51
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Yakovleva L, Shuman S. Mycobacterium smegmatis SftH exemplifies a distinctive clade of superfamily II DNA-dependent ATPases with 3' to 5' translocase and helicase activities. Nucleic Acids Res 2012; 40:7465-75. [PMID: 22641846 PMCID: PMC3424565 DOI: 10.1093/nar/gks417] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Bacterial DNA helicases are nucleic acid-dependent NTPases that play important roles in DNA replication, recombination and repair. We are interested in the DNA helicases of Mycobacteria, a genus of the phylum Actinobacteria, which includes the human pathogen Mycobacterium tuberculosis and its avirulent relative Mycobacterium smegmatis. Here, we identify and characterize M. smegmatis SftH, a superfamily II helicase with a distinctive domain structure, comprising an N-terminal NTPase domain and a C-terminal DUF1998 domain (containing a putative tetracysteine metal-binding motif). We show that SftH is a monomeric DNA-dependent ATPase/dATPase that translocates 3' to 5' on single-stranded DNA and has 3' to 5' helicase activity. SftH homologs are found in bacteria representing 12 different phyla, being especially prevalent in Actinobacteria (including M. tuberculosis). SftH homologs are evident in more than 30 genera of Archaea. Among eukarya, SftH homologs are present in plants and fungi.
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Affiliation(s)
- Lyudmila Yakovleva
- Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
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52
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Amundsen SK, Spicer T, Karabulut AC, Londoño LM, Eberhart C, Fernandez Vega V, Bannister TD, Hodder P, Smith GR. Small-molecule inhibitors of bacterial AddAB and RecBCD helicase-nuclease DNA repair enzymes. ACS Chem Biol 2012; 7:879-91. [PMID: 22443934 DOI: 10.1021/cb300018x] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The AddAB and RecBCD helicase-nucleases are related enzymes prevalent among bacteria but not eukaryotes and are instrumental in the repair of DNA double-strand breaks and in genetic recombination. Although these enzymes have been extensively studied both genetically and biochemically, inhibitors specific for this class of enzymes have not been reported. We developed a high-throughput screen based on the ability of phage T4 gene 2 mutants to grow in Escherichia coli only if the host RecBCD enzyme, or a related helicase-nuclease, is inhibited or genetically inactivated. We optimized this screen for use in 1536-well plates and screened 326,100 small molecules in the NIH molecular libraries sample collection for inhibitors of the Helicobacter pylori AddAB enzyme expressed in an E. coli recBCD deletion strain. Secondary screening used assays with cells expressing AddAB or RecBCD and a viability assay that measured the effect of compounds on cell growth without phage infection. From this screening campaign, 12 compounds exhibiting efficacy and selectivity were tested for inhibition of purified AddAB and RecBCD helicase and nuclease activities and in cell-based assays for recombination; seven were active in the 0.1-50 μM range in one or another assay. Compounds structurally related to two of these were similarly tested, and three were active in the 0.1-50 μM range. These compounds should be useful in further enzymatic, genetic, and physiological studies of these enzymes, both purified and in cells. They may also lead to useful antibacterial agents, since this class of enzymes is needed for successful bacterial infection of mammals.
