1
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Ren Y, Liao H, Yan J, Lu H, Mao X, Wang C, Li YF, Liu Y, Chen C, Chen L, Wang X, Zhou KY, Liu HM, Liu Y, Hua YM, Yu L, Xue Z. Capture of RNA-binding proteins across mouse tissues using HARD-AP. Nat Commun 2024; 15:8421. [PMID: 39341811 PMCID: PMC11438895 DOI: 10.1038/s41467-024-52765-w] [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: 11/26/2023] [Accepted: 09/20/2024] [Indexed: 10/01/2024] Open
Abstract
RNA-binding proteins (RBPs) modulate all aspects of RNA metabolism, but a comprehensive picture of RBP expression across tissues is lacking. Here, we describe our development of the method we call HARD-AP that robustly retrieves RBPs and tightly associated RNA regulatory complexes from cultured cells and fresh tissues. We successfully use HARD-AP to establish a comprehensive atlas of RBPs across mouse primary organs. We then systematically map RNA-binding sites of these RBPs using machine learning-based modeling. Notably, the modeling reveals that the LIM domain as an RNA-binding domain in many RBPs. We validate the LIM-domain-only protein Csrp1 as a tissue-dependent RNA binding protein. Taken together, HARD-AP is a powerful approach that can be used to identify RBPomes from any type of sample, allowing comprehensive and physiologically relevant networks of RNA-protein interactions.
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Affiliation(s)
- Yijia Ren
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Hongyu Liao
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jun Yan
- National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Hongyu Lu
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xiaowei Mao
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, China
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, 611731, China
- Shimmer Center, Tianfu Jiangxi Laboratory, Chengdu, Sichuan, 641419, China
| | - Chuan Wang
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yi-Fei Li
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yu Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Chong Chen
- Department of Urology, Institute of Urology, State Key Laboratory of Biotherapy and Cancer Center, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Lu Chen
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xiangfeng Wang
- National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Kai-Yu Zhou
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Han-Min Liu
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yi-Min Hua
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Lin Yu
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Zhihong Xue
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China.
- Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Chengdu, Sichuan, 610041, China.
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2
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Xiao Y, Jiang Z, Zhang M, Zhang X, Gan Q, Yang Y, Wu P, Feng X, Ni J, Dong X, She Q, Huang Q, Shen Y. The canonical single-stranded DNA-binding protein is not an essential replication factor but an RNA chaperon in Saccharolobus islandicus. iScience 2023; 26:108389. [PMID: 38034349 PMCID: PMC10684826 DOI: 10.1016/j.isci.2023.108389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/28/2023] [Accepted: 11/01/2023] [Indexed: 12/02/2023] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) have been regarded as indispensable replication factors. Herein, we report that the genes encoding the canonical SSB (SisSSB) and the non-canonical SSB (SisDBP) in Saccharolobus islandicus REY15A are not essential for cell viability. Interestingly, at a lower temperature (55°C), the protein level of SisSSB increases and the growth of ΔSisssb and ΔSisssbΔSisdbp is retarded. SisSSB exhibits melting activity on dsRNA and DNA/RNA hybrid in vitro and is able to melt RNA hairpin in Escherichia coli. Furthermore, the core SisSSB domain is able to complement the absence of cold-shock proteins in E. coli. Importantly, these activities are conserved in the canonical SSBs from Crenarchaeota species that lack bacterial Csp homologs. Overall, our study has clarified the function of the archaeal canonical SSBs which do not function as a DNA-processing factor, but play a role in the processes requiring melting of dsRNA or DNA/RNA hybrid.
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Affiliation(s)
- Yuanxi Xiao
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Zhichao Jiang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Mengqi Zhang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Xuemei Zhang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Qi Gan
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Yunfeng Yang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Pengju Wu
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Xu Feng
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Jinfeng Ni
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qunxin She
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Qihong Huang
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
| | - Yulong Shen
- CRISPR and Archaea Biology Research Center, State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao 266237, China
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3
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Madru C, Martínez-Carranza M, Laurent S, Alberti AC, Chevreuil M, Raynal B, Haouz A, Le Meur RA, Delarue M, Henneke G, Flament D, Krupovic M, Legrand P, Sauguet L. DNA-binding mechanism and evolution of replication protein A. Nat Commun 2023; 14:2326. [PMID: 37087464 PMCID: PMC10122647 DOI: 10.1038/s41467-023-38048-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/13/2023] [Indexed: 04/24/2023] Open
Abstract
Replication Protein A (RPA) is a heterotrimeric single stranded DNA-binding protein with essential roles in DNA replication, recombination and repair. Little is known about the structure of RPA in Archaea, the third domain of life. By using an integrative structural, biochemical and biophysical approach, we extensively characterize RPA from Pyrococcus abyssi in the presence and absence of DNA. The obtained X-ray and cryo-EM structures reveal that the trimerization core and interactions promoting RPA clustering on ssDNA are shared between archaea and eukaryotes. However, we also identified a helical domain named AROD (Acidic Rpa1 OB-binding Domain), and showed that, in Archaea, RPA forms an unanticipated tetrameric supercomplex in the absence of DNA. The four RPA molecules clustered within the tetramer could efficiently coat and protect stretches of ssDNA created by the advancing replisome. Finally, our results provide insights into the evolution of this primordial replication factor in eukaryotes.
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Affiliation(s)
- Clément Madru
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Markel Martínez-Carranza
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Sébastien Laurent
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), F-29280, Plouzané, France
| | - Alessandra C Alberti
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Maelenn Chevreuil
- Molecular Biophysics Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Bertrand Raynal
- Molecular Biophysics Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Ahmed Haouz
- Crystallography Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Rémy A Le Meur
- Biological NMR Platform & HDX, C2RT, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Marc Delarue
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
| | - Ghislaine Henneke
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), F-29280, Plouzané, France
| | - Didier Flament
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), F-29280, Plouzané, France
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université Paris Cité, CNRS, UMR 6047, Paris, France
| | - Pierre Legrand
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France
- Synchrotron SOLEIL, HelioBio group, L'Orme des Merisiers, 91190, Saint-Aubin, France
| | - Ludovic Sauguet
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS, UMR 3528, Paris, France.
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4
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The Impact of Single-Stranded DNA-Binding Protein SSB and Putative SSB-Interacting Proteins on Genome Integrity in the Thermophilic Crenarchaeon Sulfolobus acidocaldarius. Int J Mol Sci 2023; 24:ijms24054558. [PMID: 36901989 PMCID: PMC10003305 DOI: 10.3390/ijms24054558] [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: 01/23/2023] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
The study of DNA repair in hyperthermophiles has the potential to elucidate the mechanisms of genome integrity maintenance systems under extreme conditions. Previous biochemical studies have suggested that the single-stranded DNA-binding protein (SSB) from the hyperthermophilic crenarchaeon Sulfolobus is involved in the maintenance of genome integrity, namely, in mutation avoidance, homologous recombination (HR), and the repair of helix-distorting DNA lesions. However, no genetic study has been reported that elucidates whether SSB actually maintains genome integrity in Sulfolobus in vivo. Here, we characterized mutant phenotypes of the ssb-deleted strain Δssb in the thermophilic crenarchaeon S. acidocaldarius. Notably, an increase (29-fold) in mutation rate and a defect in HR frequency was observed in Δssb, indicating that SSB was involved in mutation avoidance and HR in vivo. We characterized the sensitivities of Δssb, in parallel with putative SSB-interacting protein-encoding gene-deleted strains, to DNA-damaging agents. The results showed that not only Δssb but also Δalhr1 and ΔSaci_0790 were markedly sensitive to a wide variety of helix-distorting DNA-damaging agents, indicating that SSB, a novel helicase SacaLhr1, and a hypothetical protein Saci_0790, were involved in the repair of helix-distorting DNA lesions. This study expands our knowledge of the impact of SSB on genome integrity and identifies novel and key proteins for genome integrity in hyperthermophilic archaea in vivo.
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5
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Lee JH. New Understandings from the Biophysical Study of the Structure, Dynamics, and Function of Nucleic Acids 2.0. Int J Mol Sci 2022; 23:ijms232415822. [PMID: 36555459 PMCID: PMC9781435 DOI: 10.3390/ijms232415822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
Nucleic acids play an essential role in all biological processes related to genetic information, such as replication, transcription, translation, repair, and recombination [...].
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Affiliation(s)
- Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Jinju 52828, Gyeongnam, Republic of Korea
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6
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Tian L, Zhu K, Chen Y, Zheng X, Zhang H, Geng Z, Li W, Ding N, Chen J, Dong Y, Cao P, Gong Y, Zhang Z. Biochemical and structural characterization of a KTSC family single-stranded DNA-binding protein from Euryarchaea. Int J Biol Macromol 2022; 216:618-628. [PMID: 35809674 DOI: 10.1016/j.ijbiomac.2022.07.015] [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: 04/14/2022] [Revised: 06/24/2022] [Accepted: 07/03/2022] [Indexed: 11/05/2022]
Abstract
The lysine (K) tRNA synthetase C-terminal (KTSC) domain containing proteins are widely spread in Bacteria, Archaea and Viruses, but the function of this short domain is unclear. The occurrence of the fusion of KTSC domain to a catalytic domain or domains related to DNA or RNA metabolisms suggests its potential role in DNA or RNA binding. Here, we report the characterization of Mvu8s from Methanolobus vulcani, which consists of a single KTSC domain. Mvu8s binds specifically to ssDNA with an affinity approximately 40- and 10-fold higher than those for dsDNA and ssRNA in vitro, respectively. It shows a slight preference to the G-rich DNA sequence but barely binds the A-stretch. Crystal structure of Mvu8s shows that it forms a homo-tetramer, with each monomer composed of a four-strand antiparallel β-sheet and a helix-turn-helix in the order of β1-β2-β3-α1-α2-β4. Four basic residues (R3, R7, K54 and K58) were found to serve important roles in ssDNA-binding. And, the spiral arrangement of the DNA interfaces in Mvu8s homo-tetramer presumably results in ssDNA wrapping. Our results not only offer clues of the functions of the KTSC domain containing proteins but also expand our knowledge on the non-oligonucleotide-binding (OB) fold single-stranded DNA-binding proteins in Archaea.
