1
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Chen Z, Hu J, Dai J, Zhou C, Hua Y, Hua X, Zhao Y. Precise CRISPR/Cpf1 genome editing system in the Deinococcus radiodurans with superior DNA repair mechanisms. Microbiol Res 2024; 284:127713. [PMID: 38608339 DOI: 10.1016/j.micres.2024.127713] [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: 12/04/2023] [Revised: 02/20/2024] [Accepted: 04/06/2024] [Indexed: 04/14/2024]
Abstract
Deinococcus radiodurans, with its high homologous recombination (HR) efficiency of double-stranded DNA breaks (DSBs), is a model organism for studying genome stability maintenance and an attractive microbe for industrial applications. Here, we developed an efficient CRISPR/Cpf1 genome editing system in D. radiodurans by evaluating and optimizing double-plasmid strategies and four Cas effector proteins from various organisms, which can precisely introduce different types of template-dependent mutagenesis without off-target toxicity. Furthermore, the role of DNA repair genes in determining editing efficiency in D. radiodurans was evaluated by introducing the CRISPR/Cpf1 system into 13 mutant strains lacking various DNA damage response and repair factors. In addition to the crucial role of RecA-dependent HR required for CRISPR/Cpf1 editing, D. radiodurans showed higher editing efficiency when lacking DdrB, the single-stranded DNA annealing (SSA) protein involved in the RecA-independent DSB repair pathway. This suggests a possible competition between HR and SSA pathways in the CRISPR editing of D. radiodurans. Moreover, off-target effects were observed during the genome editing of the pprI knockout strain, a master DNA damage response gene in Deinococcus species, which suggested that precise regulation of DNA damage response is critical for a high-fidelity genome editing system.
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Affiliation(s)
- Zijing Chen
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jing Hu
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jingli Dai
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Congli Zhou
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuejin Hua
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Ye Zhao
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China.
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2
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Shin H, La TM, Lee HJ, Kim T, Song SU, Park GH, Choi IS, Park SY, Lee JB, Lee SW. Characteristics of a Temperature-Sensitive Mutant Strain of Salmonella Enteritidis and Its Potential as a Live Vaccine Candidate. Vet Sci 2023; 10:vetsci10050313. [PMID: 37235396 DOI: 10.3390/vetsci10050313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Salmonella Enteritidis is a common foodborne pathogen transmitted through poultry products, which are its main carriers. Poultry are vaccinated against Salmonella Enteritidis in many countries, despite the absence of clinical symptoms, using commercially available live-attenuated vaccines. We previously constructed a highly attenuated temperature-sensitive (ts) Salmonella Enteritidis mutant, 2S-G10. In the present study, we describe the construction and attenuation-associated characteristics of 2S-G10. We infected 1-day-old chicks with 2S-G10 and the parental strains to evaluate the attenuation. One week after infection, 2S-G10 was not detected in the liver, cecum, or cecal tonsil tissues of the orally inoculated chicks, contrary to the parental strain. This indicates that 2S-G10 was highly attenuated when compared to the parental stain. In vitro experiments revealed the inability of 2S-G10 to grow at the normal body temperature of chickens and invade chicken liver epithelial cells. Moreover, single nucleotide polymorphism (SNP) analysis between the complete genome sequence of 2S-G10 and its parental strain revealed SNPs in bcsE, recG, rfaF, and pepD_1 genes, which are involved in epithelial cell invasion and persistence in host systems, growth, lipopolysaccharide core biosynthesis, and cellular survival under heat stress, respectively. These potential characteristics are consistent with the findings of in vitro experiments. Conclusively, chemical treatment-induced random genetic mutations highly attenuated 2S-G10, implying its potential to be developed as a novel live-attenuated vaccine against Salmonella Enteritidis.
