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Zhang Y, Ren Y, Wang B, Guo S, Wang S, Jin J, Yang L, Gao W. Purification, crystallization and preliminary crystallographic analysis of Chlamydophila pneumoniae AP endonuclease IV. Protein Expr Purif 2024; 219:106476. [PMID: 38521114 DOI: 10.1016/j.pep.2024.106476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/20/2024] [Accepted: 03/21/2024] [Indexed: 03/25/2024]
Abstract
Base excision is a crucial DNA repair process mediated by endonuclease IV in nucleotide excision. In Chlamydia pneumoniae, CpendoIV is the exclusive AP endonuclease IV, exhibiting DNA replication error-proofreading capabilities, making it a promising target for anti-chlamydial drug development. Predicting the structure of CpendoIV, molecular docking with DNA was performed, analyzing complex binding sites and protein surface electrostatic potential. Comparative structural studies were conducted with E. coli EndoIV and DNA complex containing AP sites.CpendoIV was cloned, expressed in E. coli, and purified via Ni-NTA chelation and size-exclusion chromatography. Low NaCl concentrations induced aggregation during purification, while high concentrations enhanced purity.CpendoIV recognizes and cleaving AP sites on dsDNA, and Zn2+ influences the activity. Crystallization was achieved under 8% (v/v) Tacsimate pH 5.2, 25% (w/v) polyethylene glycol 3350, and 1.91 Å resolution X-ray diffraction data was obtained at 100 K. This research is significant for provides a deeper understanding of CpendoIV involvement in the base excision repair process, offering insights into Chlamydia pneumoniae.
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Affiliation(s)
- Yitong Zhang
- School of Science, Beijing Forestry University, 35 Qinghuadong Road, Beijing, 100083, China.
| | - Yangjie Ren
- School of Science, Beijing Forestry University, 35 Qinghuadong Road, Beijing, 100083, China.
| | - Ben Wang
- School of Science, Beijing Forestry University, 35 Qinghuadong Road, Beijing, 100083, China.
| | - Shiyang Guo
- School of Science, Beijing Forestry University, 35 Qinghuadong Road, Beijing, 100083, China.
| | - Siqi Wang
- School of Science, Beijing Forestry University, 35 Qinghuadong Road, Beijing, 100083, China.
| | - Jinglin Jin
- School of Science, Beijing Forestry University, 35 Qinghuadong Road, Beijing, 100083, China.
| | - Lihong Yang
- School of Science, Beijing Forestry University, 35 Qinghuadong Road, Beijing, 100083, China.
| | - Wei Gao
- School of Science, Beijing Forestry University, 35 Qinghuadong Road, Beijing, 100083, China.
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Dymova MA, Endutkin AV, Polunovsky VV, Zakabunin AI, Khrapov EA, Torgasheva NA, Yudkina AV, Mechetin GV, Filipenko ML, Zharkov DO. Characterization of Recombinant Endonuclease IV from Mycobacterium tuberculosis. Mol Biol 2021. [DOI: 10.1134/s0026893321020059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Identification of a Novel Cobamide Remodeling Enzyme in the Beneficial Human Gut Bacterium Akkermansia muciniphila. mBio 2020; 11:mBio.02507-20. [PMID: 33293380 PMCID: PMC7733943 DOI: 10.1128/mbio.02507-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cobamides, comprising the vitamin B12 family of cobalt-containing cofactors, are required for metabolism in all domains of life, including most bacteria. Cobamides have structural variability in the lower ligand, and selectivity for particular cobamides has been observed in most organisms studied to date. The beneficial human gut bacterium Akkermansia muciniphila provides metabolites to other members of the gut microbiota by breaking down host mucin, but most of its other metabolic functions have not been investigated. A. muciniphila strain MucT is known to use cobamides, the vitamin B12 family of cofactors with structural diversity in the lower ligand. However, A. muciniphila MucT is unable to synthesize cobamides de novo, and the specific forms that can be used by A. muciniphila have not been examined. We found that the levels of growth of A. muciniphila MucT were nearly identical with each of seven cobamides tested, in contrast to nearly all bacteria that had been studied previously. Unexpectedly, this promiscuity is due to cobamide remodeling—the removal and replacement of the lower ligand—despite the absence of the canonical remodeling enzyme CbiZ in A. muciniphila. We identified a novel enzyme, CbiR, that is capable of initiating the remodeling process by hydrolyzing the phosphoribosyl bond in the nucleotide loop of cobamides. CbiR does not share similarity with other cobamide remodeling enzymes or B12-binding domains and is instead a member of the apurinic/apyrimidinic (AP) endonuclease 2 enzyme superfamily. We speculate that CbiR enables bacteria to repurpose cobamides that they cannot otherwise use in order to grow under cobamide-requiring conditions; this function was confirmed by heterologous expression of cbiR in Escherichia coli. Homologs of CbiR are found in over 200 microbial taxa across 22 phyla, suggesting that many bacteria may use CbiR to gain access to the diverse cobamides present in their environment.
