201
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Jin T, Wang Y, Li G, Du S, Yang H, Geng T, Hou P, Gong Y. Analysis of difference of association between polymorphisms in the XRCC5, RPA3 and RTEL1 genes and glioma, astrocytoma and glioblastoma. Am J Cancer Res 2015; 5:2294-300. [PMID: 26328260 PMCID: PMC4548341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 06/10/2015] [Indexed: 06/04/2023] Open
Abstract
BACKGROUND Gliomas are the most common aggressive brain tumors and have many complex pathological types. Previous reports have discovered that genetic mutations are associated with the risk of glioma. However, it is unclear whether uniform genetic mutations exist difference between glioma and its two pathological types in the Han Chinese population. MATERIALS AND METHODS We evaluated 20 SNPs of 703 glioma cases (338 astrocytoma cases, 122 glioblastoma cases) and 635 controls in a Han Chinese population using χ(2) test and genetic model analysis. RESULTS In three case-control studies, we found rs9288516 in XRCC5 gene showed a decreased risk of glioma (OR, 0.85; 95% CI, 0.73-0.99; P = 0.042) and glioblastoma (OR, 0.70; 95% CI, 0.52-0.92; P = 0.001) in the allele model. We identified rs414805 in RPA3 gene showed an increased risk of glioblastoma in allele model (OR, 1.38; 95% CI, 1.00-1.89; P = 0.047) and dominant model (OR, 1.57; 95% CI, 1.05-2.35; P = 0.027), analysis respectively. Meanwhile, rs2297440 in RTEL1 gene showed an increased risk of glioma (OR, 1.30; 95% CI, 1.10-1.54; P = 0.002) and astrocytoma (OR, 1.26; 95% CI, 1.02-1.54; P = 0.029) in the allele model. In addition, we also observed a haplotype of "GCT" in the RTEL1 gene with an increased risk of astrocytoma (P = 0.005). CONCLUSIONS Polymorphisms in the XRCC5, RPA3 and RTEL1 genes, combinating with previous reaserches, are associated with glioma developing. However, those genes mutations may play different roles in the glioma, astrocytoma and glioblastoma, respectively.
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Affiliation(s)
- Tianbo Jin
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest UniversityXi’an 710069, China
- National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest UniversityXi’an 710069, China
| | - Yuan Wang
- Department of Trauma, The Second Affiliated Hospital, Inner Mongolia Medical UniversityHohhot 010030, China
| | - Gang Li
- Department of Neurosurgery, Tangdu Hospital, The Fourth Military Medical UniversityXi’an 710038, China
| | - Shuli Du
- National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest UniversityXi’an 710069, China
| | - Hua Yang
- National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest UniversityXi’an 710069, China
| | - Tingting Geng
- National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest UniversityXi’an 710069, China
| | - Peng Hou
- Department of Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong University School of MedicineXi’an 710061, China
| | - Yongkuan Gong
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Northwest UniversityXi’an 710069, China
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202
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Xu G, Chapman JR, Brandsma I, Yuan J, Mistrik M, Bouwman P, Bartkova J, Gogola E, Warmerdam D, Barazas M, Jaspers JE, Watanabe K, Pieterse M, Kersbergen A, Sol W, Celie PHN, Schouten PC, van den Broek B, Salman A, Nieuwland M, de Rink I, de Ronde J, Jalink K, Boulton SJ, Chen J, van Gent DC, Bartek J, Jonkers J, Borst P, Rottenberg S. REV7 counteracts DNA double-strand break resection and affects PARP inhibition. Nature 2015; 521:541-544. [PMID: 25799992 PMCID: PMC4671316 DOI: 10.1038/nature14328] [Citation(s) in RCA: 435] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 02/13/2015] [Indexed: 01/01/2023]
Abstract
Error-free repair of DNA double-strand breaks (DSBs) is achieved by homologous recombination (HR), and BRCA1 is an important factor for this repair pathway. In the absence of BRCA1-mediated HR, the administration of PARP inhibitors induces synthetic lethality of tumour cells of patients with breast or ovarian cancers. Despite the benefit of this tailored therapy, drug resistance can occur by HR restoration. Genetic reversion of BRCA1-inactivating mutations can be the underlying mechanism of drug resistance, but this does not explain resistance in all cases. In particular, little is known about BRCA1-independent restoration of HR. Here we show that loss of REV7 (also known as MAD2L2) in mouse and human cell lines re-establishes CTIP-dependent end resection of DSBs in BRCA1-deficient cells, leading to HR restoration and PARP inhibitor resistance, which is reversed by ATM kinase inhibition. REV7 is recruited to DSBs in a manner dependent on the H2AX-MDC1-RNF8-RNF168-53BP1 chromatin pathway, and seems to block HR and promote end joining in addition to its regulatory role in DNA damage tolerance. Finally, we establish that REV7 blocks DSB resection to promote non-homologous end-joining during immunoglobulin class switch recombination. Our results reveal an unexpected crucial function of REV7 downstream of 53BP1 in coordinating pathological DSB repair pathway choices in BRCA1-deficient cells.
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Affiliation(s)
- Guotai Xu
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - J Ross Chapman
- The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, United Kingdom
| | - Inger Brandsma
- Department of Genetics, Erasmus, University Medical Center, Rotterdam, The Netherlands
| | - Jingsong Yuan
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Martin Mistrik
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - Peter Bouwman
- Division of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | | | - Ewa Gogola
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Daniël Warmerdam
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Marco Barazas
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Janneke E Jaspers
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Kenji Watanabe
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Mark Pieterse
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ariena Kersbergen
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Wendy Sol
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Patrick H N Celie
- Protein Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Philip C Schouten
- Division of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Bram van den Broek
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Ahmed Salman
- The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, United Kingdom
| | - Marja Nieuwland
- Deep Sequencing Core Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Iris de Rink
- Deep Sequencing Core Facility, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Jorma de Ronde
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Kees Jalink
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Simon J Boulton
- DNA Damage Response Laboratory, London Research Institute, Cancer Research UK, Clare Hall, South Mimms EN6 3LD, UK
| | - Junjie Chen
- Department of Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Dik C van Gent
- Department of Genetics, Erasmus, University Medical Center, Rotterdam, The Netherlands
| | - Jiri Bartek
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Jos Jonkers
- Division of Molecular Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Piet Borst
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
| | - Sven Rottenberg
- Division of Molecular Oncology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Laengassstrasse 122, 3012 Bern, Switzerland
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203
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Replication stress in Mammalian cells and its consequences for mitosis. Genes (Basel) 2015; 6:267-98. [PMID: 26010955 PMCID: PMC4488665 DOI: 10.3390/genes6020267] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/15/2015] [Accepted: 05/18/2015] [Indexed: 12/23/2022] Open
Abstract
The faithful transmission of genetic information to daughter cells is central to maintaining genomic stability and relies on the accurate and complete duplication of genetic material during each cell cycle. However, the genome is routinely exposed to endogenous and exogenous stresses that can impede the progression of replication. Such replication stress can be an early cause of cancer or initiate senescence. Replication stress, which primarily occurs during S phase, results in consequences during mitosis, jeopardizing chromosome segregation and, in turn, genomic stability. The traces of replication stress can be detected in the daughter cells during G1 phase. Alterations in mitosis occur in two types: 1) local alterations that correspond to breaks, rearrangements, intertwined DNA molecules or non-separated sister chromatids that are confined to the region of the replication dysfunction; 2) genome-wide chromosome segregation resulting from centrosome amplification (although centrosomes do not contain DNA), which amplifies the local replication stress to the entire genome. Here, we discuss the endogenous causes of replication perturbations, the mechanisms of replication fork restart and the consequences for mitosis, chromosome segregation and genomic stability.
