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Audry J, Zhang H, Kerr C, Berkner KL, Runge K. Ccq1 restrains Mre11-mediated degradation to distinguish short telomeres from double-strand breaks. Nucleic Acids Res 2024; 52:3722-3739. [PMID: 38321948 PMCID: PMC11040153 DOI: 10.1093/nar/gkae044] [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: 05/25/2023] [Revised: 12/21/2023] [Accepted: 01/12/2024] [Indexed: 02/08/2024] Open
Abstract
Telomeres protect chromosome ends and are distinguished from DNA double-strand breaks (DSBs) by means of a specialized chromatin composed of DNA repeats bound by a multiprotein complex called shelterin. We investigated the role of telomere-associated proteins in establishing end-protection by studying viable mutants lacking these proteins. Mutants were studied using a Schizosaccharomyces pombe model system that induces cutting of a 'proto-telomere' bearing telomere repeats to rapidly form a new stable chromosomal end, in contrast to the rapid degradation of a control DSB. Cells lacking the telomere-associated proteins Taz1, Rap1, Poz1 or Rif1 formed a chromosome end that was stable. Surprisingly, cells lacking Ccq1, or impaired for recruiting Ccq1 to the telomere, converted the cleaved proto-telomere to a rapidly degraded DSB. Ccq1 recruits telomerase, establishes heterochromatin and affects DNA damage checkpoint activation; however, these functions were separable from protection of the new telomere by Ccq1. In cells lacking Ccq1, telomere degradation was greatly reduced by eliminating the nuclease activity of Mre11 (part of the Mre11-Rad50-Nbs1/Xrs2 DSB processing complex), and higher amounts of nuclease-deficient Mre11 associated with the new telomere. These results demonstrate a novel function for S. pombe Ccq1 to effect end-protection by restraining Mre11-dependent degradation of the DNA end.
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Affiliation(s)
- Julien Audry
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Haitao Zhang
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Carly Kerr
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Kathleen L Berkner
- Department of Cardiovascular and Metabolic Sciences, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Kurt W Runge
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
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Fission Yeast Rho1p-GEFs: From Polarity and Cell Wall Synthesis to Genome Stability. Int J Mol Sci 2022; 23:ijms232213888. [PMID: 36430366 PMCID: PMC9697909 DOI: 10.3390/ijms232213888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Rho1p is a membrane-associated protein that belongs to the Rho family of small GTPases. These proteins coordinate processes such as actin remodelling and polarised secretion to maintain the shape and homeostasis of yeast cells. In response to extracellular stimuli, Rho1p undergoes conformational switching between a guanosine triphosphate (GTP)-bound active state and a guanosine diphosphate (GDP)-bound inactive state. Cycling is improved with guanine nucleotide exchange factor (GEF) activity necessary to activate signalling and GTPase activating protein (GAP) activity required for subsequent signal depletion. This review focuses on fission yeast Rho1p GEFs, Rgf1p, Rgf2p, and Rgf3p that belong to the family of DH-PH domain-containing Dbl-related GEFs. They are multi-domain proteins that detect biological signals that induce or inhibit their catalytic activity over Rho1p. Each of them activates Rho1p in different places and times. Rgf1p acts preferentially during polarised growth. Rgf2p is required for sporulation, and Rgf3p plays an essential function in septum synthesis. In addition, we outline the noncanonical roles of Rho1p-GEFs in genomic instability.
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García Fernández F, Fabre E. The Dynamic Behavior of Chromatin in Response to DNA Double-Strand Breaks. Genes (Basel) 2022; 13:genes13020215. [PMID: 35205260 PMCID: PMC8872016 DOI: 10.3390/genes13020215] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 02/05/2023] Open
Abstract
The primary functions of the eukaryotic nucleus as a site for the storage, retrieval, and replication of information require a highly dynamic chromatin organization, which can be affected by the presence of DNA damage. In response to double-strand breaks (DSBs), the mobility of chromatin at the break site is severely affected and, to a lesser extent, that of other chromosomes. The how and why of such movement has been widely studied over the last two decades, leading to different mechanistic models and proposed potential roles underlying both local and global mobility. Here, we review the state of the knowledge on current issues affecting chromatin mobility upon DSBs, and highlight its role as a crucial step in the DNA damage response (DDR).
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Affiliation(s)
- Fabiola García Fernández
- Institut Curie, CNRS UMR3664, Sorbonne Université, F-75005 Paris, France
- Correspondence: (F.G.F.); (E.F.)
| | - Emmanuelle Fabre
- Génomes Biologie Cellulaire et Thérapeutiques, CNRS UMR7212, INSERM U944, Université de Paris, F-75010 Paris, France
- Correspondence: (F.G.F.); (E.F.)
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4
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Muraszko J, Kramarz K, Argunhan B, Ito K, Baranowska G, Kurokawa Y, Murayama Y, Tsubouchi H, Lambert S, Iwasaki H, Dziadkowiec D. Rrp1 translocase and ubiquitin ligase activities restrict the genome destabilising effects of Rad51 in fission yeast. Nucleic Acids Res 2021; 49:6832-6848. [PMID: 34157114 PMCID: PMC8266636 DOI: 10.1093/nar/gkab511] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 05/27/2021] [Accepted: 06/06/2021] [Indexed: 11/20/2022] Open
Abstract
Rad51 is the key protein in homologous recombination that plays important roles during DNA replication and repair. Auxiliary factors regulate Rad51 activity to facilitate productive recombination, and prevent inappropriate, untimely or excessive events, which could lead to genome instability. Previous genetic analyses identified a function for Rrp1 (a member of the Rad5/16-like group of SWI2/SNF2 translocases) in modulating Rad51 function, shared with the Rad51 mediator Swi5-Sfr1 and the Srs2 anti-recombinase. Here, we show that Rrp1 overproduction alleviates the toxicity associated with excessive Rad51 levels in a manner dependent on Rrp1 ATPase domain. Purified Rrp1 binds to DNA and has a DNA-dependent ATPase activity. Importantly, Rrp1 directly interacts with Rad51 and removes it from double-stranded DNA, confirming that Rrp1 is a translocase capable of modulating Rad51 function. Rrp1 affects Rad51 binding at centromeres. Additionally, we demonstrate in vivo and in vitro that Rrp1 possesses E3 ubiquitin ligase activity with Rad51 as a substrate, suggesting that Rrp1 regulates Rad51 in a multi-tiered fashion.
