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Luo XC, Yu L, Xu SY, Ying SH, Feng MG. Photoreactivation Activities of Rad5, Rad16A and Rad16B Help Beauveria bassiana to Recover from Solar Ultraviolet Damage. J Fungi (Basel) 2024; 10:420. [PMID: 38921406 PMCID: PMC11205155 DOI: 10.3390/jof10060420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/02/2024] [Accepted: 06/12/2024] [Indexed: 06/27/2024] Open
Abstract
In budding yeast, Rad5 and Rad7-Rad16 play respective roles in the error-free post-replication repair and nucleotide excision repair of ultraviolet-induced DNA damage; however, their homologs have not yet been studied in non-yeast fungi. In the fungus Beauveria bassiana, a deficiency in the Rad7 homolog, Rad5 ortholog and two Rad16 paralogs (Rad16A/B) instituted an ability to help the insect-pathogenic fungus to recover from solar UVB damage through photoreactivation. The fungal lifecycle-related phenotypes were not altered in the absence of rad5, rad16A or rad16B, while severe defects in growth and conidiation were caused by the double deletion of rad16A and rad16B. Compared with the wild-type and complemented strains, the mutants showed differentially reduced activities regarding the resilience of UVB-impaired conidia at 25 °C through a 12-h incubation in a regime of visible light plus dark (L/D 3:9 h or 5:7 h for photoreactivation) or of full darkness (dark reactivation) mimicking a natural nighttime. The estimates of the median lethal UVB dose LD50 from the dark and L/D treatments revealed greater activities of Rad5 and Rad16B than of Rad16A and additive activities of Rad16A and Rad16B in either NER-dependent dark reactivation or photorepair-dependent photoreactivation. However, their dark reactivation activities were limited to recovering low UVB dose-impaired conidia but were unable to recover conidia impaired by sublethal and lethal UVB doses as did their photoreactivation activities at L/D 3:9 or 5:7, unless the night/dark time was doubled or further prolonged. Therefore, the anti-UV effects of Rad5, Rad16A and Rad16B in B. bassiana depend primarily on photoreactivation and are mechanistically distinct from those for their yeast homologs.
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Affiliation(s)
| | | | | | | | - Ming-Guang Feng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; (X.-C.L.); (L.Y.); (S.-Y.X.); (S.-H.Y.)
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Peng H, Zhang YL, Ying SH, Feng MG. Rad2, Rad14 and Rad26 recover Metarhizium robertsii from solar UV damage through photoreactivation in vivo. Microbiol Res 2024; 280:127589. [PMID: 38154444 DOI: 10.1016/j.micres.2023.127589] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 12/30/2023]
Abstract
Rad2, Rad14 and Rad26 recover ultraviolet (UV) damage by nucleotide excision repair (NER) in budding yeast but their functions in filamentous fungi have not been elucidated. Here, we report mechanistically different anti-UV effects of nucleus-specific Rad2, Rad14 and Rad26 orthologs in Metarhizium robertsii, an insect-pathogenic fungus. The null mutants of rad2, rad14 and rad26 showed a decrease of ∼90% in conidial resistance to UVB irradiation. When conidia were impaired at a UVB dose of 0.15 J/cm2, they were photoreactivated (germinated) by only 6-13% through a 5-h light plus 19-h dark incubation, whereas 100%, 80% and 70% of the wild-type conidia were photoreactivated at 0.15, 0.3 and 0.4 J/cm2, respectively. The dose-dependent photoreactivation rates were far greater than the corresponding 24-h dark reactivation rates and were largely enhanced by the overexpression (OE) of rad2, rad14 or rad26 in the wild-type strain. The OE strains exhibited markedly greater activities in photoreactivation of conidia inactivated at 0.5-0.7 J/cm2 than did the wild-type strain. Confirmed interactions of Rad2, Rad14 and Rad26 with photolyase regulators and/or Rad1 or Rad10 suggest that each of these proteins could have evolved into a component of the photolyase regulator-cored protein complex to mediate photoreactivation. The interactions inhibited in the null mutants resulted in transcriptional abolishment or repression of those factors involved in the complex. In conclusion, the anti-UV effects of Rad2, Rad14 and Rad26 depend primarily on DNA photorepair-dependent photoreactivation in M. robertsii and mechanistically differ from those of yeast orthologs depending on NER.