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204
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Brosey CA, Soss SE, Brooks S, Yan C, Ivanov I, Dorai K, Chazin WJ. Functional dynamics in replication protein A DNA binding and protein recruitment domains. Structure 2015; 23:1028-38. [PMID: 26004442 DOI: 10.1016/j.str.2015.04.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 03/30/2015] [Accepted: 04/03/2015] [Indexed: 11/29/2022]
Abstract
Replication Protein A (RPA) is an essential scaffold for many DNA processing machines; its function relies on its modular architecture. Here, we report (15)N-nuclear magnetic resonance heteronuclear relaxation analysis to characterize the movements of single-stranded (ss) DNA binding and protein interaction modules in the RPA70 subunit. Our results provide direct evidence for coordination of the motion of the tandem RPA70AB ssDNA binding domains. Moreover, binding of ssDNA substrate is found to cause dramatic reorientation and full coupling of inter-domain motion. In contrast, the RPA70N protein interaction domain remains structurally and dynamically independent of RPA70AB regardless of binding of ssDNA. This autonomy of motion between the 70N and 70AB modules supports a model in which the two binding functions of RPA are mediated fully independently, but remain differentially coordinated depending on the length of their flexible tethers. A critical role for linkers between the globular domains in determining the functional dynamics of RPA is proposed.
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Affiliation(s)
- Chris A Brosey
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37232-8725, USA
| | - Sarah E Soss
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37232-8725, USA
| | - Sonja Brooks
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Chunli Yan
- Department of Chemistry, Georgia State University, Atlanta, GA 30302-4098, USA
| | - Ivaylo Ivanov
- Department of Chemistry, Georgia State University, Atlanta, GA 30302-4098, USA
| | - Kavita Dorai
- Department of Physics, Indian Institute of Science Education and Research (IISER), Mohali, Sector 81 Manauli PO, SAS Nagar, Punjab 140306, India
| | - Walter J Chazin
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37232-8725, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA.
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205
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DNA polymerases β and λ and their roles in cell. DNA Repair (Amst) 2015; 29:112-26. [DOI: 10.1016/j.dnarep.2015.02.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 01/29/2015] [Accepted: 02/02/2015] [Indexed: 10/24/2022]
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206
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Mechanochemical regulations of RPA's binding to ssDNA. Sci Rep 2015; 5:9296. [PMID: 25787788 PMCID: PMC4365408 DOI: 10.1038/srep09296] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 02/24/2015] [Indexed: 11/10/2022] Open
Abstract
Replication protein A (RPA) is a ubiquitous eukaryotic single-stranded DNA (ssDNA) binding protein that serves to protect ssDNA from degradation and annealing, and as a template for recruitment of many downstream factors in virtually all DNA transactions in cell. During many of these transactions, DNA is tethered and is likely subject to force. Previous studies of RPA's binding behavior on ssDNA were conducted in the absence of force; therefore the RPA-ssDNA conformations regulated by force remain unclear. Here, using a combination of atomic force microscopy imaging and mechanical manipulation of single ssDNA tethers, we show that force mediates a switch of the RPA bound ssDNA from amorphous aggregation to a much more regular extended conformation. Further, we found an interesting non-monotonic dependence of the binding affinity on monovalent salt concentration in the presence of force. In addition, we discovered that zinc in micromolar concentrations drives ssDNA to a unique, highly stiff and more compact state. These results provide new mechanochemical insights into the influences and the mechanisms of action of RPA on large single ssDNA.
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207
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Piya G, Mueller EN, Haas HK, Ghospurkar PL, Wilson TM, Jensen JL, Colbert CL, Haring SJ. Characterization of the interaction between Rfa1 and Rad24 in Saccharomyces cerevisiae. PLoS One 2015; 10:e0116512. [PMID: 25719602 PMCID: PMC4342240 DOI: 10.1371/journal.pone.0116512] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 12/10/2014] [Indexed: 11/22/2022] Open
Abstract
Maintaining the integrity of the genome requires the high fidelity duplication of the genome and the ability of the cell to recognize and repair DNA lesions. The heterotrimeric single stranded DNA (ssDNA) binding complex Replication Protein A (RPA) is central to multiple DNA processes, which are coordinated by RPA through its ssDNA binding function and through multiple protein-protein interactions. Many RPA interacting proteins have been reported through large genetic and physical screens; however, the number of interactions that have been further characterized is limited. To gain a better understanding of how RPA functions in DNA replication, repair, and cell cycle regulation and to identify other potential functions of RPA, a yeast two hybrid screen was performed using the yeast 70 kDa subunit, Replication Factor A1 (Rfa1), as a bait protein. Analysis of 136 interaction candidates resulted in the identification of 37 potential interacting partners, including the cell cycle regulatory protein and DNA damage clamp loader Rad24. The Rfa1-Rad24 interaction is not dependent on ssDNA binding. However, this interaction appears affected by DNA damage. The regions of both Rfa1 and Rad24 important for this interaction were identified, and the region of Rad24 identified is distinct from the region reported to be important for its interaction with Rfc2 5. This suggests that Rad24-Rfc2-5 (Rad24-RFC) recruitment to DNA damage substrates by RPA occurs, at least partially, through an interaction between the N terminus of Rfa1 and the C terminus of Rad24. The predicted structure and location of the Rad24 C-terminus is consistent with a model in which RPA interacts with a damage substrate, loads Rad24-RFC at the 5’ junction, and then releases the Rad24-RFC complex to allow for proper loading and function of the DNA damage clamp.
