1
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Lyu XH, Suo F, Li W, Jia GS, Yang YS, Du LL. Diverse modes of chromosome terminal deletion in spontaneous canavanine-resistant Schizosaccharomyces pombe mutants. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001132. [PMID: 38404922 PMCID: PMC10884838 DOI: 10.17912/micropub.biology.001132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 02/03/2024] [Accepted: 02/02/2024] [Indexed: 02/27/2024]
Abstract
Canavanine resistance has been used to analyze mutation rates in the fission yeast Schizosaccharomyces pombe . However, the genetic basis of canavanine resistance in this organism remains incompletely understood. Here, we performed whole genome sequencing on five spontaneously arising canavanine-resistant S. pombe mutants, including the can2-1 mutant isolated in the 1970s. This analysis revealed that three mutants, including can2-1 , experienced terminal deletions of the left arm of chromosome II, leading to the loss of multiple amino acid transporter genes. Interestingly, these three mutants underwent chromosome terminal deletion through distinct mechanisms, including homology-driven translocation, homology-independent chromosome fusion, and de novo telomere addition. Our findings shed new light on the genetic basis of canavanine resistance and mechanisms underlying chromosome terminal deletions in fission yeast.
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Affiliation(s)
- Xiao-Hui Lyu
- National Institute of Biological Sciences, Beijing, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing, China
| | - Wen Li
- National Institute of Biological Sciences, Beijing, China
| | - Guo-Song Jia
- National Institute of Biological Sciences, Beijing, China
| | - Yu-Sheng Yang
- National Institute of Biological Sciences, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
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2
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Kim SM, Forsburg SL. Multiple DNA repair pathways contribute to MMS-induced post-replicative DNA synthesis in S. pombe . MICROPUBLICATION BIOLOGY 2023; 2023:10.17912/micropub.biology.000974. [PMID: 37854101 PMCID: PMC10580077 DOI: 10.17912/micropub.biology.000974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/22/2023] [Accepted: 09/29/2023] [Indexed: 10/20/2023]
Abstract
Replication stress can induce DNA synthesis outside of replicative S-phase. We have previously demonstrated that fission yeast cells stimulate DNA synthesis in G2-phase but not in M-phase in response to DNA alkylating agent MMS. In this study, we show that various DNA repair pathways, including translesion synthesis and break-induced replication contribute to post-replicative DNA synthesis. Checkpoint kinases, various repair and resection proteins, and multiple polymerases are also involved.
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Affiliation(s)
- Seong Min Kim
- Molecular and Computational Biology, University of Southern California, Los Angeles, California, United States
| | - Susan L. Forsburg
- University of Southern California, Los Angeles, California, United States
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3
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Disbennett WM, Hawk TM, Rollins PD, Nelakurti DD, Lucas BE, McPherson MT, Hylton HM, Petreaca RC. Genetic interaction of the histone chaperone hip1 + with double strand break repair genes in Schizosaccharomyces pombe. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000545. [PMID: 35622511 PMCID: PMC9005195 DOI: 10.17912/micropub.biology.000545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/15/2022] [Accepted: 03/22/2022] [Indexed: 11/06/2022]
Abstract
Schizosaccharomyces pombe hip1 + (human HIRA) is a histone chaperone and transcription factor involved in establishment of the centromeric chromatin and chromosome segregation, regulation of histone transcription, and cellular response to stress. We carried out a double mutant genetic screen of Δhip1 and mutations in double strand break repair pathway. We find that hip1 + functions after the MRN complex which initiates resection of blunt double strand break ends but before recruitment of the DNA damage repair machinery. Further, deletion of hip1 + partially suppresses sensitivity to DNA damaging agents of mutations in genes involved in Break Induced Replication (BIR), one mechanism of rescue of stalled or collapses replication forks ( rad51 + , cdc27 + ). Δhip1 also suppresses mutations in two checkpoint genes ( cds1 + , rad3 + ) on hydroxyurea a drug that stalls replication forks. Our results show that hip1 + forms complex interactions with the DNA double strand break repair genes and may be involved in facilitating communication between damage sensors and downstream factors.