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Affiliation(s)
- Hyunjin Shin
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Tae-Min La
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Hong-Jae Lee
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Taesoo Kim
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Seung-Un Song
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Gyu-Hyung Park
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - In-Soo Choi
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Seung-Yong Park
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Joong-Bok Lee
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Sang-Won Lee
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
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3
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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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4
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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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5
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Xu J, Wu C, Yang Z, Liu W, Chen H, Batool K, Yao J, Fan X, Wu J, Rao W, Huang T, Xu L, Guan X, Zhang L. For: Pesticide biochemistry and physiology recG is involved with the resistance of Bt to UV. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2020; 167:104599. [PMID: 32527443 DOI: 10.1016/j.pestbp.2020.104599] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 03/07/2020] [Accepted: 05/06/2020] [Indexed: 06/11/2023]
Abstract
As an ATP-dependent DNA helicase, RecG can repair DNA replication forks in many organisms. However, knowledge of recG in Bacillus thuringiensis (Bt) is limited. In our previous study, recG was found damaged in Bt LLP29-M19, which was more resistant to ultraviolet light (UV) after exposing Bt LLP29 to UV for 19 generations. To further understand the function of recG in the mechanism of Bt UV resistance, recG was knocked out and recovered with homologous recombination technology in Bt LLP29. Comparing the resistance of the different mutants to UVB, Bt ∆recG-LLP29 lacking recG was found more sensitive to UVB, hydroxyurea (HU) and H2O2 than LLP29 and the complementation strain. To compare the expression level of recG in the Bt strains under different UV treatments, Quantitative Real-time PCR (RT-qPCR) of recG was performed in the tested Bt strains, which showed that the expression level of recG in Bt ∆recG-LLP29 was substantially lower than that in the original strain and complementation strain. Interestingly, when exposed to UV for 20 min, RecG expression in both Bt LLP29 and Bt recG-R was the highest. The unwinding activity of recG in Bt LLP29 and the complementation strain were also found higher than that of the recG knockout strain, Bt ∆recG-LLP29. These results demonstrate that recG is involved with the resistance of Bt to UV. These findings not only enhance the understanding of the Bt UV resistance mechanism, but also provide an important theoretical basis for the application of Bt.
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Affiliation(s)
- Jin Xu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Chenxu Wu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Zhaohui Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Wencheng Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Hong Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Khadija Batool
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Junmin Yao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xiao Fan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Juan Wu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Wenhua Rao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Tianpei Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Lei Xu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xiong Guan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Lingling Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & School of Life Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
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6
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Zhou Y, Shen P, Lan Q, Deng C, Zhang Y, Li Y, Wei W, Wang Y, Su N, He F, Xie Q, Lyu Z, Yang D, Xu P. High-coverage proteomics reveals methionine auxotrophy in Deinococcus radiodurans. Proteomics 2017; 17. [PMID: 28608649 DOI: 10.1002/pmic.201700072] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 05/13/2017] [Accepted: 06/02/2017] [Indexed: 11/09/2022]
Abstract
Deinococcus radiodurans is a robust bacterium best known for its capacity to resist to radiation. In this study, the SDS-PAGE coupled with high-precision LC-MS/MS was used to study the D. radiodurans proteome. A total of 1951 proteins were identified which covers 63.18% protein-coding genes. Comparison of the identified proteins to the key enzymes in amino acid biosyntheses from KEGG database showed the methionine biosynthesis module is incomplete while other amino acid biosynthesis modules are complete, which indicated methionine auxotrophy in D. radiodurans. The subsequent amino acid-auxotrophic screening has verified methionine instead of other amino acids is essential for the growth of D. radiodurans. With molecular evolutionary genetic analysis, we found the divergence in methionine biosynthesis during the evolution of the common ancestor of bacteria. We also found D. radiodurans lost the power of synthesizing methionine because of the missing metA and metX in two types of methionine biosyntheses. For the first time, this study used high-coverage proteome analysis to identify D. radiodurans amino acid auxotrophy, which provides the important reference for the development of quantitative proteomics analysis using stable isotope labeling in metabolomics of D. radiodurans and in-depth analysis of the molecular mechanism of radiation resistance.
