1
|
Kuehner JN, Kaufman JW, Moore C. Stimulation of RNA Polymerase II ubiquitination and degradation by yeast mRNA 3'-end processing factors is a conserved DNA damage response in eukaryotes. DNA Repair (Amst) 2017; 57:151-160. [PMID: 28783563 DOI: 10.1016/j.dnarep.2017.07.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 06/18/2017] [Accepted: 07/17/2017] [Indexed: 02/09/2023]
Abstract
The quality and retrieval of genetic information is imperative to the survival and reproduction of all living cells. Ultraviolet (UV) light induces lesions that obstruct DNA access during transcription, replication, and repair. Failure to remove UV-induced lesions can abrogate gene expression and cell division, resulting in permanent DNA mutations. To defend against UV damage, cells utilize transcription-coupled nucleotide excision repair (TC-NER) to quickly target lesions within active genes. In cases of long-term genotoxic stress, a slower alternative pathway promotes degradation of RNA Polymerase II (Pol II) to allow for global genomic nucleotide excision repair (GG-NER). The crosstalk between TC-NER and GG-NER pathways and the extent of their coordination with other nuclear events has remained elusive. We aimed to identify functional links between the DNA damage response (DDR) and the mRNA 3'-end processing complex. Our labs have previously shown that UV-induced inhibition of mRNA processing is a conserved DDR between yeast and mammalian cells. Here we have identified mutations in the yeast mRNA 3'-end processing cleavage factor IA (CFIA) and cleavage and polyadenylation factor (CPF) that confer sensitivity to UV-type DNA damage. In the absence of TC-NER, CFIA and CPF mutants show reduced UV tolerance and an increased frequency of UV-induced genomic mutations, consistent with a role for RNA processing factors in an alternative DNA repair pathway. CFIA and CPF mutants impaired the ubiquitination and degradation of Pol II following DNA damage, but the co-transcriptional recruitment of Pol II degradation factors Elc1 and Def1 was undiminished. Overall these data are consistent with yeast 3'-end processing factors contributing to the removal of Pol II stalled at UV-type DNA lesions, a functional interaction that is conserved between homologous factors in yeast and human cells.
Collapse
Affiliation(s)
- Jason N Kuehner
- Department of Biology, Emmanuel College, Boston, MA 02115, United States.
| | - James W Kaufman
- Department of Biology, Emmanuel College, Boston, MA 02115, United States
| | - Claire Moore
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, United States
| |
Collapse
|
2
|
Pei N, Cao L, Liu Y, Wu J, Song Q, Zhang Z, Yuan J, Zhang X. XAB2 tagSNPs contribute to non-small cell lung cancer susceptibility in Chinese population. BMC Cancer 2015; 15:560. [PMID: 26228655 PMCID: PMC4520281 DOI: 10.1186/s12885-015-1567-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2014] [Accepted: 07/17/2015] [Indexed: 11/16/2022] Open
Abstract
Background XPA-binding protein 2 (XAB2) interacts with Cockayne syndrome complementation group A (CSA), group B (CSB) and RNA polymerase II to initiate nucleotide excision repair. This study aims to evaluate the association of XAB2 genetic variants with the risk of non-small cell lung cancer (NSCLC) using a tagging approach. Methods A hospital-based case-control study was conducted in 470 patients with NSCLC and 470 controls in Chinese population. Totally, 5 tag single nucleotide polymorphisms (SNPs) in XAB2 gene were selected by Haploview software using Hapmap database. Genotyping was performed using iPlex Gold Genotyping Asssy and Sequenom MassArray. Unconditional logistic regression was conducted to estimate odd ratios (ORs) and 95 % confidence intervals (95 % CI). Results Unconditional logistic regression analysis showed that the XAB2 genotype with rs794078 AA or at least one rs4134816 C allele were associated with the decreased risk of NSCLC with OR (95 % CI) of 0.12 (0.03–0.54) and 0.46 (0.26–0.84). When stratified by gender, we found that the subjects carrying rs4134816 CC or CT genotype had a decreased risk for developing NSCLC among males with OR (95 % CI) of 0.39 (0.18–0.82), but not among females. In age stratification analysis, we found that younger subjects (age ≤ 60) with at least one C allele had a decreased risk of NSCLC with OR (95 % CI) of 0.35 (0.17–0.74), but older subjects didn’t. We didn’t find that XAB2 4134816 C > T variant effect on the risk of NSCLC when stratified by smoking status. The environmental factors, such as age, sex and smoking had no effect on the risk of NSCLC related to XAB2 genotypes at other polymorphic sites. Conclusions The XAB2 tagSNPs (rs794078 and rs4134816) were significantly associated with the risk of NSCLC in Chinese population, which supports the XAB2 plays a significant role in the development of NSCLC.
Collapse
Affiliation(s)
- Na Pei
- Institute of Molecular Genetics, College of Life Sciences, Hebei United University, Tangshan, 063000, China. .,Department of Epidemiology, College of Public Health, Hebei United University, Tangshan, 063000, China.
| | - Lei Cao
- Institute of Molecular Genetics, College of Life Sciences, Hebei United University, Tangshan, 063000, China.
| | - Yingwen Liu
- Institute of Molecular Genetics, College of Life Sciences, Hebei United University, Tangshan, 063000, China. .,Department of Epidemiology, College of Public Health, Hebei United University, Tangshan, 063000, China.
| | - Jing Wu
- Institute of Molecular Genetics, College of Life Sciences, Hebei United University, Tangshan, 063000, China.
| | - Qinqin Song
- Tangshan Gongren Hospital, Hebei United University, Tangshan, China.
| | - Zhi Zhang
- Tangshan Gongren Hospital, Hebei United University, Tangshan, China.
| | - Juxiang Yuan
- Department of Epidemiology, College of Public Health, Hebei United University, Tangshan, 063000, China.
| | - Xuemei Zhang
- Institute of Molecular Genetics, College of Life Sciences, Hebei United University, Tangshan, 063000, China.
| |
Collapse
|
3
|
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.