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Affiliation(s)
- Susan K. Amundsen
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
98109, United States
| | - Timothy Spicer
- Scripps
Research Institute Molecular
Screening Center, Lead Identification Division, Translational Research Institute, Jupiter, Florida 33458, United States
| | - Ahmet C. Karabulut
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
98109, United States
| | - Luz Marina Londoño
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
98109, United States
| | - Christina Eberhart
- Scripps
Research Institute Molecular
Screening Center, Lead Identification Division, Translational Research Institute, Jupiter, Florida 33458, United States
| | - Virneliz Fernandez Vega
- Scripps
Research Institute Molecular
Screening Center, Lead Identification Division, Translational Research Institute, Jupiter, Florida 33458, United States
| | - Thomas D. Bannister
- Scripps Research Institute Department
of Chemistry, Translational Research Institute, Jupiter, Florida 33458, United States
| | - Peter Hodder
- Scripps
Research Institute Molecular
Screening Center, Lead Identification Division, Translational Research Institute, Jupiter, Florida 33458, United States
- Department of Molecular Therapeutics, Scripps Florida, Jupiter, Florida 33458, United States
| | - Gerald R. Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
98109, United States
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53
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Saikrishnan K, Yeeles JT, Gilhooly NS, Krajewski WW, Dillingham MS, Wigley DB. Insights into Chi recognition from the structure of an AddAB-type helicase-nuclease complex. EMBO J 2012; 31:1568-78. [PMID: 22307084 PMCID: PMC3321194 DOI: 10.1038/emboj.2012.9] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 01/04/2012] [Indexed: 12/19/2022] Open
Abstract
Homologous recombination DNA repair requires double-strand break resection by helicase–nuclease enzymes. The crystal structure of bacterial AddAB in complex with DNA substrates shows that it employs an inactive helicase site to recognize ‘Chi' recombination hotspot sequences that regulate resection. In bacterial cells, processing of double-stranded DNA breaks for repair by homologous recombination is dependent upon the recombination hotspot sequence Chi and is catalysed by either an AddAB- or RecBCD-type helicase–nuclease. Here, we report the crystal structure of AddAB bound to DNA. The structure allows identification of a putative Chi-recognition site in an inactivated helicase domain of the AddB subunit. By generating mutant protein complexes that do not respond to Chi, we show that residues responsible for Chi recognition are located in positions equivalent to the signature motifs of a conventional helicase. Comparison with the related RecBCD complex, which recognizes a different Chi sequence, provides further insight into the structural basis for sequence-specific ssDNA recognition. The structure suggests a simple mechanism for DNA break processing, explains how AddAB and RecBCD can accomplish the same overall reaction with different sets of functional modules and reveals details of the role of an Fe–S cluster in protein stability and DNA binding.
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Affiliation(s)
- Kayarat Saikrishnan
- Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, London, UK
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54
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Ordonez H, Unciuleac M, Shuman S. Mycobacterium smegmatis RqlH defines a novel clade of bacterial RecQ-like DNA helicases with ATP-dependent 3'-5' translocase and duplex unwinding activities. Nucleic Acids Res 2012; 40:4604-14. [PMID: 22287622 PMCID: PMC3378886 DOI: 10.1093/nar/gks046] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Escherichia coli RecQ DNA helicase participates in a pathway of DNA repair that operates in parallel to the recombination pathway driven by the multisubunit helicase–nuclease machine RecBCD. The model mycobacterium Mycobacterium smegmatis executes homologous recombination in the absence of its helicase–nuclease machine AdnAB, though it lacks a homolog of E. coli RecQ. Here, we identify and characterize M. smegmatis RqlH, a RecQ-like helicase with a distinctive domain structure. The 691-amino acid RqlH polypeptide consists of a RecQ-like ATPase domain (amino acids 1–346) and tetracysteine zinc-binding domain (amino acids 435–499), separated by an RqlH-specific linker. RqlH lacks the C-terminal HRDC domain found in E. coli RecQ. Rather, the RqlH C-domain resembles bacterial ComF proteins and includes a phosphoribosyltransferase-like module. We show that RqlH is a DNA-dependent ATPase/dATPase that translocates 3′–5′ on single-stranded DNA and has 3′–5′ helicase activity. These functions inhere to RqlH-(1–505), a monomeric motor unit comprising the ATPase, linker and zinc-binding domains. RqlH homologs are distributed widely among bacterial taxa. The mycobacteria that encode RqlH lack a classical RecQ, though many other Actinobacteria have both RqlH and RecQ. Whereas E. coli K12 encodes RecQ but lacks a homolog of RqlH, other strains of E. coli have both RqlH and RecQ.
