules27134270. [PMID: 35807515 PMCID: PMC9268735 DOI: 10.3390/molecules27134270] [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: 06/15/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 02/05/2023] Open
Abstract
Endonuclease III (EndoIII) is a bifunctional DNA glycosylase with specificity for a broad range of oxidized DNA lesions. The genome of an extremely radiation- and desiccation-resistant bacterium, Deinococcus radiodurans, possesses three genes encoding for EndoIII-like enzymes (DrEndoIII1, DrEndoIII2 and DrEndoIII3), which reveal different types of catalytic activities. DrEndoIII2 acts as the main EndoIII in this organism, while DrEndoIII1 and 3 demonstrate unusual and no EndoIII activity, respectively. In order to understand the role of DrEndoIII1 and DrEndoIII3 in D. radiodurans, we have generated mutants which target non-conserved residues in positions considered essential for classic EndoIII activity. In parallel, we have substituted residues coordinating the iron atoms in the [4Fe-4S] cluster in DrEndoIII2, aiming at elucidating the role of the cluster in these enzymes. Our results demonstrate that the amino acid substitutions in DrEndoIII1 reduce the enzyme activity without altering the overall structure, revealing that the residues found in the wild-type enzyme are essential for its unusual activity. The attempt to generate catalytic activity of DrEndoIII3 by re-designing its catalytic pocket was unsuccessful. A mutation of the iron-coordinating cysteine 199 in DrEndoIII2 appears to compromise the structural integrity and induce the formation of a [3Fe-4S] cluster, but apparently without affecting the activity. Taken together, we provide important structural and mechanistic insights into the three EndoIIIs, which will help us disentangle the open questions related to their presence in D. radiodurans and their particularities.
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23
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The structure of Deinococcus radiodurans transcriptional regulator HucR retold with the urate bound. Biochem Biophys Res Commun 2022; 615:63-69. [DOI: 10.1016/j.bbrc.2022.05.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 04/28/2022] [Accepted: 05/11/2022] [Indexed: 11/18/2022]
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24
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Brumwell SL, Van Belois KD, Giguere DJ, Edgell DR, Karas BJ. Conjugation-Based Genome Engineering in Deinococcus radiodurans. ACS Synth Biol 2022; 11:1068-1076. [PMID: 35254818 PMCID: PMC8939323 DOI: 10.1021/acssynbio.1c00524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Deinococcus radiodurans has become an attractive microbial platform for the study of extremophile biology and industrial bioproduction. To improve the genomic manipulation and tractability of this species, the development of tools for whole genome engineering and design is necessary. Here, we report the development of a simple and robust conjugation-based DNA transfer method from E. coli to D. radiodurans, allowing for the introduction of stable, replicating plasmids expressing antibiotic resistance markers. Using this method with nonreplicating plasmids, we developed a protocol for creating sequential gene deletions in D. radiodurans by targeting restriction-modification genes. Importantly, we demonstrated a conjugation-based method for cloning the large (178 kb), high G+C content MP1 megaplasmid from D. radiodurans in E. coli. The conjugation-based tools described here will facilitate the development of D. radiodurans strains with synthetic genomes for biological studies and industrial applications.
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Affiliation(s)
- Stephanie L Brumwell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Katherine D Van Belois
- Department of Biology, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Daniel J Giguere
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - David R Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
| | - Bogumil J Karas
- Department of Biochemistry, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario N6A 5C1, Canada
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25
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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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Joshi S, Ghosh P, Barage S, Basu B, Deobagkar DD. Genome-wide lone strand adenine methylation in Deinococcus radiodurans R1: Regulation of gene expression through DR0643-dependent adenine methylation. Microbiol Res 2022; 257:126964. [PMID: 35042054 DOI: 10.1016/j.micres.2022.126964] [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: 05/24/2021] [Revised: 12/19/2021] [Accepted: 01/11/2022] [Indexed: 10/19/2022]
Abstract
DNA methylation is a covalent modification of adenine or cytosine in the genome of an organism and is found in diverse microbes including the radiation resistant bacterium Deinococcus radiodurans R1. Although earlier findings have confirmed repression or de-repression of certain genes in adenine methyltransferase (DR_0643/Dam1DR) deficient D. radiodurans mutant however, the overall regulatory aspects of Dam1DR-mediated adenine methylation remain mostly unexplored. In the present study, we compared the genome-wide methylome and the corresponding transcriptome of D. radiodurans WT and Δdam1 mutant to explore the correlation between methylation and gene expression. In D. radiodurans, deletion of DR_0643 ORF (Δdam1) led to hypomethylation of 512 genes resulting in differential expression of 168 genes (99 genes are upregulated and 69 genes are downregulated). The modification patterns deduced for Dam1DR (DR_0643) and Dam2DR (DR_2267) were non-palindromic and atypical. Moreover, we observed methylation at opportunistic sites that show adenine methylation only in D. radiodurans Δdam1 and not in D. radiodurans WT. Correlation between the methylome and transcriptome suggests that hypomethylation at Dam1DR specific sites had both negative as well as a positive effects on gene expression. Pathways such as amino acid metabolism, transport, oxidative phosphorylation, quorum sensing, signal transduction, two-component system, glycolysis/gluconeogenesis, TCA cycle, glyoxylate and dicarboxylate metabolism were modulated by Dam1DR-mediated adenine methylation in D. radiodurans. Processes such as DNA repair, recombination, ATPase and transmembrane transporter activity were enriched when Dam1DR mutant was subjected to radiation stress. We further evaluated the molecular interactions and mode of binding between Dam1DR protein and S-adenosyl methionine using molecular docking followed by MD simulation. To get a better insight into the methylation mechanism, the Dam1DR-SAM complex was also docked with a DNA molecule to elucidate DNA-Dam1DR structural interaction during methyl-group transfer reaction. In summary, our work presents comprehensive and integrative approaches to investigate both functional and structural aspects of DNA adenine methyltransferase (Dam1DR) in D. radiodurans biology.
