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Cheng K, Sun Y, Yu H, Hu Y, He Y, Shen Y. Staphylococcus aureus SOS response: Activation, impact, and drug targets. MLIFE 2024; 3:343-366. [PMID: 39359682 PMCID: PMC11442139 DOI: 10.1002/mlf2.12137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/17/2024] [Accepted: 04/10/2024] [Indexed: 10/04/2024]
Abstract
Staphylococcus aureus is a common cause of diverse infections, ranging from superficial to invasive, affecting both humans and animals. The widespread use of antibiotics in clinical treatments has led to the emergence of antibiotic-resistant strains and small colony variants. This surge presents a significant challenge in eliminating infections and undermines the efficacy of available treatments. The bacterial Save Our Souls (SOS) response, triggered by genotoxic stressors, encompasses host immune defenses and antibiotics, playing a crucial role in bacterial survival, invasiveness, virulence, and drug resistance. Accumulating evidence underscores the pivotal role of the SOS response system in the pathogenicity of S. aureus. Inhibiting this system offers a promising approach for effective bactericidal treatments and curbing the evolution of antimicrobial resistance. Here, we provide a comprehensive review of the activation, impact, and key proteins associated with the SOS response in S. aureus. Additionally, perspectives on therapeutic strategies targeting the SOS response for S. aureus, both individually and in combination with traditional antibiotics are proposed.
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Affiliation(s)
- Kaiying Cheng
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal UniversityHangzhou Normal UniversityHangzhouChina
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of MedicineZhejiang UniversityHangzhouChina
| | - Yukang Sun
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal UniversityHangzhou Normal UniversityHangzhouChina
| | - Huan Yu
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal UniversityHangzhou Normal UniversityHangzhouChina
| | - Yingxuan Hu
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal UniversityHangzhou Normal UniversityHangzhouChina
| | - Yini He
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal UniversityHangzhou Normal UniversityHangzhouChina
| | - Yuanyuan Shen
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal UniversityHangzhou Normal UniversityHangzhouChina
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2
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Ma G, Lin T, Cao P, Oger P, Dong K, Miao L, Zhang L. Biochemical characterization and mutational analysis of the NurA protein from the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5. Res Microbiol 2024; 175:104189. [PMID: 38403006 DOI: 10.1016/j.resmic.2024.104189] [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: 10/05/2023] [Revised: 01/26/2024] [Accepted: 02/20/2024] [Indexed: 02/27/2024]
Abstract
Archaeal NurA protein plays a key role in producing 3'-single stranded DNA used for homologous recombination repair, together with HerA, Mre11, and Rad50. Herein, we describe biochemical characteristics and roles of key amino acid residues of the NurA protein from the hyperthermophilic euryarchaeon Thermococcus barophilus Ch5 (Tba-NurA). Tba-NurA possesses 5'-3' exonuclease activity for degrading DNA, displaying maximum efficiency at 45 °C-65 °C and at pH 8.0 in the presence of Mn2+. The thermostable Tba-NurA also possesses endonuclease activity capable of nicking plasmid DNA and circular ssDNA. Mutational data demonstrate that residue D49 of Tba-NurA is essential for exonuclease activity and is involved in binding ssDNA since the D49A mutant lacked exonuclease activity and reduced ssDNA binding. The R96A and R129A mutants had no detectable dsDNA binding, suggesting that residues R96 and R129 are important for binding dsDNA. The abolished degradation activity and reduced dsDNA binding of the D120A mutant suggest that residue D120 is essential for degradation activity and dsDNA binding. Additionally, residues Y392 and H400 are important for exonuclease activity since these mutations resulted in exonuclease activity loss. To our knowledge, it is the first report on biochemical characterization and mutational analysis of the NurA protein from Thermococcus.
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Affiliation(s)
- Guangyu Ma
- College of Environmental Science and Engineering, Yangzhou University, China
| | - Tan Lin
- College of Environmental Science and Engineering, Yangzhou University, China
| | - Peng Cao
- Faculty of Environment and Life, Beijing University of Technology, 100 Pingleyuan, Chaoyang District, Beijing 100124, China
| | - Philippe Oger
- Université de Lyon, INSA de Lyon, CNRS UMR, 5240 Lyon, France
| | - Kunming Dong
- College of Environmental Science and Engineering, Yangzhou University, China
| | - Li Miao
- College of Environmental Science and Engineering, Yangzhou University, China
| | - Likui Zhang
- College of Environmental Science and Engineering, Yangzhou University, China.
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3
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De March M. Crystal structure of the 3'→5' exonuclease from Methanocaldococcus jannaschii. Biochem Biophys Res Commun 2024; 712-713:149893. [PMID: 38657529 DOI: 10.1016/j.bbrc.2024.149893] [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: 04/03/2024] [Accepted: 04/03/2024] [Indexed: 04/26/2024]
Abstract
RecJ exonucleases are members of the DHH phosphodiesterase family ancestors of eukaryotic Cdc45, the key component of the CMG (Cdc45-MCM-GINS) complex at the replication fork. They are involved in DNA replication and repair, RNA maturation and Okazaki fragment degradation. Bacterial RecJs resect 5'-end ssDNA. Conversely, archaeal RecJs are more versatile being able to hydrolyse in both directions and acting on ssDNA as well as on RNA. In Methanocaldococcus jannaschii two RecJs were previously characterized: RecJ1 is a 5'→3' DNA exonuclease, MjaRecJ2 works only on 3'-end DNA/RNA with a preference for RNA. Here, I present the crystal structure of MjaRecJ2, solved at a resolution of 2.8 Å, compare it with the other RecJ structures, in particular the 5'→3' TkoGAN and the bidirectional PfuRecJ, and discuss its characteristics in light of the more recent knowledge on RecJs. This work adds new structural data that might improve the knowledge of these class of proteins.
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Affiliation(s)
- Matteo De March
- Structural Biology Laboratory, Elettra Sincrotrone Trieste S.c.p.A., 34149, Trieste, Italy; Department of Environmental and Biological Sciences, University of Nova Gorica, SI-5000, Nova Gorica, Slovenia.
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4
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Wang WW, Yi GS, Zhou H, Zhao YX, Wang QS, He JH, Yu F, Xiao X, Liu XP. The structure of the archaeal nuclease RecJ2 implicates its catalytic mechanism and inability to interact with GINS. J Biol Chem 2024; 300:107379. [PMID: 38762184 PMCID: PMC11193018 DOI: 10.1016/j.jbc.2024.107379] [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: 11/09/2023] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/20/2024] Open
Abstract
Bacterial RecJ exhibits 5'→3' exonuclease activity that is specific to ssDNA; however, archaeal RecJs show 5' or 3' exonuclease activity. The hyperthermophilic archaea Methanocaldococcus jannaschii encodes the 5'-exonuclease MjRecJ1 and the 3'-exonuclease MjRecJ2. In addition to nuclease activity, archaeal RecJ interacts with GINS, a structural subcomplex of the replicative DNA helicase complex. However, MjRecJ1 and MjRecJ2 do not interact with MjGINS. Here, we report the structural basis for the inability of the MjRecJ2 homologous dimer to interact with MjGINS and its efficient 3' hydrolysis polarity for short dinucleotides. Based on the crystal structure of MjRecJ2, we propose that the interaction surface of the MjRecJ2 dimer overlaps the potential interaction surface for MjGINS and blocks the formation of the MjRecJ2-GINS complex. Exposing the interaction surface of the MjRecJ2 dimer restores its interaction with MjGINS. The cocrystal structures of MjRecJ2 with substrate dideoxynucleotides or product dCMP/CMP show that MjRecJ2 has a short substrate binding patch, which is perpendicular to the longer patch of bacterial RecJ. Our results provide new insights into the function and diversification of archaeal RecJ/Cdc45 proteins.
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Affiliation(s)
- Wei-Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Gang-Shun Yi
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Huan Zhou
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Yi-Xuan Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; SJTU Yazhou Bay Institute of Deepsea Sci-Tech, Sanya, China
| | - Qi-Sheng Wang
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Jian-Hua He
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China; The Institute for Advanced Studies, Wuhan University, Wuhan, China
| | - Feng Yu
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; SJTU Yazhou Bay Institute of Deepsea Sci-Tech, Sanya, China; Joint International Research Laboratory of Metabolic & Developmental Sciences (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China; State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, Shanghai, China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, China
| | - Xi-Peng Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; SJTU Yazhou Bay Institute of Deepsea Sci-Tech, Sanya, China; Joint International Research Laboratory of Metabolic & Developmental Sciences (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China.
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5
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Gong J, Yang J, Lai Y, Pan T, She W. A High-Quality Assembly and Comparative Analysis of the Mitogenome of Actinidia macrosperma. Genes (Basel) 2024; 15:514. [PMID: 38674448 PMCID: PMC11049864 DOI: 10.3390/genes15040514] [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: 01/30/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The mitochondrial genome (mitogenome) of Actinidia macrosperma, a traditional medicinal plant within the Actinidia genus, remains relatively understudied. This study aimed to sequence the mitogenome of A. macrosperma, determining its assembly, informational content, and developmental expression. The results revealed that the mitogenome of A. macrosperma is circular, spanning 752,501 bp with a GC content of 46.16%. It comprises 63 unique genes, including 39 protein-coding genes (PCGs), 23 tRNA genes, and three rRNA genes. Moreover, the mitogenome was found to contain 63 SSRs, predominantly mono-nucleotides, as well as 25 tandem repeats and 650 pairs of dispersed repeats, each with lengths equal to or greater than 60, mainly comprising forward repeats and palindromic repeats. Moreover, 53 homologous fragments were identified between the mitogenome and chloroplast genome (cp-genome), with the longest segment measuring 4296 bp. This study represents the initial report on the mitogenome of the A. macrosperma, providing crucial genetic materials for phylogenetic research within the Actinidia genus and promoting the exploitation of species genetic resources.
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Affiliation(s)
- Jiangmei Gong
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.G.); (Y.L.); (T.P.)
- Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jun Yang
- College of Food and Bioengineering, Bengbu University, Bengbu 233030, China;
| | - Yan Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.G.); (Y.L.); (T.P.)
- Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tengfei Pan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.G.); (Y.L.); (T.P.)
- Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wenqin She
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (J.G.); (Y.L.); (T.P.)
- Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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6
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Bonde NJ, Kozlov AG, Cox MM, Lohman TM, Keck JL. Molecular insights into the prototypical single-stranded DNA-binding protein from E. coli. Crit Rev Biochem Mol Biol 2024; 59:99-127. [PMID: 38770626 PMCID: PMC11209772 DOI: 10.1080/10409238.2024.2330372] [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: 11/28/2023] [Accepted: 03/11/2024] [Indexed: 05/22/2024]
Abstract
The SSB protein of Escherichia coli functions to bind single-stranded DNA wherever it occurs during DNA metabolism. Depending upon conditions, SSB occurs in several different binding modes. In the course of its function, SSB diffuses on ssDNA and transfers rapidly between different segments of ssDNA. SSB interacts with many other proteins involved in DNA metabolism, with 22 such SSB-interacting proteins, or SIPs, defined to date. These interactions chiefly involve the disordered and conserved C-terminal residues of SSB. When not bound to ssDNA, SSB can aggregate to form a phase-separated biomolecular condensate. Current understanding of the properties of SSB and the functional significance of its many intermolecular interactions are summarized in this review.
