Pub Date : 2024-05-12DOI: 10.1016/j.dnarep.2024.103692
Peng Li, Xiaochun Yu
Over the past few decades, unbiased approaches such as genetic screening and protein affinity purification have unveiled numerous proteins involved in DNA double-strand break (DSB) repair and maintaining genome stability. However, despite our knowledge of these protein factors, the underlying molecular mechanisms governing key cellular events during DSB repair remain elusive. Recent evidence has shed light on the role of non-protein factors, such as RNA, in several pivotal steps of DSB repair. In this review, we provide a comprehensive summary of these recent findings, highlighting the significance of ribosomal RNA (rRNA) as a critical mediator of DNA damage response, meiosis, and mitosis. Moreover, we discuss potential mechanisms through which rRNA may influence genome integrity.
过去几十年来，基因筛选和蛋白质亲和纯化等无偏见的方法揭示了许多参与 DNA 双链断裂（DSB）修复和维持基因组稳定性的蛋白质。然而，尽管我们对这些蛋白因子有所了解，但在DSB修复过程中调控关键细胞事件的潜在分子机制仍然难以捉摸。最近的证据揭示了非蛋白因子（如 RNA）在 DSB 修复的几个关键步骤中的作用。在这篇综述中，我们全面总结了这些最新发现，强调了核糖体 RNA（rRNA）作为 DNA 损伤反应、减数分裂和有丝分裂的关键介质的重要性。此外，我们还讨论了 rRNA 影响基因组完整性的潜在机制。
{"title":"The role of rRNA in maintaining genome stability.","authors":"Peng Li, Xiaochun Yu","doi":"10.1016/j.dnarep.2024.103692","DOIUrl":"https://doi.org/10.1016/j.dnarep.2024.103692","url":null,"abstract":"<p><p>Over the past few decades, unbiased approaches such as genetic screening and protein affinity purification have unveiled numerous proteins involved in DNA double-strand break (DSB) repair and maintaining genome stability. However, despite our knowledge of these protein factors, the underlying molecular mechanisms governing key cellular events during DSB repair remain elusive. Recent evidence has shed light on the role of non-protein factors, such as RNA, in several pivotal steps of DSB repair. In this review, we provide a comprehensive summary of these recent findings, highlighting the significance of ribosomal RNA (rRNA) as a critical mediator of DNA damage response, meiosis, and mitosis. Moreover, we discuss potential mechanisms through which rRNA may influence genome integrity.</p>","PeriodicalId":93982,"journal":{"name":"DNA repair","volume":"139 ","pages":"103692"},"PeriodicalIF":0.0,"publicationDate":"2024-05-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140961115","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-01DOI: 10.1016/j.dnarep.2023.103617
Tomohiko Sugiyama, Mahima R. Sanyal
{"title":"Biochemical analysis of H2O2-induced mutation spectra revealed that multiple damages were involved in the mutational process","authors":"Tomohiko Sugiyama, Mahima R. Sanyal","doi":"10.1016/j.dnarep.2023.103617","DOIUrl":"https://doi.org/10.1016/j.dnarep.2023.103617","url":null,"abstract":"","PeriodicalId":93982,"journal":{"name":"DNA repair","volume":"528 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139023575","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-01DOI: 10.1016/j.dnarep.2023.103615
Penny Jeggo
{"title":"Contents of Previous 3 Special Issues in this Series of Perspectives.","authors":"Penny Jeggo","doi":"10.1016/j.dnarep.2023.103615","DOIUrl":"https://doi.org/10.1016/j.dnarep.2023.103615","url":null,"abstract":"","PeriodicalId":93982,"journal":{"name":"DNA repair","volume":"326 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139020311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-10-11DOI: 10.1016/j.dnarep.2023.103582
Sirelin Sillamaa, Vlad–Julian Piljukov, Iris Vaask, Tiina Sedman, Priit Jõers, Juhan Sedman
Hmi1 is a UvrD-like DNA helicase required for the maintenance of the yeast Saccharomyces cerevisiae mitochondrial DNA (mtDNA). Deletion of the HMI1 ORF leads to the formation of respiration-deficient petite mutants, which either contain a short fragment of mtDNA arranged in tandem repeats or lack mtDNA completely. Here we characterize point mutants of the helicase designed to target the ATPase or ssDNA binding activity and show that these mutations do not separately lead to complete loss of the Hmi1 function. The mutant strains support ATP production via oxidative phosphorylation and enable us to directly analyze the impact of both activities on the stability of wild-type mtDNA in this petite-positive yeast. Our data reveal that Hmi1 mutants affecting ssDNA binding display a stronger defect in the maintenance of mtDNA compared to the mutants of ATP binding/hydrolysis. Hmi1 mutants impaired in ssDNA binding demonstrate sensitivity to UV irradiation and lower levels of Cox2 encoded by the mitochondrial genome. This suggests a complex and multifarious role for Hmi1 in mtDNA maintenance-linked transactions, some of which do not require the ATP-dependent helicase activity.