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Chen Y, Chen X, Huang Q, Shao Z, Gao Y, Li Y, Yang C, Liu H, Li J, Wang Q, Ma J, Zhang YZ, Gu Y, Gan J. A unique DNA-binding mode of African swine fever virus AP endonuclease. Cell Discov 2020; 6:13. [PMID: 32194979 PMCID: PMC7076025 DOI: 10.1038/s41421-020-0146-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 02/13/2020] [Indexed: 12/31/2022] Open
Abstract
African swine fever virus (ASFV) is highly contagious and can cause lethal disease in pigs. ASFV is primarily replicated in the cytoplasm of pig macrophages, which is oxidative and caused constant damage to ASFV genome. ASFV AP endonuclease (AsfvAP) catalyzes DNA cleavage reaction at the abasic site and is a key enzyme of ASFV base excision repair (BER) system. Although it plays an essential role in ASFV survival in host cells, the basis underlying substrate binding and cleavage by AsfvAP remains unclear. Here, we reported the structural and functional studies of AsfvAP, showing that AsfvAP adopts a novel DNA-binding mode distinct from other APs. AsfvAP possesses many unique structural features, including one narrower nucleotide-binding pocket at the active site, the C16-C20 disulfide bond-containing region, and histidine-rich loop. As indicated by our mutagenesis, in vitro binding and cleavage assays, these features are important for AsfvAP to suit the acidic and oxidative environment. Owing to their functional importance, these unique features could serve as targets for designing small molecule inhibitors that could disrupt the repair process of ASFV genome and help fight against this deadly virus in the future.
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Affiliation(s)
- Yiqing Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Xi Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Qi Huang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Zhiwei Shao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Yanqing Gao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Yangyang Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Chun Yang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Hehua Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237 Shanghai, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Yong-Zhen Zhang
- Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, 200438 Shanghai, China
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, 102206 Beijing, China
| | - Yijun Gu
- National Center for Protein Science Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, 201210 Shanghai, China
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, 200438 Shanghai, China
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Mittal P, Sinha R, Kumar A, Singh P, Ngasainao MR, Singh A, Singh IK. Focusing on DNA Repair and Damage Tolerance Mechanisms in Mycobacterium tuberculosis: An Emerging Therapeutic Theme. Curr Top Med Chem 2020; 20:390-408. [PMID: 31924156 DOI: 10.2174/1568026620666200110114322] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/02/2019] [Accepted: 10/10/2019] [Indexed: 11/22/2022]
Abstract
Tuberculosis (TB) is one such disease that has become a nuisance in the world scenario and one of the most deadly diseases of the current times. The etiological agent of tuberculosis, Mycobacterium tuberculosis (M. tb) kills millions of people each year. Not only 1.7 million people worldwide are estimated to harbor M. tb in the latent form but also 5 to 15 percent of which are expected to acquire an infection during a lifetime. Though curable, a long duration of drug regimen and expense leads to low patient adherence. The emergence of multi-, extensive- and total- drug-resistant strains of M. tb further complicates the situation. Owing to high TB burden, scientists worldwide are trying to design novel therapeutics to combat this disease. Therefore, to identify new drug targets, there is a growing interest in targeting DNA repair pathways to fight this infection. Thus, this review aims to explore DNA repair and damage tolerance as an efficient target for drug development by understanding M. tb DNA repair and tolerance machinery and its regulation, its role in pathogenesis and survival, mutagenesis, and consequently, in the development of drug resistance.
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Affiliation(s)
- Pooja Mittal
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Rajesh Sinha
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Amit Kumar
- Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India
| | - Pooja Singh
- Public Health Research Institute, NJMS-Rutgers University, New Jersey, United States
| | - Moses Rinchui Ngasainao
- Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India.,Department of Molecular Ecology, Max-Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Indrakant K Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India.,Department of Molecular Ecology, Max-Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
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