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Affiliation(s)
- Lei Tian
- Department of General Surgery & Institute of General Surgery, Chinese PLA General Hospital First Medical Center, Beijing 100853, China
| | - Keli Zhu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China; Center for Multi-disciplinary Research, Institute of High Energy Physics, Chinese Academy of Sciences, 19B YuquanLu, Shijingshan District, Beijing 100049, China; Institute of Physical Science and Information Technology, Anhui University, China
| | - Yuanyuan Chen
- The Research Platform for Protein Sciences, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Xiaowei Zheng
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Heng Zhang
- Center for Multi-disciplinary Research, Institute of High Energy Physics, Chinese Academy of Sciences, 19B YuquanLu, Shijingshan District, Beijing 100049, China
| | - Zhi Geng
- Center for Multi-disciplinary Research, Institute of High Energy Physics, Chinese Academy of Sciences, 19B YuquanLu, Shijingshan District, Beijing 100049, China
| | - Wenqian Li
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture, College of Food Science and Nutrition-al Engineering, China Agricultural University, Beijing, 100083, China
| | - Niannian Ding
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China
| | - Jingyu Chen
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture, College of Food Science and Nutrition-al Engineering, China Agricultural University, Beijing, 100083, China
| | - Yuhui Dong
- Center for Multi-disciplinary Research, Institute of High Energy Physics, Chinese Academy of Sciences, 19B YuquanLu, Shijingshan District, Beijing 100049, China
| | - Peng Cao
- Faculty of Environment and Life, Beijing University of Technology, 100 Pingleyuan, Chaoyang District, Beijing 100124, China.
| | - Yong Gong
- Center for Multi-disciplinary Research, Institute of High Energy Physics, Chinese Academy of Sciences, 19B YuquanLu, Shijingshan District, Beijing 100049, China.
| | - Zhenfeng Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China.
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7
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Lin ES, Huang YH, Luo RH, Basharat Z, Huang CY. Crystal Structure of an SSB Protein from Salmonella enterica and Its Inhibition by Flavanonol Taxifolin. Int J Mol Sci 2022; 23:ijms23084399. [PMID: 35457218 PMCID: PMC9029707 DOI: 10.3390/ijms23084399] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 12/13/2022] Open
Abstract
Single-stranded DNA (ssDNA)-binding proteins (SSBs) play a central role in cells by participating in DNA metabolism, including replication, repair, recombination, and replication fork restart. SSBs are essential for cell survival and thus an attractive target for potential anti-pathogen chemotherapy. In this study, we determined the crystal structure and examined the size of the ssDNA-binding site of an SSB from Salmonella enterica serovar Typhimurium LT2 (SeSSB), a ubiquitous opportunistic pathogen which is highly resistant to antibiotics. The crystal structure was solved at a resolution of 2.8 Å (PDB ID 7F25), indicating that the SeSSB monomer possesses an oligonucleotide/oligosaccharide-binding (OB) fold domain at its N-terminus and a flexible tail at its C-terminus. The core of the OB-fold in the SeSSB is made of a six-stranded β-barrel capped by an α-helix. The crystal structure of the SeSSB contained two monomers per asymmetric unit, which may indicate the formation of a dimer. However, the gel-filtration chromatography analysis showed that the SeSSB forms a tetramer in solution. Through an electrophoretic mobility shift analysis, we characterized the stoichiometry of the SeSSB complexed with a series of ssDNA dA homopolymers, and the size of the ssDNA-binding site was determined to be around 22 nt. We also found the flavanonol taxifolin, also known as dihydroquercetin, capable of inhibiting the ssDNA-binding activity of the SeSSB. Thus, this result extended the SSB interactome to include taxifolin, a natural product with a wide range of promising pharmacological activities.
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Affiliation(s)
- En-Shyh Lin
- Department of Beauty Science, National Taichung University of Science and Technology, No. 193, Sec.1, San min Rd., Taichung City 403, Taiwan;
| | - Yen-Hua Huang
- Department of Biomedical Sciences, Chung Shan Medical University, No. 110, Sec.1, Chien-Kuo N. Rd., Taichung City 402, Taiwan; (Y.-H.H.); (R.-H.L.)
| | - Ren-Hong Luo
- Department of Biomedical Sciences, Chung Shan Medical University, No. 110, Sec.1, Chien-Kuo N. Rd., Taichung City 402, Taiwan; (Y.-H.H.); (R.-H.L.)
| | - Zarrin Basharat
- Jamil–ur–Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan;
| | - Cheng-Yang Huang
- Department of Biomedical Sciences, Chung Shan Medical University, No. 110, Sec.1, Chien-Kuo N. Rd., Taichung City 402, Taiwan; (Y.-H.H.); (R.-H.L.)
- Department of Medical Research, Chung Shan Medical University Hospital, No. 110, Sec.1, Chien-Kuo N. Rd., Taichung City 402, Taiwan
- Correspondence:
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8
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Huang C, Liu X, Chen Y, Zhou J, Li W, Ding N, Huang L, Chen J, Zhang Z. A Novel Family of Winged-Helix Single-Stranded DNA-Binding Proteins from Archaea. Int J Mol Sci 2022; 23:ijms23073455. [PMID: 35408816 PMCID: PMC8998557 DOI: 10.3390/ijms23073455] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 02/04/2023] Open
Abstract
The winged helix superfamily comprises a large number of structurally related nucleic acid-binding proteins. While these proteins are often shown to bind dsDNA, few are known to bind ssDNA. Here, we report the identification and characterization of Sul7s, a novel winged-helix single-stranded DNA binding protein family highly conserved in Sulfolobaceae. Sul7s from Sulfolobus islandicus binds ssDNA with an affinity approximately 15-fold higher than that for dsDNA in vitro. It prefers binding oligo(dT)30 over oligo(dC)30 or a dG-rich 30-nt oligonucleotide, and barely binds oligo(dA)30. Further, binding by Sul7s inhibits DNA strand annealing, but shows little effect on the melting temperature of DNA duplexes. The solution structure of Sul7s determined by NMR shows a winged helix-turn-helix fold, consisting of three α-helices, three β-strands, and two short wings. It interacts with ssDNA via a large positively charged binding surface, presumably resulting in ssDNA deformation. Our results shed significant light on not only non-OB fold single-stranded DNA binding proteins in Archaea, but also the divergence of the winged-helix proteins in both function and structure during evolution.
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Affiliation(s)
- Can Huang
- MOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (C.H.); (W.L.)
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China; (J.Z.); (N.D.); (L.H.)
| | - Xuehui Liu
- The Research Platform for Protein Sciences, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; (X.L.); (Y.C.)
| | - Yuanyuan Chen
- The Research Platform for Protein Sciences, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; (X.L.); (Y.C.)
| | - Junshi Zhou
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China; (J.Z.); (N.D.); (L.H.)
| | - Wenqian Li
- MOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (C.H.); (W.L.)
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China; (J.Z.); (N.D.); (L.H.)
| | - Niannian Ding
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China; (J.Z.); (N.D.); (L.H.)
| | - Li Huang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China; (J.Z.); (N.D.); (L.H.)
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingyu Chen
- MOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (C.H.); (W.L.)
- Correspondence: (J.C.); (Z.Z.); Tel.: +86-10-64806988 (Z.Z.)
| | - Zhenfeng Zhang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China; (J.Z.); (N.D.); (L.H.)
- College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence: (J.C.); (Z.Z.); Tel.: +86-10-64806988 (Z.Z.)
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9
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Yang MJ, Kim J, Lee Y, Lee W, Park CJ. NMR Structure and Biophysical Characterization of Thermophilic Single-Stranded DNA Binding Protein from Sulfolobus Solfataricus. Int J Mol Sci 2022; 23:ijms23063099. [PMID: 35328522 PMCID: PMC8954794 DOI: 10.3390/ijms23063099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/09/2022] [Accepted: 03/10/2022] [Indexed: 12/31/2022] Open
Abstract
Proteins from Sulfolobus solfataricus (S. solfataricus), an extremophile, are active even at high temperatures. The single-stranded DNA (ssDNA) binding protein of S. solfataricus (SsoSSB) is overexpressed to protect ssDNA during DNA metabolism. Although SsoSSB has the potential to be applied in various areas, its structural and ssDNA binding properties at high temperatures have not been studied. We present the solution structure, backbone dynamics, and ssDNA binding properties of SsoSSB at 50 °C. The overall structure is consistent with the structures previously studied at room temperature. However, the loop between the first two β sheets, which is flexible and is expected to undergo conformational change upon ssDNA binding, shows a difference from the ssDNA bound structure. The ssDNA binding ability was maintained at high temperature, but different interactions were observed depending on the temperature. Backbone dynamics at high temperature showed that the rigidity of the structured region was well maintained. The investigation of an N-terminal deletion mutant revealed that it is important for maintaining thermostability, structure, and ssDNA binding ability. The structural and dynamic properties of SsoSSB observed at high temperature can provide information on the behavior of proteins in thermophiles at the molecular level and guide the development of new experimental techniques.
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Affiliation(s)
- Min June Yang
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea; (M.J.Y.); (J.K.)
| | - Jinwoo Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea; (M.J.Y.); (J.K.)
| | - Yeongjoon Lee
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA;
| | - Woonghee Lee
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA;
- Correspondence: (W.L.); (C.-J.P.); Tel.: +1-303-315-7672 (W.L.); +82-62-715-3630 (C.-J.P.)
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea; (M.J.Y.); (J.K.)
- Correspondence: (W.L.); (C.-J.P.); Tel.: +1-303-315-7672 (W.L.); +82-62-715-3630 (C.-J.P.)
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10
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Matsuda R, Suzuki S, Kurosawa N. Genetic Study of Four Candidate Holliday Junction Processing Proteins in the Thermophilic Crenarchaeon Sulfolobus acidocaldarius. Int J Mol Sci 2022; 23:ijms23020707. [PMID: 35054893 PMCID: PMC8775617 DOI: 10.3390/ijms23020707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/24/2021] [Accepted: 01/06/2022] [Indexed: 02/01/2023] Open
Abstract
Homologous recombination (HR) is thought to be important for the repair of stalled replication forks in hyperthermophilic archaea. Previous biochemical studies identified two branch migration helicases (Hjm and PINA) and two Holliday junction (HJ) resolvases (Hjc and Hje) as HJ-processing proteins; however, due to the lack of genetic evidence, it is still unclear whether these proteins are actually involved in HR in vivo and how their functional relation is associated with the process. To address the above questions, we constructed hjc-, hje-, hjm-, and pina single-knockout strains and double-knockout strains of the thermophilic crenarchaeon Sulfolobus acidocaldarius and characterized the mutant phenotypes. Notably, we succeeded in isolating the hjm- and/or pina-deleted strains, suggesting that the functions of Hjm and PINA are not essential for cellular growth in this archaeon, as they were previously thought to be essential. Growth retardation in Δpina was observed at low temperatures (cold sensitivity). When deletion of the HJ resolvase genes was combined, Δpina Δhjc and Δpina Δhje exhibited severe cold sensitivity. Δhjm exhibited severe sensitivity to interstrand crosslinkers, suggesting that Hjm is involved in repairing stalled replication forks, as previously demonstrated in euryarchaea. Our findings suggest that the function of PINA and HJ resolvases is functionally related at lower temperatures to support robust cellular growth, and Hjm is important for the repair of stalled replication forks in vivo.
