Genomes and Genes
Experts and Doctors on dna repair in Durham, North Carolina, United States
Locale: Durham, North Carolina, United States
Topic: dna repair
- Leung M, Goldstone J, Boyd W, Freedman J, Meyer J. Caenorhabditis elegans generates biologically relevant levels of genotoxic metabolites from aflatoxin B1 but not benzo[a]pyrene in vivo. Toxicol Sci. 2010;118:444-53 pubmed publisher..Our results highlight the importance of considering differences between xenobiotic metabolism in C. elegans and mammals when using this alternative model in pharmaceutical and toxicological research. ..
- Van Houten B, Hunter S, Meyer J. Mitochondrial DNA damage induced autophagy, cell death, and disease. Front Biosci (Landmark Ed). 2016;21:42-54 pubmed..This review examines the cellular effects of persistent damage to mitochondrial genomes and discusses the very different cell fates that occur in response to different kinds of damage. ..
- Argueso J, Westmoreland J, Mieczkowski P, Gawel M, Petes T, Resnick M. Double-strand breaks associated with repetitive DNA can reshape the genome. Proc Natl Acad Sci U S A. 2008;105:11845-50 pubmed publisher..Because repeat-associated DSBs can efficiently lead to CAs and reshape the genome, they could be a rich source of evolutionary change...
- Chen A, Davies C, De Lin M, Fermor B. Oxidative DNA damage in osteoarthritic porcine articular cartilage. J Cell Physiol. 2008;217:828-33 pubmed publisher..Additionally, DNA damage induced by NO and ONOO(-) in non-OA chondrocytes does not undergo full endogenous repair. ..
- Worth L, Clark S, Radman M, Modrich P. Mismatch repair proteins MutS and MutL inhibit RecA-catalyzed strand transfer between diverged DNAs. Proc Natl Acad Sci U S A. 1994;91:3238-41 pubmed..Analysis of strand-transfer intermediates that accumulate in the presence of MutS and MutL indicates that the proteins block branch migration, presumably in response to occurrence of mispairs within newly formed heteroduplex. ..
- Iyer R, Pluciennik A, Genschel J, Tsai M, Beese L, Modrich P. MutLalpha and proliferating cell nuclear antigen share binding sites on MutSbeta. J Biol Chem. 2010;285:11730-9 pubmed publisher..These findings also indicate that MutSbeta- and MutSalpha-initiated repair events differ in fundamental ways. ..
- Mitchel K, Lehner K, Jinks Robertson S. Heteroduplex DNA position defines the roles of the Sgs1, Srs2, and Mph1 helicases in promoting distinct recombination outcomes. PLoS Genet. 2013;9:e1003340 pubmed publisher..The hDNA data are consistent with the proposed role of Sgs1 in the dissolution of double HJs, and we propose that Srs2 dismantles nicked HJs. ..
- Constantin N, Dzantiev L, Kadyrov F, Modrich P. Human mismatch repair: reconstitution of a nick-directed bidirectional reaction. J Biol Chem. 2005;280:39752-61 pubmed..Although this modest inhibition could be because of nonspecific effects, it may indicate limited dependence of bidirectional excision on an aphidicolin-sensitive DNA polymerase. ..
- York S, Modrich P. Mismatch repair-dependent iterative excision at irreparable O6-methylguanine lesions in human nuclear extracts. J Biol Chem. 2006;281:22674-83 pubmed..These results provide the first direct evidence for mismatch repair-mediated iterative processing of DNA methylator damage, an effect that may be relevant to damage signaling events triggered by this class of chemotherapeutic agent. ..
- Plank J, Wu J, Hsieh T. Topoisomerase IIIalpha and Bloom's helicase can resolve a mobile double Holliday junction substrate through convergent branch migration. Proc Natl Acad Sci U S A. 2006;103:11118-23 pubmed..This mechanism stands in contrast to classic resolvase activities that use a structure-specific endonuclease to cleave the HJs. ..
- Webb M, Plank J, Long D, Hsieh T, Kreuzer K. The phage T4 protein UvsW drives Holliday junction branch migration. J Biol Chem. 2007;282:34401-11 pubmed..Taken together, these results strongly support a role for UvsW in the branch migration of Holliday junctions that form during T4 recombination, replication, and repair...