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Affiliation(s)
- Yanxia Zhou
- College of Life Sciences, Hebei University and Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, P. R. China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, P. R. China
| | - Pan Shen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, P. R. China
| | - Qiuyan Lan
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, P. R. China.,School of Basic Medical Science, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, P. R. China
| | - Chen Deng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, P. R. China
| | - Yao Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, P. R. China.,State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, College of Ecology and Evolution, Sun Yat-Sen University, Guangzhou, P. R. China
| | - Yanchang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, P. R. China
| | - Wei Wei
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, P. R. China
| | - Yihao Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, P. R. China
| | - Na Su
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, P. R. China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, P. R. China
| | - Qiong Xie
- China Astronaut Research and Training Center, Beijing, P. R. China
| | - Zhitang Lyu
- College of Life Sciences, Hebei University and Key Laboratory of Microbial Diversity Research and Application of Hebei Province, Baoding, P. R. China
| | - Dong Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, P. R. China
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Radiation Medicine, Beijing, P. R. China.,School of Basic Medical Science, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, P. R. China
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7
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Schmier BJ, Chen X, Wolin S, Shuman S. Deletion of the rnl gene encoding a nick-sealing RNA ligase sensitizes Deinococcus radiodurans to ionizing radiation. Nucleic Acids Res 2017; 45:3812-3821. [PMID: 28126918 PMCID: PMC5397189 DOI: 10.1093/nar/gkx038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 01/23/2017] [Indexed: 11/14/2022] Open
Abstract
Deinococcus radiodurans RNA ligase (DraRnl) seals 3΄-OH/5΄-PO4 nicks in duplex nucleic acids in which the 3΄-OH nick terminus consists of two or more ribonucleotides. DraRnl exemplifies a widely distributed Rnl5 family of nick-sealing RNA ligases, the physiological functions of which are uncharted. Here we show via gene knockout that whereas DraRnl is inessential for growth of D. radiodurans, its absence sensitizes the bacterium to killing by ionizing radiation (IR). DraRnl protein is present in exponentially growing and stationary phase cells, but is depleted during the early stages of recovery from 10 kGy of IR and subsequently replenished during the late phase of post-IR genome reassembly. Absence of DraRnl elicts a delay in reconstitution of the 10 kGy IR-shattered D. radiodurans replicons that correlates with the timing of DraRnl replenishment in wild-type cells. Complementation with a catalytically dead mutant highlights that nick sealing activity is important for the radioprotective function of DraRnl. Our findings suggest a scenario in which DraRnl acts at genomic nicks resulting from gap-filling by a ribonucleotide-incorporating repair polymerase.
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Affiliation(s)
- Brad J Schmier
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
| | - Xinguo Chen
- Cell Biology Department, Yale School of Medicine, New Haven, CT 06536, USA
| | - Sandra Wolin
- Cell Biology Department, Yale School of Medicine, New Haven, CT 06536, USA
| | - Stewart Shuman
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
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8
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Kim M, Jeong S, Lim S, Sim J, Rhie HG, Lee SJ. Oxidative stress response of Deinococcus geothermalis via a cystine importer. J Microbiol 2017; 55:137-146. [PMID: 28120190 DOI: 10.1007/s12275-017-6382-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/25/2016] [Accepted: 10/26/2016] [Indexed: 11/29/2022]
Abstract
A cystine-dependent anti-oxidative stress response is characterized in Deinococcus geothermalis for the first time. Nevertheless, the same transcriptional directed Δdgeo_1985F mutant strain was revealed to have an identical phenotype to the wild-type strain, while the reverse transcriptional directed Δdgeo_1985R mutant strain was more resistant to oxidative stress at a certain concentration of H2O2 than the wild-type strain. The wild-type and mutant strains expressed equal levels of superoxide dismutase and catalase under H2O2-induced stress. Although the expression levels of the general DNA-damage response-related genes recA, pprA, ddrA, and ddrB were up-regulated by more than five-fold in the wild-type strain relative to the Δdgeo_1985R mutant strain, the mutant strain had a higher survival rate than the wild-type under H2O2 stress. The Δdgeo_1985R mutant strain highly expressed a cystine-transporter gene (dgeo_1986), at levels 150-fold higher than the wild-type strain, leading to the conclusion that this cystine transporter might be involved in the defensive response to H2O2 stress. In this study, the cystine transporter was identified and characterized through membrane protein expression analysis, a cystine-binding assay, and assays of intracellular H2O2, cysteine, and thiol levels. The genedisrupted mutant strain of the cystine importer revealed high sensitivity to H2O2 and less absorbed cystine, resulting in low concentrations of total thiol. Thus, the absorbed cystine via this cystine-specific importer may be converted into cysteine, which acts as a primitive defense substrate that non-enzymatically scavenges oxidative stress agents in D. geothermalis.