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Affiliation(s)
- Gunjan Piya
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, United States of America
| | - Erica N. Mueller
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, United States of America
| | - Heather K. Haas
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, United States of America
| | - Padmaja L. Ghospurkar
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, United States of America
| | - Timothy M. Wilson
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, United States of America
| | - Jaime L. Jensen
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, United States of America
| | - Christopher L. Colbert
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, United States of America
- Interdisciplinary Program in Cellular and Molecular Biology, North Dakota State University, Fargo, ND, 58108, United States of America
| | - Stuart J. Haring
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58108, United States of America
- Interdisciplinary Program in Cellular and Molecular Biology, North Dakota State University, Fargo, ND, 58108, United States of America
- * E-mail:
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208
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Ning B, Feldkamp MD, Cortez D, Chazin WJ, Friedman KL, Fanning E. Simian virus Large T antigen interacts with the N-terminal domain of the 70 kD subunit of Replication Protein A in the same mode as multiple DNA damage response factors. PLoS One 2015; 10:e0116093. [PMID: 25706313 PMCID: PMC4337903 DOI: 10.1371/journal.pone.0116093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/04/2014] [Indexed: 11/18/2022] Open
Abstract
Simian virus 40 (SV40) serves as an important model organism for studying eukaryotic DNA replication. Its helicase, Large T-antigen (Tag), is a multi-functional protein that interacts with multiple host proteins, including the ubiquitous ssDNA binding protein Replication Protein A (RPA). Tag recruits RPA, actively loads it onto the unwound DNA, and together they promote priming of the template. Although interactions of Tag with RPA have been mapped, no interaction between Tag and the N-terminal protein interaction domain of the RPA 70kDa subunit (RPA70N) has been reported. Here we provide evidence of direct physical interaction of Tag with RPA70N and map the binding sites using a series of pull-down and mutational experiments. In addition, a monoclonal anti-Tag antibody, the epitope of which overlaps with the binding site, blocks the binding of Tag to RPA70N. We use NMR chemical shift perturbation analysis to show that Tag uses the same basic cleft in RPA70N as multiple of DNA damage response proteins. Mutations in the binding sites of both RPA70N and Tag demonstrate that specific charge reversal substitutions in either binding partner strongly diminish the interaction. These results expand the known repertoire of contacts between Tag and RPA, which mediate the many critical roles of Tag in viral replication.
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Affiliation(s)
- Boting Ning
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Michael D. Feldkamp
- Departments of Biochemistry, Chemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - David Cortez
- Department of Biochemistry, Vanderbilt University Medical School, Nashville, Tennessee, United States of America
| | - Walter J. Chazin
- Departments of Biochemistry, Chemistry, and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail: (KLF); (WJC)
| | - Katherine L. Friedman
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail: (KLF); (WJC)
| | - Ellen Fanning
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
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209
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Waterson AG, Kennedy JP, Patrone JD, Pelz NF, Feldkamp MD, Frank AO, Vangamudi B, Souza-Fagundes EM, Rossanese OW, Chazin WJ, Fesik SW. Diphenylpyrazoles as replication protein a inhibitors. ACS Med Chem Lett 2015; 6:140-5. [PMID: 25699140 DOI: 10.1021/ml5003629] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 11/11/2014] [Indexed: 01/16/2023] Open
Abstract
Replication Protein A is the primary eukaryotic ssDNA binding protein that has a central role in initiating the cellular response to DNA damage. RPA recruits multiple proteins to sites of DNA damage via the N-terminal domain of the 70 kDa subunit (RPA70N). Here we describe the optimization of a diphenylpyrazole carboxylic acid series of inhibitors of these RPA-protein interactions. We evaluated substituents on the aromatic rings as well as the type and geometry of the linkers used to combine fragments, ultimately leading to submicromolar inhibitors of RPA70N protein-protein interactions.
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Affiliation(s)
- Alex G. Waterson
- Department of Biochemistry, ‡Department of Pharmacology, Vanderbilt University School of
Medicine, and §Department of
Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - J. Phillip Kennedy
- Department of Biochemistry, ‡Department of Pharmacology, Vanderbilt University School of
Medicine, and §Department of
Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - James D. Patrone
- Department of Biochemistry, ‡Department of Pharmacology, Vanderbilt University School of
Medicine, and §Department of
Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Nicholas F. Pelz
- Department of Biochemistry, ‡Department of Pharmacology, Vanderbilt University School of
Medicine, and §Department of
Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Michael D. Feldkamp
- Department of Biochemistry, ‡Department of Pharmacology, Vanderbilt University School of
Medicine, and §Department of
Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Andreas O. Frank
- Department of Biochemistry, ‡Department of Pharmacology, Vanderbilt University School of
Medicine, and §Department of
Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Bhavatarini Vangamudi
- Department of Biochemistry, ‡Department of Pharmacology, Vanderbilt University School of
Medicine, and §Department of
Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Elaine M. Souza-Fagundes
- Department of Biochemistry, ‡Department of Pharmacology, Vanderbilt University School of
Medicine, and §Department of
Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Olivia W. Rossanese
- Department of Biochemistry, ‡Department of Pharmacology, Vanderbilt University School of
Medicine, and §Department of
Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Walter J. Chazin
- Department of Biochemistry, ‡Department of Pharmacology, Vanderbilt University School of
Medicine, and §Department of
Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Stephen W. Fesik
- Department of Biochemistry, ‡Department of Pharmacology, Vanderbilt University School of
Medicine, and §Department of
Chemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
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210
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Georgescu R, Langston L, O'Donnell M. A proposal: Evolution of PCNA's role as a marker of newly replicated DNA. DNA Repair (Amst) 2015; 29:4-15. [PMID: 25704660 DOI: 10.1016/j.dnarep.2015.01.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 01/28/2015] [Accepted: 01/30/2015] [Indexed: 11/26/2022]
Abstract
Processivity clamps that hold DNA polymerases to DNA for processivity were the first proteins known to encircle the DNA duplex. At the time, polymerase processivity was thought to be the only function of ring shaped processivity clamps. But studies from many laboratories have identified numerous proteins that bind and function with sliding clamps. Among these processes are mismatch repair and nucleosome assembly. Interestingly, there exist polymerases that are highly processive and do not require clamps. Hence, DNA polymerase processivity does not intrinsically require that sliding clamps evolved for this purpose. We propose that polymerases evolved to require clamps as a way of ensuring that clamps are deposited on newly replicated DNA. These clamps are then used on the newly replicated daughter strands, for processes important to genomic integrity, such as mismatch repair and the assembly of nucleosomes to maintain epigenetic states of replicating cells during development.
