1
|
Robins WP, Meader BT, Toska J, Mekalanos JJ. DdmABC-dependent death triggered by viral palindromic DNA sequences. Cell Rep 2024; 43:114450. [PMID: 39002129 DOI: 10.1016/j.celrep.2024.114450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 04/24/2024] [Accepted: 06/20/2024] [Indexed: 07/15/2024] Open
Abstract
Defense systems that recognize viruses provide important insights into both prokaryotic and eukaryotic innate immunity mechanisms. Such systems that restrict foreign DNA or trigger cell death have recently been recognized, but the molecular signals that activate many of these remain largely unknown. Here, we characterize one such system in pandemic Vibrio cholerae responsible for triggering cell density-dependent death (CDD) of cells in response to the presence of certain genetic elements. We show that the key component is the Lamassu DdmABC anti-phage/plasmid defense system. We demonstrate that signals that trigger CDD were palindromic DNA sequences in phages and plasmids that are predicted to form stem-loop hairpins from single-stranded DNA. Our results suggest that agents that damage DNA also trigger DdmABC activation and inhibit cell growth. Thus, any infectious process that results in damaged DNA, particularly during DNA replication, can in theory trigger DNA restriction and death through the DdmABC abortive infection system.
Collapse
Affiliation(s)
- William P Robins
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
| | - Bradley T Meader
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Jonida Toska
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - John J Mekalanos
- Department of Microbiology, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
| |
Collapse
|
2
|
Duardo RC, Guerra F, Pepe S, Capranico G. Non-B DNA structures as a booster of genome instability. Biochimie 2023; 214:176-192. [PMID: 37429410 DOI: 10.1016/j.biochi.2023.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023]
Abstract
Non-canonical secondary structures (NCSs) are alternative nucleic acid structures that differ from the canonical B-DNA conformation. NCSs often occur in repetitive DNA sequences and can adopt different conformations depending on the sequence. The majority of these structures form in the context of physiological processes, such as transcription-associated R-loops, G4s, as well as hairpins and slipped-strand DNA, whose formation can be dependent on DNA replication. It is therefore not surprising that NCSs play important roles in the regulation of key biological processes. In the last years, increasing published data have supported their biological role thanks to genome-wide studies and the development of bioinformatic prediction tools. Data have also highlighted the pathological role of these secondary structures. Indeed, the alteration or stabilization of NCSs can cause the impairment of transcription and DNA replication, modification in chromatin structure and DNA damage. These events lead to a wide range of recombination events, deletions, mutations and chromosomal aberrations, well-known hallmarks of genome instability which are strongly associated with human diseases. In this review, we summarize molecular processes through which NCSs trigger genome instability, with a focus on G-quadruplex, i-motif, R-loop, Z-DNA, hairpin, cruciform and multi-stranded structures known as triplexes.
Collapse
Affiliation(s)
- Renée C Duardo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Federico Guerra
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Simona Pepe
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126, Bologna, Italy.
| |
Collapse
|
3
|
Amarh V, Abbey BA, Acheampong SA, Debrah MA, Amarquaye GN, Arthur PK. Codeine dysregulates ribosome biogenesis in Escherichia coli with DNA double-strand breaks to chart path to new classes of antibiotics. FUTURE DRUG DISCOVERY 2023; 5:FDD84. [PMID: 38464684 PMCID: PMC10918497 DOI: 10.4155/fdd-2023-0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/26/2023] [Indexed: 03/12/2024] Open
Abstract
Aim A bacterial genetics-guided approach was utilized for the discovery of new compounds affecting bacterial genome stability. Materials & methods Fungal extracts and fractions were tested for genome instability-mediated antibacterial activity. Interaction assays and RT-qPCR were used to identify compounds that boost the activity of sub-minimum inhibitory concentration streptomycin and obtain insights on the molecular mechanisms of the primary hit compound, respectively. Results Several extracts and fractions caused bacterial genome instability. Codeine, in synergy with streptomycin, regulates double-strand break (DSB) repair and causes bacterial ribosome dysfunction in the absence of DSBs, and dysregulation of ribosome biogenesis in a DSB-dependent manner. Conclusion This study demonstrates a potential viable strategy that we are exploring for the discovery of new chemical entities with activities against Escherichia coli and other bacterial pathogens.
Collapse
Affiliation(s)
- Vincent Amarh
- Department of Biochemistry, Cell & Molecular Biology, West African Center for Cell Biology of Infectious Pathogens, University of Ghana, PO Box LG54, Legon, Accra, Ghana
| | - Benaiah Annertey Abbey
- Department of Biochemistry, Cell & Molecular Biology, West African Center for Cell Biology of Infectious Pathogens, University of Ghana, PO Box LG54, Legon, Accra, Ghana
| | - Samuel Akwasi Acheampong
- Department of Biochemistry, Cell & Molecular Biology, West African Center for Cell Biology of Infectious Pathogens, University of Ghana, PO Box LG54, Legon, Accra, Ghana
| | - Michael Acheampong Debrah
- Department of Biochemistry, Cell & Molecular Biology, West African Center for Cell Biology of Infectious Pathogens, University of Ghana, PO Box LG54, Legon, Accra, Ghana
| | - Gwendolyn Nita Amarquaye
- Department of Biochemistry, Cell & Molecular Biology, West African Center for Cell Biology of Infectious Pathogens, University of Ghana, PO Box LG54, Legon, Accra, Ghana
| | - Patrick Kobina Arthur
- Department of Biochemistry, Cell & Molecular Biology, West African Center for Cell Biology of Infectious Pathogens, University of Ghana, PO Box LG54, Legon, Accra, Ghana
| |
Collapse
|
4
|
Ait Saada A, Guo W, Costa AB, Yang J, Wang J, Lobachev K. Widely spaced and divergent inverted repeats become a potent source of chromosomal rearrangements in long single-stranded DNA regions. Nucleic Acids Res 2023; 51:3722-3734. [PMID: 36919609 PMCID: PMC10164571 DOI: 10.1093/nar/gkad153] [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: 11/11/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/16/2023] Open
Abstract
DNA inverted repeats (IRs) are widespread across many eukaryotic genomes. Their ability to form stable hairpin/cruciform secondary structures is causative in triggering chromosome instability leading to several human diseases. Distance and sequence divergence between IRs are inversely correlated with their ability to induce gross chromosomal rearrangements (GCRs) because of a lesser probability of secondary structure formation and chromosomal breakage. In this study, we demonstrate that structural parameters that normally constrain the instability of IRs are overcome when the repeats interact in single-stranded DNA (ssDNA). We established a system in budding yeast whereby >73 kb of ssDNA can be formed in cdc13-707fs mutants. We found that in ssDNA, 12 bp or 30 kb spaced Alu-IRs show similarly high levels of GCRs, while heterology only beyond 25% suppresses IR-induced instability. Mechanistically, rearrangements arise after cis-interaction of IRs leading to a DNA fold-back and the formation of a dicentric chromosome, which requires Rad52/Rad59 for IR annealing as well as Rad1-Rad10, Slx4, Msh2/Msh3 and Saw1 proteins for nonhomologous tail removal. Importantly, using structural characteristics rendering IRs permissive to DNA fold-back in yeast, we found that ssDNA regions mapped in cancer genomes contain a substantial number of potentially interacting and unstable IRs.
Collapse
Affiliation(s)
- Anissia Ait Saada
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Wenying Guo
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alex B Costa
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Jiaxin Yang
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Jianrong Wang
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Kirill S Lobachev
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| |
Collapse
|
5
|
Wang G, Vasquez KM. Dynamic alternative DNA structures in biology and disease. Nat Rev Genet 2023; 24:211-234. [PMID: 36316397 DOI: 10.1038/s41576-022-00539-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2022] [Indexed: 11/06/2022]
Abstract
Repetitive elements in the human genome, once considered 'junk DNA', are now known to adopt more than a dozen alternative (that is, non-B) DNA structures, such as self-annealed hairpins, left-handed Z-DNA, three-stranded triplexes (H-DNA) or four-stranded guanine quadruplex structures (G4 DNA). These dynamic conformations can act as functional genomic elements involved in DNA replication and transcription, chromatin organization and genome stability. In addition, recent studies have revealed a role for these alternative structures in triggering error-generating DNA repair processes, thereby actively enabling genome plasticity. As a driving force for genetic variation, non-B DNA structures thus contribute to both disease aetiology and evolution.
Collapse
Affiliation(s)
- Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Paediatric Research Institute, Austin, TX, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Paediatric Research Institute, Austin, TX, USA.
| |
Collapse
|
6
|
Mre11-Rad50: the DNA end game. Biochem Soc Trans 2023; 51:527-538. [PMID: 36892213 DOI: 10.1042/bst20220754] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/09/2023] [Accepted: 02/17/2023] [Indexed: 03/10/2023]
Abstract
The Mre11-Rad50-(Nbs1/Xrs2) complex is an evolutionarily conserved factor for the repair of DNA double-strand breaks and other DNA termini in all kingdoms of life. It is an intricate DNA associated molecular machine that cuts, among other functions, a large variety of free and obstructed DNA termini for DNA repair by end joining or homologous recombination, yet leaves undamaged DNA intact. Recent years have brought progress in both the structural and functional analyses of Mre11-Rad50 orthologs, revealing mechanisms of DNA end recognition, endo/exonuclease activities, nuclease regulation and DNA scaffolding. Here, I review our current understanding and recent progress on the functional architecture Mre11-Rad50 and how this chromosome associated coiled-coil ABC ATPase acts as DNA topology specific endo-/exonuclease.