- Culligan K, Britt A. Both ATM and ATR promote the efficient and accurate processing of programmed meiotic double-strand breaks. Plant J. 2008;55:629-38 pubmed publisher..They also indicate that ATM and ATR act redundantly to inhibit sustained interactions between non-homologous chromatids, and that these ectopic interactions require SPO11 activity. ..
- Yan S, Wang W, Marques J, Mohan R, Saleh A, Durrant W, et al. Salicylic acid activates DNA damage responses to potentiate plant immunity. Mol Cell. 2013;52:602-10 pubmed publisher..Our study suggests that activation of DNA damage responses is an intrinsic component of the plant immune responses. ..
- Genschel J, Modrich P. Functions of MutLalpha, replication protein A (RPA), and HMGB1 in 5'-directed mismatch repair. J Biol Chem. 2009;284:21536-44 pubmed publisher..Assay of extracts derived from HMGB1(+/+) and HMGB1(-/-) mouse embryo fibroblast cells indicates that HMGB1 is not essential for mismatch repair. ..
- Feng J, Wakeman T, Yong S, Wu X, Kornbluth S, Wang X. Protein phosphatase 2A-dependent dephosphorylation of replication protein A is required for the repair of DNA breaks induced by replication stress. Mol Cell Biol. 2009;29:5696-709 pubmed publisher..These data indicate that PP2A-mediated RPA32 dephosphorylation is required for the efficient DNA damage repair. ..
- Guo X, Hum Y, Lehner K, Jinks Robertson S. Regulation of hetDNA Length during Mitotic Double-Strand Break Repair in Yeast. Mol Cell. 2017;67:539-549.e4 pubmed publisher..Data are most consistent with the extent of DNA synthesis from the invading end being the primary determinant of hetDNA length during SDSA. ..
- Gawel D, Seed P. Urinary tract infection drives genome instability in uropathogenic Escherichia coli and necessitates translesion synthesis DNA polymerase IV for virulence. Virulence. 2011;2:222-32 pubmed
- Longley M, Pierce A, Modrich P. DNA polymerase delta is required for human mismatch repair in vitro. J Biol Chem. 1997;272:10917-21 pubmed..However, due to the presence of DNA polymerases alpha and epsilon in the depleted extract, potential involvement of one or both of these activities in the reaction cannot be excluded. ..
- Bjornson K, Modrich P. Differential and simultaneous adenosine di- and triphosphate binding by MutS. J Biol Chem. 2003;278:18557-62 pubmed..These findings suggest that the protein exists primarily as the ATP.MutS.ADP ternary complex in solution and that this may be the form of the protein that is involved in DNA encounters in vivo. ..
- Anderson D, Trujillo K, Sung P, Erickson H. Structure of the Rad50 x Mre11 DNA repair complex from Saccharomyces cerevisiae by electron microscopy. J Biol Chem. 2001;276:37027-33 pubmed..We also demonstrate that Mre11 binds as a dimer between the catalytic domains of Rad50, bringing the nuclease activities of Mre11 in close proximity to the ATPase and DNA binding activities of Rad50. ..
- Kreuzer K. DNA damage responses in prokaryotes: regulating gene expression, modulating growth patterns, and manipulating replication forks. Cold Spring Harb Perspect Biol. 2013;5:a012674 pubmed publisher..Finally, some recent advances that relate to the replication and repair of damaged DNA will be summarized. ..
- Grilley M, Griffith J, Modrich P. Bidirectional excision in methyl-directed mismatch repair. J Biol Chem. 1993;268:11830-7 pubmed..The extent of excision is therefore controlled by one or more components of the repair system. ..
- Yamaguchi M, Dao V, Modrich P. MutS and MutL activate DNA helicase II in a mismatch-dependent manner. J Biol Chem. 1998;273:9197-201 pubmed..Although DNA helicase II and Rep helicase share substantial sequence homology and features of mechanism, Rep helicase is inactive in this reaction. ..