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Affiliation(s)
- Heather Ordonez
- Molecular Biology Program, Sloan-Kettering Institute, NY 10065, USA
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55
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Blackwood JK, Rzechorzek NJ, Abrams AS, Maman JD, Pellegrini L, Robinson NP. Structural and functional insights into DNA-end processing by the archaeal HerA helicase-NurA nuclease complex. Nucleic Acids Res 2011; 40:3183-96. [PMID: 22135300 PMCID: PMC3326311 DOI: 10.1093/nar/gkr1157] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Helicase–nuclease systems dedicated to DNA end resection in preparation for homologous recombination (HR) are present in all kingdoms of life. In thermophilic archaea, the HerA helicase and NurA nuclease cooperate with the highly conserved Mre11 and Rad50 proteins during HR-dependent DNA repair. Here we show that HerA and NurA must interact in a complex with specific subunit stoichiometry to process DNA ends efficiently. We determine crystallographically that NurA folds in a toroidal dimer of intertwined RNaseH-like domains. The central channel of the NurA dimer is too narrow for double-stranded DNA but appears well suited to accommodate one or two strands of an unwound duplex. We map a critical interface of the complex to an exposed hydrophobic epitope of NurA abutting the active site. Based upon the presented evidence, we propose alternative mechanisms of DNA end processing by the HerA-NurA complex.
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Affiliation(s)
- John K Blackwood
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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56
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Cardenas PP, Carzaniga T, Zangrossi S, Briani F, Garcia-Tirado E, Dehò G, Alonso JC. Polynucleotide phosphorylase exonuclease and polymerase activities on single-stranded DNA ends are modulated by RecN, SsbA and RecA proteins. Nucleic Acids Res 2011; 39:9250-61. [PMID: 21859751 PMCID: PMC3241651 DOI: 10.1093/nar/gkr635] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Bacillus subtilis pnpA gene product, polynucleotide phosphorylase (PNPase), is involved in double-strand break (DSB) repair via homologous recombination (HR) or non-homologous end-joining (NHEJ). RecN is among the first responders to localize at the DNA DSBs, with PNPase facilitating the formation of a discrete RecN focus per nucleoid. PNPase, which co-purifies with RecA and RecN, was able to degrade single-stranded (ss) DNA with a 3′ → 5′ polarity in the presence of Mn2+ and low inorganic phosphate (Pi) concentration, or to extend a 3′-OH end in the presence dNDP·Mn2+. Both PNPase activities were observed in evolutionarily distant bacteria (B. subtilis and Escherichia coli), suggesting conserved functions. The activity of PNPase was directed toward ssDNA degradation or polymerization by manipulating the Pi/dNDPs concentrations or the availability of RecA or RecN. In its dATP-bound form, RecN stimulates PNPase-mediated polymerization. ssDNA phosphorolysis catalyzed by PNPase is stimulated by RecA, but inhibited by SsbA. Our findings suggest that (i) the PNPase degradative and polymerizing activities might play a critical role in the transition from DSB sensing to end resection via HR and (ii) by blunting a 3′-tailed duplex DNA, in the absence of HR, B. subtilis PNPase might also contribute to repair via NHEJ.
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Affiliation(s)
- Paula P Cardenas
- Centro Nacional de Biotecnología-CSIC, Darwin 3, 28049 Madrid, Spain
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57
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Stallings CL, Chu L, Li LX, Glickman MS. Catalytic and non-catalytic roles for the mono-ADP-ribosyltransferase Arr in the mycobacterial DNA damage response. PLoS One 2011; 6:e21807. [PMID: 21789183 PMCID: PMC3138739 DOI: 10.1371/journal.pone.0021807] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 06/07/2011] [Indexed: 01/28/2023] Open
Abstract
Recent evidence indicates that the mycobacterial response to DNA double strand breaks (DSBs) differs substantially from previously characterized bacteria. These differences include the use of three DSB repair pathways (HR, NHEJ, SSA), and the CarD pathway, which integrates DNA damage with transcription. Here we identify a role for the mono-ADP-ribosyltransferase Arr in the mycobacterial DNA damage response. Arr is transcriptionally induced following DNA damage and cellular stress. Although Arr is not required for induction of a core set of DNA repair genes, Arr is necessary for suppression of a set of ribosomal protein genes and rRNA during DNA damage, placing Arr in a similar pathway as CarD. Surprisingly, the catalytic activity of Arr is not required for this function, as catalytically inactive Arr was still able to suppress ribosomal protein and rRNA expression during DNA damage. In contrast, Arr substrate binding and catalytic activities were required for regulation of a small subset of other DNA damage responsive genes, indicating that Arr has both catalytic and noncatalytic roles in the DNA damage response. Our findings establish an endogenous cellular function for a mono-ADP-ribosyltransferase apart from its role in mediating Rifampin resistance.