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Affiliation(s)
- Han Peng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Clinical Research Institute, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, China
| | - Yi-Lu Zhang
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Sheng-Hua Ying
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ming-Guang Feng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
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Lanz MC, Dibitetto D, Smolka MB. DNA damage kinase signaling: checkpoint and repair at 30 years. EMBO J 2019; 38:e101801. [PMID: 31393028 PMCID: PMC6745504 DOI: 10.15252/embj.2019101801] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 07/03/2019] [Accepted: 07/24/2019] [Indexed: 12/27/2022] Open
Abstract
From bacteria to mammalian cells, damaged DNA is sensed and targeted by DNA repair pathways. In eukaryotes, kinases play a central role in coordinating the DNA damage response. DNA damage signaling kinases were identified over two decades ago and linked to the cell cycle checkpoint concept proposed by Weinert and Hartwell in 1988. Connections between the DNA damage signaling kinases and DNA repair were scant at first, and the initial perception was that the importance of these kinases for genome integrity was largely an indirect effect of their roles in checkpoints, DNA replication, and transcription. As more substrates of DNA damage signaling kinases were identified, it became clear that they directly regulate a wide range of DNA repair factors. Here, we review our current understanding of DNA damage signaling kinases, delineating the key substrates in budding yeast and humans. We trace the progress of the field in the last 30 years and discuss our current understanding of the major substrate regulatory mechanisms involved in checkpoint responses and DNA repair.
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Affiliation(s)
- Michael Charles Lanz
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Diego Dibitetto
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Marcus Bustamante Smolka
- Department of Molecular Biology and GeneticsWeill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
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Poli J, Gerhold CB, Tosi A, Hustedt N, Seeber A, Sack R, Herzog F, Pasero P, Shimada K, Hopfner KP, Gasser SM. Mec1, INO80, and the PAF1 complex cooperate to limit transcription replication conflicts through RNAPII removal during replication stress. Genes Dev 2016; 30:337-54. [PMID: 26798134 PMCID: PMC4743062 DOI: 10.1101/gad.273813.115] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 12/21/2015] [Indexed: 12/11/2022]
Abstract
Poli et al. present genetic and proteomic analyses from budding yeast that uncover links between the DNA replication checkpoint sensor Mec1–Ddc2 (ATR–ATRIP), the chromatin remodeling complex INO80C, and the transcription complex PAF1C. A subset of chromatin-bound RNAPII is degraded in a manner dependent on Mec1, INO80, and PAF1 complexes in cells exposed to hydroxyurea. Little is known about how cells ensure DNA replication in the face of RNA polymerase II (RNAPII)-mediated transcription, especially under conditions of replicative stress. Here we present genetic and proteomic analyses from budding yeast that uncover links between the DNA replication checkpoint sensor Mec1–Ddc2 (ATR–ATRIP), the chromatin remodeling complex INO80C (INO80 complex), and the transcription complex PAF1C (PAF1 complex). We found that a subset of chromatin-bound RNAPII is degraded in a manner dependent on Mec1, INO80, and PAF1 complexes in cells exposed to hydroxyurea (HU). On HU, Mec1 triggers the efficient removal of PAF1C and RNAPII from transcribed genes near early firing origins. Failure to evict RNAPII correlates inversely with recovery from replication stress: paf1Δ cells, like ino80 and mec1 mutants, fail to restart forks efficiently after stalling. Our data reveal unexpected synergies between INO80C, Mec1, and PAF1C in the maintenance of genome integrity and suggest a mechanism of RNAPII degradation that reduces transcription–replication fork collision.