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Affiliation(s)
- Nina J. Bonde
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Alexander G. Kozlov
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Michael M. Cox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Timothy M. Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - James L. Keck
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
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7
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Liu C, Hauk G, Yan Q, Berger JM. Structure of Escherichia coli exonuclease VII. Proc Natl Acad Sci U S A 2024; 121:e2319644121. [PMID: 38271335 PMCID: PMC10835039 DOI: 10.1073/pnas.2319644121] [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: 11/08/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
Exonuclease VII (ExoVII) is a ubiquitous bacterial nuclease. Encoded by the xseA and xseB genes, ExoVII participates in multiple nucleic acid-dependent pathways including the processing of multicopy single-stranded DNA and the repair of covalent DNA-protein crosslinks (DPCs). Although many biochemical properties of ExoVII have been defined, little is known about its structure/function relationships. Here, we use cryoelectron microscopy (cryoEM) to determine that Escherichia coli ExoVII comprises a highly elongated XseA4·XseB24 holo-complex. Each XseA subunit dimerizes through a central extended α-helical segment decorated by six XseB subunits and a C-terminal, domain-swapped β-barrel element; two XseA2·XseB12 subcomplexes further associate using N-terminal OB (oligonucleotide/oligosaccharide-binding) folds and catalytic domains to form a spindle-shaped, catenated octaicosamer. The catalytic domains of XseA, which adopt a nuclease fold related to 3-dehydroquinate dehydratases, are sequestered in the center of the complex and accessible only through large pores formed between XseA tetramers. The architectural organization of ExoVII, combined with biochemical studies, indicate that substrate selectivity is controlled by steric access to its nuclease elements and that tetramer dissociation results from substrate DNA binding. Despite a lack of sequence and fold homology, the physical organization of ExoVII is reminiscent of Mre11·Rad50/SbcCD ATP (adenosine triphosphate)-dependent nucleases used in the repair of double-stranded DNA breaks, including those formed by DPCs through aberrant topoisomerase activity, suggesting that there may have been convergent evolutionary pressure to contend with such damage events.
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Affiliation(s)
- Chuan Liu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Glenn Hauk
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Qianyun Yan
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205
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8
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Liu S, Wang F, Chen H, Yang Z, Ning Y, Chang C, Yang D. New Insights into Radio-Resistance Mechanism Revealed by (Phospho)Proteome Analysis of Deinococcus Radiodurans after Heavy Ion Irradiation. Int J Mol Sci 2023; 24:14817. [PMID: 37834265 PMCID: PMC10572868 DOI: 10.3390/ijms241914817] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/23/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Deinococcus radiodurans (D. radiodurans) can tolerate various extreme environments including radiation. Protein phosphorylation plays an important role in radiation resistance mechanisms; however, there is currently a lack of systematic research on this topic in D. radiodurans. Based on label-free (phospho)proteomics, we explored the dynamic changes of D. radiodurans under various doses of heavy ion irradiation and at different time points. In total, 2359 proteins and 1110 high-confidence phosphosites were identified, of which 66% and 23% showed significant changes, respectively, with the majority being upregulated. The upregulated proteins at different states (different doses or time points) were distinct, indicating that the radio-resistance mechanism is dose- and stage-dependent. The protein phosphorylation level has a much higher upregulation than protein abundance, suggesting phosphorylation is more sensitive to irradiation. There were four distinct dynamic changing patterns of phosphorylation, most of which were inconsistent with protein levels. Further analysis revealed that pathways related to RNA metabolism and antioxidation were activated after irradiation, indicating their importance in radiation response. We also screened some key hub phosphoproteins and radiation-responsive kinases for further study. Overall, this study provides a landscape of the radiation-induced dynamic change of protein expression and phosphorylation, which provides a basis for subsequent functional and applied studies.
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Affiliation(s)
- Shihao Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (S.L.); (H.C.); (Y.N.); (C.C.)
| | - Fei Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (S.L.); (H.C.); (Y.N.); (C.C.)
| | - Heye Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (S.L.); (H.C.); (Y.N.); (C.C.)
| | - Zhixiang Yang
- College of Life Sciences, Hebei University, Baoding 071002, China;
| | - Yifan Ning
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (S.L.); (H.C.); (Y.N.); (C.C.)
- College of Life Sciences, Hebei University, Baoding 071002, China;
| | - Cheng Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (S.L.); (H.C.); (Y.N.); (C.C.)
| | - Dong Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China; (S.L.); (H.C.); (Y.N.); (C.C.)
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9
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Jia H, Dantuluri S, Margulies S, Smith V, Lever R, Allers T, Koh J, Chen S, Maupin-Furlow JA. RecJ3/4-aRNase J form a Ubl-associated nuclease complex functioning in survival against DNA damage in Haloferax volcanii. mBio 2023; 14:e0085223. [PMID: 37458473 PMCID: PMC10470531 DOI: 10.1128/mbio.00852-23] [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: 04/05/2023] [Accepted: 06/02/2023] [Indexed: 09/02/2023] Open
Abstract
Nucleases are strictly regulated and often localized in the cell to avoid the uncontrolled degradation of DNA and RNA. Here, a new type of nuclease complex, composed of RecJ3, RecJ4, and aRNase J, was identified through its ATP-dependent association with the ubiquitin-like SAMP1 and AAA-ATPase Cdc48a. The complex was discovered in Haloferax volcanii, an archaeon lacking an RNA exosome. Genetic analysis revealed aRNase J to be essential and RecJ3, RecJ4, and Cdc48a to function in the recovery from DNA damage including genotoxic agents that generate double-strand breaks. The RecJ3:RecJ4:aRNase J complex (isolated in 2:2:1 stoichiometry) functioned primarily as a 3'-5' exonuclease in hydrolyzing RNA and ssDNA, with the mechanism non-processive for ssDNA. aRNase J could also be purified as a homodimer that catalyzed endoribonuclease activity and, thus, was not restricted to the 5'-3' exonuclease activity typical of aRNase J homologs. Moreover, RecJ3 and RecJ4 could be purified as a 560-kDa subcomplex in equimolar subunit ratio with nuclease activities mirroring the full RecJ3/4-aRNase J complex. These findings prompted reconstitution assays that suggested RecJ3/4 could suppress, alter, and/or outcompete the nuclease activities of aRNase J. Based on the phenotypic results, this control mechanism of aRNase J by RecJ3/4 is not necessary for cell growth but instead appears important for DNA repair. IMPORTANCE Nucleases are critical for various cellular processes including DNA replication and repair. Here, a dynamic type of nuclease complex is newly identified in the archaeon Haloferax volcanii, which is missing the canonical RNA exosome. The complex, composed of RecJ3, RecJ4, and aRNase J, functions primarily as a 3'-5' exonuclease and was discovered through its ATP-dependent association with the ubiquitin-like SAMP1 and Cdc48a. aRNase J alone forms a homodimer that has endonuclease function and, thus, is not restricted to 5'-3' exonuclease activity typical of other aRNase J enzymes. RecJ3/4 appears to suppress, alter, and/or outcompete the nuclease activities of aRNase J. While aRNase J is essential for growth, RecJ3/4, Cdc48a, and SAMPs are important for recovery against DNA damage. These biological distinctions may correlate with the regulated nuclease activity of aRNase J in the RecJ3/4-aRNaseJ complex.
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Affiliation(s)
- Huiyong Jia
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, USA
| | - Swathi Dantuluri
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, USA
| | - Shae Margulies
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, USA
| | - Victoria Smith
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Rebecca Lever
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Jin Koh
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
| | - Sixue Chen
- Proteomics and Mass Spectrometry, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
- Department of Biology, College of Liberal Arts and Sciences, University of Florida, Gainesville, Florida, USA
| | - Julie A. Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, Florida, USA
- Genetics Institute, University of Florida, Gainesville, Florida, USA
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10
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Cox MM, Goodman MF, Keck JL, van Oijen A, Lovett ST, Robinson A. Generation and Repair of Postreplication Gaps in Escherichia coli. Microbiol Mol Biol Rev 2023; 87:e0007822. [PMID: 37212693 PMCID: PMC10304936 DOI: 10.1128/mmbr.00078-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
When replication forks encounter template lesions, one result is lesion skipping, where the stalled DNA polymerase transiently stalls, disengages, and then reinitiates downstream to leave the lesion behind in a postreplication gap. Despite considerable attention in the 6 decades since postreplication gaps were discovered, the mechanisms by which postreplication gaps are generated and repaired remain highly enigmatic. This review focuses on postreplication gap generation and repair in the bacterium Escherichia coli. New information to address the frequency and mechanism of gap generation and new mechanisms for their resolution are described. There are a few instances where the formation of postreplication gaps appears to be programmed into particular genomic locations, where they are triggered by novel genomic elements.
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Affiliation(s)
- Michael M. Cox
- Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Myron F. Goodman
- Department of Biological Sciences, University of Southern California, University Park, Los Angeles, California, USA
- Department of Chemistry, University of Southern California, University Park, Los Angeles, California, USA
| | - James L. Keck
- Department of Biological Chemistry, University of Wisconsin—Madison School of Medicine, Madison, Wisconsin, USA
| | - Antoine van Oijen
- Molecular Horizons, University of Wollongong, Wollongong, New South Wales, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
| | - Susan T. Lovett
- Department of Biology, Brandeis University, Waltham, Massachusetts, USA
| | - Andrew Robinson
- Molecular Horizons, University of Wollongong, Wollongong, New South Wales, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
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11
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Zhang X, Shan Y, Li J, Qin Q, Yu J, Deng H. Assembly of the Complete Mitochondrial Genome of Pereskia aculeata Revealed That Two Pairs of Repetitive Elements Mediated the Recombination of the Genome. Int J Mol Sci 2023; 24:ijms24098366. [PMID: 37176072 PMCID: PMC10179450 DOI: 10.3390/ijms24098366] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
Pereskia aculeata is a potential new crop species that has both food and medicinal (antinociceptive activity) properties. However, comprehensive genomic research on P. aculeata is still lacking, particularly concerning its organelle genome. In this study, P. aculeata was studied to sequence the mitochondrial genome (mitogenome) and to ascertain the assembly, informational content, and developmental expression of the mitogenome. The findings revealed that the mitogenome of P. aculeata is circular and measures 515,187 bp in length with a GC content of 44.05%. It contains 52 unique genes, including 33 protein-coding genes, 19 tRNA genes, and three rRNA genes. Additionally, the mitogenome analysis identified 165 SSRs, primarily consisting of tetra-nucleotides, and 421 pairs of dispersed repeats with lengths greater than or equal to 30, which were mainly forward repeats. Based on long reads and PCR experiments, we confirmed that two pairs of long-fragment repetitive elements were highly involved with the mitogenome recombination process. Furthermore, there were 38 homologous fragments detected between the mitogenome and chloroplast genome, and the longest fragment was 3962 bp. This is the first report on the mitogenome in the family Cactaceae. The decoding of the mitogenome of P. aculeata will provide important genetic materials for phylogenetic studies of Cactaceae and promote the utilization of species germplasm resources.