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A Complexed Crystal Structure of a Single-Stranded DNA-Binding Protein with Quercetin and the Structural Basis of Flavonol Inhibition Specificity. Int J Mol Sci 2022; 23:ijms23020588. [PMID: 35054774 PMCID: PMC8775380 DOI: 10.3390/ijms23020588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/29/2021] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
Single-stranded DNA (ssDNA)-binding protein (SSB) plays a crucial role in DNA replication, repair, and recombination as well as replication fork restarts. SSB is essential for cell survival and, thus, is an attractive target for potential antipathogen chemotherapy. Whether naturally occurring products can inhibit SSB remains unknown. In this study, the effect of the flavonols myricetin, quercetin, kaempferol, and galangin on the inhibition of Pseudomonas aeruginosa SSB (PaSSB) was investigated. Furthermore, SSB was identified as a novel quercetin-binding protein. Through an electrophoretic mobility shift analysis, myricetin could inhibit the ssDNA binding activity of PaSSB with an IC50 of 2.8 ± 0.4 μM. The effect of quercetin, kaempferol, and galangin was insignificant. To elucidate the flavonol inhibition specificity, the crystal structure of PaSSB complexed with the non-inhibitor quercetin was solved using the molecular replacement method at a resolution of 2.3 Å (PDB entry 7VUM) and compared with a structure with the inhibitor myricetin (PDB entry 5YUN). Although myricetin and quercetin bound PaSSB at a similar site, their binding poses were different. Compared with myricetin, the aromatic ring of quercetin shifted by a distance of 4.9 Å and an angle of 31° for hydrogen bonding to the side chain of Asn108 in PaSSB. In addition, myricetin occupied and interacted with the ssDNA binding sites Lys7 and Glu80 in PaSSB whereas quercetin did not. This result might explain why myricetin could, but quercetin could not, strongly inhibit PaSSB. This molecular evidence reveals the flavonol inhibition specificity and also extends the interactomes of the natural anticancer products myricetin and quercetin to include the OB-fold protein SSB.
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12
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Genetic and Biochemical Characterizations of aLhr1 Helicase in the Thermophilic Crenarchaeon Sulfolobus acidocaldarius. Catalysts 2021. [DOI: 10.3390/catal12010034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Homologous recombination (HR) refers to the process of information exchange between homologous DNA duplexes and is composed of four main steps: end resection, strand invasion and formation of a Holliday junction (HJ), branch migration, and resolution of the HJ. Within each step of HR in Archaea, the helicase-promoting branch migration is not fully understood. Previous biochemical studies identified three candidates for archaeal helicase promoting branch migration in vitro: Hjm/Hel308, PINA, and archaeal long helicase related (aLhr) 2. However, there is no direct evidence of their involvement in HR in vivo. Here, we identified a novel helicase encoded by Saci_0814, isolated from the thermophilic crenarchaeon Sulfolobus acidocaldarius; the helicase dissociated a synthetic HJ. Notably, HR frequency in the Saci_0814-deleted strain was lower than that of the parent strain (5-fold decrease), indicating that Saci_0814 may be involved in HR in vivo. Saci_0814 is classified as an aLhr1 under superfamily 2 helicases; its homologs are conserved among Archaea. Purified protein produced in Escherichia coli showed branch migration activity in vitro. Based on both genetic and biochemical evidence, we suggest that aLhr1 is involved in HR and may function as a branch migration helicase in S. acidocaldarius.
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Lin ES, Huang YH, Huang CY. Characterization of the Chimeric PriB-SSBc Protein. Int J Mol Sci 2021; 22:ijms221910854. [PMID: 34639195 PMCID: PMC8509808 DOI: 10.3390/ijms221910854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 01/27/2023] Open
Abstract
PriB is a primosomal protein required for the replication fork restart in bacteria. Although PriB shares structural similarity with SSB, they bind ssDNA differently. SSB consists of an N-terminal ssDNA-binding/oligomerization domain (SSBn) and a flexible C-terminal protein–protein interaction domain (SSBc). Apparently, the largest difference in structure between PriB and SSB is the lack of SSBc in PriB. In this study, we produced the chimeric PriB-SSBc protein in which Klebsiella pneumoniae PriB (KpPriB) was fused with SSBc of K. pneumoniae SSB (KpSSB) to characterize the possible SSBc effects on PriB function. The crystal structure of KpSSB was solved at a resolution of 2.3 Å (PDB entry 7F2N) and revealed a novel 114-GGRQ-117 motif in SSBc that pre-occupies and interacts with the ssDNA-binding sites (Asn14, Lys74, and Gln77) in SSBn. As compared with the ssDNA-binding properties of KpPriB, KpSSB, and PriB-SSBc, we observed that SSBc could significantly enhance the ssDNA-binding affinity of PriB, change the binding behavior, and further stimulate the PriA activity (an initiator protein in the pre-primosomal step of DNA replication), but not the oligomerization state, of PriB. Based on these experimental results, we discuss reasons why the properties of PriB can be retrofitted when fusing with SSBc.
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Affiliation(s)
- En-Shyh Lin
- Department of Beauty Science, National Taichung University of Science and Technology, No. 193, Sec.1, San-Min Rd., Taichung City 403, Taiwan;
| | - Yen-Hua Huang
- School of Biomedical Sciences, Chung Shan Medical University, No. 110, Sec.1, Chien-Kuo N. Rd., Taichung City 402, Taiwan;
| | - Cheng-Yang Huang
- School of Biomedical Sciences, Chung Shan Medical University, No. 110, Sec.1, Chien-Kuo N. Rd., Taichung City 402, Taiwan;
- Department of Medical Research, Chung Shan Medical University Hospital, No. 110, Sec.1, Chien-Kuo N. Rd., Taichung City 402, Taiwan
- Correspondence:
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14
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Andreassen PR, Seo J, Wiek C, Hanenberg H. Understanding BRCA2 Function as a Tumor Suppressor Based on Domain-Specific Activities in DNA Damage Responses. Genes (Basel) 2021; 12:genes12071034. [PMID: 34356050 PMCID: PMC8307705 DOI: 10.3390/genes12071034] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/23/2021] [Accepted: 06/29/2021] [Indexed: 01/14/2023] Open
Abstract
BRCA2 is an essential genome stability gene that has various functions in cells, including roles in homologous recombination, G2 checkpoint control, protection of stalled replication forks, and promotion of cellular resistance to numerous types of DNA damage. Heterozygous mutation of BRCA2 is associated with an increased risk of developing cancers of the breast, ovaries, pancreas, and other sites, thus BRCA2 acts as a classic tumor suppressor gene. However, understanding BRCA2 function as a tumor suppressor is severely limited by the fact that ~70% of the encoded protein has not been tested or assigned a function in the cellular DNA damage response. Remarkably, even the specific role(s) of many known domains in BRCA2 are not well characterized, predominantly because stable expression of the very large BRCA2 protein in cells, for experimental purposes, is challenging. Here, we review what is known about these domains and the assay systems that are available to study the cellular roles of BRCA2 domains in DNA damage responses. We also list criteria for better testing systems because, ultimately, functional assays for assessing the impact of germline and acquired mutations identified in genetic screens are important for guiding cancer prevention measures and for tailored cancer treatments.
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Affiliation(s)
- Paul R. Andreassen
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA;
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
- Correspondence: ; Tel.: +1-(513)-636-0499
| | - Joonbae Seo
- Division of Experimental Hematology and Cancer Biology, Cancer and Blood Diseases Institute, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA;
| | - Constanze Wiek
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich Heine University, 40225 Düsseldorf, Germany; (C.W.); (H.H.)
| | - Helmut Hanenberg
- Department of Otorhinolaryngology and Head/Neck Surgery, Heinrich Heine University, 40225 Düsseldorf, Germany; (C.W.); (H.H.)
- Department of Pediatrics III, Children’s Hospital, University of Duisburg-Essen, 45122 Essen, Germany
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15
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Yang MJ, Lee W, Park CJ. Resonance assignments and secondary structure of thermophile single-stranded DNA binding protein from Sulfolobus solfataricus at 323K. BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:159-164. [PMID: 33405014 DOI: 10.1007/s12104-020-09999-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Single-stranded DNA (ssDNA)-binding proteins (SSBs) are essential for DNA replication, recombination, and repair processes in all organisms. Sulfolobus solfataricus (S. solfataricus), a hyperthermophilic species, overexpresses its SSB (S. solfataricus SSB (SsoSSB)) to protect ssDNA during DNA metabolisms. Even though the crystal structure of apo SsoSSB and its ssDNA-bound solution structure have been reported at room temperature, structural information at high temperature is not yet available. To find out how SsoSSB maintains its structure and ssDNA binding affinity at high temperatures, we performed multidimensional NMR experiments for SsoSSB at 323K. In this study, we present the backbone and side chain chemical shifts and predict the secondary structure of SsoSSB from the chemical shifts. We found that SsoSSB is ordered, even at high temperatures, and has the same fold at high temperature as at room temperature. Our data will help improve structural analyses and our understanding of the features of thermophilic proteins.
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Affiliation(s)
- Min June Yang
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 61005, Korea
| | - Woonghee Lee
- Department of Chemistry, University of Colorado Denver, Denver, CO, 80217-3364, USA.
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 61005, Korea.
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16
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Abstract
Single-stranded (ss) DNA-binding proteins are found in all three domains of life where they play vital roles in nearly all aspects of DNA metabolism by binding to and stabilizing exposed ssDNA and acting as platforms onto which DNA-processing activities can assemble. The ssDNA-binding factors SSB and RPA are extremely well conserved across bacteria and eukaryotes, respectively, and comprise one or more OB-fold ssDNA-binding domains. In the third domain of life, the archaea, multiple types of ssDNA-binding protein are found with a variety of domain architectures and subunit compositions, with OB-fold ssDNA-binding domains being a characteristic of most, but not all. This chapter summarizes current knowledge of the distribution, structure, and biological function of the archaeal ssDNA-binding factors, highlighting key features shared between clades and those that distinguish the proteins of different clades from one another. The likely cellular functions of the proteins are discussed and gaps in current knowledge identified.
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Affiliation(s)
- Najwa Taib
- Unit Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, Paris, France
- Hub Bioinformatics and Biostatistics, Department of Computational Biology, Institut Pasteur, Paris, France
| | - Simonetta Gribaldo
- Unit Evolutionary Biology of the Microbial Cell, Department of Microbiology, Institut Pasteur, Paris, France
| | - Stuart A MacNeill
- Biomedical Sciences Research Complex, School of Biology, University of St Andrews, St Andrews, UK.
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17
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Oliveira MT, Ciesielski GL. The Essential, Ubiquitous Single-Stranded DNA-Binding Proteins. Methods Mol Biol 2021; 2281:1-21. [PMID: 33847949 DOI: 10.1007/978-1-0716-1290-3_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Maintenance of genomes is fundamental for all living organisms. The diverse processes related to genome maintenance entail the management of various intermediate structures, which may be deleterious if unresolved. The most frequent intermediate structures that result from the melting of the DNA duplex are single-stranded (ss) DNA stretches. These are thermodynamically less stable and can spontaneously fold into secondary structures, which may obstruct a variety of genome processes. In addition, ssDNA is more prone to breaking, which may lead to the formation of deletions or DNA degradation. Single-stranded DNA-binding proteins (SSBs) bind and stabilize ssDNA, preventing the abovementioned deleterious consequences and recruiting the appropriate machinery to resolve that intermediate molecule. They are present in all forms of life and are essential for their viability, with very few exceptions. Here we present an introductory chapter to a volume of the Methods in Molecular Biology dedicated to SSBs, in which we provide a general description of SSBs from various taxa.