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Affiliation(s)
| | - Karol Kramarz
- Institut Curie, Université PSL, CNRS UMR3348, 91400 Orsay, France.,Université Paris-Saclay, CNRS UMR3348, 91400 Orsay, France
| | - Bilge Argunhan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Kentaro Ito
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | | | - Yumiko Kurokawa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Yasuto Murayama
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Hideo Tsubouchi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
| | - Sarah Lambert
- Institut Curie, Université PSL, CNRS UMR3348, 91400 Orsay, France.,Université Paris-Saclay, CNRS UMR3348, 91400 Orsay, France
| | - Hiroshi Iwasaki
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Japan
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Zhu W, Hu J, Chi J, Li Y, Yang B, Hu W, Chen F, Xu C, Chai L, Bao Y. Label-Free Proteomics Reveals the Molecular Mechanism of Subculture Induced Strain Degeneration and Discovery of Indicative Index for Degeneration in Pleurotus ostreatus. Molecules 2020; 25:molecules25214920. [PMID: 33114310 PMCID: PMC7660624 DOI: 10.3390/molecules25214920] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 10/13/2020] [Accepted: 10/19/2020] [Indexed: 11/16/2022] Open
Abstract
Pleurotus ostreatus is one of the widely cultivated edible fungi across the world. Mycelial subculture is an indispensable part in the process of cultivation and production for all kinds of edible fungi. However, successive subcultures usually lead to strain degeneration. The degenerated strains usually have a decrease in stress resistance, yield, and an alteration in fruiting time, which will subsequently result in tremendous economic loss. Through proteomic analysis, we identified the differentially expressed proteins (DEPs) in the mycelium of Pleurotus ostreatus from different subcultured generations. We found that the DNA damage repair system, especially the double-strand breaks (DSBs), repairs via homologous recombination, was impaired in the subcultured mycelium, and gradual accumulation of the DSBs would lead to the strain degeneration after successive subculture. The TUNEL assay further confirmed our finding about the DNA breaks in the subcultured mycelium. Interestingly, the enzyme activity of laccase, carboxylic ester hydrolase, α-galactosidase, and catalase directly related to passage number could be used as the characteristic index for strain degeneration determination. Our results not only reveal for the first time at the molecular level that genomic instability is the cause of degeneration, but also provide an applicable approach for monitoring strain degeneration in process of edible fungi cultivation and production.
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Affiliation(s)
- Weiwei Zhu
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China;
- Microbial Research Institute of Liaoning Province, Chaoyang 122000, China; (J.C.); (Y.L.); (F.C.); (C.X.); (L.C.)
| | - Jinbo Hu
- Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; (J.H.); (B.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingliang Chi
- Microbial Research Institute of Liaoning Province, Chaoyang 122000, China; (J.C.); (Y.L.); (F.C.); (C.X.); (L.C.)
| | - Yang Li
- Microbial Research Institute of Liaoning Province, Chaoyang 122000, China; (J.C.); (Y.L.); (F.C.); (C.X.); (L.C.)
| | - Bing Yang
- Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; (J.H.); (B.Y.)
| | - Wenli Hu
- Core Facility Center, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China;
| | - Fei Chen
- Microbial Research Institute of Liaoning Province, Chaoyang 122000, China; (J.C.); (Y.L.); (F.C.); (C.X.); (L.C.)
| | - Chong Xu
- Microbial Research Institute of Liaoning Province, Chaoyang 122000, China; (J.C.); (Y.L.); (F.C.); (C.X.); (L.C.)
| | - Linshan Chai
- Microbial Research Institute of Liaoning Province, Chaoyang 122000, China; (J.C.); (Y.L.); (F.C.); (C.X.); (L.C.)
| | - Yongming Bao
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China;
- School of Ocean Science and Technology, Dalian University of Technology, Panjin 124021, China
- Correspondence: ; Tel.: +86-427-2631777; Fax: +86-411-84706365
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Abstract
The fission yeast Schizosaccharomyces pombe is an excellent model organism to study DNA metabolism, in which the DNA replication and repair mechanisms are evolutionarily conserved. In this introduction we describe a range of methods commonly used to study aspects of DNA metabolism in fission yeast, focusing on approaches used for the analysis of genome stability, DNA replication, and DNA repair. We describe the use of a minichromosome, Ch16, for monitoring different aspects of genome stability. We introduce two-dimensional gel electrophoresis and immunofluorescent visualization of combed DNA molecules for the analysis of DNA replication. Further, we introduce a pulsed field gel electrophoresis (PFGE) assay to physically monitor chromosome integrity, which can be used in conjunction with a DNA double-strand break (DSB) repair assay to genetically quantitate different DSB repair and misrepair outcomes, including gross chromosomal rearrangements, in fission yeast.
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Affiliation(s)
- Francisco Antequera
- Instituto de Biología Funcional y Genómica, CSIC/Universidad de Salamanca, Salamanca 37007, Spain
| | - Timothy C Humphrey
- CRUK-MRC Oxford Institute for Radiation Oncology, University of Oxford, OX3 7DQ, United Kingdom
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7
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Manjón E, Edreira T, Muñoz S, Sánchez Y. Rgf1p (Rho1p GEF) is required for double-strand break repair in fission yeast. Nucleic Acids Res 2017; 45:5269-5284. [PMID: 28334931 PMCID: PMC5435928 DOI: 10.1093/nar/gkx176] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 03/07/2017] [Indexed: 12/04/2022] Open
Abstract
Rho GTPases are conserved molecules that control cytoskeletal dynamics. These functions are expedited by Rho GEFs that stimulate the release of GDP to enable GTP binding, thereby allowing Rho proteins to initiate intracellular signaling. How Rho GEFs and Rho GTPases protect cells from DNA damage is unknown. Here, we explore the extreme sensitivity of a deletion mutation in the Rho1p exchange factor Rgf1p to the DNA break/inducing antibiotic phleomycin (Phl). The Rgf1p mutant cells are defective in reentry into the cell cycle following the induction of severe DNA damage. This phenotype correlates with the inability of rgf1Δ cells to efficiently repair fragmented chromosomes after Phl treatment. Consistent with this observation Rad11p (ssDNA binding protein, RPA), Rad52p, Rad54p and Rad51p, which facilitate strand invasion in the process of homology-directed repair (HDR), are permanently stacked in Phl-induced foci in rgf1Δ cells. These phenotypes are phenocopied by genetic inhibition of Rho1p. Our data provide evidence that Rgf1p/Rho1p activity positively controls a repair function that confers resistance against the anti-cancer drug Phl.