- Genschel J, Modrich P. Mechanism of 5'-directed excision in human mismatch repair. Mol Cell. 2003;12:1077-86 pubmed..As observed in the purified system, excision directed by a 5' strand break in HeLa nuclear extract can proceed in the absence of MutLalpha or PCNA, although 3' excision in the extract system requires both proteins. ..
- Drummond J, Li G, Longley M, Modrich P. Isolation of an hMSH2-p160 heterodimer that restores DNA mismatch repair to tumor cells. Science. 1995;268:1909-12 pubmed
- Sharma N, Lebedeva M, Thomas T, Kovalenko O, Stumpf J, Shadel G, et al. Intrinsic mitochondrial DNA repair defects in Ataxia Telangiectasia. DNA Repair (Amst). 2014;13:22-31 pubmed publisher..A-T is thus the first disease characterized by diminished Lig3. ..
- Henriksson S, Rassoolzadeh H, HedstrÃ¶m E, Coucoravas C, Julner A, Goldstein M, et al. The scaffold protein WRAP53Î² orchestrates the ubiquitin response critical for DNA double-strand break repair. Genes Dev. 2014;28:2726-38 pubmed publisher..Our findings establish WRAP53Î² as a novel regulator of DSB repair by providing a scaffold for DNA repair factors. ..
- Scarbrough P, Weber R, Iversen E, Brhane Y, Amos C, Kraft P, et al. A Cross-Cancer Genetic Association Analysis of the DNA Repair and DNA Damage Signaling Pathways for Lung, Ovary, Prostate, Breast, and Colorectal Cancer. Cancer Epidemiol Biomarkers Prev. 2016;25:193-200 pubmed publisher..Results suggest that many common variants in DNA repair genes are likely associated with cancer susceptibility through small effect sizes that do not meet stringent significance testing criteria. ..
- Kadyrov F, Dzantiev L, Constantin N, Modrich P. Endonucleolytic function of MutLalpha in human mismatch repair. Cell. 2006;126:297-308 pubmed..Therefore, the mode of excision initiation may differ in these organisms. ..
- Martik D, Baitinger C, Modrich P. Differential specificities and simultaneous occupancy of human MutSalpha nucleotide binding sites. J Biol Chem. 2004;279:28402-10 pubmed..These findings imply that MutSalpha has two nucleotide binding sites with differential specificities for ADP and ATP and suggest that the ADP.MutSalpha.ATP ternary complex has an important role in mismatch repair. ..
- Lee P, Greenwell P, Dominska M, Gawel M, Hamilton M, Petes T. A fine-structure map of spontaneous mitotic crossovers in the yeast Saccharomyces cerevisiae. PLoS Genet. 2009;5:e1000410 pubmed publisher..In addition, about 40% of the conversion events have patterns of marker segregation that are most simply explained as reflecting the repair of a chromosome that was broken in G1 of the cell cycle...
- Lahue R, Au K, Modrich P. DNA mismatch correction in a defined system. Science. 1989;245:160-4 pubmed..This set of proteins can process seven of the eight base-base mismatches in a strand-specific reaction that is directed by the state of methylation of a single d(GATC) sequence located 1 kilobase from the mispair. ..
- da Silva M, Wilds C, Noronha A, Colvin O, Miller P, Gamcsik M. Accommodation of mispair aligned N3T-ethyl-N3T DNA interstrand cross link. Biochemistry. 2004;43:12549-54 pubmed..Thus, this synthetic DNA is a valuable structural probe to study mechanisms of repair. ..
- Au K, Clark S, Miller J, Modrich P. Escherichia coli mutY gene encodes an adenine glycosylase active on G-A mispairs. Proc Natl Acad Sci U S A. 1989;86:8877-81 pubmed..MutY, a 5'-apurinic/apyrimidinic-site endonuclease, DNA polymerase I, and DNA ligase are sufficient to reconstitute MutY-dependent G-A to G.C repair in vitro. ..
- Zhang J, Bao S, Furumai R, Kucera K, Ali A, Dean N, et al. Protein phosphatase 5 is required for ATR-mediated checkpoint activation. Mol Cell Biol. 2005;25:9910-9 pubmed..Taken together, our results suggest that PP5 plays a critical role in the ATR-mediated checkpoint activation. ..