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Affiliation(s)
- Minwook Kim
- Department of Biology, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Sunwook Jeong
- Division of Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Sangyong Lim
- Division of Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Jeonggu Sim
- Department of Visual Optics, Baekseok University, Cheonan, 31065, Republic of Korea
| | - Ho-Gun Rhie
- Department of Biology, Kyung Hee University, Seoul, 02447, Republic of Korea
| | - Sung-Jae Lee
- Department of Biology, Kyung Hee University, Seoul, 02447, Republic of Korea. .,Department of Life and Nanopharmaceutical Sciences, Kyung Hee University, Seoul, 02447, Republic of Korea.
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9
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Beyene GT, Balasingham SV, Frye SA, Namouchi A, Homberset H, Kalayou S, Riaz T, Tønjum T. Characterization of the Neisseria meningitidis Helicase RecG. PLoS One 2016; 11:e0164588. [PMID: 27736945 PMCID: PMC5063381 DOI: 10.1371/journal.pone.0164588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 09/27/2016] [Indexed: 11/19/2022] Open
Abstract
Neisseria meningitidis (Nm) is a Gram-negative oral commensal that opportunistically can cause septicaemia and/or meningitis. Here, we overexpressed, purified and characterized the Nm DNA repair/recombination helicase RecG (RecGNm) and examined its role during genotoxic stress. RecGNm possessed ATP-dependent DNA binding and unwinding activities in vitro on a variety of DNA model substrates including a Holliday junction (HJ). Database searching of the Nm genomes identified 49 single nucleotide polymorphisms (SNPs) in the recGNm including 37 non-synonymous SNPs (nsSNPs), and 7 of the nsSNPs were located in the codons for conserved active site residues of RecGNm. A transient reduction in transformation of DNA was observed in the Nm ΔrecG strain as compared to the wildtype. The gene encoding recGNm also contained an unusually high number of the DNA uptake sequence (DUS) that facilitate transformation in neisserial species. The differentially abundant protein profiles of the Nm wildtype and ΔrecG strains suggest that expression of RecGNm might be linked to expression of other proteins involved in DNA repair, recombination and replication, pilus biogenesis, glycan biosynthesis and ribosomal activity. This might explain the growth defect that was observed in the Nm ΔrecG null mutant.
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Affiliation(s)
| | | | - Stephan A. Frye
- Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
| | - Amine Namouchi
- Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
| | | | - Shewit Kalayou
- Department of Microbiology, University of Oslo, Oslo, Norway
| | - Tahira Riaz
- Department of Microbiology, University of Oslo, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, University of Oslo, Oslo, Norway
- Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway
- * E-mail:
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10
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Agapov AA, Kulbachinskiy AV. Mechanisms of Stress Resistance and Gene Regulation in the Radioresistant Bacterium Deinococcus radiodurans. BIOCHEMISTRY (MOSCOW) 2016; 80:1201-16. [PMID: 26567564 DOI: 10.1134/s0006297915100016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The bacterium Deinococcus radiodurans reveals extraordinary resistance to ionizing radiation, oxidative stress, desiccation, and other damaging conditions. In this review, we consider the main molecular mechanisms underlying such resistance, including the action of specific DNA repair and antioxidation systems, and transcription regulation during the anti-stress response.
