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De Falco M, De Felice M. Take a Break to Repair: A Dip in the World of Double-Strand Break Repair Mechanisms Pointing the Gaze on Archaea. Int J Mol Sci 2021; 22:ijms222413296. [PMID: 34948099 PMCID: PMC8708640 DOI: 10.3390/ijms222413296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/24/2022] Open
Abstract
All organisms have evolved many DNA repair pathways to counteract the different types of DNA damages. The detection of DNA damage leads to distinct cellular responses that bring about cell cycle arrest and the induction of DNA repair mechanisms. In particular, DNA double-strand breaks (DSBs) are extremely toxic for cell survival, that is why cells use specific mechanisms of DNA repair in order to maintain genome stability. The choice among the repair pathways is mainly linked to the cell cycle phases. Indeed, if it occurs in an inappropriate cellular context, it may cause genome rearrangements, giving rise to many types of human diseases, from developmental disorders to cancer. Here, we analyze the most recent remarks about the main pathways of DSB repair with the focus on homologous recombination. A thorough knowledge in DNA repair mechanisms is pivotal for identifying the most accurate treatments in human diseases.
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Pennell S, Déclais AC, Li J, Haire LF, Berg W, Saldanha JW, Taylor IA, Rouse J, Lilley DMJ, Smerdon SJ. FAN1 activity on asymmetric repair intermediates is mediated by an atypical monomeric virus-type replication-repair nuclease domain. Cell Rep 2014; 8:84-93. [PMID: 24981866 PMCID: PMC4103454 DOI: 10.1016/j.celrep.2014.06.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 05/08/2014] [Accepted: 06/03/2014] [Indexed: 11/29/2022] Open
Abstract
FAN1 is a structure-selective DNA repair nuclease with 5' flap endonuclease activity, involved in the repair of interstrand DNA crosslinks. It is the only eukaryotic protein with a virus-type replication-repair nuclease ("VRR-Nuc") "module" that commonly occurs as a standalone domain in many bacteria and viruses. Crystal structures of three representatives show that they structurally resemble Holliday junction resolvases (HJRs), are dimeric in solution, and are able to cleave symmetric four-way junctions. In contrast, FAN1 orthologs are monomeric and cleave 5' flap structures in vitro, but not Holliday junctions. Modeling of the VRR-Nuc domain of FAN1 reveals that it has an insertion, which packs against the dimerization interface observed in the structures of the viral/bacterial VRR-Nuc proteins. We propose that these additional structural elements in FAN1 prevent dimerization and bias specificity toward flap structures.
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Affiliation(s)
- Simon Pennell
- Division of Molecular Structure, MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK.
| | - Anne-Cécile Déclais
- CRUK Nucleic Acids Structure Research Group, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Jiejin Li
- Division of Molecular Structure, MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
| | - Lesley F Haire
- Division of Molecular Structure, MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
| | - Wioletta Berg
- Division of Molecular Structure, MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
| | - José W Saldanha
- Division of Mathematical Biology, MRC National Institute for Medical Research, London NW7 1AA, UK
| | - Ian A Taylor
- Division of Molecular Structure, MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
| | - John Rouse
- MRC Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - David M J Lilley
- CRUK Nucleic Acids Structure Research Group, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Stephen J Smerdon
- Division of Molecular Structure, MRC National Institute for Medical Research, The Ridgeway, London NW7 1AA, UK
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Gardner AF, Guan C, Jack WE. Biochemical characterization of a structure-specific resolving enzyme from Sulfolobus islandicus rod-shaped virus 2. PLoS One 2011; 6:e23668. [PMID: 21858199 PMCID: PMC3157427 DOI: 10.1371/journal.pone.0023668] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Accepted: 07/22/2011] [Indexed: 11/19/2022] Open
Abstract
Sulfolobus islandicus rod shaped virus 2 (SIRV2) infects the archaeon Sulfolobus islandicus at extreme temperature (70°C–80°C) and acidity (pH 3). SIRV2 encodes a Holliday junction resolving enzyme (SIRV2 Hjr) that has been proposed as a key enzyme in SIRV2 genome replication. The molecular mechanism for SIRV2 Hjr four-way junction cleavage bias, minimal requirements for four-way junction cleavage, and substrate specificity were determined. SIRV2 Hjr cleaves four-way DNA junctions with a preference for cleavage of exchange strand pairs, in contrast to host-derived resolving enzymes, suggesting fundamental differences in substrate recognition and cleavage among closely related Sulfolobus resolving enzymes. Unlike other viral resolving enzymes, such as T4 endonuclease VII or T7 endonuclease I, that cleave branched DNA replication intermediates, SIRV2 Hjr cleavage is specific to four-way DNA junctions and inactive on other branched DNA molecules. In addition, a specific interaction was detected between SIRV2 Hjr and the SIRV2 virion body coat protein (SIRV2gp26). Based on this observation, a model is proposed linking SIRV2 Hjr genome resolution to viral particle assembly.