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Affiliation(s)
- Elvira Manjón
- Instituto de Biología Funcional y Genómica, CSIC. Departamento de Microbiología y Genética, Universidad de Salamanca. C/Zacarías González, s/n. Salamanca, Spain
| | - Tomás Edreira
- Instituto de Biología Funcional y Genómica, CSIC. Departamento de Microbiología y Genética, Universidad de Salamanca. C/Zacarías González, s/n. Salamanca, Spain
| | - Sofía Muñoz
- Instituto de Biología Funcional y Genómica, CSIC. Departamento de Microbiología y Genética, Universidad de Salamanca. C/Zacarías González, s/n. Salamanca, Spain
| | - Yolanda Sánchez
- Instituto de Biología Funcional y Genómica, CSIC. Departamento de Microbiología y Genética, Universidad de Salamanca. C/Zacarías González, s/n. Salamanca, Spain
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Nonhomologous End-Joining with Minimal Sequence Loss Is Promoted by the Mre11-Rad50-Nbs1-Ctp1 Complex in Schizosaccharomyces pombe. Genetics 2017; 206:481-496. [PMID: 28292918 DOI: 10.1534/genetics.117.200972] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 02/24/2017] [Indexed: 11/18/2022] Open
Abstract
While the Mre11-Rad50-Nbs1 (MRN) complex has known roles in repair processes like homologous recombination and microhomology-mediated end-joining, its role in nonhomologous end-joining (NHEJ) is unclear as Saccharomyces cerevisiae, Schizosaccharomyces pombe, and mammals have different requirements for repairing cut DNA ends. Most double-strand breaks (DSBs) require nucleolytic processing prior to DNA ligation. Therefore, we studied repair using the Hermes transposon, whose excision leaves a DSB capped by hairpin ends similar to structures generated by palindromes and trinucleotide repeats. We generated single Hermes insertions using a novel S. pombe transient transfection system, and used Hermes excision to show a requirement for MRN in the NHEJ of nonligatable ends. NHEJ repair was indicated by the >1000-fold decrease in excision in cells lacking Ku or DNA ligase 4. Most repaired excision sites had <5 bp of sequence loss or mutation, characteristic for NHEJ and similar excision events in metazoans, and in contrast to the more extensive loss seen in S. cerevisiaeS. pombe NHEJ was reduced >1000-fold in cells lacking each MRN subunit, and loss of MRN-associated Ctp1 caused a 30-fold reduction. An Mre11 dimer is thought to hold DNA ends together for repair, and Mre11 dimerization domain mutations reduced repair 300-fold. In contrast, a mre11 mutant defective in endonucleolytic activity, the same mutant lacking Ctp1, or the triple mutant also lacking the putative hairpin nuclease Pso2 showed wild-type levels of repair. Thus, MRN may act to recruit the hairpin opening activity that allows subsequent repair.
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9
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Bhattacharjee S, Nandi S. Choices have consequences: the nexus between DNA repair pathways and genomic instability in cancer. Clin Transl Med 2016; 5:45. [PMID: 27921283 PMCID: PMC5136664 DOI: 10.1186/s40169-016-0128-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 11/22/2016] [Indexed: 11/10/2022] Open
Abstract
Background The genome is under constant assault from a multitude of sources that can lead to the formation of DNA double-stand breaks (DSBs). DSBs are cytotoxic lesions, which if left unrepaired could lead to genomic instability, cancer and even cell death. However, erroneous repair of DSBs can lead to chromosomal rearrangements and loss of heterozygosity, which in turn can also cause cancer and cell death. Hence, although the repair of DSBs is crucial for the maintenance of genome integrity the process of repair need to be well regulated and closely monitored. Main body The two most commonly used pathways to repair DSBs in higher eukaryotes include non-homologous end joining (NHEJ) and homologous recombination (HR). NHEJ is considered to be error-prone, intrinsically mutagenic quick fix remedy to seal together the broken DNA ends and restart replication. In contrast, HR is a high-fidelity process that has been very well conserved from phage to humans. Here we review HR and its sub-pathways. We discuss what factors determine the sub pathway choice including etiology of the DSB, chromatin structure at the break site, processing of the DSBs and the mechanisms regulating the sub-pathway choice. We also elaborate on the potential of targeting HR genes for cancer therapy and anticancer strategies. Conclusion The DNA repair field is a vibrant one, and the stage is ripe for scrutinizing the potential treatment efficacy and future clinical applications of the pharmacological inhibitors of HR enzymes as mono- or combinatorial therapy regimes. Electronic supplementary material The online version of this article (doi:10.1186/s40169-016-0128-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Saikat Nandi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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10
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Genome-Wide Estimates of Mutation Rates and Spectrum in Schizosaccharomyces pombe Indicate CpG Sites are Highly Mutagenic Despite the Absence of DNA Methylation. G3-GENES GENOMES GENETICS 2015; 6:149-60. [PMID: 26564949 PMCID: PMC4704713 DOI: 10.1534/g3.115.022129] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We accumulated mutations for 1952 generations in 79 initially identical, haploid lines of the fission yeast Schizosaccharomyces pombe, and then performed whole-genome sequencing to determine the mutation rates and spectrum. We captured 696 spontaneous mutations across the 79 mutation accumulation (MA) lines. We compared the mutation spectrum and rate to a recently published equivalent experiment on the same species, and to another model ascomycetous yeast, the budding yeast Saccharomyces cerevisiae. While the two species are approximately 600 million years diverged from each other, they share similar life histories, genome size and genomic G/C content. We found that Sc. pombe and S. cerevisiae have similar mutation rates, but Sc. pombe exhibits a stronger insertion bias. Intriguingly, we observed an increased mutation rate at cytosine nucleotides, specifically CpG nucleotides, which is also seen in S. cerevisiae. However, the absence of methylation in Sc. pombe and the pattern of mutation at these sites, primarily C → A as opposed to C → T, strongly suggest that the increased mutation rate is not caused by deamination of methylated cytosines. This result implies that the high mutability of CpG dinucleotides in other species may be caused in part by a methylation-independent mechanism. Many of our findings mirror those seen in the recent study, despite the use of different passaging conditions, indicating that MA is a reliable method for estimating mutation rates and spectra.
