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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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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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