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Affiliation(s)
- A A Agapov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
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11
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Jeong SW, Seo HS, Kim MK, Choi JI, Lim HM, Lim S. PprM is necessary for up-regulation of katE1, encoding the major catalase of Deinococcus radiodurans, under unstressed culture conditions. J Microbiol 2016; 54:426-31. [PMID: 27225459 DOI: 10.1007/s12275-016-6175-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 05/19/2016] [Accepted: 05/19/2016] [Indexed: 01/07/2023]
Abstract
Deinococcus radiodurans is a poly-extremophilic organism, capable of tolerating a wide variety of different stresses, such as gamma/ultraviolet radiation, desiccation, and oxidative stress. PprM, a cold shock protein homolog, is involved in the radiation resistance of D. radiodurans, but its role in the oxidative stress response has not been investigated. In this study, we investigated the effect of pprM mutation on catalase gene expression. pprM disruption decreased the mRNA and protein levels of KatE1, which is the major catalase in D. radiodurans, under normal culture conditions. A pprM mutant strain (pprM MT) exhibited decreased catalase activity, and its resistance to hydrogen peroxide (H2O2) decreased accordingly compared with that of the wild-type strain. We confirmed that RecG helicase negatively regulates katE1 under normal culture conditions. Among katE1 transcriptional regulators, the positive regulator drRRA was not altered in pprM (-), while the negative regulators perR, dtxR, and recG were activated more than 2.5-fold in pprM MT. These findings suggest that PprM is necessary for KatE1 production under normal culture conditions by down-regulation of katE1 negative regulators.
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Affiliation(s)
- Sun-Wook Jeong
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea.,Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Ho Seong Seo
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Min-Kyu Kim
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea
| | - Jong-Il Choi
- Department of Biotechnology and Bioengineering, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Heon-Man Lim
- Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, 34134, Republic of Korea.
| | - Sangyong Lim
- Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup, 56212, Republic of Korea.
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12
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Cheng J, Wang H, Xu X, Wang L, Tian B, Hua Y. Characteristics of dr1790 disruptant and its functional analysis in Deinococcus radiodurans. Braz J Microbiol 2015; 46:601-11. [PMID: 26273280 PMCID: PMC4507557 DOI: 10.1590/s1517-838246220131018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 12/19/2014] [Indexed: 11/22/2022] Open
Abstract
Deinococcus radiodurans (DR) is an extremophile that is well
known for its resistance to radiation, oxidants and desiccation. The gene
dr1790 of D. radiodurans
was predicted to encode a yellow-related protein. The primary objective of the
present study was to characterize the biological function of the DR1790 protein,
which is a member of the ancient yellow/major royal jelly (MRJ) protein family,
in prokaryotes. Fluorescence labeling demonstrated that the yellow-related
protein encoded by dr1790 is a membrane protein. The deletion
of the dr1790 gene decreased the cell growth rate and
sensitivity to hydrogen peroxide and radiation and increased the membrane
permeability of D. radiodurans. Transcript
profiling by microarray and RT-PCR analyses of the dr1790
deletion mutant suggested that some genes that are involved in protein secretion
and transport were strongly suppressed, while other genes that are involved in
protein quality control, such as chaperones and proteases, were induced. In
addition, the expression of genes with predicted functions that are involved in
antioxidant systems, electron transport, and energy metabolism was significantly
altered through the disruption of dr1790. Moreover, the results
of proteomic analyses using 2-DE and MS also demonstrated that DR1790
contributed to D. radiodurans survival. Taken
together, these results indicate that the DR1790 protein from the ancient yellow
protein family plays a pleiotropic role in the survival of prokaryotic cells and
contributes to the extraordinary resistance of D. radiodurans
against oxidative and radiation stresses.