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Affiliation(s)
- Suraj Joshi
- Molecular Biology Research Laboratory, Department of Zoology, Savitribai Phule Pune University, Pune, India; Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India; Bioinformatics Centre, Savitribai Phule Pune University, Pune, India
| | - Payel Ghosh
- Bioinformatics Centre, Savitribai Phule Pune University, Pune, India.
| | - Sagar Barage
- Amity Institute of Biotechnology, Amity University, Mumbai - Pune Expressway, Bhatan, Post-Somathne, Panvel, Maharashtra, 410206, India
| | - Bhakti Basu
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Deepti D Deobagkar
- Molecular Biology Research Laboratory, Department of Zoology, Savitribai Phule Pune University, Pune, India.
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Basu B. The radiophiles of Deinococcaceae family: Resourceful microbes for innovative biotechnological applications. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100153. [PMID: 35909625 PMCID: PMC9325910 DOI: 10.1016/j.crmicr.2022.100153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/24/2022] [Accepted: 06/29/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Bhakti Basu
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
- Corresponding author.
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Butts CT, Martin RW. Bayesian estimation of the hydroxyl radical diffusion coefficient at low temperature and high pressure from atomistic molecular dynamics. J Chem Phys 2021; 155:194504. [PMID: 34800943 DOI: 10.1063/5.0064995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The hydroxyl radical is the primary reactive oxygen species produced by the radiolysis of water and is a significant source of radiation damage to living organisms. Mobility of the hydroxyl radical at low temperatures and/or high pressures is hence a potentially important factor in determining the challenges facing psychrophilic and/or barophilic organisms in high-radiation environments (e.g., ice-interface or undersea environments in which radiative heating is a potential heat and energy source). Here, we estimate the diffusion coefficient for the hydroxyl radical in aqueous solution using a hierarchical Bayesian model based on atomistic molecular dynamics trajectories in TIP4P/2005 water over a range of temperatures and pressures.
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Affiliation(s)
- Carter T Butts
- Departments of Sociology, Statistics, Computer Science, and EECS, University of California, Irvine, California 92697, USA
| | - Rachel W Martin
- Departments of Chemistry and Molecular Biology and Biochemistry, University of California, Irvine, California 92697, USA
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Structural and Biochemical Characterization of Thioredoxin-2 from Deinococcus radiodurans. Antioxidants (Basel) 2021; 10:antiox10111843. [PMID: 34829714 PMCID: PMC8615215 DOI: 10.3390/antiox10111843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 12/19/2022] Open
Abstract
Thioredoxin (Trx), a ubiquitous protein showing disulfide reductase activity, plays critical roles in cellular redox control and oxidative stress response. Trx is a member of the Trx system, comprising Trx, Trx reductase (TrxR), and a cognate reductant (generally reduced nicotinamide adenine dinucleotide phosphate, NADPH). Bacterial Trx1 contains only the Trx-fold domain, in which the active site CXXC motif that is critical for the disulfide reduction activity is located. Bacterial Trx2 contains an N-terminal extension, which forms a zinc-finger domain, including two additional CXXC motifs. The multi-stress resistant bacterium Deinococcus radiodurans encodes both Trx1 (DrTrx1) and Trx2 (DrTrx2), which act as members of the enzymatic antioxidant systems. In this study, we constructed Δdrtrx1 and Δdrtrx2 mutants and examined their survival rates under H2O2 treated conditions. Both drtrx1 and drtrx2 genes were induced following H2O2 treatment, and the Δdrtrx1 and Δdrtrx2 mutants showed a decrease in resistance toward H2O2, compared to the wild-type. Native DrTrx1 and DrTrx2 clearly displayed insulin and DTNB reduction activity, whereas mutant DrTrx1 and DrTrx2, which harbors the substitution of conserved cysteine to serine in its active site CXXC motif, showed almost no reduction activity. Mutations in the zinc binding cysteines did not fully eliminate the reduction activities of DrTrx2. Furthermore, we solved the crystal structure of full-length DrTrx2 at 1.96 Å resolution. The N-terminal zinc-finger domain of Trx2 is thought to be involved in Trx-target interaction and, from our DrTrx2 structure, the orientation of the zinc-finger domain of DrTrx2 and its interdomain interaction, between the Trx-fold domain and the zinc-finger domain, is clearly distinguished from those of the other Trx2 structures.
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Ye T, Wang B, Li C, Bian P, Chen L, Wang G. Exposure of cyanobacterium Nostoc sp. to the Mars-like stratosphere environment. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2021; 224:112307. [PMID: 34649187 DOI: 10.1016/j.jphotobiol.2021.112307] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/25/2021] [Accepted: 09/09/2021] [Indexed: 01/19/2023]
Abstract
During the HH-19-2 flight mission of the Chinese Scientific Experimental System, dried Nostoc sp. cells were exposed to the stratosphere environment (32,508 m altitude) for 3 h and 22 min. The atmospheric pressure, temperature, relative humidity, and ionizing and non-ionizing radiation levels at that altitude are similar to those on the surface of Mars. Although analyses revealed decreased photosynthetic activity, a decline in autofluorescence, and damage to the cellular morphology in the flight-exposed sample, the death rate was low (28%). Physiological changes were not obvious after the exposure to the Mars-like vacuum conditions. The ground-exposed samples showed a similar trend to the flight-exposed samples, but the damage was relatively slight. RNA-sequencing data revealed a number of affected metabolic pathways: photosynthetic system and CO2 fixation function, activation of antioxidant systems, heat shock protein, DNA repair, and protein synthesis. Results suggest that Nostoc sp. has the potential to survive in a Mars-like environment and that it may be a suitable pioneer species to colonize Mars in the future in closed life-support systems (base) or in localities with relatively suitable conditions for life, such as localities with water available.