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Affiliation(s)
- Jérôme Poli
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | | | - Alessandro Tosi
- Gene Center, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Nicole Hustedt
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Andrew Seeber
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Ragna Sack
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Franz Herzog
- Gene Center, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Philippe Pasero
- UPR 1142, Institut de Génétique Humaine, Centre National de la Recherche Scientifique, 30396 Montpellier, France
| | - Kenji Shimada
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Karl-Peter Hopfner
- Gene Center, Ludwig Maximilian University of Munich, 81377 Munich, Germany
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland; Faculty of Natural Sciences, University of Basel, CH-4056 Basel, Switzerland
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Transcription coupled nucleotide excision repair in the yeast Saccharomyces cerevisiae: The ambiguous role of Rad26. DNA Repair (Amst) 2015; 36:43-48. [DOI: 10.1016/j.dnarep.2015.09.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Waters R, van Eijk P, Reed S. Histone modification and chromatin remodeling during NER. DNA Repair (Amst) 2015; 36:105-113. [DOI: 10.1016/j.dnarep.2015.09.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Bélanger F, Angers JP, Fortier É, Hammond-Martel I, Costantino S, Drobetsky E, Wurtele H. Mutations in Replicative Stress Response Pathways Are Associated with S Phase-specific Defects in Nucleotide Excision Repair. J Biol Chem 2015; 291:522-37. [PMID: 26578521 DOI: 10.1074/jbc.m115.685883] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Indexed: 01/02/2023] Open
Abstract
Nucleotide excision repair (NER) is a highly conserved pathway that removes helix-distorting DNA lesions induced by a plethora of mutagens, including UV light. Our laboratory previously demonstrated that human cells deficient in either ATM and Rad3-related (ATR) kinase or translesion DNA polymerase η (i.e. key proteins that promote the completion of DNA replication in response to UV-induced replicative stress) are characterized by profound inhibition of NER exclusively during S phase. Toward elucidating the mechanistic basis of this phenomenon, we developed a novel assay to quantify NER kinetics as a function of cell cycle in the model organism Saccharomyces cerevisiae. Using this assay, we demonstrate that in yeast, deficiency of the ATR homologue Mec1 or of any among several other proteins involved in the cellular response to replicative stress significantly abrogates NER uniquely during S phase. Moreover, initiation of DNA replication is required for manifestation of this defect, and S phase NER proficiency is correlated with the capacity of individual mutants to respond to replicative stress. Importantly, we demonstrate that partial depletion of Rfa1 recapitulates defective S phase-specific NER in wild type yeast; moreover, ectopic RPA1-3 overexpression rescues such deficiency in either ATR- or polymerase η-deficient human cells. Our results strongly suggest that reduction of NER capacity during periods of enhanced replicative stress, ostensibly caused by inordinate sequestration of RPA at stalled DNA replication forks, represents a conserved feature of the multifaceted eukaryotic DNA damage response.
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Affiliation(s)
- François Bélanger
- From the Centre de Recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, Québec H1T 2M4, Canada and
| | - Jean-Philippe Angers
- From the Centre de Recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, Québec H1T 2M4, Canada and the Programme de Biologie Moléculaire
| | - Émile Fortier
- From the Centre de Recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, Québec H1T 2M4, Canada and
| | - Ian Hammond-Martel
- From the Centre de Recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, Québec H1T 2M4, Canada and
| | - Santiago Costantino
- From the Centre de Recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, Québec H1T 2M4, Canada and Département d'ophtalmologie, and
| | - Elliot Drobetsky
- From the Centre de Recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, Québec H1T 2M4, Canada and Département de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Hugo Wurtele
- From the Centre de Recherche de l'Hôpital Maisonneuve-Rosemont, Montréal, Québec H1T 2M4, Canada and Département de Médecine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
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Mao P, Smerdon MJ. Rescue of DNA damage-stalled RNA Pol II: histone H2B in action. RNA & DISEASE (HOUSTON, TEX.) 2015; 1. [PMID: 25705722 DOI: 10.14800/rd.422;] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
RNA Pol II elongation in eukaryotes is coupled with a series of histone modifications. Elongating RNA Pol II can be strongly stalled by lesions on the DNA template. However, it is unclear whether RNA Pol II stalling affects elongation-associated histone modifications. We have explored this important question by investigating the function of histone H2B mono-ubiquitylation (H2Bub), a well-characterized epigenetic mark associated with RNA Pol II elongation, in the cellular response to DNA lesions induced by ultraviolet (UV) radiation. We found that, in contrast to transcription elongation, RNA Pol II stalling induced by UV lesions triggers rapid and significant H2B deubiquitylation that removes ubiquitin from H2B. Interestingly, in yeast mutant cells that lack H2B deubiquitylation enzymes, rescue of the stalled RNA Pol II by transcription-coupled repair (TCR) is significantly impaired. Thus, our study has established a direct connection between RNA Pol II stalling and a histone modification response.
