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Schumacher MA, Cannistraci E, Salinas R, Lloyd D, Messner E, Gozzi K. Structure of the WYL-domain containing transcription activator, DriD, in complex with ssDNA effector and DNA target site. Nucleic Acids Res 2024; 52:1435-1449. [PMID: 38142455 PMCID: PMC10853764 DOI: 10.1093/nar/gkad1198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/20/2023] [Accepted: 12/01/2023] [Indexed: 12/26/2023] Open
Abstract
Transcription regulators play central roles in orchestrating responses to changing environmental conditions. Recently the Caulobacter crescentus transcription activator DriD, which belongs to the newly defined WYL-domain family, was shown to regulate DNA damage responses independent of the canonical SOS pathway. However, the molecular mechanisms by which DriD and other WYL-regulators sense environmental signals and recognize DNA are not well understood. We showed DriD DNA-binding is triggered by its interaction with ssDNA, which is produced during DNA damage. Here we describe the structure of the full-length C. crescentus DriD bound to both target DNA and effector ssDNA. DriD consists of an N-terminal winged-HTH (wHTH) domain, linker region, three-helix bundle, WYL-domain and C-terminal WCX-dimer domain. Strikingly, DriD binds DNA using a novel, asymmetric DNA-binding mechanism that results from different conformations adopted by the linker. Although the linker does not touch DNA, our data show that contacts it makes with the wHTH are key for specific DNA binding. The structure indicates how ssDNA-effector binding to the WYL-domain impacts wHTH DNA binding. In conclusion, we present the first structure of a WYL-activator bound to both effector and target DNA. The structure unveils a unique, asymmetric DNA binding mode that is likely conserved among WYL-activators.
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Affiliation(s)
- Maria A Schumacher
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC 27710, USA
| | - Emily Cannistraci
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC 27710, USA
| | - Raul Salinas
- Department of Biochemistry, 307 Research Dr., Box 3711, Duke University Medical Center, Durham, NC 27710, USA
| | - Devin Lloyd
- 100 Edwin H Land Blvd, Rowland Institute at Harvard, Harvard University, Cambridge, Cambridge, MA 02142, USA
| | - Ella Messner
- 100 Edwin H Land Blvd, Rowland Institute at Harvard, Harvard University, Cambridge, Cambridge, MA 02142, USA
| | - Kevin Gozzi
- 100 Edwin H Land Blvd, Rowland Institute at Harvard, Harvard University, Cambridge, Cambridge, MA 02142, USA
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2
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Aicart-Ramos C, Hormeno S, Wilkinson OJ, Dillingham MS, Moreno-Herrero F. Long DNA constructs to study helicases and nucleic acid translocases using optical tweezers. Methods Enzymol 2022; 673:311-358. [DOI: 10.1016/bs.mie.2022.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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3
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Wilkinson OJ, Carrasco C, Aicart-Ramos C, Moreno-Herrero F, Dillingham MS. Bulk and single-molecule analysis of a bacterial DNA2-like helicase-nuclease reveals a single-stranded DNA looping motor. Nucleic Acids Res 2020; 48:7991-8005. [PMID: 32621607 PMCID: PMC7430649 DOI: 10.1093/nar/gkaa562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 06/12/2020] [Accepted: 06/19/2020] [Indexed: 11/14/2022] Open
Abstract
DNA2 is an essential enzyme involved in DNA replication and repair in eukaryotes. In a search for homologues of this protein, we identified and characterised Geobacillus stearothermophilus Bad, a bacterial DNA helicase-nuclease with similarity to human DNA2. We show that Bad contains an Fe-S cluster and identify four cysteine residues that are likely to co-ordinate the cluster by analogy to DNA2. The purified enzyme specifically recognises ss-dsDNA junctions and possesses ssDNA-dependent ATPase, ssDNA binding, ssDNA endonuclease, 5' to 3' ssDNA translocase and 5' to 3' helicase activity. Single molecule analysis reveals that Bad is a processive DNA motor capable of moving along DNA for distances of >4 kb at a rate of ∼200 bp per second at room temperature. Interestingly, as reported for the homologous human and yeast DNA2 proteins, the DNA unwinding activity of Bad is cryptic and can be unmasked by inactivating the intrinsic nuclease activity. Strikingly, our experiments show that the enzyme loops DNA while translocating, which is an emerging feature of processive DNA unwinding enzymes. The bacterial Bad enzymes will provide an excellent model system for understanding the biochemical properties of DNA2-like helicase-nucleases and DNA looping motor proteins in general.