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Affiliation(s)
| | - Tila M. Hawk
- James Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | - P. Daniel Rollins
- Molecular Genetics Undergraduate Program, The Ohio State University, Columbus, OH
| | - Devi D Nelakurti
- Biomedical Science Undergraduate Program, The Ohio State University Medical School, Columbus, OH
| | - Bailey E Lucas
- James Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | | | - Hannah M Hylton
- Biology Undergraduate Program, The Ohio State University, Marion, OH
| | - Ruben C Petreaca
- Department of Molecular Genetics, The Ohio State University, Marion, OH
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4
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Yang YS, Ning SK, Lyu XH, Suo F, Jia GS, Li W, Du LL. Canavanine resistance mutation can1-1 in Schizosaccharomyces pombe is a missense mutation in the ubiquitin ligase adaptor gene any1. MICROPUBLICATION BIOLOGY 2022; 2022:10.17912/micropub.biology.000538. [PMID: 35300005 PMCID: PMC8922049 DOI: 10.17912/micropub.biology.000538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/05/2022] [Accepted: 03/09/2022] [Indexed: 11/18/2022]
Abstract
In Schizosaccharomyces pombe, the can1-1 mutation confers resistance to the toxic arginine analog canavanine. This mutation has been assumed to disrupt a gene encoding an arginine transporter. In PomBase, the gene SPBC18H10.16 is currently designated can1. Here, we sequenced the genomes of three can1-1 strains. No mutations were found in SPBC18H10.16. Instead, these strains harbor an R175C mutation in the gene any1 (SPBC18H10.20c). any1 encodes an α-arrestin that acts as a ubiquitin ligase adaptor to downregulate plasma membrane amino acid transporters. Our findings indicate that can1-1 is not a loss-of-function mutation in an amino acid transporter gene, but a possible gain-of-function mutation in a gene encoding a negative regulator of amino acid transporters.
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Affiliation(s)
- Yu-Sheng Yang
- National Institute of Biological Sciences, Beijing, China
| | - Shao-Kai Ning
- National Institute of Biological Sciences, Beijing, China
| | - Xiao-Hui Lyu
- National Institute of Biological Sciences, Beijing, China
| | - Fang Suo
- National Institute of Biological Sciences, Beijing, China
| | - Guo-Song Jia
- National Institute of Biological Sciences, Beijing, China
| | - Wen Li
- National Institute of Biological Sciences, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
,
Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
,
Correspondence to: Li-Lin Du (
)
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5
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Gan T, Wang Y, Liu Y, Schatz DG, Hu J. RAG2 abolishes RAG1 aggregation to facilitate V(D)J recombination. Cell Rep 2021; 37:109824. [PMID: 34644584 DOI: 10.1016/j.celrep.2021.109824] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 02/09/2021] [Accepted: 09/21/2021] [Indexed: 11/26/2022] Open
Abstract
RAG1 and RAG2 form a tetramer nuclease to initiate V(D)J recombination in developing T and B lymphocytes. The RAG1 protein evolves from a transposon ancestor and possesses nuclease activity that requires interaction with RAG2. Here, we show that the human RAG1 aggregates in the nucleus in the absence of RAG2, exhibiting an extremely low V(D)J recombination activity. In contrast, RAG2 does not aggregate by itself, but it interacts with RAG1 to disrupt RAG1 aggregates and thereby activate robust V(D)J recombination. Moreover, RAG2 from mouse and zebrafish could not disrupt the aggregation of human RAG1 as efficiently as human RAG2 did, indicating a species-specific regulatory mechanism for RAG1 by RAG2. Therefore, we propose that RAG2 coevolves with RAG1 to release inert RAG1 from aggregates and thereby activate V(D)J recombination to generate diverse antigen receptors in lymphocytes.