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MESH Headings
- Amino Acid Sequence
- Base Sequence
- Biocatalysis
- Capsid Proteins/chemistry
- Capsid Proteins/genetics
- Capsid Proteins/metabolism
- DNA, Cruciform/chemistry
- DNA, Cruciform/genetics
- DNA, Cruciform/metabolism
- DNA, Viral/chemistry
- DNA, Viral/genetics
- DNA, Viral/metabolism
- Electrophoresis, Polyacrylamide Gel
- Holliday Junction Resolvases/chemistry
- Holliday Junction Resolvases/genetics
- Holliday Junction Resolvases/metabolism
- Immunoprecipitation
- Maltose-Binding Proteins/chemistry
- Maltose-Binding Proteins/genetics
- Maltose-Binding Proteins/metabolism
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation
- Protein Binding
- Protein Multimerization
- Protein Structure, Quaternary
- Recombinant Fusion Proteins/chemistry
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Rudiviridae/enzymology
- Rudiviridae/genetics
- Sequence Homology, Amino Acid
- Substrate Specificity
- Sulfolobus/virology
- Viral Proteins/chemistry
- Viral Proteins/genetics
- Viral Proteins/metabolism
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Affiliation(s)
- Andrew F Gardner
- New England Biolabs, Inc., Ipswich, Massachusetts, United States of America.
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Wijeratne AJ, Chen C, Zhang W, Timofejeva L, Ma H. The Arabidopsis thaliana PARTING DANCERS gene encoding a novel protein is required for normal meiotic homologous recombination. Mol Biol Cell 2006; 17:1331-43. [PMID: 16394097 PMCID: PMC1382321 DOI: 10.1091/mbc.e05-09-0902] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Recent studies of meiotic recombination in the budding yeast and the model plant Arabidopsis thaliana indicate that meiotic crossovers (COs) occur through two genetic pathways: the interference-sensitive pathway and the interference-insensitive pathway. However, few genes have been identified in either pathway. Here, we describe the identification of the PARTING DANCERS (PTD) gene, as a gene with an elevated expression level in meiocytes. Analysis of two independently generated transferred DNA insertional lines in PTD showed that the mutants had reduced fertility. Further cytological analysis of male meiosis in the ptd mutants revealed defects in meiosis, including reduced formation of chiasmata, the cytological appearance of COs. The residual chiasmata in the mutants were distributed randomly, indicating that the ptd mutants are defective for CO formation in the interference-sensitive pathway. In addition, transmission electron microscopic analysis of the mutants detected no obvious abnormality of synaptonemal complexes and apparently normal late recombination nodules at the pachytene stage, suggesting that the mutant's defects in bivalent formation were postsynaptic. Comparison to other genes with limited sequence similarity raises the possibility that PTD may present a previously unknown function conserved in divergent eukaryotic organisms.
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Affiliation(s)
- Asela J Wijeratne
- Intercollege Graduate Program in Plant Physiology, The Pennsylvania State University, University Park, PA 16802, USA
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Parker JL, White MF. The endonuclease Hje catalyses rapid, multiple turnover resolution of Holliday junctions. J Mol Biol 2005; 350:1-6. [PMID: 15921693 DOI: 10.1016/j.jmb.2005.04.056] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2005] [Revised: 04/20/2005] [Accepted: 04/26/2005] [Indexed: 10/25/2022]
Abstract
Holliday junction-resolving enzymes are ubiquitous, structure-specific endonucleases that resolve four-way DNA junctions by the introduction of paired nicks in opposing strands, and are required for homologous recombination, double-strand break repair, recombination-dependent restart of stalled or collapsed DNA replication forks, and phage DNA processing. Here, we present the first steady-state kinetic characterisation of a junction-resolving enzyme; the Hje endonuclease from Sulfolobus solfataricus. We demonstrate that substrate turnover by Hje is sequence-independent and limited largely by the rate of cleavage of the phosphodiester bonds of the bound Holliday junction substrate, rather than substrate association or product dissociation. Reaction rates under multiple turnover conditions compare favourably with type II restriction enzymes. These properties, coupled with a high level of specificity for four-way junctions over all other DNA substrates, make Hje a suitable enzyme for applications requiring the detection and cleavage of Holliday junctions in vitro.