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Affiliation(s)
- Christina L. Stallings
- Department of Molecular Microbiology Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Linda Chu
- Immunology program, Sloan Kettering Institute, New York, New York, United States of America
| | - Lucy X. Li
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Summer Undergraduate Research Program, New York, New York, United States of America
| | - Michael S. Glickman
- Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Immunology program, Sloan Kettering Institute, New York, New York, United States of America
- * E-mail:
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58
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Ayora S, Carrasco B, Cárdenas PP, César CE, Cañas C, Yadav T, Marchisone C, Alonso JC. Double-strand break repair in bacteria: a view from Bacillus subtilis. FEMS Microbiol Rev 2011; 35:1055-81. [PMID: 21517913 DOI: 10.1111/j.1574-6976.2011.00272.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
In all living organisms, the response to double-strand breaks (DSBs) is critical for the maintenance of chromosome integrity. Homologous recombination (HR), which utilizes a homologous template to prime DNA synthesis and to restore genetic information lost at the DNA break site, is a complex multistep response. In Bacillus subtilis, this response can be subdivided into five general acts: (1) recognition of the break site(s) and formation of a repair center (RC), which enables cells to commit to HR; (2) end-processing of the broken end(s) by different avenues to generate a 3'-tailed duplex and RecN-mediated DSB 'coordination'; (3) loading of RecA onto single-strand DNA at the RecN-induced RC and concomitant DNA strand exchange; (4) branch migration and resolution, or dissolution, of the recombination intermediates, and replication restart, followed by (5) disassembly of the recombination apparatus formed at the dynamic RC and segregation of sister chromosomes. When HR is impaired or an intact homologous template is not available, error-prone nonhomologous end-joining directly rejoins the two broken ends by ligation. In this review, we examine the functions that are known to contribute to DNA DSB repair in B. subtilis, and compare their properties with those of other bacterial phyla.
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Affiliation(s)
- Silvia Ayora
- Departmento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, Cantoblanco, Madrid, Spain
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59
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Touzain F, Petit MA, Schbath S, El Karoui M. DNA motifs that sculpt the bacterial chromosome. Nat Rev Microbiol 2011; 9:15-26. [PMID: 21164534 DOI: 10.1038/nrmicro2477] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
During the bacterial cell cycle, the processes of chromosome replication, DNA segregation, DNA repair and cell division are coordinated by precisely defined events. Tremendous progress has been made in recent years in identifying the mechanisms that underlie these processes. A striking feature common to these processes is that non-coding DNA motifs play a central part, thus 'sculpting' the bacterial chromosome. Here, we review the roles of these motifs in the mechanisms that ensure faithful transmission of genetic information to daughter cells. We show how their chromosomal distribution is crucial for their function and how it can be analysed quantitatively. Finally, the potential roles of these motifs in bacterial chromosome evolution are discussed.
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Affiliation(s)
- Fabrice Touzain
- INRA, UMR 1319, Institut Micalis, FR-78352, Jouy-en-Josas, France
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60
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Mimitou EP, Symington LS. DNA end resection--unraveling the tail. DNA Repair (Amst) 2011; 10:344-8. [PMID: 21227759 DOI: 10.1016/j.dnarep.2010.12.004] [Citation(s) in RCA: 156] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 12/01/2010] [Accepted: 12/13/2010] [Indexed: 12/25/2022]
Abstract
Homology-dependent repair of DNA double-strand breaks (DSBs) initiates by the 5'-3' resection of the DNA ends to create single-stranded DNA (ssDNA), the substrate for Rad51/RecA binding. Long tracts of ssDNA are also required for activation of the ATR-mediated checkpoint response. Thus, identifying the proteins required and the underlying mechanism for DNA end resection has been an intense area of investigation. Genetic studies in Saccharomyces cerevisiae show that end resection takes place in two steps. Initially, a short oligonucleotide tract is removed from the 5' strand to create an early intermediate with a short 3' overhang. Then in a second step the early intermediate is rapidly processed generating an extensive tract of ssDNA. The first step is dependent on the highly conserved Mre11-Rad50-Xrs2 complex and Sae2, while the second step employs the exonuclease Exo1 and/or the helicase-topoisomerase complex Sgs1-Top3-Rmi1 with the endonuclease Dna2. Here we review recent in vitro and in vivo findings that shed more light into the mechanisms of DSB processing in mitotic and meiotic DSB repair as well as in telomere metabolism.