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Affiliation(s)
- Roxana Georgescu
- Rockefeller University and HHMI, 1230 York Avenue, Box 228, New York, NY 10065, United States
| | - Lance Langston
- Rockefeller University and HHMI, 1230 York Avenue, Box 228, New York, NY 10065, United States
| | - Mike O'Donnell
- Rockefeller University and HHMI, 1230 York Avenue, Box 228, New York, NY 10065, United States.
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211
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The DNA damage response and checkpoint adaptation in Saccharomyces cerevisiae: distinct roles for the replication protein A2 (Rfa2) N-terminus. Genetics 2015; 199:711-27. [PMID: 25595672 PMCID: PMC4349066 DOI: 10.1534/genetics.114.173211] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In response to DNA damage, two general but fundamental processes occur in the cell: (1) a DNA lesion is recognized and repaired, and (2) concomitantly, the cell halts the cell cycle to provide a window of opportunity for repair to occur. An essential factor for a proper DNA-damage response is the heterotrimeric protein complex Replication Protein A (RPA). Of particular interest is hyperphosphorylation of the 32-kDa subunit, called RPA2, on its serine/threonine-rich amino (N) terminus following DNA damage in human cells. The unstructured N-terminus is often referred to as the phosphorylation domain and is conserved among eukaryotic RPA2 subunits, including Rfa2 in Saccharomyces cerevisiae. An aspartic acid/alanine-scanning and genetic interaction approach was utilized to delineate the importance of this domain in budding yeast. It was determined that the Rfa2 N-terminus is important for a proper DNA-damage response in yeast, although its phosphorylation is not required. Subregions of the Rfa2 N-terminus important for the DNA-damage response were also identified. Finally, an Rfa2 N-terminal hyperphosphorylation-mimetic mutant behaves similarly to another Rfa1 mutant (rfa1-t11) with respect to genetic interactions, DNA-damage sensitivity, and checkpoint adaptation. Our data indicate that post-translational modification of the Rfa2 N-terminus is not required for cells to deal with "repairable" DNA damage; however, post-translational modification of this domain might influence whether cells proceed into M-phase in the continued presence of unrepaired DNA lesions as a "last-resort" mechanism for cell survival.
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212
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Li P, Ma X, Adams IR, Yuan P. A tight control of Rif1 by Oct4 and Smad3 is critical for mouse embryonic stem cell stability. Cell Death Dis 2015; 6:e1588. [PMID: 25569105 PMCID: PMC4669749 DOI: 10.1038/cddis.2014.551] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2014] [Revised: 11/03/2014] [Accepted: 11/17/2014] [Indexed: 12/20/2022]
Abstract
Prolonged culture of embryonic stem cells (ESCs) leads them to adopt embryonal carcinoma cell features, creating enormous dangers for their further application. The mechanism involved in ESC stability has not, however, been extensively studied. We previously reported that SMAD family member 3 (Smad3) has an important role in maintaining mouse ESC stability, as depletion of Smad3 results in cancer cell-like properties in ESCs and Smad3-/- ESCs are prone to grow large, malignant teratomas. To understand how Smad3 contributes to ESC stability, we performed microarray analysis to compare the transcriptome of wild-type and Smad3-/- ESCs. We found that Rif1 (RAP1-associated protein 1), a factor important for genomic stability, is significantly upregulated in Smad3-/- ESCs. The expression level of Rif1 needs to be tightly controlled in ESCs, as a low level of Rif1 is associated with ESC differentiation, but a high level of Rif1 is linked to ESC transformation. In ESCs, Oct4 activates Rif1, whereas Smad3 represses its expression. Oct4 recruits Smad3 to bind to Rif1 promoter, but Smad3 joining facilitates the loading of a polycomb complex that generates a repressive epigenetic modification on Rif1 promoter, and thus maintains the expression of Rif1 at a proper level in ESCs. Interestingly, Rif1 short hairpin RNA (shRNA)-transduced Smad3-/- ESCs showed less malignant properties than the control shRNA-transduced Smad3-/- ESCs, suggesting a critical role of Rif1 in maintaining the stability of ESCs during proliferation.
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Affiliation(s)
- P Li
- 1] Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China [2] Department of Chemical Pathology, Stem Cell and Functional Genomics, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China [3] The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - X Ma
- 1] Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China [2] Department of Chemical Pathology, Stem Cell and Functional Genomics, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - I R Adams
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - P Yuan
- 1] Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China [2] Department of Chemical Pathology, Stem Cell and Functional Genomics, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China [3] The Chinese University of Hong Kong Shenzhen Research Institute, Shenzhen, China [4] School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
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213
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Qiao M, Luo D, Kuang Y, Feng H, Luo G, Liang P. Cell cycle specific distribution of killin: evidence for negative regulation of both DNA and RNA synthesis. Cell Cycle 2015; 14:1823-9. [PMID: 25945611 PMCID: PMC4614363 DOI: 10.1080/15384101.2015.1038686] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 03/28/2015] [Accepted: 04/02/2015] [Indexed: 12/13/2022] Open
Abstract
p53 tumor-suppressor gene is a master transcription factor which controls cell cycle progression and apoptosis. killin was discovered as one of the p53 target genes implicated in S-phase control coupled to cell death. Due to its extreme proximity to pten tumor-suppressor gene on human chromosome 10, changes in epigenetic modification of killin have also been linked to Cowden syndrome as well as other human cancers. Previous studies revealed that Killin is a high-affinity DNA-binding protein with preference to single-stranded DNA, and it inhibits DNA synthesis in vitro and in vivo. Here, co-localization studies of RFP-Killin with either GFP-PCNA or endogenous single-stranded DNA binding protein RPA during S-phase show that Killin always adopts a mutually exclusive punctuated nuclear expression pattern with the 2 accessory proteins in DNA replication. In contrast, when cells are not in S-phase, RFP-Killin largely congregates in the nucleolus where rRNA transcription normally occurs. Both of these cell cycle specific localization patterns of RFP-Killin are stable under high salt condition, consistent with Killin being tightly associated with nucleic acids within cell nuclei. Together, these cell biological results provide a molecular basis for Killin in competitively inhibiting the formation of DNA replication forks during S-phase, as well as potentially negatively regulate RNA synthesis during other cell cycle phases.