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Affiliation(s)
- Jianhui Cheng
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China, Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hu Wang
- Institute of Ageing Research, Hangzhou Normal University, Hangzhou, China, Institute of Ageing Research, Hangzhou Normal University, Hangzhou, China
| | - Xin Xu
- Zhejiang University, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Liangyan Wang
- Zhejiang University, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Bing Tian
- Zhejiang University, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
| | - Yuejin Hua
- Zhejiang University, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China, Institute of Nuclear-Agricultural Sciences, Zhejiang University, Hangzhou, China
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13
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Im S, Joe M, Kim D, Park DH, Lim S. Transcriptome analysis of salt-stressed Deinococcus radiodurans and characterization of salt-sensitive mutants. Res Microbiol 2013; 164:923-32. [DOI: 10.1016/j.resmic.2013.07.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 06/27/2013] [Indexed: 01/30/2023]
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14
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Yang P, Chen Z, Shan Z, Ding X, Liu L, Guo J. Effects of FMN riboswitch on antioxidant activity in Deinococcus radiodurans under H₂O₂ stress. Microbiol Res 2013; 169:411-6. [PMID: 24103862 DOI: 10.1016/j.micres.2013.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/05/2013] [Accepted: 09/07/2013] [Indexed: 10/26/2022]
Abstract
The flavin mononucleotide (FMN) riboswitch is structured noncoding RNA domains that control gene expression by selectively binding FMN or sensing surrounding changes without protein factors, which are involved in the biosynthesis and transport of riboflavin and related compounds. We constructed the deletion mutant of FMN riboswitch to investigate its possible role in response to H₂O₂ stress in Deinococcus radiodurans. The results showed that the deletion of FMN riboswitch resulted in an obvious growth delay in D. radiodurans. Compared with the survival rate of 56% of D. radiodurans, only 40% of the mutant survived after treated with 50 mM of H₂O₂, indicating that deletion of FMN riboswitch obviously increased the susceptibility to H₂O₂. Compared with the wild type R1 strain of D. radiodurans, FMN riboswitch knockout cells accumulated a higher level of intracellular reactive oxygen species (ROS) while their total catalase activity reduced significantly. Results from quantitative real-time PCR analysis implies structural alterations of in response to H₂O₂ challenge. Our data suggest a critical role of FMN riboswitch in the oxidation tolerance system of D. radiodurans.
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Affiliation(s)
- Peng Yang
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, PR China
| | - Zhouwei Chen
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, PR China
| | - Zhan Shan
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, PR China
| | - Xianfeng Ding
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, PR China
| | - Lili Liu
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, PR China
| | - Jiangfeng Guo
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, PR China.
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15
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Zegeye ED, Balasingham SV, Laerdahl JK, Homberset H, Tønjum T. Mycobacterium tuberculosis RecG binds and unwinds model DNA substrates with a preference for Holliday junctions. MICROBIOLOGY-SGM 2012; 158:1982-1993. [PMID: 22628485 PMCID: PMC3542137 DOI: 10.1099/mic.0.058693-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The RecG enzyme, a superfamily 2 helicase, is present in nearly all bacteria. Here we report for the first time that the recG gene is also present in the genomes of most vascular plants as well as in green algae, but is not found in other eukaryotes or archaea. The precise function of RecG is poorly understood, although ample evidence shows that it plays critical roles in DNA repair, recombination and replication. We further demonstrate that Mycobacterium tuberculosis RecG (RecGMtb) DNA binding activity had a broad substrate specificity, whereas it only unwound branched-DNA substrates such as Holliday junctions (HJs), replication forks, D-loops and R-loops, with a strong preference for the HJ as a helicase substrate. In addition, RecGMtb preferentially bound relatively long (≥40 nt) ssDNA, exhibiting a higher affinity for the homopolymeric nucleotides poly(dT), poly(dG) and poly(dC) than for poly(dA). RecGMtb helicase activity was supported by hydrolysis of ATP or dATP in the presence of Mg2+, Mn2+, Cu2+ or Fe2+. Like its Escherichia coli orthologue, RecGMtb is also a strictly DNA-dependent ATPase.