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Affiliation(s)
- Eleni P Mimitou
- Department of Microbiology and Immunology, Columbia University Medical Center, 701 W. 168th St., New York, NY 10032, USA
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61
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Gupta R, Barkan D, Redelman-Sidi G, Shuman S, Glickman MS. Mycobacteria exploit three genetically distinct DNA double-strand break repair pathways. Mol Microbiol 2010; 79:316-30. [PMID: 21219454 DOI: 10.1111/j.1365-2958.2010.07463.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Bacterial pathogens rely on their DNA repair pathways to resist genomic damage inflicted by the host. DNA double-strand breaks (DSBs) are especially threatening to bacterial viability. DSB repair by homologous recombination (HR) requires nucleases that resect DSB ends and a strand exchange protein that facilitates homology search. RecBCD and RecA perform these functions in Escherichia coli and constitute the major pathway of error-free DSB repair. Mycobacteria, including the human pathogen M. tuberculosis, elaborate an additional error-prone pathway of DSB repair via non-homologous end-joining (NHEJ) catalysed by Ku and DNA ligase D (LigD). Little is known about the relative contributions of HR and NHEJ to mycobacterial chromosome repair, the factors that dictate pathway choice, or the existence of additional DSB repair pathways. Here we demonstrate that Mycobacterium smegmatis has three DSB repair pathway options: HR, NHEJ and a novel mechanism of single-strand annealing (SSA). Inactivation of NHEJ or SSA is compensated by elevated HR. We find that mycobacterial RecBCD does not participate in HR or confer resistance to ionizing radiation (IR), but is required for the RecA-independent SSA pathway. In contrast, the mycobacterial helicase-nuclease AdnAB participates in the RecA-dependent HR pathway, and is a major determinant of resistance to IR and oxidative DNA damage. These findings reveal distinctive features of mycobacterial DSB repair, most notably the dedication of the RecBCD and AdnAB helicase-nuclease machines to distinct repair pathways.
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Affiliation(s)
- Richa Gupta
- Immunology Program Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA
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62
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Abstract
Genotoxic agents from endogenous and exogenous sources cause double-strand breaks (DSBs) in chromosomal DNA. Given the threat these lesions pose to viability, it is not surprising that multiple, conserved mechanisms exist for their detection, processing and repair. Previous studies have established both functional non-homologous end-joining (NHEJ) and homologous recombination (HR) systems in mycobacteria. However, relative pathway utilization in these organisms, which include the major human pathogen Mycobacterium tuberculosis, remains unclear. In this issue, Glickman and colleagues describe an elegant assay to distinguish DSB repair outcomes through simple phenotypic screening. By applying their novel reporter system to a panel of repair pathway mutants, they identify an unexpected role for single-strand annealing (SSA) in the related non-pathogen, Mycobacterium smegmatis. As such, these results expand the mycobacterial DSB repair pathway complement to three mechanisms that are distinguishable by their differential requirements for the DSB-resecting, helicase-nuclease machines, AdnAB and RecBCD. Notably, in an unexpected departure from classical models, they establish that mycobacterial RecBCD is a dedicated SSA nuclease, while AdnAB is required for RecA-dependent HR. Here, we consider the implications of their observations, which include the asymmetric cross-regulation of pathway function, for the role of DSB repair in mycobacterial pathogenesis.
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Affiliation(s)
- Digby F Warner
- MRC/NHLS/WITS Molecular Mycobacteriology Research Unit and DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, PO Box 1038, Johannesburg 2000, South Africa.