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Affiliation(s)
- Oliver J Wilkinson
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Carolina Carrasco
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Cantoblanco, Madrid, Spain
| | - Mark S Dillingham
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, UK
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4
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Chen YT, Yang H, Chu JW. Structure-mechanics statistical learning unravels the linkage between local rigidity and global flexibility in nucleic acids. Chem Sci 2020; 11:4969-4979. [PMID: 34122953 PMCID: PMC8159235 DOI: 10.1039/d0sc00480d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The mechanical properties of nucleic acids underlie biological processes ranging from genome packaging to gene expression, but tracing their molecular origin has been difficult due to the structural and chemical complexity. We posit that concepts from machine learning can help to tackle this long-standing challenge. Here, we demonstrate the feasibility and advantage of this strategy through developing a structure-mechanics statistical learning scheme to elucidate how local rigidity in double-stranded (ds)DNA and dsRNA may lead to their global flexibility in bend, stretch, and twist. Specifically, the mechanical parameters in a heavy-atom elastic network model are computed from the trajectory data of all-atom molecular dynamics simulation. The results show that the inter-atomic springs for backbone and ribose puckering in dsRNA are stronger than those in dsDNA, but are similar in strengths for base-stacking and base-pairing. Our analysis shows that the experimental observation of dsDNA being easier to bend but harder to stretch than dsRNA comes mostly from the respective B- and A-form topologies. The computationally resolved composition of local rigidity indicates that the flexibility of both nucleic acids is mostly due to base-stacking. But for properties like twist-stretch coupling, backbone springs are shown to play a major role instead. The quantitative connection between local rigidity and global flexibility sets foundation for understanding how local binding and chemical modification of genetic materials effectuate longer-ranged regulatory signals. The mechanical properties of nucleic acids underlie biological processes ranging from genome packaging to gene expression. We devise structural mechanics statistical learning method to reveal their molecular origin in terms of chemical interactions.![]()
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Affiliation(s)
- Yi-Tsao Chen
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University Hsinchu Taiwan 30068 Republic of China
| | - Haw Yang
- Department of Chemistry, Princeton University Princeton NJ 08544 USA
| | - Jhih-Wei Chu
- Institute of Bioinformatics and Systems Biology, Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, National Chiao Tung University Hsinchu Taiwan 30068 Republic of China +886 3 5712121 ext. 56996
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5
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Carrasco C, Pastrana CL, Aicart-Ramos C, Leuba SH, Khan S, Moreno-Herrero F. Dynamics of DNA nicking and unwinding by the RepC-PcrA complex. Nucleic Acids Res 2020; 48:2013-2025. [PMID: 31930301 PMCID: PMC7038956 DOI: 10.1093/nar/gkz1200] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 12/10/2019] [Accepted: 12/18/2019] [Indexed: 01/22/2023] Open
Abstract
The rolling-circle replication is the most common mechanism for the replication of small plasmids carrying antibiotic resistance genes in Gram-positive bacteria. It is initiated by the binding and nicking of double-stranded origin of replication by a replication initiator protein (Rep). Duplex unwinding is then performed by the PcrA helicase, whose processivity is critically promoted by its interaction with Rep. How Rep and PcrA proteins interact to nick and unwind the duplex is not fully understood. Here, we have used magnetic tweezers to monitor PcrA helicase unwinding and its relationship with the nicking activity of Staphylococcus aureus plasmid pT181 initiator RepC. Our results indicate that PcrA is a highly processive helicase prone to stochastic pausing, resulting in average translocation rates of 30 bp s-1, while a typical velocity of 50 bp s-1 is found in the absence of pausing. Single-strand DNA binding protein did not affect PcrA translocation velocity but slightly increased its processivity. Analysis of the degree of DNA supercoiling required for RepC nicking, and the time between RepC nicking and DNA unwinding, suggests that RepC and PcrA form a protein complex on the DNA binding site before nicking. A comprehensive model that rationalizes these findings is presented.
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Affiliation(s)
- Carolina Carrasco
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Cantoblanco, Madrid, Spain
| | - Cesar L Pastrana
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Cantoblanco, Madrid, Spain
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Cantoblanco, Madrid, Spain
| | - Sanford H Leuba
- Departments of Cell Biology and Bioengineering, UPMC Hillman Cancer Center, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Pittsburgh, PA 15213, USA
| | - Saleem A Khan
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, CSIC, Darwin 3, 28049 Cantoblanco, Madrid, Spain
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6
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Selective loading and processing of prespacers for precise CRISPR adaptation. Nature 2020; 579:141-145. [PMID: 32076262 DOI: 10.1038/s41586-020-2018-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 12/19/2019] [Indexed: 01/08/2023]
Abstract
CRISPR-Cas immunity protects prokaryotes against invading genetic elements1. It uses the highly conserved Cas1-Cas2 complex to establish inheritable memory (spacers)2-5. How Cas1-Cas2 acquires spacers from foreign DNA fragments (prespacers) and integrates them into the CRISPR locus in the correct orientation is unclear6,7. Here, using the high spatiotemporal resolution of single-molecule fluorescence, we show that Cas1-Cas2 selects precursors of prespacers from DNA in various forms-including single-stranded DNA and partial duplexes-in a manner that depends on both the length of the DNA strand and the presence of a protospacer adjacent motif (PAM) sequence. We also identify DnaQ exonucleases as enzymes that process the Cas1-Cas2-loaded prespacer precursors into mature prespacers of a suitable size for integration. Cas1-Cas2 protects the PAM sequence from maturation, which results in the production of asymmetrically trimmed prespacers and the subsequent integration of spacers in the correct orientation. Our results demonstrate the kinetic coordination of prespacer precursor selection and PAM trimming, providing insight into the mechanisms that underlie the integration of functional spacers in the CRISPR loci.
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7
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Abstract
Many bacteria and archaea have the unique ability to heritably alter their genomes by incorporating small fragments of foreign DNA, called spacers, into CRISPR loci. Once transcribed and processed into individual CRISPR RNAs, spacer sequences guide Cas effector nucleases to destroy complementary, invading nucleic acids. Collectively, these two processes are known as the CRISPR-Cas immune response. In this Progress article, we review recent studies that have advanced our understanding of the molecular mechanisms underlying spacer acquisition and that have revealed a fundamental link between the two phases of CRISPR immunity that ensures optimal immunity from newly acquired spacers. Finally, we highlight important open questions and discuss the potential basic and applied impact of spacer acquisition research.