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Affiliation(s)
- Man Qiao
- Center for Growth, Metabolism and Aging; Department of Biochemistry & Molecular Biology; School of Life Sciences; Sichuan University; Chengdu, China
| | - Dan Luo
- Center for Growth, Metabolism and Aging; Department of Biochemistry & Molecular Biology; School of Life Sciences; Sichuan University; Chengdu, China
| | - Yi Kuang
- Center for Growth, Metabolism and Aging; Department of Biochemistry & Molecular Biology; School of Life Sciences; Sichuan University; Chengdu, China
| | - Haiyan Feng
- Center for Growth, Metabolism and Aging; Department of Biochemistry & Molecular Biology; School of Life Sciences; Sichuan University; Chengdu, China
| | - Guangping Luo
- State Key Laboratory for Gene and Cell Therapy; Sichuan University; Chengdu, China
| | - Peng Liang
- Center for Growth, Metabolism and Aging; Department of Biochemistry & Molecular Biology; School of Life Sciences; Sichuan University; Chengdu, China
- Clover Biopharmaceuticals; Chengdu, China
- State Key Laboratory for Gene and Cell Therapy; Sichuan University; Chengdu, China
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214
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Mukherjee B, Tomimatsu N, Burma S. Immunofluorescence-based methods to monitor DNA end resection. Methods Mol Biol 2015; 1292:67-75. [PMID: 25804748 DOI: 10.1007/978-1-4939-2522-3_5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Double-strand breaks (DSBs) are the most deleterious among all types of DNA damage that can occur in the cell. These breaks arise from both endogenous (e.g., DNA replication stress) and exogenous insults (e.g., ionizing radiation). DSBs are principally repaired by one of two major pathways: nonhomologous end joining (NHEJ) or homologous recombination (HR). NHEJ is an error-prone process that can occur in all phases of the cell cycle, while HR is limited to the S and G2 phases of the cell cycle when a sister chromatid is available as a template for error-free repair. The first step in HR is "DNA end resection," a process during which the broken DNA end is converted into a long stretch of 3'-ended single-stranded DNA (ssDNA). In recent years, DNA end resection has been identified as a pivotal step that controls "repair pathway choice," i.e., the appropriate choice between NHEJ and HR for DSB repair. Therefore, methods to quantitatively or semiquantitatively assess DNA end resection have gained importance in laboratories working on DNA repair. In this chapter, we describe two simple immunofluorescence-based techniques to monitor DNA end resection in mammalian cells. The first technique involves immuno-detection of replication protein A (RPA), an ssDNA-binding protein that binds to resected DNA. The second technique involves labeling of genomic DNA with 5-bromo-2'-deoxyuridine (BrdU) that can be detected by anti-BrdU antibody only after the DNA becomes single stranded due to resection. These methods are not complicated, do not involve sophisticated instrumentation or reporter constructs, and can be applied to most mammalian cell lines and, therefore, should be of broad utility as simple ways of monitoring DNA end resection in vivo.
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Affiliation(s)
- Bipasha Mukherjee
- Division of Molecular Radiation Biology, Department of Radiation Oncology, University of Texas Southwestern Medical Center, 2201 Inwood Road, NC7.208, Dallas, TX, 75390, USA
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215
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Bhat KP, Bétous R, Cortez D. High-affinity DNA-binding domains of replication protein A (RPA) direct SMARCAL1-dependent replication fork remodeling. J Biol Chem 2014; 290:4110-7. [PMID: 25552480 DOI: 10.1074/jbc.m114.627083] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SMARCAL1 catalyzes replication fork remodeling to maintain genome stability. It is recruited to replication forks via an interaction with replication protein A (RPA), the major ssDNA-binding protein in eukaryotic cells. In addition to directing its localization, RPA also activates SMARCAL1 on some fork substrates but inhibits it on others, thereby conferring substrate specificity to SMARCAL1 fork-remodeling reactions. We investigated the mechanism by which RPA regulates SMARCAL1. Our results indicate that although an interaction between SMARCAL1 and RPA is essential for SMARCAL1 activation, the location of the interacting surface on RPA is not. Counterintuitively, high-affinity DNA binding of RPA DNA-binding domain (DBD) A and DBD-B near the fork junction makes it easier for SMARCAL1 to remodel the fork, which requires removing RPA. We also found that RPA DBD-C and DBD-D are not required for SMARCAL1 regulation. Thus, the orientation of the high-affinity RPA DBDs at forks dictates SMARCAL1 substrate specificity.
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Affiliation(s)
- Kamakoti P Bhat
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Rémy Bétous
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - David Cortez
- From the Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
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216
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Sugitani N, Chazin WJ. Characteristics and concepts of dynamic hub proteins in DNA processing machinery from studies of RPA. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 117:206-211. [PMID: 25542993 DOI: 10.1016/j.pbiomolbio.2014.12.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 12/15/2014] [Accepted: 12/16/2014] [Indexed: 11/26/2022]
Abstract
DNA replication, damage response and repair require the coordinated action of multi-domain proteins operating within dynamic multi-protein machines that act upon the DNA substrate. These modular proteins contain flexible linkers of various lengths, which enable changes in the spatial distribution of the globular domains (architecture) that harbor their essential biochemical functions. This mobile architecture is uniquely suited to follow the evolving substrate landscape present over the course of the specific process performed by the multi-protein machinery. A fundamental advance in understanding of protein machinery is the realization of the pervasive role of dynamics. Not only is the machine undergoing dynamic transformations, but the proteins themselves are flexible and constantly adapting to the progression through the steps of the overall process. Within this dynamic context the activity of the constituent proteins must be coordinated, a role typically played by hub proteins. A number of important characteristics of modular proteins and concepts about the operation of dynamic machinery have been discerned. These provide the underlying basis for the action of the machinery that reads DNA, and responds to and repairs DNA damage. Here, we introduce a number of key characteristics and concepts, including the modularity of the proteins, linkage of weak binding sites, direct competition between sites, and allostery, using the well recognized hub protein replication protein A (RPA).
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Affiliation(s)
- Norie Sugitani
- Center for Structural Biology and Departments of Biochemistry and Chemistry, Vanderbilt University, Nashville, TN, USA
| | - Walter J Chazin
- Center for Structural Biology and Departments of Biochemistry and Chemistry, Vanderbilt University, Nashville, TN, USA.