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63
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Yeeles JTP, Gwynn EJ, Webb MR, Dillingham MS. The AddAB helicase-nuclease catalyses rapid and processive DNA unwinding using a single Superfamily 1A motor domain. Nucleic Acids Res 2010; 39:2271-85. [PMID: 21071401 PMCID: PMC3064778 DOI: 10.1093/nar/gkq1124] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The oligomeric state of Superfamily I DNA helicases is the subject of considerable and ongoing debate. While models based on crystal structures imply that a single helicase core domain is sufficient for DNA unwinding activity, biochemical data from several related enzymes suggest that a higher order oligomeric species is required. In this work we characterize the helicase activity of the AddAB helicase–nuclease, which is involved in the repair of double-stranded DNA breaks in Bacillus subtilis. We show that the enzyme is functional as a heterodimer of the AddA and AddB subunits, that it is a rapid and processive DNA helicase, and that it catalyses DNA unwinding using one single-stranded DNA motor of 3′→5′ polarity located in the AddA subunit. The AddB subunit contains a second putative ATP-binding pocket, but this does not contribute to the observed helicase activity and may instead be involved in the recognition of recombination hotspot sequences.
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Affiliation(s)
- Joseph T P Yeeles
- DNA-Protein Interactions Unit, School of Biochemistry, Medical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, UK
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64
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Abstract
Nucleases cleave the phosphodiester bonds of nucleic acids and may be endo or exo, DNase or RNase, topoisomerases, recombinases, ribozymes, or RNA splicing enzymes. In this review, I survey nuclease activities with known structures and catalytic machinery and classify them by reaction mechanism and metal-ion dependence and by their biological function ranging from DNA replication, recombination, repair, RNA maturation, processing, interference, to defense, nutrient regeneration or cell death. Several general principles emerge from this analysis. There is little correlation between catalytic mechanism and biological function. A single catalytic mechanism can be adapted in a variety of reactions and biological pathways. Conversely, a single biological process can often be accomplished by multiple tertiary and quaternary folds and by more than one catalytic mechanism. Two-metal-ion-dependent nucleases comprise the largest number of different tertiary folds and mediate the most diverse set of biological functions. Metal-ion-dependent cleavage is exclusively associated with exonucleases producing mononucleotides and endonucleases that cleave double- or single-stranded substrates in helical and base-stacked conformations. All metal-ion-independent RNases generate 2',3'-cyclic phosphate products, and all metal-ion-independent DNases form phospho-protein intermediates. I also find several previously unnoted relationships between different nucleases and shared catalytic configurations.
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65
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Unciuleac MC, Shuman S. Double strand break unwinding and resection by the mycobacterial helicase-nuclease AdnAB in the presence of single strand DNA-binding protein (SSB). J Biol Chem 2010; 285:34319-29. [PMID: 20736178 DOI: 10.1074/jbc.m110.162925] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mycobacterial AdnAB is a heterodimeric DNA helicase-nuclease and 3' to 5' DNA translocase implicated in the repair of double strand breaks (DSBs). The AdnA and AdnB subunits are each composed of an N-terminal motor domain and a C-terminal nuclease domain. Inclusion of mycobacterial single strand DNA-binding protein (SSB) in reactions containing linear plasmid dsDNA allowed us to study the AdnAB helicase under conditions in which the unwound single strands are coated by SSB and thereby prevented from reannealing or promoting ongoing ATP hydrolysis. We found that the AdnAB motor catalyzed processive unwinding of 2.7-11.2-kbp linear duplex DNAs at a rate of ∼250 bp s(-1), while hydrolyzing ∼5 ATPs per bp unwound. Crippling the AdnA phosphohydrolase active site did not affect the rate of unwinding but lowered energy consumption slightly, to ∼4.2 ATPs bp(-1). Mutation of the AdnB phosphohydrolase abolished duplex unwinding, consistent with a model in which the "leading" AdnB motor propagates a Y-fork by translocation along the 3' DNA strand, ahead of the "lagging" AdnA motor domain. By tracking the resection of the 5' and 3' strands at the DSB ends, we illuminated a division of labor among the AdnA and AdnB nuclease modules during dsDNA unwinding, whereby the AdnA nuclease processes the unwound 5' strand to liberate a short oligonucleotide product, and the AdnB nuclease incises the 3' strand on which the motor translocates. These results extend our understanding of presynaptic DSB processing by AdnAB and engender instructive comparisons with the RecBCD and AddAB clades of bacterial helicase-nuclease machines.