Collapse
|
7
|
Goswami S, Gowrishankar J. Role for DNA double strand end-resection activity of RecBCD in control of aberrant chromosomal replication initiation in Escherichia coli. Nucleic Acids Res 2022; 50:8643-8657. [PMID: 35929028 PMCID: PMC9410895 DOI: 10.1093/nar/gkac670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 07/13/2022] [Accepted: 08/03/2022] [Indexed: 11/12/2022] Open
Abstract
Replication of the circular bacterial chromosome is initiated from a locus oriC with the aid of an essential protein DnaA. One approach to identify factors acting to prevent aberrant oriC-independent replication initiation in Escherichia coli has been that to obtain mutants which survive loss of DnaA. Here, we show that a ΔrecD mutation, associated with attenuation of RecBCD’s DNA double strand end-resection activity, provokes abnormal replication and rescues ΔdnaA lethality in two situations: (i) in absence of 5′-3′ single-strand DNA exonuclease RecJ, or (ii) when multiple two-ended DNA double strand breaks (DSBs) are generated either by I-SceI endonucleolytic cleavages or by radiomimetic agents phleomycin or bleomycin. One-ended DSBs in the ΔrecD mutant did not rescue ΔdnaA lethality. With two-ended DSBs in the ΔrecD strain, ΔdnaA viability was retained even after linearization of the chromosome. Data from genome-wide DNA copy number determinations in ΔdnaA-rescued cells lead us to propose a model that nuclease-mediated DNA resection activity of RecBCD is critical for prevention of a σ-mode of rolling-circle over-replication when convergent replication forks merge and fuse, as may be expected to occur during normal replication at the chromosomal terminus region or during repair of two-ended DSBs following ‘ends-in’ replication.
Collapse
Affiliation(s)
- Sayantan Goswami
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India.,Graduate Studies, Manipal Academy of Higher Education, Manipal 576104, India.,Indian Institute of Science Education and Research Mohali, SAS Nagar 140306, India
| | - Jayaraman Gowrishankar
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India.,Indian Institute of Science Education and Research Mohali, SAS Nagar 140306, India
| |
Collapse
|
8
|
Structural mechanism of endonucleolytic processing of blocked DNA ends and hairpins by Mre11-Rad50. Mol Cell 2022; 82:3513-3522.e6. [DOI: 10.1016/j.molcel.2022.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 06/10/2022] [Accepted: 07/23/2022] [Indexed: 11/17/2022]
|
9
|
Bowater RP, Bohálová N, Brázda V. Interaction of Proteins with Inverted Repeats and Cruciform Structures in Nucleic Acids. Int J Mol Sci 2022; 23:ijms23116171. [PMID: 35682854 PMCID: PMC9180970 DOI: 10.3390/ijms23116171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/26/2022] [Accepted: 05/30/2022] [Indexed: 01/27/2023] Open
Abstract
Cruciforms occur when inverted repeat sequences in double-stranded DNA adopt intra-strand hairpins on opposing strands. Biophysical and molecular studies of these structures confirm their characterization as four-way junctions and have demonstrated that several factors influence their stability, including overall chromatin structure and DNA supercoiling. Here, we review our understanding of processes that influence the formation and stability of cruciforms in genomes, covering the range of sequences shown to have biological significance. It is challenging to accurately sequence repetitive DNA sequences, but recent advances in sequencing methods have deepened understanding about the amounts of inverted repeats in genomes from all forms of life. We highlight that, in the majority of genomes, inverted repeats are present in higher numbers than is expected from a random occurrence. It is, therefore, becoming clear that inverted repeats play important roles in regulating many aspects of DNA metabolism, including replication, gene expression, and recombination. Cruciforms are targets for many architectural and regulatory proteins, including topoisomerases, p53, Rif1, and others. Notably, some of these proteins can induce the formation of cruciform structures when they bind to DNA. Inverted repeat sequences also influence the evolution of genomes, and growing evidence highlights their significance in several human diseases, suggesting that the inverted repeat sequences and/or DNA cruciforms could be useful therapeutic targets in some cases.
Collapse
Affiliation(s)
- Richard P. Bowater
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK;
| | - Natália Bohálová
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, 61265 Brno, Czech Republic;
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Václav Brázda
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, 61265 Brno, Czech Republic;
- Correspondence:
| |
Collapse
|
10
|
Jaramillo‐Riveri S, Broughton J, McVey A, Pilizota T, Scott M, El Karoui M. Growth-dependent heterogeneity in the DNA damage response in Escherichia coli. Mol Syst Biol 2022; 18:e10441. [PMID: 35620827 PMCID: PMC9136515 DOI: 10.15252/msb.202110441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 04/13/2022] [Accepted: 04/27/2022] [Indexed: 11/16/2022] Open
Abstract
In natural environments, bacteria are frequently exposed to sub-lethal levels of DNA damage, which leads to the induction of a stress response (the SOS response in Escherichia coli). Natural environments also vary in nutrient availability, resulting in distinct physiological changes in bacteria, which may have direct implications on their capacity to repair their chromosomes. Here, we evaluated the impact of varying the nutrient availability on the expression of the SOS response induced by chronic sub-lethal DNA damage in E. coli. We found heterogeneous expression of the SOS regulon at the single-cell level in all growth conditions. Surprisingly, we observed a larger fraction of high SOS-induced cells in slow growth as compared with fast growth, despite a higher rate of SOS induction in fast growth. The result can be explained by the dynamic balance between the rate of SOS induction and the division rates of cells exposed to DNA damage. Taken together, our data illustrate how cell division and physiology come together to produce growth-dependent heterogeneity in the DNA damage response.
Collapse
Affiliation(s)
| | - James Broughton
- Institute of Cell Biology and SynthSysUniversity of EdinburghEdinburghUK
| | - Alexander McVey
- Institute of Cell Biology and SynthSysUniversity of EdinburghEdinburghUK
- Present address:
OGI Bio LtdEdinburghUK
| | - Teuta Pilizota
- Institute of Cell Biology and SynthSysUniversity of EdinburghEdinburghUK
| | - Matthew Scott
- Department of Applied MathematicsUniversity of WaterlooWaterlooONCanada
| | - Meriem El Karoui
- Institute of Cell Biology and SynthSysUniversity of EdinburghEdinburghUK
| |
Collapse
|
11
|
Rissone P, Bizarro CV, Ritort F. Stem-loop formation drives RNA folding in mechanical unzipping experiments. Proc Natl Acad Sci U S A 2022; 119:e2025575119. [PMID: 35022230 PMCID: PMC8784153 DOI: 10.1073/pnas.2025575119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 11/29/2021] [Indexed: 12/22/2022] Open
Abstract
Accurate knowledge of RNA hybridization is essential for understanding RNA structure and function. Here we mechanically unzip and rezip a 2-kbp RNA hairpin and derive the 10 nearest-neighbor base pair (NNBP) RNA free energies in sodium and magnesium with 0.1 kcal/mol precision using optical tweezers. Notably, force-distance curves (FDCs) exhibit strong irreversible effects with hysteresis and several intermediates, precluding the extraction of the NNBP energies with currently available methods. The combination of a suitable RNA synthesis with a tailored pulling protocol allowed us to obtain the fully reversible FDCs necessary to derive the NNBP energies. We demonstrate the equivalence of sodium and magnesium free-energy salt corrections at the level of individual NNBP. To characterize the irreversibility of the unzipping-rezipping process, we introduce a barrier energy landscape of the stem-loop structures forming along the complementary strands, which compete against the formation of the native hairpin. This landscape correlates with the hysteresis observed along the FDCs. RNA sequence analysis shows that base stacking and base pairing stabilize the stem-loops that kinetically trap the long-lived intermediates observed in the FDC. Stem-loops formation appears as a general mechanism to explain a wide range of behaviors observed in RNA folding.
Collapse
Affiliation(s)
- Paolo Rissone
- Small Biosystems Laboratory, Condensed Matter Physics Department, University of Barcelona, Barcelona 08028, Spain
| | - Cristiano V Bizarro
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Centro de Pesquisas em Biologia Molecular e Funcional, Pontifícia Universidade Católica do Rio Grande do Sul, 90616-900 Porto Alegre, Brazil
| | - Felix Ritort
- Small Biosystems Laboratory, Condensed Matter Physics Department, University of Barcelona, Barcelona 08028, Spain;
| |
Collapse
|
12
|
Yasmin T, Azeroglu B, Cockram CA, Leach DRF. Distribution of Holliday junctions and repair forks during Escherichia coli DNA double-strand break repair. PLoS Genet 2021; 17:e1009717. [PMID: 34432790 PMCID: PMC8386832 DOI: 10.1371/journal.pgen.1009717] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/14/2021] [Indexed: 11/21/2022] Open
Abstract
Accurate repair of DNA double-strand breaks (DSBs) is crucial for cell survival and genome integrity. In Escherichia coli, DSBs are repaired by homologous recombination (HR), using an undamaged sister chromosome as template. The DNA intermediates of this pathway are expected to be branched molecules that may include 4-way structures termed Holliday junctions (HJs), and 3-way structures such as D-loops and repair forks. Using a tool creating a site-specific, repairable DSB on only one of a pair of replicating sister chromosomes, we have determined how these branched DNA intermediates are distributed across a DNA region that is undergoing DSB repair. In cells, where branch migration and cleavage of HJs are limited by inactivation of the RuvABC complex, HJs and repair forks are principally accumulated within a distance of 12 kb from sites of recombination initiation, known as Chi, on each side of the engineered DSB. These branched DNA structures can even be detected in the region of DNA between the Chi sites flanking the DSB, a DNA segment not expected to be engaged in recombination initiation, and potentially degraded by RecBCD nuclease action. This is observed even in the absence of the branch migration and helicase activities of RuvAB, RadA, RecG, RecQ and PriA. The detection of full-length DNA fragments containing HJs in this central region implies that DSB repair can restore the two intact chromosomes, into which HJs can relocate prior to their resolution. The distribution of recombination intermediates across the 12kb region beyond Chi is altered in xonA, recJ and recQ mutants suggesting that, in the RecBCD pathway of DSB repair, exonuclease I stimulates the formation of repair forks and that RecJQ promotes strand-invasion at a distance from the recombination initiation sites.