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Affiliation(s)
- Tingting Gan
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yuhong Wang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yang Liu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - David G Schatz
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Jiazhi Hu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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6
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Zheng L, Meng Y, Campbell JL, Shen B. Multiple roles of DNA2 nuclease/helicase in DNA metabolism, genome stability and human diseases. Nucleic Acids Res 2020; 48:16-35. [PMID: 31754720 PMCID: PMC6943134 DOI: 10.1093/nar/gkz1101] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 10/23/2019] [Accepted: 11/12/2019] [Indexed: 12/25/2022] Open
Abstract
DNA2 nuclease/helicase is a structure-specific nuclease, 5'-to-3' helicase, and DNA-dependent ATPase. It is involved in multiple DNA metabolic pathways, including Okazaki fragment maturation, replication of 'difficult-to-replicate' DNA regions, end resection, stalled replication fork processing, and mitochondrial genome maintenance. The participation of DNA2 in these different pathways is regulated by its interactions with distinct groups of DNA replication and repair proteins and by post-translational modifications. These regulatory mechanisms induce its recruitment to specific DNA replication or repair complexes, such as DNA replication and end resection machinery, and stimulate its efficient cleavage of various structures, for example, to remove RNA primers or to produce 3' overhangs at telomeres or double-strand breaks. Through these versatile activities at replication forks and DNA damage sites, DNA2 functions as both a tumor suppressor and promoter. In normal cells, it suppresses tumorigenesis by maintaining the genomic integrity. Thus, DNA2 mutations or functional deficiency may lead to cancer initiation. However, DNA2 may also function as a tumor promoter, supporting cancer cell survival by counteracting replication stress. Therefore, it may serve as an ideal target to sensitize advanced DNA2-overexpressing cancers to current chemo- and radiotherapy regimens.
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Affiliation(s)
- Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Yuan Meng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Judith L Campbell
- Divisions of Chemistry and Chemical Engineering and Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
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7
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Pohl TJ, Zakian VA. Pif1 family DNA helicases: A helpmate to RNase H? DNA Repair (Amst) 2019; 84:102633. [PMID: 31231063 DOI: 10.1016/j.dnarep.2019.06.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/14/2019] [Accepted: 06/14/2019] [Indexed: 01/21/2023]
Abstract
An R-loop is a structure that forms when an RNA transcript stays bound to the DNA strand that encodes it and leaves the complementary strand exposed as a loop of single stranded DNA. R-loops accumulate when the processing of RNA transcripts is impaired. The failure to remove these RNA-DNA hybrids can lead to replication fork stalling and genome instability. Resolution of R-loops is thought to be mediated mainly by RNase H enzymes through the removal and degradation of the RNA in the hybrid. However, DNA helicases can also dismantle R-loops by displacing the bound RNA. In particular, the Pif1 family DNA helicases have been shown to regulate R-loop formation at specific genomic loci, such as tRNA genes and centromeres. Here we review the roles of Pif1 family helicases in vivo and in vitro and discuss evidence that Pif1 family helicases act on RNA-DNA hybrids and highlight their potential roles in complementing RNase H for R-loop resolution.
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Affiliation(s)
- Thomas J Pohl
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, United States
| | - Virginia A Zakian
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, United States.
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8
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DNA Replication Through Strand Displacement During Lagging Strand DNA Synthesis in Saccharomyces cerevisiae. Genes (Basel) 2019; 10:genes10020167. [PMID: 30795600 PMCID: PMC6409922 DOI: 10.3390/genes10020167] [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: 01/11/2019] [Revised: 02/14/2019] [Accepted: 02/18/2019] [Indexed: 01/21/2023] Open
Abstract
This review discusses a set of experimental results that support the existence of extended strand displacement events during budding yeast lagging strand DNA synthesis. Starting from introducing the mechanisms and factors involved in leading and lagging strand DNA synthesis and some aspects of the architecture of the eukaryotic replisome, we discuss studies on bacterial, bacteriophage and viral DNA polymerases with potent strand displacement activities. We describe proposed pathways of Okazaki fragment processing via short and long flaps, with a focus on experimental results obtained in Saccharomyces cerevisiae that suggest the existence of frequent and extended strand displacement events during eukaryotic lagging strand DNA synthesis, and comment on their implications for genome integrity.