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Tosti E, Katakowski JA, Schaetzlein S, Kim HS, Ryan CJ, Shales M, Roguev A, Krogan NJ, Palliser D, Keogh MC, Edelmann W. Evolutionarily conserved genetic interactions with budding and fission yeast MutS identify orthologous relationships in mismatch repair-deficient cancer cells. Genome Med 2014; 6:68. [PMID: 25302077 PMCID: PMC4189729 DOI: 10.1186/s13073-014-0068-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 08/28/2014] [Indexed: 12/13/2022] Open
Abstract
Background The evolutionarily conserved DNA mismatch repair (MMR) system corrects base-substitution and insertion-deletion mutations generated during erroneous replication. The mutation or inactivation of many MMR factors strongly predisposes to cancer, where the resulting tumors often display resistance to standard chemotherapeutics. A new direction to develop targeted therapies is the harnessing of synthetic genetic interactions, where the simultaneous loss of two otherwise non-essential factors leads to reduced cell fitness or death. High-throughput screening in human cells to directly identify such interactors for disease-relevant genes is now widespread, but often requires extensive case-by-case optimization. Here we asked if conserved genetic interactors (CGIs) with MMR genes from two evolutionary distant yeast species (Saccharomyces cerevisiae and Schizosaccharomyzes pombe) can predict orthologous genetic relationships in higher eukaryotes. Methods High-throughput screening was used to identify genetic interaction profiles for the MutSα and MutSβ heterodimer subunits (msh2Δ, msh3Δ, msh6Δ) of fission yeast. Selected negative interactors with MutSβ (msh2Δ/msh3Δ) were directly analyzed in budding yeast, and the CGI with SUMO-protease Ulp2 further examined after RNA interference/drug treatment in MSH2-deficient and -proficient human cells. Results This study identified distinct genetic profiles for MutSα and MutSβ, and supports a role for the latter in recombinatorial DNA repair. Approximately 28% of orthologous genetic interactions with msh2Δ/msh3Δ are conserved in both yeasts, a degree consistent with global trends across these species. Further, the CGI between budding/fission yeast msh2 and SUMO-protease Ulp2 is maintained in human cells (MSH2/SENP6), and enhanced by Olaparib, a PARP inhibitor that induces the accumulation of single-strand DNA breaks. This identifies SENP6 as a promising new target for the treatment of MMR-deficient cancers. Conclusion Our findings demonstrate the utility of employing evolutionary distance in tractable lower eukaryotes to predict orthologous genetic relationships in higher eukaryotes. Moreover, we provide novel insights into the genome maintenance functions of a critical DNA repair complex and propose a promising targeted treatment for MMR deficient tumors. Electronic supplementary material The online version of this article (doi:10.1186/s13073-014-0068-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elena Tosti
- Department of Cell Biology, Albert Einstein College of Medicine, New York, USA
| | - Joseph A Katakowski
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, New York, USA
| | - Sonja Schaetzlein
- Department of Cell Biology, Albert Einstein College of Medicine, New York, USA
| | - Hyun-Soo Kim
- Department of Cell Biology, Albert Einstein College of Medicine, New York, USA
| | - Colm J Ryan
- Department of Cellular & Molecular Pharmacology, UCSF, San Francisco, USA ; California Institute for Quantitative Biosciences, San Francisco, USA ; School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Michael Shales
- Department of Cellular & Molecular Pharmacology, UCSF, San Francisco, USA
| | - Assen Roguev
- Department of Cellular & Molecular Pharmacology, UCSF, San Francisco, USA
| | - Nevan J Krogan
- Department of Cellular & Molecular Pharmacology, UCSF, San Francisco, USA ; California Institute for Quantitative Biosciences, San Francisco, USA ; J. David Gladstone Institutes, San Francisco, USA
| | - Deborah Palliser
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, New York, USA
| | | | - Winfried Edelmann
- Department of Cell Biology, Albert Einstein College of Medicine, New York, USA
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12
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Pears CJ, Lakin ND. Emerging models for DNA repair: Dictyostelium discoideum as a model for nonhomologous end-joining. DNA Repair (Amst) 2014; 17:121-31. [DOI: 10.1016/j.dnarep.2014.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 01/09/2014] [Accepted: 01/24/2014] [Indexed: 02/03/2023]
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13
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Dziadkowiec D, Kramarz K, Kanik K, Wisniewski P, Carr AM. Involvement of Schizosaccharomyces pombe rrp1+ and rrp2+ in the Srs2- and Swi5/Sfr1-dependent pathway in response to DNA damage and replication inhibition. Nucleic Acids Res 2013; 41:8196-209. [PMID: 23828040 PMCID: PMC3783160 DOI: 10.1093/nar/gkt564] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Previously we identified Rrp1 and Rrp2 as two proteins required for the Sfr1/Swi5-dependent branch of homologous recombination (HR) in Schizosaccharomyces pombe. Here we use a yeast two-hybrid approach to demonstrate that Rrp1 and Rrp2 can interact with each other and with Swi5, an HR mediator protein. Rrp1 and Rrp2 form co-localizing methyl methanesulphonate-induced foci in nuclei, further suggesting they function as a complex. To place the Rrp1/2 proteins more accurately within HR sub-pathways, we carried out extensive epistasis analysis between mutants defining Rrp1/2, Rad51 (recombinase), Swi5 and Rad57 (HR-mediators) plus the anti-recombinogenic helicases Srs2 and Rqh1. We confirm that Rrp1 and Rrp2 act together with Srs2 and Swi5 and independently of Rad57 and show that Rqh1 also acts independently of Rrp1/2. Mutants devoid of Srs2 are characterized by elevated recombination frequency with a concomitant increase in the percentage of conversion-type recombinants. Strains devoid of Rrp1 or Rrp2 did not show a change in HR frequency, but the number of conversion-type recombinants was increased, suggesting a possible function for Rrp1/2 with Srs2 in counteracting Rad51 activity. Our data allow us to propose a model placing Rrp1 and Rrp2 functioning together with Swi5 and Srs2 in a synthesis-dependent strand annealing HR repair pathway.
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Affiliation(s)
- Dorota Dziadkowiec
- Faculty of Biotechnology, Wrocław University, Przybyszewskiego 63-77, 51-148 Wrocław, Poland, Institute of Low Temperature and Structure Research, Polish Academy of Sciences, PO Box 1410, 50-950 Wrocław, Poland and Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
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Schonbrun M, Kolesnikov M, Kupiec M, Weisman R. TORC2 is required to maintain genome stability during S phase in fission yeast. J Biol Chem 2013; 288:19649-60. [PMID: 23703609 DOI: 10.1074/jbc.m113.464974] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA damage can occur due to environmental insults or intrinsic metabolic processes and is a major threat to genome stability. The DNA damage response is composed of a series of well coordinated cellular processes that include activation of the DNA damage checkpoint, transient cell cycle arrest, DNA damage repair, and reentry into the cell cycle. Here we demonstrate that mutant cells defective for TOR complex 2 (TORC2) or the downstream AGC-like kinase, Gad8, are highly sensitive to chronic replication stress but are insensitive to ionizing radiation. We show that in response to replication stress, TORC2 is dispensable for Chk1-mediated cell cycle arrest but is required for the return to cell cycle progression. Rad52 is a DNA repair and recombination protein that forms foci at DNA damage sites and stalled replication forks. TORC2 mutant cells show increased spontaneous nuclear Rad52 foci, particularly during S phase, suggesting that TORC2 protects cells from DNA damage that occurs during normal DNA replication. Consistently, the viability of TORC2-Gad8 mutant cells is dependent on the presence of the homologous recombination pathway and other proteins that are required for replication restart following fork replication stalling. Our findings indicate that TORC2 is required for genome integrity. This may be relevant for the growing amount of evidence implicating TORC2 in cancer development.
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Affiliation(s)
- Miriam Schonbrun
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Ramat Aviv, Israel
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15
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Tay Z, Eng RJ, Sajiki K, Lim KK, Tang MY, Yanagida M, Chen ES. Cellular robustness conferred by genetic crosstalk underlies resistance against chemotherapeutic drug doxorubicin in fission yeast. PLoS One 2013; 8:e55041. [PMID: 23365689 PMCID: PMC3554685 DOI: 10.1371/journal.pone.0055041] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 12/18/2012] [Indexed: 11/28/2022] Open
Abstract
Doxorubicin is an anthracycline antibiotic that is among one of the most commonly used chemotherapeutic agents in the clinical setting. The usage of doxorubicin is faced with many problems including severe side effects and chemoresistance. To overcome these challenges, it is important to gain an understanding of the underlying molecular mechanisms with regards to the mode of action of doxorubicin. To facilitate this aim, we identified the genes that are required for doxorubicin resistance in the fission yeast Schizosaccharomyces pombe. We further demonstrated interplay between factors controlling various aspects of chromosome metabolism, mitochondrial respiration and membrane transport. In the nucleus we observed that the subunits of the Ino80, RSC, and SAGA complexes function in the similar epistatic group that shares significant overlap with the homologous recombination genes. However, these factors generally act in synergistic manner with the chromosome segregation regulator DASH complex proteins, possibly forming two major arms for regulating doxorubicin resistance in the nucleus. Simultaneous disruption of genes function in membrane efflux transport or the mitochondrial respiratory chain integrity in the mutants defective in either Ino80 or HR function resulted in cumulative upregulation of drug-specific growth defects, suggesting a rewiring of pathways that synergize only when the cells is exposed to the cytotoxic stress. Taken together, our work not only identified factors that are required for survival of the cells in the presence of doxorubicin but has further demonstrated that an extensive molecular crosstalk exists between these factors to robustly confer doxorubicin resistance.
