A Synthetic Interaction between CDC20 and RAD4 in Saccharomyces cerevisiae upon UV Irradiation

Regulation of DNA repair can be achieved through ubiquitin-mediated degradation of transiently induced proteins. In Saccharomyces cerevisiae, Rad4 is involved in damage recognition during nucleotide excision repair (NER) and, in conjunction with Rad23, recruits other proteins to the site of damage. We identified a synthetic interaction upon UV exposure between Rad4 and Cdc20, a protein that modulates the activity of the anaphase promoting complex (APC/C), a multisubunit E3 ubiquitin ligase complex. The moderately UV sensitive Δrad4 strain became highly sensitive when cdc20-1 was present, and was rescued by overexpression of CDC20. The double mutant is also deficient in elicting RNR3-lacZ transcription upon exposure to UV irradiation or 4-NQO compared with the Δrad4 single mutant. We demonstrate that the Δrad4/cdc20-1 double mutant is defective in double strand break repair by way of a plasmid end-joining assay, indicating that Rad4 acts to ensure that damaged DNA is repaired via a Cdc20-mediated mechanism. This study is the first to present evidence that Cdc20 may play a role in the degradation of proteins involved in nucleotide excision repair.

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RAD1 and RAD10, but not other excision repair genes, are required for double-strand break-induced recombination in Saccharomyces cerevisiae.

Molecular and Cellular Biology ◽

10.1128/mcb.15.4.2245 ◽

1995 ◽

Vol 15 (4) ◽

pp. 2245-2251 ◽

Cited By ~ 136

Author(s):

E L Ivanov ◽

J E Haber

Keyword(s):

Saccharomyces Cerevisiae ◽

Nucleotide Excision Repair ◽

Excision Repair ◽

Strand Break ◽

Single Strand ◽

Repair Gene ◽

Yeast Saccharomyces Cerevisiae ◽

Nucleotide Excision ◽

Single Strand Annealing ◽

Strand Annealing

HO endonuclease-induced double-strand breaks (DSBs) in the yeast Saccharomyces cerevisiae can be repaired by the process of gap repair or, alternatively, by single-strand annealing if the site of the break is flanked by directly repeated homologous sequences. We have shown previously (J. Fishman-Lobell and J. E. Haber, Science 258:480-484, 1992) that during the repair of an HO-induced DSB, the excision repair gene RAD1 is needed to remove regions of nonhomology from the DSB ends. In this report, we present evidence that among nine genes involved in nucleotide excision repair, only RAD1 and RAD10 are required for removal of nonhomologous sequences from the DSB ends. rad1 delta and rad10 delta mutants displayed a 20-fold reduction in the ability to execute both gap repair and single-strand annealing pathways of HO-induced recombination. Mutations in RAD2, RAD3, and RAD14 reduced HO-induced recombination by about twofold. We also show that RAD7 and RAD16, which are required to remove UV photodamage from the silent HML, locus, are not required for MAT switching with HML or HMR as a donor. Our results provide a molecular basis for understanding the role of yeast nucleotide excision repair gene and their human homologs in DSB-induced recombination and repair.

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Transcription-coupled nucleotide excision repair is coordinated by ubiquitin and SUMO in response to ultraviolet irradiation

Nucleic Acids Research ◽

10.1093/nar/gkz977 ◽

2019 ◽

Cited By ~ 1

Author(s):

Frauke Liebelt ◽

Joost Schimmel ◽

Matty Verlaan – de Vries ◽

Esra Klemann ◽

Martin E van Royen ◽

...

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Nucleotide Excision Repair ◽

Uv Irradiation ◽

Excision Repair ◽

Premature Aging ◽

Dependent Manner ◽

Ubiquitin Ligase Complex ◽

Nucleotide Excision ◽

Damage Response

Abstract Cockayne Syndrome (CS) is a severe neurodegenerative and premature aging autosomal-recessive disease, caused by inherited defects in the CSA and CSB genes, leading to defects in transcription-coupled nucleotide excision repair (TC-NER) and consequently hypersensitivity to ultraviolet (UV) irradiation. TC-NER is initiated by lesion-stalled RNA polymerase II, which stabilizes the interaction with the SNF2/SWI2 ATPase CSB to facilitate recruitment of the CSA E3 Cullin ubiquitin ligase complex. However, the precise biochemical connections between CSA and CSB are unknown. The small ubiquitin-like modifier SUMO is important in the DNA damage response. We found that CSB, among an extensive set of other target proteins, is the most dynamically SUMOylated substrate in response to UV irradiation. Inhibiting SUMOylation reduced the accumulation of CSB at local sites of UV irradiation and reduced recovery of RNA synthesis. Interestingly, CSA is required for the efficient clearance of SUMOylated CSB. However, subsequent proteomic analysis of CSA-dependent ubiquitinated substrates revealed that CSA does not ubiquitinate CSB in a UV-dependent manner. Surprisingly, we found that CSA is required for the ubiquitination of the largest subunit of RNA polymerase II, RPB1. Combined, our results indicate that the CSA, CSB, RNA polymerase II triad is coordinated by ubiquitin and SUMO in response to UV irradiation. Furthermore, our work provides a resource of SUMO targets regulated in response to UV or ionizing radiation.