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Affiliation(s)
- Joanne L Parker
- Centre for Biomolecular Sciences, University of St Andrews, North Haugh, St Andrews, Fife KY16 9ST, UK
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Middleton CL, Parker JL, Richard DJ, White MF, Bond CS. Substrate recognition and catalysis by the Holliday junction resolving enzyme Hje. Nucleic Acids Res 2004; 32:5442-51. [PMID: 15479781 PMCID: PMC524281 DOI: 10.1093/nar/gkh869] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Two archaeal Holliday junction resolving enzymes, Holliday junction cleavage (Hjc) and Holliday junction endonuclease (Hje), have been characterized. Both are members of a nuclease superfamily that includes the type II restriction enzymes, although their DNA cleaving activity is highly specific for four-way junction structure and not nucleic acid sequence. Despite 28% sequence identity, Hje and Hjc cleave junctions with distinct cutting patterns--they cut different strands of a four-way junction, at different distances from the junction centre. We report the high-resolution crystal structure of Hje from Sulfolobus solfataricus. The structure provides a basis to explain the differences in substrate specificity of Hje and Hjc, which result from changes in dimer organization, and suggests a viral origin for the Hje gene. Structural and biochemical data support the modelling of an Hje:DNA junction complex, highlighting a flexible loop that interacts intimately with the junction centre. A highly conserved serine residue on this loop is shown to be essential for the enzyme's activity, suggesting a novel variation of the nuclease active site. The loop may act as a conformational switch, ensuring that the active site is completed only on binding a four-way junction, thus explaining the exquisite specificity of these enzymes.
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Affiliation(s)
- Claire L Middleton
- Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
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Serre MC, Duguet M. Enzymes That Cleave and Religate DNA at High Temperature: The Same Story with Different Actors. ACTA ACUST UNITED AC 2003; 74:37-81. [PMID: 14510073 DOI: 10.1016/s0079-6603(03)01010-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Affiliation(s)
- Marie-Claude Serre
- Laboratoire d'Enzymologie des Acides Nucléiques, Institut de Génétique et Microbiologie, Université Paris-Sud, 91405 Orsay Cedex, France
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Kvaratskhelia M, Wardleworth BN, Bond CS, Fogg JM, Lilley DMJ, White MF. Holliday junction resolution is modulated by archaeal chromatin components in vitro. J Biol Chem 2002; 277:2992-6. [PMID: 11709558 DOI: 10.1074/jbc.m109496200] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Holliday junction-resolving enzyme Hjc is conserved in the archaea and probably plays a role analogous to that of Escherichia coli RuvC in the pathway of homologous recombination. Hjc specifically recognizes four-way DNA junctions, cleaving them without sequence preference to generate recombinant DNA duplex products. Hjc imposes an X-shaped global conformation on the bound DNA junction and distorts base stacking around the point of cleavage, three nucleotides 3' of the junction center. We show that Hjc is autoinhibitory under single turnover assay conditions and that this can be relieved by the addition of either competitor duplex DNA or the architectural double-stranded DNA-binding protein Sso7d (i.e. by approximating in vivo conditions more closely). Using a combination of isothermal titration calorimetry and fluorescent resonance energy transfer, we demonstrate that multiple Hjc dimers can bind to each synthetic four-way junction and provide evidence for significant distortion of the junction structure at high protein:DNA ratios. Analysis of crystal packing interactions in the crystal structure of Hjc suggests a molecular basis for this autoinhibition. The wider implications of these findings for the quantitative study of DNA-protein interactions is discussed.
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Affiliation(s)
- Mamuka Kvaratskhelia
- Centre for Biomolecular Science, University of Saint Andrews, North Haugh, Saint Andrews, KY16 9ST, United Kingdom
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Abstract
Junction-resolving enzymes are ubiquitous nucleases that are important for DNA repair and recombination and act on DNA molecules containing branch points, especially four-way junctions. They show a pronounced selectivity for the structure of the DNA substrate but, despite its importance, the structural selectivity is not well understood. This poses an intriguing challenge in molecular recognition on a relatively large scale.
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Affiliation(s)
- D M Lilley
- CRC Nucleic Acid Structure Research Group, Department of Biochemistry, University of Dundee, Dundee DD1 5EH, UK.
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