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Affiliation(s)
- Xue Zhang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
| | - Yuanyu Shan
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
| | - Jingling Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
| | - Qiulin Qin
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
| | - Jie Yu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400716, China
- Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River, Ministry of Education, Southwest University, Chongqing 400715, China
| | - Hongping Deng
- Center for Biodiversity Conservation and Utilization, School of Life Sciences, Southwest University, Chongqing 400715, China
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12
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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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13
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Kumar A, Rajaram H. Insights into the presence of multiple RecQ helicases in the ancient cyanobacterium, Nostoc sp. strain PCC7120: bioinformatics and expression analysis approach. Mol Genet Genomics 2023; 298:37-47. [PMID: 36264383 DOI: 10.1007/s00438-022-01963-6] [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: 05/09/2022] [Accepted: 10/09/2022] [Indexed: 01/11/2023]
Abstract
Owing to their crucial role in genome maintenance, RecQ helicases are ubiquitous and present across organisms. Though the multiplicity of RecQ helicases is well known in higher organisms, it is rare among bacteria. The ancient cyanobacterium Nostoc sp. strain PCC7120 was found to have three annotated RecQ helicases. This study aims at understanding its structural differences and evolution through bioinformatics approach and functionality through expression analysis studies. Nostoc RecQ helicases were found to be transcriptionally regulated by LexA and DNA damage inducing stresses. Bioinformatic analysis revealed that all three RecQ helicases of Nostoc possess helicases_C and Zn+2-binding domains. Two of the helicases (AnRecQ and AnRecQ2) lacked the complete RQC and HRDC domains, and AnRecQ2 had an additional Phosphoribosyl transferase domain (Pribosyltran), also seen in RecQ-like helicase (RqlH) protein of Mycobacterium smegmatis. AnRecQ1, which was similar to most bacterial RecQ helicases, differed in having a long C-terminal tail. STRING analysis revealed that the proteins also differed in their predicted protein interactome. Phylogenetic analysis suggested that the multiple recQ genes may have been acquired through duplication and acquisition of additional domains from the smallest of the RecQ helicases (AnRecQ) to cater multiple functions required to deal with the harsh environmental conditions. In course of evolution, however, the multiplicity was lost with the modern-day bacteria and lower eukaryotes which retained fewer RecQ helicases, while further duplication of the acquired RECQ occurred in higher animals and plants to deal with cellular complexity.
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Affiliation(s)
- Arvind Kumar
- Cyanobacterial Stress Biology and Biotechnology Section, Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, Trombay, 400085, India
| | - Hema Rajaram
- Cyanobacterial Stress Biology and Biotechnology Section, Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, Trombay, 400085, India. .,Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India.
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14
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Schons-Fonseca L, Lazova MD, Smith JL, Anderson ME, Grossman AD. Beneficial and detrimental genes in the cellular response to replication arrest. PLoS Genet 2022; 18:e1010564. [PMID: 36574412 PMCID: PMC9836290 DOI: 10.1371/journal.pgen.1010564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/12/2023] [Accepted: 12/09/2022] [Indexed: 12/28/2022] Open
Abstract
DNA replication is essential for all living organisms. Several events can disrupt replication, including DNA damage (e.g., pyrimidine dimers, crosslinking) and so-called "roadblocks" (e.g., DNA-binding proteins or transcription). Bacteria have several well-characterized mechanisms for repairing damaged DNA and then restoring functional replication forks. However, little is known about the repair of stalled or arrested replication forks in the absence of chemical alterations to DNA. Using a library of random transposon insertions in Bacillus subtilis, we identified 35 genes that affect the ability of cells to survive exposure to an inhibitor that arrests replication elongation, but does not cause chemical alteration of the DNA. Genes identified include those involved in iron-sulfur homeostasis, cell envelope biogenesis, and DNA repair and recombination. In B. subtilis, and many bacteria, two nucleases (AddAB and RecJ) are involved in early steps in repairing replication forks arrested by chemical damage to DNA and loss of either nuclease causes increased sensitivity to DNA damaging agents. These nucleases resect DNA ends, leading to assembly of the recombinase RecA onto the single-stranded DNA. Notably, we found that disruption of recJ increased survival of cells following replication arrest, indicating that in the absence of chemical damage to DNA, RecJ is detrimental to survival. In contrast, and as expected, disruption of addA decreased survival of cells following replication arrest, indicating that AddA promotes survival. The different phenotypes of addA and recJ mutants appeared to be due to differences in assembly of RecA onto DNA. RecJ appeared to promote too much assembly of RecA filaments. Our results indicate that in the absence of chemical damage to DNA, RecA is dispensable for cells to survive replication arrest and that the stable RecA nucleofilaments favored by the RecJ pathway may lead to cell death by preventing proper processing of the arrested replication fork.
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Affiliation(s)
- Luciane Schons-Fonseca
- Department of Biology Massachusetts Institute of Technology Cambridge, Massachusetts, United States of America
| | - Milena D. Lazova
- Department of Biology Massachusetts Institute of Technology Cambridge, Massachusetts, United States of America
| | - Janet L. Smith
- Department of Biology Massachusetts Institute of Technology Cambridge, Massachusetts, United States of America
| | - Mary E. Anderson
- Department of Biology Massachusetts Institute of Technology Cambridge, Massachusetts, United States of America
| | - Alan D. Grossman
- Department of Biology Massachusetts Institute of Technology Cambridge, Massachusetts, United States of America
- * E-mail:
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15
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Yuan LG, Liu NN, Xi XG. Biochemical and functional characterization of an exonuclease from Chaetomium thermophilum. Biochem Biophys Res Commun 2022; 636:17-24. [DOI: 10.1016/j.bbrc.2022.10.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 10/13/2022] [Indexed: 11/30/2022]
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16
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Crystal Structure of the Recombination Mediator Protein RecO from Campylobacter jejuni and Its Interaction with DNA and a Zinc Ion. Int J Mol Sci 2022; 23:ijms23179667. [PMID: 36077065 PMCID: PMC9456098 DOI: 10.3390/ijms23179667] [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: 08/05/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/23/2022] Open
Abstract
Homologous recombination is involved in repairing DNA damage, contributing to maintaining the integrity and stability of viral and cellular genomes. In bacteria, the recombination mediator proteins RecO and RecR are required to load the RecA recombinase on ssDNA for homologous recombination. To structurally and functionally characterize RecO, we determined the crystal structure of RecO from Campylobacter jejuni (cjRecO) at a 1.8 Å resolution and biochemically assessed its capacity to interact with DNA and a metal ion. cjRecO folds into a curved rod-like structure that consists of an N-terminal domain (NTD), C-terminal domain (CTD), and Zn2+-binding domain (ZnD). The ZnD at the end of the rod-like structure coordinates three cysteine residues and one histidine residue to accommodate a Zn2+ ion. Based on an extensive comparative analysis of RecO structures and sequences, we propose that the Zn2+-binding consensus sequence of RecO is CxxC…C/HxxC/H/D. The interaction with Zn2+ is indispensable for the protein stability of cjRecO but does not seem to be required for the recombination mediator function. cjRecO also interacts with ssDNA as part of its biological function, potentially using the positively charged patch in the NTD and CTD. However, cjRecO displays a low ssDNA-binding affinity, suggesting that cjRecO requires RecR to efficiently recognize ssDNA for homologous recombination.
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17
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Wang BB, Xu JZ, Zhang F, Liu S, Liu J, Zhang WG. Review of DNA repair enzymes in bacteria: With a major focus on AddAB and RecBCD. DNA Repair (Amst) 2022; 118:103389. [PMID: 36030574 DOI: 10.1016/j.dnarep.2022.103389] [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: 03/14/2022] [Revised: 07/18/2022] [Accepted: 08/20/2022] [Indexed: 11/03/2022]
Abstract
DNA recombination repair systems are essential for organisms to maintain genomic stability. In recent years, we have improved our understanding of the mechanisms of RecBCD/AddAB family-mediated DNA double-strand break repair. In E. coli, it is RecBCD that plays a central role, and in Firmicute Bacillus subtilis it is the AddAB complex that functions. However, there are open questions about the mechanism of DNA repair in bacteria. For example, how bacteria containing crossover hotspot instigator (Chi) sites regulate the activity of proteins. In addition, we still do not know the exact process by which the RecB nuclease or AddA nuclease structural domains load RecA onto DNA. We also know little about the mechanism of DNA repair in the industrially important production bacterium Corynebacterium glutamicum (C. glutamicum). Therefore, exploring DNA repair mechanisms in bacteria may not only deepen our understanding of the DNA repair process in this species but also guide us in the targeted treatment of diseases associated with recombination defects, such as cancer. In this paper, we firstly review the classical proteins RecBCD and AddAB involved in DNA recombination repair, secondly focus on the novel helical nuclease AdnAB found in the genus Mycobacterium.
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Affiliation(s)
- Bing-Bing Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, WuXi 214122, People's Republic of China
| | - Jian-Zhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, WuXi 214122, People's Republic of China.
| | - Feng Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, WuXi 214122, People's Republic of China
| | - Shuai Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, WuXi 214122, People's Republic of China
| | - Jie Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, WuXi 214122, People's Republic of China
| | - Wei-Guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, WuXi 214122, People's Republic of China.
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18
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Xu Y, Xu L, Qin C, Wang L, Guo J, Hua Y, Zhao Y. Mechanisms of helicase activated DNA end resection in bacteria. Structure 2022; 30:1298-1306.e3. [PMID: 35841886 DOI: 10.1016/j.str.2022.06.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/26/2022] [Accepted: 06/21/2022] [Indexed: 12/01/2022]
Abstract
DNA end resection mediated by the coordinated action of nuclease and helicase is a crucial step in initiating homologous recombination. The end-resection apparatus NurA nuclease and HerA helicase are present in both archaea and bacteria. Here, we report the cryo-electron microscopy structure of a bacterial HerA-NurA complex from Deinococcus radiodurans. The structure reveals a barrel-like hexameric HerA and a distinctive NurA dimer subcomplex, which has a unique extended N-terminal region (ENR) involved in bacterial NurA dimerization and activation. In addition to the long protruding linking loop and the C-terminal α helix of NurA, the flexible ENR is close to the HerA-NurA interface and divides the central channel of the DrNurA dimer into two halves, suggesting a possible mechanism of DNA end processing. In summary, this work provides new insights into the structure, assembly, and activation mechanisms of bacterial DNA end resection mediated by a minimal end-resection apparatus.