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Affiliation(s)
- Zoey Tay
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- National University Health System, Singapore
| | - Ru Jun Eng
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- National University Health System, Singapore
| | - Kenichi Sajiki
- G0 Cell Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Kim Kiat Lim
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- National University Health System, Singapore
| | - Ming Yi Tang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- National University Health System, Singapore
| | - Mitsuhiro Yanagida
- G0 Cell Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Ee Sin Chen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- National University Health System, Singapore
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16
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Pan X, Lei B, Zhou N, Feng B, Yao W, Zhao X, Yu Y, Lu H. Identification of novel genes involved in DNA damage response by screening a genome-wide Schizosaccharomyces pombe deletion library. BMC Genomics 2012; 13:662. [PMID: 23173672 PMCID: PMC3536581 DOI: 10.1186/1471-2164-13-662] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 10/24/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA damage response (DDR) plays pivotal roles in maintaining genome integrity and stability. An effective DDR requires the involvement of hundreds of genes that compose a complicated network. Because DDR is highly conserved in evolution, studies in lower eukaryotes can provide valuable information to elucidate the mechanism in higher organisms. Fission yeast (Schizosaccharomyces pombe) has emerged as an excellent model for DDR research in recent years. To identify novel genes involved in DDR, we screened a genome-wide S. pombe haploid deletion library against six different DNA damage reagents. The library covered 90.5% of the nonessential genes of S. pombe. RESULTS We have identified 52 genes that were actively involved in DDR. Among the 52 genes, 20 genes were linked to DDR for the first time. Flow cytometry analysis of the repair defective mutants revealed that most of them exhibited a defect in cell cycle progression, and some caused genome instability. Microarray analysis and genetic complementation assays were carried out to characterize 6 of the novel DDR genes in more detail. Data suggested that SPBC2A9.02 and SPAC27D7.08c were required for efficient DNA replication initiation because they interacted genetically with DNA replication initiation proteins Abp1 and Abp2. In addition, deletion of sgf73+, meu29+, sec65+ or pab1+ caused improper cytokinesis and DNA re-replication, which contributed to the diploidization in the mutants. CONCLUSIONS A genome-wide screen of genes involved in DDR emphasized the key role of cell cycle control in the DDR network. Characterization of novel genes identified in the screen helps to elucidate the mechanism of the DDR network and provides valuable clues for understanding genome stability in higher eukaryotes.
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Affiliation(s)
- Xian Pan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China
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17
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Tange Y, Kurabayashi A, Goto B, Hoe KL, Kim DU, Park HO, Hayles J, Chikashige Y, Tsutumi C, Hiraoka Y, Yamao F, Nurse P, Niwa O. The CCR4-NOT complex is implicated in the viability of aneuploid yeasts. PLoS Genet 2012; 8:e1002776. [PMID: 22737087 PMCID: PMC3380822 DOI: 10.1371/journal.pgen.1002776] [Citation(s) in RCA: 12] [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: 03/16/2012] [Accepted: 05/05/2012] [Indexed: 12/23/2022] Open
Abstract
To identify the genes required to sustain aneuploid viability, we screened a deletion library of non-essential genes in the fission yeast Schizosaccharomyces pombe, in which most types of aneuploidy are eventually lethal to the cell. Aneuploids remain viable for a period of time and can form colonies by reducing the extent of the aneuploidy. We hypothesized that a reduction in colony formation efficiency could be used to screen for gene deletions that compromise aneuploid viability. Deletion mutants were used to measure the effects on the viability of spores derived from triploid meiosis and from a chromosome instability mutant. We found that the CCR4-NOT complex, an evolutionarily conserved general regulator of mRNA turnover, and other related factors, including poly(A)-specific nuclease for mRNA decay, are involved in aneuploid viability. Defective mutations in CCR4-NOT complex components in the distantly related yeast Saccharomyces cerevisiae also affected the viability of spores produced from triploid cells, suggesting that this complex has a conserved role in aneuploids. In addition, our findings suggest that the genes required for homologous recombination repair are important for aneuploid viability.
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Affiliation(s)
- Yoshie Tange
- Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | | | - Bunshiro Goto
- Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
| | - Kwang-Lae Hoe
- Chungnam National University, Graduate School of New Drug Discovery and Development, Yusong-gu, Daejeon, Korea
| | - Dong-Uk Kim
- Aging Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yusong-gu, Daejeon, Korea
| | | | - Jacqueline Hayles
- Cancer Research UK, The London Research Institute, London, United Kingdom
| | - Yuji Chikashige
- National Institute of Information and Communications Technology, Kobe, Japan
| | - Chihiro Tsutumi
- National Institute of Information and Communications Technology, Kobe, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- National Institute of Information and Communications Technology, Kobe, Japan
| | - Fumiaki Yamao
- National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Paul Nurse
- Cancer Research UK, The London Research Institute, London, United Kingdom
- The Rockefeller University, New York, New York, United States of America
| | - Osami Niwa
- Kazusa DNA Research Institute, Kisarazu, Chiba, Japan
- The Rockefeller University, New York, New York, United States of America
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18
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Sunder S, Greeson-Lott NT, Runge KW, Sanders SL. A new method to efficiently induce a site-specific double-strand break in the fission yeast Schizosaccharomyces pombe. Yeast 2012; 29:275-91. [PMID: 22674789 DOI: 10.1002/yea.2908] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 05/03/2012] [Indexed: 12/16/2022] Open
Abstract
Double-strand DNA breaks are a serious threat to cellular viability and yeast systems have proved invaluable in helping to understand how these potentially toxic lesions are sensed and repaired. An important method to study the processing of DNA breaks in the budding yeast Saccharomyces cerevisiae is to introduce a unique double-strand break into the genome by regulating the expression of the site-specific HO endonuclease with a galactose inducible promoter. Variations of the HO site-specific DSB assay have been adapted to many organisms, but the methodology has seen only limited use in the fission yeast Schizosaccharomyces pombe because of the lack of a promoter capable of inducing endonuclease expression on a relatively short time scale (~1 h). We have overcome this limitation by developing a new assay in which expression of the homing endonuclease I-PpoI is tightly regulated with a tetracycline-inducible promoter. We show that induction of the I-PpoI endonuclease produces rapid cutting of a defined cleavage site (> 80% after 1 h), efficient cell cycle arrest and significant accumulation of the checkpoint protein Crb2 at break-adjacent regions in a manner that is analogous to published findings with DSBs produced by an acute exposure to ionizing irradiation. This assay provides an important new tool for the fission yeast community and, because many aspects of mammalian chromatin organization have been well-conserved in Sz. pombe but not in S. cerevisiae, also offers an attractive system to decipher the role of chromatin structure in modulating the repair of double-stranded DNA breaks.