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Affiliation(s)
- Marcos T Oliveira
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil
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18
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Amir M, Mohammad T, Dohare R, Islam A, Ahmad F, Imtaiyaz Hassan M. Structure, function and therapeutic implications of OB-fold proteins: A lesson from past to present. Brief Funct Genomics 2020; 19:377-389. [PMID: 32393969 DOI: 10.1093/bfgp/elaa008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Oligonucleotide/oligosaccharide-binding (OB)-fold proteins play essential roles in the regulation of genome and its correct transformation to the subsequent generation. To maintain the genomic stability, OB-fold proteins are implicated in various cellular processes including DNA replication, DNA repair, cell cycle regulation and maintenance of telomere. The diverse functional spectrums of OB-fold proteins are mainly due to their involvement in protein-DNA and protein-protein complexes. Mutations and consequential structural alteration in the OB-fold proteins often lead to severe diseases. Here, we have investigated the structure, function and mode of action of OB-fold proteins (RPA, BRCA2, DNA ligases and SSBs1/2) in cellular pathways and their relationship with diseases and their possible use in therapeutic intervention. Due to the crucial role of OB-fold proteins in regulating the key physiological process, a detailed structural understanding in the context of underlying mechanism of action and cellular complexity offers a new avenue to target OB-proteins for therapeutic intervention.
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19
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Tan C, Wang T, Yang W, Deng L. PredPSD: A Gradient Tree Boosting Approach for Single-Stranded and Double-Stranded DNA Binding Protein Prediction. Molecules 2019; 25:molecules25010098. [PMID: 31888057 PMCID: PMC6982935 DOI: 10.3390/molecules25010098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 12/20/2019] [Accepted: 12/21/2019] [Indexed: 11/16/2022] Open
Abstract
Interactions between proteins and DNAs play essential roles in many biological processes. DNA binding proteins can be classified into two categories. Double-stranded DNA-binding proteins (DSBs) bind to double-stranded DNA and are involved in a series of cell functions such as gene expression and regulation. Single-stranded DNA-binding proteins (SSBs) are necessary for DNA replication, recombination, and repair and are responsible for binding to the single-stranded DNA. Therefore, the effective classification of DNA-binding proteins is helpful for functional annotations of proteins. In this work, we propose PredPSD, a computational method based on sequence information that accurately predicts SSBs and DSBs. It introduces three novel feature extraction algorithms. In particular, we use the autocross-covariance (ACC) transformation to transform feature matrices into fixed-length vectors. Then, we put the optimal feature subset obtained by the minimal-redundancy-maximal-relevance criterion (mRMR) feature selection algorithm into the gradient tree boosting (GTB). In 10-fold cross-validation based on a benchmark dataset, PredPSD achieves promising performances with an AUC score of 0.956 and an accuracy of 0.912, which are better than those of existing methods. Moreover, our method has significantly improved the prediction accuracy in independent testing. The experimental results show that PredPSD can significantly recognize the binding specificity and differentiate DSBs and SSBs.
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Affiliation(s)
- Changgeng Tan
- School of Computer Science and Engineering, Central South University, Changsha 410075, China; (C.T.); (T.W.); (W.Y.)
| | - Tong Wang
- School of Computer Science and Engineering, Central South University, Changsha 410075, China; (C.T.); (T.W.); (W.Y.)
| | - Wenyi Yang
- School of Computer Science and Engineering, Central South University, Changsha 410075, China; (C.T.); (T.W.); (W.Y.)
| | - Lei Deng
- School of Computer Science and Engineering, Central South University, Changsha 410075, China; (C.T.); (T.W.); (W.Y.)
- School of Software, Xinjiang University, Urumqi 830008, China
- Correspondence: ; Tel.: +86-731-82539736
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20
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Barbero Barcenilla B, Shippen DE. Back to the future: The intimate and evolving connection between telomere-related factors and genotoxic stress. J Biol Chem 2019; 294:14803-14813. [PMID: 31434740 DOI: 10.1074/jbc.aw119.008145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The conversion of circular genomes to linear chromosomes during molecular evolution required the invention of telomeres. This entailed the acquisition of factors necessary to fulfill two new requirements: the need to fully replicate terminal DNA sequences and the ability to distinguish chromosome ends from damaged DNA. Here we consider the multifaceted functions of factors recruited to perpetuate and stabilize telomeres. We discuss recent theories for how telomere factors evolved from existing cellular machineries and examine their engagement in nontelomeric functions such as DNA repair, replication, and transcriptional regulation. We highlight the remarkable versatility of protection of telomeres 1 (POT1) proteins that was fueled by gene duplication and divergence events that occurred independently across several eukaryotic lineages. Finally, we consider the relationship between oxidative stress and telomeres and the enigmatic role of telomere-associated proteins in mitochondria. These findings point to an evolving and intimate connection between telomeres and cellular physiology and the strong drive to maintain chromosome integrity.
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Affiliation(s)
- Borja Barbero Barcenilla
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128
| | - Dorothy E Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843-2128
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21
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Suzuki S, Kurosawa N. Robust growth of archaeal cells lacking a canonical single-stranded DNA-binding protein. FEMS Microbiol Lett 2019; 366:5511891. [DOI: 10.1093/femsle/fnz124] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 06/04/2019] [Indexed: 12/17/2022] Open
Abstract
AbstractCanonical single-stranded DNA-binding proteins (SSBs) are universally conserved helix-destabilizing proteins that play critical roles in DNA replication, recombination and repair. Many biochemical and genetic studies have demonstrated the importance of functional SSBs for all life forms. Herein, we report successful deletion of the gene encoding the only canonical SSB of the thermophilic crenarchaeon Sulfolobus acidocaldarius. Genomic sequencing of the ssb-deficient strain using illumina sequencing revealed that the canonical ssb gene is completely deleted from the genome of S. acidocaldarius. Phenotypic characterization demonstrated robust growth of the thermophilic archaeal cells lacking a canonical SSB, thereby demonstrating tolerance to the loss of a universal protein that is generally considered to be essential. Therefore, our work provides evidence that canonical SSBs are not essential for all life forms. Furthermore, on the basis of universal distribution and essentiality pattern of canonical SSBs, our findings can provide a conceptual understanding of the characteristics of early life forms before the last universal common ancestor.
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Affiliation(s)
- Shoji Suzuki
- Department of Science and Engineering for Sustainable Development, Faculty of Science and Engineering, Soka University, 1–236 Tangi-machi, Hachioji, Tokyo 192–8577, Japan
| | - Norio Kurosawa
- Department of Science and Engineering for Sustainable Development, Faculty of Science and Engineering, Soka University, 1–236 Tangi-machi, Hachioji, Tokyo 192–8577, Japan
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22
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Nagata M, Ishino S, Yamagami T, Ishino Y. Replication protein A complex in Thermococcus kodakarensis interacts with DNA polymerases and helps their effective strand synthesis. Biosci Biotechnol Biochem 2019; 83:695-704. [DOI: 10.1080/09168451.2018.1559722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
ABSTRACT
Replication protein A (RPA) is an essential component of DNA metabolic processes. RPA binds to single-stranded DNA (ssDNA) and interacts with multiple DNA-binding proteins. In this study, we showed that two DNA polymerases, PolB and PolD, from the hyperthermophilic archaeon Thermococcus kodakarensis interact directly with RPA in vitro. RPA was expected to play a role in resolving the secondary structure, which may stop the DNA synthesis reaction, in the template ssDNA. Our in vitro DNA synthesis assay showed that the pausing was resolved by RPA for both PolB and PolD. These results supported the fact that RPA interacts with DNA polymerases as a member of the replisome and is involved in the normal progression of DNA replication forks.
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Affiliation(s)
- Mariko Nagata
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Takeshi Yamagami
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
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23
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Lawson T, El-Kamand S, Kariawasam R, Richard DJ, Cubeddu L, Gamsjaeger R. A Structural Perspective on the Regulation of Human Single-Stranded DNA Binding Protein 1 (hSSB1, OBFC2B) Function in DNA Repair. Comput Struct Biotechnol J 2019; 17:441-446. [PMID: 30996823 PMCID: PMC6451162 DOI: 10.1016/j.csbj.2019.03.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 12/11/2022] Open
Abstract
Single-stranded DNA binding (SSB) proteins are essential to protect singe-stranded DNA (ssDNA) that exists as a result of several important DNA repair pathways in living cells. In humans, besides the well-characterised Replication Protein A (RPA) we have described another SSB termed human SSB1 (hSSB1, OBFC2B) and have shown that this protein is an important player in the maintenance of the genome. In this review we define the structural and biophysical details of how hSSB1 interacts with both DNA and other essential proteins. While the presence of the oligonucleotide/oligosaccharide (OB) domain ensures ssDNA binding by hSSB1, it has also been shown to self-oligomerise as well as interact with and being modified by several proteins highlighting the versatility that hSSB1 displays in the context of DNA repair. A detailed structural understanding of these processes will likely lead to the designs of tailored hSSB1 inhibitors as anti-cancer drugs in the near future.
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Affiliation(s)
- Teegan Lawson
- School of Science and Health, Western Sydney University, Sydney, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Serene El-Kamand
- School of Science and Health, Western Sydney University, Sydney, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Ruvini Kariawasam
- School of Science and Health, Western Sydney University, Sydney, Locked Bag 1797, Penrith, NSW 2751, Australia
| | - Derek J Richard
- Genome Stability Laboratory, Cancer and Ageing Research Program, Institute of Health and Biomedical Innovation, Translational Research Institute, Queensland University of Technology, Woolloongabba, Queensland 4102, Australia
| | - Liza Cubeddu
- School of Science and Health, Western Sydney University, Sydney, Locked Bag 1797, Penrith, NSW 2751, Australia.,School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Roland Gamsjaeger
- School of Science and Health, Western Sydney University, Sydney, Locked Bag 1797, Penrith, NSW 2751, Australia.,School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
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24
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Delpech F, Collien Y, Mahou P, Beaurepaire E, Myllykallio H, Lestini R. Snapshots of archaeal DNA replication and repair in living cells using super-resolution imaging. Nucleic Acids Res 2018; 46:10757-10770. [PMID: 30212908 PMCID: PMC6237752 DOI: 10.1093/nar/gky829] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 09/03/2018] [Accepted: 09/07/2018] [Indexed: 12/17/2022] Open
Abstract
Using the haloarchaeon Haloferax volcanii as a model, we developed nascent DNA labeling and the functional GFP-labeled single-stranded binding protein RPA2 as novel tools to gain new insight into DNA replication and repair in live haloarchaeal cells. Our quantitative fluorescence microscopy data revealed that RPA2 forms distinct replication structures that dynamically responded to replication stress and DNA damaging agents. The number of the RPA2 foci per cell followed a probabilistic Poisson distribution, implying hitherto unnoticed stochastic cell-to-cell variation in haloarchaeal DNA replication and repair processes. The size range of haloarchaeal replication structures is very similar to those observed earlier in eukaryotic cells. The improved lateral resolution of 3D-SIM fluorescence microscopy allowed proposing that inhibition of DNA synthesis results in localized replication foci clustering and facilitated observation of RPA2 complexes brought about by chemical agents creating DNA double-strand breaks. Altogether our in vivo observations are compatible with earlier in vitro studies on archaeal single-stranded DNA binding proteins. Our work thus underlines the great potential of live cell imaging for unraveling the dynamic nature of transient molecular interactions that underpin fundamental molecular processes in the Third domain of life.