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9
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Zhang H, Hua Y, Li R, Kong D. Cdc24 Is Essential for Long-range End Resection in the Repair of Double-stranded DNA Breaks. J Biol Chem 2016; 291:24961-24973. [PMID: 27729451 DOI: 10.1074/jbc.m116.755991] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/07/2016] [Indexed: 11/06/2022] Open
Abstract
Double-stranded DNA breaks (DSBs) are highly detrimental DNA lesions, which may be repaired by the homologous recombination-mediated repair pathway. The 5' to 3' direction of long-range end resection on one DNA strand, in which 3'-single-stranded DNA overhangs are created from broken DNA ends, is an essential step in this pathway. Dna2 has been demonstrated as an essential nuclease in this event, but the molecular mechanism of how Dna2 is recruited to DNA break sites in vivo has not been elucidated. In this study, a novel recombination factor called Cdc24 was identified in fission yeast. We demonstrated that Cdc24 localizes to DNA break sites during the repair of DNA breaks and is an essential factor in long-range end resection. We also determined that Cdc24 plays a direct role in recruiting Dna2 to DNA break sites through its interaction with Dna2 and replication protein A (RPA). Further, this study revealed that RPA acts as the foundation for assembling the machinery for long-range end resection by its essential role in recruiting Cdc24 and Dna2 to DNA break sites. These results define Cdc24 as an essential factor for long-range end resection in the repair of DSBs, opening the door for further investigations into the enzymes involved in long-range end resection for DSB repair.
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Affiliation(s)
- Huimin Zhang
- From the Peking-Tsinghua Center for Life Sciences, National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Yu Hua
- From the Peking-Tsinghua Center for Life Sciences, National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Rui Li
- From the Peking-Tsinghua Center for Life Sciences, National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Daochun Kong
- From the Peking-Tsinghua Center for Life Sciences, National Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
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10
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Onaka AT, Toyofuku N, Inoue T, Okita AK, Sagawa M, Su J, Shitanda T, Matsuyama R, Zafar F, Takahashi TS, Masukata H, Nakagawa T. Rad51 and Rad54 promote noncrossover recombination between centromere repeats on the same chromatid to prevent isochromosome formation. Nucleic Acids Res 2016; 44:10744-10757. [PMID: 27697832 PMCID: PMC5159554 DOI: 10.1093/nar/gkw874] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 09/06/2016] [Accepted: 09/21/2016] [Indexed: 12/14/2022] Open
Abstract
Centromeres consist of DNA repeats in many eukaryotes. Non-allelic homologous recombination (HR) between them can result in gross chromosomal rearrangements (GCRs). In fission yeast, Rad51 suppresses isochromosome formation that occurs between inverted repeats in the centromere. However, how the HR enzyme prevents homology-mediated GCRs remains unclear. Here, we provide evidence that Rad51 with the aid of the Swi/Snf-type motor protein Rad54 promotes non-crossover recombination between centromere repeats to prevent isochromosome formation. Mutations in Rad51 and Rad54 epistatically increased the rates of isochromosome formation and chromosome loss. In sharp contrast, these mutations decreased gene conversion between inverted repeats in the centromere. Remarkably, analysis of recombinant DNAs revealed that rad51 and rad54 increase the proportion of crossovers. In the absence of Rad51, deletion of the structure-specific endonuclease Mus81 decreased both crossovers and isochromosomes, while the cdc27/pol32-D1 mutation, which impairs break-induced replication, did not. We propose that Rad51 and Rad54 promote non-crossover recombination between centromere repeats on the same chromatid, thereby suppressing crossover between non-allelic repeats on sister chromatids that leads to chromosomal rearrangements. Furthermore, we found that Rad51 and Rad54 are required for gene silencing in centromeres, suggesting that HR also plays a role in the structure and function of centromeres.