Collapse
Affiliation(s)
- Tahirah Yasmin
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King’s Buildings, Edinburgh, United Kingdom
| | - Benura Azeroglu
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King’s Buildings, Edinburgh, United Kingdom
| | - Charlotte A. Cockram
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King’s Buildings, Edinburgh, United Kingdom
| | - David R. F. Leach
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King’s Buildings, Edinburgh, United Kingdom
| |
Collapse
|
13
|
Al-Zain AM, Symington LS. The dark side of homology-directed repair. DNA Repair (Amst) 2021; 106:103181. [PMID: 34311272 DOI: 10.1016/j.dnarep.2021.103181] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/16/2021] [Accepted: 07/16/2021] [Indexed: 10/20/2022]
Abstract
DNA double strand breaks (DSB) are cytotoxic lesions that can lead to genome rearrangements and genomic instability, which are hallmarks of cancer. The two main DSB repair pathways are non-homologous end joining and homologous recombination (HR). While HR is generally highly accurate, it has the potential for rearrangements that occur directly or through intermediates generated during the repair process. Whole genome sequencing of cancers has revealed numerous types of structural rearrangement signatures that are often indicative of repair mediated by sequence homology. However, it can be challenging to delineate repair mechanisms from sequence analysis of rearrangement end products from cancer genomes, or even model systems, because the same rearrangements can be generated by different pathways. Here, we review homology-directed repair pathways and their consequences. Exploring those pathways can lead to a greater understanding of rearrangements that occur in cancer cells.
Collapse
Affiliation(s)
- Amr M Al-Zain
- Program in Biological Sciences, Columbia University, New York, NY, 10027, United States; Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, United States
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY, 10032, United States; Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY, 10032, United States.
| |
Collapse
|
14
|
Ait Saada A, Costa AB, Sheng Z, Guo W, Haber JE, Lobachev K. Structural parameters of palindromic repeats determine the specificity of nuclease attack of secondary structures. Nucleic Acids Res 2021; 49:3932-3947. [PMID: 33772579 PMCID: PMC8053094 DOI: 10.1093/nar/gkab168] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/24/2021] [Accepted: 03/02/2021] [Indexed: 12/15/2022] Open
Abstract
Palindromic sequences are a potent source of chromosomal instability in many organisms and are implicated in the pathogenesis of human diseases. In this study, we investigate which nucleases are responsible for cleavage of the hairpin and cruciform structures and generation of double-strand breaks at inverted repeats in Saccharomyces cerevisiae. We demonstrate that the involvement of structure-specific nucleases in palindrome fragility depends on the distance between inverted repeats and their transcriptional status. The attack by the Mre11 complex is constrained to hairpins with loops <9 nucleotides. This restriction is alleviated upon RPA depletion, indicating that RPA controls the stability and/or formation of secondary structures otherwise responsible for replication fork stalling and DSB formation. Mus81-Mms4 cleavage of cruciforms occurs at divergently but not convergently transcribed or nontranscribed repeats. Our study also reveals the third pathway for fragility at perfect and quasi-palindromes, which involves cruciform resolution during the G2 phase of the cell cycle.
Collapse
Affiliation(s)
- Anissia Ait Saada
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GE 30332, USA
| | - Alex B Costa
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GE 30332, USA
| | - Ziwei Sheng
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GE 30332, USA
| | - Wenying Guo
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GE 30332, USA
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Waltham, MA 02454-9110, USA
| | - Kirill S Lobachev
- School of Biological Sciences and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GE 30332, USA
| |
Collapse
|
15
|
Svetec Miklenić M, Svetec IK. Palindromes in DNA-A Risk for Genome Stability and Implications in Cancer. Int J Mol Sci 2021; 22:2840. [PMID: 33799581 PMCID: PMC7999016 DOI: 10.3390/ijms22062840] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/04/2021] [Accepted: 03/08/2021] [Indexed: 02/07/2023] Open
Abstract
A palindrome in DNA consists of two closely spaced or adjacent inverted repeats. Certain palindromes have important biological functions as parts of various cis-acting elements and protein binding sites. However, many palindromes are known as fragile sites in the genome, sites prone to chromosome breakage which can lead to various genetic rearrangements or even cell death. The ability of certain palindromes to initiate genetic recombination lies in their ability to form secondary structures in DNA which can cause replication stalling and double-strand breaks. Given their recombinogenic nature, it is not surprising that palindromes in the human genome are involved in genetic rearrangements in cancer cells as well as other known recurrent translocations and deletions associated with certain syndromes in humans. Here, we bring an overview of current understanding and knowledge on molecular mechanisms of palindrome recombinogenicity and discuss possible implications of DNA palindromes in carcinogenesis. Furthermore, we overview the data on known palindromic sequences in the human genome and efforts to estimate their number and distribution, as well as underlying mechanisms of genetic rearrangements specific palindromic sequences cause.
Collapse
Affiliation(s)
| | - Ivan Krešimir Svetec
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia;
| |
Collapse
|
16
|
Ghosh S, Ejaz A, Repeta L, Shuman S. Pseudomonas putida MPE, a manganese-dependent endonuclease of the binuclear metallophosphoesterase superfamily, incises single-strand DNA in two orientations to yield a mixture of 3'-PO4 and 3'-OH termini. Nucleic Acids Res 2021; 49:1023-1032. [PMID: 33367848 PMCID: PMC7826289 DOI: 10.1093/nar/gkaa1214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/25/2020] [Accepted: 11/30/2020] [Indexed: 11/14/2022] Open
Abstract
Pseudomonas putida MPE exemplifies a novel clade of manganese-dependent single-strand DNA endonuclease within the binuclear metallophosphoesterase superfamily. MPE is encoded within a widely conserved DNA repair operon. Via structure-guided mutagenesis, we identify His113 and His81 as essential for DNA nuclease activity, albeit inessential for hydrolysis of bis-p-nitrophenylphosphate. We propose that His113 contacts the scissile phosphodiester and serves as a general acid catalyst to expel the OH leaving group of the product strand. We find that MPE cleaves the 3′ and 5′ single-strands of tailed duplex DNAs and that MPE can sense and incise duplexes at sites of short mismatch bulges and opposite a nick. We show that MPE is an ambidextrous phosphodiesterase capable of hydrolyzing the ssDNA backbone in either orientation to generate a mixture of 3′-OH and 3′-PO4 cleavage products. The directionality of phosphodiester hydrolysis is dictated by the orientation of the water nucleophile vis-à-vis the OH leaving group, which must be near apical for the reaction to proceed. We propose that the MPE active site and metal-bound water nucleophile are invariant and the enzyme can bind the ssDNA productively in opposite orientations.
Collapse
Affiliation(s)
- Shreya Ghosh
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Anam Ejaz
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lucas Repeta
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Stewart Shuman
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| |
Collapse
|
17
|
Ye Z, Moreb EA, Li S, Lebeau J, Menacho-Melgar R, Munson M, Lynch MD. Escherichia coli Cas1/2 Endonuclease Complex Modifies Self-Targeting CRISPR/Cascade Spacers Reducing Silencing Guide Stability. ACS Synth Biol 2021; 10:29-37. [PMID: 33331764 DOI: 10.1021/acssynbio.0c00398] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
CRISPR-based interference has become common in various applications from genetic circuits to dynamic metabolic control. In E. coli, the native CRISPR Cascade system can be utilized for silencing by deletion of the cas3 nuclease along with expression of guide RNA arrays, where multiple genes can be silenced from a single transcript. We notice the loss of spacer sequences from guide arrays utilized for dynamic silencing. We report that unstable guide arrays are due to expression of the Cas1/2 endonuclease complex. We propose a model wherein basal Cas1/2 endonuclease activity results in the loss of spacers from guide arrays. Subsequently, mutant guide arrays can be amplified through selection. Replacing a constitutive promoter driving Cascade complex expression with a tightly controlled inducible promoter improves guide array stability, while minimizing leaky gene silencing. Additionally, these results demonstrate the potential of Cas1/2 mediated guide deletion as a mechanism to avoid CRISPR based autoimmunity.
Collapse
Affiliation(s)
- Zhixia Ye
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
- DMC Biotechnologies, Inc., Durham, North Carolina 27701, United States
| | - Eirik A Moreb
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Shuai Li
- DMC Biotechnologies, Inc., Durham, North Carolina 27701, United States
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Juliana Lebeau
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Romel Menacho-Melgar
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Matthew Munson
- DMC Biotechnologies, Inc., Durham, North Carolina 27701, United States
| | - Michael D Lynch
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| |
Collapse
|
18
|
Alternative DNA Structures In Vivo: Molecular Evidence and Remaining Questions. Microbiol Mol Biol Rev 2020; 85:85/1/e00110-20. [PMID: 33361270 DOI: 10.1128/mmbr.00110-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Duplex DNA naturally folds into a right-handed double helix in physiological conditions. Some sequences of unusual base composition may nevertheless form alternative structures, as was shown for many repeated sequences in vitro However, evidence for the formation of noncanonical structures in living cells is difficult to gather. It mainly relies on genetic assays demonstrating their function in vivo or through genetic instability reflecting particular properties of such structures. Efforts were made to reveal their existence directly in a living cell, mainly by generating antibodies specific to secondary structures or using chemical ligands selected for their affinity to these structures. Among secondary structure-forming DNAs are G-quadruplexes, human fragile sites containing minisatellites, AT-rich regions, inverted repeats able to form cruciform structures, hairpin-forming CAG/CTG triplet repeats, and triple helices formed by homopurine-homopyrimidine GAA/TTC trinucleotide repeats. Many of these alternative structures are involved in human pathologies, such as neurological or developmental disorders, as in the case of trinucleotide repeats, or cancers triggered by translocations linked to fragile sites. This review will discuss and highlight evidence supporting the formation of alternative DNA structures in vivo and will emphasize the role of the mismatch repair machinery in binding mispaired DNA duplexes, triggering genetic instability.