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Affiliation(s)
- Floriane Delpech
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645 – INSERM U1182, 91128 Palaiseau Cedex, France
| | - Yoann Collien
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645 – INSERM U1182, 91128 Palaiseau Cedex, France
| | - Pierre Mahou
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645 – INSERM U1182, 91128 Palaiseau Cedex, France
| | - Emmanuel Beaurepaire
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645 – INSERM U1182, 91128 Palaiseau Cedex, France
| | - Hannu Myllykallio
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645 – INSERM U1182, 91128 Palaiseau Cedex, France
| | - Roxane Lestini
- Laboratoire d’Optique et Biosciences, Ecole Polytechnique, CNRS UMR7645 – INSERM U1182, 91128 Palaiseau Cedex, France
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25
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Li D, Gao D, Qi J, Chai R, Zhan Y, Xing C. Conjugated Polymer/Graphene Oxide Complexes for Photothermal Activation of DNA Unzipping and Binding to Protein. ACS APPLIED BIO MATERIALS 2018. [DOI: 10.1021/acsabm.8b00047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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Antony E, Lohman TM. Dynamics of E. coli single stranded DNA binding (SSB) protein-DNA complexes. Semin Cell Dev Biol 2018; 86:102-111. [PMID: 29588158 DOI: 10.1016/j.semcdb.2018.03.017] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 01/25/2023]
Abstract
Single stranded DNA binding proteins (SSB) are essential to the cell as they stabilize transiently open single stranded DNA (ssDNA) intermediates, recruit appropriate DNA metabolism proteins, and coordinate fundamental processes such as replication, repair and recombination. Escherichia coli single stranded DNA binding protein (EcSSB) has long served as the prototype for the study of SSB function. The structure, functions, and DNA binding properties of EcSSB are well established: The protein is a stable homotetramer with each subunit possessing an N-terminal DNA binding core, a C-terminal protein-protein interaction tail, and an intervening intrinsically disordered linker (IDL). EcSSB wraps ssDNA in multiple DNA binding modes and can diffuse along DNA to remove secondary structures and remodel other protein-DNA complexes. This review provides an update on these features based on recent findings, with special emphasis on the functional and mechanistic relevance of the IDL and DNA binding modes.
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Affiliation(s)
- Edwin Antony
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53201, USA.
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
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27
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Touma C, Adams MN, Ashton NW, Mizzi M, El-Kamand S, Richard DJ, Cubeddu L, Gamsjaeger R. A data-driven structural model of hSSB1 (NABP2/OBFC2B) self-oligomerization. Nucleic Acids Res 2017; 45:8609-8620. [PMID: 28609781 PMCID: PMC5737504 DOI: 10.1093/nar/gkx526] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 06/05/2017] [Indexed: 12/19/2022] Open
Abstract
The maintenance of genome stability depends on the ability of the cell to repair DNA efficiently. Single-stranded DNA binding proteins (SSBs) play an important role in DNA processing events such as replication, recombination and repair. While the role of human single-stranded DNA binding protein 1 (hSSB1/NABP2/OBFC2B) in the repair of double-stranded breaks has been well established, we have recently shown that it is also essential for the base excision repair (BER) pathway following oxidative DNA damage. However, unlike in DSB repair, the formation of stable hSSB1 oligomers under oxidizing conditions is an important prerequisite for its proper function in BER. In this study, we have used solution-state NMR in combination with biophysical and functional experiments to obtain a structural model of hSSB1 self-oligomerization. We reveal that hSSB1 forms a tetramer that is structurally similar to the SSB from Escherichia coli and is stabilized by two cysteines (C81 and C99) as well as a subset of charged and hydrophobic residues. Our structural and functional data also show that hSSB1 oligomerization does not preclude its function in DSB repair, where it can interact with Ints3, a component of the SOSS1 complex, further establishing the versatility that hSSB1 displays in maintaining genome integrity.
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Affiliation(s)
- Christine Touma
- School of Science and Health, Western Sydney University, Penrith, NSW 2751, Australia
| | - Mark N Adams
- School of Biomedical Research, Institute of Health and Biomedical Innovation at the Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD 4102, Australia
| | - Nicholas W Ashton
- School of Biomedical Research, Institute of Health and Biomedical Innovation at the Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD 4102, Australia
| | - Michael Mizzi
- School of Science and Health, Western Sydney University, Penrith, NSW 2751, Australia
| | - Serene El-Kamand
- School of Science and Health, Western Sydney University, Penrith, NSW 2751, Australia
| | - Derek J Richard
- School of Biomedical Research, Institute of Health and Biomedical Innovation at the Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD 4102, Australia
| | - Liza Cubeddu
- School of Science and Health, Western Sydney University, Penrith, NSW 2751, Australia.,School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
| | - Roland Gamsjaeger
- School of Science and Health, Western Sydney University, Penrith, NSW 2751, Australia.,School of Life and Environmental Sciences, University of Sydney, NSW 2006, Australia
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28
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Staphylococcus aureus single-stranded DNA-binding protein SsbA can bind but cannot stimulate PriA helicase. PLoS One 2017; 12:e0182060. [PMID: 28750050 PMCID: PMC5531588 DOI: 10.1371/journal.pone.0182060] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/11/2017] [Indexed: 12/02/2022] Open
Abstract
Single-stranded DNA-binding protein (SSB) and PriA helicase play important roles in bacterial DNA replication restart process. The mechanism by which PriA helicase is bound and stimulated by SSB in Escherichia coli (Ec) has been established, but information on this process in Gram-positive bacteria are limited. We characterized the properties of SSB from Staphylococcus aureus (SaSsbA, a counterpart of EcSSB) and analyzed its interaction with SaPriA. The gel filtration chromatography analysis of purified SaSsbA showed a stable tetramer in solution. The crystal structure of SaSsbA determined at 1.82 Å resolution (PDB entry 5XGT) reveals that the classic oligonucleotide/oligosaccharide-binding folds are formed in the N-terminal DNA-binding domain, but the entire C-terminal domain is disordered. Unlike EcSSB, which can stimulate EcPriA via a physical interaction between EcPriA and the C-terminus of EcSSB (SSB-Ct), SaSsbA does not affect the activity of SaPriA. We also found that SaPriA can be bound by SaSsbA, but not by SaSsbA-Ct. Although no effect was found with SaSsbA, SaPriA can be significantly stimulated by the Gram-negative Klebsiella pneumoniae SSB (KpSSB). In addition, we found that the conserved SSB-Ct binding site of KpPriA (Trp82, Tyr86, Lys370, Arg697, and Gln701) is not present in SaPriA. Arg697 in KpPriA is known to play a critical role in altering the SSB35/SSB65 distribution, but this corresponding residue in SaPriA is Glu767 instead, which has an opposite charge to Arg. SaPriA E767R mutant was constructed and analyzed; however, it still cannot be stimulated by SaSsbA. Finally, we found that the conserved MDFDDDIPF motif in the Gram-negative bacterial SSB is DISDDDLPF in SaSsbA, i.e., F172 in EcSSB and F168 in KpSSB is S161 in SaSsbA, not F. When acting with SaSsbA S161F mutant, the activity of SaPriA was dramatically enhanced elevenfold. Overall, the conserved binding sites, both in EcPriA and EcSSB, are not present in SaPriA and SaSsbA, thereby no stimulation occurs. Our observations through structure-sequence comparison and mutational analyses indicate that the case of EcPriA-EcSSB is not applicable to SaPriA-SaSsbA because of inherent differences among the species.
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29
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Wang W, Sun L, Zhang S, Zhang H, Shi J, Xu T, Li K. Analysis and prediction of single-stranded and double-stranded DNA binding proteins based on protein sequences. BMC Bioinformatics 2017; 18:300. [PMID: 28606086 PMCID: PMC5469069 DOI: 10.1186/s12859-017-1715-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 06/06/2017] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND DNA-binding proteins perform important functions in a great number of biological activities. DNA-binding proteins can interact with ssDNA (single-stranded DNA) or dsDNA (double-stranded DNA), and DNA-binding proteins can be categorized as single-stranded DNA-binding proteins (SSBs) and double-stranded DNA-binding proteins (DSBs). The identification of DNA-binding proteins from amino acid sequences can help to annotate protein functions and understand the binding specificity. In this study, we systematically consider a variety of schemes to represent protein sequences: OAAC (overall amino acid composition) features, dipeptide compositions, PSSM (position-specific scoring matrix profiles) and split amino acid composition (SAA), and then we adopt SVM (support vector machine) and RF (random forest) classification model to distinguish SSBs from DSBs. RESULTS Our results suggest that some sequence features can significantly differentiate DSBs and SSBs. Evaluated by 10 fold cross-validation on the benchmark datasets, our prediction method can achieve the accuracy of 88.7% and AUC (area under the curve) of 0.919. Moreover, our method has good performance in independent testing. CONCLUSIONS Using various sequence-derived features, a novel method is proposed to distinguish DSBs and SSBs accurately. The method also explores novel features, which could be helpful to discover the binding specificity of DNA-binding proteins.
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Affiliation(s)
- Wei Wang
- College of Computer and Information Engineering, Henan Normal University, Xinxiang, Henan Province 453007 China
- Laboratory of Computation Intelligence and Information Processing, Engineering Technology Research Center for Computing Intelligence and Data Mining, Xinxiang, Henan Province 453007 China
| | - Lin Sun
- College of Computer and Information Engineering, Henan Normal University, Xinxiang, Henan Province 453007 China
| | - Shiguang Zhang
- College of Computer and Information Engineering, Henan Normal University, Xinxiang, Henan Province 453007 China
| | - Hongjun Zhang
- School of Aviation Engineering, Anyang University, Anyang, Henan Province 455000 China
| | - Jinling Shi
- School of International Education, Xuchang University, Xuchang, Henan Province 461000 China
| | - Tianhe Xu
- College of Computer and Information Engineering, Henan Normal University, Xinxiang, Henan Province 453007 China
| | - Keliang Li
- College of Computer and Information Engineering, Henan Normal University, Xinxiang, Henan Province 453007 China
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30
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Morten MJ, Gamsjaeger R, Cubeddu L, Kariawasam R, Peregrina J, Penedo JC, White MF. High-affinity RNA binding by a hyperthermophilic single-stranded DNA-binding protein. Extremophiles 2017; 21:369-379. [PMID: 28074284 PMCID: PMC5346138 DOI: 10.1007/s00792-016-0910-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/19/2016] [Indexed: 12/30/2022]
Abstract
Single-stranded DNA-binding proteins (SSBs), including replication protein A (RPA) in eukaryotes, play a central role in DNA replication, recombination, and repair. SSBs utilise an oligonucleotide/oligosaccharide-binding (OB) fold domain to bind DNA, and typically oligomerise in solution to bring multiple OB fold domains together in the functional SSB. SSBs from hyperthermophilic crenarchaea, such as Sulfolobus solfataricus, have an unusual structure with a single OB fold coupled to a flexible C-terminal tail. The OB fold resembles those in RPA, whilst the tail is reminiscent of bacterial SSBs and mediates interaction with other proteins. One paradigm in the field is that SSBs bind specifically to ssDNA and much less strongly to RNA, ensuring that their functions are restricted to DNA metabolism. Here, we use a combination of biochemical and biophysical approaches to demonstrate that the binding properties of S. solfataricus SSB are essentially identical for ssDNA and ssRNA. These features may represent an adaptation to a hyperthermophilic lifestyle, where DNA and RNA damage is a more frequent event.
