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Derevensky M, Fasullo M. DNA damaging agents trigger the expression of the HML silent mating type locus in Saccharomyces cerevisiae. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2018; 835:16-20. [PMID: 30249477 DOI: 10.1016/j.mrgentox.2018.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 08/22/2018] [Accepted: 08/22/2018] [Indexed: 12/11/2022]
Abstract
Many DNA damaging agents also react with RNA and protein, and could thus cause epigenetic as well as genotoxic changes. To investigate which DNA damaging agents alter epigenetic states, we studied the chemical-induced changes in expression of the yeast silent mating type locus HMLα, which can be triggered by inhibiting yeast Sir2. We observed that the alkylating agent methyl methane sulfonate (MMS) can result in HMLα expression, using a colony sector assay that results from expression of a HML-positioned cre gene. Using single-cell imaging we also observed that alkylating agents, including MMS and methyl-3-nitro-1-nitrosoguanidine (MNNG), as well as short-wave UV, also decreased HML silencing. We suggest that chemical-induced alterations in heterochromatin structure could confer transient phenotypic changes that affect the cellular responses to DNA damaging agents.
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Affiliation(s)
- Michael Derevensky
- College of Nanoscale Sciences and Engineering, SUNY Polytechnic Institute, 257 Fuller Road, Albany, NY 12205, United States
| | - Michael Fasullo
- College of Nanoscale Sciences and Engineering, SUNY Polytechnic Institute, 257 Fuller Road, Albany, NY 12205, United States.
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2
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Spasskaya DS, Karpov DS, Mironov AS, Karpov VL. Transcription factor Rpn4 promotes a complex antistress response in Saccharomyces cerevisiae cells exposed to methyl methanesulfonate. Mol Biol 2014. [DOI: 10.1134/s0026893314010130] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Srivas R, Costelloe T, Carvunis AR, Sarkar S, Malta E, Sun SM, Pool M, Licon K, van Welsem T, van Leeuwen F, McHugh PJ, van Attikum H, Ideker T. A UV-induced genetic network links the RSC complex to nucleotide excision repair and shows dose-dependent rewiring. Cell Rep 2013; 5:1714-24. [PMID: 24360959 DOI: 10.1016/j.celrep.2013.11.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2013] [Revised: 10/05/2013] [Accepted: 11/20/2013] [Indexed: 12/24/2022] Open
Abstract
Efficient repair of UV-induced DNA damage requires the precise coordination of nucleotide excision repair (NER) with numerous other biological processes. To map this crosstalk, we generated a differential genetic interaction map centered on quantitative growth measurements of >45,000 double mutants before and after different doses of UV radiation. Integration of genetic data with physical interaction networks identified a global map of 89 UV-induced functional interactions among 62 protein complexes, including a number of links between the RSC complex and several NER factors. We show that RSC is recruited to both silenced and transcribed loci following UV damage where it facilitates efficient repair by promoting nucleosome remodeling. Finally, a comparison of the response to high versus low levels of UV shows that the degree of genetic rewiring correlates with dose of UV and reveals a network of dose-specific interactions. This study makes available a large resource of UV-induced interactions, and it illustrates a methodology for identifying dose-dependent interactions based on quantitative shifts in genetic networks.
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Affiliation(s)
- Rohith Srivas
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Thomas Costelloe
- Department of Toxicogenetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | | | - Sovan Sarkar
- Department of Oncology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Erik Malta
- Department of Toxicogenetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Su Ming Sun
- Department of Toxicogenetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Marijke Pool
- Department of Toxicogenetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Katherine Licon
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Tibor van Welsem
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands
| | - Peter J McHugh
- Department of Oncology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK
| | - Haico van Attikum
- Department of Toxicogenetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands.
| | - Trey Ideker
- Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92037, USA.