Collapse
|
19
|
Kuzmenko A, Oguienko A, Esyunina D, Yudin D, Petrova M, Kudinova A, Maslova O, Ninova M, Ryazansky S, Leach D, Aravin AA, Kulbachinskiy A. DNA targeting and interference by a bacterial Argonaute nuclease. Nature 2020; 587:632-637. [PMID: 32731256 DOI: 10.1038/s41586-020-2605-1] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 07/24/2020] [Indexed: 12/21/2022]
Abstract
Members of the conserved Argonaute protein family use small RNA guides to locate their mRNA targets and regulate gene expression and suppress mobile genetic elements in eukaryotes1,2. Argonautes are also present in many bacterial and archaeal species3-5. Unlike eukaryotic proteins, several prokaryotic Argonaute proteins use small DNA guides to cleave DNA, a process known as DNA interference6-10. However, the natural functions and targets of DNA interference are poorly understood, and the mechanisms of DNA guide generation and target discrimination remain unknown. Here we analyse the activity of a bacterial Argonaute nuclease from Clostridium butyricum (CbAgo) in vivo. We show that CbAgo targets multicopy genetic elements and suppresses the propagation of plasmids and infection by phages. CbAgo induces DNA interference between homologous sequences and triggers DNA degradation at double-strand breaks in the target DNA. The loading of CbAgo with locus-specific small DNA guides depends on both its intrinsic endonuclease activity and the cellular double-strand break repair machinery. A similar interaction was reported for the acquisition of new spacers during CRISPR adaptation, and prokaryotic genomes that encode Ago nucleases are enriched in CRISPR-Cas systems. These results identify molecular mechanisms that generate guides for DNA interference and suggest that the recognition of foreign nucleic acids by prokaryotic defence systems involves common principles.
Collapse
Affiliation(s)
- Anton Kuzmenko
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia. .,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | - Anastasiya Oguienko
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Daria Esyunina
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Denis Yudin
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia.,Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Mayya Petrova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Alina Kudinova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Olga Maslova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Maria Ninova
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Sergei Ryazansky
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - David Leach
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Alexei A Aravin
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia. .,Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
| | | |
Collapse
|
20
|
Yu TY, Garcia VE, Symington LS. CDK and Mec1/Tel1-catalyzed phosphorylation of Sae2 regulate different responses to DNA damage. Nucleic Acids Res 2020; 47:11238-11249. [PMID: 31552432 PMCID: PMC6868371 DOI: 10.1093/nar/gkz814] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 09/09/2019] [Accepted: 09/20/2019] [Indexed: 11/14/2022] Open
Abstract
Sae2 functions in the DNA damage response by controlling Mre11-Rad50-Xrs2 (MRX)-catalyzed end resection, an essential step for homology-dependent repair of double-strand breaks (DSBs), and by attenuating DNA damage checkpoint signaling. Phosphorylation of Sae2 by cyclin-dependent kinase (CDK1/Cdc28) activates the Mre11 endonuclease, while the physiological role of Sae2 phosphorylation by Mec1 and Tel1 checkpoint kinases is not fully understood. Here, we compare the phenotype of sae2 mutants lacking the main CDK (sae2-S267A) or Mec1 and Tel1 phosphorylation sites (sae2-5A) with sae2Δ and Mre11 nuclease defective (mre11-nd) mutants. The phosphorylation-site mutations confer DNA damage sensitivity, but not to the same extent as sae2Δ. The sae2-S267A mutation is epistatic to mre11-nd for camptothecin (CPT) sensitivity and synergizes with sgs1Δ, whereas sae2-5A synergizes with mre11-nd and exhibits epistasis with sgs1Δ. We find that attenuation of checkpoint signaling by Sae2 is mostly independent of Mre11 endonuclease activation but requires Mec1 and Tel1-dependent phosphorylation of Sae2. These results support a model whereby CDK-catalyzed phosphorylation of Sae2 activates resection via Mre11 endonuclease, whereas Sae2 phosphorylation by Mec1 and Tel1 promotes resection by the Dna2-Sgs1 and Exo1 pathways indirectly by dampening the DNA damage response.
Collapse
Affiliation(s)
- Tai-Yuan Yu
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Valerie E Garcia
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA.,Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY 10032, USA
| |
Collapse
|
21
|
Svetec Miklenić M, Gatalica N, Matanović A, Žunar B, Štafa A, Lisnić B, Svetec IK. Size-dependent antirecombinogenic effect of short spacers on palindrome recombinogenicity. DNA Repair (Amst) 2020; 90:102848. [PMID: 32388488 DOI: 10.1016/j.dnarep.2020.102848] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 03/21/2020] [Accepted: 03/28/2020] [Indexed: 01/01/2023]
Abstract
Palindromic sequences in DNA can instigate genetic recombination and genome instability, which can result in devastating conditions such as the Emmanuel syndrome. Palindrome recombinogenicity increases with its size and sequence similarity between palindrome arms, while quasipalindromes with long spacers are less recombinogenic. However, the minimal spacer length, which could reduce or abolish palindrome recombinogenicity in the eukaryotic genome, was never determined. Therefore, we constructed a series of palindromes containing spacers of lengths ranging from 0 (perfect palindrome) to 10 bp and tested their recombinogenicity in yeast Saccharomyces cerevisiae. We found that a 7 bp spacer significantly reduces 126 bp palindrome recombinogenicity, while a 10 bp spacer completely stabilizes palindromes up to 150 bp long. Additionally, we showed that palindrome stimulated recombination rate is not dependent on Mus81 and Yen1 endonucleases. We also compared the recombinogenicity of a perfect 126 bp palindrome and a corresponding quasipalindrome consisting of the same palindrome arms with a stabilising 10 bp spacer in sgs1Δ and rad27Δ backgrounds, since both Sgs1 helicase and Rad27 endonuclease are implicated in preventing hairpin formation at palindromic sequences during replication.
Collapse
Affiliation(s)
- Marina Svetec Miklenić
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Nikolina Gatalica
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Angela Matanović
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Bojan Žunar
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Anamarija Štafa
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Berislav Lisnić
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia
| | - Ivan Krešimir Svetec
- Laboratory for Biology and Microbial Genetics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia.
| |
Collapse
|
22
|
Sinha AK, Possoz C, Leach DRF. The Roles of Bacterial DNA Double-Strand Break Repair Proteins in Chromosomal DNA Replication. FEMS Microbiol Rev 2020; 44:351-368. [PMID: 32286623 PMCID: PMC7326373 DOI: 10.1093/femsre/fuaa009] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/09/2020] [Indexed: 02/06/2023] Open
Abstract
It is well established that DNA double-strand break (DSB) repair is required to underpin chromosomal DNA replication. Because DNA replication forks are prone to breakage, faithful DSB repair and correct replication fork restart are critically important. Cells, where the proteins required for DSB repair are absent or altered, display characteristic disturbances to genome replication. In this review, we analyze how bacterial DNA replication is perturbed in DSB repair mutant strains and explore the consequences of these perturbations for bacterial chromosome segregation and cell viability. Importantly, we look at how DNA replication and DSB repair processes are implicated in the striking recent observations of DNA amplification and DNA loss in the chromosome terminus of various mutant Escherichia coli strains. We also address the mutant conditions required for the remarkable ability to copy the entire E. coli genome, and to maintain cell viability, even in the absence of replication initiation from oriC, the unique origin of DNA replication in wild type cells. Furthermore, we discuss the models that have been proposed to explain these phenomena and assess how these models fit with the observed data, provide new insights and enhance our understanding of chromosomal replication and termination in bacteria.
Collapse
Affiliation(s)
- Anurag Kumar Sinha
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen, 2200, Denmark
| | - Christophe Possoz
- Evolution and maintenance of circular chromosomes, Genome biology department, Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, 1 avenue de la Terrasse Building 26, 91198 Gif-sur-Yvette, France
| | - David R F Leach
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King's Buildings, Edinburgh, EH9 3FF, United Kingdom
| |
Collapse
|
23
|
Chen SH, Goller CC. Harnessing single-stranded DNA binding protein to explore protein-protein and protein-DNA interactions. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 48:181-190. [PMID: 31850676 DOI: 10.1002/bmb.21324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/29/2019] [Accepted: 12/03/2019] [Indexed: 06/10/2023]
Abstract
Proteins must interact with a variety of other cellular components to properly perform their functions. We have developed a series of five experiments based on the robust bacterial single-stranded DNA binding protein (SSB) to characterize both known and unknown protein-protein and protein-DNA interactions. Students work in groups to generate and process data from electrophoretic mobility shift assays (EMSA), yeast two-hybrid, far Western, chromatin immunoprecipitation (ChIP), and fluorescence microscopy experiments, including choosing a novel condition for each. A gamification approach was used to encourage student participation and laboratory safety. Student learning was assessed using pre- and post-surveys and course grade data. The results indicate a clear increase in both content knowledge and confidence in the topics presented. Ranking of course activities indicated that performing the hands-on laboratory exercises was the most valuable course component, and over half of the students would choose to take another course with a similar gamification component. Each of the five laboratory experiments can be performed in combination with each other or integrated separately into a related course, and the gamification structure can be applied to any course.
Collapse
Affiliation(s)
- Stefanie H Chen
- Biotechnology Program, North Carolina State University, Raleigh, North Carolina
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina
| | - Carlos C Goller
- Biotechnology Program, North Carolina State University, Raleigh, North Carolina
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina
| |
Collapse
|
24
|
White MA, Darmon E, Lopez-Vernaza MA, Leach DRF. DNA double strand break repair in Escherichia coli perturbs cell division and chromosome dynamics. PLoS Genet 2020; 16:e1008473. [PMID: 31895943 PMCID: PMC6959608 DOI: 10.1371/journal.pgen.1008473] [Citation(s) in RCA: 4] [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: 10/09/2019] [Revised: 01/14/2020] [Accepted: 12/16/2019] [Indexed: 11/18/2022] Open
Abstract
To prevent the transmission of damaged genomic material between generations, cells require a system for accommodating DNA repair within their cell cycles. We have previously shown that Escherichia coli cells subject to a single, repairable site-specific DNA double-strand break (DSB) per DNA replication cycle reach a new average cell length, with a negligible effect on population growth rate. We show here that this new cell size distribution is caused by a DSB repair-dependent delay in completion of cell division. This delay occurs despite unperturbed cell size regulated initiation of both chromosomal DNA replication and cell division. Furthermore, despite DSB repair altering the profile of DNA replication across the genome, the time required to complete chromosomal duplication is invariant. The delay in completion of cell division is accompanied by a DSB repair-dependent delay in individualization of sister nucleoids. We suggest that DSB repair events create inter-sister connections that persist until those chromosomes are separated by a closing septum.