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Affiliation(s)
- Michael J Morten
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Roland Gamsjaeger
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, 2006, Australia
| | - Liza Cubeddu
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, 2006, Australia
| | - Ruvini Kariawasam
- School of Science and Health, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
- School of Molecular Bioscience, University of Sydney, Sydney, NSW, 2006, Australia
| | - Jose Peregrina
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - J Carlos Penedo
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, KY16 9ST, UK.
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31
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Korzhnev DM, Neculai D, Dhe-Paganon S, Arrowsmith CH, Bezsonova I. Solution NMR structure of the HLTF HIRAN domain: a conserved module in SWI2/SNF2 DNA damage tolerance proteins. JOURNAL OF BIOMOLECULAR NMR 2016; 66:209-219. [PMID: 27771863 DOI: 10.1007/s10858-016-0070-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/17/2016] [Indexed: 06/06/2023]
Abstract
HLTF is a SWI2/SNF2-family ATP-dependent chromatin remodeling enzyme that acts in the error-free branch of DNA damage tolerance (DDT), a cellular mechanism that enables replication of damaged DNA while leaving damage repair for a later time. Human HLTF and a closely related protein SHPRH, as well as their yeast homologue Rad5, are multi-functional enzymes that share E3 ubiquitin-ligase activity required for activation of the error-free DDT. HLTF and Rad5 also function as ATP-dependent dsDNA translocases and possess replication fork reversal activities. Thus, they can convert Y-shaped replication forks into X-shaped Holliday junction structures that allow error-free replication over DNA lesions. The fork reversal activity of HLTF is dependent on 3'-ssDNA-end binding activity of its N-terminal HIRAN domain. Here we present the solution NMR structure of the human HLTF HIRAN domain, an OB-like fold module found in organisms from bacteria (as a stand-alone domain) to plants, fungi and metazoan (in combination with SWI2/SNF2 helicase-like domain). The obtained structure of free HLTF HIRAN is similar to recently reported structures of its DNA bound form, while the NMR analysis also reveals that the DNA binding site of the free domain exhibits conformational heterogeneity. Sequence comparison of N-terminal regions of HLTF, SHPRH and Rad5 aided by knowledge of the HLTF HIRAN structure suggests that the SHPRH N-terminus also includes an uncharacterized structured module, exhibiting weak sequence similarity with HIRAN regions of HLTF and Rad5, and potentially playing a similar functional role.
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Affiliation(s)
- Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, University of Connecticut Health, Farmington, CT, 06030, USA
| | - Dante Neculai
- School of Medicine, Zhejiang University, Hangzhou, China
| | - Sirano Dhe-Paganon
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
- Department of Medical Biophysics, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Irina Bezsonova
- Department of Molecular Biology and Biophysics, University of Connecticut Health, Farmington, CT, 06030, USA.
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32
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hSSB1 (NABP2/OBFC2B) is regulated by oxidative stress. Sci Rep 2016; 6:27446. [PMID: 27273218 PMCID: PMC4897654 DOI: 10.1038/srep27446] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/18/2016] [Indexed: 12/17/2022] Open
Abstract
The maintenance of genome stability is an essential cellular process to prevent the development of diseases including cancer. hSSB1 (NABP2/ OBFC2A) is a critical component of the DNA damage response where it participates in the repair of double-strand DNA breaks and in base excision repair of oxidized guanine residues (8-oxoguanine) by aiding the localization of the human 8-oxoguanine glycosylase (hOGG1) to damaged DNA. Here we demonstrate that following oxidative stress, hSSB1 is stabilized as an oligomer which is required for hSSB1 to function in the removal of 8-oxoguanine. Monomeric hSSB1 shows a decreased affinity for oxidized DNA resulting in a cellular 8-oxoguanine-repair defect and in the absence of ATM signaling initiation. While hSSB1 oligomerization is important for the removal of 8-oxoguanine from the genome, it is not required for the repair of double-strand DNA-breaks by homologous recombination. These findings demonstrate a novel hSSB1 regulatory mechanism for the repair of damaged DNA.
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33
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Wang W, Liu J, Sun L. Surface shapes and surrounding environment analysis of single- and double-stranded DNA-binding proteins in protein-DNA interface. Proteins 2016; 84:979-89. [PMID: 27038080 DOI: 10.1002/prot.25045] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/15/2016] [Accepted: 03/25/2016] [Indexed: 11/12/2022]
Abstract
Protein-DNA bindings are critical to many biological processes. However, the structural mechanisms underlying these interactions are not fully understood. Here, we analyzed the residues shape (peak, flat, or valley) and the surrounding environment of double-stranded DNA-binding proteins (DSBs) and single-stranded DNA-binding proteins (SSBs) in protein-DNA interfaces. In the results, we found that the interface shapes, hydrogen bonds, and the surrounding environment present significant differences between the two kinds of proteins. Built on the investigation results, we constructed a random forest (RF) classifier to distinguish DSBs and SSBs with satisfying performance. In conclusion, we present a novel methodology to characterize protein interfaces, which will deepen our understanding of the specificity of proteins binding to ssDNA (single-stranded DNA) or dsDNA (double-stranded DNA). Proteins 2016; 84:979-989. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Wei Wang
- Department of Computer Science and Technology, College of Computer and Information Engineering, Henan Normal University, Xinxiang, 453007, China.,Laboratory of Computation Intelligence and Information Processing, Engineering Technology Research Center for Computing Intelligence and Data Mining, Henan Province, China
| | - Juan Liu
- Institute of Computer Software, School of Computer, Wuhan University, Wuhan, 430072, China
| | - Lin Sun
- Department of Computer Science and Technology, College of Computer and Information Engineering, Henan Normal University, Xinxiang, 453007, China.,Laboratory of Computation Intelligence and Information Processing, Engineering Technology Research Center for Computing Intelligence and Data Mining, Henan Province, China
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34
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Ma C, Pathak C, Lee SJ, Lee KY, Jang SB, Nam M, Im H, Yoon HJ, Lee BJ. Alba from Thermoplasma volcanium belongs to α-NAT's: An insight into the structural aspects of Tv Alba and its acetylation by Tv Ard1. Arch Biochem Biophys 2016; 590:90-100. [DOI: 10.1016/j.abb.2015.11.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Revised: 11/04/2015] [Accepted: 11/26/2015] [Indexed: 01/30/2023]
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35
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Purification and characterization of oligonucleotide binding (OB)-fold protein from medicinal plant Tinospora cordifolia. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 1008:38-44. [PMID: 26613539 DOI: 10.1016/j.jchromb.2015.11.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 11/09/2015] [Accepted: 11/12/2015] [Indexed: 12/11/2022]
Abstract
The oligonucleotide binding fold (OB-fold) is a small structural motif present in many proteins. It is originally named for its oligonucleotide or oligosaccharide binding properties. These proteins have been identified as essential for replication, recombination and repair of DNA. We have successfully purified a protein contains OB-fold from the stem of Tinospora cordifolia, a medicinal plants of north India. Stems were crushed and centrifuged, and fraction obtained at 60% ammonium sulphate was extensively dialyzed and applied to the weak anion exchange chromatography on Hi-Trap DEAE-FF in 50mM Tris-HCl buffer at pH 8.0. Eluted fractions were concentrated and applied to gel filtration column to get pure protein. We observed a single band of 20-kDa on SDS-PAGE. Finally, the protein was identified as OB-fold by MALDI-TOF. The purified OB-fold protein was characterized for its secondary structural elements using circular dichroism (CD) in the far-UV region. Generally the OB-fold has a characteristic feature as five-stranded beta-sheet coiled to form a closed beta- barrel. To estimate its chemical stability, guanidinium chloride-induced denaturation curve was followed by observing changes in the far-UV CD as a function of the denaturant concentration. Analysis of this denaturation curve gave values of 8.90±0.25kcalmol(-1) and 3.78±0.18M for ΔGD° (Gibbs free energy change at 25°C) and Cm (midpoint of denaturation), respectively. To determine heat stability parameters of OB-fold protein, differential scanning calorimetry was performed. Calorimetric values of ΔGD°, Tm (midpoint of denaturation), ΔHm (enthalpy change at Tm), and ΔCp (constant-pressure heat capacity change) are 9.05±0.27kcalmol(-1), 85.2±0,3°C, 105±4kcalmol(-1) and 1.6±0.08kcalmol(-1)K(-1). This is the first report on the isolation, purification and characterization of OB-fold protein from a medicinal plant T. cordifolia.
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36
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Morten MJ, Peregrina JR, Figueira-Gonzalez M, Ackermann K, Bode BE, White MF, Penedo JC. Binding dynamics of a monomeric SSB protein to DNA: a single-molecule multi-process approach. Nucleic Acids Res 2015; 43:10907-24. [PMID: 26578575 PMCID: PMC4678828 DOI: 10.1093/nar/gkv1225] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 10/29/2015] [Indexed: 01/28/2023] Open
Abstract
Single-stranded DNA binding proteins (SSBs) are ubiquitous across all organisms and are characterized by the presence of an OB (oligonucleotide/oligosaccharide/oligopeptide) binding motif to recognize single-stranded DNA (ssDNA). Despite their critical role in genome maintenance, our knowledge about SSB function is limited to proteins containing multiple OB-domains and little is known about single OB-folds interacting with ssDNA. Sulfolobus solfataricus SSB (SsoSSB) contains a single OB-fold and being the simplest representative of the SSB-family may serve as a model to understand fundamental aspects of SSB:DNA interactions. Here, we introduce a novel approach based on the competition between Förster resonance energy transfer (FRET), protein-induced fluorescence enhancement (PIFE) and quenching to dissect SsoSSB binding dynamics at single-monomer resolution. We demonstrate that SsoSSB follows a monomer-by-monomer binding mechanism that involves a positive-cooperativity component between adjacent monomers. We found that SsoSSB dynamic behaviour is closer to that of Replication Protein A than to Escherichia coli SSB; a feature that might be inherited from the structural analogies of their DNA-binding domains. We hypothesize that SsoSSB has developed a balance between high-density binding and a highly dynamic interaction with ssDNA to ensure efficient protection of the genome but still allow access to ssDNA during vital cellular processes.