Collapse
Affiliation(s)
- Shivani Malik
- a Department of Biochemistry and Molecular Biology ; Southern Illinois University School of Medicine ; Carbondale , IL USA
| | | |
Collapse
|
4
|
Karakasili E, Burkert-Kautzsch C, Kieser A, Sträßer K. Degradation of DNA damage-independently stalled RNA polymerase II is independent of the E3 ligase Elc1. Nucleic Acids Res 2014; 42:10503-15. [PMID: 25120264 PMCID: PMC4176355 DOI: 10.1093/nar/gku731] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 07/28/2014] [Accepted: 07/29/2014] [Indexed: 11/21/2022] Open
Abstract
Transcription elongation is a highly dynamic and discontinuous process, which includes frequent pausing of RNA polymerase II (RNAPII). RNAPII complexes that stall persistently on a gene during transcription elongation block transcription and thus have to be removed. It has been proposed that the cellular pathway for removal of these DNA damage-independently stalled RNAPII complexes is similar or identical to the removal of RNAPII complexes stalled due to DNA damage. Here, we show that-consistent with previous data-DNA damage-independent stalling causes polyubiquitylation and proteasome-mediated degradation of Rpb1, the largest subunit of RNAPII, using Saccharomyces cerevisiae as model system. Moreover, recruitment of the proteasome to RNAPII and transcribed genes is increased when transcription elongation is impaired indicating that Rpb1 degradation takes place at the gene. Importantly, in contrast to the DNA damage-dependent pathway Rpb1 degradation of DNA damage-independently stalled RNAPII is independent of the E3 ligase Elc1. In addition, deubiquitylation of RNAPII is also independent of the Elc1-antagonizing deubiquitylase Ubp3. Thus, the pathway for degradation of DNA damage-independently stalled RNAPII is overlapping yet distinct from the previously described pathway for degradation of RNAPII stalled due to DNA damage. Taken together, we provide the first evidence that the cell discriminates between DNA damage-dependently and -independently stalled RNAPII.
Collapse
Affiliation(s)
- Eleni Karakasili
- Gene Center and Munich Center for Integrated Protein Science CIPSM at the Department of Biochemistry of the Ludwig-Maximilians-University of Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Cornelia Burkert-Kautzsch
- Gene Center and Munich Center for Integrated Protein Science CIPSM at the Department of Biochemistry of the Ludwig-Maximilians-University of Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Anja Kieser
- Gene Center and Munich Center for Integrated Protein Science CIPSM at the Department of Biochemistry of the Ludwig-Maximilians-University of Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Katja Sträßer
- Gene Center and Munich Center for Integrated Protein Science CIPSM at the Department of Biochemistry of the Ludwig-Maximilians-University of Munich, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| |
Collapse
|
5
|
Nucleotide excision repair: why is it not used to predict response to platinum-based chemotherapy? Cancer Lett 2014; 346:163-71. [PMID: 24462818 DOI: 10.1016/j.canlet.2014.01.005] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/07/2014] [Accepted: 01/13/2014] [Indexed: 02/07/2023]
Abstract
Platinum based therapy is one of the most effectively used chemotherapeutic treatments for cancer. The mechanism of action of platinum compounds is to damage DNA and drive cells into apoptosis. The most commonly used platinum containing agents are cis-diammine-dichloroplatinum (II)], more commonly known as cisplatin, its analogue carboplatin, and oxaliplatin. Cisplatin is used to treat a wide variety of tumours such as ovarian, testicular, head and neck and non-small cell lung cancers (NSCLCs). In addition, it forms the basis of most combined treatment regimes. Despite this, cisplatin and its analogues are extremely toxic and although some patients benefit substantially from treatment, a large proportion suffer the toxic side effects without any therapeutic benefit. Nucleotide excision repair (NER) is a versatile DNA repair system that recognises DNA damage induced by platinum based therapy. For many years the components of the NER pathway have been studied to determine mRNA and protein expression levels in response or resistance to cisplatin in many forms of cancer; particularly testicular, ovarian and NSCLCs. Despite the consistent finding that over or under expression of subsets of NER proteins and mRNA highly correlate with response to cisplatin, the translation of these findings into the clinical setting has not been forthcoming. This review summarises the results of previous investigations into NER in cisplatin response and clinical trials where the expression of NER proteins were compared to the response to platinum therapies in treatment.
Collapse
|
6
|
Abstract
Many of the biochemical details of nucleotide excision repair (NER) have been established using purified proteins and DNA substrates. In cells however, DNA is tightly packaged around histones and other chromatin-associated proteins, which can be an obstacle to efficient repair. Several cooperating mechanisms enhance the efficiency of NER by altering chromatin structure. Interestingly, many of the players involved in modifying chromatin at sites of DNA damage were originally identified as regulators of transcription. These include ATP-dependent chromatin remodelers, histone modifying enzymes and several transcription factors. The p53 and E2F1 transcription factors are well known for their abilities to regulate gene expression in response to DNA damage. This review will highlight the underappreciated, transcription-independent functions of p53 and E2F1 in modifying chromatin structure in response to DNA damage to promote global NER.
Collapse
|
7
|
Siaud N, Dubois E, Massot S, Richaud A, Dray E, Collier J, Doutriaux MP. The SOS screen in Arabidopsis: a search for functions involved in DNA metabolism. DNA Repair (Amst) 2010; 9:567-78. [PMID: 20227352 DOI: 10.1016/j.dnarep.2010.02.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Revised: 02/08/2010] [Accepted: 02/10/2010] [Indexed: 11/19/2022]
Abstract
The SOS screen, as originally described by Perkins et al. (1999) [7], was setup with the aim of identifying Arabidopsis functions that might potentially be involved in the DNA metabolism. Such functions, when expressed in bacteria, are prone to disturb replication and thus trigger the SOS response. Consistently, expression of AtRAD51 and AtDMC1 induced the SOS response in bacteria, even affecting E. coli viability. 100 SOS-inducing cDNAs were isolated from a cDNA library constructed from an Arabidopsis cell suspension that was found to highly express meiotic genes. A large proportion of these SOS(+) candidates are clearly related to the DNA metabolism, others could be involved in the RNA metabolism, while the remaining cDNAs encode either totally unknown proteins or proteins that were considered as irrelevant. Seven SOS(+) candidate genes are induced following gamma irradiation. The in planta function of several of the SOS-inducing clones was investigated using T-DNA insertional mutants or RNA interference. Only one SOS(+) candidate, among those examined, exhibited a defined phenotype: silenced plants for DUT1 were sensitive to 5-fluoro-uracil (5FU), as is the case of the leaky dut-1 mutant in E. coli that are affected in dUTPase activity. dUTPase is essential to prevent uracil incorporation in the course of DNA replication.