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Affiliation(s)
- Jon McGinn
- Laboratory of Bacteriology, The Rockefeller University, New York, NY, USA
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8
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Wilkinson OJ, Martín-González A, Kang H, Northall SJ, Wigley DB, Moreno-Herrero F, Dillingham MS. CtIP forms a tetrameric dumbbell-shaped particle which bridges complex DNA end structures for double-strand break repair. eLife 2019; 8:42129. [PMID: 30601117 PMCID: PMC6344080 DOI: 10.7554/elife.42129] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 01/01/2019] [Indexed: 12/16/2022] Open
Abstract
CtIP is involved in the resection of broken DNA during the S and G2 phases of the cell cycle for repair by recombination. Acting with the MRN complex, it plays a particularly important role in handling complex DNA end structures by localised nucleolytic processing of DNA termini in preparation for longer range resection. Here we show that human CtIP is a tetrameric protein adopting a dumbbell architecture in which DNA binding domains are connected by long coiled-coils. The protein complex binds two short DNA duplexes with high affinity and bridges DNA molecules in trans. DNA binding is potentiated by dephosphorylation and is not specific for DNA end structures per se. However, the affinity for linear DNA molecules is increased if the DNA terminates with complex structures including forked ssDNA overhangs and nucleoprotein conjugates. This work provides a biochemical and structural basis for the function of CtIP at complex DNA breaks.
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Affiliation(s)
| | - Alejandro Martín-González
- Department of Macromolecular Structures, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain
| | - Haejoo Kang
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Sarah J Northall
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Dale B Wigley
- Department of Medicine, Imperial College London, London, United Kingdom
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain
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9
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Pisano S, Gilson E. Analysis of DNA-Protein Complexes by Atomic Force Microscopy Imaging: The Case of TRF2-Telomeric DNA Wrapping. Methods Mol Biol 2019; 1886:75-97. [PMID: 30374863 DOI: 10.1007/978-1-4939-8894-5_5] [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] [Indexed: 06/08/2023]
Abstract
Atomic force microscopy (AFM) is a non-optical microscopy that enables the acquisition at the nanoscale level of a 3D topographical image of the sample. For 30 years, AFM has been a valuable tool in life sciences to study biological samples in the field of tissue, cellular and molecular imaging, of mechanical properties and of force spectroscopy. Since the early beginnings of the technique, AFM has been extensively exploited as an imaging tool for structural studies of nucleic acids and nucleoprotein complexes. The morphometric analysis performed on the images can unveil specific structural and functional aspects of the sample, such as the multimerization state of proteins bound to DNA, or DNA conformational changes led by the DNA-binding proteins. Herein, a method for analyzing a complex formed by a telomeric DNA sequence wrapped around the TRF2 binding protein is presented. The described procedure could be applied to the study of any type of DNA-protein complex.
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Affiliation(s)
- Sabrina Pisano
- Université Côte d'Azur, CNRS UMR 7284/INSERM U108, Institute for Research on Cancer and Aging, Nice (IRCAN), Medical School, Nice, France.
| | - Eric Gilson
- Université Côte d'Azur, CNRS UMR 7284/INSERM U108, Institute for Research on Cancer and Aging, Nice (IRCAN), Medical School, Nice, France
- International Laboratory in Hematology and Cancer, Pôle Sino-Français de Recherche en Sciences du Vivant et Génomique, Shanghai Ruijin Hospital, Shanghai Jiao Tong University School of Medicine/Ruijin Hospital/CNRS/INSERM/Nice University, Shanghai, China
- Department of Genetics, CHU Nice, Université Côte d'Azur, Nice, France
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10
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Xie P. Modeling DNA Unwinding by AddAB Helicase-Nuclease and Modulation by Chi Sequences: Comparison with AdnAB and RecBCD. Cell Mol Bioeng 2018; 12:179-191. [PMID: 31719908 DOI: 10.1007/s12195-018-00563-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/29/2018] [Indexed: 01/28/2023] Open
Abstract
Introduction AddAB enzyme is a helicase-nuclease complex that initiates recombinational repair of double-stranded DNA breaks. It catalyzes processive DNA unwinding and concomitant resection of the unwound strands, which are modulated by the recognition of a recombination hotspot called Chi in the 3'-terminated strand. Despite extensive structural, biochemical and single molecule studies, the detailed molecular mechanism of DNA unwinding by the complex and modulation by Chi sequence remains unclear. Methods A model of DNA unwinding by the AddAB complex and modulation by Chi recognition was presented, based on which the dynamics of AddAB complex was studied analytically. Results The theoretical results explain well the available experimental data on effect of DNA sequence on velocity, effect of Chi recognition on velocity, static disorder peculiar to the AddAB complex, and dynamics of pausing of wild-type and mutant AddAB complexes occurring at Chi or Chi-like sequence. Predictions were provided. Comparisons of AddAB complex with other helicase-nuclease complexes such as RecBCD and AdnAB were made. Conclusions The study has strong implications for the molecular mechanism of DNA unwinding by the AddAB complex. The intriguing issues are addressed of why Chi recognition is an inefficient process, how AddAB complex pauses upon recognizing Chi sequence, how the paused state transits to the translocating state, why the mutant AddAB with a stronger affinity to Chi sequence has a shorter pausing lifetime, why the pausing lifetime is sensitive to the solution temperature, and so on.