- Bjornson K, Allen D, Modrich P. Modulation of MutS ATP hydrolysis by DNA cofactors. Biochemistry. 2000;39:3176-83 pubmed..These results, together with kinetic findings, indicate nonequivalence of subunits within a MutS oligomer with respect to ATP hydrolysis and DNA binding. ..
- Aklilu B, Soderquist R, Culligan K. Genetic analysis of the Replication Protein A large subunit family in Arabidopsis reveals unique and overlapping roles in DNA repair, meiosis and DNA replication. Nucleic Acids Res. 2014;42:3104-18 pubmed publisher..We show these defects in the rpa1b rpa1d mutant are likely the result of defective DNA replication leading to reduction in cell division. ..
- Bartz R, Suliman H, Fu P, Welty Wolf K, Carraway M, Macgarvey N, et al. Staphylococcus aureus sepsis and mitochondrial accrual of the 8-oxoguanine DNA glycosylase DNA repair enzyme in mice. Am J Respir Crit Care Med. 2011;183:226-33 pubmed publisher..These studies identify OGG1 as an early mitochondrial response protein during sepsis under regulation by the NRF-1 and NRF-2? transcription factors that regulate mitochondrial biogenesis. ..
- Wakeman T, Wang Q, Feng J, Wang X. Bat3 facilitates H3K79 dimethylation by DOT1L and promotes DNA damage-induced 53BP1 foci at G1/G2 cell-cycle phases. EMBO J. 2012;31:2169-81 pubmed publisher..Taken together, our findings identify a novel role for Bat3 in regulating DOT1L function, which plays a critical role in DNA damage response. ..
- Dzantiev L, Constantin N, Genschel J, Iyer R, Burgers P, Modrich P. A defined human system that supports bidirectional mismatch-provoked excision. Mol Cell. 2004;15:31-41 pubmed..By contrast, RFC and PCNA have only a limited effect on 5' to 3' excision directed by a 5' strand break. ..
- Cooper D, Lahue R, Modrich P. Methyl-directed mismatch repair is bidirectional. J Biol Chem. 1993;268:11823-9 pubmed..To our knowledge, these experiments represent the first instance in which exonuclease I, exonuclease VII, and RecJ have been implicated in a particular DNA metabolic pathway. ..
- Kim N, Jinks Robertson S. Abasic sites in the transcribed strand of yeast DNA are removed by transcription-coupled nucleotide excision repair. Mol Cell Biol. 2010;30:3206-15 pubmed publisher..Such transcription-coupled NER of AP sites may explain previously suggested links between the BER pathway and transcription. ..
- COLON RAMOS D, Shenvi C, Weitzel D, Gan E, Matts R, Cate J, et al. Direct ribosomal binding by a cellular inhibitor of translation. Nat Struct Mol Biol. 2006;13:103-11 pubmed..This function of Reaper may modulate gene expression programs to affect cell fate. ..
- Genschel J, Bazemore L, Modrich P. Human exonuclease I is required for 5' and 3' mismatch repair. J Biol Chem. 2002;277:13302-11 pubmed..The involvement of hEXOI in 3'-heteroduplex repair suggests that it has a regulatory/structural role in assembly of the 3'-excision complex or that the protein possesses a cryptic 3' to 5' hydrolytic activity. ..
- Au K, Welsh K, Modrich P. Initiation of methyl-directed mismatch repair. J Biol Chem. 1992;267:12142-8 pubmed
- St Charles J, Petes T. High-resolution mapping of spontaneous mitotic recombination hotspots on the 1.1 Mb arm of yeast chromosome IV. PLoS Genet. 2013;9:e1003434 pubmed publisher..We also show that different genetic elements are associated with reciprocal crossover conversion tracts depending on the cell cycle timing of the initiating DSB. ..
- Kozmin S, Jinks Robertson S. The mechanism of nucleotide excision repair-mediated UV-induced mutagenesis in nonproliferating cells. Genetics. 2013;193:803-17 pubmed publisher..The requirement for specific DNA-damage checkpoint proteins suggests roles in recruiting and/or activating factors required to fill such gaps. ..