Collapse
Affiliation(s)
- Nicolas Siaud
- Institut de Biologie des Plantes, CNRS UMR8618, Bâtiment 630, Université Paris Sud 11, 91405 Orsay Cedex, France.
| | | | | | | | | | | | | |
Collapse
|
8
|
Andressoo JO, Hoeijmakers JHJ, de Waard H. Nucleotide excision repair and its connection with cancer and ageing. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2008; 570:45-83. [PMID: 18727498 DOI: 10.1007/1-4020-3764-3_3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Jaan-Olle Andressoo
- MGC Department of Cell Biology and Genetics, Center for Biomedical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | | |
Collapse
|
9
|
Sordet O, Larochelle S, Nicolas E, Stevens EV, Zhang C, Shokat KM, Fisher RP, Pommier Y. Hyperphosphorylation of RNA polymerase II in response to topoisomerase I cleavage complexes and its association with transcription- and BRCA1-dependent degradation of topoisomerase I. J Mol Biol 2008; 381:540-9. [PMID: 18588899 DOI: 10.1016/j.jmb.2008.06.028] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 06/05/2008] [Accepted: 06/11/2008] [Indexed: 02/06/2023]
Abstract
The progression of RNA polymerase II can be blocked by lesions on the DNA template. In this study, we focused on the modifications of the largest subunit of RNA polymerase II, Rpb1, in response to stabilized topoisomerase I (Top1)-DNA cleavage complexes. In addition to DNA modifications (base damages and strand breaks), Top1 cleavage complexes can be trapped by camptothecin (CPT) and its derivatives used in cancer treatment. We found that, within a few minutes, CPT produces the complete hyperphosphorylation of Rpb1 in both primary and transformed cancer cells. Hyperphosphorylation is rapidly reversible following CPT removal. Hyperphosphorylation occurs selectively on the serine 5 residue of the conserved heptapeptide repeats in the Rpb1 carboxy-terminal domain and is mediated principally by the transcription factor IIH-associated cyclin-dependent kinase Cdk7. Hyperphosphorylated Rpb1 is not primarily targeted for proteosomal degradation and instead is subjected to cycles of phosphorylation and dephosphorylation as long as Top1 cleavage complexes are trapped by CPT. Finally, we show that transcription-induced degradation of Top1 is Brca1 dependent, suggesting a role for Brca1 in the repair or removal of transcription-blocking Top1-DNA cleavage complexes.
Collapse
Affiliation(s)
- Olivier Sordet
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892-4255, USA
| | | | | | | | | | | | | | | |
Collapse
|
10
|
Malik S, Bagla S, Chaurasia P, Duan Z, Bhaumik SR. Elongating RNA Polymerase II Is Disassembled through Specific Degradation of Its Largest but Not Other Subunits in Response to DNA Damage in Vivo. J Biol Chem 2008; 283:6897-905. [DOI: 10.1074/jbc.m707649200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
|
11
|
Mirkin N, Fonseca D, Mohammed S, Cevher MA, Manley JL, Kleiman FE. The 3' processing factor CstF functions in the DNA repair response. Nucleic Acids Res 2008; 36:1792-804. [PMID: 18252771 PMCID: PMC2330234 DOI: 10.1093/nar/gkn005] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Following DNA damage, mRNA levels decrease, reflecting a coordinated interaction of the DNA repair, transcription and RNA processing machineries. In this study, we provide evidence that transcription and polyadenylation of mRNA precursors are both affected in vivo by UV treatment. We next show that the polyadenylation factor CstF, plays a direct role in the DNA damage response. Cells with reduced levels of CstF display decreased viability following UV treatment, reduced ability to ubiquitinate RNA polymerase II (RNAP II), and defects in repair of DNA damage. Furthermore, we show that CstF, RNAP II and BARD1 are all found at sites of repaired DNA. Our results indicate that CstF plays an active role in the response to DNA damage, providing a link between transcription-coupled RNA processing and DNA repair.
Collapse
Affiliation(s)
- Nurit Mirkin
- Chemistry Department, Hunter College, City University of New York, New York, NY 10027, USA
| | | | | | | | | | | |
Collapse
|
12
|
Gill EE, Fast NM. Stripped-down DNA repair in a highly reduced parasite. BMC Mol Biol 2007; 8:24. [PMID: 17374165 PMCID: PMC1851970 DOI: 10.1186/1471-2199-8-24] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2007] [Accepted: 03/20/2007] [Indexed: 11/30/2022] Open
Abstract
Background Encephalitozoon cuniculi is a member of a distinctive group of single-celled parasitic eukaryotes called microsporidia, which are closely related to fungi. Some of these organisms, including E. cuniculi, also have uniquely small genomes that are within the prokaryotic range. Thus, E. cuniculi has undergone a massive genome reduction which has resulted in a loss of genes from diverse biological pathways, including those that act in DNA repair. DNA repair is essential to any living cell. A loss of these mechanisms invariably results in accumulation of mutations and/or cell death. Six major pathways of DNA repair in eukaryotes include: non-homologous end joining (NHEJ), homologous recombination repair (HRR), mismatch repair (MMR), nucleotide excision repair (NER), base excision repair (BER) and methyltransferase repair. DNA polymerases are also critical players in DNA repair processes. Given the close relationship between microsporidia and fungi, the repair mechanisms present in E. cuniculi were compared to those of the yeast Saccharomyces cerevisiae to ascertain how the process of genome reduction has affected the DNA repair pathways. Results E. cuniculi lacks 16 (plus another 6 potential absences) of the 56 DNA repair genes sought via BLASTP and PSI-BLAST searches. Six of 14 DNA polymerases or polymerase subunits are also absent in E. cuniculi. All of these genes are relatively well conserved within eukaryotes. The absence of genes is not distributed equally among the different repair pathways; some pathways lack only one protein, while there is a striking absence of many proteins that are components of both double strand break repair pathways. All specialized repair polymerases are also absent. Conclusion Given the large number of DNA repair genes that are absent from the double strand break repair pathways, E. cuniculi is a prime candidate for the study of double strand break repair with minimal machinery. Strikingly, all of the double strand break repair genes that have been retained by E. cuniculi participate in other biological pathways.