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Affiliation(s)
- Ping Xie
- Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190 China
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11
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Understanding the mechanical response of double-stranded DNA and RNA under constant stretching forces using all-atom molecular dynamics. Proc Natl Acad Sci U S A 2017. [PMID: 28634300 DOI: 10.1073/pnas.1705642114] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Multiple biological processes involve the stretching of nucleic acids (NAs). Stretching forces induce local changes in the molecule structure, inhibiting or promoting the binding of proteins, which ultimately affects their functionality. Understanding how a force induces changes in the structure of NAs at the atomic level is a challenge. Here, we use all-atom, microsecond-long molecular dynamics to simulate the structure of dsDNA and dsRNA subjected to stretching forces up to 20 pN. We determine all of the elastic constants of dsDNA and dsRNA and provide an explanation for three striking differences in the mechanical response of these two molecules: the threefold softer stretching constant obtained for dsRNA, the opposite twist-stretch coupling, and its nontrivial force dependence. The lower dsRNA stretching resistance is linked to its more open structure, whereas the opposite twist-stretch coupling of both molecules is due to the very different evolution of molecules' interstrand distance with the stretching force. A reduction of this distance leads to overwinding in dsDNA. In contrast, dsRNA is not able to reduce its interstrand distance and can only elongate by unwinding. Interstrand distance is directly correlated with the slide base-pair parameter and its different behavior in dsDNA and dsRNA traced down to changes in the sugar pucker angle of these NAs.
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12
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Badrinarayanan A, Le TBK, Spille JH, Cisse II, Laub MT. Global analysis of double-strand break processing reveals in vivo properties of the helicase-nuclease complex AddAB. PLoS Genet 2017; 13:e1006783. [PMID: 28489851 PMCID: PMC5443536 DOI: 10.1371/journal.pgen.1006783] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 05/24/2017] [Accepted: 04/26/2017] [Indexed: 12/03/2022] Open
Abstract
In bacteria, double-strand break (DSB) repair via homologous recombination is thought to be initiated through the bi-directional degradation and resection of DNA ends by a helicase-nuclease complex such as AddAB. The activity of AddAB has been well-studied in vitro, with translocation speeds between 400–2000 bp/s on linear DNA suggesting that a large section of DNA around a break site is processed for repair. However, the translocation rate and activity of AddAB in vivo is not known, and how AddAB is regulated to prevent excessive DNA degradation around a break site is unclear. To examine the functions and mechanistic regulation of AddAB inside bacterial cells, we developed a next-generation sequencing-based approach to assay DNA processing after a site-specific DSB was introduced on the chromosome of Caulobacter crescentus. Using this assay we determined the in vivo rates of DSB processing by AddAB and found that putative chi sites attenuate processing in a RecA-dependent manner. This RecA-mediated regulation of AddAB prevents the excessive loss of DNA around a break site, limiting the effects of DSB processing on transcription. In sum, our results, taken together with prior studies, support a mechanism for regulating AddAB that couples two key events of DSB repair–the attenuation of DNA-end processing and the initiation of homology search by RecA–thereby helping to ensure that genomic integrity is maintained during DSB repair. Double-strand breaks (DSBs) are a threat to genome integrity and are faithfully repaired via homologous recombination. The initial processing of DSB ends that prepares them for recombination has been well-studied in vitro, but is less well characterized in vivo. We describe a deep sequencing-based assay for assessing the early steps of DSB processing in bacterial cells by the helicase-nuclease complex AddAB. We find that a combination of chi site recognition and RecA loading is required to attenuate AddAB activity. In the absence of RecA, the chromosome is excessively degraded with a concomitant loss in transcription. Our results, along with prior studies, support a model for how chi recognition and RecA together regulate AddAB to maintain genome integrity and facilitate recombination.
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Affiliation(s)
- Anjana Badrinarayanan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- National Centre for Biological Sciences (NCBS), Tata Institute of Fundamental Research, Bangalore, India
| | - Tung B. K. Le
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Jan-Hendrik Spille
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Ibrahim I. Cisse
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Michael T. Laub
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, United States of America
- * E-mail:
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13
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Gupta R, Unciuleac MC, Shuman S, Glickman MS. Homologous recombination mediated by the mycobacterial AdnAB helicase without end resection by the AdnAB nucleases. Nucleic Acids Res 2016; 45:762-774. [PMID: 27899634 PMCID: PMC5314763 DOI: 10.1093/nar/gkw1130] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 10/26/2016] [Accepted: 10/29/2016] [Indexed: 01/31/2023] Open
Abstract
Current models of bacterial homologous recombination (HR) posit that extensive resection of a DNA double-strand break (DSB) by a multisubunit helicase–nuclease machine (e.g. RecBCD, AddAB or AdnAB) generates the requisite 3′ single-strand DNA substrate for RecA-mediated strand invasion. AdnAB, the helicase–nuclease implicated in mycobacterial HR, consists of two subunits, AdnA and AdnB, each composed of an N-terminal ATPase domain and a C-terminal nuclease domain. DSB unwinding by AdnAB in vitro is stringently dependent on the ATPase activity of the ‘lead’ AdnB motor translocating on the 3′ ssDNA strand, but not on the putative ‘lagging’ AdnA ATPase. Here, we queried genetically which activities of AdnAB are pertinent to its role in HR and DNA damage repair in vivo by inactivating each of the four catalytic domains. Complete nuclease-dead AdnAB enzyme can sustain recombination in vivo, as long as its AdnB motor is intact and RecO and RecR are available. We conclude that AdnAB's processive DSB unwinding activity suffices for AdnAB function in HR. Albeit not excluding the agency of a backup nuclease, our findings suggest that mycobacterial HR can proceed via DSB unwinding and protein capture of the displaced 3′-OH single strand, without a need for extensive end-resection.