{"title":"UvrD-like helicase Hmi1 Has an ATP independent role in yeast mitochondrial DNA maintenance","authors":"Sirelin Sillamaa, Vlad–Julian Piljukov, Iris Vaask, Tiina Sedman, Priit Jõers, Juhan Sedman","doi":"10.1016/j.dnarep.2023.103582","DOIUrl":"https://doi.org/10.1016/j.dnarep.2023.103582","url":null,"abstract":"<div><p><span><span>Hmi1 is a UvrD-like DNA </span>helicase required for the maintenance of the yeast </span><span><em>Saccharomyces cerevisiae</em></span> mitochondrial DNA (mtDNA). Deletion of the <em>HMI1</em> ORF leads to the formation of respiration-deficient <em>petite</em><span><span><span> mutants, which either contain a short fragment of mtDNA arranged in tandem repeats<span> or lack mtDNA completely. Here we characterize point mutants of the helicase designed to target the ATPase or ssDNA </span></span>binding activity and show that these mutations do not separately lead to complete loss of the Hmi1 function. The mutant strains support ATP production via </span>oxidative phosphorylation and enable us to directly analyze the impact of both activities on the stability of wild-type mtDNA in this </span><em>petite</em><span>-positive yeast. Our data reveal that Hmi1 mutants affecting ssDNA binding display a stronger defect in the maintenance of mtDNA compared to the mutants of ATP binding/hydrolysis. Hmi1 mutants impaired in ssDNA binding demonstrate sensitivity to UV irradiation and lower levels of Cox2 encoded by the mitochondrial genome. This suggests a complex and multifarious role for Hmi1 in mtDNA maintenance-linked transactions, some of which do not require the ATP-dependent helicase activity.</span></p></div>","PeriodicalId":93982,"journal":{"name":"DNA repair","volume":"132 ","pages":"Article 103582"},"PeriodicalIF":0.0,"publicationDate":"2023-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41227818","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-05-05DOI: 10.21203/RS.3.RS-495251/V1
Simon Keane, H. de Weerd, K. Ejeskär
BACKGROUND In primary neuroblastoma, deletions on chromosome 11q are known to result in an increase in the total number of chromosomal breaks. The DNA double-strand break repair pathways mediated by NHEJ are often upregulated in cancer. DLG2, a candidate tumor suppressor gene on chromosome 11q, has previously been implicated in DNA repair. METHODS We evaluated an association between gene expression and neuroblastoma patient outcome, risk categorization, and 11q status using publicly available microarray data from independent neuroblastoma patient datasets. Functional studies were conducted using comet assay and H2AX phosphorylation in neuroblastoma cell lines and in the fruit fly with UVC-induced DNA breaks. RESULTS We show that the NHEJ genes PARP1 and FEN1 are over expressed in neuroblastoma and restoration of DLG2 impairs their gene and protein expression. When exposed to UVC radiation, cells with DLG2 over expression show less DNA fragmentation and induce apoptosis in a p53 S46 dependent manner. We could also confirm that DLG2 over expression results in CHK1 phosphorylation consistent with previous reports of G2/M maintenance. CONCLUSIONS Taken together, we show that DLG2 over expression increases p53 mediated apoptosis in response to etoposide and UVC mediated genotoxicity and reduced DNA replication machinery.