Collapse
Affiliation(s)
- Erin E Gill
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Naomi M Fast
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
13
|
Wu W, Nishikawa H, Hayami R, Sato K, Honda A, Aratani S, Nakajima T, Fukuda M, Ohta T. BRCA1 ubiquitinates RPB8 in response to DNA damage. Cancer Res 2007; 67:951-8. [PMID: 17283126 DOI: 10.1158/0008-5472.can-06-3187] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The breast and ovarian tumor suppressor BRCA1 catalyzes untraditional polyubiquitin chains that could be a signal for processes other than proteolysis. However, despite intense investigations, the mechanisms regulated by the enzyme activity remain only partially understood. Here, we report that BRCA1-BARD1 mediates polyubiquitination of RPB8, a common subunit of RNA polymerases, in response to DNA damage. A proteomics screen identified RPB8 as a protein modified after epirubicin treatment in BRCA1-dependent manner. RPB8 interacted with BRCA1-BARD1 and was polyubiquitinated by BRCA1-BARD1 in vivo and in vitro. BRCA1-BARD1 did not destabilize RPB8 in vivo but rather caused an increase in the amount of soluble RPB8. Importantly, RPB8 was polyubiquitinated immediately after UV irradiation in a manner sensitive to BRCA1 knockdown by RNA interference. Substitution of five lysine residues of RPB8 with arginine residues abolished its ability to be ubiquitinated while preserving its polymerase activity. HeLa cell lines stably expressing this ubiquitin-resistant form of RPB8 exhibited UV hypersensitivity accompanied by up-regulated caspase activity. Our findings suggest that ubiquitination of a common subunit of RNA polymerases is a mechanism underlying BRCA1-dependent cell survival after DNA damage.
Collapse
Affiliation(s)
- Wenwen Wu
- Division of Breast and Endocrine Surgery, Institute of Medical Science, St. Marianna University School of Medicine, Kawasaki 216-8511, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Dürr H, Flaus A, Owen-Hughes T, Hopfner KP. Snf2 family ATPases and DExx box helicases: differences and unifying concepts from high-resolution crystal structures. Nucleic Acids Res 2006; 34:4160-7. [PMID: 16935875 PMCID: PMC1616948 DOI: 10.1093/nar/gkl540] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Proteins with sequence similarity to the yeast Snf2 protein form a large family of ATPases that act to alter the structure of a diverse range of DNA–protein structures including chromatin. Snf2 family enzymes are related in sequence to DExx box helicases, yet they do not possess helicase activity. Recent biochemical and structural studies suggest that the mechanism by which these enzymes act involves ATP-dependent translocation on DNA. Crystal structures suggest that these enzymes travel along the minor groove, a process that can generate the torque or energy in remodelling processes. We review the recent structural and biochemical findings which suggest a common mechanistic basis underlies the action of many of both Snf2 family and DExx box helicases.
Collapse
Affiliation(s)
- Harald Dürr
- Gene Center, University of MunichFeodor-Lynen-Strasse 25, D-81377 Munich, Germany
- Department of Chemistry and Biochemistry, University of MunichFeodor-Lynen-Strasse 25, D-81377 Munich, Germany
| | - Andrew Flaus
- Division of Gene Regulation and Expression, School of Life Sciences, University of DundeeDundee DD1 5EH, UK
| | - Tom Owen-Hughes
- Division of Gene Regulation and Expression, School of Life Sciences, University of DundeeDundee DD1 5EH, UK
- To whom correspondence should be addressed. Tel: +49 89 218076953; Fax: +49 89 218076999;
| | - Karl-Peter Hopfner
- Gene Center, University of MunichFeodor-Lynen-Strasse 25, D-81377 Munich, Germany
- Department of Chemistry and Biochemistry, University of MunichFeodor-Lynen-Strasse 25, D-81377 Munich, Germany
- Correspondence may also be addressed to: Tom Owen-Hughes.Tel: +44 1382 385796; Fax: +44 1382 388072;
| |
Collapse
|
15
|
Andressoo JO, Mitchell JR, de Wit J, Hoogstraten D, Volker M, Toussaint W, Speksnijder E, Beems RB, van Steeg H, Jans J, de Zeeuw CI, Jaspers NGJ, Raams A, Lehmann AR, Vermeulen W, Hoeijmakers JHJ, van der Horst GTJ. An Xpd mouse model for the combined xeroderma pigmentosum/Cockayne syndrome exhibiting both cancer predisposition and segmental progeria. Cancer Cell 2006; 10:121-32. [PMID: 16904611 DOI: 10.1016/j.ccr.2006.05.027] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2005] [Revised: 04/05/2006] [Accepted: 05/17/2006] [Indexed: 10/24/2022]
Abstract
Inborn defects in nucleotide excision DNA repair (NER) can paradoxically result in elevated cancer incidence (xeroderma pigmentosum [XP]) or segmental progeria without cancer predisposition (Cockayne syndrome [CS] and trichothiodystrophy [TTD]). We report generation of a knockin mouse model for the combined disorder XPCS with a G602D-encoding mutation in the Xpd helicase gene. XPCS mice are the most skin cancer-prone NER model to date, and we postulate an unusual NER dysfunction that is likely responsible for this susceptibility. XPCS mice also displayed symptoms of segmental progeria, including cachexia and progressive loss of germinal epithelium. Like CS fibroblasts, XPCS and TTD fibroblasts from human and mouse showed evidence of defective repair of oxidative DNA lesions that may underlie these segmental progeroid symptoms.