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Affiliation(s)
- Ying Xu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Lingyi Xu
- Department of Biophysics, Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Chen Qin
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Liangyan Wang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jiangtao Guo
- Department of Biophysics, Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.
| | - Yuejin Hua
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Ye Zhao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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19
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Laureti L, Lee L, Philippin G, Kahi M, Pagès V. Single strand gap repair: The presynaptic phase plays a pivotal role in modulating lesion tolerance pathways. PLoS Genet 2022; 18:e1010238. [PMID: 35653392 PMCID: PMC9203016 DOI: 10.1371/journal.pgen.1010238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 06/16/2022] [Accepted: 05/05/2022] [Indexed: 11/17/2022] Open
Abstract
During replication, the presence of unrepaired lesions results in the formation of single stranded DNA (ssDNA) gaps that need to be repaired to preserve genome integrity and cell survival. All organisms have evolved two major lesion tolerance pathways to continue replication: Translesion Synthesis (TLS), potentially mutagenic, and Homology Directed Gap Repair (HDGR), that relies on homologous recombination. In Escherichia coli, the RecF pathway repairs such ssDNA gaps by processing them to produce a recombinogenic RecA nucleofilament during the presynaptic phase. In this study, we show that the presynaptic phase is crucial for modulating lesion tolerance pathways since the competition between TLS and HDGR occurs at this stage. Impairing either the extension of the ssDNA gap (mediated by the nuclease RecJ and the helicase RecQ) or the loading of RecA (mediated by RecFOR) leads to a decrease in HDGR and a concomitant increase in TLS. Hence, we conclude that defects in the presynaptic phase delay the formation of the D-loop and increase the time window allowed for TLS. In contrast, we show that a defect in the postsynaptic phase that impairs HDGR does not lead to an increase in TLS. Unexpectedly, we also reveal a strong genetic interaction between recF and recJ genes, that results in a recA deficient-like phenotype in which HDGR is almost completely abolished.
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Affiliation(s)
- Luisa Laureti
- Team DNA Damage and Genome Instability, Cancer Research Center of Marseille (CRCM); CNRS, Aix Marseille Univ, INSERM, Institut Paoli-Calmettes, Marseille, France
| | - Lara Lee
- Team DNA Damage and Genome Instability, Cancer Research Center of Marseille (CRCM); CNRS, Aix Marseille Univ, INSERM, Institut Paoli-Calmettes, Marseille, France
| | - Gaëlle Philippin
- Team DNA Damage and Genome Instability, Cancer Research Center of Marseille (CRCM); CNRS, Aix Marseille Univ, INSERM, Institut Paoli-Calmettes, Marseille, France
| | - Michel Kahi
- Team DNA Damage and Genome Instability, Cancer Research Center of Marseille (CRCM); CNRS, Aix Marseille Univ, INSERM, Institut Paoli-Calmettes, Marseille, France
| | - Vincent Pagès
- Team DNA Damage and Genome Instability, Cancer Research Center of Marseille (CRCM); CNRS, Aix Marseille Univ, INSERM, Institut Paoli-Calmettes, Marseille, France
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20
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Yang Y, Yu Q, Wang M, Zhao R, Liu H, Xun L, Xia Y. Escherichia coli BW25113 Competent Cells Prepared Using a Simple Chemical Method Have Unmatched Transformation and Cloning Efficiencies. Front Microbiol 2022; 13:838698. [PMID: 35401484 PMCID: PMC8989280 DOI: 10.3389/fmicb.2022.838698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 03/01/2022] [Indexed: 11/26/2022] Open
Abstract
Escherichia coli recA− strains are usually used for cloning to prevent insert instability via RecA-dependent recombination. Here, we report that E. coli BW25113 (recA+) competent cells prepared by using a previously reported transformation and storage solution (TSS) had 100-fold or higher transformation efficiency than the commonly used E. coli cloning strains, including XL1-Blue MRF’. The cloning success rates with E. coli BW25113 were 440 to 1,267-fold higher than those with E. coli XL1-Blue MRF’ when several inserts were assembled into four vectors by using a simple DNA assembly method. The difference was in part due to RecA, as the recA deletion in E. coli BW25113 reduced the transformation efficiency by 16 folds and cloning success rate by about 10 folds. However, the transformation efficiency and the cloning success rate of the recA deletion mutant of E. coli BW25113 are still 12- and >48-fold higher than those of E. coli XL1-Blue MRF’, which is a commonly used cloning strain. The cloned inserts with different lengths of homologous sequences were assembled into four vectors and transformed into E. coli BW25113, and they were stably maintained in BW25113. Thus, we recommend using E. coli BW25113 for efficient cloning and DNA assembly.
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Affiliation(s)
- Yuqing Yang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Institute of Marine Science and Technology, Shandong University, Qingdao, China
| | - Qiaoli Yu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Min Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Rui Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Huaiwei Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Luying Xun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- School of Molecular Biosciences, Washington State University, Pullman, WA, United States
- *Correspondence: Luying Xun, Yongzhen Xia,
| | - Yongzhen Xia
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- *Correspondence: Luying Xun, Yongzhen Xia,
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21
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The rarA gene as part of an expanded RecFOR recombination pathway: Negative epistasis and synthetic lethality with ruvB, recG, and recQ. PLoS Genet 2021; 17:e1009972. [PMID: 34936656 PMCID: PMC8735627 DOI: 10.1371/journal.pgen.1009972] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 01/06/2022] [Accepted: 12/01/2021] [Indexed: 11/19/2022] Open
Abstract
The RarA protein, homologous to human WRNIP1 and yeast MgsA, is a AAA+ ATPase and one of the most highly conserved DNA repair proteins. With an apparent role in the repair of stalled or collapsed replication forks, the molecular function of this protein family remains obscure. Here, we demonstrate that RarA acts in late stages of recombinational DNA repair of post-replication gaps. A deletion of most of the rarA gene, when paired with a deletion of ruvB or ruvC, produces a growth defect, a strong synergistic increase in sensitivity to DNA damaging agents, cell elongation, and an increase in SOS induction. Except for SOS induction, these effects are all suppressed by inactivating recF, recO, or recJ, indicating that RarA, along with RuvB, acts downstream of RecA. SOS induction increases dramatically in a rarA ruvB recF/O triple mutant, suggesting the generation of large amounts of unrepaired ssDNA. The rarA ruvB defects are not suppressed (and in fact slightly increased) by recB inactivation, suggesting RarA acts primarily downstream of RecA in post-replication gaps rather than in double strand break repair. Inactivating rarA, ruvB and recG together is synthetically lethal, an outcome again suppressed by inactivation of recF, recO, or recJ. A rarA ruvB recQ triple deletion mutant is also inviable. Together, the results suggest the existence of multiple pathways, perhaps overlapping, for the resolution or reversal of recombination intermediates created by RecA protein in post-replication gaps within the broader RecF pathway. One of these paths involves RarA.
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22
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Yasmin T, Azeroglu B, Cockram CA, Leach DRF. Distribution of Holliday junctions and repair forks during Escherichia coli DNA double-strand break repair. PLoS Genet 2021; 17:e1009717. [PMID: 34432790 PMCID: PMC8386832 DOI: 10.1371/journal.pgen.1009717] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/14/2021] [Indexed: 11/21/2022] Open
Abstract
Accurate repair of DNA double-strand breaks (DSBs) is crucial for cell survival and genome integrity. In Escherichia coli, DSBs are repaired by homologous recombination (HR), using an undamaged sister chromosome as template. The DNA intermediates of this pathway are expected to be branched molecules that may include 4-way structures termed Holliday junctions (HJs), and 3-way structures such as D-loops and repair forks. Using a tool creating a site-specific, repairable DSB on only one of a pair of replicating sister chromosomes, we have determined how these branched DNA intermediates are distributed across a DNA region that is undergoing DSB repair. In cells, where branch migration and cleavage of HJs are limited by inactivation of the RuvABC complex, HJs and repair forks are principally accumulated within a distance of 12 kb from sites of recombination initiation, known as Chi, on each side of the engineered DSB. These branched DNA structures can even be detected in the region of DNA between the Chi sites flanking the DSB, a DNA segment not expected to be engaged in recombination initiation, and potentially degraded by RecBCD nuclease action. This is observed even in the absence of the branch migration and helicase activities of RuvAB, RadA, RecG, RecQ and PriA. The detection of full-length DNA fragments containing HJs in this central region implies that DSB repair can restore the two intact chromosomes, into which HJs can relocate prior to their resolution. The distribution of recombination intermediates across the 12kb region beyond Chi is altered in xonA, recJ and recQ mutants suggesting that, in the RecBCD pathway of DSB repair, exonuclease I stimulates the formation of repair forks and that RecJQ promotes strand-invasion at a distance from the recombination initiation sites.
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Affiliation(s)
- Tahirah Yasmin
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King’s Buildings, Edinburgh, United Kingdom
| | - Benura Azeroglu
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King’s Buildings, Edinburgh, United Kingdom
| | - Charlotte A. Cockram
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King’s Buildings, Edinburgh, United Kingdom
| | - David R. F. Leach
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King’s Buildings, Edinburgh, United Kingdom
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23
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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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24
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Yang Y, Wang T, Yu Q, Liu H, Xun L, Xia Y. The pathway of recombining short homologous ends in Escherichia coli revealed by the genetic study. Mol Microbiol 2021; 115:1309-1322. [PMID: 33372330 DOI: 10.1111/mmi.14677] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/17/2020] [Accepted: 12/23/2020] [Indexed: 11/30/2022]
Abstract
The recombination of short homologous ends in Escherichia coli has been known for 30 years, and it is often used for both site-directed mutagenesis and in vivo cloning. For cloning, a plasmid and target DNA fragments were converted into linear DNA fragments with short homologous ends, which are joined via recombination inside E. coli after transformation. Here this mechanism of joining homologous ends in E. coli was determined by a linearized plasmid with short homologous ends. Two 3'-5' exonucleases ExoIII and ExoX with nonprocessive activity digested linear dsDNA to generate 5' single-strand overhangs, which annealed with each other. The polymerase activity of DNA polymerase I (Pol I) was exclusively employed to fill in the gaps. The strand displacement activity and the 5'-3' exonuclease activity of Pol I were also required, likely to generate 5' phosphate termini for subsequent ligation. Ligase A (LigA) joined the nicks to finish the process. The model involving 5' single-stranded overhangs is different from established recombination pathways that all generate 3' single-stranded overhangs. This recombination is likely common in bacteria since the involved enzymes are ubiquitous.