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217
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Manfrini N, Trovesi C, Wery M, Martina M, Cesena D, Descrimes M, Morillon A, d'Adda di Fagagna F, Longhese MP. RNA-processing proteins regulate Mec1/ATR activation by promoting generation of RPA-coated ssDNA. EMBO Rep 2014; 16:221-31. [PMID: 25527408 DOI: 10.15252/embr.201439458] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Eukaryotic cells respond to DNA double-strand breaks (DSBs) by activating a checkpoint that depends on the protein kinases Tel1/ATM and Mec1/ATR. Mec1/ATR is activated by RPA-coated single-stranded DNA (ssDNA), which arises upon nucleolytic degradation (resection) of the DSB. Emerging evidences indicate that RNA-processing factors play critical, yet poorly understood, roles in genomic stability. Here, we provide evidence that the Saccharomyces cerevisiae RNA decay factors Xrn1, Rrp6 and Trf4 regulate Mec1/ATR activation by promoting generation of RPA-coated ssDNA. The lack of Xrn1 inhibits ssDNA generation at the DSB by preventing the loading of the MRX complex. By contrast, DSB resection is not affected in the absence of Rrp6 or Trf4, but their lack impairs the recruitment of RPA, and therefore of Mec1, to the DSB. Rrp6 and Trf4 inactivation affects neither Rad51/Rad52 association nor DSB repair by homologous recombination (HR), suggesting that full Mec1 activation requires higher amount of RPA-coated ssDNA than HR-mediated repair. Noteworthy, deep transcriptome analyses do not identify common misregulated gene expression that could explain the observed phenotypes. Our results provide a novel link between RNA processing and genome stability.
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Affiliation(s)
- Nicola Manfrini
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Camilla Trovesi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Maxime Wery
- Institut Curie, CNRS UMR3244 Université Pierre et Marie Curie, Paris Cedex 05, France
| | - Marina Martina
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Daniele Cesena
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Marc Descrimes
- Institut Curie, CNRS UMR3244 Université Pierre et Marie Curie, Paris Cedex 05, France
| | - Antonin Morillon
- Institut Curie, CNRS UMR3244 Université Pierre et Marie Curie, Paris Cedex 05, France
| | - Fabrizio d'Adda di Fagagna
- IFOM Foundation-FIRC Institute of Molecular Oncology Foundation, Milan, Italy Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
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218
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Nocua PA, Ramirez CA, Barreto GE, González J, Requena JM, Puerta CJ. Leishmania braziliensis replication protein A subunit 1: molecular modelling, protein expression and analysis of its affinity for both DNA and RNA. Parasit Vectors 2014; 7:573. [PMID: 25498946 PMCID: PMC4269926 DOI: 10.1186/s13071-014-0573-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 11/26/2014] [Indexed: 11/28/2022] Open
Abstract
Background Replication factor A (RPA) is a single-strand DNA binding protein involved in DNA replication, recombination and repair processes. It is composed by the subunits RPA-1, RPA-2 and RPA-3; the major DNA-binding activity resides in the subunit 1 of the heterotrimeric RPA complex. In yeast and higher eukaryotes, besides the three basic structural DNA-binding domains, the RPA-1 subunit contains an N-terminal region involved in protein-protein interactions with a fourth DNA-binding domain. Remarkably, the N-terminal extension is absent in the RPA-1 of the pathogenic protozoan Leishmania (Leishmania) amazonensis; however, the protein maintains its ability to bind ssDNA. In a recent work, we identify Leishmania (Viannia) braziliensis RPA-1 by its specific binding to the untranslated regions of the HSP70 mRNAs, suggesting that this protein might be also an RNA-binding protein. Methods Both rLbRPA-1 purified by His-tag affinity chromatography as well as the in vitro transcribed L. braziliensis 3′ HSP70-II UTR were used to perform pull down assays to asses nucleic acid binding properties. Also, homology modeling was carried out to construct the LbRPA-1 tridimensional structure to search relevant amino acid residues to bind nucleic acids. Results In this work, after obtaining the recombinant L. braziliensis RPA-1 protein under native conditions, competitive and non-competitive pull-down assays confirmed the single-stranded DNA binding activity of this protein and demonstrated its interaction with the 3′ UTR from the HSP70-II mRNA. As expected, this protein exhibits a high affinity for ssDNA, but we have found that RPA-1 interacts also with RNA. Additionally, we carried out a structural analysis of L. braziliensis RPA-1 protein using the X-ray diffraction structure of Ustilago maydis homologous protein as a template. Our results indicate that, in spite of the evolutionary divergence between both organisms, the structure of these two RPA-1 proteins seems to be highly conserved. Conclusion The LbRPA-1 protein is a ssDNA binding protein, but also it shows affinity in vitro for the HSP70 mRNA; this finding supports a possible in vivo role in the HSP70 mRNA metabolism. On the other hand, the three dimensional model of Leishmania RPA-1 serves as a starting point for both functional analysis and its exploration as a chemotherapeutic target to combat leishmaniasis.
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Affiliation(s)
- Paola A Nocua
- Laboratorio de Parasitología Molecular, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7 No 43-82, Edificio 50, Laboratorio 113, Bogotá, Colombia.
| | - Cesar A Ramirez
- Laboratorio de Parasitología Molecular, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7 No 43-82, Edificio 50, Laboratorio 113, Bogotá, Colombia.
| | - George E Barreto
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia.
| | - Janneth González
- Departamento de Nutrición y Bioquímica, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá, Colombia.
| | - José M Requena
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma de Madrid, Madrid, Spain.
| | - Concepción J Puerta
- Laboratorio de Parasitología Molecular, Facultad de Ciencias, Pontificia Universidad Javeriana, Carrera 7 No 43-82, Edificio 50, Laboratorio 113, Bogotá, Colombia.