Collapse
Affiliation(s)
- Martin A. White
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, The King’s Buildings, Edinburgh, United Kingdom
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA, United States of America
| | - Elise Darmon
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, The King’s Buildings, Edinburgh, United Kingdom
| | - Manuel A. Lopez-Vernaza
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, The King’s Buildings, Edinburgh, United Kingdom
| | - David R. F. Leach
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, The King’s Buildings, Edinburgh, United Kingdom
- * E-mail:
| |
Collapse
|
25
|
Wang Y, Luo L, Li Q, Wang H, Wang Y, Sun H, Xu J, Lan R, Ye C. Genomic dissection of the most prevalent Listeria monocytogenes clone, sequence type ST87, in China. BMC Genomics 2019; 20:1014. [PMID: 31870294 PMCID: PMC6929445 DOI: 10.1186/s12864-019-6399-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 12/15/2019] [Indexed: 12/27/2022] Open
Abstract
Background Listeria monocytogenes consists of four lineages that occupy a wide variety of ecological niches. Sequence type (ST) 87 (serotype 1/2b), belonging to lineage I, is one of the most common STs isolated from food products, food associated environments and sporadic listeriosis in China. Here, we performed a comparative genomic analysis of the L. monocytogenes ST87 clone by sequencing 71 strains representing a diverse range of sources, different geographical locations and isolation years. Results The core genome and pan genome of ST87 contained 2667 genes and 3687 genes respectively. Phylogenetic analysis based on core genome SNPs divided the 71 strains into 10 clades. The clinical strains were distributed among multiple clades. Four clades contained strains from multiple geographic regions and showed high genetic diversity. The major gene content variation of ST87 genomes was due to putative prophages, with eleven hotspots of the genome that harbor prophages. All strains carry an intact CRISRP/Cas system. Two major CRISPR spacer profiles were found which were not clustered phylogenetically. A large plasmid of about 90 Kb, which carried heavy metal resistance genes, was found in 32.4% (23/71) of the strains. All ST87 strains harbored the Listeria pathogenicity island (LIPI)-4 and a unique 10-open read frame (ORF) genomic island containing a novel restriction-modification system. Conclusion Whole genome sequence analysis of L. monocytogenes ST87 enabled a clearer understanding of the population structure and the evolutionary history of ST87 L. monocytogenes in China. The novel genetic elements identified may contribute to its virulence and adaptation to different environmental niches. Our findings will be useful for the development of effective strategies for the prevention and treatment of listeriosis caused by this prevalent clone.
Collapse
Affiliation(s)
- Yan Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Lijuan Luo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Qun Li
- Zigong Center for Disease Control and Prevention, Zigong, 643000, Sichuan Province, China
| | - Hong Wang
- Zigong Center for Disease Control and Prevention, Zigong, 643000, Sichuan Province, China
| | - Yiqian Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Hui Sun
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Jianguo Xu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2052, Australia.
| | - Changyun Ye
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| |
Collapse
|
26
|
Käshammer L, Saathoff JH, Lammens K, Gut F, Bartho J, Alt A, Kessler B, Hopfner KP. Mechanism of DNA End Sensing and Processing by the Mre11-Rad50 Complex. Mol Cell 2019; 76:382-394.e6. [DOI: 10.1016/j.molcel.2019.07.035] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 06/17/2019] [Accepted: 07/25/2019] [Indexed: 02/01/2023]
|
27
|
Genome Maintenance Proteins Modulate Autoimmunity Mediated Primed Adaptation by the Escherichia coli Type I-E CRISPR-Cas System. Genes (Basel) 2019; 10:genes10110872. [PMID: 31683605 PMCID: PMC6896009 DOI: 10.3390/genes10110872] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/22/2019] [Accepted: 10/28/2019] [Indexed: 12/21/2022] Open
Abstract
Bacteria and archaea use CRISPR-Cas adaptive immunity systems to interfere with viruses, plasmids, and other mobile genetic elements. During the process of adaptation, CRISPR-Cas systems acquire immunity by incorporating short fragments of invaders’ genomes into CRISPR arrays. The acquisition of fragments of host genomes leads to autoimmunity and may drive chromosomal rearrangements, negative cell selection, and influence bacterial evolution. In this study, we investigated the role of proteins involved in genome stability maintenance in spacer acquisition by the Escherichia coli type I-E CRISPR-Cas system targeting its own genome. We show here, that the deletion of recJ decreases adaptation efficiency and affects accuracy of spacers incorporation into CRISPR array. Primed adaptation efficiency is also dramatically inhibited in double mutants lacking recB and sbcD but not in single mutants suggesting independent involvement and redundancy of RecBCD and SbcCD pathways in spacer acquisition. While the presence of at least one of two complexes is crucial for efficient primed adaptation, RecBCD and SbcCD affect the pattern of acquired spacers. Overall, our data suggest distinct roles of the RecBCD and SbcCD complexes and of RecJ in spacer precursor selection and insertion into CRISPR array and highlight the functional interplay between CRISPR-Cas systems and host genome maintenance mechanisms.
Collapse
|
28
|
DNA double-strand break formation and repair as targets for novel antibiotic combination chemotherapy. Future Sci OA 2019; 5:FSO411. [PMID: 31534779 PMCID: PMC6745595 DOI: 10.2144/fsoa-2019-0034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
An unrepaired DNA double-strand break (DSB) is lethal to cells. In bacteria, DSBs are usually repaired either via an error-prone pathway, which ligates the ends of the break or an accurate recombination pathway. Due to this lethality, drugs that induce persistent DSBs have been successful in bacterial infection treatment. However, recurrent usage of these drugs has led to emergence of resistant strains. Several articles have thoroughly reviewed the causes, mechanisms and effects of bacterial drug resistance while others have also discussed approaches for facilitating drug discovery and development. Here, we focus on a hypothetical chemotherapeutic strategy that can be explored for minimizing development of resistance to novel DSB-inducing compounds. We also highlight the possibility of utilizing bacterial DSB repair pathways as targets for the discovery and development of novel antibiotics. Our health systems face a huge challenge in the form of antimicrobial resistance, which may result in many common infections becoming untreatable. The same antibiotics that gave modern medicine its power are fast losing their hold on the germs that cause disease. Many options are being developed to restore the control that antibiotics have on the microbes that cause many diseases. In this perspective, we outline a concept that is built around the way and manner in which bacteria mend their DNA whenever there is a break in the DNA chain. We discuss the merits of finding a new class of drugs that obstruct bacterial ability to mend their broken DNA. In this scenario, a combination of these new drugs with existing drugs or other new drugs that cause breaks in bacterial DNA would become a powerful therapeutic regimen. This concept, when fully developed, will offer hope in our effort to combat antimicrobial-resistant infections.
Collapse
|
29
|
White MA, Azeroglu B, Lopez-Vernaza MA, Hasan AMM, Leach DRF. RecBCD coordinates repair of two ends at a DNA double-strand break, preventing aberrant chromosome amplification. Nucleic Acids Res 2019; 46:6670-6682. [PMID: 29901759 PMCID: PMC6061781 DOI: 10.1093/nar/gky463] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 06/08/2018] [Indexed: 12/23/2022] Open
Abstract
DNA double-strand break (DSB) repair is critical for cell survival. A diverse range of organisms from bacteria to humans rely on homologous recombination for accurate DSB repair. This requires both coordinate action of the two ends of a DSB and stringent control of the resultant DNA replication to prevent unwarranted DNA amplification and aneuploidy. In Escherichia coli, RecBCD enzyme is responsible for the initial steps of homologous recombination. Previous work has revealed recD mutants to be nuclease defective but recombination proficient. Despite this proficiency, we show here that a recD null mutant is defective for the repair of a two-ended DSB and that this defect is associated with unregulated chromosome amplification and defective chromosome segregation. Our results demonstrate that RecBCD plays an important role in avoiding this amplification by coordinating the two recombining ends in a manner that prevents divergent replication forks progressing away from the DSB site.
Collapse
Affiliation(s)
- Martin A White
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3FF, UK
| | - Benura Azeroglu
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3FF, UK
| | - Manuel A Lopez-Vernaza
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3FF, UK
| | - A M Mahedi Hasan
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3FF, UK
| | - David R F Leach
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh EH9 3FF, UK
| |
Collapse
|
30
|
Ejaz A, Goldgur Y, Shuman S. Activity and structure of Pseudomonas putida MPE, a manganese-dependent single-strand DNA endonuclease encoded in a nucleic acid repair gene cluster. J Biol Chem 2019; 294:7931-7941. [PMID: 30894417 DOI: 10.1074/jbc.ra119.008049] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/20/2019] [Indexed: 02/04/2023] Open
Abstract
A recently identified and widely prevalent prokaryal gene cluster encodes a suite of enzymes with imputed roles in nucleic acid repair. The enzymes are as follows: MPE, a DNA endonuclease; Lhr-Core, a 3'-5' DNA helicase; LIG, an ATP-dependent DNA ligase; and Exo, a metallo-β-lactamase-family nuclease. Bacterial and archaeal MPE proteins belong to the binuclear metallophosphoesterase superfamily that includes the well-studied DNA repair nucleases Mre11 and SbcD. Here, we report that the Pseudomonas putida MPE protein is a manganese-dependent DNA endonuclease that incises either linear single strands or the single-strand loops of stem-loop DNA structures. MPE has feeble activity on duplex DNA. A crystal structure of MPE at 2.2 Å resolution revealed that the active site includes two octahedrally coordinated manganese ions. Seven signature amino acids of the binuclear metallophosphoesterase superfamily serve as the enzymic metal ligands in MPE: Asp33, His35, Asp78, Asn112, His124, His146, and His158 A swath of positive surface potential on either side of the active site pocket suggests a binding site for the single-strand DNA substrate. The structure of MPE differs from Mre11 and SbcD in several key respects: (i) MPE is a monomer, whereas Mre11 and SbcD are homodimers; (ii) MPE lacks the capping domain present in Mre11 and SbcD; and (iii) the topology of the β sandwich that comprises the core of the metallophosphoesterase fold differs in MPE vis-à-vis Mre11 and SbcD. We surmise that MPE exemplifies a novel clade of DNA endonuclease within the binuclear metallophosphoesterase superfamily.