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Affiliation(s)
- Atsushi T Onaka
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Naoko Toyofuku
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Takahiro Inoue
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Akiko K Okita
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Minami Sagawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Jie Su
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Takeshi Shitanda
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Rei Matsuyama
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Faria Zafar
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Tatsuro S Takahashi
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hisao Masukata
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Takuro Nakagawa
- Department of Biological Sciences, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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11
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Zhang JM, Liu XM, Ding YH, Xiong LY, Ren JY, Zhou ZX, Wang HT, Zhang MJ, Yu Y, Dong MQ, Du LL. Fission yeast Pxd1 promotes proper DNA repair by activating Rad16XPF and inhibiting Dna2. PLoS Biol 2014; 12:e1001946. [PMID: 25203555 PMCID: PMC4159138 DOI: 10.1371/journal.pbio.1001946] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 07/31/2014] [Indexed: 01/31/2023] Open
Abstract
Structure-specific nucleases play crucial roles in many DNA repair pathways. They must be precisely controlled to ensure optimal repair outcomes; however, mechanisms of their regulation are not fully understood. Here, we report a fission yeast protein, Pxd1, that binds to and regulates two structure-specific nucleases: Rad16XPF-Swi10ERCC1 and Dna2-Cdc24. Strikingly, Pxd1 influences the activities of these two nucleases in opposite ways: It activates the 3' endonuclease activity of Rad16-Swi10 but inhibits the RPA-mediated activation of the 5' endonuclease activity of Dna2. Pxd1 is required for Rad16-Swi10 to function in single-strand annealing, mating-type switching, and the removal of Top1-DNA adducts. Meanwhile, Pxd1 attenuates DNA end resection mediated by the Rqh1-Dna2 pathway. Disabling the Dna2-inhibitory activity of Pxd1 results in enhanced use of a break-distal repeat sequence in single-strand annealing and a greater loss of genetic information. We propose that Pxd1 promotes proper DNA repair by differentially regulating two structure-specific nucleases.
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Affiliation(s)
- Jia-Min Zhang
- National Institute of Biological Sciences, Beijing, China
- Graduate School of Peking Union Medical College, Beijing, China
| | - Xiao-Man Liu
- National Institute of Biological Sciences, Beijing, China
| | - Yue-He Ding
- National Institute of Biological Sciences, Beijing, China
| | | | - Jing-Yi Ren
- National Institute of Biological Sciences, Beijing, China
| | - Zhi-Xiong Zhou
- National Institute of Biological Sciences, Beijing, China
| | - Hai-Tao Wang
- National Institute of Biological Sciences, Beijing, China
| | - Mei-Jun Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Yang Yu
- National Institute of Biological Sciences, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China
| | - Li-Lin Du
- National Institute of Biological Sciences, Beijing, China
- Graduate School of Peking Union Medical College, Beijing, China
- * E-mail:
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12
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Lee CH, Lee M, Kang HJ, Kim DH, Kang YH, Bae SH, Seo YS. The N-terminal 45-kDa domain of Dna2 endonuclease/helicase targets the enzyme to secondary structure DNA. J Biol Chem 2013; 288:9468-81. [PMID: 23344960 DOI: 10.1074/jbc.m112.418715] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The removal of initiating primers from the 5'-ends of each Okazaki fragment, required for the generation of contiguous daughter strands, can be catalyzed by the combined action of DNA polymerase δ and Fen1. When the flaps generated by displacement of DNA synthesis activity of polymerase δ become long enough to bind replication protein A or form hairpin structures, the helicase/endonuclease enzyme, Dna2, becomes critical because of its ability to remove replication protein A-coated or secondary structure flaps. In this study, we show that the N-terminal 45-kDa domain of Dna2 binds hairpin structures, allowing the enzyme to target secondary structure flap DNA. We found that this activity was essential for the efficient removal of hairpin flaps by the endonuclease activity of Dna2 with the aid of its helicase activity. Thus, the efficient removal of hairpin structure flaps requires the coordinated action of all three functional domains of Dna2. We also found that deletion of the N-terminal 45-kDa domain of Dna2 led to a partial loss of the intra-S-phase checkpoint function and an increased rate of homologous recombination in yeast. We discuss the potential roles of the N-terminal domain of Dna2 in the maintenance of genomic stability.