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Affiliation(s)
- Yuqing Yang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China.,Institute of Marine Science and Technology, Shandong University, Qingdao, People's Republic of China
| | - Tianqi Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Qiaoli Yu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Huaiwei Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Luying Xun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China.,School of Molecular Biosciences, Washington State University, Pullman, WA, USA
| | - Yongzhen Xia
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
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25
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Double strand break (DSB) repair in Cyanobacteria: Understanding the process in an ancient organism. DNA Repair (Amst) 2020; 95:102942. [DOI: 10.1016/j.dnarep.2020.102942] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 07/19/2020] [Accepted: 07/26/2020] [Indexed: 02/07/2023]
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26
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Gurung D, Blumenthal RM. Distribution of RecBCD and AddAB recombination-associated genes among bacteria in 33 phyla. MICROBIOLOGY-SGM 2020; 166:1047-1064. [PMID: 33085588 DOI: 10.1099/mic.0.000980] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Homologous recombination plays key roles in fundamental processes such as recovery from DNA damage and in bacterial horizontal gene transfer, yet there are still open questions about the distribution of recognized components of recombination machinery among bacteria and archaea. RecBCD helicase-nuclease plays a central role in recombination among Gammaproteobacteria like Escherichia coli; while bacteria in other phyla, like the Firmicute Bacillus subtilis, use the related AddAB complex. The activity of at least some of these complexes is controlled by short DNA sequences called crossover hotspot instigator (Chi) sites. When RecBCD or AddAB complexes encounter an autologous Chi site during unwinding, they introduce a nick such that ssDNA with a free end is available to invade another duplex. If homologous DNA is present, RecA-dependent homologous recombination is promoted; if not (or if no autologous Chi site is present) the RecBCD/AddAB complex eventually degrades the DNA. We examined the distribution of recBCD and addAB genes among bacteria, and sought ways to distinguish them unambiguously. We examined bacterial species among 33 phyla, finding some unexpected distribution patterns. RecBCD and addAB are less conserved than recA, with the orthologous recB and addA genes more conserved than the recC or addB genes. We were able to classify RecB vs. AddA and RecC vs. AddB in some bacteria where this had not previously been done. We used logo analysis to identify sequence segments that are conserved, but differ between the RecBC and AddAB proteins, to help future differentiation between members of these two families.
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Affiliation(s)
- Deepti Gurung
- Present address: Department of Cancer Biology, College of Medicine & Life Sciences, The University of Toledo, Toledo OH 43614-1021, USA.,Department of Medical Microbiology & Immunology, and Program in Bioinformatics, College of Medicine & Life Sciences, The University of Toledo, Toledo OH 43614-1021, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology & Immunology, and Program in Bioinformatics, College of Medicine & Life Sciences, The University of Toledo, Toledo OH 43614-1021, USA
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27
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Chen Z, Tang Y, Hua Y, Zhao Y. Structural features and functional implications of proteins enabling the robustness of Deinococcus radiodurans. Comput Struct Biotechnol J 2020; 18:2810-2817. [PMID: 33133422 PMCID: PMC7575645 DOI: 10.1016/j.csbj.2020.09.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 12/21/2022] Open
Abstract
Deinococcus radiodurans can survive under extreme conditions, including high doses of DNA damaging agents and ionizing radiation, desiccation, and oxidative stress. Both the efficient cellular DNA repair machinery and antioxidation systems contribute to the extreme resistance of this bacterium, making it an ideal organism for studying the cellular mechanisms of environmental adaptation. The number of stress-related proteins identified in this bacterium has mushroomed in the past two decades. The newly identified proteins reveal both commonalities and diversity of structure, mechanism, and function, which impact a wide range of cellular functions. Here, we review the unique and general structural features of these proteins and discuss how these studies improve our understanding of the environmental stress adaptation mechanisms of D. radiodurans.
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Affiliation(s)
- Zijing Chen
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuyue Tang
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuejin Hua
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
| | - Ye Zhao
- Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, Zhejiang, China
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28
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Recombinational Repair of Nuclease-Generated Mitotic Double-Strand Breaks with Different End Structures in Yeast. G3-GENES GENOMES GENETICS 2020; 10:3821-3829. [PMID: 32826304 PMCID: PMC7534431 DOI: 10.1534/g3.120.401603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mitotic recombination is the predominant mechanism for repairing double-strand breaks in Saccharomyces cerevisiae. Current recombination models are largely based on studies utilizing the enzyme I-SceI or HO to create a site-specific break, each of which generates broken ends with 3′ overhangs. In this study sequence-diverged ectopic substrates were used to assess whether the frequent Pol δ-mediated removal of a mismatch 8 nucleotides from a 3′ end affects recombination outcomes and whether the presence of a 3′ vs. 5′ overhang at the break site alters outcomes. Recombination outcomes monitored were the distributions of recombination products into crossovers vs. noncrossovers, and the position/length of transferred sequence (heteroduplex DNA) in noncrossover products. A terminal mismatch that was 22 nucleotides from the 3′ end was rarely removed and the greater distance from the end did not affect recombination outcomes. To determine whether the recombinational repair of breaks with 3′ vs. 5′ overhangs differs, we compared the well-studied 3′ overhang created by I-SceI to a 5′ overhang created by a ZFN (Zinc Finger Nuclease). Initiation with the ZFN yielded more recombinants, consistent with more efficient cleavage and potentially faster repair rate relative to I-SceI. While there were proportionally more COs among ZFN- than I-SceI-initiated events, NCOs in the two systems were indistinguishable in terms of the extent of strand transfer. These data demonstrate that the method of DSB induction and the resulting differences in end polarity have little effect on mitotic recombination outcomes despite potential differences in repair rate.
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29
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Cheng K, Xu Y, Chen X, Lu H, He Y, Wang L, Hua Y. Participation of RecJ in the base excision repair pathway of Deinococcus radiodurans. Nucleic Acids Res 2020; 48:9859-9871. [PMID: 32870272 PMCID: PMC7515722 DOI: 10.1093/nar/gkaa714] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 08/07/2020] [Accepted: 08/20/2020] [Indexed: 12/03/2022] Open
Abstract
RecJ reportedly participates in the base excision repair (BER) pathway, but structural and functional data are scarce. Herein, the Deinococcus radiodurans RecJ (drRecJ) deletion strain exhibited extreme sensitivity to hydrogen peroxide and methyl-methanesulphonate, as well as a high spontaneous mutation rate and an accumulation of unrepaired abasic sites in vivo, indicating the involvement of drRecJ in the BER pathway. The binding affinity and nuclease activity preference of drRecJ toward DNA substrates containing a 5'-P-dSpacer group, a 5'-deoxyribose-phosphate (dRP) mimic, were established. A 1.9 Å structure of drRecJ in complex with 5'-P-dSpacer-modified single-stranded DNA (ssDNA) revealed a 5'-monophosphate binding pocket and occupancy of 5'-dRP in the drRecJ nuclease core. The mechanism for RecJ 5'-dRP catalysis was explored using structural and biochemical data, and the results implied that drRecJ is not a canonical 5'-dRP lyase. Furthermore, in vitro reconstitution assays indicated that drRecJ tends to participate in the long-patch BER pathway rather than the short-patch BER pathway.
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Affiliation(s)
- Kaiying Cheng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, China
| | - Ying Xu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, China
| | - Xuanyi Chen
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, China
| | - Huizhi Lu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, China
| | - Yuan He
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, China
| | - Liangyan Wang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, China
| | - Yuejin Hua
- MOE Key Laboratory of Biosystems Homeostasis & Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, China
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30
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Rogers CM, Lee CY, Parkins S, Buehler NJ, Wenzel S, Martínez-Márquez F, Takagi Y, Myong S, Bochman ML. The yeast Hrq1 helicase stimulates Pso2 translesion nuclease activity and thereby promotes DNA interstrand crosslink repair. J Biol Chem 2020; 295:8945-8957. [PMID: 32371399 PMCID: PMC7335788 DOI: 10.1074/jbc.ra120.013626] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/05/2020] [Indexed: 12/11/2022] Open
Abstract
DNA interstrand crosslink (ICL) repair requires a complex network of DNA damage response pathways. Removal of the ICL lesions is vital, as they are physical barriers to essential DNA processes that require the separation of duplex DNA, such as replication and transcription. The Fanconi anemia (FA) pathway is the principal mechanism for ICL repair in metazoans and is coupled to DNA replication. In Saccharomyces cerevisiae, a vestigial FA pathway is present, but ICLs are predominantly repaired by a pathway involving the Pso2 nuclease, which is hypothesized to use its exonuclease activity to digest through the lesion to provide access for translesion polymerases. However, Pso2 lacks translesion nuclease activity in vitro, and mechanistic details of this pathway are lacking, especially relative to FA. We recently identified the Hrq1 helicase, a homolog of the disease-linked enzyme RecQ-like helicase 4 (RECQL4), as a component of Pso2-mediated ICL repair. Here, using genetic, biochemical, and biophysical approaches, including single-molecule FRET (smFRET)- and gel-based nuclease assays, we show that Hrq1 stimulates the Pso2 nuclease through a mechanism that requires Hrq1 catalytic activity. Importantly, Hrq1 also stimulated Pso2 translesion nuclease activity through a site-specific ICL in vitro We noted that stimulation of Pso2 nuclease activity is specific to eukaryotic RecQ4 subfamily helicases, and genetic and biochemical data suggest that Hrq1 likely interacts with Pso2 through their N-terminal domains. These results advance our understanding of FA-independent ICL repair and establish a role for the RecQ4 helicases in the repair of these detrimental DNA lesions.
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Affiliation(s)
- Cody M Rogers
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana, USA
| | - Chun-Ying Lee
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Samuel Parkins
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Nicholas J Buehler
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana, USA
| | - Sabine Wenzel
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Francisco Martínez-Márquez
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Yuichiro Takagi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Sua Myong
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Matthew L Bochman
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, Indiana, USA.
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31
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Wang W, Ma L, Wang L, Zheng L, Zheng M. RecJ from Bacillus halodurans possesses endonuclease activity at moderate temperature. FEBS Lett 2020; 594:2303-2310. [PMID: 32394489 DOI: 10.1002/1873-3468.13809] [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: 02/26/2020] [Revised: 04/17/2020] [Accepted: 04/21/2020] [Indexed: 11/11/2022]
Abstract
RecJ homologs, which occur in virtually all prokaryotes and eukaryotes, play key roles in DNA damage repair and recombination. Current evidence shows that RecJ family proteins exhibit exonuclease activity, degrading single-stranded nucleic acids. Here, we report a novel RecJ isolated from Bacillus halodurans, which utilizes double-stranded DNA as a substrate and functions as an endonuclease. Bacillus halodurans RecJ (BhRecJ) cleaves supercoiled plasmids into open circular and linear forms. Besides the typical domains of DHH, DHHA1, and oligonucleotide-binding-fold, BhRecJ possesses a C-terminal domain with unknown function, which might form the core of the endonuclease activity. Using mutational analysis, we mapped several essential residues for BhRecJ endonuclease activity. Our findings suggest that BhRecJ may be involved in biological processes not typically associated with RecJ proteins.