Collapse
Affiliation(s)
| | - Yehuda Goldgur
- Structural Biology Programs, Sloan Kettering Institute, New York, New York 10065
| | | |
Collapse
|
31
|
Saathoff JH, Käshammer L, Lammens K, Byrne RT, Hopfner KP. The bacterial Mre11-Rad50 homolog SbcCD cleaves opposing strands of DNA by two chemically distinct nuclease reactions. Nucleic Acids Res 2018; 46:11303-11314. [PMID: 30277537 PMCID: PMC6265447 DOI: 10.1093/nar/gky878] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 09/14/2018] [Accepted: 09/19/2018] [Indexed: 12/22/2022] Open
Abstract
The Mre11-Rad50 complex is a DNA double-strand break sensor that cleaves blocked DNA ends and hairpins by an ATP-dependent endo/exonuclease activity for subsequent repair. For that, Mre11-Rad50 complexes, including the Escherichia coli homolog SbcCD, can endonucleolytically cleave one or both strands near a protein block and process free DNA ends via a 3'-5' exonuclease, but a unified basis for these distinct activities is lacking. Here we analyzed DNA binding, ATPase and nuclease reactions on different DNA substrates. SbcCD clips terminal bases of both strands of the DNA end in the presence of ATPγS. It introduces a DNA double-strand break around 20-25 bp from a blocked end after multiple rounds of ATP hydrolysis in a reaction that correlates with local DNA meltability. Interestingly, we find that nuclease reactions on opposing strands are chemically distinct, leaving a 5' phosphate on one strand, but a 3' phosphate on the other strand. Collectively, our results identify an unexpected chemical variability of the nuclease, indicating that the complex is oriented at a free DNA end and facing a block with opposite polarity. This suggests a unified model for ATP-dependent endo- and exonuclease reactions at internal DNA near a block and at free DNA ends.
Collapse
Affiliation(s)
- Jan-Hinnerk Saathoff
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
| | - Lisa Käshammer
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
| | - Katja Lammens
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
| | - Robert Thomas Byrne
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
| | - Karl-Peter Hopfner
- Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
- Gene Center, Ludwig-Maximilians-Universität München, Feodor Lynen Straße 25, 81377 Munich, Germany
- Center for Integrated Protein Science, Munich, Germany
| |
Collapse
|
32
|
Oh J, Symington LS. Role of the Mre11 Complex in Preserving Genome Integrity. Genes (Basel) 2018; 9:E589. [PMID: 30501098 PMCID: PMC6315862 DOI: 10.3390/genes9120589] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 11/26/2018] [Accepted: 11/27/2018] [Indexed: 12/12/2022] Open
Abstract
DNA double-strand breaks (DSBs) are hazardous lesions that threaten genome integrity and cell survival. The DNA damage response (DDR) safeguards the genome by sensing DSBs, halting cell cycle progression and promoting repair through either non-homologous end joining (NHEJ) or homologous recombination (HR). The Mre11-Rad50-Xrs2/Nbs1 (MRX/N) complex is central to the DDR through its structural, enzymatic, and signaling roles. The complex tethers DNA ends, activates the Tel1/ATM kinase, resolves protein-bound or hairpin-capped DNA ends, and maintains telomere homeostasis. In addition to its role at DSBs, MRX/N associates with unperturbed replication forks, as well as stalled replication forks, to ensure complete DNA synthesis and to prevent chromosome rearrangements. Here, we summarize the significant progress made in characterizing the MRX/N complex and its various activities in chromosome metabolism.
Collapse
Affiliation(s)
- Julyun Oh
- Biological Sciences Program, Columbia University, New York, NY 10027, USA.
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA.
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA.
| |
Collapse
|
33
|
Hasan AMM, Azeroglu B, Leach DRF. Genomic Analysis of DNA Double-Strand Break Repair in Escherichia coli. Methods Enzymol 2018; 612:523-554. [PMID: 30502957 DOI: 10.1016/bs.mie.2018.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Counting DNA whole genome sequencing reads is providing new insight into DNA double-strand break repair (DSBR) in the model organism Escherichia coli. We describe the application of RecA chromatin immunoprecipitation coupled to genomic DNA sequencing (RecA-ChIP-seq) and marker frequency analysis (MFA) to analyze the genomic consequences of DSBR. We provide detailed procedures for the preparation of DNA and the analysis of data. We compare different ways of visualizing ChIP data and show that alternative protocols for the preparation of DNA for MFA differentially affect the recovery of branched DNA molecules containing Holliday junctions.
Collapse
Affiliation(s)
- A M Mahedi Hasan
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King's Buildings, Edinburgh, United Kingdom
| | - Benura Azeroglu
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King's Buildings, Edinburgh, United Kingdom
| | - David R F Leach
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, King's Buildings, Edinburgh, United Kingdom.
| |
Collapse
|
34
|
Paull TT. 20 Years of Mre11 Biology: No End in Sight. Mol Cell 2018; 71:419-427. [PMID: 30057197 DOI: 10.1016/j.molcel.2018.06.033] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/18/2018] [Accepted: 06/21/2018] [Indexed: 01/01/2023]
Abstract
The Mre11 nuclease has been the subject of intensive investigation for the past 20 years because of the central role that Mre11/Rad50 complexes play in genome maintenance. The last two decades of work on this complex has led to a much deeper understanding of the structure, biochemical activities, and regulation of Mre11/Rad50 complexes from archaea, bacteria, and eukaryotic cells. This review will discuss some of the important findings over recent years that have illuminated roles for the Mre11 nuclease in these different contexts as well as the insights from structural biology that have helped us to understand its mechanisms of action.
Collapse
Affiliation(s)
- Tanya T Paull
- Howard Hughes Medical Institute; Department of Molecular Biosciences and Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA.
| |
Collapse
|
35
|
Lovett ST. Between sisters: Watching replication-associated recombinational DNA repair. J Cell Biol 2018; 217:2225-2227. [PMID: 29895696 PMCID: PMC6028551 DOI: 10.1083/jcb.201805091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Lovett previews work from Amarh et al. describing the dynamics of RecA-mediated repair at replication-dependent breaks. Amarh et al. (2018. J. Cell Biol.https://doi.org/10.1083/jcb.201803020) visualize for the first time the repair of double-strand breaks during DNA replication. As viewed by live-cell fluorescent imaging of Escherichia coli, repair of replication-dependent breaks is extraordinarily rapid and localized within the cell.
Collapse
Affiliation(s)
- Susan T Lovett
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, MA
| |
Collapse
|
36
|
Amarh V, White MA, Leach DRF. Dynamics of RecA-mediated repair of replication-dependent DNA breaks. J Cell Biol 2018; 217:2299-2307. [PMID: 29789437 PMCID: PMC6028544 DOI: 10.1083/jcb.201803020] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/27/2018] [Accepted: 04/30/2018] [Indexed: 11/22/2022] Open
Abstract
Spontaneous DNA double-strand breaks form during DNA replication and are largely repaired by recombination with a sister chromosome. Using live-cell fluorescence imaging, Amarh et al. show that repair of a replication-dependent break is rapid, localized, and involves a transient RecA focus. Chromosomal replication is the major source of spontaneous DNA double-strand breaks (DSBs) in living cells. Repair of these DSBs is essential for cell viability, and accuracy of repair is critical to avoid chromosomal rearrangements. Repair of replication-dependent DSBs occurs primarily by homologous recombination with a sister chromosome. However, this reaction has never been visualized at a defined chromosomal locus, so little is known about its spatial or temporal dynamics. Repair of a replication-independent DSB generated in Escherichia coli by a rare-cutting endonuclease leads to the formation of a bundle of RecA filaments. In this study, we show that in contrast, repair of a replication-dependent DSB involves a transient RecA focus localized in the central region of the cell in which the DNA is replicated. The recombining loci remain centrally located with restricted movement before segregating with little extension to the period of postreplicative sister-chromosome cohesion. The spatial and temporal efficiency of this reaction is remarkable.
Collapse
Affiliation(s)
- Vincent Amarh
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, UK
| | - Martin A White
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, UK
| | - David R F Leach
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, UK
| |
Collapse
|
37
|
Windgassen TA, Wessel SR, Bhattacharyya B, Keck JL. Mechanisms of bacterial DNA replication restart. Nucleic Acids Res 2018; 46:504-519. [PMID: 29202195 PMCID: PMC5778457 DOI: 10.1093/nar/gkx1203] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 11/15/2017] [Accepted: 11/20/2017] [Indexed: 12/21/2022] Open
Abstract
Multi-protein DNA replication complexes called replisomes perform the essential process of copying cellular genetic information prior to cell division. Under ideal conditions, replisomes dissociate only after the entire genome has been duplicated. However, DNA replication rarely occurs without interruptions that can dislodge replisomes from DNA. Such events produce incompletely replicated chromosomes that, if left unrepaired, prevent the segregation of full genomes to daughter cells. To mitigate this threat, cells have evolved 'DNA replication restart' pathways that have been best defined in bacteria. Replication restart requires recognition and remodeling of abandoned replication forks by DNA replication restart proteins followed by reloading of the replicative DNA helicase, which subsequently directs assembly of the remaining replisome subunits. This review summarizes our current understanding of the mechanisms underlying replication restart and the proteins that drive the process in Escherichia coli (PriA, PriB, PriC and DnaT).