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Affiliation(s)
- Chul-Hwan Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
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13
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Rahmeh AA, Zhou Y, Xie B, Li H, Lee EYC, Lee MYWT. Phosphorylation of the p68 Subunit of Pol δ Acts as a Molecular Switch To Regulate Its Interaction with PCNA. Biochemistry 2011; 51:416-24. [DOI: 10.1021/bi201638e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amal A. Rahmeh
- Department
of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595, United States
| | - Yajing Zhou
- Department
of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595, United States
| | - Bin Xie
- Department
of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595, United States
| | - Hao Li
- Department
of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595, United States
| | - Ernest Y. C. Lee
- Department
of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595, United States
| | - Marietta Y. W. T. Lee
- Department
of Biochemistry and Molecular Biology, New York Medical College, Valhalla, New York 10595, United States
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14
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Kang YH, Lee CH, Seo YS. Dna2 on the road to Okazaki fragment processing and genome stability in eukaryotes. Crit Rev Biochem Mol Biol 2010; 45:71-96. [PMID: 20131965 DOI: 10.3109/10409230903578593] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
DNA replication is a primary mechanism for maintaining genome integrity, but it serves this purpose best by cooperating with other proteins involved in DNA repair and recombination. Unlike leading strand synthesis, lagging strand synthesis has a greater risk of faulty replication for several reasons: First, a significant part of DNA is synthesized by polymerase alpha, which lacks a proofreading function. Second, a great number of Okazaki fragments are synthesized, processed and ligated per cell division. Third, the principal mechanism of Okazaki fragment processing is via generation of flaps, which have the potential to form a variety of structures in their sequence context. Finally, many proteins for the lagging strand interact with factors involved in repair and recombination. Thus, lagging strand DNA synthesis could be the best example of a converging place of both replication and repair proteins. To achieve the risky task with extraordinary fidelity, Okazaki fragment processing may depend on multiple layers of redundant, but connected pathways. An essential Dna2 endonuclease/helicase plays a pivotal role in processing common structural intermediates that occur during diverse DNA metabolisms (e.g. lagging strand synthesis and telomere maintenance). Many roles of Dna2 suggest that the preemptive removal of long or structured flaps ultimately contributes to genome maintenance in eukaryotes. In this review, we describe the function of Dna2 in Okazaki fragment processing, and discuss its role in the maintenance of genome integrity with an emphasis on its functional interactions with other factors required for genome maintenance.
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Affiliation(s)
- Young-Hoon Kang
- Center for DNA Replication and Genome Instability, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
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15
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Tinline-Purvis H, Savory AP, Cullen JK, Davé A, Moss J, Bridge WL, Marguerat S, Bähler J, Ragoussis J, Mott R, Walker CA, Humphrey TC. Failed gene conversion leads to extensive end processing and chromosomal rearrangements in fission yeast. EMBO J 2009; 28:3400-12. [PMID: 19798055 DOI: 10.1038/emboj.2009.265] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Accepted: 08/17/2009] [Indexed: 01/06/2023] Open
Abstract
Loss of heterozygosity (LOH), a causal event in cancer and human genetic diseases, frequently encompasses multiple genetic loci and whole chromosome arms. However, the mechanisms by which such extensive LOH arises, and how it is suppressed in normal cells is poorly understood. We have developed a genetic system to investigate the mechanisms of DNA double-strand break (DSB)-induced extensive LOH, and its suppression, using a non-essential minichromosome, Ch(16), in fission yeast. We find extensive LOH to arise from a new break-induced mechanism of isochromosome formation. Our data support a model in which Rqh1 and Exo1-dependent end processing from an unrepaired DSB leads to removal of the broken chromosome arm and to break-induced replication of the intact arm from the centromere, a considerable distance from the initial lesion. This process also promotes genome-wide copy number variation. A genetic screen revealed Rhp51, Rhp55, Rhp57 and the MRN complex to suppress both isochromosome formation and chromosome loss, in accordance with these events resulting from extensive end processing associated with failed homologous recombination repair.