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Affiliation(s)
- Richa Gupta
- Immunology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Mihaela-Carmen Unciuleac
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Michael S Glickman
- Immunology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA .,Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
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14
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Gilhooly NS, Carrasco C, Gollnick B, Wilkinson M, Wigley DB, Moreno-Herrero F, Dillingham MS. Chi hotspots trigger a conformational change in the helicase-like domain of AddAB to activate homologous recombination. Nucleic Acids Res 2016; 44:2727-41. [PMID: 26762979 PMCID: PMC4824097 DOI: 10.1093/nar/gkv1543] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 12/27/2015] [Indexed: 11/29/2022] Open
Abstract
In bacteria, the repair of double-stranded DNA breaks is modulated by Chi sequences. These are recognised by helicase-nuclease complexes that process DNA ends for homologous recombination. Chi activates recombination by changing the biochemical properties of the helicase-nuclease, transforming it from a destructive exonuclease into a recombination-promoting repair enzyme. This transition is thought to be controlled by the Chi-dependent opening of a molecular latch, which enables part of the DNA substrate to evade degradation beyond Chi. Here, we show that disruption of the latch improves Chi recognition efficiency and stabilizes the interaction of AddAB with Chi, even in mutants that are impaired for Chi binding. Chi recognition elicits a structural change in AddAB that maps to a region of AddB which resembles a helicase domain, and which harbours both the Chi recognition locus and the latch. Mutation of the latch potentiates the change and moderately reduces the duration of a translocation pause at Chi. However, this mutant displays properties of Chi-modified AddAB even in the complete absence of bona fide hotspot sequences. The results are used to develop a model for AddAB regulation in which allosteric communication between Chi binding and latch opening ensures quality control during recombination hotspot recognition.
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Affiliation(s)
| | - Carolina Carrasco
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, 28049 Cantoblanco, Madrid, Spain
| | - Benjamin Gollnick
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, 28049 Cantoblanco, Madrid, Spain
| | - Martin Wilkinson
- Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK Section of Structural Biology, Department of Medicine, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Dale B Wigley
- Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK Section of Structural Biology, Department of Medicine, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Cientificas, 28049 Cantoblanco, Madrid, Spain
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15
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Abstract
AddAB and RecBCD-type helicase-nuclease complexes control the first stage of bacterial homologous recombination (HR) – the resection of double strand DNA breaks. A switch in the activities of the complexes to initiate repair by HR is regulated by a short, species-specific DNA sequence known as a Crossover Hotspot Instigator (Chi) site. It has been shown that, upon encountering Chi, AddAB and RecBCD pause translocation before resuming at a reduced rate. Recently, the structure of B.subtilis AddAB in complex with its regulatory Chi sequence revealed the nature of Chi binding and the paused translocation state. Here the structural features associated with Chi binding are described in greater detail and discussed in relation to the related E.coli RecBCD system.
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Affiliation(s)
- Martin Wilkinson
- a Division of Structural Biology; Institute of Cancer Research; Chester Beatty Laboratories ; London , UK
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16
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Carrasco B, Yadav T, Serrano E, Alonso JC. Bacillus subtilis RecO and SsbA are crucial for RecA-mediated recombinational DNA repair. Nucleic Acids Res 2015; 43:5984-97. [PMID: 26001966 PMCID: PMC4499154 DOI: 10.1093/nar/gkv545] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/12/2015] [Indexed: 11/13/2022] Open
Abstract
Genetic data have revealed that the absence of Bacillus subtilis RecO and one of the end-processing avenues (AddAB or RecJ) renders cells as sensitive to DNA damaging agents as the null recA, suggesting that both end-resection pathways require RecO for recombination. RecA, in the rATP·Mg(2+) bound form (RecA·ATP), is inactive to catalyze DNA recombination between linear double-stranded (ds) DNA and naked complementary circular single-stranded (ss) DNA. We showed that RecA·ATP could not nucleate and/or polymerize on SsbA·ssDNA or SsbB·ssDNA complexes. RecA·ATP nucleates and polymerizes on RecO·ssDNA·SsbA complexes more efficiently than on RecO·ssDNA·SsbB complexes. Limiting SsbA concentrations were sufficient to stimulate RecA·ATP assembly on the RecO·ssDNA·SsbB complexes. RecO and SsbA are necessary and sufficient to 'activate' RecA·ATP to catalyze DNA strand exchange, whereas the AddAB complex, RecO alone or in concert with SsbB was not sufficient. In presence of AddAB, RecO and SsbA are still necessary for efficient RecA·ATP-mediated three-strand exchange recombination. Based on genetic and biochemical data, we proposed that SsbA and RecO (or SsbA, RecO and RecR in vivo) are crucial for RecA activation for both, AddAB and RecJ-RecQ (RecS) recombinational repair pathways.
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Affiliation(s)
- Begoña Carrasco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Street, 28049 Madrid, Spain
| | - Tribhuwan Yadav
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Street, 28049 Madrid, Spain
| | - Ester Serrano
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Street, 28049 Madrid, Spain
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Street, 28049 Madrid, Spain
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17
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Gollnick B, Carrasco C, Zuttion F, Gilhooly NS, Dillingham MS, Moreno-Herrero F. Probing DNA helicase kinetics with temperature-controlled magnetic tweezers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:1273-84. [PMID: 25400244 PMCID: PMC4473356 DOI: 10.1002/smll.201402686] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Indexed: 05/04/2023]
Abstract
Motor protein functions like adenosine triphosphate (ATP) hydrolysis or translocation along molecular substrates take place at nanometric scales and consequently depend on the amount of available thermal energy. The associated rates can hence be investigated by actively varying the temperature conditions. In this article, a thermally controlled magnetic tweezers (MT) system for single-molecule experiments at up to 40 °C is presented. Its compact thermostat module yields a precision of 0.1 °C and can in principle be tailored to any other surface-coupled microscopy technique, such as tethered particle motion (TPM), nanopore-based sensing of biomolecules, or super-resolution fluorescence imaging. The instrument is used to examine the temperature dependence of translocation along double-stranded (ds)DNA by individual copies of the protein complex AddAB, a helicase-nuclease motor involved in dsDNA break repair. Despite moderately lower mean velocities measured at sub-saturating ATP concentrations, almost identical estimates of the enzymatic reaction barrier (around 21-24 k(B)T) are obtained by comparing results from MT and stopped-flow bulk assays. Single-molecule rates approach ensemble values at optimized chemical energy conditions near the motor, which can withstand opposing loads of up to 14 piconewtons (pN). Having proven its reliability, the temperature-controlled MT described herein will eventually represent a routinely applied method within the toolbox for nano-biotechnology.