{"title":"DLG2 impairs dsDNA break repair and maintains genome integrity in neuroblastoma.","authors":"Simon Keane, H. de Weerd, K. Ejeskär","doi":"10.21203/RS.3.RS-495251/V1","DOIUrl":"https://doi.org/10.21203/RS.3.RS-495251/V1","url":null,"abstract":"BACKGROUND\u0000In primary neuroblastoma, deletions on chromosome 11q are known to result in an increase in the total number of chromosomal breaks. The DNA double-strand break repair pathways mediated by NHEJ are often upregulated in cancer. DLG2, a candidate tumor suppressor gene on chromosome 11q, has previously been implicated in DNA repair.\u0000\u0000\u0000METHODS\u0000We evaluated an association between gene expression and neuroblastoma patient outcome, risk categorization, and 11q status using publicly available microarray data from independent neuroblastoma patient datasets. Functional studies were conducted using comet assay and H2AX phosphorylation in neuroblastoma cell lines and in the fruit fly with UVC-induced DNA breaks.\u0000\u0000\u0000RESULTS\u0000We show that the NHEJ genes PARP1 and FEN1 are over expressed in neuroblastoma and restoration of DLG2 impairs their gene and protein expression. When exposed to UVC radiation, cells with DLG2 over expression show less DNA fragmentation and induce apoptosis in a p53 S46 dependent manner. We could also confirm that DLG2 over expression results in CHK1 phosphorylation consistent with previous reports of G2/M maintenance.\u0000\u0000\u0000CONCLUSIONS\u0000Taken together, we show that DLG2 over expression increases p53 mediated apoptosis in response to etoposide and UVC mediated genotoxicity and reduced DNA replication machinery.","PeriodicalId":93982,"journal":{"name":"DNA repair","volume":"112 1","pages":"103302"},"PeriodicalIF":0.0,"publicationDate":"2021-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47504505","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. L. Hamm, Anarosa A. Garcia, Rachel Gilbert, Manavi Johri, M. Ricart, Samantha L. Sholes, Laura A. Murray-Nerger, Eugene Wu
Abstract 8-oxo-2′-deoxyguanosine (OdG) is a prominent DNA lesion that can direct the incorporation of dCTP or dATP during replication. As the latter reaction can lead to mutation, the ratio of dCTP/dATP incorporation can significantly affect the mutagenic potential of OdG. Previous work with the A-family polymerase BF and seven analogues of OdG identified a major groove amino acid, Ile716, which likely influences the dCTP/dATP incorporation ratio opposite OdG. To further probe the importance of this amino acid, dCTP and dATP incorporations opposite the same seven analogues were tested with two BF mutants, I716M and I716A. Results from these studies support the presence of clashing interactions between Ile716 and the C8-oxygen and C2-amine during dCTP and dATP incorporations, respectively. Crystallographic analysis suggests that residue 716 alters the conformation of the template base prior to insertion into the active site, thereby affecting enzymatic efficiency. These results are also consistent with previous work with A-family polymerases, which indicate they have tight, rigid active sites that are sensitive to template perturbations.