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Affiliation(s)
- Sham Sunder
- Department of Biochemistry and Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
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19
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Kamisugi Y, Schaefer DG, Kozak J, Charlot F, Vrielynck N, Holá M, Angelis KJ, Cuming AC, Nogué F. MRE11 and RAD50, but not NBS1, are essential for gene targeting in the moss Physcomitrella patens. Nucleic Acids Res 2011; 40:3496-510. [PMID: 22210882 PMCID: PMC3333855 DOI: 10.1093/nar/gkr1272] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The moss Physcomitrella patens is unique among plant models for the high frequency with which targeted transgene insertion occurs via homologous recombination. Transgene integration is believed to utilize existing machinery for the detection and repair of DNA double-strand breaks (DSBs). We undertook targeted knockout of the Physcomitrella genes encoding components of the principal sensor of DNA DSBs, the MRN complex. Loss of function of PpMRE11 or PpRAD50 strongly and specifically inhibited gene targeting, whilst rates of untargeted transgene integration were relatively unaffected. In contrast, disruption of the PpNBS1 gene retained the wild-type capacity to integrate transforming DNA efficiently at homologous loci. Analysis of the kinetics of DNA-DSB repair in wild-type and mutant plants by single-nucleus agarose gel electrophoresis revealed that bleomycin-induced fragmentation of genomic DNA was repaired at approximately equal rates in each genotype, although both the Ppmre11 and Pprad50 mutants exhibited severely restricted growth and development and enhanced sensitivity to UV-B and bleomycin-induced DNA damage, compared with wild-type and Ppnbs1 plants. This implies that while extensive DNA repair can occur in the absence of a functional MRN complex; this is unsupervised in nature and results in the accumulation of deleterious mutations incompatible with normal growth and development.
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Affiliation(s)
- Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, Leeds University, Leeds LS2 9JT, UK
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20
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DNA double-strand break repair and the evolution of intron density. Trends Genet 2010; 27:1-6. [PMID: 21106271 PMCID: PMC3020277 DOI: 10.1016/j.tig.2010.10.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 10/18/2010] [Accepted: 10/18/2010] [Indexed: 01/23/2023]
Abstract
The density of introns is both an important feature of genome architecture and a highly variable trait across eukaryotes. This heterogeneity has posed an evolutionary puzzle for the last 30 years. Recent evidence is consistent with novel introns being the outcome of the error-prone repair of DNA double-stranded breaks (DSBs) via non-homologous end joining (NHEJ). Here we suggest that deletion of pre-existing introns could occur via the same pathway. We propose a novel framework in which species-specific differences in the activity of NHEJ and homologous recombination (HR) during the repair of DSBs underlie changes in intron density.
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21
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Rowan BA, Oldenburg DJ, Bendich AJ. RecA maintains the integrity of chloroplast DNA molecules in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2010; 61:2575-88. [PMID: 20406785 PMCID: PMC2882256 DOI: 10.1093/jxb/erq088] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Revised: 03/15/2010] [Accepted: 03/16/2010] [Indexed: 05/18/2023]
Abstract
Although our understanding of mechanisms of DNA repair in bacteria and eukaryotic nuclei continues to improve, almost nothing is known about the DNA repair process in plant organelles, especially chloroplasts. Since the RecA protein functions in DNA repair for bacteria, an analogous function may exist for chloroplasts. The effects on chloroplast DNA (cpDNA) structure of two nuclear-encoded, chloroplast-targeted homologues of RecA in Arabidopsis were examined. A homozygous T-DNA insertion mutation in one of these genes (cpRecA) resulted in altered structural forms of cpDNA molecules and a reduced amount of cpDNA, while a similar mutation in the other gene (DRT100) had no effect. Double mutants exhibited a similar phenotype to cprecA single mutants. The cprecA mutants also exhibited an increased amount of single-stranded cpDNA, consistent with impaired RecA function. After four generations, the cprecA mutant plants showed signs of reduced chloroplast function: variegation and necrosis. Double-stranded breaks in cpDNA of wild-type plants caused by ciprofloxacin (an inhibitor of Escherichia coli gyrase, a type II topoisomerase) led to an alteration of cpDNA structure that was similar to that seen in cprecA mutants. It is concluded that the process by which damaged DNA is repaired in bacteria has been retained in their endosymbiotic descendent, the chloroplast.
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Affiliation(s)
| | | | - Arnold J. Bendich
- Department of Biology, University of Washington, Seattle, WA 91895 USA
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22
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Deshpande GP, Hayles J, Hoe KL, Kim DU, Park HO, Hartsuiker E. Screening a genome-wide S. pombe deletion library identifies novel genes and pathways involved in genome stability maintenance. DNA Repair (Amst) 2009; 8:672-9. [PMID: 19264558 DOI: 10.1016/j.dnarep.2009.01.016] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2008] [Revised: 01/19/2009] [Accepted: 01/20/2009] [Indexed: 11/27/2022]
Abstract
The maintenance of genome stability is essential for an organism to avoid cell death and cancer. Based on screens for mutant sensitivity against DNA damaging agents a large number of DNA repair and DNA damage checkpoint genes have previously been identified in genetically amenable model organisms. These screens have however not been exhaustive and various genes have been, and remain to be, identified by other means. We therefore screened a genome-wide Schizosaccharomyces pombe deletion library for mutants sensitive against various DNA damaging agents. Screening the library on different concentrations of these genotoxins allowed us to assign a semi-quantitative score to each mutant expressing the degree of sensitivity. We isolated a total of 229 mutants which show sensitivity to one or more of the DNA damaging agents used. This set of mutants was significantly enriched for processes involved in DNA replication, DNA repair, DNA damage checkpoint, response to UV, mating type switching, telomere length maintenance and meiosis, and also for processes involved in the establishment and maintenance of chromatin architecture (notably members of the SAGA complex), transcription (members of the CCR4-Not complex) and microtubule related processes (members of the DASH complex). We also identified 23 sensitive mutants which had previously been classified as "sequence orphan" or as "conserved hypothetical". Among these, we identified genes showing extensive homology to CtIP, Stra13, Ybp1/Ybp2, Human Fragile X mental retardation interacting protein NUFIP1, and Aprataxin. The identification of these homologues will provide a basis for the further characterisation of the role of these conserved proteins in the genetically amenable model organism S. pombe.