Collapse
Affiliation(s)
- Jaan-Olle Andressoo
- Medical Genetics Center, Department of Cell Biology and Genetics, Center of Biomedical Genetics, Cancer Genomics Center, Erasmus Medical Center, Dr. Molewaterplein 50, 3015 GE, Rotterdam, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Abstract
Biochemical and structural progress over the last years has revealed that SWI2/SNF2 family chromatin remodeling or DNA repair enzymes are molecular motors that transport duplex DNA along a helicase-like domain using ATP-hydrolysis. The screw motion of DNA along the active site probably generates the force to disrupt chromatin or other protein:DNA complexes. In this chapter, we describe biochemical and structural approaches to study the molecular mechanism of SWI2/SNF2 enzymes. In particular, we describe assays to monitor DNA dependent ATPase activity, translocation on duplex DNA, and DNA distortion activity. We also describe recent progress in the crystallization and structure determination of SWI2/SNF2 enzymes in complex with duplex DNA.
Collapse
Affiliation(s)
- Harald Dürr
- Department of Chemistry and Biochemistry, Gene Center, Ludwig Maximilians University of Munich, Munich, Germany
| | | |
Collapse
|
17
|
Pommier Y, Barcelo J, Rao VA, Sordet O, Jobson AG, Thibaut L, Miao Z, Seiler J, Zhang H, Marchand C, Agama K, Redon C. Repair of topoisomerase I-mediated DNA damage. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 2006; 81:179-229. [PMID: 16891172 PMCID: PMC2576451 DOI: 10.1016/s0079-6603(06)81005-6] [Citation(s) in RCA: 226] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Topoisomerase I (Top1) is an abundant and essential enzyme. Top1 is the selective target of camptothecins, which are effective anticancer agents. Top1-DNA cleavage complexes can also be trapped by various endogenous and exogenous DNA lesions including mismatches, abasic sites and carcinogenic adducts. Tyrosyl-DNA phosphodiesterase (Tdp1) is one of the repair enzymes for Top1-DNA covalent complexes. Tdp1 forms a multiprotein complex that includes poly(ADP) ribose polymerase (PARP). PARP-deficient cells are hypersensitive to camptothecins and functionally deficient for Tdp1. We will review recent developments in several pathways involved in the repair of Top1 cleavage complexes and the role of Chk1 and Chk2 checkpoint kinases in the cellular responses to Top1 inhibitors. The genes conferring camptothecin hypersensitivity are compiled for humans, budding yeast and fission yeast.
Collapse
Affiliation(s)
- Yves Pommier
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Juana Barcelo
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - V. Ashutosh Rao
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Olivier Sordet
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Andrew G. Jobson
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Laurent Thibaut
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Zheyong Miao
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Jennifer Seiler
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Hongliang Zhang
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Christophe Marchand
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Keli Agama
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| | - Christophe Redon
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, DHHS
| |
Collapse
|
18
|
Dürr H, Körner C, Müller M, Hickmann V, Hopfner KP. X-ray structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase core and its complex with DNA. Cell 2005; 121:363-73. [PMID: 15882619 DOI: 10.1016/j.cell.2005.03.026] [Citation(s) in RCA: 214] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2004] [Revised: 02/28/2005] [Accepted: 03/17/2005] [Indexed: 11/22/2022]
Abstract
SWI2/SNF2 ATPases remodel chromatin or other DNA:protein complexes by a poorly understood mechanism that involves ATP-dependent DNA translocation and generation of superhelical torsion. Crystal structures of a dsDNA-translocating SWI2/SNF2 ATPase core from Sulfolobus solfataricus reveal two helical SWI2/SNF2 specific subdomains, fused to a DExx box helicase-related ATPase core. Fully base paired duplex DNA binds along a central cleft via both minor groove strands, indicating that SWI2/SNF2 ATPases travel along the dsDNA minor groove without strand separation. A structural switch, linking DNA binding and the active site DExx motif, may account for the stimulation of ATPase activity by dsDNA. Our results suggest that torque in remodeling processes is generated by an ATP-driven screw motion of DNA along the active site cleft. The structures also redefine SWI2/SNF2 functional motifs and uncover unexpected structural correlation of mutations in Cockayne and X-linked mental retardation syndromes.
Collapse
Affiliation(s)
- Harald Dürr
- Gene Center and Department of Chemistry and Biochemistry, University of Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | | | | | | | | |
Collapse
|
19
|
Kleiman FE, Wu-Baer F, Fonseca D, Kaneko S, Baer R, Manley JL. BRCA1/BARD1 inhibition of mRNA 3' processing involves targeted degradation of RNA polymerase II. Genes Dev 2005; 19:1227-37. [PMID: 15905410 PMCID: PMC1132008 DOI: 10.1101/gad.1309505] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Mammalian cells exhibit a complex response to DNA damage. The tumor suppressor BRCA1 and associated protein BARD1 are thought to play an important role in this response, and our previous work demonstrated that this includes transient inhibition of the pre-mRNA 3' processing machinery. Here we provide evidence that this inhibition involves proteasomal degradation of a component necessary for processing, RNA polymerase II (RNAP II). We further show that RNAP IIO, the elongating form of the enzyme, is a specific in vitro target of the BRCA1/BARD1 ubiquitin ligase activity. Significantly, siRNA-mediated knockdown of BRCA1 and BARD1 resulted in stabilization of RNAP II after DNA damage. In addition, inhibition of 3' cleavage induced by DNA damage was reverted in extracts of BRCA1-, BARD1-, or BRCA1/BARD1-depleted cells. We also describe corresponding changes in the nuclear localization and/or accumulation of these factors following DNA damage. Our results support a model in which a BRCA1/BARD1-containing complex functions to initiate degradation of stalled RNAP IIO, inhibiting the coupled transcription-RNA processing machinery and facilitating repair.