{"title":"Bacillus Fragment DNA polymerase mutant I716M","authors":"M. L. Hamm, Anarosa A. Garcia, Rachel Gilbert, Manavi Johri, M. Ricart, Samantha L. Sholes, Laura A. Murray-Nerger, Eugene Wu","doi":"10.2210/pdb6p5c/pdb","DOIUrl":"https://doi.org/10.2210/pdb6p5c/pdb","url":null,"abstract":"Abstract 8-oxo-2′-deoxyguanosine (OdG) is a prominent DNA lesion that can direct the incorporation of dCTP or dATP during replication. As the latter reaction can lead to mutation, the ratio of dCTP/dATP incorporation can significantly affect the mutagenic potential of OdG. Previous work with the A-family polymerase BF and seven analogues of OdG identified a major groove amino acid, Ile716, which likely influences the dCTP/dATP incorporation ratio opposite OdG. To further probe the importance of this amino acid, dCTP and dATP incorporations opposite the same seven analogues were tested with two BF mutants, I716M and I716A. Results from these studies support the presence of clashing interactions between Ile716 and the C8-oxygen and C2-amine during dCTP and dATP incorporations, respectively. Crystallographic analysis suggests that residue 716 alters the conformation of the template base prior to insertion into the active site, thereby affecting enzymatic efficiency. These results are also consistent with previous work with A-family polymerases, which indicate they have tight, rigid active sites that are sensitive to template perturbations.","PeriodicalId":93982,"journal":{"name":"DNA repair","volume":"89 1","pages":"102826-102826"},"PeriodicalIF":0.0,"publicationDate":"2020-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43135037","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
T. Rao, S. Longerich, Weixing Zhao, H. Aihara, P. Sung, Y. Xiong
Fanconi-associated nuclease 1 (FAN1) removes interstrand DNA crosslinks (ICLs) through its DNA flap endonuclease and exonuclease activities. Crystal structures of human and bacterial FAN1 bound to a DNA flap have been solved. The Pseudomonas aeruginosa bacterial FAN1 and human FAN1 (hFAN1) missing a flexible loop are monomeric, while intact hFAN1 is homo-dimeric in structure. Importantly, the monomeric and dimeric forms of FAN1 exhibit very different DNA binding modes. Here, we interrogate the functional differences between monomeric and dimeric forms of FAN1 and provide an explanation for the discrepancy in oligomeric state between the two hFAN1 structures. Specifically, we show that the flexible loop in question is needed for hFAN1 dimerization. While monomeric and dimeric bacterial or human FAN1 proteins cleave a short 5’ flap strand with similar efficiency, optimal cleavage of a long 5’ flap strand is contingent upon protein dimerization. Our study therefore furnishes biochemical evidence for a role of hFAN1 homodimerization in biological processes that involve 5’ DNA Flap cleavage.
{"title":"Importance of homo-dimerization of Fanconi-associated nuclease 1 in DNA flap cleavage","authors":"T. Rao, S. Longerich, Weixing Zhao, H. Aihara, P. Sung, Y. Xiong","doi":"10.1101/236208","DOIUrl":"https://doi.org/10.1101/236208","url":null,"abstract":"Fanconi-associated nuclease 1 (FAN1) removes interstrand DNA crosslinks (ICLs) through its DNA flap endonuclease and exonuclease activities. Crystal structures of human and bacterial FAN1 bound to a DNA flap have been solved. The Pseudomonas aeruginosa bacterial FAN1 and human FAN1 (hFAN1) missing a flexible loop are monomeric, while intact hFAN1 is homo-dimeric in structure. Importantly, the monomeric and dimeric forms of FAN1 exhibit very different DNA binding modes. Here, we interrogate the functional differences between monomeric and dimeric forms of FAN1 and provide an explanation for the discrepancy in oligomeric state between the two hFAN1 structures. Specifically, we show that the flexible loop in question is needed for hFAN1 dimerization. While monomeric and dimeric bacterial or human FAN1 proteins cleave a short 5’ flap strand with similar efficiency, optimal cleavage of a long 5’ flap strand is contingent upon protein dimerization. Our study therefore furnishes biochemical evidence for a role of hFAN1 homodimerization in biological processes that involve 5’ DNA Flap cleavage.","PeriodicalId":93982,"journal":{"name":"DNA repair","volume":"64 1","pages":"53 - 58"},"PeriodicalIF":0.0,"publicationDate":"2017-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45479686","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
扫码关注我们
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号