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Mazumder A, Pesudo LQ, McRee S, Bathe M, Samson LD. Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S. cerevisiae. Nucleic Acids Res 2013; 41:9310-24. [PMID: 23935119 PMCID: PMC3814357 DOI: 10.1093/nar/gkt715] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
An effective response to DNA damaging agents involves modulating numerous facets of cellular homeostasis in addition to DNA repair and cell-cycle checkpoint pathways. Fluorescence microscopy-based imaging offers the opportunity to simultaneously interrogate changes in both protein level and subcellular localization in response to DNA damaging agents at the single-cell level. We report here results from screening the yeast Green Fluorescent Protein (GFP)-fusion library to investigate global cellular protein reorganization on exposure to the alkylating agent methyl methanesulfonate (MMS). Broad groups of induced, repressed, nucleus- and cytoplasm-enriched proteins were identified. Gene Ontology and interactome analyses revealed the underlying cellular processes. Transcription factor (TF) analysis identified principal regulators of the response, and targets of all major stress-responsive TFs were enriched amongst the induced proteins. An unexpected partitioning of biological function according to the number of TFs targeting individual genes was revealed. Finally, differential modulation of ribosomal proteins depending on methyl methanesulfonate dose was shown to correlate with cell growth and with the translocation of the Sfp1 TF. We conclude that cellular responses can navigate different routes according to the extent of damage, relying on both expression and localization changes of specific proteins.
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Affiliation(s)
- Aprotim Mazumder
- Department of Biological Engineering, Center for Environmental Health Sciences, Laboratory for Computational Biology and Biophysics, Department of Biology and The David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Golla U, Singh V, Azad GK, Singh P, Verma N, Mandal P, Chauhan S, Tomar RS. Sen1p contributes to genomic integrity by regulating expression of ribonucleotide reductase 1 (RNR1) in Saccharomyces cerevisiae. PLoS One 2013; 8:e64798. [PMID: 23741394 PMCID: PMC3669351 DOI: 10.1371/journal.pone.0064798] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 04/18/2013] [Indexed: 12/29/2022] Open
Abstract
Gene expression is a multi-step process which requires recruitment of several factors to promoters. One of the factors, Sen1p is an RNA/DNA helicase implicated in transcriptional termination and RNA processing in yeast. In the present study, we have identified a novel function of Sen1p that regulates the expression of ribonucleotide reductase RNR1 gene, which is essential for maintaining genomic integrity. Cells with mutation in the helicase domain or lacking N-terminal domain of Sen1p displayed a drastic decrease in the basal level transcription of RNR1 gene and showed enhanced sensitivity to various DNA damaging agents. Moreover, SEN1 mutants [Sen1-1 (G1747D), Sen1-2 (Δ1-975)] exhibited defects in DNA damage checkpoint activation. Surprisingly, CRT1 deletion in Sen1p mutants (Sen1-1, Sen1-2) was partly able to rescue the slow growth phenotype upon genotoxic stress. Altogether, our observations suggest that Sen1p is required for cell protection against DNA damage by regulating the expression of DNA repair gene RNR1. Thus, the misregulation of Sen1p regulated genes can cause genomic instability that may lead to neurological disorders and premature aging.
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Affiliation(s)
- Upendarrao Golla
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Vikash Singh
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Gajendra Kumar Azad
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Prabhat Singh
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Naveen Verma
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Papita Mandal
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Sakshi Chauhan
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
| | - Raghuvir S. Tomar
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
- * E-mail:
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Azad GK, Singh V, Golla U, Tomar RS. Depletion of cellular iron by curcumin leads to alteration in histone acetylation and degradation of Sml1p in Saccharomyces cerevisiae. PLoS One 2013; 8:e59003. [PMID: 23520547 PMCID: PMC3592818 DOI: 10.1371/journal.pone.0059003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 02/08/2013] [Indexed: 12/26/2022] Open
Abstract
Curcumin, a naturally occurring polyphenolic compound, is known to possess diverse pharmacological properties. There is a scarcity of literature documenting the exact mechanism by which curcumin modulates its biological effects. In the present study, we have used yeast as a model organism to dissect the mechanism underlying the action of curcumin. We found that the yeast mutants of histone proteins and chromatin modifying enzymes were sensitive to curcumin and further supplementation of iron resulted in reversal of the changes induced by curcumin. Additionally, treatment of curcumin caused the iron starvation induced expression of FET3, FRE1 genes. We also demonstrated that curcumin induces degradation of Sml1p, a ribonucleotide reductase inhibitor involved in regulating dNTPs production. The degradation of Sml1p was mediated through proteasome and vacuole dependent protein degradation pathways. Furthermore, curcumin exerts biological effect by altering global proteome profile without affecting chromatin architecture. These findings suggest that the medicinal properties of curcumin are largely contributed by its cumulative effect of iron starvation and epigenetic modifications.
