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Shi C, Wang L, Xu H, Zhao Y, Tian B, Hua Y. Characterization of a Novel N4-Methylcytosine Restriction-Modification System in Deinococcus radiodurans. Int J Mol Sci 2024; 25:1660. [PMID: 38338939 PMCID: PMC10855626 DOI: 10.3390/ijms25031660] [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: 12/21/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Deinococcus radiodurans is an extremophilic microorganism that possesses a unique DNA damage repair system, conferring a strong resistance to radiation, desiccation, oxidative stress, and chemical damage. Recently, we discovered that D. radiodurans possesses an N4-methylation (m4C) methyltransferase called M.DraR1, which recognizes the 5'-CCGCGG-3' sequence and methylates the second cytosine. Here, we revealed its cognate restriction endonuclease R.DraR1 and recognized that it is the only endonuclease specially for non-4C-methylated 5'-CCGCGG-3' sequence so far. We designated the particular m4C R.DraR1-M.DraR1 as the DraI R-M system. Bioinformatics searches displayed the rarity of the DraI R-M homologous system. Meanwhile, recombination and transformation efficiency experiments demonstrated the important role of the DraI R-M system in response to oxidative stress. In addition, in vitro activity experiments showed that R.DraR1 could exceptionally cleave DNA substrates with a m5C-methlated 5'-CCGCGG-3' sequence instead of its routine activity, suggesting that this particular R-M component possesses a broader substrate choice. Furthermore, an imbalance of the DraI R-M system led to cell death through regulating genes involved in the maintenance of cell survival such as genome stability, transporter, and energy production. Thus, our research revealed a novel m4C R-M system that plays key roles in maintaining cell viability and defending foreign DNA in D. radiodurans.
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Affiliation(s)
- Chenxiang Shi
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (C.S.); (H.X.); (Y.Z.); (B.T.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Liangyan Wang
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (C.S.); (H.X.); (Y.Z.); (B.T.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Hong Xu
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (C.S.); (H.X.); (Y.Z.); (B.T.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Ye Zhao
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (C.S.); (H.X.); (Y.Z.); (B.T.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Bing Tian
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (C.S.); (H.X.); (Y.Z.); (B.T.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Yuejin Hua
- MOE Key Laboratory of Biosystems Homeostasis and Protection, Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (C.S.); (H.X.); (Y.Z.); (B.T.)
- Cancer Center, Zhejiang University, Hangzhou 310058, China
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Li S, Cai J, Lu H, Mao S, Dai S, Hu J, Wang L, Hua X, Xu H, Tian B, Zhao Y, Hua Y. N 4-Cytosine DNA Methylation Is Involved in the Maintenance of Genomic Stability in Deinococcus radiodurans. Front Microbiol 2019; 10:1905. [PMID: 31497001 PMCID: PMC6712171 DOI: 10.3389/fmicb.2019.01905] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/05/2019] [Indexed: 12/16/2022] Open
Abstract
DNA methylation serves as a vital component of restriction-modification (R-M) systems in bacteria, where it plays a crucial role in defense against foreign DNA. Recent studies revealed that DNA methylation has a global impact on gene expression. Deinococcus radiodurans, an ideal model organism for studying DNA repair and genomic stability, possesses unparalleled resistance to DNA-damaging agents such as irradiation and strong oxidation. However, details on the methylome of this bacterium remain unclear. Here, we demonstrate that N 4-cytosine is the major methylated form (4mC) in D. radiodurans. A novel methylated motif, "C4mCGCGG" was identified that was fully attributed to M.DraR1 methyltransferase. M.DraR1 can specifically bind and methylate the second cytosine at N 4 atom of "CCGCGG" motif, preventing its digestion by a cognate restriction endonuclease. Cells deficient in 4mC modification displayed higher spontaneous rifampin mutation frequency and enhanced DNA recombination and transformation efficiency. And genes involved in the maintenance of genomic stability were differentially expressed in conjunction with the loss of M.DraR1. This study provides evidence that N 4-cytosine DNA methylation contributes to genomic stability of D. radiodurans and lays the foundation for further research on the mechanisms of epigenetic regulation by R-M systems in bacteria.
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Affiliation(s)
- Shengjie Li
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, China
| | - Jianling Cai
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, China
| | - Huizhi Lu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, China
| | - Shuyu Mao
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, China
| | - Shang Dai
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, China
| | - Jing Hu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, China
| | - Liangyan Wang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Hong Xu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, China
| | - Bing Tian
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, China
| | - Ye Zhao
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, China
| | - Yuejin Hua
- The MOE Key Laboratory of Biosystems Homeostasis & Protection, Zhejiang University, Hangzhou, China
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Deinococcus radiodurans HD-Pnk, a Nucleic Acid End-Healing Enzyme, Abets Resistance to Killing by Ionizing Radiation and Mitomycin C. J Bacteriol 2018; 200:JB.00151-18. [PMID: 29891641 DOI: 10.1128/jb.00151-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 06/06/2018] [Indexed: 12/11/2022] Open
Abstract
5'- and 3'-end healing are key steps in nucleic acid break repair in which 5'-OH and 3'-PO4 or 2',3'-cyclic-PO4 ends are converted to 5'-PO4 and 3'-OH termini suitable for sealing by polynucleotide ligases. Here, we characterize Deinococcus radiodurans HD-Pnk as a bifunctional end-healing enzyme composed of N-terminal HD (histidine-aspartate) phosphoesterase and C-terminal P-loop polynucleotide kinase (Pnk) domains. HD-Pnk phosphorylates 5'-OH DNA in the presence of ATP and magnesium. HD-Pnk has 3'-phosphatase and 2',3'-cyclic-phosphodiesterase activity in the presence of transition metals, optimally cobalt or copper, and catalyzes copper-dependent hydrolysis of p-nitrophenylphosphate. HD-Pnk is encoded by the LIG-PARG-HD-Pnk three-gene operon, which includes polynucleotide ligase and poly(ADP-ribose) glycohydrolase genes. We show that whereas HD-Pnk is inessential for Deinococcus growth, its absence sensitizes by 80-fold bacteria to killing by 9 kGy of ionizing radiation (IR). HD-Pnk protein is depleted during early stages of post-IR recovery and then replenished at 15 h, after reassembly of the genome from shattered fragments. ΔHD-Pnk mutant cells are competent for genome reassembly, as gauged by pulsed-field gel electrophoresis. Our findings suggest a role for HD-Pnk in repairing residual single-strand gaps or nicks in the reassembled genome. HD-Pnk-Ala mutations that ablate kinase or phosphoesterase activity sensitize Deinococcus to killing by mitomycin C.IMPORTANCE End healing is a process whereby nucleic acid breaks with "dirty" 3'-PO4 or 2',3'-cyclic-PO4 and 5'-OH ends are converted to 3'-OH and 5'-PO4 termini that are amenable to downstream repair reactions. Deinococcus radiodurans is resistant to massive doses of ionizing radiation (IR) that generate hundreds of dirty DNA double-strand breaks and thousands of single-strand breaks. This study highlights Deinococcus HD-Pnk as a bifunctional 3'- and 5'-end-healing enzyme that helps protect against killing by IR. HD-Pnk appears to act late in the process of post-IR recovery, subsequent to genome reassembly from shattered fragments. HD-Pnk also contributes to resistance to killing by mitomycin C. These findings are significant in that they establish a role for end-healing enzymes in bacterial DNA damage repair.
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