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Affiliation(s)
- Peng Mao
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520
| | - Michael J Smerdon
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520
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Shivange G, Kodipelli N, Monisha M, Anindya R. A role for Saccharomyces cerevisiae Tpa1 protein in direct alkylation repair. J Biol Chem 2014; 289:35939-52. [PMID: 25381260 DOI: 10.1074/jbc.m114.590216] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Alkylating agents induce cytotoxic DNA base adducts. In this work, we provide evidence to suggest, for the first time, that Saccharomyces cerevisiae Tpa1 protein is involved in DNA alkylation repair. Little is known about Tpa1 as a repair protein beyond the initial observation from a high-throughput analysis indicating that deletion of TPA1 causes methyl methane sulfonate sensitivity in S. cerevisiae. Using purified Tpa1, we demonstrate that Tpa1 repairs both single- and double-stranded methylated DNA. Tpa1 is a member of the Fe(II) and 2-oxoglutarate-dependent dioxygenase family, and we show that mutation of the amino acid residues involved in cofactor binding abolishes the Tpa1 DNA repair activity. Deletion of TPA1 along with the base excision repair pathway DNA glycosylase MAG1 renders the tpa1Δmag1Δ double mutant highly susceptible to methylation-induced toxicity. We further demonstrate that the trans-lesion synthesis DNA polymerase Polζ (REV3) plays a key role in tolerating DNA methyl-base lesions and that tpa1Δmag1revΔ3 triple mutant is extremely susceptible to methylation-induced toxicity. Our results indicate a synergism between the base excision repair pathway and direct alkylation repair by Tpa1 in S. cerevisiae. We conclude that Tpa1 is a hitherto unidentified DNA repair protein in yeast and that it plays a crucial role in reverting alkylated DNA base lesions and cytotoxicity.
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Affiliation(s)
- Gururaj Shivange
- From the Department of Biotechnology, Indian Institute of Technology Hyderabad, Ordnance Factory Estate, Yeddumailaram 502205, Hyderabad, India
| | - Naveena Kodipelli
- From the Department of Biotechnology, Indian Institute of Technology Hyderabad, Ordnance Factory Estate, Yeddumailaram 502205, Hyderabad, India
| | - Mohan Monisha
- From the Department of Biotechnology, Indian Institute of Technology Hyderabad, Ordnance Factory Estate, Yeddumailaram 502205, Hyderabad, India
| | - Roy Anindya
- From the Department of Biotechnology, Indian Institute of Technology Hyderabad, Ordnance Factory Estate, Yeddumailaram 502205, Hyderabad, India
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Abstract
Rad26p is a SWI/SNF-like ATPase in yeast, and is conserved among eukaryotes. Both Rad26p and its human homolog CSB (Cockayne syndrome group B) are involved in regulation of chromatin structure, transcription and DNA repair. Thus, mutations or malfunctions of these proteins have significant effects on cellular functions. Mutations in CSB are associated with Cockayne syndrome (CS) that is characterized by heterogeneous pathologies such as mental and physical retardation, sun sensitivity, premature aging, muscular and skeletal abnormalities, and progressive decline in neurological and cognitive functions. Therefore, many research groups focused their studies to understand the mechanisms of Rad26p/CSB functions to illuminate the molecular bases of CS. These studies have provided significant functional and mechanistic insights of Rad26p/CSB in regulation of gene expression and genome integrity as described here.
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Affiliation(s)
- Shivani Malik
- a Department of Biochemistry and Molecular Biology ; Southern Illinois University School of Medicine ; Carbondale , IL USA
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Abstract
DNA repair mechanisms are critical for maintaining the integrity of genomic DNA, and their loss is associated with cancer predisposition syndromes. Studies in Saccharomyces cerevisiae have played a central role in elucidating the highly conserved mechanisms that promote eukaryotic genome stability. This review will focus on repair mechanisms that involve excision of a single strand from duplex DNA with the intact, complementary strand serving as a template to fill the resulting gap. These mechanisms are of two general types: those that remove damage from DNA and those that repair errors made during DNA synthesis. The major DNA-damage repair pathways are base excision repair and nucleotide excision repair, which, in the most simple terms, are distinguished by the extent of single-strand DNA removed together with the lesion. Mistakes made by DNA polymerases are corrected by the mismatch repair pathway, which also corrects mismatches generated when single strands of non-identical duplexes are exchanged during homologous recombination. In addition to the true repair pathways, the postreplication repair pathway allows lesions or structural aberrations that block replicative DNA polymerases to be tolerated. There are two bypass mechanisms: an error-free mechanism that involves a switch to an undamaged template for synthesis past the lesion and an error-prone mechanism that utilizes specialized translesion synthesis DNA polymerases to directly synthesize DNA across the lesion. A high level of functional redundancy exists among the pathways that deal with lesions, which minimizes the detrimental effects of endogenous and exogenous DNA damage.