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Affiliation(s)
- Gajendra Kumar Azad
- Laboratory of Chromatin Biology, Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, India
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Kouranti I, Peyroche A. Protein degradation in DNA damage response. Semin Cell Dev Biol 2012; 23:538-45. [PMID: 22353182 DOI: 10.1016/j.semcdb.2012.02.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Revised: 01/31/2012] [Accepted: 02/07/2012] [Indexed: 12/17/2022]
Abstract
DNA damage is a major threat to genome integrity. To reduce its deleterious effects, cells have developed coordinated responses, collectively referred to as the "DNA damage response" pathway (DDR). In multicellular organisms, the DDR pathway has a critical role in preventing tumorigenesis, which accounts for the wide use of drugs targeting DDR factors in anti-cancer therapy. Post-translational modifications such as phosphorylation, ubiquitylation, acetylation, sumoylation are integral part of the DDR pathway. Ubiquitylation of DDR-related factors has recently emerged both as a switch initiating signaling cascades and as a proteolytic signal coordinating recruitment and disassembly of those proteins. In this review we will present evidence supporting an increasingly important role for the ubiquitin-proteasome-mediated degradation in regulating DDR at different levels.
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Dyavaiah M, Rooney JP, Chittur SV, Lin Q, Begley TJ. Autophagy-dependent regulation of the DNA damage response protein ribonucleotide reductase 1. Mol Cancer Res 2011; 9:462-75. [PMID: 21343333 DOI: 10.1158/1541-7786.mcr-10-0473] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Protein synthesis and degradation are posttranscriptional pathways used by cells to regulate protein levels. We have developed a systems biology approach to identify targets of posttranscriptional regulation and we have employed this system in Saccharomyces cerevisiae to study the DNA damage response. We present evidence that 50% to 75% of the transcripts induced by alkylation damage are regulated posttranscriptionally. Significantly, we demonstrate that two transcriptionally-induced DNA damage response genes, RNR1 and RNR4, fail to show soluble protein level increases after DNA damage. To determine one of the associated mechanisms of posttranscriptional regulation, we tracked ribonucleotide reductase 1 (Rnr1) protein levels during the DNA damage response. We show that RNR1 is actively translated after damage and that a large fraction of the corresponding Rnr1 protein is packaged into a membrane-bound structure and transported to the vacuole for degradation, with these last two steps dependent on autophagy proteins. We found that inhibition of target of rapamycin (TOR) signaling and subsequent induction of autophagy promoted an increase in targeting of Rnr1 to the vacuole and a decrease in soluble Rnr1 protein levels. In addition, we demonstrate that defects in autophagy result in an increase in soluble Rnr1 protein levels and a DNA damage phenotype. Our results highlight roles for autophagy and TOR signaling in regulating a specific protein and demonstrate the importance of these pathways in optimizing the DNA damage response.
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Affiliation(s)
- Madhu Dyavaiah
- Department of Biomedical Sciences, University at Albany, State University of New York, Rensselaer, New York 12144, USA
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Ravi D, Wiles AM, Bhavani S, Ruan J, Leder P, Bishop AJR. A network of conserved damage survival pathways revealed by a genomic RNAi screen. PLoS Genet 2009; 5:e1000527. [PMID: 19543366 PMCID: PMC2688755 DOI: 10.1371/journal.pgen.1000527] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2009] [Accepted: 05/19/2009] [Indexed: 11/18/2022] Open
Abstract
Damage initiates a pleiotropic cellular response aimed at cellular survival when appropriate. To identify genes required for damage survival, we used a cell-based RNAi screen against the Drosophila genome and the alkylating agent methyl methanesulphonate (MMS). Similar studies performed in other model organisms report that damage response may involve pleiotropic cellular processes other than the central DNA repair components, yet an intuitive systems level view of the cellular components required for damage survival, their interrelationship, and contextual importance has been lacking. Further, by comparing data from different model organisms, identification of conserved and presumably core survival components should be forthcoming. We identified 307 genes, representing 13 signaling, metabolic, or enzymatic pathways, affecting cellular survival of MMS-induced damage. As expected, the majority of these pathways are involved in DNA repair; however, several pathways with more diverse biological functions were also identified, including the TOR pathway, transcription, translation, proteasome, glutathione synthesis, ATP synthesis, and Notch signaling, and these were equally important in damage survival. Comparison with genomic screen data from Saccharomyces cerevisiae revealed no overlap enrichment of individual genes between the species, but a conservation of the pathways. To demonstrate the functional conservation of pathways, five were tested in Drosophila and mouse cells, with each pathway responding to alkylation damage in both species. Using the protein interactome, a significant level of connectivity was observed between Drosophila MMS survival proteins, suggesting a higher order relationship. This connectivity was dramatically improved by incorporating the components of the 13 identified pathways within the network. Grouping proteins into "pathway nodes" qualitatively improved the interactome organization, revealing a highly organized "MMS survival network." We conclude that identification of pathways can facilitate comparative biology analysis when direct gene/orthologue comparisons fail. A biologically intuitive, highly interconnected MMS survival network was revealed after we incorporated pathway data in our interactome analysis.