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66
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Rupnik A, Lowndes NF, Grenon M. MRN and the race to the break. Chromosoma 2010; 119:115-35. [PMID: 19862546 DOI: 10.1007/s00412-009-0242-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Revised: 09/12/2009] [Accepted: 09/21/2009] [Indexed: 10/20/2022]
Abstract
In all living cells, DNA is constantly threatened by both endogenous and exogenous agents. In order to protect genetic information, all cells have developed a sophisticated network of proteins, which constantly monitor genomic integrity. This network, termed the DNA damage response, senses and signals the presence of DNA damage to effect numerous biological responses, including DNA repair, transient cell cycle arrests ("checkpoints") and apoptosis. The MRN complex (MRX in yeast), composed of Mre11, Rad50 and Nbs1 (Xrs2), is a key component of the immediate early response to DNA damage, involved in a cross-talk between the repair and checkpoint machinery. Using its ability to bind DNA ends, it is ideally placed to sense and signal the presence of double strand breaks and plays an important role in DNA repair and cellular survival. Here, we summarise recent observation on MRN structure, function, regulation and emerging mechanisms by which the MRN nano-machinery protects genomic integrity. Finally, we discuss the biological significance of the unique MRN structure and summarise the emerging sequence of early events of the response to double strand breaks orchestrated by the MRN complex.
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Affiliation(s)
- Agnieszka Rupnik
- Centre for Chromosome Biology, School of Natural Science, National University of Ireland Galway, University Road, Galway, Ireland
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Reuter M, Parry F, Dryden DTF, Blakely GW. Single-molecule imaging of Bacteroides fragilis AddAB reveals the highly processive translocation of a single motor helicase. Nucleic Acids Res 2010; 38:3721-31. [PMID: 20185564 PMCID: PMC2887965 DOI: 10.1093/nar/gkq100] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The AddAB helicase and nuclease complex is used for repairing double-strand DNA breaks in the many bacteria that do not possess RecBCD. Here, we show that AddAB, from the Gram-negative opportunistic pathogen Bacteroides fragilis, can rescue the ultraviolet sensitivity of an Escherichia coli recBCD mutant and that addAB is required for survival of B. fragilis following DNA damage. Using single-molecule observations we demonstrate that AddAB can translocate along DNA at up to 250 bp per second and can unwind an average of 14,000 bp, with some complexes capable of unwinding 40,000 bp. These results demonstrate the importance of processivity for facilitating encounters with recognition sequences that modify enzyme function during homologous recombination.
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Affiliation(s)
- Marcel Reuter
- EastChem School of Chemistry and COSMIC, The University of Edinburgh, The King's Buildings, Edinburgh EH9 3JR, UK
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69
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Yeeles JTP, Dillingham MS. The processing of double-stranded DNA breaks for recombinational repair by helicase-nuclease complexes. DNA Repair (Amst) 2010; 9:276-85. [PMID: 20116346 DOI: 10.1016/j.dnarep.2009.12.016] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Double-stranded DNA breaks are prepared for recombinational repair by nucleolytic digestion to form single-stranded DNA overhangs that are substrates for RecA/Rad51-mediated strand exchange. This processing can be achieved through the activities of multiple helicases and nucleases. In bacteria, the function is mainly provided by a stable multi-protein complex of which there are two structural classes; AddAB- and RecBCD-type enzymes. These helicase-nucleases are of special interest with respect to DNA helicase mechanism because they are exceptionally powerful DNA translocation motors, and because they serve as model systems for both single molecule studies and for understanding how DNA helicases can be coupled to other protein machinery. This review discusses recent developments in our understanding of the AddAB and RecBCD complexes, focussing on their distinctive strategies for processing DNA ends. We also discuss the extent to which bacterial DNA end resection mechanisms may parallel those used in eukaryotic cells.