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Affiliation(s)
- Tong Ye
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bo Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Caiyan Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Po Bian
- Key Laboratory of Ion Beam Bio-engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, Hefei, Anhui 230031, China
| | - Lanzhou Chen
- School of Resource & Environmental Sciences, Wuhan University, Wuhan 430079, PR China
| | - Gaohong Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Eugénie N, Zivanovic Y, Lelandais G, Coste G, Bouthier de la Tour C, Bentchikou E, Servant P, Confalonieri F. Characterization of the Radiation Desiccation Response Regulon of the Radioresistant Bacterium Deinococcus radiodurans by Integrative Genomic Analyses. Cells 2021; 10:cells10102536. [PMID: 34685516 PMCID: PMC8533742 DOI: 10.3390/cells10102536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 12/02/2022] Open
Abstract
Numerous genes are overexpressed in the radioresistant bacterium Deinococcus radiodurans after exposure to radiation or prolonged desiccation. It was shown that the DdrO and IrrE proteins play a major role in regulating the expression of approximately twenty genes. The transcriptional repressor DdrO blocks the expression of these genes under normal growth conditions. After exposure to genotoxic agents, the IrrE metalloprotease cleaves DdrO and relieves gene repression. At present, many questions remain, such as the number of genes regulated by DdrO. Here, we present the first ChIP-seq analysis performed at the genome level in Deinococcus species coupled with RNA-seq, which was achieved in the presence or not of DdrO. We also resequenced our laboratory stock strain of D. radiodurans R1 ATCC 13939 to obtain an accurate reference for read alignments and gene expression quantifications. We highlighted genes that are directly under the control of this transcriptional repressor and showed that the DdrO regulon in D. radiodurans includes numerous other genes than those previously described, including DNA and RNA metabolism proteins. These results thus pave the way to better understand the radioresistance pathways encoded by this bacterium and to compare the stress-induced responses mediated by this pair of proteins in diverse bacteria.
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Dai S, Chen Q, Jiang M, Wang B, Xie Z, Yu N, Zhou Y, Li S, Wang L, Hua Y, Tian B. Colonized extremophile Deinococcus radiodurans alleviates toxicity of cadmium and lead by suppressing heavy metal accumulation and improving antioxidant system in rice. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 284:117127. [PMID: 33892465 DOI: 10.1016/j.envpol.2021.117127] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/09/2021] [Accepted: 04/08/2021] [Indexed: 06/12/2023]
Abstract
Cadmium (Cd) and lead (Pb) are the major toxic heavy metals accumulated in rice and pose a serious threat to human health. The most important remediation strategy is to reduce the translocation of these heavy metals from polluted soil to rice. Bioremediation using microorganisms had been widely used for preventing environmental heavy metal pollution, and the interaction between microorganisms and plants is critical to reduce the heavy metal stress. In this study, we demonstrated that an extremophile Deinococcus radiodurans, especially its mutant strain-Δdr2577 which is deficient in cell surface-layer, could efficiently prevent the translocation and damages of Cd or Pb in rice. The bacterial cells efficiently removed Cd or Pb from culture medium. Following colonization of Δdr2577 cells in rice root, Cd level decreased to 71.6% in root and 60.9% in shoot, comparing to the plants treated with Cd alone; Pb level decreased to 73.3% in root and 56.9% in shoot, comparing to the plants treated with Pb alone. Meanwhile, the bacterial cells released their intracellular antioxidant-related molecules including glutamate and manganese ions into culture medium. Accumulation of glutamate and manganese ions detected in rice root and shoot ameliorate Cd/Pb-induced oxidative stress as indicated by reduced levels of ROS and enhanced activities of antioxidant enzymes in rice. Our results provide a potential application of an extremophile bacterium in alleviating heavy metal toxicity in rice. The main findings of the work reveal the interaction between the D. radiodurans and rice, as well as the alleviating mechanism of Cd and Pb toxicity through suppressing heavy metal accumulation and improving the antioxidant system in rice by the extremophile bacterium.
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Affiliation(s)
- Shang Dai
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qi Chen
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Meng Jiang
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Binqiang Wang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhenming Xie
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ning Yu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yulong Zhou
- Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, School of Chemistry and Chemical Engineering, Shihezi University, Shihezi, China
| | - Shan Li
- National Key Laboratory of Rice Biology, Institute of Crop Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Liangyan Wang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yuejin Hua
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Bing Tian
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China; Key Laboratory for Green Processing of Chemical Engineering of Xinjiang Bingtuan, School of Chemistry and Chemical Engineering, Shihezi University, Shihezi, China.
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Jung JH, Jeong S, Im S, Kim MK, Seo HS, Lim S. Lack of the Bacterial Phytochrome Protein Decreases Deinococcus radiodurans Resistance to Mitomycin C. Front Microbiol 2021; 12:659233. [PMID: 34394020 PMCID: PMC8363230 DOI: 10.3389/fmicb.2021.659233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Deinococcus radiodurans known for its extraordinary resistance to ionizing radiation contains bacterial phytochrome (BphP), a member of the family of red/far-red light-sensing proteins. In this study, we constructed a bphP mutant strain (ΔbphP) to investigate the role of D. radiodurans BphP (DrBphP) in the DNA damage response. When cells were incubated under light and dark conditions following exposure to DNA damaging agents, such as γ- and UV-radiation and mitomycin C (MMC), no significant difference in cell survival was observed between the wild-type D. radiodurans strain (WT) and ΔbphP. However, when continuously exposed to MMC under light conditions, the WT strain notably exhibited increased survival compared to cells grown in the dark. The increased survival was not observed in the ΔbphP strain. These results are indicative of the protective role of light-activated DrBphP in the presence of MMC. Site-directed mutagenesis revealed that the conserved amino acids Cys-24 and His-532 involved in chromophore binding and signal transduction, respectively, were essential for the protective function of DrBphP. Inactivation of the cognate response regulator (RR; DrBphR) of DrBphP increased MMC resistance in the dark. In trans complementation of the bphP bphR double mutant strain (ΔbphPR) with DrBphR decreased MMC resistance. Considering that DrBphP acts as a light-activated phosphatase that dephosphorylates DrBphR, it appears that phosphorylated DrBphR exerts a negative effect on cell survival in the presence of MMC. DrBphP overexpression resulted in an increase in MMC resistance of ΔbphPR, implying that other RRs might be involved in the DrBphP-mediated signaling pathway. A mutant lacking the dr_0781 gene (Δdr_0781) demonstrated the same MMC phenotype as ΔbphR. Survival was further increased in the bphR dr_0781 double mutant strain compared to each single mutant ΔbphR or Δdr_0781, suggesting that DR_0781 is also involved in the DrBphP-dependent MMC sensitivity. This study uncovered a previously unknown phenomenon of red/far-red light-dependent DNA damage survival mediated by BphP by identifying the conditions under which DrBphP exhibits a fitness advantage.