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Affiliation(s)
- Benjamin Gollnick
- Centro Nacional de Biotecnología, CSIC, Darwin 3, Campus de Cantoblanco, 28049, Madrid, Spain
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18
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Accessory Replicative Helicases and the Replication of Protein-Bound DNA. J Mol Biol 2014; 426:3917-3928. [DOI: 10.1016/j.jmb.2014.10.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 09/29/2014] [Accepted: 10/06/2014] [Indexed: 12/29/2022]
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19
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Green M, Gilhooly NS, Abedeen S, Scott DJ, Dillingham MS, Soultanas P. Engineering a reagentless biosensor for single-stranded DNA to measure real-time helicase activity in Bacillus. Biosens Bioelectron 2014; 61:579-86. [PMID: 24953846 PMCID: PMC4103019 DOI: 10.1016/j.bios.2014.06.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 05/28/2014] [Accepted: 06/03/2014] [Indexed: 10/27/2022]
Abstract
Single-stranded DNA-binding protein (SSB) is a well characterized ubiquitous and essential bacterial protein involved in almost all aspects of DNA metabolism. Using the Bacillus subtilis SSB we have generated a reagentless SSB biosensor that can be used as a helicase probe in B. subtilis and closely related gram positive bacteria. We have demonstrated the utility of the probe in a DNA unwinding reaction using a helicase from Bacillus and for the first time, characterized the B. subtilis SSB's DNA binding mode switching and stoichiometry. The importance of SSB in DNA metabolism is not limited to simply binding and protecting ssDNA during DNA replication, as previously thought. It interacts with an array of partner proteins to coordinate many different aspects of DNA metabolism. In most cases its interactions with partner proteins is species-specific and for this reason, knowing how to produce and use cognate reagentless SSB biosensors in different bacteria is critical. Here we explain how to produce a B. subtilis SSB probe that exhibits 9-fold fluorescence increase upon binding to single stranded DNA and can be used in all related gram positive firmicutes which employ drastically different DNA replication and repair systems than the widely studied Escherichia coli. The materials to produce the B. subtilis SSB probe are commercially available, so the methodology described here is widely available unlike previously published methods for the E. coli SSB.
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Affiliation(s)
- Matthew Green
- School of Chemistry, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Neville S Gilhooly
- School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Shahriar Abedeen
- School of Chemistry, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - David J Scott
- School of Biosciences, University of Nottingham, Sutton Bonington, Leicestershire LE12 5RD, UK
| | - Mark S Dillingham
- School of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, UK
| | - Panos Soultanas
- School of Chemistry, Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK.
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20
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Gilhooly NS, Dillingham MS. Recombination hotspots attenuate the coupled ATPase and translocase activities of an AddAB-type helicase-nuclease. Nucleic Acids Res 2014; 42:5633-43. [PMID: 24682829 PMCID: PMC4027173 DOI: 10.1093/nar/gku188] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In all domains of life, the resection of double-stranded DNA breaks to form long 3′-ssDNA overhangs in preparation for recombinational repair is catalyzed by the coordinated activities of DNA helicases and nucleases. In bacterial cells, this resection reaction is modulated by the recombination hotspot sequence Chi. The Chi sequence is recognized in cis by translocating helicase–nuclease complexes such as the Bacillus subtilis AddAB complex. Binding of Chi to AddAB results in the attenuation of nuclease activity on the 3′-terminated strand, thereby promoting recombination. In this work, we used stopped-flow methods to monitor the coupling of adenosine triphosphate (ATP) hydrolysis and DNA translocation and how this is affected by Chi recognition. We show that in the absence of Chi sequences, AddAB translocates processively on DNA at ∼2000 bp s−1 and hydrolyses approximately 1 ATP molecule per base pair travelled. The recognition of recombination hotspots results in a sustained decrease in the translocation rate which is accompanied by a decrease in the ATP hydrolysis rate, such that the coupling between these activities and the net efficiency of DNA translocation is largely unchanged by Chi.
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Affiliation(s)
- Neville S Gilhooly
- DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Mark S Dillingham
- DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
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21
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Carrasco C, Dillingham MS, Moreno-Herrero F. Single molecule approaches to monitor the recognition and resection of double-stranded DNA breaks during homologous recombination. DNA Repair (Amst) 2014; 20:119-129. [PMID: 24569169 DOI: 10.1016/j.dnarep.2014.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 01/31/2014] [Accepted: 02/01/2014] [Indexed: 11/30/2022]
Abstract
The fate of a cell depends on its ability to repair the many double-stranded DNA breaks (DSBs) that occur during normal metabolism. Improper DSB repair may result in genomic instability, cancer, or other genetic diseases. The repair of a DSB can be initiated by the recognition and resection of a duplex DNA end to form a 3'-terminated single-stranded DNA overhang. This task is carried out by different single-strand exonucleases, endonucleases, and helicases that work in a coordinated manner. This manuscript reviews the different single-molecule approaches that have been employed to characterize the structural features of these molecular machines, as well as the intermediates and products formed during the process of DSB repair. Imaging techniques have unveiled the structural organization of complexes involved in the tethering and recognition of DSBs. In addition to that static picture, single molecule studies on the dynamics of helicase-nuclease complexes responsible for the processive resection of DSBs have provided detailed mechanistic insights into their function.
