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Aniukwu J, Glickman MS, Shuman S. The pathways and outcomes of mycobacterial NHEJ depend on the structure of the broken DNA ends. Genes Dev 2008; 22:512-27. [PMID: 18281464 DOI: 10.1101/gad.1631908] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Mycobacteria can repair DNA double-strand breaks (DSBs) via a nonhomologous end-joining (NHEJ) system that includes a dedicated DNA ligase (LigD) and the DNA end-binding protein Ku. Here we exploit an improved plasmid-based NHEJ assay and a collection of Mycobacterium smegmatis strains bearing deletions or mutations in Ku or the DNA ligases to interrogate the contributions of LigD's three catalytic activities (polymerase, ligase, and 3' phosphoesterase) and structural domains (POL, LIG, and PE) to the efficiency and molecular outcomes of NHEJ in vivo. By analyzing in parallel the repair of blunt, 5' overhang, and 3' overhang DSBs, we discovered a novel end-joining pathway specific to breaks with 3' overhangs that is Ku- and LigD-independent and perfectly faithful. This 3' overhang NHEJ pathway is independent of ligases B and C; we surmise that it relies on NAD(+)-dependent LigA, the essential replicative ligase. We find that efficient repair of blunt and 5' overhang DSBs depends stringently on Ku and the LigD POL domain, but not on the LigD polymerase activity, which mainly serves to promote NHEJ infidelity. The lack of an effect of PE-inactivating LigD mutations on NHEJ outcomes, especially the balance between deletions and insertions at blunt or 5' overhang breaks, argues against LigD being the catalyst of deletion formation. Ligase-inactivating LigD mutations (or deletion of the LIG domain) have a modest impact on the efficiency of blunt and 5' overhang DSB repair, because the strand sealing activity can be provided in trans by one of the other resident ATP-dependent ligases (likely LigC). Reliance on the backup ligase is accompanied by a drastic loss of fidelity during blunt end and 5' overhang DSB repair. We conclude that the mechanisms of mycobacterial NHEJ are many and the outcomes depend on the initial structures of the DSBs and the available ensemble of end-processing and end-sealing components, which are not limited to Ku and LigD.
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Affiliation(s)
- Jideofor Aniukwu
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA
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Gioia J, Yerrapragada S, Qin X, Jiang H, Igboeli OC, Muzny D, Dugan-Rocha S, Ding Y, Hawes A, Liu W, Perez L, Kovar C, Dinh H, Lee S, Nazareth L, Blyth P, Holder M, Buhay C, Tirumalai MR, Liu Y, Dasgupta I, Bokhetache L, Fujita M, Karouia F, Eswara Moorthy P, Siefert J, Uzman A, Buzumbo P, Verma A, Zwiya H, McWilliams BD, Olowu A, Clinkenbeard KD, Newcombe D, Golebiewski L, Petrosino JF, Nicholson WL, Fox GE, Venkateswaran K, Highlander SK, Weinstock GM. Paradoxical DNA repair and peroxide resistance gene conservation in Bacillus pumilus SAFR-032. PLoS One 2007; 2:e928. [PMID: 17895969 PMCID: PMC1976550 DOI: 10.1371/journal.pone.0000928] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Accepted: 08/31/2007] [Indexed: 11/25/2022] Open
Abstract
Background Bacillus spores are notoriously resistant to unfavorable conditions such as UV radiation, γ-radiation, H2O2, desiccation, chemical disinfection, or starvation. Bacillus pumilus SAFR-032 survives standard decontamination procedures of the Jet Propulsion Lab spacecraft assembly facility, and both spores and vegetative cells of this strain exhibit elevated resistance to UV radiation and H2O2 compared to other Bacillus species. Principal Findings The genome of B. pumilus SAFR-032 was sequenced and annotated. Lists of genes relevant to DNA repair and the oxidative stress response were generated and compared to B. subtilis and B. licheniformis. Differences in conservation of genes, gene order, and protein sequences are highlighted because they potentially explain the extreme resistance phenotype of B. pumilus. The B. pumilus genome includes genes not found in B. subtilis or B. licheniformis and conserved genes with sequence divergence, but paradoxically lacks several genes that function in UV or H2O2 resistance in other Bacillus species. Significance This study identifies several candidate genes for further research into UV and H2O2 resistance. These findings will help explain the resistance of B. pumilus and are applicable to understanding sterilization survival strategies of microbes.
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Affiliation(s)
- Jason Gioia
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Shailaja Yerrapragada
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Huaiyang Jiang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Okezie C. Igboeli
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Shannon Dugan-Rocha
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Yan Ding
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Alicia Hawes
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Wen Liu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lesette Perez
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Christie Kovar
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Huyen Dinh
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sandra Lee
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lynne Nazareth
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Peter Blyth
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Michael Holder
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Christian Buhay
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Madhan R. Tirumalai
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Yamei Liu
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Indrani Dasgupta
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Lina Bokhetache
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Masaya Fujita
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Fathi Karouia
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Prahathees Eswara Moorthy
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Johnathan Siefert
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Akif Uzman
- Department of Natural Sciences, University of Houston‐Downtown, Houston, Texas, United States of America
| | - Prince Buzumbo
- Department of Natural Sciences, University of Houston‐Downtown, Houston, Texas, United States of America
| | - Avani Verma
- Department of Natural Sciences, University of Houston‐Downtown, Houston, Texas, United States of America
| | - Hiba Zwiya
- Department of Natural Sciences, University of Houston‐Downtown, Houston, Texas, United States of America
| | - Brian D. McWilliams
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Adeola Olowu
- University of St. Thomas, Houston Texas, United States of America
| | - Kenneth D. Clinkenbeard
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - David Newcombe
- University of Idaho Coeur d'Alene, Coeur d'Alene, Idaho, United States of America
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, United States of America
| | - Lisa Golebiewski
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph F. Petrosino
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Wayne L. Nicholson
- Department of Microbiology and Cell Science, University of Florida Space Life Sciences Laboratory, Kennedy Space Center, Florida, United States of America
| | - George E. Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Kasthuri Venkateswaran
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, United States of America
| | - Sarah K. Highlander
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - George M. Weinstock
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- * To whom correspondence should be addressed. E-mail:
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