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Affiliation(s)
- Jong-Hyun Jung
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea.,Department of Radiation Science and Technology, University of Science and Technology, Daejeon, South Korea
| | - Soyoung Jeong
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea.,Department of Food and Animal Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Seonghun Im
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| | - Min-Kyu Kim
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| | - Ho Seong Seo
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea.,Department of Radiation Science and Technology, University of Science and Technology, Daejeon, South Korea
| | - Sangyong Lim
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea.,Department of Radiation Science and Technology, University of Science and Technology, Daejeon, South Korea
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Aoyagi Blue Y, Kusumi J, Satake A. Copy number analyses of DNA repair genes reveal the role of poly(ADP-ribose) polymerase (PARP) in tree longevity. iScience 2021; 24:102779. [PMID: 34278274 PMCID: PMC8271160 DOI: 10.1016/j.isci.2021.102779] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 05/22/2021] [Accepted: 06/22/2021] [Indexed: 11/29/2022] Open
Abstract
Long-lived organisms are exposed to the risk of accumulating mutations due to DNA damage. Previous studies in animals have revealed the positive relationship between the copy number of DNA repair genes and longevity. However, the role of DNA repair in the lifespan of plants remains poorly understood. Using the recent accumulation of the complete genome sequences of diverse plant species, we performed systematic comparative analyses of the copy number variations of DNA repair genes in 61 plant species with different lifespans. Among 121 DNA repair gene families, PARP gene family was identified as a unique gene that exhibits significant expansion in trees compared to annual and perennial herbs. Among three paralogs of plant PARPs, PARP1 showed a close association with growth rate. PARPs catalyze poly(ADP-ribosyl)ation and play pivotal roles in DNA repair and antipathogen defense. Our study suggests the conserved role of PARPs in longevity between plants and animals. Comparing the copy number variations of DNA repair genes in diverse plant species PARP gene family showed higher copy number in trees compared to herbs There was negative correlation between copy number of PARP1 and growth rate in trees Increased copy number of PARP would be evolutionary favored in plant longevity
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Affiliation(s)
- Yuta Aoyagi Blue
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Fukuoka, 819-0395, Japan
| | - Junko Kusumi
- Department of Environmental Changes, Faculty of Social and Cultural Studies, Kyushu University, 744 Motooka, Fukuoka819-0395, Japan
| | - Akiko Satake
- Department of Biology, Kyushu University, 744 Motooka, Fukuoka819-0395, Japan
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DivIVA Regulates Its Expression and the Orientation of New Septum Growth in Deinococcus radiodurans. J Bacteriol 2021; 203:e0016321. [PMID: 34031039 DOI: 10.1128/jb.00163-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In rod-shaped Gram-negative bacteria, FtsZ localization at midcell position is regulated by the gradient of MinCDE complex across the poles. In round-shaped bacteria, which lack predefined poles, the next plane of cell division is perpendicular to the previous plane, and determination of the FtsZ assembly site is still intriguing. Deinococcus radiodurans, a coccus bacterium, is characterized by its extraordinary resistance to DNA damage. DivIVA, a putative component of the Min system in this bacterium, interacts with cognate cell division and genome segregation proteins. Here, we report that deletion of a chromosomal copy of DivIVA was possible only when the wild-type copy of DivIVA was expressed in trans on a plasmid. However, deletion of the C-terminal domain (CTD) of DivIVA (CTD mutant) was possible but produced distinguishable phenotypes, like smaller cells, slower growth, and tilted septum orientation, in D. radiodurans. In trans expression of DivIVA in the CTD mutant could restore these features of the wild type. Interestingly, the overexpression of DivIVA led to delayed separation of tetrads from an octet state in both trans-complemented divIVA-mutant and wild-type cells. The CTD mutant showed upregulation of the yggS-divIVAN operon. Both the wild type and CTD mutant formed FtsZ foci; however, unlike wild type, the position of foci in the mutant cells was found to be away from conjectural midcell position in cocci. Notably, DivIVA-red fluorescent protein (DivIVA-RFP) localizes to the septum during cell division at the new division site. These results suggested that DivIVA is an essential protein in D. radiodurans, and its C-terminal domain plays an important role in the regulation of its expression and orientation of new septal growth in this bacterium. IMPORTANCE In rod-shaped Gram-negative bacteria, the midcell position for binary fission is relatively easy to model. In cocci that do not have predefined poles, the plane of next cell division is shown to be perpendicular to the previous plane. However, the molecular basis of perpendicularity is not known in cocci. The DivIVA protein of Deinococcus radiodurans, a coccus bacterium, physically interacts with the septum and establishes macromolecular interactions with genome segregation proteins through its N-terminal domain and with MinC through the C-terminal domain. Here, we have brought forth some evidence to suggest that DivIVA is essential for growth and plays an important role in cell polarity determination, and its C-terminal domain plays a crucial role in the growth of new septa in the correct orientation as well as in the regulation of DivIVA expression.
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Fernandes A, Piotrowski Y, Williamson A, Frade K, Moe E. Studies of multifunctional DNA polymerase I from the extremely radiation resistant Deinococcus radiodurans: Recombinant expression, purification and characterization of the full-length protein and its large fragment. Protein Expr Purif 2021; 187:105925. [PMID: 34175440 DOI: 10.1016/j.pep.2021.105925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 05/27/2021] [Accepted: 05/29/2021] [Indexed: 11/19/2022]
Abstract
Deinococcus radiodurans is a bacterium with extreme resistance to desiccation and radiation. Although the origins of this extreme resistance have not been fully elucidated, an efficient DNA repair machinery that includes the enzyme DNA polymerase I, is potentially crucial as part of a protection mechanism. Here we have cloned and performed small, medium, and large-scale expression of full-length D. radiodurans DNA polymerase I (DrPolI) as well as the large/Klenow fragment (DrKlenow). We then carried out functional characterization of 5' exonuclease, DNA strand displacement and polymerase activities of these proteins using gel-based and molecular beacon-based biochemical assays. With the same expression and purification strategy, we got higher yield in the production of DrKlenow than of the full-length protein, approximately 2.5 mg per liter of culture. Moreover, we detected a prominent 5' exonuclease activity of DrPolI in vitro. This activity and, DrKlenow strand displacement and DNA polymerase activities are preferentially stimulated at pH 8.0-8.5 and are reduced by addition of NaCl. Interestingly, both protein variants are more thermostable at pH 6.0-6.5. The characterization of DrPolI's multiple functions provides new insights into the enzyme's role in DNA repair pathways, and how the modulation of these functions is potentially used by D. radiodurans as a survival strategy.