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Affiliation(s)
- Carolina Carrasco
- Centro Nacional de Biotecnología, CSIC, Campus UAM, Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Mark S Dillingham
- School of Biochemistry, Medical Sciences Building, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Fernando Moreno-Herrero
- Centro Nacional de Biotecnología, CSIC, Campus UAM, Darwin 3, Cantoblanco, 28049 Madrid, Spain.
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22
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Hormeño S, Penedo M, Manzano CV, Luna M. Gold nanoparticle coated silicon tips for Kelvin probe force microscopy in air. NANOTECHNOLOGY 2013; 24:395701. [PMID: 24008394 DOI: 10.1088/0957-4484/24/39/395701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The tip apex dimensions and geometry of the conductive probe remain the major limitation to the resolution of Kelvin probe force microscopy (KPFM). One of the possible strategies to improve the spatial resolution of surface potential images consists in the development of thinner and more durable conductive tips. In an effort to improve the lateral resolution of topography and surface potential maps, we have evaluated high aspect ratio conductive tips created by depositing gold nanoparticles on standard silicon tips. Besides the already known general topographic resolution enhancement offered by these modified tips, an improvement of surface potential lateral resolution and signal-to-noise ratio is reported here for a variety of samples as compared to other regular conductive probes. We have also observed that the modified conductive tips have a significant auto-regeneration capability, which stems from a certain level of mobility of the nanoparticle coating. This property makes the modified tips highly resistant to degradation during scanning, thus increasing their durability. As demonstrated by the heterogeneous set of structures measured in the present study performed in air, the nanoparticle coated tips are suitable for KPFM analysis. In particular, surface potential difference determination on graphene deposited on silicon, gold sputtered on a salt surface, large and mildly rough areas of ZnO films and small DNA molecules on insulating mica have been achieved with enhanced resolution.
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Affiliation(s)
- Silvia Hormeño
- IMM-Instituto de Microelectrónica de Madrid (CNM-CSIC), Isaac Newton 8, PTM, E-28760 Tres Cantos, Madrid, Spain
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23
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On the mechanism of recombination hotspot scanning during double-stranded DNA break resection. Proc Natl Acad Sci U S A 2013; 110:E2562-71. [PMID: 23798400 DOI: 10.1073/pnas.1303035110] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Double-stranded DNA break repair by homologous recombination is initiated by resection of free DNA ends to produce a 3'-ssDNA overhang. In bacteria, this reaction is catalyzed by helicase-nuclease complexes such as AddAB in a manner regulated by specific recombination hotspot sequences called Crossover hotspot instigator (Chi). We have used magnetic tweezers to investigate the dynamics of AddAB translocation and hotspot scanning during double-stranded DNA break resection. AddAB was prone to stochastic pausing due to transient recognition of Chi-like sequences, unveiling an antagonistic relationship between DNA translocation and sequence-specific DNA recognition. Pauses at bona fide Chi sequences were longer, were nonexponentially distributed, and resulted in an altered velocity upon restart of translocation downstream of Chi. We propose a model for the recognition of Chi sequences to explain the origin of pausing during failed and successful hotspot recognition.
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24
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AFM volumetric methods for the characterization of proteins and nucleic acids. Methods 2013; 60:113-21. [DOI: 10.1016/j.ymeth.2013.02.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/28/2013] [Accepted: 02/14/2013] [Indexed: 11/19/2022] Open
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25
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Early steps of double-strand break repair in Bacillus subtilis. DNA Repair (Amst) 2013; 12:162-76. [PMID: 23380520 DOI: 10.1016/j.dnarep.2012.12.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 12/04/2012] [Accepted: 12/14/2012] [Indexed: 11/22/2022]
Abstract
All organisms rely on integrated networks to repair DNA double-strand breaks (DSBs) in order to preserve the integrity of the genetic information, to re-establish replication, and to ensure proper chromosomal segregation. Genetic, cytological, biochemical and structural approaches have been used to analyze how Bacillus subtilis senses DNA damage and responds to DSBs. RecN, which is among the first responders to DNA DSBs, promotes the ordered recruitment of repair proteins to the site of a lesion. Cells have evolved different mechanisms for efficient end processing to create a 3'-tailed duplex DNA, the substrate for RecA binding, in the repair of one- and two-ended DSBs. Strand continuity is re-established via homologous recombination (HR), utilizing an intact homologous DNA molecule as a template. In the absence of transient diploidy or of HR, however, two-ended DSBs can be directly re-ligated via error-prone non-homologous end-joining. Here we review recent findings that shed light on the early stages of DSB repair in Firmicutes.
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26
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Abstract
From microbes to multicellular eukaryotic organisms, all cells contain pathways responsible for genome maintenance. DNA replication allows for the faithful duplication of the genome, whereas DNA repair pathways preserve DNA integrity in response to damage originating from endogenous and exogenous sources. The basic pathways important for DNA replication and repair are often conserved throughout biology. In bacteria, high-fidelity repair is balanced with low-fidelity repair and mutagenesis. Such a balance is important for maintaining viability while providing an opportunity for the advantageous selection of mutations when faced with a changing environment. Over the last decade, studies of DNA repair pathways in bacteria have demonstrated considerable differences between Gram-positive and Gram-negative organisms. Here we review and discuss the DNA repair, genome maintenance, and DNA damage checkpoint pathways of the Gram-positive bacterium Bacillus subtilis. We present their molecular mechanisms and compare the functions and regulation of several pathways with known information on other organisms. We also discuss DNA repair during different growth phases and the developmental program of sporulation. In summary, we present a review of the function, regulation, and molecular mechanisms of DNA repair and mutagenesis in Gram-positive bacteria, with a strong emphasis on B. subtilis.