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Regulation of Mitotic Homeologous Recombination in Yeast: Functions of Mismatch Repair and Nucleotide Excision Repair Genes

Genetics ◽

10.1093/genetics/154.1.133 ◽

2000 ◽

Vol 154 (1) ◽

pp. 133-146 ◽

Cited By ~ 1

Author(s):

Ainsley Nicholson ◽

Miyono Hendrix ◽

Sue Jinks-Robertson ◽

Gray F Crouse

Keyword(s):

Saccharomyces Cerevisiae ◽

Mismatch Repair ◽

Nucleotide Excision Repair ◽

Excision Repair ◽

Mitotic Recombination ◽

Inverted Repeats ◽

Replication Errors ◽

Nucleotide Excision ◽

Homeologous Recombination ◽

Repair Genes

Abstract The Saccharomyces cerevisiae homologs of the bacterial mismatch repair proteins MutS and MutL correct replication errors and prevent recombination between homeologous (nonidentical) sequences. Previously, we demonstrated that Msh2p, Msh3p, and Pms1p regulate recombination between 91% identical inverted repeats, and here use the same substrates to show that Mlh1p and Msh6p have important antirecombination roles. In addition, substrates containing defined types of mismatches (base-base mismatches; 1-, 4-, or 12-nt insertion/deletion loops; or 18-nt palindromes) were used to examine recognition of these mismatches in mitotic recombination intermediates. Msh2p was required for recognition of all types of mismatches, whereas Msh6p recognized only base-base mismatches and 1-nt insertion/deletion loops. Msh3p was involved in recognition of the palindrome and all loops, but also had an unexpected antirecombination role when the potential heteroduplex contained only base-base mismatches. In contrast to their similar antimutator roles, Pms1p consistently inhibited recombination to a lesser degree than did Msh2p. In addition to the yeast MutS and MutL homologs, the exonuclease Exo1p and the nucleotide excision repair proteins Rad1p and Rad10p were found to have roles in inhibiting recombination between mismatched substrates.

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Photolyases from Saccharomyces cerevisiae and Escherichia coli recognize common binding determinants in DNA containing pyrimidine dimers.

Molecular and Cellular Biology ◽

10.1128/mcb.9.11.4777 ◽

1989 ◽

Vol 9 (11) ◽

pp. 4777-4788 ◽

Cited By ~ 23

Author(s):

M Baer ◽

G B Sancar

Keyword(s):

Escherichia Coli ◽

Saccharomyces Cerevisiae ◽

Nucleotide Excision Repair ◽

Excision Repair ◽

Spectroscopic Studies ◽

Pyrimidine Dimer ◽

Nucleotide Sequence Analysis ◽

Binding Motif ◽

Pyrimidine Dimers ◽

Nucleotide Excision

DNA photolyases catalyze the light-dependent repair of pyrimidine dimers in DNA. The results of nucleotide sequence analysis and spectroscopic studies demonstrated that photolyases from Saccharomyces cerevisiae and Escherichia coli share 37% amino acid sequence homology and contain identical chromophores. Do the similarities between these two enzymes extend to their interactions with DNA containing pyrimidine dimers, or does the organization of DNA into nucleosomes in S. cerevisiae necessitate alternative or additional recognition determinants? To answer this question, we used chemical and enzymatic techniques to identify the contacts made on DNA by S. cerevisiae photolyase when it is bound to a pyrimidine dimer and compared these contacts with those made by E. coli photolyase and by a truncated derivative of the yeast enzyme when bound to the same substrate. We found evidence for a common set of interactions between the photolyases and specific phosphates in the backbones of both strands as well as for interactions with bases in both the major and minor grooves of dimer-containing DNA. Superimposed on this common pattern were significant differences in the contributions of specific contacts to the overall binding energy, in the interactions of the enzymes with groups on the complementary strand, and in the extent to which other DNA-binding proteins were excluded from the region around the dimer. These results provide strong evidence both for a conserved dimer-binding motif and for the evolution of new interactions that permit photolyases to also act as accessory proteins in nucleotide excision repair. The locations of the specific contacts made by the yeast enzyme indicate that the mechanism of nucleotide excision repair in this organism involves incision(s) at a distance from the pyrimidine dimer.