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Affiliation(s)
- A Fernandes
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Y Piotrowski
- UiT - The Artic University of Norway, Tromsø, Norway
| | - A Williamson
- UiT - The Artic University of Norway, Tromsø, Norway; University of Waikato, Hamilton, New Zealand
| | - K Frade
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - E Moe
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal; UiT - The Artic University of Norway, Tromsø, Norway.
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de la Tour CB, Mathieu M, Servant P, Coste G, Norais C, Confalonieri F. Characterization of the DdrD protein from the extremely radioresistant bacterium Deinococcus radiodurans. Extremophiles 2021; 25:343-355. [PMID: 34052926 PMCID: PMC8254717 DOI: 10.1007/s00792-021-01233-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/16/2021] [Indexed: 10/25/2022]
Abstract
Here, we report the in vitro and in vivo characterization of the DdrD protein from the extraordinary stress-resistant bacterium, D. radiodurans. DdrD is one of the most highly induced proteins following cellular irradiation or desiccation. We confirm that DdrD belongs to the Radiation Desiccation Response (RDR) regulon protein family whose expression is regulated by the IrrE/DdrO proteins after DNA damage. We show that DdrD is a DNA binding protein that binds to single-stranded DNA In vitro, but not to duplex DNA unless it has a 5' single-stranded extension. In vivo, we observed no significant effect of the absence of DdrD on the survival of D. radiodurans cells after exposure to γ-rays or UV irradiation in different genetic contexts. However, genome reassembly is affected in a ∆ddrD mutant when cells recover from irradiation in the absence of nutrients. Thus, DdrD likely contributes to genome reconstitution after irradiation, but only under starvation conditions. Lastly, we show that the absence of the DdrD protein partially restores the frequency of plasmid transformation of a ∆ddrB mutant, suggesting that DdrD could also be involved in biological processes other than the response to DNA damage.
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Affiliation(s)
- Claire Bouthier de la Tour
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198, Gif sur Yvette, France.
| | - Martine Mathieu
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198, Gif sur Yvette, France
| | - Pascale Servant
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198, Gif sur Yvette, France
| | - Geneviève Coste
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198, Gif sur Yvette, France
| | - Cédric Norais
- Department of Biochemistry, University of Wisconsin, Madison, WI, 53706, USA.,SAT Lyon, Promega France, 24 Chemin des Verrieres, 69260, Charbonnières les Bains, France
| | - Fabrice Confalonieri
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198, Gif sur Yvette, France
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38
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Repar J, Zahradka D, Sović I, Zahradka K. Characterization of gross genome rearrangements in Deinococcus radiodurans recA mutants. Sci Rep 2021; 11:10939. [PMID: 34035321 PMCID: PMC8149714 DOI: 10.1038/s41598-021-89173-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/21/2021] [Indexed: 02/04/2023] Open
Abstract
Genome stability in radioresistant bacterium Deinococcus radiodurans depends on RecA, the main bacterial recombinase. Without RecA, gross genome rearrangements occur during repair of DNA double-strand breaks. Long repeated (insertion) sequences have been identified as hot spots for ectopic recombination leading to genome rearrangements, and single-strand annealing (SSA) postulated to be the most likely mechanism involved in this process. Here, we have sequenced five isolates of D. radiodurans recA mutant carrying gross genome rearrangements to precisely characterize the rearrangements and to elucidate the underlying repair mechanism. The detected rearrangements consisted of large deletions in chromosome II in all the sequenced recA isolates. The mechanism behind these deletions clearly differs from the classical SSA; it utilized short (4-11 bp) repeats as opposed to insertion sequences or other long repeats. Moreover, it worked over larger linear DNA distances from those previously tested. Our data are most compatible with alternative end-joining, a recombination mechanism that operates in eukaryotes, but is also found in Escherichia coli. Additionally, despite the recA isolates being preselected for different rearrangement patterns, all identified deletions were found to overlap in a 35 kb genomic region. We weigh the evidence for mechanistic vs. adaptive reasons for this phenomenon.
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Affiliation(s)
- Jelena Repar
- grid.4905.80000 0004 0635 7705Laboratory for Molecular Microbiology, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Davor Zahradka
- grid.4905.80000 0004 0635 7705Laboratory for Molecular Microbiology, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Ivan Sović
- Digital BioLogic d.o.o, Ivanić-Grad, Croatia
| | - Ksenija Zahradka
- grid.4905.80000 0004 0635 7705Laboratory for Molecular Microbiology, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
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39
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Castillo H, Li X, Smith GB. Deinococcus radiodurans UWO298 Dependence on Background Radiation for Optimal Growth. Front Genet 2021; 12:644292. [PMID: 34025716 PMCID: PMC8136434 DOI: 10.3389/fgene.2021.644292] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 03/02/2021] [Indexed: 01/04/2023] Open
Abstract
Ionizing radiation is a major environmental variable for cells on Earth, and so organisms have adapted to either prevent or to repair damages caused by it, primarily from the appearance and accumulation of reactive oxygen species (ROS). In this study, we measured the differential gene expression in Deinococcus radiodurans UWO298 cultures deprived of background ionizing radiation (IR) while growing 605 m underground at the Waste Isolation Pilot Plant (WIPP), reducing the dose rate from 72.1 to 0.9 nGy h–1 from control to treatment, respectively. This reduction in IR dose rate delayed the entry into the exponential phase of the IR-shielded cultures, resulting in a lower biomass accumulation for the duration of the experiment. The RNASeq-based transcriptome analysis showed the differential expression of 0.2 and 2.7% of the D. radiodurans genome after 24 and 34 h of growth in liquid culture, respectively. Gene expression regulation after 34 h was characterized by the downregulation of genes involved in folding newly synthesized and denatured/misfolded proteins, in the assimilation of nitrogen for amino acid synthesis and in the control of copper transport and homeostasis to prevent oxidative stress. We also observed the upregulation of genes coding for proteins with transport and cell wall assembly roles. These results show that D. radiodurans is sensitive to the absence of background levels of ionizing radiation and suggest that its transcriptional response is insufficient to maintain optimal growth.