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Affiliation(s)
- Ephrem Debebe Zegeye
- Centre for Molecular Biology and Neuroscience and Department of Microbiology, University of Oslo, Oslo, Norway
| | - Seetha V Balasingham
- Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway.,Centre for Molecular Biology and Neuroscience and Department of Microbiology, University of Oslo, Oslo, Norway
| | - Jon K Laerdahl
- Bioinformatics Core Facility, Department of Informatics, University of Oslo, Oslo, Norway.,Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway.,Centre for Molecular Biology and Neuroscience and Department of Microbiology, University of Oslo, Oslo, Norway
| | - Håvard Homberset
- Centre for Molecular Biology and Neuroscience and Department of Microbiology, University of Oslo, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, Oslo University Hospital (Rikshospitalet), Oslo, Norway.,Centre for Molecular Biology and Neuroscience and Department of Microbiology, University of Oslo, Oslo, Norway
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16
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Maisch T, Shimizu T, Mitra A, Heinlin J, Karrer S, Li YF, Morfill G, Zimmermann JL. Contact-free cold atmospheric plasma treatment of Deinococcus radiodurans. J Ind Microbiol Biotechnol 2012; 39:1367-75. [PMID: 22584820 DOI: 10.1007/s10295-012-1137-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 04/18/2012] [Indexed: 01/10/2023]
Abstract
In this study we investigated the sensitivity of Deinococcus radiodurans to contact-free cold atmospheric plasma treatment as part of a project to establish new efficient procedures for disinfection of inanimate surfaces. The Gram-positive D. radiodurans is one of the most resistant microorganisms worldwide. Stationary phases of D. radiodurans were exposed to cold atmospheric plasma for different time intervals or to ultraviolet C (UVC) radiation at dose rates of 0.001-0.0656 J cm⁻², respectively. A methicillin-resistant Staphylococcus aureus strain (MRSA) served as control for Gram-positive bacteria. The surface microdischarge plasma technology was used for generation of cold atmospheric plasma. A plasma discharge was ignited using ambient air. Surprisingly, D. radiodurans was sensitive to the cold atmospheric plasma treatment in the same range as the MRSA strain. Survival of both bacteria decreased with increasing plasma exposure times up to 6 log₁₀ cycles (>99.999 %) within 20 s of plasma treatment. In contrast, UVC radiation of both bacteria demonstrated that D. radiodurans was more resistant to UVC treatment than MRSA. Cold atmospheric plasma seems to be a promising tool for industrial and clinical purposes where time-saving is a critical point to achieve efficient disinfection of inanimate surfaces and where protection from corrosive materials is needed.
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Affiliation(s)
- Tim Maisch
- Department of Dermatology, Regensburg University Hospital, Franz-Josef-Strauss-Allee 11, 93053 Regensburg, Germany.
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17
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Abstract
Deinococcus radiodurans is a robust bacterium best known for its capacity to repair massive DNA damage efficiently and accurately. It is extremely resistant to many DNA-damaging agents, including ionizing radiation and UV radiation (100 to 295 nm), desiccation, and mitomycin C, which induce oxidative damage not only to DNA but also to all cellular macromolecules via the production of reactive oxygen species. The extreme resilience of D. radiodurans to oxidative stress is imparted synergistically by an efficient protection of proteins against oxidative stress and an efficient DNA repair mechanism, enhanced by functional redundancies in both systems. D. radiodurans assets for the prevention of and recovery from oxidative stress are extensively reviewed here. Radiation- and desiccation-resistant bacteria such as D. radiodurans have substantially lower protein oxidation levels than do sensitive bacteria but have similar yields of DNA double-strand breaks. These findings challenge the concept of DNA as the primary target of radiation toxicity while advancing protein damage, and the protection of proteins against oxidative damage, as a new paradigm of radiation toxicity and survival. The protection of DNA repair and other proteins against oxidative damage is imparted by enzymatic and nonenzymatic antioxidant defense systems dominated by divalent manganese complexes. Given that oxidative stress caused by the accumulation of reactive oxygen species is associated with aging and cancer, a comprehensive outlook on D. radiodurans strategies of combating oxidative stress may open new avenues for antiaging and anticancer treatments. The study of the antioxidation protection in D. radiodurans is therefore of considerable potential interest for medicine and public health.
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18
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Chang X, Yang L, Zhao Q, Fu W, Chen H, Qiu Z, Chen JA, Hu R, Shu W. Involvement of recF in 254 nm Ultraviolet Radiation Resistance in Deinococcus radiodurans and Escherichia coli. Curr Microbiol 2010; 61:458-64. [DOI: 10.1007/s00284-010-9638-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 03/24/2010] [Indexed: 11/28/2022]
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