Collapse
Affiliation(s)
- Frida E Kleiman
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | | | | | | | | | | |
Collapse
|
20
|
Beerens N, Hoeijmakers JHJ, Kanaar R, Vermeulen W, Wyman C. The CSB protein actively wraps DNA. J Biol Chem 2004; 280:4722-9. [PMID: 15548521 DOI: 10.1074/jbc.m409147200] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The CSB protein is a member of the SWI2/SNF2 family of ATP-dependent chromatin remodeling factors and is essential for transcription-coupled DNA repair. The role of CSB in this DNA repair process is unclear, but the protein was found to remodel nucleosomes and alter DNA double helix conformation upon binding. Elucidating the nature of the change in DNA structure induced by CSB is of great interest for understanding the CSB mechanism of action. We analyzed the CSB.DNA complex by scanning force microscopy and measured a shortening of DNA contour length upon CSB binding in the presence of ATP. This DNA length reduction most likely results from DNA wrapping around the protein. Shorter DNA molecules were observed more frequently in the presence of non-hydrolyzable ATP analogues. These results suggest that DNA wrapping depends on ATP binding, whereas ATP hydrolysis results in unwrapping. We also provide evidence suggesting that CSB binds DNA as a dimer. DNA wrapping and unwrapping allows CSB to actively alter the DNA double helix conformation, which could influence nucleosomes and other protein-DNA interactions.
Collapse
Affiliation(s)
- Nancy Beerens
- Department of Cell Biology and Genetics and Radiation Oncology, Erasmus Medical Center, P. O. Box 1738, 3000 DR Rotterdam, The Netherlands
| | | | | | | | | |
Collapse
|
21
|
Koeppel F, Poindessous V, Lazar V, Raymond E, Sarasin A, Larsen AK. Irofulven cytotoxicity depends on transcription-coupled nucleotide excision repair and is correlated with XPG expression in solid tumor cells. Clin Cancer Res 2004; 10:5604-13. [PMID: 15328203 DOI: 10.1158/1078-0432.ccr-04-0442] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Irofulven is a novel alkylating agent with promising clinical activity, particularly toward ovarian and hormone-refractory prostate cancers. To facilitate additional clinical development, we have aimed to identify biological markers associated with sensitivity to the compound. METHODS Fibroblasts derived from patients with xeroderma pigmentosum or Cockayne's syndrome along with a panel of 20 human cancer cell lines (eight different tumor types) were examined to establish the importance of nucleotide excision repair proteins in the sensitivity to irofulven. RESULTS Human cells deficient in nucleotide excision repair are up to 30-fold more sensitive to the cytotoxic effects of irofulven compared with repair-proficient controls, clearly indicating that nucleotide excision repair plays a crucial role in the sensitivity to the drug. Interestingly, our results show that irofulven-induced lesions are recognized by transcription-coupled repair but not by global genome repair. Another unique feature is the pronounced sensitivity of XPD and XPB helicase-deficient cells to the drug. Comparison of the IC50 values for irofulven, cisplatin, and ecteinascidin 743 with the expression levels of ERCC1, XPD, and XPG genes in different solid tumor cell lines shows no correlation between the expression levels of any of the three nucleotide excision repair proteins and the sensitivity to ecteinascidin 743. In contrast, expression of the XPG endonuclease was correlated with the cytotoxicity for irofulven and, to a lesser degree, for cisplatin. Importantly, XPG expression was also correlated with cellular nucleotide excision repair activity. CONCLUSIONS Increasing evidence indicates that compromised nucleotide excision repair activity is frequent in several solid tumor types. The results presented here suggest that XPG expression in such tumors may be a useful marker to predict their sensitivity to irofulven.
Collapse
Affiliation(s)
- Florence Koeppel
- Group of Biology and Pharmacogenetics of Human Tumors, Centre National de la Recherche Scientifique, UMR 8113, Institut Gustave-Roussy, Villejuif, France
| | | | | | | | | | | |
Collapse
|
22
|
Salmon TB, Evert BA, Song B, Doetsch PW. Biological consequences of oxidative stress-induced DNA damage in Saccharomyces cerevisiae. Nucleic Acids Res 2004; 32:3712-23. [PMID: 15254273 PMCID: PMC484183 DOI: 10.1093/nar/gkh696] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Reactive oxygen species (ROS), generated by endogenous and exogenous sources, cause significant damage to macromolecules, including DNA. To determine the cellular effects of induced, oxidative DNA damage, we established a relationship between specific oxidative DNA damage levels and biological consequences produced by acute H2O2 exposures in yeast strains defective in one or two DNA damage-handling pathways. We observed that unrepaired, spontaneous DNA damage interferes with the normal cellular response to exogenous oxidative stress. In addition, when base excision repair (BER) is compromised, there is a preference for using recombination (REC) over translesion synthesis (TLS) for handling H2O2-induced DNA damage. The global genome transcriptional response of these strains to exogenous H2O2 exposure allowed for the identification of genes responding specifically to induced, oxidative DNA damage. We also found that the presence of DNA damage alone was sufficient to cause an increase in intracellular ROS levels. These results, linking DNA damage and intracellular ROS production, may provide insight into the role of DNA damage in tumor progression and aging. To our knowledge, this is the first report establishing a relationship between H2O2-induced biological endpoints and specific oxidative DNA damage levels present in the genome.