- Hunter S, Gustafson M, Margillo K, Lee S, Ryde I, Meyer J. In vivo repair of alkylating and oxidative DNA damage in the mitochondrial and nuclear genomes of wild-type and glycosylase-deficient Caenorhabditis elegans. DNA Repair (Amst). 2012;11:857-63 pubmed publisher..We also failed to detect increased lethality or growth inhibition in nth-1 nematodes after exposure to oxidative or alkylating damage, suggesting the existence of at least one additional as-yet undetected glycosylase...
- Carles Kinch K, George J, Kreuzer K. Bacteriophage T4 UvsW protein is a helicase involved in recombination, repair and the regulation of DNA replication origins. EMBO J. 1997;16:4142-51 pubmed..In support of this model, a partially purified GST/UvsW fusion protein, but not a GST/UvsW-K141R fusion, displays ssDNA-dependent ATPase activity and is able to unwind a branched DNA substrate. ..
- Kim N, Jinks Robertson S. Transcription as a source of genome instability. Nat Rev Genet. 2012;13:204-14 pubmed publisher..Here we review the diverse ways in which the essential process of transcription alters the underlying DNA template and thereby modifies the genetic landscape. ..
- Dao V, Modrich P. Mismatch-, MutS-, MutL-, and helicase II-dependent unwinding from the single-strand break of an incised heteroduplex. J Biol Chem. 1998;273:9202-7 pubmed..MutS and MutL are thus sufficient to coordinate mismatch recognition to the orientation-dependent activation of helicase II unwinding at a single-strand break located a kilobase from the mispair. ..
- Capp C, Wu J, Hsieh T. RecQ4: the second replicative helicase?. Crit Rev Biochem Mol Biol. 2010;45:233-42 pubmed publisher..Thus, it is clear that two helicases, RecQ4 and Mcm2-7, are integral to replication. The nature of the simultaneous involvement of these two helicases remains to be determined, and possible models will be proposed. ..
- Heitman J, Ivanenko T, Kiss A. DNA nicks inflicted by restriction endonucleases are repaired by a RecA- and RecB-dependent pathway in Escherichia coli. Mol Microbiol. 1999;33:1141-51 pubmed..These observations suggest that an increased number of DNA nicks can overwhelm the repair capacity of DNA ligase, resulting in the conversion of a proportion of DNA nicks into DNA lesions that require recombination for repair. ..
- Blackwell L, Bjornson K, Allen D, Modrich P. Distinct MutS DNA-binding modes that are differentially modulated by ATP binding and hydrolysis. J Biol Chem. 2001;276:34339-47 pubmed..Conversely, the highest mismatch specificity is observed in the absence of nucleotide or in the presence of ADP. ADP has only a limited effect on heteroduplex affinity but reduces MutS affinity for homoduplex DNA. ..
- Fang Y, Tsao C, Goodman B, Furumai R, Tirado C, Abraham R, et al. ATR functions as a gene dosage-dependent tumor suppressor on a mismatch repair-deficient background. EMBO J. 2004;23:3164-74 pubmed..These results demonstrate that MMR proteins and ATR functionally interact during the cellular response to genotoxic stress, and that ATR serves as a haploinsufficient tumor suppressor in MMR-deficient cells. ..
- Song J, Durrant W, Wang S, Yan S, Tan E, Dong X. DNA repair proteins are directly involved in regulation of gene expression during plant immune response. Cell Host Microbe. 2011;9:115-24 pubmed publisher..Given that the SSN2-RAD51D complex is conserved in eukaryotes, their dual function in homologous recombination and transcription regulation of plant-defense genes suggests a general link between these two stress responses. ..
- Burdett V, Baitinger C, Viswanathan M, Lovett S, Modrich P. In vivo requirement for RecJ, ExoVII, ExoI, and ExoX in methyl-directed mismatch repair. Proc Natl Acad Sci U S A. 2001;98:6765-70 pubmed
- O Reilly E, Kreuzer K. Isolation of SOS constitutive mutants of Escherichia coli. J Bacteriol. 2004;186:7149-60 pubmed..This study also provides a quantitative comparison of the extent of SOS expression caused by inactivation of many different genes in a common genetic background. ..