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The mechanism of nucleotide excision repair-mediated UV-induced mutagenesis in nonproliferating cells. Genetics 2013; 193:803-17. [PMID: 23307894 DOI: 10.1534/genetics.112.147421] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Following the irradiation of nondividing yeast cells with ultraviolet (UV) light, most induced mutations are inherited by both daughter cells, indicating that complementary changes are introduced into both strands of duplex DNA prior to replication. Early analyses demonstrated that such two-strand mutations depend on functional nucleotide excision repair (NER), but the molecular mechanism of this unique type of mutagenesis has not been further explored. In the experiments reported here, an ade2 adeX colony-color system was used to examine the genetic control of UV-induced mutagenesis in nondividing cultures of Saccharomyces cerevisiae. We confirmed a strong suppression of two-strand mutagenesis in NER-deficient backgrounds and demonstrated that neither mismatch repair nor interstrand crosslink repair affects the production of these mutations. By contrast, proteins involved in the error-prone bypass of DNA damage (Rev3, Rev1, PCNA, Rad18, Pol32, and Rad5) and in the early steps of the DNA-damage checkpoint response (Rad17, Mec3, Ddc1, Mec1, and Rad9) were required for the production of two-strand mutations. There was no involvement, however, for the Pol η translesion synthesis DNA polymerase, the Mms2-Ubc13 postreplication repair complex, downstream DNA-damage checkpoint factors (Rad53, Chk1, and Dun1), or the Exo1 exonuclease. Our data support models in which UV-induced mutagenesis in nondividing cells occurs during the Pol ζ-dependent filling of lesion-containing, NER-generated gaps. The requirement for specific DNA-damage checkpoint proteins suggests roles in recruiting and/or activating factors required to fill such gaps.
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Gaillard H, Aguilera A. Transcription coupled repair at the interface between transcription elongation and mRNP biogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:141-50. [PMID: 23046879 DOI: 10.1016/j.bbagrm.2012.09.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 09/19/2012] [Accepted: 09/22/2012] [Indexed: 01/13/2023]
Abstract
During transcription, the nascent pre-mRNA associates with mRNA-binding proteins and undergoes a series of processing steps, resulting in export competent mRNA ribonucleoprotein complexes (mRNPs) that are transported into the cytoplasm. Throughout transcription elongation, RNA polymerases frequently deal with a number of obstacles that need to be removed for transcription resumption. One important type of hindrance consists of helix-distorting DNA lesions. Transcription-coupled repair (TC-NER), a specific sub-pathway of nucleotide excision repair, ensures a fast repair of such transcription-blocking lesions. While the nucleotide excision repair reaction is fairly well understood, its regulation and the way it deals with DNA transcription remains largely unknown. In this review, we update our current understanding of the factors involved in TC-NER and discuss their functional interplay with the processes of transcription elongation and mRNP biogenesis. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.
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Waters R, Evans K, Bennett M, Yu S, Reed S. Nucleotide excision repair in cellular chromatin: studies with yeast from nucleotide to gene to genome. Int J Mol Sci 2012; 13:11141-11164. [PMID: 23109843 PMCID: PMC3472735 DOI: 10.3390/ijms130911141] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Revised: 08/22/2012] [Accepted: 08/24/2012] [Indexed: 11/16/2022] Open
Abstract
Here we review our development of, and results with, high resolution studies on global genome nucleotide excision repair (GGNER) in Saccharomyces cerevisiae. We have focused on how GGNER relates to histone acetylation for its functioning and we have identified the histone acetyl tranferase Gcn5 and acetylation at lysines 9/14 of histone H3 as a major factor in enabling efficient repair. We consider results employing primarily MFA2 as a model gene, but also those with URA3 located at subtelomeric sequences. In the latter case we also see a role for acetylation at histone H4. We then go on to outline the development of a high resolution genome-wide approach that enables one to examine correlations between histone modifications and the nucleotide excision repair (NER) of UV-induced cyclobutane pyrimidine dimers throughout entire genomes. This is an approach that will enable rapid advances in understanding the complexities of how compacted chromatin in chromosomes is processed to access DNA damage and then returned to its pre-damaged status to maintain epigenetic codes.