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Affiliation(s)
- Helen Tinline-Purvis
- CRUK-MRC Gray Institute for Radiation Oncology and Biology, University of Oxford, Oxford, Oxfordshire, UK
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16
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Sanchez Garcia J, Baranovskiy AG, Knatko EV, Gray FC, Tahirov TH, MacNeill SA. Functional mapping of the fission yeast DNA polymerase delta B-subunit Cdc1 by site-directed and random pentapeptide insertion mutagenesis. BMC Mol Biol 2009; 10:82. [PMID: 19686603 PMCID: PMC2734569 DOI: 10.1186/1471-2199-10-82] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Accepted: 08/17/2009] [Indexed: 11/25/2022] Open
Abstract
Background DNA polymerase δ plays an essential role in chromosomal DNA replication in eukaryotic cells, being responsible for synthesising the bulk of the lagging strand. In fission yeast, Pol δ is a heterotetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1. Pol3 binds directly to the B-subunit, Cdc1, which in turn binds the C-subunit, Cdc27. Human Pol δ comprises the same four subunits, and the crystal structure was recently reported of a complex of human p50 and the N-terminal domain of p66, the human orthologues of Cdc1 and Cdc27, respectively. Results To gain insights into the structure and function of Cdc1, random and directed mutagenesis techniques were used to create a collection of thirty alleles encoding mutant Cdc1 proteins. Each allele was tested for function in fission yeast and for binding of the altered protein to Pol3 and Cdc27 using the two-hybrid system. Additionally, the locations of the amino acid changes in each protein were mapped onto the three-dimensional structure of human p50. The results obtained from these studies identify amino acid residues and regions within the Cdc1 protein that are essential for interaction with Pol3 and Cdc27 and for in vivo function. Mutations specifically defective in Pol3-Cdc1 interactions allow the identification of a possible Pol3 binding surface on Cdc1. Conclusion In the absence of a three-dimensional structure of the entire Pol δ complex, the results of this study highlight regions in Cdc1 that are vital for protein function in vivo and provide valuable clues to possible protein-protein interaction surfaces on the Cdc1 protein that will be important targets for further study.
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Affiliation(s)
- Javier Sanchez Garcia
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, King's Buildings, Mayfield Road, Edinburgh, EH9 3JR, UK.
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17
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Budd ME, Reis CC, Smith S, Myung K, Campbell JL. Evidence suggesting that Pif1 helicase functions in DNA replication with the Dna2 helicase/nuclease and DNA polymerase delta. Mol Cell Biol 2006; 26:2490-500. [PMID: 16537895 PMCID: PMC1430326 DOI: 10.1128/mcb.26.7.2490-2500.2006] [Citation(s) in RCA: 168] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The precise machineries required for two aspects of eukaryotic DNA replication, Okazaki fragment processing (OFP) and telomere maintenance, are poorly understood. In this work, we present evidence that Saccharomyces cerevisiae Pif1 helicase plays a wider role in DNA replication than previously appreciated and that it likely functions in conjunction with Dna2 helicase/nuclease as a component of the OFP machinery. In addition, we show that Dna2, which is known to associate with telomeres in a cell-cycle-specific manner, may be a new component of the telomere replication apparatus. Specifically, we show that deletion of PIF1 suppresses the lethality of a DNA2-null mutant. The pif1delta dna2delta strain remains methylmethane sulfonate sensitive and temperature sensitive; however, these phenotypes can be suppressed by further deletion of a subunit of pol delta, POL32. Deletion of PIF1 also suppresses the cold-sensitive lethality and hydroxyurea sensitivity of the pol32delta strain. Dna2 is thought to function by cleaving long flaps that arise during OFP due to excessive strand displacement by pol delta and/or by an as yet unidentified helicase. Thus, suppression of dna2delta can be rationalized if deletion of POL32 and/or PIF1 results in a reduction in long flaps that require Dna2 for processing. We further show that deletion of DNA2 suppresses the long-telomere phenotype and the high rate of formation of gross chromosomal rearrangements in pif1Delta mutants, suggesting a role for Dna2 in telomere elongation in the absence of Pif1.
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Affiliation(s)
- Martin E Budd
- Braun Laboratories, 147-75, California Institute of Technology, Pasadena, California 91125, USA
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18
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Budd ME, Tong AHY, Polaczek P, Peng X, Boone C, Campbell JL. A network of multi-tasking proteins at the DNA replication fork preserves genome stability. PLoS Genet 2005; 1:e61. [PMID: 16327883 PMCID: PMC1298934 DOI: 10.1371/journal.pgen.0010061] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Accepted: 10/12/2005] [Indexed: 11/18/2022] Open
Abstract
To elucidate the network that maintains high fidelity genome replication, we have introduced two conditional mutant alleles of DNA2, an essential DNA replication gene, into each of the approximately 4,700 viable yeast deletion mutants and determined the fitness of the double mutants. Fifty-six DNA2-interacting genes were identified. Clustering analysis of genomic synthetic lethality profiles of each of 43 of the DNA2-interacting genes defines a network (consisting of 322 genes and 876 interactions) whose topology provides clues as to how replication proteins coordinate regulation and repair to protect genome integrity. The results also shed new light on the functions of the query gene DNA2, which, despite many years of study, remain controversial, especially its proposed role in Okazaki fragment processing and the nature of its in vivo substrates. Because of the multifunctional nature of virtually all proteins at the replication fork, the meaning of any single genetic interaction is inherently ambiguous. The multiplexing nature of the current studies, however, combined with follow-up supporting experiments, reveals most if not all of the unique pathways requiring Dna2p. These include not only Okazaki fragment processing and DNA repair but also chromatin dynamics.