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Affiliation(s)
- Hugo Castillo
- Human Factors and Behavioral Neurobiology Department, Embry-Riddle Aeronautical University, Daytona Beach, FL, United States
| | - Xiaoping Li
- Virginia Tech Hampton Roads Agriculture Research and Extension Center, Virginia Tech, Blacksburg, VA, United States
| | - Geoffrey B Smith
- Department of Biology, New Mexico State University, Las Cruces, NM, United States
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40
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Ujaoney AK, Padwal MK, Basu B. An in vivo Interaction Network of DNA-Repair Proteins: A Snapshot at Double Strand Break Repair in Deinococcus radiodurans. J Proteome Res 2021; 20:3242-3255. [PMID: 33929844 DOI: 10.1021/acs.jproteome.1c00078] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An extremophile Deinococcus radiodurans survives massive DNA damage by efficiently mending hundreds of double strand breaks through homology-dependent DNA repair pathways. Although DNA repair proteins that contribute to its impressive DNA repair capacity are fairly known, interactions among them or with proteins related to other relevant pathways remain unexplored. Here, we report in vivo cross-linking of the interactomes of key DNA repair proteins DdrA, DdrB, RecA, and Ssb (baits) in D. radiodurans cells recovering from gamma irradiation. The protein-protein interactions were systematically investigated through co-immunoprecipitation experiments coupled to mass spectrometry. From a total of 399 proteins co-eluted with the baits, we recovered interactions among diverse biological pathways such as DNA repair, transcription, translation, chromosome partitioning, cell division, antioxidation, protein folding/turnover, metabolism, cell wall architecture, membrane transporters, and uncharacterized proteins. Among these, about 80 proteins were relevant to the DNA damage resistance of the organism based on integration of data on inducible expression following DNA damage, radiation sensitive phenotype of deletion mutant, etc. Further, we cloned ORFs of 23 interactors in heterologous E. coli and expressed corresponding proteins with N-terminal His-tag, which were used for pull-down assays. A total of 95 interactions were assayed, in which we confirmed 25 previously unknown binary interactions between the proteins associated with radiation resistance, and 2 known interactions between DdrB and Ssb or DR_1245. Among these, five interactions were positive even under non-stress conditions. The confirmed interactions cover a wide range of biological processes such as DNA repair, negative regulation of cell division, chromosome partitioning, membrane anchorage, etc., and their functional relevance is discussed from the perspective of DNA repair. Overall, the study substantially advances our understanding on the cross-talk between different homology-dependent DNA repair pathways and other relevant biological processes that essentially contribute to the extraordinary DNA damage repair capability of D. radiodurans. The data sets generated and analyzed in this study have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD021822.
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Affiliation(s)
- Aman Kumar Ujaoney
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Mahesh Kumar Padwal
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Bhakti Basu
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
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41
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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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42
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Selveshwari S, Lele K, Dey S. Genomic signatures of UV resistance evolution in
Escherichia coli
depend on the growth phase during exposure. J Evol Biol 2021; 34:953-967. [DOI: 10.1111/jeb.13764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 12/27/2020] [Accepted: 01/13/2021] [Indexed: 11/28/2022]
Affiliation(s)
- S Selveshwari
- Population Biology Laboratory, Biology Division Indian Institute of Science Education and Research Pune Maharashtra India
| | - Kasturi Lele
- Population Biology Laboratory, Biology Division Indian Institute of Science Education and Research Pune Maharashtra India
| | - Sutirth Dey
- Population Biology Laboratory, Biology Division Indian Institute of Science Education and Research Pune Maharashtra India
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43
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Jeong SW, Kim MK, Zhao L, Yang SK, Jung JH, Lim HM, Lim S. Effects of Conserved Wedge Domain Residues on DNA Binding Activity of Deinococcus radiodurans RecG Helicase. Front Genet 2021; 12:634615. [PMID: 33613647 PMCID: PMC7889586 DOI: 10.3389/fgene.2021.634615] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 01/18/2021] [Indexed: 11/13/2022] Open
Abstract
Deinococcus radiodurans is extremely resistant to ionizing radiation and has an exceptional ability to repair DNA damage caused by various DNA-damaging agents. D. radiodurans uses the same DNA-repair strategies as other prokaryotes, but certain proteins involved in the classical DNA repair machinery have characteristics different from their counterparts. RecG helicase, which unwinds a variety of branched DNA molecules, such as Holliday junctions (HJ) and D-loops, plays important roles in DNA repair, recombination, and replication. Primary sequence analysis of RecG from a number of bacterial species revealed that three amino acids (QPW) in the DNA-binding wedge domain (WD) are well-conserved across the Deinococcus RecG proteins. Interactions involving these conserved residues and DNA substrates were predicted in modeled domain structures of D. radiodurans RecG (DrRecG). Compared to the WD of Escherichia coli RecG protein (EcRecG) containing FSA amino acids corresponding to QPW in DrRecG, the HJ binding activity of DrRecG-WD was higher than that of EcRecG-WD. Reciprocal substitution of FSA and QPW increased and decreased the HJ binding activity of the mutant WDs, EcRecG-WDQPW, and DrRecG-WDFSA, respectively. Following γ-irradiation treatment, the reduced survival rate of DrRecG mutants (ΔrecG) was fully restored by the expression of DrRecG, but not by that of EcRecG. EcRecGQPW also enhanced γ-radioresistance of ΔrecG, whereas DrRecGFSA did not. ΔrecG cells complemented in trans by DrRecG and EcRecGQPW reconstituted an intact genome within 3 h post-irradiation, as did the wild-type strain, but ΔrecG with EcRecG and DrRecGFSA exhibited a delay in assembly of chromosomal fragments induced by γ-irradiation. These results suggested that the QPW residues facilitate the association of DrRecG with DNA junctions, thereby enhancing the DNA repair efficiency of DrRecG.