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Affiliation(s)
- Wen Wang
- College of Environmental Science and Engineering, Qingdao University, Qingdao, 266071, China.,Marine Bioresources and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Liya Ma
- College of Environmental Science and Engineering, Qingdao University, Qingdao, 266071, China.,Marine Bioresources and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Ling Wang
- College of Environmental Science and Engineering, Qingdao University, Qingdao, 266071, China
| | - Li Zheng
- Marine Bioresources and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Minggang Zheng
- Marine Bioresources and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
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32
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Chevigny N, Schatz-Daas D, Lotfi F, Gualberto JM. DNA Repair and the Stability of the Plant Mitochondrial Genome. Int J Mol Sci 2020; 21:E328. [PMID: 31947741 PMCID: PMC6981420 DOI: 10.3390/ijms21010328] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 12/27/2019] [Accepted: 01/01/2020] [Indexed: 12/13/2022] Open
Abstract
The mitochondrion stands at the center of cell energy metabolism. It contains its own genome, the mtDNA, that is a relic of its prokaryotic symbiotic ancestor. In plants, the mitochondrial genetic information influences important agronomic traits including fertility, plant vigor, chloroplast function, and cross-compatibility. Plant mtDNA has remarkable characteristics: It is much larger than the mtDNA of other eukaryotes and evolves very rapidly in structure. This is because of recombination activities that generate alternative mtDNA configurations, an important reservoir of genetic diversity that promotes rapid mtDNA evolution. On the other hand, the high incidence of ectopic recombination leads to mtDNA instability and the expression of gene chimeras, with potential deleterious effects. In contrast to the structural plasticity of the genome, in most plant species the mtDNA coding sequences evolve very slowly, even if the organization of the genome is highly variable. Repair mechanisms are probably responsible for such low mutation rates, in particular repair by homologous recombination. Herein we review some of the characteristics of plant organellar genomes and of the repair pathways found in plant mitochondria. We further discuss how homologous recombination is involved in the evolution of the plant mtDNA.
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Affiliation(s)
| | | | | | - José Manuel Gualberto
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67081 Strasbourg, France; (N.C.); (D.S.-D.); (F.L.)
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33
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Feng L, Chang CC, Song D, Jiang C, Song Y, Wang CF, Deng W, Zou YJ, Chen HF, Xiao X, Wang FP, Liu XP. The trimeric Hef-associated nuclease HAN is a 3'→5' exonuclease and is probably involved in DNA repair. Nucleic Acids Res 2019; 46:9027-9043. [PMID: 30102394 PMCID: PMC6158738 DOI: 10.1093/nar/gky707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 08/01/2018] [Indexed: 12/26/2022] Open
Abstract
Nucleases play important roles in nucleic acid metabolism. Some archaea encode a conserved protein known as Hef-associated nuclease (HAN). In addition to its C-terminal DHH nuclease domain, HAN also has three N-terminal domains, including a DnaJ-Zinc-finger, ribosomal protein S1-like, and oligonucleotide/oligosaccharide-binding fold. To further understand HAN’s function, we biochemically characterized the enzymatic properties of HAN from Pyrococcus furiosus (PfuHAN), solved the crystal structure of its DHH nuclease domain, and examined its role in DNA repair. Our results show that PfuHAN is a Mn2+-dependent 3′-exonuclease specific to ssDNA and ssRNA with no activity on blunt and 3′-recessive double-stranded DNA. Domain truncation confirmed that the intrinsic nuclease activity is dependent on the C-terminal DHH nuclease domain. The crystal structure of the DHH nuclease domain adopts a trimeric topology, with each subunit adopting a classical DHH phosphoesterase fold. Yeast two hybrid assay confirmed that the DHH domain interacts with the IDR peptide of Hef nuclease. Knockout of the han gene or its C-terminal DHH nuclease domain in Haloferax volcanii resulted in increased sensitivity to the DNA damage reagent MMS. Our results imply that HAN nuclease might be involved in repairing stalled replication forks in archaea.
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Affiliation(s)
- Lei Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Chen-Chen Chang
- Institute of Precision Medicine,The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine
| | - Dong Song
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Chuang Jiang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Yang Song
- Institute of Precision Medicine,The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine
| | - Chao-Fan Wang
- Institute of Precision Medicine,The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine
| | - Wei Deng
- Institute of Precision Medicine,The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine
| | - Ya-Juan Zou
- Instrumental Analysis Center, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Feng-Ping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
| | - Xi-Peng Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai 200240, China
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34
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Li MJ, Yi GS, Yu F, Zhou H, Chen JN, Xu CY, Wang FP, Xiao X, He JH, Liu XP. The crystal structure of Pyrococcus furiosus RecJ implicates it as an ancestor of eukaryotic Cdc45. Nucleic Acids Res 2019; 45:12551-12564. [PMID: 30053256 PMCID: PMC5716160 DOI: 10.1093/nar/gkx887] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 10/01/2017] [Indexed: 12/27/2022] Open
Abstract
RecJ nucleases specifically degrade single-stranded (ss) DNA in the 5′ to 3′ direction. Archaeal RecJ is different from bacterial RecJ in sequence, domain organization, and substrate specificity. The RecJ from archaea Pyrococcus furiosus (PfuRecJ) also hydrolyzes RNA strands in the 3′ to 5′ direction. Like eukaryotic Cdc45 protein, archaeal RecJ forms a complex with MCM helicase and GINS. Here, we report the crystal structures of PfuRecJ and the complex of PfuRecJ and two CMPs. PfuRecJ bind one or two divalent metal ions in its crystal structure. A channel consisting of several positively charged residues is identified in the complex structure, and might be responsible for binding substrate ssDNA and/or releasing single nucleotide products. The deletion of the complex interaction domain (CID) increases the values of kcat/Km of 5′ exonuclease activity on ssDNA and 3′ exonuclease activity on ssRNA by 5- and 4-fold, respectively, indicating that the CID functions as a regulator of enzymatic activity. The DHH domain of PfuRecJ interacts with the C-terminal beta-sheet domain of the GINS51 subunit in the tetrameric GINS complex. The relationship of archaeal and bacterial RecJs, as well as eukaryotic Cdc45, is discussed based on biochemical and structural results.
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Affiliation(s)
- Min-Jun Li
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China
| | - Gang-Shun Yi
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, China
| | - Feng Yu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China
| | - Huan Zhou
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China
| | - Jia-Nan Chen
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, China
| | - Chun-Yan Xu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China
| | - Feng-Ping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, China
| | - Xiang Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, China
| | - Jian-Hua He
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 239 Zhangheng Road, Shanghai 201204, China
| | - Xi-Peng Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, China.,State Key Laboratory of Ocean Engineering, School of Naval Architecture, Ocean and Civil Engineering, Shanghai Jiao Tong University, No. 800 Dongchuan Road, Shanghai 200240, China
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35
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Muenter MM, Aiken A, Akanji JO, Baig S, Bellou S, Carlson A, Conway C, Cowell CM, DeLateur NA, Hester A, Joshi C, Kramer C, Leifer BS, Nash E, Qi MH, Travers M, Wong KC, Hu M, Gou N, Giese RW, Gu AZ, Beuning PJ. The response of Escherichia coli to the alkylating agents chloroacetaldehyde and styrene oxide. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2019; 840:1-10. [PMID: 30857727 DOI: 10.1016/j.mrgentox.2019.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 02/06/2019] [Accepted: 02/06/2019] [Indexed: 10/27/2022]
Abstract
DNA damage is ubiquitous and can arise from endogenous or exogenous sources. DNA-damaging alkylating agents are present in environmental toxicants as well as in cancer chemotherapy drugs and are a constant threat, which can lead to mutations or cell death. All organisms have multiple DNA repair and DNA damage tolerance pathways to resist the potentially negative effects of exposure to alkylating agents. In bacteria, many of the genes in these pathways are regulated as part of the SOS reponse or the adaptive response. In this work, we probed the cellular responses to the alkylating agents chloroacetaldehyde (CAA), which is a metabolite of 1,2-dichloroethane used to produce polyvinyl chloride, and styrene oxide (SO), a major metabolite of styrene used in the production of polystyrene and other polymers. Vinyl chloride and styrene are produced on an industrial scale of billions of kilograms annually and thus have a high potential for environmental exposure. To identify stress response genes in E. coli that are responsible for tolerance to the reactive metabolites CAA and SO, we used libraries of transcriptional reporters and gene deletion strains. In response to both alkylating agents, genes associated with several different stress pathways were upregulated, including protein, membrane, and oxidative stress, as well as DNA damage. E. coli strains lacking genes involved in base excision repair and nucleotide excision repair were sensitive to SO, whereas strains lacking recA and the SOS gene ybfE were sensitive to both alkylating agents tested. This work indicates the varied systems involved in cellular responses to alkylating agents, and highlights the specific DNA repair genes involved in the responses.
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Affiliation(s)
- Mark M Muenter
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Ariel Aiken
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Jadesola O Akanji
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Samir Baig
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Sirine Bellou
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Alyssa Carlson
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Charles Conway
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Courtney M Cowell
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Nicholas A DeLateur
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Alexis Hester
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Christopher Joshi
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Caitlin Kramer
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Becky S Leifer
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Emma Nash
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Macee H Qi
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Meghan Travers
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Kelly C Wong
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA
| | - Man Hu
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, 02115 USA
| | - Na Gou
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, 02115 USA; School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14850, USA
| | - Roger W Giese
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA, 02115 USA
| | - April Z Gu
- Department of Civil and Environmental Engineering, Northeastern University, Boston, MA, 02115 USA; School of Civil and Environmental Engineering, Cornell University, Ithaca, NY, 14850, USA
| | - Penny J Beuning
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA, 02115 USA.
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Weaver GM, Mettrick KA, Corocher TA, Graham A, Grainge I. Replication fork collapse at a protein-DNA roadblock leads to fork reversal, promoted by the RecQ helicase. Mol Microbiol 2018; 111:455-472. [PMID: 30466158 DOI: 10.1111/mmi.14166] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2018] [Indexed: 11/27/2022]
Abstract
Proteins that bind DNA are the cause of the majority of impediments to replication fork progression and can lead to subsequent collapse of the replication fork. Failure to deal with fork collapse efficiently leads to mutation or cell death. Several models have been proposed for how a cell processes a stalled or collapsed replication fork; eukaryotes and bacteria are not dissimilar in terms of the general pathways undertaken to deal with these events. This study shows that replication fork regression, the combination of replication fork reversal leading to formation of a Holliday Junction along with exonuclease digestion, is the preferred pathway for dealing with a collapsed fork in Escherichia coli. Direct endo-nuclease activity at the replication fork was not observed. The protein that had the greatest effect on these fork processing events was the RecQ helicase, while RecG and RuvABC, which have previously been implicated in this process, were found to play a lesser role. Eukaryotic RecQ homologues, BLM and WRN, have also been implicated in processing events following replication fork collapse and may reflect a conserved mechanism. Finally, the SOS response was not induced by the protein-DNA roadblock under these conditions, so did not affect fork processing.