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Affiliation(s)
- Martin E Budd
- Braun Laboratories, California Institute of Technology, Pasadena, California, United States of America
| | - Amy Hin Yan Tong
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario, Canada
| | - Piotr Polaczek
- Braun Laboratories, California Institute of Technology, Pasadena, California, United States of America
| | - Xiao Peng
- Braun Laboratories, California Institute of Technology, Pasadena, California, United States of America
| | - Charles Boone
- Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Genetics and Microbiology, University of Toronto, Toronto, Ontario, Canada
| | - Judith L Campbell
- Braun Laboratories, California Institute of Technology, Pasadena, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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Kim J, Robertson K, Mylonas KJL, Gray FC, Charapitsa I, MacNeill SA. Contrasting effects of Elg1-RFC and Ctf18-RFC inactivation in the absence of fully functional RFC in fission yeast. Nucleic Acids Res 2005; 33:4078-89. [PMID: 16040599 PMCID: PMC1179736 DOI: 10.1093/nar/gki728] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2005] [Revised: 06/16/2005] [Accepted: 07/05/2005] [Indexed: 12/02/2022] Open
Abstract
Proliferating cell nuclear antigen loading onto DNA by replication factor C (RFC) is a key step in eukaryotic DNA replication and repair processes. In this study, the C-terminal domain (CTD) of the large subunit of fission yeast RFC is shown to be essential for its function in vivo. Cells carrying a temperature-sensitive mutation in the CTD, rfc1-44, arrest with incompletely replicated chromosomes, are sensitive to DNA damaging agents, are synthetically lethal with other DNA replication mutants, and can be suppressed by mutations in rfc5. To assess the contribution of the RFC-like complexes Elg1-RFC and Ctf18-RFC to the viability of rfc1-44, genes encoding the large subunits of these complexes have been deleted and overexpressed. Inactivation of Ctf18-RFC by the deletion of ctf18+, dcc1+ or ctf8+ is lethal in an rfc1-44 background showing that full Ctf18-RFC function is required in the absence of fully functional RFC. In contrast, rfc1-44 elg1Delta cells are viable and overproduction of Elg1 in rfc1-44 is lethal, suggesting that Elg1-RFC plays a negative role when RFC function is inhibited. Consistent with this, the deletion of elg1+ is shown to restore viability to rfc1-44 ctf18Delta cells.
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Affiliation(s)
- Jiyoung Kim
- Wellcome Trust Centre for Cell Biology, University of EdinburghMichael Swann Building, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Kathryn Robertson
- Wellcome Trust Centre for Cell Biology, University of EdinburghMichael Swann Building, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Katie J. L. Mylonas
- Wellcome Trust Centre for Cell Biology, University of EdinburghMichael Swann Building, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Fiona C. Gray
- Wellcome Trust Centre for Cell Biology, University of EdinburghMichael Swann Building, Mayfield Road, Edinburgh EH9 3JR, UK
- Institute of Molecular Biology and Physiology, University of CopenhagenSølvgade 83H, DK-1307 Copenhagen K, Denmark
| | - Iryna Charapitsa
- Wellcome Trust Centre for Cell Biology, University of EdinburghMichael Swann Building, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Stuart A. MacNeill
- Wellcome Trust Centre for Cell Biology, University of EdinburghMichael Swann Building, Mayfield Road, Edinburgh EH9 3JR, UK
- Institute of Molecular Biology and Physiology, University of CopenhagenSølvgade 83H, DK-1307 Copenhagen K, Denmark
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20
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Current awareness on yeast. Yeast 2005; 22:745-52. [PMID: 16106592 DOI: 10.1002/yea.1165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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