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Affiliation(s)
- Sun-Wook Jeong
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea.,Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Min-Kyu Kim
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| | - Lei Zhao
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| | - Seul-Ki Yang
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea
| | - Jong-Hyun Jung
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea.,Department of Radiation Science and Technology, University of Science and Technology, Daejeon, South Korea
| | - Heon-Man Lim
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, South Korea
| | - Sangyong Lim
- Radiation Research Division, Korea Atomic Energy Research Institute, Jeongeup, South Korea.,Department of Radiation Science and Technology, University of Science and Technology, Daejeon, South Korea
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44
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Kumari N, Raghavan SC. G-quadruplex DNA structures and their relevance in radioprotection. Biochim Biophys Acta Gen Subj 2021; 1865:129857. [PMID: 33508382 DOI: 10.1016/j.bbagen.2021.129857] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND DNA, the genetic material of most of the organisms, is the crucial element of life. Integrity of DNA needs to be maintained for transmission of genetic material from one generation to another. All organisms are constantly challenged by the environmental conditions which can lead to the induction of DNA damage. Ionizing radiation (IR) has been known to induce DNA damage and IR sensitivity varies among different organisms. The causes for differential radiosensitivity among various organisms have not been studied in great detail. SCOPE OF REVIEW We discuss DNA secondary structure formation, GC content of the genome, role of G-quadruplex formation, and its relationship with radiosensitivity of the genome. MAJOR CONCLUSION In Deinococcus radiodurans, the bacterium that exhibits maximum radio resistance, multiple G-quadruplex forming motifs are reported. In human cells, G-quadruplex formation led to differential radiosensitivity. In this article, we have discussed, the role of secondary DNA structure formation like G-quadruplex in shielding the genome from radiation and its implications in understanding evolution of radio protective effect of an organism. We also discuss role of GC content and its correlation with radio resistance. GENERAL SIGNIFICANCE This review provides an insight into the role of G-quadruplexes in providing differential radiosensitivity at different site of the genome and in different organisms. It further discusses the possibility of higher GC content contributing towards reduced radiosensitivity in different organisms, evolution of radiosensitivity, and regulation of multiple cellular processes.
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Affiliation(s)
- Nitu Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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45
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Chaudhary R, Mishra S, Kota S, Misra H. Molecular interactions and their predictive roles in cell pole determination in bacteria. Crit Rev Microbiol 2021; 47:141-161. [PMID: 33423591 DOI: 10.1080/1040841x.2020.1857686] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Bacterial cell cycle is divided into well-coordinated phases; chromosome duplication and segregation, cell elongation, septum formation, and cytokinesis. The temporal separation of these phases depends upon the growth rates and doubling time in different bacteria. The entire process of cell division starts with the assembly of divisome complex at mid-cell position followed by constriction of the cell wall and septum formation. In the mapping of mid-cell position for septum formation, the gradient of oscillating Min proteins across the poles plays a pivotal role in several bacteria genus. The cues in the cell that defines the poles and plane of cell division are not fully characterized in cocci. Recent studies have shed some lights on molecular interactions at the poles and the underlying mechanisms involved in pole determination in non-cocci. In this review, we have brought forth recent findings on these aspects together, which would suggest a model to explain the mechanisms of pole determination in rod shaped bacteria and could be extrapolated as a working model in cocci.
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Affiliation(s)
- Reema Chaudhary
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute, Mumbai, India
| | - Shruti Mishra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute, Mumbai, India
| | - Swathi Kota
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute, Mumbai, India
| | - Hari Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Life Sciences, Homi Bhabha National Institute, Mumbai, India
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46
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Bioinformatics Tools for Gene and Genome Annotation Analysis of Microbes for Synthetic Biology and Cancer Biology Applications. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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47
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Maurya GK, Chaudhary R, Pandey N, Misra HS. Molecular insights into replication initiation in a multipartite genome harboring bacterium Deinococcus radiodurans. J Biol Chem 2021; 296:100451. [PMID: 33626388 PMCID: PMC7988490 DOI: 10.1016/j.jbc.2021.100451] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/12/2021] [Accepted: 02/18/2021] [Indexed: 11/23/2022] Open
Abstract
Deinococcus radiodurans harbors a multipartite ploid genome system consisting of two chromosomes and two plasmids present in multiple copies. How these discrete genome elements are maintained and inherited is not well understood. PprA, a pleiotropic protein involved in radioresistance, has been characterized for its roles in DNA repair, genome segregation, and cell division in this bacterium. Here, we show that PprA regulates ploidy of chromosome I and II and inhibits the activity of drDnaA, the initiator protein in D. radiodurans. We found that pprA deletion resulted in an increased genomic content and ploidy of both the chromosomal elements. Expression of PprA in trans rescued the phenotypes of the pprA mutant. To understand the molecular mechanism underlying these phenotypes, we characterized drDnaA and drDnaB. As expected for an initiator protein, recombinant drDnaA showed sequence-specific interactions with the putative oriC sequence in chromosome I (oriCI). Both drDnaA and drDnaB showed ATPase activity, also typical of initiator proteins, but only drDnaB exhibited 5'→3' dsDNA helicase activity in vitro. drDnaA and drDnaB showed homotypic and heterotypic interactions with each other, which were perturbed by PprA. Interestingly, PprA has inhibited the ATPase activity of drDnaA but showed no effect on the activity of drDnaB. Regulation of chromosome copy number and inhibition of the initiator protein functions by PprA strongly suggest that it plays a role as a checkpoint regulator of the DNA replication initiation in D. radiodurans perhaps through its interaction with the replication initiation machinery.
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Affiliation(s)
- Ganesh K Maurya
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India; Life Sciences, Homi Bhabha National Institute, Mumbai, India
| | - Reema Chaudhary
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India; Life Sciences, Homi Bhabha National Institute, Mumbai, India
| | - Neha Pandey
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India; Life Sciences, University of Mumbai, Mumbai, India
| | - Hari S Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India; Life Sciences, Homi Bhabha National Institute, Mumbai, India.
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48
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Maurya GK, Misra HS. Characterization of ori and parS-like functions in secondary genome replicons in Deinococcus radiodurans. Life Sci Alliance 2020; 4:4/1/e202000856. [PMID: 33199509 PMCID: PMC7671480 DOI: 10.26508/lsa.202000856] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 11/04/2020] [Accepted: 11/04/2020] [Indexed: 12/27/2022] Open
Abstract
The mechanisms underlying multipartite genome maintenance and its functional significance in extraordinary radioresistance of Deinococcus radiodurans are not well understood. The sequences upstream to parAB operons in chrII (cisII) and MP (cisMP) could stabilize an otherwise, non-replicative colE1 plasmid, in D. radiodurans DnaA and cognate ParB proteins bound specifically with cisII and cisMP elements. The ΔcisII and ΔcisMP cells showed the reduced copy number of cognate replicons and radioresistance as compared with wild type. Fluorescent reporter-operator system inserted in chrI, chrII, and MP in wild type and cisII mutants showed the presence of all three replicons in wild-type cells. Although chrI was present in all the ΔcisII and ΔcisMP cells, nearly half of these cells had chrII and MP, respectively, and the other half had the reduced number of foci representing these replications. These results suggested that cisII and cisMP elements contain both origin of replication and parS-like functions and the secondary genome replicons (chrII and MP) are maintained independent of chrI and have roles in radioresistance of D. radiodurans.