Collapse
Affiliation(s)
- Tiffany B Salmon
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | | | | |
Collapse
|
23
|
van den Boom V, Citterio E, Hoogstraten D, Zotter A, Egly JM, van Cappellen WA, Hoeijmakers JHJ, Houtsmuller AB, Vermeulen W. DNA damage stabilizes interaction of CSB with the transcription elongation machinery. ACTA ACUST UNITED AC 2004; 166:27-36. [PMID: 15226310 PMCID: PMC2172148 DOI: 10.1083/jcb.200401056] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Cockayne syndrome B (CSB) protein is essential for transcription-coupled DNA repair (TCR), which is dependent on RNA polymerase II elongation. TCR is required to quickly remove the cytotoxic transcription-blocking DNA lesions. Functional GFP-tagged CSB, expressed at physiological levels, was homogeneously dispersed throughout the nucleoplasm in addition to bright nuclear foci and nucleolar accumulation. Photobleaching studies showed that GFP-CSB, as part of a high molecular weight complex, transiently interacts with the transcription machinery. Upon (DNA damage-induced) transcription arrest CSB binding these interactions are prolonged, most likely reflecting actual engagement of CSB in TCR. These findings are consistent with a model in which CSB monitors progression of transcription by regularly probing elongation complexes and becomes more tightly associated to these complexes when TCR is active.
Collapse
Affiliation(s)
- Vincent van den Boom
- Department of Cell Biology and Genetics, Erasmus MC, P.O. Box 1738, 3000 DR Rotterdam, Netherlands
| | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Briggs GS, Mahdi AA, Weller GR, Wen Q, Lloyd RG. Interplay between DNA replication, recombination and repair based on the structure of RecG helicase. Philos Trans R Soc Lond B Biol Sci 2004; 359:49-59. [PMID: 15065656 PMCID: PMC1693295 DOI: 10.1098/rstb.2003.1364] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Recent studies in Escherichia coli indicate that the interconversion of DNA replication fork and Holliday junction structures underpins chromosome duplication and helps secure faithful transmission of the genome from one generation to the next. It facilitates interplay between DNA replication, recombination and repair, and provides means to rescue replication forks stalled by lesions in or on the template DNA. Insight into how this interconversion may be catalysed has emerged from genetic, biochemical and structural studies of RecG protein, a member of superfamily 2 of DNA and RNA helicases. We describe how a single molecule of RecG might target a branched DNA structure and translocate a single duplex arm to drive branch migration of a Holliday junction, interconvert replication fork and Holliday junction structures and displace the invading strand from a D loop formed during recombination at a DNA end. We present genetic evidence suggesting how the latter activity may provide an efficient pathway for the repair of DNA double-strand breaks that avoids crossing over, thus facilitating chromosome segregation at cell division.
Collapse
Affiliation(s)
- Geoffrey S Briggs
- Institute of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | | | | | | | | |
Collapse
|
25
|
Taylor MS, Ponting CP, Copley RR. Occurrence and consequences of coding sequence insertions and deletions in Mammalian genomes. Genome Res 2004; 14:555-66. [PMID: 15059996 PMCID: PMC383299 DOI: 10.1101/gr.1977804] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2003] [Accepted: 11/17/2003] [Indexed: 11/24/2022]
Abstract
Nucleotide insertion and deletion (indel) events, together with substitutions, represent the major mutational processes of gene evolution. Through the alignment of 8148 orthologous genes from human, mouse, and rat, we have identified 1743 indel events within rodent protein-coding sequences. Using human as an out-group, we reconstructed the mutational event underlying each of these indels. Overall, we found an excess of deletions over insertions, particularly for the rat lineage (70% excess). Sequence slippage accounts for at least 52% of insertions and 38% of deletions. We have also evaluated the selective tolerance of identifiable protein structures to indels. Transmembrane domains are the least, and low complexity regions, the most tolerant. Mapping of indels onto known protein structures demonstrated that structural cores are markedly less tolerant to indels than are loop regions. There is a specific enrichment of CpG dinucleotides in close proximity to insertion events, and both insertions and deletions are more common in higher G+C content sequences.
Collapse
Affiliation(s)
- Martin S Taylor
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.
| | | | | |
Collapse
|
26
|
Tremeau-Bravard A, Riedl T, Egly JM, Dahmus ME. Fate of RNA polymerase II stalled at a cisplatin lesion. J Biol Chem 2003; 279:7751-9. [PMID: 14672951 DOI: 10.1074/jbc.m309853200] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Elongating RNA polymerase II blocked by DNA damage in the transcribed DNA strand is thought to initiate the transcription-coupled repair process. The objective of this study is to better understand the sequence of events that occurs during repair from the time RNA polymerase II first encounters the lesion. This study establishes that an immobilized DNA template containing a unique cisplatin lesion can serve as an in vitro substrate for both transcription and DNA repair. RNA polymerase II is quantitatively stalled at the cisplatin lesion during transcription and can be released from the template, along with the nascent transcript, in an ATP-dependent manner. RNA polymerase II stalled at a lesion and containing a dephosphorylated repetitive carboxyl-terminal domain (CTD) appears to be more sensitive toward release. However, a dephosphorylated CTD can become readily phosphorylated in front of the lesion by CTD kinases in the presence of ATP. The observation that RNA polymerase II and transcript release occurs in a TFIIH-deficient repair extract but not in a reconstituted repair system demonstrates that disassembly of the elongation complex can occur independently of the repair process and vice versa. Indeed, the presence of RNA polymerase II at the lesion does not prevent dual incision from occurring. Finally, we also propose that the Cockayne's syndrome B protein factor, believed to be the mammalian transcription repair coupling factor, is neither involved in transcript release nor required for dual incision in the presence of lesionstalled RNA polymerase II in vitro. More likely, it prevents RNA polymerase from backing up when it encounters the lesion. The ability to transcribe and repair the same damaged DNA molecule fixed on beads, along with the fact that the reaction conditions can be freely altered, provides a powerful tool to study the fate of RNA polymerase II blocked on the cisplatin lesion.