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Roles for Gcn5p and Ada2p in transcription and nucleotide excision repair at the Saccharomyces cerevisiae MET16 gene

Nucleic Acids Research ◽

10.1093/nar/gkj501 ◽

2006 ◽

Vol 34 (3) ◽

pp. 976-985 ◽

Cited By ~ 15

Author(s):

J. A. Ferreiro

Keyword(s):

Saccharomyces Cerevisiae ◽

Nucleotide Excision Repair ◽

Excision Repair ◽

Nucleotide Excision

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The NR4A2 Nuclear Receptor Is Recruited to Novel Nuclear Foci in Response to UV Irradiation and Participates in Nucleotide Excision Repair

PLoS ONE ◽

10.1371/journal.pone.0078075 ◽

2013 ◽

Vol 8 (11) ◽

pp. e78075 ◽

Cited By ~ 27

Author(s):

Kasturee Jagirdar ◽

Kelvin Yin ◽

Matthew Harrison ◽

Wen Lim ◽

George E. O. Muscat ◽

...

Keyword(s):

Nucleotide Excision Repair ◽

Nuclear Receptor ◽

Uv Irradiation ◽

Excision Repair ◽

Nucleotide Excision ◽

Nuclear Foci

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Growth Retardation, Early Death, and DNA Repair Defects in Mice Deficient for the Nucleotide Excision Repair Enzyme XPF

Molecular and Cellular Biology ◽

10.1128/mcb.24.3.1200-1205.2004 ◽

2004 ◽

Vol 24 (3) ◽

pp. 1200-1205 ◽

Cited By ~ 109

Author(s):

Ming Tian ◽

Reiko Shinkura ◽

Nobuhiko Shinkura ◽

Frederick W. Alt

Keyword(s):

Dna Repair ◽

Nucleotide Excision Repair ◽

Uv Irradiation ◽

Excision Repair ◽

Genetic Defect ◽

Growth Defect ◽

Human Genetic Disease ◽

Nucleotide Excision ◽

Deficient Mice

ABSTRACT Xeroderma pigmentosum (XP) is a human genetic disease which is caused by defects in nucleotide excision repair. Since this repair pathway is responsible for removing UV irradiation-induced damage to DNA, XP patients are hypersensitive to sunlight and are prone to develop skin cancer. Based on the underlying genetic defect, the disease can be divided into the seven complementation groups XPA through XPG. XPF, in association with ERCC1, constitutes a structure-specific endonuclease that makes an incision 5′ to the photodamage. XPF-ERCC1 has also been implicated in both removal of interstrand DNA cross-links and homology-mediated recombination and in immunoglobulin class switch recombination (CSR). To study the function of XPF in vivo, we inactivated the XPF gene in mice. XPF-deficient mice showed a severe postnatal growth defect and died approximately 3 weeks after birth. Histological examination revealed that the liver of mutant animals contained abnormal cells with enlarged nuclei. Furthermore, embryonic fibroblasts defective in XPF are hypersensitive to UV irradiation and mitomycin C treatment. No defect in CSR was detected, suggesting that the nuclease is dispensable for this recombination process. These phenotypes are identical to those exhibited by the ERCC1-deficient mice, consistent with the functional association of the two proteins. The complex phenotype suggests that XPF-ERCC1 is involved in multiple DNA repair processes.

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Nucleotide excision repair in the yeast Saccharomyces cerevisiae : its relationship to specialized mitotic recombination and RNA polymerase II basal transcription

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.1995.0010 ◽

1995 ◽

Vol 347 (1319) ◽

pp. 63-68 ◽

Cited By ~ 27

Keyword(s):

Saccharomyces Cerevisiae ◽

Rna Polymerase ◽

Rna Polymerase Ii ◽

Nucleotide Excision Repair ◽

Excision Repair ◽

Gene Products ◽

Basal Transcription ◽

Yeast Saccharomyces Cerevisiae ◽

Nucleotide Excision ◽

Yeast Genes

Nucleotide excision repair (ner) in eukaryotes is a biochemically complex process involving multiple gene products. The budding yeast Saccharomyces cerevisiae is an informative model for this process. Multiple genes and in some cases gene products that are indispensable for ner have been isolated from this organism. Homologues of many of these yeast genes are structurally and functionally conserved in higher organisms, including humans. The yeast Rad1/Rad10 heterodimeric protein complex is an endonuclease that is believed to participate in damage-specific incision of DNA during ner . This endonuclease is also required for specialized types of recombination. The products of the RAD3, SSL2(RAD25) SSL1 and TFB1 genes have dual roles in ner and in RNA polymerase II-dependent basal transcription.

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