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Affiliation(s)
- Joseph T P Yeeles
- DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol, BS8 1TD, United Kingdom
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70
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Zhu H, Shuman S. Gap filling activities of Pseudomonas DNA ligase D (LigD) polymerase and functional interactions of LigD with the DNA end-binding Ku protein. J Biol Chem 2009; 285:4815-25. [PMID: 20018881 DOI: 10.1074/jbc.m109.073874] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Many bacterial pathogens, including Pseudomonas aeruginosa, have a nonhomologous end joining (NHEJ) system of DNA double strand break (DSB) repair driven by Ku and DNA ligase D (LigD). LigD is a multifunctional enzyme composed of a ligase domain fused to an autonomous polymerase module (POL) that adds ribonucleotides or deoxyribonucleotides to DSB ends and primer-templates. LigD POL and the eukaryal NHEJ polymerase lambda are thought to bridge broken DNA ends via contacts with a duplex DNA segment downstream of the primer terminus, a scenario analogous to gap repair. Here, we characterized the gap repair activity of Pseudomonas LigD POL, which is more efficient than simple templated primer extension and relies on a 5'-phosphate group on the distal gap strand end to confer apparent processivity in filling gaps of 3 or 4 nucleotides. Mutations of the His-553, Arg-556, and Lys-566 side chains implicated in DNA 5'-phosphate binding eliminate the preferential filling of 5'-phosphate gaps. Mutating Phe-603, which is imputed to stack on the nucleobase of the template strand that includes the 1st bp of the downstream gap duplex segment, selectively affects incorporation of the final gap-closing nucleotide. We find that Pseudomonas Ku stimulates POL-catalyzed ribonucleotide addition to a plasmid DSB end and promotes plasmid end joining by full-length Pseudomonas LigD. A series of incremental truncations from the C terminus of the 293-amino acid Ku polypeptide identifies Ku-(1-229) as sufficient for homodimerization and LigD stimulation. The slightly longer Ku-(1-253) homodimer forms stable complexes at both ends of linear plasmid DNA that protect the DSBs from digestion by 5'- and 3'-exonucleases.
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Affiliation(s)
- Hui Zhu
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10021, USA
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71
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Unciuleac MC, Shuman S. Characterization of the mycobacterial AdnAB DNA motor provides insights into the evolution of bacterial motor-nuclease machines. J Biol Chem 2009; 285:2632-41. [PMID: 19920138 DOI: 10.1074/jbc.m109.076133] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Mycobacterial AdnAB exemplifies a family of heterodimeric motor-nucleases involved in processing DNA double strand breaks (DSBs). The AdnA and AdnB subunits are each composed of an N-terminal UvrD-like motor domain and a C-terminal RecB-like nuclease module. Here we conducted a biochemical characterization of the AdnAB motor, using a nuclease-inactivated heterodimer. AdnAB is a vigorous single strand DNA (ssDNA)-dependent ATPase (k(cat) 415 s(-1)), and the affinity of the motor for the ssDNA cofactor increases 140-fold as DNA length is extended from 12 to 44 nucleotides. Using a streptavidin displacement assay, we demonstrate that AdnAB is a 3' --> 5' translocase on ssDNA. AdnAB binds stably to DSB ends. In the presence of ATP, the motor unwinds the DNA duplex without requiring an ssDNA loading strand. We integrate these findings into a model of DSB unwinding in which the "leading" AdnB and "lagging" AdnA motor domains track in tandem, 3' to 5', along the same DNA single strand. This contrasts with RecBCD, in which the RecB and RecD motors track in parallel along the two separated DNA single strands. The effects of 5' and 3' terminal obstacles on ssDNA cleavage by wild-type AdnAB suggest that the AdnA nuclease receives and processes the displaced 5' strand, while the AdnB nuclease cleaves the displaced 3' strand. We present evidence that the distinctive "molecular ruler" function of the ATP-dependent single strand DNase, whereby AdnAB measures the distance from the 5'-end to the sites of incision, reflects directional pumping of the ssDNA through the AdnAB motor into the AdnB nuclease. These and other findings suggest a scenario for the descent of the RecBCD- and AddAB-type DSB-processing machines from an ancestral AdnAB-like enzyme.
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72
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Niu H, Raynard S, Sung P. Multiplicity of DNA end resection machineries in chromosome break repair. Genes Dev 2009; 23:1481-6. [PMID: 19571177 DOI: 10.1101/gad.1824209] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
DNA end resection is critical for chromosome break repair by homologous recombination and influences the efficiency of repair by nonhomologous DNA end joining. An elegant study by Sinha and colleagues (pp. 1423-1437) published in the June 15, 2009, issue of Genes & Development identified a novel mycobacterial DNA end resection protein complex, AdnAB, that harbors dual DNA motor and dual nuclease functions. Sinha and colleagues also demonstrated that the DNA end-binding protein complex Ku regulates the activity of AdnAB.
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Affiliation(s)
- Hengyao Niu
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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