Collapse
Affiliation(s)
- Tricia A Windgassen
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Sarah R Wessel
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
- Department of Biochemistry, Vanderbilt School of Medicine, Nashville, TN 37205, USA
| | - Basudeb Bhattacharyya
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
- Department of Chemistry and Biochemistry, University of Wisconsin-La Crosse, La Crosse, WI 54601, USA
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| |
Collapse
|
38
|
Vahanian N, Oh CS, Sippy J, Feiss M. Natural history of a viral cohesive end site: cosN of the λ-like phages. Virology 2017. [PMID: 28646648 DOI: 10.1016/j.virol.2017.06.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The base pairs of cosN, the site where the 12 base-long cohesive ends are generated in λ-like phages, show partial-two fold rotational symmetry. In a bioinformatic survey, we found that the cosN changes in 12 natural cosN variants are restricted to bp 6-to-12 of the cohesive end sequence. In contrast, bp 1-5 of the cohesive end sequence are strictly conserved (13/13), as are the two bp flanking the left nicking site (bp -2 and -1). The bp flanking the right nick site (bp 13 and 14) are conserved in 12 of 13 variants. Five cosN variants differing by as many as five bp were used to replace lambda's cosN. No significant effects of the cosN changes on λ's virus yield were found. In sum, bp -2 to 5 are critical cosN function, and bp 6-12 of the cohesive end sequence are not critical for terminase recognition or virus fitness.
Collapse
Affiliation(s)
- Nicole Vahanian
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA 52242, USA
| | - Choon Seok Oh
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA 52242, USA
| | - Jean Sippy
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA 52242, USA
| | - Michael Feiss
- Department of Microbiology, Roy J. and Lucille A. Carver College of Medicine University of Iowa, Iowa City, IA 52242, USA.
| |
Collapse
|
39
|
Azeroglu B, Leach DRF. RecG controls DNA amplification at double-strand breaks and arrested replication forks. FEBS Lett 2017; 591:1101-1113. [PMID: 28155219 PMCID: PMC5412681 DOI: 10.1002/1873-3468.12583] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 01/13/2017] [Accepted: 01/28/2017] [Indexed: 12/16/2022]
Abstract
DNA amplification is a powerful mutational mechanism that is a hallmark of cancer and drug resistance. It is therefore important to understand the fundamental pathways that cells employ to avoid over‐replicating sections of their genomes. Recent studies demonstrate that, in the absence of RecG, DNA amplification is observed at sites of DNA double‐strand break repair (DSBR) and of DNA replication arrest that are processed to generate double‐strand ends. RecG also plays a role in stabilising joint molecules formed during DSBR. We propose that RecG prevents a previously unrecognised mechanism of DNA amplification that we call reverse‐restart, which generates DNA double‐strand ends from incorrect loading of the replicative helicase at D‐loops formed by recombination, and at arrested replication forks.
Collapse
Affiliation(s)
- Benura Azeroglu
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, UK
| | - David R F Leach
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, UK
| |
Collapse
|
40
|
Molin WT, Wright AA, Lawton-Rauh A, Saski CA. The unique genomic landscape surrounding the EPSPS gene in glyphosate resistant Amaranthus palmeri: a repetitive path to resistance. BMC Genomics 2017; 18:91. [PMID: 28095770 PMCID: PMC5240378 DOI: 10.1186/s12864-016-3336-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 11/23/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The expanding number and global distributions of herbicide resistant weedy species threaten food, fuel, fiber and bioproduct sustainability and agroecosystem longevity. Amongst the most competitive weeds, Amaranthus palmeri S. Wats has rapidly evolved resistance to glyphosate primarily through massive amplification and insertion of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene across the genome. Increased EPSPS gene copy numbers results in higher titers of the EPSPS enzyme, the target of glyphosate, and confers resistance to glyphosate treatment. To understand the genomic unit and mechanism of EPSPS gene copy number proliferation, we developed and used a bacterial artificial chromosome (BAC) library from a highly resistant biotype to sequence the local genomic landscape flanking the EPSPS gene. RESULTS By sequencing overlapping BACs, a 297 kb sequence was generated, hereafter referred to as the "EPSPS cassette." This region included several putative genes, dense clusters of tandem and inverted repeats, putative helitron and autonomous replication sequences, and regulatory elements. Whole genome shotgun sequencing (WGS) of two biotypes exhibiting high and no resistance to glyphosate was performed to compare genomic representation across the EPSPS cassette. Mapping of sequences for both biotypes to the reference EPSPS cassette revealed significant differences in upstream and downstream sequences relative to EPSPS with regard to both repetitive units and coding content between these biotypes. The differences in sequence may have resulted from a compounded-building mechanism such as repetitive transpositional events. The association of putative helitron sequences with the cassette suggests a possible amplification and distribution mechanism. Flow cytometry revealed that the EPSPS cassette added measurable genomic content. CONCLUSIONS The adoption of glyphosate resistant cropping systems in major crops such as corn, soybean, cotton and canola coupled with excessive use of glyphosate herbicide has led to evolved glyphosate resistance in several important weeds. In Amaranthus palmeri, the amplification of the EPSPS cassette, characterized by a complex array of repetitive elements and putative helitron sequences, suggests an adaptive structural genomic mechanism that drives amplification and distribution around the genome. The added genomic content not found in glyphosate sensitive plants may be driving evolution through genome expansion.
Collapse
Affiliation(s)
- William T Molin
- United States Department of Agriculture, Crop Production Systems Research Unit, Stoneville, MS, USA.
| | - Alice A Wright
- United States Department of Agriculture, Crop Production Systems Research Unit, Stoneville, MS, USA
| | - Amy Lawton-Rauh
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, USA
| | - Christopher A Saski
- Institute of Translational Genomics, Genomics and Computational Biology Lab, Clemson University, Clemson, SC, USA.
| |
Collapse
|
41
|
Deshpande RA, Lee JH, Arora S, Paull TT. Nbs1 Converts the Human Mre11/Rad50 Nuclease Complex into an Endo/Exonuclease Machine Specific for Protein-DNA Adducts. Mol Cell 2016; 64:593-606. [PMID: 27814491 DOI: 10.1016/j.molcel.2016.10.010] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 07/22/2016] [Accepted: 10/05/2016] [Indexed: 11/26/2022]
Abstract
The human Mre11/Rad50/Nbs1 (hMRN) complex is critical for the sensing, processing, and signaling of DNA double-strand breaks. The nuclease activity of Mre11 is essential for mammalian development and cell viability, although the regulation and substrate specificity of Mre11 have been difficult to define. Here we show that hMRN catalyzes sequential endonucleolytic and exonucleolytic activities on both 5' and 3' strands of DNA ends containing protein adducts, and that Nbs1, ATP, and adducts are essential for this function. In contrast, Nbs1 inhibits Mre11/Rad50-catalyzed 3'-to-5' exonucleolytic degradation of clean DNA ends. The hMRN endonucleolytic cleavage events are further stimulated by the phosphorylated form of the human C-terminal binding protein-interacting protein (CtIP) DNA repair enzyme, establishing a role for CtIP in regulating hMRN activity. These results illuminate the important role of Nbs1 and CtIP in determining the substrates and consequences of human Mre11/Rad50 nuclease activities on protein-DNA lesions.
Collapse
Affiliation(s)
- Rajashree A Deshpande
- Howard Hughes Medical Institute and Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Ji-Hoon Lee
- Howard Hughes Medical Institute and Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Sucheta Arora
- Howard Hughes Medical Institute and Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Tanya T Paull
- Howard Hughes Medical Institute and Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
| |
Collapse
|
42
|
Xrs2 Dependent and Independent Functions of the Mre11-Rad50 Complex. Mol Cell 2016; 64:405-415. [PMID: 27746018 DOI: 10.1016/j.molcel.2016.09.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 07/22/2016] [Accepted: 09/08/2016] [Indexed: 02/04/2023]
Abstract
The Mre11-Rad50-Xrs2/Nbs1 (MRX/N) complex orchestrates the cellular response to DSBs through its structural, enzymatic, and signaling roles. Xrs2/Nbs1 is essential for nuclear translocation of Mre11, but its role as a component of the complex is not well defined. Here, we demonstrate that nuclear localization of Mre11 (Mre11-NLS) is able to bypass several functions of Xrs2, including DNA end resection, meiosis, hairpin resolution, and cellular resistance to clastogens. Using purified components, we show that the MR complex has equivalent activity to MRX in cleavage of protein-blocked DNA ends. Although Xrs2 physically interacts with Sae2, we found that end resection in its absence remains Sae2 dependent in vivo and in vitro. MRE11-NLS was unable to rescue the xrs2Δ defects in Tel1/ATM kinase signaling and non-homologous end joining, consistent with the role of Xrs2 as a chaperone and adaptor protein coordinating interactions between the MR complex and other repair proteins.
Collapse
|
43
|
Myler LR, Finkelstein IJ. Eukaryotic resectosomes: A single-molecule perspective. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2016; 127:119-129. [PMID: 27498169 DOI: 10.1016/j.pbiomolbio.2016.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 08/02/2016] [Indexed: 12/13/2022]
Abstract
DNA double-strand breaks (DSBs) disrupt the physical and genetic continuity of the genome. If unrepaired, DSBs can lead to cellular dysfunction and malignant transformation. Homologous recombination (HR) is a universally conserved DSB repair mechanism that employs the information in a sister chromatid to catalyze error-free DSB repair. To initiate HR, cells assemble the resectosome: a multi-protein complex composed of helicases, nucleases, and regulatory proteins. The resectosome nucleolytically degrades (resects) the free DNA ends for downstream homologous recombination. Several decades of intense research have identified the core resectosome components in eukaryotes, archaea, and bacteria. More recently, these proteins have been characterized via single-molecule approaches. Here, we focus on recent single-molecule studies that have begun to unravel how nucleases, helicases, processivity factors, and other regulatory proteins dictate the extent and efficiency of DNA resection in eukaryotic cells. We conclude with a discussion of outstanding questions that can be addressed via single-molecule approaches.