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Affiliation(s)
- Raymond Waters
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +44-29-2068-7336; Fax: +44-29-2074-4276
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Malik S, Chaurasia P, Lahudkar S, Uprety B, Bhaumik SR. Rad26p regulates the occupancy of histone H2A-H2B dimer at the active genes in vivo. Nucleic Acids Res 2011; 40:3348-63. [PMID: 22199252 PMCID: PMC3333851 DOI: 10.1093/nar/gkr1244] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Recently, we have demonstrated a predominant association of Rad26p with the coding sequences but not promoters of several GAL genes following transcriptional induction. Here, we show that the occupancy of histone H2A–H2B dimer at the coding sequences of these genes is not altered following transcriptional induction in the absence of Rad26p. A histone H2A–H2B dimer-enriched chromatin in Δrad26 is correlated to decreased association of RNA polymerase II with the active coding sequences (and hence transcription). However, the reduced association of RNA polymerase II with the active coding sequence in the absence of Rad26p is not due to the defect in formation of transcription complex at the promoter. Thus, Rad26p regulates the occupancy of histone H2A–H2B dimer, which is correlated to the association of elongating RNA polymerase II with active GAL genes. Similar results are also found at other inducible non-GAL genes. Collectively, our results define a new role of Rad26p in orchestrating chromatin structure and hence transcription in vivo.
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Affiliation(s)
- Shivani Malik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
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Novarina D, Amara F, Lazzaro F, Plevani P, Muzi-Falconi M. Mind the gap: keeping UV lesions in check. DNA Repair (Amst) 2011; 10:751-9. [PMID: 21602108 PMCID: PMC3171152 DOI: 10.1016/j.dnarep.2011.04.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Cells respond to genotoxic insults by triggering a DNA damage checkpoint surveillance mechanism and by activating repair pathways. Recent findings indicate that the two processes are more related than originally thought. Here we discuss the mechanisms involved in responding to UV-induced lesions in different phases of the cell cycle and summarize the most recent data in a model where Nucleotide Excision Repair (NER) and exonucleolytic activities act in sequence leading to checkpoint activation in non replicating cells. The critical trigger is likely represented by problematic intermediates that cannot be completely or efficiently repaired by NER. In S phase cells, on the other hand, the replicative polymerases, blocked by bulky UV lesions, re-initiate DNA synthesis downstream of the lesions, leaving behind a ssDNA tract. If these gaps are not rapidly refilled, checkpoint kinases will be activated.
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Affiliation(s)
- Daniele Novarina
- Dipartimento di Scienze Biomolecolari e Biotecnologie, Università degli Studi di Milano. Via Celoria 26, 20133 Milano, Italy
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Current awareness on yeast. Yeast 2010. [DOI: 10.1002/yea.1718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Svejstrup JQ. The interface between transcription and mechanisms maintaining genome integrity. Trends Biochem Sci 2010; 35:333-8. [PMID: 20194025 DOI: 10.1016/j.tibs.2010.02.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Revised: 02/03/2010] [Accepted: 02/05/2010] [Indexed: 12/27/2022]
Abstract
Maintaining genome integrity is crucial for correctly regulated gene expression. Conversely, the process of transcription fundamentally impinges on genome stability, necessitating cellular mechanisms that lessen the genome destabilizing effect of reading genes. This review provides an overview of our present knowledge of how eukaryotic RNA polymerase II transcription affects, and is affected by, other DNA-related processes such as chromatin remodeling, DNA repair, recombination and replication.
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Affiliation(s)
- Jesper Q Svejstrup
- Clare Hall Laboratories, Cancer Research UK London Research Institute, Blanche Lane, South Mimms, EN6 3LD, UK.
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