Collapse
|
27
|
Jung Y, Lippard SJ. Multiple states of stalled T7 RNA polymerase at DNA lesions generated by platinum anticancer agents. J Biol Chem 2003; 278:52084-92. [PMID: 14534300 DOI: 10.1074/jbc.m310120200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Transcription inhibition by DNA adducts of cisplatin is considered to be one of the major routes by which this anticancer drug kills cancer cells. Stalled RNA polymerases at platinum-DNA lesions evoke various cellular responses such as nucleotide excision repair, polymerase degradation, and apoptosis. T7 RNA polymerase and site-specifically platinated DNA templates immobilized on a solid support were used to study stalled transcription elongation complexes. In vitro transcription studies were performed in both a promoter-dependent and -independent manner. An elongation complex is strongly blocked by cisplatin 1,2-intrastrand d(GpG) and 1,3-intrastrand d(GpTpG) cross-links located on the template strand. Polymerase action is inhibited at multiple sites in the vicinity of the platinum lesion, the nature of which can be altered by the choice and concentration of NTPs. The [(1R,2R-diaminocyclohexane)Pt]2+ DNA adducts formed by oxaliplatin, which carries a stereochemically more demanding spectator ligand than the ammine groups in cisplatin, also strongly block the polymerase with measurable differences compared with cis-[(NH3)2Pt]2+ lesions. Elongation complexes stopped at sites of platinum damage were isolated and characterized. The stalled polymerase can be dissociated from the DNA by subsequent polymerases initiated from the same template. We also discovered that a polymerase stalled at the platinum-DNA lesion can resume transcription after the platinum adduct is chemically removed from the template.
Collapse
Affiliation(s)
- Yongwon Jung
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
| | | |
Collapse
|
28
|
Mitchell JR, Hoeijmakers JHJ, Niedernhofer LJ. Divide and conquer: nucleotide excision repair battles cancer and ageing. Curr Opin Cell Biol 2003; 15:232-40. [PMID: 12648680 DOI: 10.1016/s0955-0674(03)00018-8] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Protection from cancer and ensured longevity are tightly linked in mammals. One of the fundamental mechanisms contributing to both is the cellular response to DNA damage. The appropriate response is an initial attempt at repair, but if the damage is too extensive or compromises DNA metabolism, a signalling cascade triggers cellular senescence or death. Evidence in mice and humans suggests a division of tasks amongst DNA repair pathways: transcription-coupled repair and interstrand crosslink repair of cytotoxic lesions are predominantly responsible for longevity assurance, whereas excision repair of mutagenic lesions provides protection against cancer. Similarly, the signalling component of the DNA-damage response might contribute unequally to organismal outcomes depending on its set point: an inadequate response to DNA damage sanctions carcinogenesis but might limit local ageing, whereas overzealous signalling provides cancer protection but accelerates ageing.
Collapse
Affiliation(s)
- James R Mitchell
- Department of Cell Biology and Genetics, Erasmus University Rotterdam, PO Box 1738, 3000 DR, Rotterdam, The Netherlands
| | | | | |
Collapse
|
29
|
Moore T, McGlynn P, Ngo HP, Sharples GJ, Lloyd RG. The RdgC protein of Escherichia coli binds DNA and counters a toxic effect of RecFOR in strains lacking the replication restart protein PriA. EMBO J 2003; 22:735-45. [PMID: 12554673 PMCID: PMC140733 DOI: 10.1093/emboj/cdg048] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
PriA protein provides a means to load the DnaB replicative helicase at DNA replication fork and D loop structures, and is therefore a key factor in the rescue of stalled or broken forks and subsequent replication restart. We show that the nucleoid-associated RdgC protein binds non-specifically to single-stranded (ss) DNA and double-stranded DNA. It is also essential for growth of a strain lacking PriA, indicating that it might affect replication fork progression or fork rescue. dnaC suppressors of priA overcome this inviability, especially when RecF, RecO or RecR is inactivated, indicating that RdgC avoids or counters a toxic effect of these proteins. Mutations modifying ssDNA-binding (SSB) protein also negate this toxic effect, suggesting that the toxicity reflects inappropriate loading of RecA on SSB-coated ssDNA, leading to excessive or untimely RecA activity. We suggest that binding of RdgC to DNA limits RecA loading, avoiding problems at replication forks that would otherwise require PriA to promote replication restart. Mutations in RNA polymerase also reduce the toxic effect of RecFOR, providing a further link between DNA replication, transcription and repair.
Collapse
Affiliation(s)
| | | | | | - Gary J. Sharples
- Institute of Genetics, University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK
Present address: Centre for Infectious Diseases, University of Durham, Wolfson Research Institute, Queen’s Campus, Stockton-on-Tees TS17 6BH, UK Corresponding author e-mail:
| | - Robert G. Lloyd
- Institute of Genetics, University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK
Present address: Centre for Infectious Diseases, University of Durham, Wolfson Research Institute, Queen’s Campus, Stockton-on-Tees TS17 6BH, UK Corresponding author e-mail:
| |
Collapse
|
30
|
Trautinger BW, Lloyd RG. Modulation of DNA repair by mutations flanking the DNA channel through RNA polymerase. EMBO J 2002; 21:6944-53. [PMID: 12486015 PMCID: PMC139083 DOI: 10.1093/emboj/cdf654] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The RuvABC and RecBCD proteins promote rescue of stalled or broken DNA replication forks in Escherichia coli. Strains lacking these proteins cope poorly with DNA damage and have problems with chromosome segregation and cell division. We show how these difficulties are overcome to varying degrees by a sub-class of RNA polymerase mutations selected for their stringent phenotype. Thirty-five mutations were sequenced. All but one change single amino acids in RpoB or RpoC that lie on or near the path taken by DNA through the enzyme, indicating they may affect the stability of transcription complexes. Four mutant enzymes are shown to form unstable open complexes at the lambdacro promoter. At least one may also release stalled complexes or limit their formation, as it reduces the need for reactivation of transcription by GreA or GreB, and for transcription-coupled DNA repair of UV damage by Mfd. The results shed light on the interplay between DNA replication and transcription and suggest ways in which conflicts between these two vital cellular processes are avoided or resolved.
Collapse
Affiliation(s)
| | - Robert G. Lloyd
- Institute of Genetics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2UH, UK
Corresponding author e-mail:
| |
Collapse
|