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Affiliation(s)
- Michael J Morten
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Jose R Peregrina
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Maria Figueira-Gonzalez
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Katrin Ackermann
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Bela E Bode
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK EaStCHEM School of Chemistry and Centre of Magnetic Resonance, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - Malcolm F White
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK
| | - J Carlos Penedo
- Biomedical Sciences Research Complex, University of St Andrews, St Andrews, Fife KY16 9ST, UK SUPA School of Physics and Astronomy, University of St Andrews, St Andrews, Fife KY16 9SS, UK
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Vidhyasagar V, He Y, Guo M, Ding H, Talwar T, Nguyen V, Nwosu J, Katselis G, Wu Y. C-termini are essential and distinct for nucleic acid binding of human NABP1 and NABP2. Biochim Biophys Acta Gen Subj 2015; 1860:371-83. [PMID: 26550690 DOI: 10.1016/j.bbagen.2015.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 10/30/2015] [Accepted: 11/04/2015] [Indexed: 01/03/2023]
Abstract
BACKGROUND Human Nucleic Acid Binding Protein 1 and 2 (hNABP1 and 2; also known as hSSB2 and 1, respectively) are two newly identified single-stranded (ss) DNA binding proteins (SSB). Both NABP1 and NABP2 have a conserved oligonucleotide/oligosaccharide-binding (OB)-fold domain and a divergent carboxy-terminal domain, the functional importance of which is unknown. METHODS Recombinant hNABP1/2 proteins were purified using affinity and size exclusion chromatography and their identities confirmed by mass spectrometry. Oligomerization state was checked by sucrose gradient centrifugation. Secondary structure was determined by circular dichroism spectroscopy. Nucleic acid binding ability was examined by EMSA and ITC. RESULTS Both hNABP1 and hNABP2 exist as monomers in solution; however, hNABP2 exhibits anomalous behavior. CD spectroscopy revealed that the C-terminus of hNABP2 is highly disordered. Deletion of the C-terminal tail diminishes the DNA binding ability and protein stability of hNABP2. Although both hNABP1 and hNABP2 prefer to bind ssDNA than double-stranded (ds) DNA, hNABP1 has a higher affinity for ssDNA than hNABP2. Unlike hNABP2, hNABP1 protein binds and multimerizes on ssDNA with the C-terminal tail responsible for its multimerization. Both hNABP1 and hNABP2 are able to bind single-stranded RNA, with hNABP2 having a higher affinity than hNABP1. CONCLUSIONS Biochemical evidence suggests that the C-terminal region of NABP1 and NABP2 is essential for their functionality and may lead to different roles in DNA and RNA metabolism. GENERAL SIGNIFICANCE This is the first report demonstrating the regulation and functional properties of the C-terminal domain of hNABP1/2, which might be a general characteristic of OB-fold proteins.
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Affiliation(s)
- Venkatasubramanian Vidhyasagar
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Yujiong He
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Manhong Guo
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Hao Ding
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Tanu Talwar
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Vi Nguyen
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Jessica Nwosu
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - George Katselis
- Department of Medicine, University of Saskatchewan, Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada; Canadian Centre for Health and Safety in Agriculture, University of Saskatchewan, Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
| | - Yuliang Wu
- Department of Biochemistry, University of Saskatchewan, Health Sciences Building, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada.
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Abstract
DNA replication is essential for all life forms. Although the process is fundamentally conserved in the three domains of life, bioinformatic, biochemical, structural, and genetic studies have demonstrated that the process and the proteins involved in archaeal DNA replication are more similar to those in eukaryal DNA replication than in bacterial DNA replication, but have some archaeal-specific features. The archaeal replication system, however, is not monolithic, and there are some differences in the replication process between different species. In this review, the current knowledge of the mechanisms governing DNA replication in Archaea is summarized. The general features of the replication process as well as some of the differences are discussed.
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Affiliation(s)
- Lori M Kelman
- Program in Biotechnology, Montgomery College, Germantown, Maryland 20876;
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Olszewski M, Balsewicz J, Nowak M, Maciejewska N, Cyranka-Czaja A, Zalewska-Piątek B, Piątek R, Kur J. Characterization of a Single-Stranded DNA-Binding-Like Protein from Nanoarchaeum equitans--A Nucleic Acid Binding Protein with Broad Substrate Specificity. PLoS One 2015; 10:e0126563. [PMID: 25973760 PMCID: PMC4431734 DOI: 10.1371/journal.pone.0126563] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 04/03/2015] [Indexed: 11/18/2022] Open
Abstract
Background SSB (single-stranded DNA-binding) proteins play an essential role in all living cells and viruses, as they are involved in processes connected with ssDNA metabolism. There has recently been an increasing interest in SSBs, since they can be applied in molecular biology techniques and analytical methods. Nanoarchaeum equitans, the only known representative of Archaea phylum Nanoarchaeota, is a hyperthermophilic, nanosized, obligatory parasite/symbiont of Ignicoccus hospitalis. Results This paper reports on the ssb-like gene cloning, gene expression and characterization of a novel nucleic acid binding protein from Nanoarchaeum equitans archaeon (NeqSSB-like protein). This protein consists of 243 amino acid residues and one OB fold per monomer. It is biologically active as a monomer like as SSBs from some viruses. The NeqSSB-like protein displays a low sequence similarity to the Escherichia coli SSB, namely 10% identity and 29% similarity, and is the most similar to the Sulfolobus solfataricus SSB (14% identity and 32% similarity). The NeqSSB-like protein binds to ssDNA, although it can also bind mRNA and, surprisingly, various dsDNA forms, with no structure-dependent preferences as evidenced by gel mobility shift assays. The size of the ssDNA binding site, which was estimated using fluorescence spectroscopy, is 7±1 nt. No salt-dependent binding mode transition was observed. NeqSSB-like protein probably utilizes a different model for ssDNA binding than the SSB proteins studied so far. This protein is highly thermostable; the half-life of the ssDNA binding activity is 5 min at 100°C and melting temperature (Tm) is 100.2°C as shown by differential scanning calorimetry (DSC) analysis. Conclusion NeqSSB-like protein is a novel highly thermostable protein which possesses a unique broad substrate specificity and is able to bind all types of nucleic acids.
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Affiliation(s)
- Marcin Olszewski
- Gdańsk University of Technology, Chemical Faculty, Department of Molecular Biotechnology and Microbiology, 80–233, Gdańsk, Poland
- * E-mail:
| | - Jan Balsewicz
- Gdańsk University of Technology, Chemical Faculty, Department of Molecular Biotechnology and Microbiology, 80–233, Gdańsk, Poland
| | - Marta Nowak
- Gdańsk University of Technology, Chemical Faculty, Department of Molecular Biotechnology and Microbiology, 80–233, Gdańsk, Poland
| | - Natalia Maciejewska
- Gdańsk University of Technology, Chemical Faculty, Department of Molecular Biotechnology and Microbiology, 80–233, Gdańsk, Poland
| | - Anna Cyranka-Czaja
- University of Wroclaw, Faculty of Biotechnology, Department of Protein Engineering, 50–138, Wrocław, Poland
| | - Beata Zalewska-Piątek
- Gdańsk University of Technology, Chemical Faculty, Department of Molecular Biotechnology and Microbiology, 80–233, Gdańsk, Poland
| | - Rafał Piątek
- Gdańsk University of Technology, Chemical Faculty, Department of Molecular Biotechnology and Microbiology, 80–233, Gdańsk, Poland
| | - Józef Kur
- Gdańsk University of Technology, Chemical Faculty, Department of Molecular Biotechnology and Microbiology, 80–233, Gdańsk, Poland
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Chakraborty K, Bandyopadhyay S. Correlated Conformational Motions of the KH Domains of Far Upstream Element Binding Protein Complexed with Single-Stranded DNA Oligomers. J Phys Chem B 2015; 119:10998-1009. [DOI: 10.1021/acs.jpcb.5b01687] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Kaushik Chakraborty
- Molecular Modeling Laboratory,
Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
| | - Sanjoy Bandyopadhyay
- Molecular Modeling Laboratory,
Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302, India
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The structural basis of DNA binding by the single-stranded DNA-binding protein from Sulfolobus solfataricus. Biochem J 2015; 465:337-46. [DOI: 10.1042/bj20141140] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We present the 3D solution structure of the canonical SSB from the crenarchaeote Sulfolobus solfataricus bound to single-stranded DNA and compare this structure with human homologues.
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Wang W, Liu J, Xiong Y, Zhu L, Zhou X. Analysis and classification of DNA-binding sites in single-stranded and double-stranded DNA-binding proteins using protein information. IET Syst Biol 2014; 8:176-83. [PMID: 25075531 DOI: 10.1049/iet-syb.2013.0048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) and double-stranded DNA-binding proteins (DSBs) play different roles in biological processes when they bind to single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA). However, the underlying binding mechanisms of SSBs and DSBs have not yet been fully understood. Here, the authors firstly constructed two groups of ssDNA and dsDNA specific binding sites from two non-redundant sets of SSBs and DSBs. They further analysed the relationship between the two classes of binding sites and a newly proposed set of features (residue charge distribution, secondary structure and spatial shape). To assess and utilise the predictive power of these features, they trained a classification model using support vector machine to make predictions about the ssDNA and the dsDNA binding sites. The author's analysis and prediction results indicated that the two classes of binding sites can be distinguishable by the three types of features, and the final classifier using all the features achieved satisfactory performance. In conclusion, the proposed features will deepen their understanding of the specificity of proteins which bind to ssDNA or dsDNA.
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Affiliation(s)
- Wei Wang
- School of Computer, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Juan Liu
- School of Computer, Wuhan University, Wuhan, Hubei, People's Republic of China.
| | - Yi Xiong
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA
| | - Lida Zhu
- School of Computer, Wuhan University, Wuhan, Hubei, People's Republic of China
| | - Xionghui Zhou
- School of Computer, Wuhan University, Wuhan, Hubei, People's Republic of China
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Wang W, Liu J, Zhou X. Identification of single-stranded and double-stranded DNA binding proteins based on protein structure. BMC Bioinformatics 2014; 15 Suppl 12:S4. [PMID: 25474071 PMCID: PMC4243121 DOI: 10.1186/1471-2105-15-s12-s4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Background Protein-DNA interactions are essential for many biological processes. However, the structural mechanisms underlying these interactions are not fully understood. DNA binding proteins can be classified into double-stranded DNA binding proteins (DSBs) and single-stranded DNA binding proteins (SSBs), and they take part in different biological functions. DSBs usually act as transcriptional factors to regulate the genes' expressions, while SSBs usually play roles in DNA replication, recombination, and repair, etc. Understanding the binding specificity of a DNA binding protein is helpful for the research of protein functions. Results In this paper, we investigated the differences between DSBs and SSBs on surface tunnels as well as the OB-fold domain information. We detected the largest clefts on the protein surfaces, to obtain several features to be used for distinguishing the potential interfaces between SSBs and DSBs, and compared its structure with each of the six OB-fold protein templates, and use the maximal alignment score TM-score as the OB-fold feature of the protein, based on which, we constructed the support vector machine (SVM) classification model to automatically distinguish these two kinds of proteins, with prediction accuracy of 87%,83% and 83% for HOLO-set, APO-set and Mixed-set respectively. Conclusions We found that they have different ranges of tunnel lengths and tunnel curvatures; moreover, the alignment results with OB-fold templates have also found to be the discriminative feature of SSBs and DSBs. Experimental results on 10-fold cross validation indicate that the new feature set are effective to describe DNA binding proteins. The evaluation results on both bound (DNA-bound) and non-bound (DNA-free) proteins have shown the satisfactory performance of our method.