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Affiliation(s)
- Georgia M Weaver
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, Australia
| | - Karla A Mettrick
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, Australia
| | - Tayla-Ann Corocher
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, Australia
| | - Adam Graham
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, Australia
| | - Ian Grainge
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, Australia
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Resistance to UV Irradiation Caused by Inactivation of nurA and herA Genes in Thermus thermophilus. J Bacteriol 2018; 200:JB.00201-18. [PMID: 29844033 DOI: 10.1128/jb.00201-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 05/23/2018] [Indexed: 11/20/2022] Open
Abstract
NurA and HerA are thought to be essential proteins for DNA end resection in archaeal homologous recombination systems. Thermus thermophilus, an extremely thermophilic eubacterium, has proteins that exhibit significant sequence similarity to archaeal NurA and HerA. To unveil the cellular function of NurA and HerA in T. thermophilus, we performed phenotypic analysis of disruptant mutants of nurA and herA with or without DNA-damaging agents. The nurA and herA genes were not essential for survival, and their deletion had no effect on cell growth and genome integrity. Unexpectedly, these disruptants of T. thermophilus showed increased resistance to UV irradiation and mitomycin C treatment. Further, these disruptants and the wild type displayed no difference in sensitivity to oxidative stress and a DNA replication inhibitor. T. thermophilus NurA had nuclease activity, and HerA had ATPase. The overexpression of loss-of-function mutants of nurA and herA in the respective disruptants showed no complementation, suggesting their enzymatic activities were involved in the UV sensitivity. In addition, T. thermophilus NurA and HerA interacted with each other in vitro and in vivo, forming a complex with 2:6 stoichiometry. These results suggest that the NurA-HerA complex has an architecture similar to that of archaeal counterparts but that it impairs, rather than promotes, the repair of photoproducts and DNA cross-links in T. thermophilus cells. This cellular function is distinctly different from that of archaeal NurA and HerA.IMPORTANCE Many nucleases and helicases are engaged in homologous recombination-mediated DNA repair. Previous in vitro analyses in archaea indicated that NurA and HerA are the recombination-related nuclease and helicase. However, their cellular function had not been fully understood, especially in bacterial cells. In this study, we performed in vivo analyses to address the cellular function of nurA and herA in an extremely thermophilic bacterium, Thermus thermophilus As a result, T. thermophilus NurA and HerA exhibited an interfering effect on the repair of several instances of DNA damage in the cell, which is in contrast to the results in archaea. This finding will facilitate our understanding of the diverse cellular functions of the recombination-related nucleases and helicases.
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Mills M, Harami GM, Seol Y, Gyimesi M, Martina M, Kovács ZJ, Kovács M, Neuman KC. RecQ helicase triggers a binding mode change in the SSB-DNA complex to efficiently initiate DNA unwinding. Nucleic Acids Res 2017; 45:11878-11890. [PMID: 29059328 PMCID: PMC5714189 DOI: 10.1093/nar/gkx939] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 09/29/2017] [Accepted: 10/09/2017] [Indexed: 11/12/2022] Open
Abstract
The single-stranded DNA binding protein (SSB) of Escherichia coli plays essential roles in maintaining genome integrity by sequestering ssDNA and mediating DNA processing pathways through interactions with DNA-processing enzymes. Despite its DNA-sequestering properties, SSB stimulates the DNA processing activities of some of its binding partners. One example is the genome maintenance protein RecQ helicase. Here, we determine the mechanistic details of the RecQ-SSB interaction using single-molecule magnetic tweezers and rapid kinetic experiments. Our results reveal that the SSB-RecQ interaction changes the binding mode of SSB, thereby allowing RecQ to gain access to ssDNA and facilitating DNA unwinding. Conversely, the interaction of RecQ with the SSB C-terminal tail increases the on-rate of RecQ-DNA binding and has a modest stimulatory effect on the unwinding rate of RecQ. We propose that this bidirectional communication promotes efficient DNA processing and explains how SSB stimulates rather than inhibits RecQ activity.
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Affiliation(s)
- Maria Mills
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gábor M. Harami
- Department of Biochemistry, ELTE-MTA “Momentum” Motor Enzymology Research Group, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
| | - Yeonee Seol
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Máté Gyimesi
- Department of Biochemistry, ELTE-MTA “Momentum” Motor Enzymology Research Group, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
| | - Máté Martina
- Department of Biochemistry, ELTE-MTA “Momentum” Motor Enzymology Research Group, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
| | - Zoltán J. Kovács
- Department of Biochemistry, ELTE-MTA “Momentum” Motor Enzymology Research Group, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
| | - Mihály Kovács
- Department of Biochemistry, ELTE-MTA “Momentum” Motor Enzymology Research Group, Eötvös Loránd University, Pázmány P. s. 1/c, H-1117 Budapest, Hungary
| | - Keir C. Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Hong Y, Li L, Luan G, Drlica K, Zhao X. Contribution of reactive oxygen species to thymineless death in Escherichia coli. Nat Microbiol 2017; 2:1667-1675. [PMID: 28970486 PMCID: PMC5705385 DOI: 10.1038/s41564-017-0037-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 09/05/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Yuzhi Hong
- Public Health Research Institute and Department of Microbiology, Biochemistry & Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ, 07103, USA
| | - Liping Li
- Public Health Research Institute and Department of Microbiology, Biochemistry & Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ, 07103, USA
| | - Gan Luan
- Public Health Research Institute and Department of Microbiology, Biochemistry & Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ, 07103, USA
| | - Karl Drlica
- Public Health Research Institute and Department of Microbiology, Biochemistry & Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ, 07103, USA
| | - Xilin Zhao
- Public Health Research Institute and Department of Microbiology, Biochemistry & Molecular Genetics, New Jersey Medical School, Rutgers University, 225 Warren Street, Newark, NJ, 07103, USA. .,State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health, Xiamen University, South Xiang-An Road, Xiang-An District, Xiamen, Fujian Province, 361102, China.
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40
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Rogers CM, Wang JCY, Noguchi H, Imasaki T, Takagi Y, Bochman ML. Yeast Hrq1 shares structural and functional homology with the disease-linked human RecQ4 helicase. Nucleic Acids Res 2017; 45:5217-5230. [PMID: 28334827 PMCID: PMC5605238 DOI: 10.1093/nar/gkx151] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 02/22/2017] [Indexed: 12/14/2022] Open
Abstract
The five human RecQ helicases participate in multiple processes required to maintain genome integrity. Of these, the disease-linked RecQ4 is the least studied because it poses many technical challenges. We previously demonstrated that the yeast Hrq1 helicase displays similar functions to RecQ4 in vivo, and here, we report the biochemical and structural characterization of these enzymes. In vitro, Hrq1 and RecQ4 are DNA-stimulated ATPases and robust helicases. Further, these activities were sensitive to DNA sequence and structure, with the helicases preferentially unwinding D-loops. Consistent with their roles at telomeres, telomeric repeat sequence DNA also stimulated binding and unwinding by these enzymes. Finally, electron microscopy revealed that Hrq1 and RecQ4 share similar structural features. These results solidify Hrq1 as a true RecQ4 homolog and position it as the premier model to determine how RecQ4 mutations lead to genomic instability and disease.
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Affiliation(s)
- Cody M Rogers
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
| | | | - Hiroki Noguchi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Tsuyoshi Imasaki
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Yuichiro Takagi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Matthew L Bochman
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, USA
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41
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Đermić E, Zahradka D, Vujaklija D, Ivanković S, Đermić D. 3'-Terminated Overhangs Regulate DNA Double-Strand Break Processing in Escherichia coli. G3 (BETHESDA, MD.) 2017; 7:3091-3102. [PMID: 28710290 PMCID: PMC5592934 DOI: 10.1534/g3.117.043521] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 07/11/2017] [Indexed: 01/18/2023]
Abstract
Double-strand breaks (DSBs) are lethal DNA lesions, which are repaired by homologous recombination in Escherichia coli To study DSB processing in vivo, we induced DSBs into the E. coli chromosome by γ-irradiation and measured chromosomal degradation. We show that the DNA degradation is regulated by RecA protein concentration and its rate of association with single-stranded DNA (ssDNA). RecA decreased DNA degradation in wild-type, recB, and recD strains, indicating that it is a general phenomenon in E. coli On the other hand, DNA degradation was greatly reduced and unaffected by RecA in the recB1080 mutant (which produces long overhangs) and in a strain devoid of four exonucleases that degrade a 3' tail (ssExos). 3'-5' ssExos deficiency is epistatic to RecA deficiency concerning DNA degradation, suggesting that bound RecA is shielding the 3' tail from degradation by 3'-5' ssExos. Since 3' tail preservation is common to all these situations, we infer that RecA polymerization constitutes a subset of mechanisms for preserving the integrity of 3' tails emanating from DSBs, along with 3' tail's massive length, or prevention of their degradation by inactivation of 3'-5' ssExos. Thus, we conclude that 3' overhangs are crucial in controlling the extent of DSB processing in E. coli This study suggests a regulatory mechanism for DSB processing in E. coli, wherein 3' tails impose a negative feedback loop on DSB processing reactions, specifically on helicase reloading onto dsDNA ends.
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Affiliation(s)
- Edyta Đermić
- Department of Plant Pathology, Faculty of Agriculture, University of Zagreb, 10000, Croatia
| | - Davor Zahradka
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Dušica Vujaklija
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Siniša Ivanković
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Damir Đermić
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia
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42
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Two Archaeal RecJ Nucleases from Methanocaldococcus jannaschii Show Reverse Hydrolysis Polarity: Implication to Their Unique Function in Archaea. Genes (Basel) 2017; 8:genes8090211. [PMID: 28837073 PMCID: PMC5615345 DOI: 10.3390/genes8090211] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 08/16/2017] [Accepted: 08/17/2017] [Indexed: 12/05/2022] Open
Abstract
Bacterial nuclease RecJ, which exists in almost all bacterial species, specifically degrades single-stranded (ss) DNA in the 5′ to 3′ direction. Some archaeal phyla, except Crenarchaea, also encode RecJ homologs. Compared with bacterial RecJ, archaeal RecJ exhibits a largely different amino acid sequence and domain organization. Archaeal RecJs from Thermococcus kodakarensis and Pyrococcus furiosus show 5′→3′ exonuclease activity on ssDNA. Interestingly, more than one RecJ exists in some Euryarchaeota classes, such as Methanomicrobia, Methanococci, Methanomicrobia, Methanobacteria, and Archaeoglobi. Here we report the biochemical characterization of two RecJs from Methanocaldococcus jannaschii, the long RecJ1 (MJ0977) and short RecJ2 (MJ0831) to understand their enzymatic properties. RecJ1 is a 5′→3′ exonuclease with a preference to ssDNA; however, RecJ2 is a 3′→5′ exonuclease with a preference to ssRNA. The 5′ terminal phosphate promotes RecJ1 activity, but the 3′ terminal phosphate inhibits RecJ2 nuclease. Go-Ichi-Ni-San (GINS) complex does not interact with two RecJs and does not promote their nuclease activities. Finally, we discuss the diversity, function, and molecular evolution of RecJ in archaeal taxonomy. Our analyses provide insight into the function and evolution of conserved archaeal RecJ/eukaryotic Cdc45 protein.