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219
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Ghospurkar PL, Wilson TM, Liu S, Herauf A, Steffes J, Mueller EN, Oakley GG, Haring SJ. Phosphorylation and cellular function of the human Rpa2 N-terminus in the budding yeast Saccharomyces cerevisiae. Exp Cell Res 2014; 331:183-199. [PMID: 25499885 DOI: 10.1016/j.yexcr.2014.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 11/29/2014] [Accepted: 12/02/2014] [Indexed: 11/18/2022]
Abstract
Maintenance of genome integrity is critical for proper cell growth. This occurs through accurate DNA replication and repair of DNA lesions. A key factor involved in both DNA replication and the DNA damage response is the heterotrimeric single-stranded DNA (ssDNA) binding complex Replication Protein A (RPA). Although the RPA complex appears to be structurally conserved throughout eukaryotes, the primary amino acid sequence of each subunit can vary considerably. Examination of sequence differences along with the functional interchangeability of orthologous RPA subunits or regions could provide insight into important regions and their functions. This might also allow for study in simpler systems. We determined that substitution of yeast Replication Factor A (RFA) with human RPA does not support yeast cell viability. Exchange of a single yeast RFA subunit with the corresponding human RPA subunit does not function due to lack of inter-species subunit interactions. Substitution of yeast Rfa2 with domains/regions of human Rpa2 important for Rpa2 function (i.e., the N-terminus and the loop 3-4 region) supports viability in yeast cells, and hybrid proteins containing human Rpa2 N-terminal phospho-mutations result in similar DNA damage phenotypes to analogous yeast Rfa2 N-terminal phospho-mutants. Finally, the human Rpa2 N-terminus (NT) fused to yeast Rfa2 is phosphorylated in a manner similar to human Rpa2 in human cells, indicating that conserved kinases recognize the human domain in yeast. The implication is that budding yeast represents a potential model system for studying not only human Rpa2 N-terminal phosphorylation, but also phosphorylation of Rpa2 N-termini from other eukaryotic organisms.
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Affiliation(s)
- Padmaja L Ghospurkar
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA
| | - Timothy M Wilson
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA
| | - Shengqin Liu
- Department of Oral Biology, University of Nebraska Medical Center, Lincoln, NE 68583, USA
| | - Anna Herauf
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA
| | - Jenna Steffes
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA
| | - Erica N Mueller
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA
| | - Gregory G Oakley
- Department of Oral Biology, University of Nebraska Medical Center, Lincoln, NE 68583, USA
| | - Stuart J Haring
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA; Interdisciplinary Cellular and Molecular Biology Program, North Dakota State University, Fargo, ND 58108, USA.
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220
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Maréchal A, Zou L. RPA-coated single-stranded DNA as a platform for post-translational modifications in the DNA damage response. Cell Res 2014; 25:9-23. [PMID: 25403473 DOI: 10.1038/cr.2014.147] [Citation(s) in RCA: 315] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The Replication Protein A (RPA) complex is an essential regulator of eukaryotic DNA metabolism. RPA avidly binds to single-stranded DNA (ssDNA) through multiple oligonucleotide/oligosaccharide-binding folds and coordinates the recruitment and exchange of genome maintenance factors to regulate DNA replication, recombination and repair. The RPA-ssDNA platform also constitutes a key physiological signal which activates the master ATR kinase to protect and repair stalled or collapsed replication forks during replication stress. In recent years, the RPA complex has emerged as a key target and an important regulator of post-translational modifications in response to DNA damage, which is critical for its genome guardian functions. Phosphorylation and SUMOylation of the RPA complex, and more recently RPA-regulated ubiquitination, have all been shown to control specific aspects of DNA damage signaling and repair by modulating the interactions between RPA and its partners. Here, we review our current understanding of the critical functions of the RPA-ssDNA platform in the maintenance of genome stability and its regulation through an elaborate network of covalent modifications.
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Affiliation(s)
- Alexandre Maréchal
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Lee Zou
- 1] Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA [2] Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
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221
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RPA-1 from Leishmania amazonensis (LaRPA-1) structurally differs from other eukaryote RPA-1 and interacts with telomeric DNA via its N-terminal OB-fold domain. FEBS Lett 2014; 588:4740-8. [PMID: 25451229 DOI: 10.1016/j.febslet.2014.11.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/25/2014] [Accepted: 11/06/2014] [Indexed: 12/18/2022]
Abstract
Replication protein A-1 (RPA-1) is a single-stranded DNA-binding protein involved in DNA metabolism. We previously demonstrated the interaction between LaRPA-1 and telomeric DNA. Here, we expressed and purified truncated mutants of LaRPA-1 and used circular dichroism measurements and molecular dynamics simulations to demonstrate that the tertiary structure of LaRPA-1 differs from human and yeast RPA-1. LaRPA-1 interacts with telomeric ssDNA via its N-terminal OB-fold domain, whereas RPA from higher eukaryotes show different binding modes to ssDNA. Our results show that LaRPA-1 is evolutionary distinct from other RPA-1 proteins and can potentially be used for targeting trypanosomatid telomeres.
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222
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Deng SK, Chen H, Symington LS. Replication protein A prevents promiscuous annealing between short sequence homologies: Implications for genome integrity. Bioessays 2014; 37:305-13. [PMID: 25400143 DOI: 10.1002/bies.201400161] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Replication protein A (RPA) is the main eukaryotic single-stranded DNA (ssDNA) binding protein, having essential roles in all DNA metabolic reactions involving ssDNA. RPA binds ssDNA with high affinity, thereby preventing the formation of secondary structures and protecting ssDNA from the action of nucleases, and directly interacts with other DNA processing proteins. Here, we discuss recent results supporting the idea that one function of RPA is to prevent annealing between short repeats that can lead to chromosome rearrangements by microhomology-mediated end joining or the formation of hairpin structures that are substrates for structure-selective nucleases. We suggest that replication fork catastrophe caused by depletion of RPA could result from cleavage of secondary structures by nucleases, and that failure to cleave hairpin structures formed at DNA ends could lead to gene amplification. These studies highlight the important role RPA plays in maintaining genome integrity.