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Gamsjaeger R, Kariawasam R, Touma C, Kwan AH, White MF, Cubeddu L. Backbone and side-chain ¹H, ¹³C and ¹⁵N resonance assignments of the OB domain of the single stranded DNA binding protein from Sulfolobus solfataricus and chemical shift mapping of the DNA-binding interface. BIOMOLECULAR NMR ASSIGNMENTS 2014; 8:243-246. [PMID: 23749431 DOI: 10.1007/s12104-013-9492-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 06/03/2013] [Indexed: 06/02/2023]
Abstract
Single stranded DNA binding proteins (SSBs) are present in all known cellular organisms and are critical for DNA replication, recombination and repair. The SSB from the hyperthermophilic crenarchaeote Sulfolobus solfataricus (SsoSSB) has an unusual domain structure with a single DNA-binding oligonucleotide binding (OB) fold coupled to a flexible C-terminal tail. This 'simple' domain organisation differs significantly from other known SSBs, such as human replication protein A (RPA). However, it is conserved in another important human SSB, hSSB1, which we have recently discovered and shown to be essential in the DNA damage response. In this study we report the solution-state backbone and side-chain chemical shift assignments of the OB domain of SsoSSB. In addition, using the recently determined crystal structure, we have utilized NMR to reveal the DNA-binding interface of SsoSSB. These data will allow us to elucidate the structural basis of DNA-binding and shed light onto the molecular mechanism by which these 'simple' SSBs interact with single-stranded DNA.
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Affiliation(s)
- Roland Gamsjaeger
- School of Science and Health, University of Western Sydney, Penrith, NSW, 2751, Australia,
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Raymann K, Forterre P, Brochier-Armanet C, Gribaldo S. Global phylogenomic analysis disentangles the complex evolutionary history of DNA replication in archaea. Genome Biol Evol 2014; 6:192-212. [PMID: 24398374 PMCID: PMC3914693 DOI: 10.1093/gbe/evu004] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The archaeal machinery responsible for DNA replication is largely homologous to that of eukaryotes and is clearly distinct from its bacterial counterpart. Moreover, it shows high diversity in the various archaeal lineages, including different sets of components, heterogeneous taxonomic distribution, and a large number of additional copies that are sometimes highly divergent. This has made the evolutionary history of this cellular system particularly challenging to dissect. Here, we have carried out an exhaustive identification of homologs of all major replication components in over 140 complete archaeal genomes. Phylogenomic analysis allowed assigning them to either a conserved and probably essential core of replication components that were mainly vertically inherited, or to a variable and highly divergent shell of extra copies that have likely arisen from integrative elements. This suggests that replication proteins are frequently exchanged between extrachromosomal elements and cellular genomes. Our study allowed clarifying the history that shaped this key cellular process (ancestral components, horizontal gene transfers, and gene losses), providing important evolutionary and functional information. Finally, our precise identification of core components permitted to show that the phylogenetic signal carried by DNA replication is highly consistent with that harbored by two other key informational machineries (translation and transcription), strengthening the existence of a robust organismal tree for the Archaea.
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Affiliation(s)
- Kasie Raymann
- Département de Microbiologie, Institut Pasteur, Unité Biologie Moléculaire du Gene chez les Extrêmophiles, Paris, France
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C-terminal domain swapping of SSB changes the size of the ssDNA binding site. BIOMED RESEARCH INTERNATIONAL 2014; 2014:573936. [PMID: 25162017 PMCID: PMC4137731 DOI: 10.1155/2014/573936] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 07/09/2014] [Indexed: 01/29/2023]
Abstract
Single-stranded DNA-binding protein (SSB) plays an important role in DNA metabolism, including DNA replication, repair, and recombination, and is therefore essential for cell survival. Bacterial SSB consists of an N-terminal ssDNA-binding/oligomerization domain and a flexible C-terminal protein-protein interaction domain. We characterized the ssDNA-binding properties of Klebsiella pneumoniae SSB (KpSSB), Salmonella enterica Serovar Typhimurium LT2 SSB (StSSB), Pseudomonas aeruginosa PAO1 SSB (PaSSB), and two chimeric KpSSB proteins, namely, KpSSBnStSSBc and KpSSBnPaSSBc. The C-terminal domain of StSSB or PaSSB was exchanged with that of KpSSB through protein chimeragenesis. By using the electrophoretic mobility shift assay, we characterized the stoichiometry of KpSSB, StSSB, PaSSB, KpSSBnStSSBc, and KpSSBnPaSSBc, complexed with a series of ssDNA homopolymers. The binding site sizes were determined to be 26 ± 2, 21 ± 2, 29 ± 2, 21 ± 2, and 29 ± 2 nucleotides (nt), respectively. Comparison of the binding site sizes of KpSSB, KpSSBnStSSBc, and KpSSBnPaSSBc showed that the C-terminal domain swapping of SSB changes the size of the binding site. Our observations suggest that not only the conserved N-terminal domain but also the C-terminal domain of SSB is an important determinant for ssDNA binding.
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Structural insight into the DNA-binding mode of the primosomal proteins PriA, PriB, and DnaT. BIOMED RESEARCH INTERNATIONAL 2014; 2014:195162. [PMID: 25136561 PMCID: PMC4129139 DOI: 10.1155/2014/195162] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 06/20/2014] [Accepted: 07/01/2014] [Indexed: 01/31/2023]
Abstract
Replication restart primosome is a complex dynamic system that is essential for bacterial survival. This system uses various proteins to reinitiate chromosomal DNA replication to maintain genetic integrity after DNA damage. The replication restart primosome in Escherichia coli is composed of PriA helicase, PriB, PriC, DnaT, DnaC, DnaB helicase, and DnaG primase. The assembly of the protein complexes within the forked DNA responsible for reloading the replicative DnaB helicase anywhere on the chromosome for genome duplication requires the coordination of transient biomolecular interactions. Over the last decade, investigations on the structure and mechanism of these nucleoproteins have provided considerable insight into primosome assembly. In this review, we summarize and discuss our current knowledge and recent advances on the DNA-binding mode of the primosomal proteins PriA, PriB, and DnaT.
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Diversity of the DNA replication system in the Archaea domain. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2014; 2014:675946. [PMID: 24790526 PMCID: PMC3984812 DOI: 10.1155/2014/675946] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 02/16/2014] [Indexed: 12/11/2022]
Abstract
The precise and timely duplication of the genome is essential for cellular life. It is achieved by DNA replication, a complex process that is conserved among the three domains of life. Even though the cellular structure of archaea closely resembles that of bacteria, the information processing machinery of archaea is evolutionarily more closely related to the eukaryotic system, especially for the proteins involved in the DNA replication process. While the general DNA replication mechanism is conserved among the different domains of life, modifications in functionality and in some of the specialized replication proteins are observed. Indeed, Archaea possess specific features unique to this domain. Moreover, even though the general pattern of the replicative system is the same in all archaea, a great deal of variation exists between specific groups.
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Ren W, Chen H, Sun Q, Tang X, Lim SC, Huang J, Song H. Structural basis of SOSS1 complex assembly and recognition of ssDNA. Cell Rep 2014; 6:982-991. [PMID: 24630995 DOI: 10.1016/j.celrep.2014.02.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 02/06/2014] [Accepted: 02/14/2014] [Indexed: 01/03/2023] Open
Abstract
The SOSS1 complex comprising SOSSA, SOSSB1, and SOSSC senses single-stranded DNA (ssDNA) and promotes repair of DNA double-strand breaks (DSBs). But how SOSS1 is assembled and recognizes ssDNA remains elusive. The crystal structure of the N-terminal half of SOSSA (SOSSAN) in complex with SOSSB1 and SOSSC showed that SOSSAN serves as a scaffold to bind both SOSSB1 and SOSSC for assembly of the SOSS1 complex. The structures of SOSSAN/B1 in complex with a 12 nt ssDNA and SOSSAN/B1/C in complex with a 35 nt ssDNA showed that SOSSB1 interacts with both SOSSAN and ssDNA via two distinct surfaces. Recognition of ssDNA with a length of up to nine nucleotides is mediated solely by SOSSB1, whereas neither SOSSC nor SOSSAN are critical for ssDNA binding. These results reveal the structural basis of SOSS1 assembly and provide a framework for further study of the mechanism governing longer ssDNA recognition by the SOSS1 complex during DSB repair.
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Affiliation(s)
- Wendan Ren
- Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China; Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Hongxia Chen
- Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China
| | - Qiangzu Sun
- Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China
| | - Xuhua Tang
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Siew Choo Lim
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Jun Huang
- Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China.
| | - Haiwei Song
- Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China; Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore; Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore 117543, Singapore.
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Spies M. Two steps forward, one step back: determining XPD helicase mechanism by single-molecule fluorescence and high-resolution optical tweezers. DNA Repair (Amst) 2014; 20:58-70. [PMID: 24560558 DOI: 10.1016/j.dnarep.2014.01.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 12/31/2013] [Accepted: 01/13/2014] [Indexed: 11/17/2022]
Abstract
XPD-like helicases constitute a prominent DNA helicase family critical for many aspects of genome maintenance. These enzymes share a unique structural feature, an auxiliary domain stabilized by an iron-sulphur (FeS) cluster, and a 5'-3' polarity of DNA translocation and duplex unwinding. Biochemical analyses alongside two single-molecule approaches, total internal reflection fluorescence microscopy and high-resolution optical tweezers, have shown how the unique structural features of XPD helicase and its specific patterns of substrate interactions tune the helicase for its specific cellular function and shape its molecular mechanism. The FeS domain forms a duplex separation wedge and contributes to an extended DNA binding site. Interactions within this site position the helicase in an orientation to unwind the duplex, control the helicase rate, and verify the integrity of the translocating strand. Consistent with its cellular role, processivity of XPD is limited and is defined by an idiosyncratic stepping kinetics. DNA duplex separation occurs in single base pair steps punctuated by frequent backward steps and conformational rearrangements of the protein-DNA complex. As such, the helicase in isolation mainly stabilizes spontaneous base pair opening and exhibits a limited ability to unwind stable DNA duplexes. The presence of a cognate ssDNA binding protein converts XPD into a vigorous helicase by destabilizing the upstream dsDNA as well as by trapping the unwound strands. Remarkably, the two proteins can co-exist on the same DNA strand without competing for binding. The current model of the XPD unwinding mechanism will be discussed along with possible modifications to this mechanism by the helicase interacting partners and unique features of such bio-medically important XPD-like helicases as FANCJ (BACH1), RTEL1 and CHLR1 (DDX11).
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Affiliation(s)
- Maria Spies
- Department of Biochemistry, University of Iowa Carver College of Medicine, IA 52242, United States.
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