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Affiliation(s)
- Gaurang P Deshpande
- Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK
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23
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Dziadkowiec D, Petters E, Dyjankiewicz A, Karpiński P, Garcia V, Watson A, Carr AM. The role of novel genes rrp1(+) and rrp2(+) in the repair of DNA damage in Schizosaccharomyces pombe. DNA Repair (Amst) 2009; 8:627-36. [PMID: 19185548 DOI: 10.1016/j.dnarep.2008.12.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2008] [Revised: 12/08/2008] [Accepted: 12/16/2008] [Indexed: 10/21/2022]
Abstract
We identified two predicted proteins in Schizosaccharomyces pombe, Rrp1 (SPAC17A2.12) and Rrp2 (SPBC23E6.02) that share 34% and 36% similarity to Saccharomyces cerevisiae Ris1p, respectively. Ris1p is a DNA-dependent ATP-ase involved in gene silencing and DNA repair. Rrp1 and Rrp2 also share similarity with S. cerevisiae Rad5 and S. pombe Rad8, containing SNF2-N, RING finger and Helicase-C domains. To investigate the function of the Rrp proteins, we studied the DNA damage sensitivities and genetic interactions of null mutants with known DNA repair mutants. Single Deltarrp1 and Deltarrp2 mutants were not sensitive to CPT, 4NQO, CDPP, MMS, HU, UV or IR. The double mutants Deltarrp1 Deltarhp51 and Deltarrp2 Deltarhp51 plus the triple Deltarrp1 Deltarrp2 Deltarhp51 mutant did not display significant additional sensitivity. However, the double mutants Deltarrp1 Deltarhp57 and Deltarrp2 Deltarhp57 were significantly more sensitive to MMS, CPT, HU and IR than the Deltarhp57 single mutant. The checkpoint response in these strains was functional. In S. pombe, Rhp55/57 acts in parallel with a second mediator complex, Swi5/Sfr1, to facilitate Rhp51-dependent DNA repair. Deltarrp1 Deltasfr1 and Deltarrp2 Deltasfr1 double mutants did not show significant additional sensitivity, suggesting a function for Rrp proteins in the Swi5/Sfr1 pathway of DSB repair. Consistent with this, Deltarrp1 Deltarhp57 and Deltarrp2 Deltarhp57 mutants, but not Deltarrp1 Deltasfr1 or Deltarrp2 Deltasfr1 double mutants, exhibited slow growth and aberrations in cell and nuclear morphology that are typical of Deltarhp51.
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Affiliation(s)
- Dorota Dziadkowiec
- Faculty of Biotechnology, Wrocław University, Przybyszewskiego 63-77, 51-148 Wrocław, Poland.
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24
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Conaway RC, Conaway JW. The INO80 chromatin remodeling complex in transcription, replication and repair. Trends Biochem Sci 2008; 34:71-7. [PMID: 19062292 DOI: 10.1016/j.tibs.2008.10.010] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 10/28/2008] [Accepted: 10/29/2008] [Indexed: 01/05/2023]
Abstract
The Ino80 ATPase is a member of the SNF2 family of ATPases and functions as an integral component of a multisubunit ATP-dependent chromatin remodeling complex. Although INO80 complexes from yeast and higher eukaryotes share a common core of conserved subunits, the complexes have diverged substantially during evolution and have acquired new subunits with apparently species-specific functions. Recent studies have shown that the INO80 complex contributes to a wide variety of chromatin-dependent nuclear transactions, including transcription, DNA repair and DNA replication.
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Affiliation(s)
- Ronald C Conaway
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, KS 66160, USA
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25
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Willis N, Rhind N. Mus81, Rhp51(Rad51), and Rqh1 form an epistatic pathway required for the S-phase DNA damage checkpoint. Mol Biol Cell 2008; 20:819-33. [PMID: 19037101 DOI: 10.1091/mbc.e08-08-0798] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The S-phase DNA damage checkpoint slows the rate of DNA synthesis in response to damage during replication. In the fission yeast Schizosaccharomyces pombe, Cds1, the S-phase-specific checkpoint effector kinase, is required for checkpoint signaling and replication slowing; upon treatment with the alkylating agent methyl methane sulfonate, cds1Delta mutants display a complete checkpoint defect. We have identified proteins downstream of Cds1 required for checkpoint-dependant slowing, including the structure-specific endonuclease Mus81 and the helicase Rqh1, which are implicated in replication fork stability and the negative regulation of recombination. Removing Rhp51, the Rad51 recombinase homologue, suppresses the slowing defect of rqh1Delta mutants, but not that of mus81Delta mutant, defining an epistatic pathway in which mus81 is epistatic to rhp51 and rhp51 is epistatic to rqh1. We propose that restraining recombination is required for the slowing of replication in response to DNA damage.
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Affiliation(s)
- Nicholas Willis
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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26
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Xrs2 facilitates crossovers during DNA double-strand gap repair in yeast. DNA Repair (Amst) 2008; 7:1563-77. [PMID: 18599383 DOI: 10.1016/j.dnarep.2008.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2007] [Revised: 06/02/2008] [Accepted: 06/04/2008] [Indexed: 11/23/2022]
Abstract
Xrs2 is a member of the MRX complex (Mre11/Rad50/Xrs2) in Saccharomyces cerevisiae. In this study we demonstrate the important role of the MRX complex and in more detail of Xrs2 for the repair of radiation-induced chromosomal double-strand breaks by pulsed field gel electrophoresis. By using a newly designed in vivo plasmid-chromosome recombination system, we could show that gap repair efficiency and the association with crossovers were reduced in the MRX null mutants, but repair accuracy was unaffected. For these processes, an intact Mre11-binding domain of Xrs2 is crucial, whereas the FHA- and BRCT-domains as well as the Tel1-binding domain of Xrs2 are dispensable. Obviously, the Mre11-binding domain of the Xrs2 protein is crucial for the analysed functions and our results suggest a new role of the MRX complex for the formation of crossovers. Analysis of double mutants showed that the phenotype of the Deltaxrs2 null mutant concerning the crossover frequency is dominant over the phenotypes of Deltasrs2 and Deltasgs1 null mutants. Thus, the complex seems to be involved in early steps of double-strand break and gap repair, and we propose that it has a regulatory role for the selection of homologous recombination pathways.