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43
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Ogino H, Ishino S, Kohda D, Ishino Y. The RecJ2 protein in the thermophilic archaeon Thermoplasma acidophilum is a 3'-5' exonuclease that associates with a DNA replication complex. J Biol Chem 2017; 292:7921-7931. [PMID: 28302716 DOI: 10.1074/jbc.m116.767921] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 03/15/2017] [Indexed: 11/06/2022] Open
Abstract
RecJ/cell division cycle 45 (Cdc45) proteins are widely conserved in the three domains of life, i.e. in bacteria, Eukarya, and Archaea. Bacterial RecJ is a 5'-3' exonuclease and functions in DNA repair pathways by using its 5'-3' exonuclease activity. Eukaryotic Cdc45 has no identified enzymatic activity but participates in the CMG complex, so named because it is composed of Cdc45, minichromosome maintenance protein complex (MCM) proteins 2-7, and GINS complex proteins (Sld5, Psf11-3). Eukaryotic Cdc45 and bacterial/archaeal RecJ share similar amino acid sequences and are considered functional counterparts. In Archaea, a RecJ homolog in Thermococcus kodakarensis was shown to associate with GINS and accelerate its nuclease activity and was, therefore, designated GAN (GINS-associated nuclease); however, to date, no archaeal RecJ·MCM·GINS complex has been isolated. The thermophilic archaeon Thermoplasma acidophilum has two RecJ-like proteins, designated TaRecJ1 and TaRecJ2. TaRecJ1 exhibited DNA-specific 5'-3' exonuclease activity, whereas TaRecJ2 had 3'-5' exonuclease activity and preferred RNA over DNA. TaRecJ2, but not TaRecJ1, formed a stable complex with TaGINS in a 2:1 molar ratio. Furthermore, the TaRecJ2·TaGINS complex stimulated activity of TaMCM (T. acidophilum MCM) helicase in vitro, and the TaRecJ2·TaMCM·TaGINS complex was also observed in vivo However, TaRecJ2 did not interact with TaMCM directly and was not required for the helicase activation in vitro These findings suggest that the function of archaeal RecJ in DNA replication evolved divergently from Cdc45 despite conservation of the CMG-like complex formation between Archaea and Eukarya.
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Affiliation(s)
- Hiromi Ogino
- From the Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashiku, Fukuoka 812-8581, Japan and
| | - Sonoko Ishino
- From the Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashiku, Fukuoka 812-8581, Japan and
| | - Daisuke Kohda
- the Medical Institute of Bioregulation, Kyushu University, 3-1-1, Maidashi, Higashiku, Fukuoka 812-8582, Japan
| | - Yoshizumi Ishino
- From the Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, 6-10-1 Hakozaki, Higashiku, Fukuoka 812-8581, Japan and .,the Medical Institute of Bioregulation, Kyushu University, 3-1-1, Maidashi, Higashiku, Fukuoka 812-8582, Japan
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44
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Shuttling along DNA and directed processing of D-loops by RecQ helicase support quality control of homologous recombination. Proc Natl Acad Sci U S A 2017; 114:E466-E475. [PMID: 28069956 DOI: 10.1073/pnas.1615439114] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cells must continuously repair inevitable DNA damage while avoiding the deleterious consequences of imprecise repair. Distinction between legitimate and illegitimate repair processes is thought to be achieved in part through differential recognition and processing of specific noncanonical DNA structures, although the mechanistic basis of discrimination remains poorly defined. Here, we show that Escherichia coli RecQ, a central DNA recombination and repair enzyme, exhibits differential processing of DNA substrates based on their geometry and structure. Through single-molecule and ensemble biophysical experiments, we elucidate how the conserved domain architecture of RecQ supports geometry-dependent shuttling and directed processing of recombination-intermediate [displacement loop (D-loop)] substrates. Our study shows that these activities together suppress illegitimate recombination in vivo, whereas unregulated duplex unwinding is detrimental for recombination precision. Based on these results, we propose a mechanism through which RecQ helicases achieve recombination precision and efficiency.
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45
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Pavankumar TL, Exell JC, Kowalczykowski SC. Direct Fluorescent Imaging of Translocation and Unwinding by Individual DNA Helicases. Methods Enzymol 2016; 581:1-32. [PMID: 27793277 DOI: 10.1016/bs.mie.2016.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The unique translocation and DNA unwinding properties of DNA helicases can be concealed by the stochastic behavior of enzyme molecules within the necessarily large populations used in ensemble experiments. With recent technological advances, the direct visualization of helicases acting on individual DNA molecules has contributed significantly to the current understanding of their mechanisms of action and biological functions. The combination of single-molecule techniques that enable both manipulation of individual protein or DNA molecules and visualization of their actions has made it possible to literally see novel and unique biochemical characteristics that were previously masked. Here, we describe the execution and use of single-molecule fluorescence imaging techniques, focusing on methods that include optical trapping in conjunction with epifluorescent imaging, and also surface immobilization in conjunction with total internal reflection fluorescence visualization. Combined with microchannel flow cells and microfluidic control, these methods allow individual fluorescently labeled protein and DNA molecules to be imaged and tracked, affording measurement of DNA unwinding and translocation at single-molecule resolution.
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Affiliation(s)
| | - J C Exell
- University of California, Davis, CA, United States
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46
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Rotman E, Webber DM, Seifert HS. Analyzing Neisseria gonorrhoeae Pilin Antigenic Variation Using 454 Sequencing Technology. J Bacteriol 2016; 198:2470-82. [PMID: 27381912 PMCID: PMC4999939 DOI: 10.1128/jb.00330-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 06/28/2016] [Indexed: 01/04/2023] Open
Abstract
UNLABELLED Many pathogens use homologous recombination to vary surface antigens in order to avoid immune surveillance. Neisseria gonorrhoeae, the bacterium responsible for the sexually transmitted infection gonorrhea, achieves this in part by changing the sequence of the major subunit of the type IV pilus in a process termed pilin antigenic variation (Av). The N. gonorrhoeae chromosome contains one expression locus (pilE) and many promoterless, partial-coding silent copies (pilS) that act as reservoirs for variant pilin information. Pilin Av occurs by high-frequency gene conversion reactions, which transfer pilS sequences into the pilE locus. We have developed a 454 sequencing-based assay to analyze the frequency and characteristics of pilin Av that allows a more robust analysis of pilin Av than previous assays. We used this assay to analyze mutations and conditions previously shown to affect pilin Av, confirming many but not all of the previously reported phenotypes. We show that mutations or conditions that cause growth defects can result in Av phenotypes when analyzed by phase variation-based assays. Adapting the 454 sequencing to analyze pilin Av demonstrates the utility of this technology to analyze any diversity generation system that uses recombination to develop biological diversity. IMPORTANCE Measuring and analyzing complex recombination-based systems constitute a major barrier to understanding the mechanisms used to generate diversity. We have analyzed the contributions of many gonococcal mutations or conditions to the process of pilin antigenic variation.
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Affiliation(s)
- Ella Rotman
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | | | - H Steven Seifert
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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47
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Pinto C, Kasaciunaite K, Seidel R, Cejka P. Human DNA2 possesses a cryptic DNA unwinding activity that functionally integrates with BLM or WRN helicases. eLife 2016; 5. [PMID: 27612385 PMCID: PMC5030094 DOI: 10.7554/elife.18574] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 09/08/2016] [Indexed: 12/13/2022] Open
Abstract
Human DNA2 (hDNA2) contains both a helicase and a nuclease domain within the same polypeptide. The nuclease of hDNA2 is involved in a variety of DNA metabolic processes. Little is known about the role of the hDNA2 helicase. Using bulk and single-molecule approaches, we show that hDNA2 is a processive helicase capable of unwinding kilobases of dsDNA in length. The nuclease activity prevents the engagement of the helicase by competing for the same substrate, hence prominent DNA unwinding by hDNA2 alone can only be observed using the nuclease-deficient variant. We show that the helicase of hDNA2 functionally integrates with BLM or WRN helicases to promote dsDNA degradation by forming a heterodimeric molecular machine. This collectively suggests that the hDNA2 motor promotes the enzyme's capacity to degrade dsDNA in conjunction with BLM or WRN and thus promote the repair of broken DNA. DOI:http://dx.doi.org/10.7554/eLife.18574.001
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Affiliation(s)
- Cosimo Pinto
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | | | - Ralf Seidel
- Institute of Experimental Physics I, University of Leipzig, Leipzig, Germany
| | - Petr Cejka
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
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48
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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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49
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Remodeling and Control of Homologous Recombination by DNA Helicases and Translocases that Target Recombinases and Synapsis. Genes (Basel) 2016; 7:genes7080052. [PMID: 27548227 PMCID: PMC4999840 DOI: 10.3390/genes7080052] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 07/24/2016] [Accepted: 08/12/2016] [Indexed: 11/16/2022] Open
Abstract
Recombinase enzymes catalyse invasion of single-stranded DNA (ssDNA) into homologous duplex DNA forming "Displacement loops" (D-loops), a process called synapsis. This triggers homologous recombination (HR), which can follow several possible paths to underpin DNA repair and restart of blocked and collapsed DNA replication forks. Therefore, synapsis can be a checkpoint for controlling whether or not, how far, and by which pathway, HR proceeds to overcome an obstacle or break in a replication fork. Synapsis can be antagonized by limiting access of a recombinase to ssDNA and by dissociation of D-loops or heteroduplex formed by synapsis. Antagonists include DNA helicases and translocases that are identifiable in eukaryotes, bacteria and archaea, and which target synaptic and pre-synaptic DNA structures thereby controlling HR at early stages. Here we survey these events with emphasis on enabling DNA replication to be resumed from sites of blockage or collapse. We also note how knowledge of anti-recombination activities could be useful to improve efficiency of CRISPR-based genome editing.
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Abstract
The repair of DNA by homologous recombination is an essential, efficient, and high-fidelity process that mends DNA lesions formed during cellular metabolism; these lesions include double-stranded DNA breaks, daughter-strand gaps, and DNA cross-links. Genetic defects in the homologous recombination pathway undermine genomic integrity and cause the accumulation of gross chromosomal abnormalities-including rearrangements, deletions, and aneuploidy-that contribute to cancer formation. Recombination proceeds through the formation of joint DNA molecules-homologously paired but metastable DNA intermediates that are processed by several alternative subpathways-making recombination a versatile and robust mechanism to repair damaged chromosomes. Modern biophysical methods make it possible to visualize, probe, and manipulate the individual molecules participating in the intermediate steps of recombination, revealing new details about the mechanics of genetic recombination. We review and discuss the individual stages of homologous recombination, focusing on common pathways in bacteria, yeast, and humans, and place particular emphasis on the molecular mechanisms illuminated by single-molecule methods.
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Affiliation(s)
- Jason C Bell
- Department of Microbiology and Molecular Genetics, and Department of Molecular and Cellular Biology, University of California, Davis, California 95616;
| | - Stephen C Kowalczykowski
- Department of Microbiology and Molecular Genetics, and Department of Molecular and Cellular Biology, University of California, Davis, California 95616;
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