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Affiliation(s)
- Dashnamoorthy Ravi
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Amy M. Wiles
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Selvaraj Bhavani
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Jianhua Ruan
- Department of Computer Science, University of Texas at San Antonio, San Antonio, Texas, United States of America
| | - Philip Leder
- Harvard Medical School, Department of Genetics, Harvard University, Boston, Massachusetts, United States of America
| | - Alexander J. R. Bishop
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
- Harvard Medical School, Department of Genetics, Harvard University, Boston, Massachusetts, United States of America
- * E-mail:
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10
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Vlachostergios PJ, Patrikidou A, Daliani DD, Papandreou CN. The ubiquitin-proteasome system in cancer, a major player in DNA repair. Part 2: transcriptional regulation. J Cell Mol Med 2009; 13:3019-31. [PMID: 19522844 PMCID: PMC4516462 DOI: 10.1111/j.1582-4934.2009.00825.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA repair is an indispensable part of a cell’s defence system against the devastating effects of DNA-damaging conditions. The regulation of this function is a really demanding situation, particularly when the stressing factors persist for a long time. In such cases, the depletion of existing DNA repair proteins has to be compensated by the induction of the analogous gene products. In addition, the arrest of transcription, which is another result of many DNA-damaging agents, needs to be overcome through regulation of transcription-specific DNA repair pathways. The involvement of the ubiquitin-proteasome system (UPS) in cancer- and chemotherapy-related DNA-damage repair relevant to the above transcriptional modification mechanisms are illustrated in this review. Furthermore, the contribution of UPS to the regulation of localization and accessibility of DNA repair proteins to chromatin, in response to cellular stress is discussed.
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Putnam CD, Jaehnig EJ, Kolodner RD. Perspectives on the DNA damage and replication checkpoint responses in Saccharomyces cerevisiae. DNA Repair (Amst) 2009; 8:974-82. [PMID: 19477695 DOI: 10.1016/j.dnarep.2009.04.021] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The DNA damage and replication checkpoints are believed to primarily slow the progression of the cell cycle to allow DNA repair to occur. Here we summarize known aspects of the Saccharomyces cerevisiae checkpoints including how these responses are integrated into downstream effects on the cell cycle, chromatin, DNA repair, and cytoplasmic targets. Analysis of the transcriptional response demonstrates that it is far more complex and less relevant to the repair of DNA damage than the bacterial SOS response. We also address more speculative questions regarding potential roles of the checkpoint during the normal S-phase and how current evidence hints at a checkpoint activation mechanism mediated by positive feedback that amplifies initial damage signals above a minimum threshold.
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Affiliation(s)
- Christopher D Putnam
- Ludwig Institute for Cancer Research, Department of Medicine and Cancer Center, University of California School of Medicine, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0669, United States.
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Dantuma NP, Heinen C, Hoogstraten D. The ubiquitin receptor Rad23: at the crossroads of nucleotide excision repair and proteasomal degradation. DNA Repair (Amst) 2009; 8:449-60. [PMID: 19223247 DOI: 10.1016/j.dnarep.2009.01.005] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A protein that exemplifies the intimate link between the ubiquitin/proteasome system (UPS) and DNA repair is the yeast nucleotide excision repair (NER) protein Rad23 and its human orthologs hHR23A and hHR23B. Rad23, which was originally identified as an important factor involved in the recognition of DNA lesions, also plays a central role in targeting ubiquitylated proteins for proteasomal degradation, an activity that it shares with other ubiquitin receptors like Dsk2 and Ddi1. Although the finding that Rad23 serves as a ubiquitin receptor explains to a large extent its importance in proteasomal degradation, the precise mode of action of Rad23 in NER and the possible link with the UPS is less clear. In this review, we discuss our present knowledge on the functions of Rad23 in protein degradation and DNA repair and speculate on the importance of the dual roles of Rad23 for the cell's ability to cope with stress conditions.