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Affiliation(s)
- Ganesh K Maurya
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.,Homi Bhabha National Institute, Mumbai, India
| | - Hari S Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India .,Homi Bhabha National Institute, Mumbai, India
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49
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Joshi S, Ujaoney AK, Ghosh P, Deobagkar DD, Basu B. N6-methyladenine and epigenetic immunity of Deinococcus radiodurans. Res Microbiol 2020; 172:103789. [PMID: 33188877 DOI: 10.1016/j.resmic.2020.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 10/29/2020] [Accepted: 10/31/2020] [Indexed: 10/23/2022]
Abstract
DNA methylation is ubiquitously found in all three domains of life. This epigenetic modification on adenine or cytosine residues serves to regulate gene expression or to defend against invading DNA in bacteria. Here, we report the significance of N6-methyladenine (6mA) to epigenetic immunity in Deinococcus radiodurans. Putative protein encoded by DR_2267 ORF (Dam2DR) contributed 35% of genomic 6mA in D. radiodurans but did not influence gene expression or radiation resistance. Dam2DR was characterized to be a functional S-adenosyl methionine (SAM)-dependent N6-adenine DNA methyltransferase (MTase) but with no endonuclease activity. Adenine methylation from Dam2DR or Dam1DR (N6-adenine MTase encoded by DR_0643) improved DNA uptake during natural transformation. To the contrary, methylation from Escherichia coli N6-adenine MTase (DamEC that methylates adenine in GATC sequence) on donor plasmid drastically reduced DNA uptake in D. radiodurans, even in presence of Dam2DR or Dam1DR methylated adenines. With these results, we conclude that self-type N6-adenine methylation on donor DNA had a protective effect in absence of additional foreign methylation, a separate methylation-dependent Restriction Modification (R-M) system effectively identifies and limits uptake of G6mATC sequence containing donor DNA. This is the first report demonstrating presence of epigenetic immunity in D. radiodurans.
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Affiliation(s)
- Suraj Joshi
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Molecular Biology Research Laboratory, Department of Zoology, SPPU, Pune 411007, India; Bioinformatics Centre, SPPU, Pune 411007, India.
| | - Aman Kumar Ujaoney
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India.
| | - Payel Ghosh
- Bioinformatics Centre, SPPU, Pune 411007, India.
| | - Deepti D Deobagkar
- Molecular Biology Research Laboratory, Department of Zoology, SPPU, Pune 411007, India.
| | - Bhakti Basu
- Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India.
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50
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Ott E, Kawaguchi Y, Kölbl D, Rabbow E, Rettberg P, Mora M, Moissl-Eichinger C, Weckwerth W, Yamagishi A, Milojevic T. Molecular repertoire of Deinococcus radiodurans after 1 year of exposure outside the International Space Station within the Tanpopo mission. MICROBIOME 2020; 8:150. [PMID: 33121542 PMCID: PMC7597052 DOI: 10.1186/s40168-020-00927-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/24/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND The extraordinarily resistant bacterium Deinococcus radiodurans withstands harsh environmental conditions present in outer space. Deinococcus radiodurans was exposed for 1 year outside the International Space Station within Tanpopo orbital mission to investigate microbial survival and space travel. In addition, a ground-based simulation experiment with conditions, mirroring those from low Earth orbit, was performed. METHODS We monitored Deinococcus radiodurans cells during early stage of recovery after low Earth orbit exposure using electron microscopy tools. Furthermore, proteomic, transcriptomic and metabolomic analyses were performed to identify molecular mechanisms responsible for the survival of Deinococcus radiodurans in low Earth orbit. RESULTS D. radiodurans cells exposed to low Earth orbit conditions do not exhibit any morphological damage. However, an accumulation of numerous outer-membrane-associated vesicles was observed. On levels of proteins and transcripts, a multi-faceted response was detected to alleviate cell stress. The UvrABC endonuclease excision repair mechanism was triggered to cope with DNA damage. Defense against reactive oxygen species is mirrored by the increased abundance of catalases and is accompanied by the increased abundance of putrescine, which works as reactive oxygen species scavenging molecule. In addition, several proteins and mRNAs, responsible for regulatory and transporting functions showed increased abundances. The decrease in primary metabolites indicates alternations in the energy status, which is needed to repair damaged molecules. CONCLUSION Low Earth orbit induced molecular rearrangements trigger multiple components of metabolic stress response and regulatory networks in exposed microbial cells. Presented results show that the non-sporulating bacterium Deinococcus radiodurans survived long-term low Earth orbit exposure if wavelength below 200 nm are not present, which mirrors the UV spectrum of Mars, where CO2 effectively provides a shield below 190 nm. These results should be considered in the context of planetary protection concerns and the development of new sterilization techniques for future space missions. Video Abstract.
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Affiliation(s)
- Emanuel Ott
- Space Biochemistry Group, Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Yuko Kawaguchi
- Planetary Exploration Research Center (PERC), Chiba Institute of Technology (CIT), Chiba, Japan
| | - Denise Kölbl
- Space Biochemistry Group, Department of Biophysical Chemistry, University of Vienna, Vienna, Austria
| | - Elke Rabbow
- Institute of Aerospace Medicine, Radiation Biology Department, German Aerospace Center, Cologne, Germany
| | - Petra Rettberg
- Institute of Aerospace Medicine, Radiation Biology Department, German Aerospace Center, Cologne, Germany
| | - Maximilian Mora
- Department of Internal Medicine, Section of Infectious Diseases and Tropical Medicine, Medical University Graz, Graz, Austria
| | - Christine Moissl-Eichinger
- Department of Internal Medicine, Section of Infectious Diseases and Tropical Medicine, Medical University Graz, Graz, Austria
| | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Akihiko Yamagishi
- Department of Life Science, Tokyo Institute of Technology, Nagatsuta, Yokohama, Japan
| | - Tetyana Milojevic
- Space Biochemistry Group, Department of Biophysical Chemistry, University of Vienna, Vienna, Austria.
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