Collapse
Affiliation(s)
- Logan R Myler
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, 78712, USA.
| |
Collapse
|
44
|
Deng SK, Yin Y, Petes TD, Symington LS. Mre11-Sae2 and RPA Collaborate to Prevent Palindromic Gene Amplification. Mol Cell 2016; 60:500-8. [PMID: 26545079 DOI: 10.1016/j.molcel.2015.09.027] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 08/20/2015] [Accepted: 09/28/2015] [Indexed: 12/17/2022]
Abstract
Foldback priming at DNA double-stranded breaks is one mechanism proposed to initiate palindromic gene amplification, a common feature of cancer cells. Here, we show that small (5-9 bp) inverted repeats drive the formation of large palindromic duplications, the major class of chromosomal rearrangements recovered from yeast cells lacking Sae2 or the Mre11 nuclease. RPA dysfunction increased the frequency of palindromic duplications in Sae2 or Mre11 nuclease-deficient cells by ∼ 1,000-fold, consistent with intra-strand annealing to create a hairpin-capped chromosome that is subsequently replicated to form a dicentric isochromosome. The palindromic duplications were frequently associated with duplication of a second chromosome region bounded by a repeated sequence and a telomere, suggesting the dicentric chromosome breaks and repairs by recombination between dispersed repeats to acquire a telomere. We propose secondary structures within single-stranded DNA are potent instigators of genome instability, and RPA and Mre11-Sae2 play important roles in preventing their formation and propagation, respectively.
Collapse
Affiliation(s)
- Sarah K Deng
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Yi Yin
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Thomas D Petes
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY 10032, USA.
| |
Collapse
|
45
|
Azeroglu B, Mawer JSP, Cockram CA, White MA, Hasan AMM, Filatenkova M, Leach DRF. RecG Directs DNA Synthesis during Double-Strand Break Repair. PLoS Genet 2016; 12:e1005799. [PMID: 26872352 PMCID: PMC4752480 DOI: 10.1371/journal.pgen.1005799] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 12/19/2015] [Indexed: 11/19/2022] Open
Abstract
Homologous recombination provides a mechanism of DNA double-strand break repair (DSBR) that requires an intact, homologous template for DNA synthesis. When DNA synthesis associated with DSBR is convergent, the broken DNA strands are replaced and repair is accurate. However, if divergent DNA synthesis is established, over-replication of flanking DNA may occur with deleterious consequences. The RecG protein of Escherichia coli is a helicase and translocase that can re-model 3-way and 4-way DNA structures such as replication forks and Holliday junctions. However, the primary role of RecG in live cells has remained elusive. Here we show that, in the absence of RecG, attempted DSBR is accompanied by divergent DNA replication at the site of an induced chromosomal DNA double-strand break. Furthermore, DNA double-stand ends are generated in a recG mutant at sites known to block replication forks. These double-strand ends, also trigger DSBR and the divergent DNA replication characteristic of this mutant, which can explain over-replication of the terminus region of the chromosome. The loss of DNA associated with unwinding joint molecules previously observed in the absence of RuvAB and RecG, is suppressed by a helicase deficient PriA mutation (priA300), arguing that the action of RecG ensures that PriA is bound correctly on D-loops to direct DNA replication rather than to unwind joint molecules. This has led us to put forward a revised model of homologous recombination in which the re-modelling of branched intermediates by RecG plays a fundamental role in directing DNA synthesis and thus maintaining genomic stability.
Collapse
Affiliation(s)
- Benura Azeroglu
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Julia S. P. Mawer
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Charlotte A. Cockram
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Martin A. White
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - A. M. Mahedi Hasan
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Milana Filatenkova
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - David R. F. Leach
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
46
|
Lai PJ, Lim CT, Le HP, Katayama T, Leach DRF, Furukohri A, Maki H. Long inverted repeat transiently stalls DNA replication by forming hairpin structures on both leading and lagging strands. Genes Cells 2016; 21:136-45. [PMID: 26738888 DOI: 10.1111/gtc.12326] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 11/18/2015] [Indexed: 11/27/2022]
Abstract
Long inverted repeats (LIRs), often found in eukaryotic genomes, are unstable in Escherichia coli where they are recognized by the SbcCD (the bacterial Mre11/Rad50 homologue), an endonuclease/exonuclease capable of cleaving hairpin DNA. It has long been postulated that LIRs form hairpin structures exclusively on the lagging-strand template during DNA replication, and SbcCD cleaves these hairpin-containing lagging strands to generate DNA double-strand breaks. Using a reconstituted oriC plasmid DNA replication system, we have examined how a replication fork behaves when it meets a LIR on DNA. We have shown that leading-strand synthesis stalls transiently within the upstream half of the LIR. Pausing of lagging-strand synthesis at the LIR was not clearly observed, but the pattern of priming sites for Okazaki fragment synthesis was altered within the downstream half of the LIR. We have found that the LIR on a replicating plasmid was cleaved by SbcCD with almost equal frequency on both the leading- and lagging-strand templates. These data strongly suggest that the LIR is readily converted to a cruciform DNA, before the arrival of the fork, creating SbcCD-sensitive hairpin structures on both leading and lagging strands. We propose a model for the replication-dependent extrusion of LIRs to form cruciform structures that transiently impede replication fork movement.
Collapse
Affiliation(s)
- Pey Jiun Lai
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Chew Theng Lim
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Hang Phuong Le
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Tsutomu Katayama
- Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - David R F Leach
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Kings Buildings, Edinburgh, EH9 3JR, UK
| | - Asako Furukohri
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Hisaji Maki
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| |
Collapse
|
47
|
Abstract
DNA exonucleases, enzymes that hydrolyze phosphodiester bonds in DNA from a free end, play important cellular roles in DNA repair, genetic recombination and mutation avoidance in all organisms. This article reviews the structure, biochemistry, and biological functions of the 17 exonucleases currently identified in the bacterium Escherichia coli. These include the exonucleases associated with DNA polymerases I (polA), II (polB), and III (dnaQ/mutD); Exonucleases I (xonA/sbcB), III (xthA), IV, VII (xseAB), IX (xni/xgdG), and X (exoX); the RecBCD, RecJ, and RecE exonucleases; SbcCD endo/exonucleases; the DNA exonuclease activities of RNase T (rnt) and Endonuclease IV (nfo); and TatD. These enzymes are diverse in terms of substrate specificity and biochemical properties and have specialized biological roles. Most of these enzymes fall into structural families with characteristic sequence motifs, and members of many of these families can be found in all domains of life.
Collapse
|
48
|
Lim CT, Lai PJ, Leach DRF, Maki H, Furukohri A. A novel mode of nuclease action is revealed by the bacterial Mre11/Rad50 complex. Nucleic Acids Res 2015; 43:9804-16. [PMID: 26319016 PMCID: PMC4787754 DOI: 10.1093/nar/gkv855] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Accepted: 08/12/2015] [Indexed: 11/14/2022] Open
Abstract
The Mre11/Rad50 complex is a central player in various genome maintenance pathways. Here, we report a novel mode of nuclease action found for the Escherichia coli Mre11/Rad50 complex, SbcC2/D2 complex (SbcCD). SbcCD cuts off the top of a cruciform DNA by making incisions on both strands and continues cleaving the dsDNA stem at ∼10-bp intervals. Using linear-shaped DNA substrates, we observed that SbcCD cleaved dsDNA using this activity when the substrate was 110 bp long, but that on shorter substrates the cutting pattern was changed to that predicted for the activity of a 3′-5′ exonuclease. Our results suggest that SbcCD processes hairpin and linear dsDNA ends with this novel DNA end-dependent binary endonuclease activity in response to substrate length rather than using previously reported activities. We propose a model for this mode of nuclease action, which provides new insight into SbcCD activity at a dsDNA end.
Collapse
Affiliation(s)
- Chew Theng Lim
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Pey Jiun Lai
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - David R F Leach
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Kings Buildings, Edinburgh EH9 3JR, UK
| | - Hisaji Maki
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Asako Furukohri
- Division of Systems Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| |
Collapse
|
49
|
Quantitative genomic analysis of RecA protein binding during DNA double-strand break repair reveals RecBCD action in vivo. Proc Natl Acad Sci U S A 2015; 112:E4735-42. [PMID: 26261330 PMCID: PMC4553759 DOI: 10.1073/pnas.1424269112] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Understanding molecular mechanisms in the context of living cells requires the development of new methods of in vivo biochemical analysis to complement established in vitro biochemistry. A critically important molecular mechanism is genetic recombination, required for the beneficial reassortment of genetic information and for DNA double-strand break repair (DSBR). Central to recombination is the RecA (Rad51) protein that assembles into a spiral filament on DNA and mediates genetic exchange. Here we have developed a method that combines chromatin immunoprecipitation with next-generation sequencing (ChIP-Seq) and mathematical modeling to quantify RecA protein binding during the active repair of a single DSB in the chromosome of Escherichia coli. We have used quantitative genomic analysis to infer the key in vivo molecular parameters governing RecA loading by the helicase/nuclease RecBCD at recombination hot-spots, known as Chi. Our genomic analysis has also revealed that DSBR at the lacZ locus causes a second RecBCD-mediated DSBR event to occur in the terminus region of the chromosome, over 1 Mb away.
Collapse
|
50
|
Abstract
The mammalian CtIP protein and its orthologs in other eukaryotes promote the resection of DNA double-strand breaks and are essential for meiotic recombination. Here we review the current literature supporting the role of CtIP in DNA end processing and the importance of CtIP endonuclease activity in DNA repair. We also examine the regulation of CtIP function by post-translational modifications, and its involvement in transcription- and replication-dependent functions through association with other protein complexes. The tumor suppressor function of CtIP likely is dependent on a combination of these roles in many aspects of DNA metabolism.
Collapse
|