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Affiliation(s)
- Nico P Dantuma
- Department of Cell and Molecular Biology, The Medical Nobel Institute, Karolinska Institutet, Von Eulers väg 3, S-17177 Stockholm, Sweden.
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Rooney JP, George AD, Patil A, Begley U, Bessette E, Zappala MR, Huang X, Conklin DA, Cunningham RP, Begley TJ. Systems based mapping demonstrates that recovery from alkylation damage requires DNA repair, RNA processing, and translation associated networks. Genomics 2009; 93:42-51. [PMID: 18824089 PMCID: PMC2633870 DOI: 10.1016/j.ygeno.2008.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Revised: 08/29/2008] [Accepted: 09/03/2008] [Indexed: 12/31/2022]
Abstract
The identification of cellular responses to damage can promote mechanistic insight into stress signalling. We have screened a library of 3968 Escherichia coli gene-deletion mutants to identify 99 gene products that modulate the toxicity of the alkylating agent methyl methanesulfonate (MMS). We have developed an ontology mapping approach to identify functional categories over-represented with MMS-toxicity modulating proteins and demonstrate that, in addition to DNA re-synthesis (replication, recombination, and repair), proteins involved in mRNA processing and translation influence viability after MMS damage. We have also mapped our MMS-toxicity modulating proteins onto an E. coli protein interactome and identified a sub-network consisting of 32 proteins functioning in DNA repair, mRNA processing, and translation. Clustering coefficient analysis identified seven highly connected MMS-toxicity modulating proteins associated with translation and mRNA processing, with the high connectivity suggestive of a coordinated response. Corresponding results from reporter assays support the idea that the SOS response is influenced by activities associated with the mRNA-translation interface.
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Affiliation(s)
- John P. Rooney
- Department of Biomedical Sciences, University at Albany, State University of New York, Rensselaer NY 12144-3456
- Gen*NY*Sis Center for Excellence in Cancer Genomics, University at Albany, State University of New York, Rensselaer NY 12144-3456
| | - Ajish D. George
- Department of Biomedical Sciences, University at Albany, State University of New York, Rensselaer NY 12144-3456
- Gen*NY*Sis Center for Excellence in Cancer Genomics, University at Albany, State University of New York, Rensselaer NY 12144-3456
| | - Ashish Patil
- Department of Biomedical Sciences, University at Albany, State University of New York, Rensselaer NY 12144-3456
- Gen*NY*Sis Center for Excellence in Cancer Genomics, University at Albany, State University of New York, Rensselaer NY 12144-3456
| | - Ulrike Begley
- Department of Biomedical Sciences, University at Albany, State University of New York, Rensselaer NY 12144-3456
- Gen*NY*Sis Center for Excellence in Cancer Genomics, University at Albany, State University of New York, Rensselaer NY 12144-3456
| | - Erin Bessette
- Department of Biomedical Sciences, University at Albany, State University of New York, Rensselaer NY 12144-3456
- Gen*NY*Sis Center for Excellence in Cancer Genomics, University at Albany, State University of New York, Rensselaer NY 12144-3456
| | - Maria R. Zappala
- Gen*NY*Sis Center for Excellence in Cancer Genomics, University at Albany, State University of New York, Rensselaer NY 12144-3456
- Department of Biological Sciences, University at Albany, State University of New York, Albany NY 12222
| | - Xin Huang
- Gen*NY*Sis Center for Excellence in Cancer Genomics, University at Albany, State University of New York, Rensselaer NY 12144-3456
- Department of Biological Sciences, University at Albany, State University of New York, Albany NY 12222
| | - Douglas A. Conklin
- Department of Biomedical Sciences, University at Albany, State University of New York, Rensselaer NY 12144-3456
- Gen*NY*Sis Center for Excellence in Cancer Genomics, University at Albany, State University of New York, Rensselaer NY 12144-3456
| | - Richard P. Cunningham
- Gen*NY*Sis Center for Excellence in Cancer Genomics, University at Albany, State University of New York, Rensselaer NY 12144-3456
- Department of Biological Sciences, University at Albany, State University of New York, Albany NY 12222
| | - Thomas J. Begley
- Department of Biomedical Sciences, University at Albany, State University of New York, Rensselaer NY 12144-3456
- Gen*NY*Sis Center for Excellence in Cancer Genomics, University at Albany, State University of New York, Rensselaer NY 12144-3456
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