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27
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Sakaguchi C, Morishita T, Shinagawa H, Hishida T. Essential and distinct roles of the F-box and helicase domains of Fbh1 in DNA damage repair. BMC Mol Biol 2008; 9:27. [PMID: 18312697 PMCID: PMC2294136 DOI: 10.1186/1471-2199-9-27] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Accepted: 03/03/2008] [Indexed: 11/12/2022] Open
Abstract
Background DNA double-strand breaks (DSBs) are induced by exogenous insults such as ionizing radiation and chemical exposure, and they can also arise as a consequence of stalled or collapsed DNA replication forks. Failure to repair DSBs can lead to genomic instability or cell death and cancer in higher eukaryotes. The Schizosaccharomyces pombe fbh1 gene encodes an F-box DNA helicase previously described to play a role in the Rhp51 (an orthologue of S. cerevisiae RAD51)-dependent recombinational repair of DSBs. Fbh1 fused to GFP localizes to discrete nuclear foci following DNA damage. Results To determine the functional roles of the highly conserved F-box and helicase domains, we have characterized fbh1 mutants carrying specific mutations in these domains. We show that the F-box mutation fbh1-fb disturbs the nuclear localization of Fbh1, conferring an fbh1 null-like phenotype. Moreover, nuclear foci do not form in fbh1-fb cells with DNA damage even if Fbh1-fb is targeted to the nucleus by fusion to a nuclear localization signal sequence. In contrast, the helicase mutation fbh1-hl causes the accumulation of Fbh1 foci irrespective of the presence of DNA damage and confers damage sensitivity greater than that conferred by the null allele. Additional mutation of the F-box alleviates the hypermorphic phenotype of the fbh1-hl mutant. Conclusion These results suggest that the F-box and DNA helicase domains play indispensable but distinct roles in Fbh1 function. Assembly of the SCFFbh1 complex is required for both the nuclear localization and DNA damage-induced focus formation of Fbh1 and is therefore prerequisite for the Fbh1 recombination function.
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Affiliation(s)
- Chikako Sakaguchi
- Laboratory of Genome Dynamics, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan.
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28
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Buhler C, Borde V, Lichten M. Mapping meiotic single-strand DNA reveals a new landscape of DNA double-strand breaks in Saccharomyces cerevisiae. PLoS Biol 2008; 5:e324. [PMID: 18076285 PMCID: PMC2121111 DOI: 10.1371/journal.pbio.0050324] [Citation(s) in RCA: 186] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2007] [Accepted: 10/25/2007] [Indexed: 11/19/2022] Open
Abstract
DNA double-strand breaks (DSBs), which are formed by the Spo11 protein, initiate meiotic recombination. Previous DSB-mapping studies have used rad50S or sae2Δ mutants, which are defective in break processing, to accumulate Spo11-linked DSBs, and report large (≥ 50 kb) “DSB-hot” regions that are separated by “DSB-cold” domains of similar size. Substantial recombination occurs in some DSB-cold regions, suggesting that DSB patterns are not normal in rad50S or sae2Δ mutants. We therefore developed a novel method to map genome-wide, single-strand DNA (ssDNA)–associated DSBs that accumulate in processing-capable, repair-defective dmc1Δ and dmc1Δ rad51Δ mutants. DSBs were observed at known hot spots, but also in most previously identified “DSB-cold” regions, including near centromeres and telomeres. Although approximately 40% of the genome is DSB-cold in rad50S mutants, analysis of meiotic ssDNA from dmc1Δ shows that most of these regions have substantial DSB activity. Southern blot assays of DSBs in selected regions in dmc1Δ, rad50S, and wild-type cells confirm these findings. Thus, DSBs are distributed much more uniformly than was previously believed. Comparisons of DSB signals in dmc1, dmc1 rad51, and dmc1 spo11 mutant strains identify Dmc1 as a critical strand-exchange activity genome-wide, and confirm previous conclusions that Spo11-induced lesions initiate all meiotic recombination. During meiosis, the two copies of each chromosome present in the full (diploid) genome come together and then separate, forming haploid gametes (sperm and eggs, in animals). Recombination, which swaps DNA between chromosomes, is critical for chromosome pairing and separation, and also promotes genetic diversity in the next generation, providing the feedstock for evolution. DNA double-strand breaks (DSBs), which are formed by the conserved Spo11 nuclease, initiate meiotic recombination. DSB mapping is thus an alternative to standard genetic analysis for determining where meiotic recombination occurs. DSBs have been most extensively mapped in budding yeast mutants that fail to remove Spo11 from break ends, blocking further recombination steps. Paradoxically, those studies indicated that DSBs are absent from large regions where recombination was known to occur. We developed a new DSB mapping method that purifies and analyzes the single-strand DNA formed at breaks after Spo11 removal. This new map shows that DSBs (and by inference, recombination) actually occur frequently throughout almost all of the budding yeast genome, in a distribution that is consistent with recombination's roles in chromosome pairing and in generating genetic diversity. This new mapping method will be useful for studying meiotic recombination and DNA damage repair in other organisms. The authors developed a new method to detect DNA damage genome-wide, and they used it to show that meiotic recombination is more uniformly distributed in budding yeast than was previously believed.
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Affiliation(s)
- Cyril Buhler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Valérie Borde
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Michael Lichten
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * To whom correspondence should be addressed. E-mail:
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Ward JD, Barber LJ, Petalcorin MIR, Yanowitz J, Boulton SJ. Replication blocking lesions present a unique substrate for homologous recombination. EMBO J 2007; 26:3384-96. [PMID: 17611606 PMCID: PMC1933397 DOI: 10.1038/sj.emboj.7601766] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2007] [Accepted: 05/24/2007] [Indexed: 02/06/2023] Open
Abstract
Homologous recombination (HR) plays a critical role in the restart of blocked replication forks, but how this is achieved remains poorly understood. We show that mutants in the single Rad51 paralog in Caenorhabditis elegans, rfs-1, permit discrimination between HR substrates generated at DNA double-strand breaks (DSBs), or following replication fork collapse from HR substrates assembled at replication fork barriers (RFBs). Unexpectedly, RFS-1 is dispensable for RAD-51 recruitment to meiotic and ionizing radiation (IR)-induced DSBs and following replication fork collapse, yet, is essential for RAD-51 recruitment to RFBs formed by DNA crosslinking agents and other replication blocking lesions. Deletion of rfs-1 also suppresses the accumulation of toxic HR intermediates in him-6; top-3 mutants and accelerates deletion formation at presumed endogenous RFBs formed by poly G/C tracts in the absence of DOG-1. These data suggest that RFS-1 is not a general mediator of HR-dependent DSB repair, but acts specifically to promote HR at RFBs. HR substrates generated at conventional DSBs or following replication fork collapse are therefore intrinsically different from those produced during normal repair of blocked replication forks.
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Affiliation(s)
- Jordan D Ward
- DNA Damage Response Laboratory, Cancer Research UK, The London Research Institute, Clare Hall Laboratories, South Mimms, Herts, UK
| | - Louise J Barber
- DNA Damage Response Laboratory, Cancer Research UK, The London Research Institute, Clare Hall Laboratories, South Mimms, Herts, UK
| | - Mark IR Petalcorin
- DNA Damage Response Laboratory, Cancer Research UK, The London Research Institute, Clare Hall Laboratories, South Mimms, Herts, UK
| | - Judith Yanowitz
- Carnegie Institution, Department of Embryology, Baltimore, MD, USA
| | - Simon J Boulton
- DNA Damage Response Laboratory, Cancer Research UK, The London Research Institute, Clare Hall Laboratories, South Mimms, Herts, UK
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30
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Current awareness on yeast. Yeast 2007. [DOI: 10.1002/yea.1326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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