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27
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Bacterial DNA repair: recent insights into the mechanism of RecBCD, AddAB and AdnAB. Nat Rev Microbiol 2012. [DOI: 10.1038/nrmicro2917] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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28
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Kidane D, Ayora S, Sweasy JB, Graumann PL, Alonso JC. The cell pole: the site of cross talk between the DNA uptake and genetic recombination machinery. Crit Rev Biochem Mol Biol 2012; 47:531-55. [PMID: 23046409 DOI: 10.3109/10409238.2012.729562] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Natural transformation is a programmed mechanism characterized by binding of free double-stranded (ds) DNA from the environment to the cell pole in rod-shaped bacteria. In Bacillus subtilis some competence proteins, which process the dsDNA and translocate single-stranded (ss) DNA into the cytosol, recruit a set of recombination proteins mainly to one of the cell poles. A subset of single-stranded binding proteins, working as "guardians", protects ssDNA from degradation and limit the RecA recombinase loading. Then, the "mediators" overcome the inhibitory role of guardians, and recruit RecA onto ssDNA. A RecA·ssDNA filament searches for homology on the chromosome and, in a process that is controlled by "modulators", catalyzes strand invasion with the generation of a displacement loop (D-loop). A D-loop resolvase or "resolver" cleaves this intermediate, limited DNA replication restores missing information and a DNA ligase seals the DNA ends. However, if any step fails, the "rescuers" will repair the broken end to rescue chromosomal transformation. If the ssDNA does not share homology with resident DNA, but it contains information for autonomous replication, guardian and mediator proteins catalyze plasmid establishment after inhibition of RecA. DNA replication and ligation reconstitute the molecule (plasmid transformation). In this review, the interacting network that leads to a cross talk between proteins of the uptake and genetic recombination machinery will be placed into prospective.
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Affiliation(s)
- Dawit Kidane
- Departments of Therapeutic Radiology and Genetics, Yale University School of Medicine, New Haven, CT, USA
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29
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Nicholson WL, Moeller R, Horneck G. Transcriptomic responses of germinating Bacillus subtilis spores exposed to 1.5 years of space and simulated martian conditions on the EXPOSE-E experiment PROTECT. ASTROBIOLOGY 2012; 12:469-86. [PMID: 22680693 DOI: 10.1089/ast.2011.0748] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Because of their ubiquity and resistance to spacecraft decontamination, bacterial spores are considered likely potential forward contaminants on robotic missions to Mars. Thus, it is important to understand their global responses to long-term exposure to space or martian environments. As part of the PROTECT experiment, spores of B. subtilis 168 were exposed to real space conditions and to simulated martian conditions for 559 days in low-Earth orbit mounted on the EXPOSE-E exposure platform outside the European Columbus module on the International Space Station. Upon return, spores were germinated, total RNA extracted, fluorescently labeled, and used to probe a custom Bacillus subtilis microarray to identify genes preferentially activated or repressed relative to ground control spores. Increased transcript levels were detected for a number of stress-related regulons responding to DNA damage (SOS response, SPβ prophage induction), protein damage (CtsR/Clp system), oxidative stress (PerR regulon), and cell envelope stress (SigV regulon). Spores exposed to space demonstrated a much broader and more severe stress response than spores exposed to simulated martian conditions. The results are discussed in the context of planetary protection for a hypothetical journey of potential forward contaminant spores from Earth to Mars and their subsequent residence on Mars.
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Affiliation(s)
- Wayne L Nicholson
- Department of Microbiology and Cell Science, University of Florida, Space Life Sciences Laboratory, Kennedy Space Center, FL 32899, USA.
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30
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Fuentes-Perez ME, Gwynn EJ, Dillingham MS, Moreno-Herrero F. Using DNA as a fiducial marker to study SMC complex interactions with the atomic force microscope. Biophys J 2012; 102:839-48. [PMID: 22385855 DOI: 10.1016/j.bpj.2012.01.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 01/10/2012] [Accepted: 01/17/2012] [Indexed: 01/21/2023] Open
Abstract
Atomic force microscopy can potentially provide information on protein volumes, shapes, and interactions but is susceptible to variable tip-induced artifacts. In this study, we present an atomic force microscopy approach that can measure volumes of nonglobular polypeptides such as structural maintenance of chromosomes (SMC) proteins, and use it to study the interactions that occur within and between SMC complexes. Together with the protein of interest, we coadsorb a DNA molecule and use it as a fiducial marker to account for tip-induced artifacts that affect both protein and DNA, allowing normalization of protein volumes from images taken on different days and with different tips. This approach significantly reduced the error associated with volume analysis, and allowed determination of the oligomeric states and architecture of the Bacillus subtilis SMC complex, formed by the SMC protein, and by the smaller ScpA and ScpB subunits. This work reveals that SMC and ScpB are dimers and that ScpA is a stable monomer. Moreover, whereas ScpA binds directly to SMC, ScpB only binds to SMC in the presence of ScpA. Notably, the presence of both ScpA and ScpB favored the formation of higher-order structures of SMC complexes, suggesting a role for these subunits in the organization of SMC oligomers.
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Affiliation(s)
- M E Fuentes-Perez
- Department of Macromolecular Structures, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid, Spain
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31
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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: 52] [Impact Index Per Article: 4.3] [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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