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Affiliation(s)
- Sarah K Deng
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, USA
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223
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Mishra AK, Dormi SS, Turchi AM, Woods DS, Turchi JJ. Chemical inhibitor targeting the replication protein A-DNA interaction increases the efficacy of Pt-based chemotherapy in lung and ovarian cancer. Biochem Pharmacol 2014; 93:25-33. [PMID: 25449597 DOI: 10.1016/j.bcp.2014.10.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 10/22/2014] [Accepted: 10/23/2014] [Indexed: 01/28/2023]
Abstract
Platinum-based chemotherapeutics exert their therapeutic efficacy via the formation of DNA adducts which interfere with DNA replication, transcription and cell division and ultimately induce cell death. Repair and tolerance of these Pt-DNA lesions by nucleotide excision repair (NER) and homologous recombination (HR) can substantially reduce the effectiveness of therapy. Inhibition of these repair pathways, therefore, holds the potential to sensitize cancer cells to Pt treatment and increase clinical efficacy. Replication Protein A (RPA) plays essential roles in both NER and HR, along with its role in DNA replication and DNA damage checkpoint activation. Each of these functions is, in part, mediated by RPA binding to single-stranded DNA (ssDNA). Here we report the synthesis and characterization of novel derivatives of RPA small molecule inhibitors and their activity in models of epithelial ovarian cancer (EOC) and non-small cell lung cancer (NSCLC). We have synthesized analogs of our previously reported RPA inhibitor TDRL-505 and determined the structure-activity relationships. These data led us to the identification of TDRL-551, which exhibited a greater than 2-fold increase in in vitro activity. TDRL-551 showed synergy with Pt in tissue culture models of EOC and in vivo efficacy, as a single agent and in combination with platinum, in a NSCLC xenograft model. These data demonstrate the utility of RPA inhibition in EOC and NSCLC and the potential in developing novel anticancer therapeutics that target RPA-DNA interactions.
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Affiliation(s)
- Akaash K Mishra
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Silvana S Dormi
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Alaina M Turchi
- NERx Biosciences Inc. 351W. 10th Street, Suite 510, Indianapolis, IN 46202, USA
| | - Derek S Woods
- NERx Biosciences Inc. 351W. 10th Street, Suite 510, Indianapolis, IN 46202, USA
| | - John J Turchi
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA; Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202, USA; NERx Biosciences Inc. 351W. 10th Street, Suite 510, Indianapolis, IN 46202, USA.
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224
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Witosch J, Wolf E, Mizuno N. Architecture and ssDNA interaction of the Timeless-Tipin-RPA complex. Nucleic Acids Res 2014; 42:12912-27. [PMID: 25348395 PMCID: PMC4227788 DOI: 10.1093/nar/gku960] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The Timeless-Tipin (Tim-Tipin) complex, also referred to as the fork protection complex, is involved in coordination of DNA replication. Tim-Tipin is suggested to be recruited to replication forks via Replication Protein A (RPA) but details of the interaction are unknown. Here, using cryo-EM and biochemical methods, we characterized complex formation of Tim-Tipin, RPA and single-stranded DNA (ssDNA). Tim-Tipin and RPA form a 258 kDa complex with a 1:1:1 stoichiometry. The cryo-EM 3D reconstruction revealed a globular architecture of the Tim-Tipin-RPA complex with a ring-like and a U-shaped domain covered by a RPA lid. Interestingly, RPA in the complex adopts a horse shoe-like shape resembling its conformation in the presence of long ssDNA (>30 nucleotides). Furthermore, the recruitment of the Tim-Tipin-RPA complex to ssDNA is modulated by the RPA conformation and requires RPA to be in the more compact 30 nt ssDNA binding mode. The dynamic formation and disruption of the Tim-Tipin-RPA-ssDNA complex implicates the RPA-based recruitment of Tim-Tipin to the replication fork.
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Affiliation(s)
- Justine Witosch
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Eva Wolf
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany Department of Physiological Chemistry and Center For Integrated Protein Science Munich (CIPSM), Butenandt Institute, Ludwig Maximilians University of Munich, Butenandtstrasse 5, 81377 Munich, Germany Institut für allgemeine Botanik, Johannes Gutenberg-University, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany and Institute of Molecular Biology (IMB), Mainz, Germany
| | - Naoko Mizuno
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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225
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226
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Liu T, Huang J. Quality control of homologous recombination. Cell Mol Life Sci 2014; 71:3779-97. [PMID: 24858417 PMCID: PMC11114062 DOI: 10.1007/s00018-014-1649-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 05/09/2014] [Indexed: 12/21/2022]
Abstract
Exogenous and endogenous genotoxic agents, such as ionizing radiation and numerous chemical agents, cause DNA double-strand breaks (DSBs), which are highly toxic and lead to genomic instability or tumorigenesis if not repaired accurately and efficiently. Cells have over evolutionary time developed certain repair mechanisms in response to DSBs to maintain genomic integrity. Major DSB repair mechanisms include non-homologous end joining and homologous recombination (HR). Using sister homologues as templates, HR is a high-fidelity repair pathway that can rejoin DSBs without introducing mutations. However, HR execution without appropriate guarding may lead to more severe gross genome rearrangements. Here we review current knowledge regarding the factors and mechanisms required for accomplishment of accurate HR.
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Affiliation(s)
- Ting Liu
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang China
| | - Jun Huang
- Life Sciences Institute, Zhejiang University, Hangzhou, 310058 Zhejiang China
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227
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Wang WC, Wu CY, Lai YC, Lin NS, Hsu YH, Hu CC. Characterization of the cryptic AV3 promoter of ageratum yellow vein virus in prokaryotic and eukaryotic systems. PLoS One 2014; 9:e108608. [PMID: 25268755 PMCID: PMC4182527 DOI: 10.1371/journal.pone.0108608] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 08/25/2014] [Indexed: 11/19/2022] Open
Abstract
A cryptic prokaryotic promoter, designated AV3 promoter, has been previously identified in certain begomovirus genus, including ageratum yellow vein virus isolate NT (AYVV-NT). In this study, we demonstrated that the core nucleotides in the putative -10 and -35 boxes are necessary but not sufficient for promoter activity in Escherichia coli, and showed that AYVV-NT AV3 promoter could specifically interact with single-stranded DNA-binding protein and sigma 70 of E. coli involved in transcription. Several AYVV-NT-encoded proteins were found to increase the activity of AV3 promoter. The transcription start sites downstream to AV3 promoter were mapped to nucleotide positions 803 or 805 in E. coli, and 856 in Nicotiana benthamiana. The eukaryotic activity of AV3 promoter and the translatability of a short downstream open reading frame were further confirmed by using a green fluorescent protein reporter construct in yeast (Saccharomyces cerevisiae) cells. These results suggested that AV3 promoter might be a remnant of evolution that retained cryptic activity at present.
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Affiliation(s)
- Wei-Chen Wang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Chia-Ying Wu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Yi-Chin Lai
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Na-Sheng Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Chung-Chi Hu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
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228
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Chen R, Wold MS. Replication protein A: single-stranded DNA's first responder: dynamic DNA-interactions allow replication protein A to direct single-strand DNA intermediates into different pathways for synthesis or repair. Bioessays 2014; 36:1156-61. [PMID: 25171654 DOI: 10.1002/bies.201400107] [Citation(s) in RCA: 197] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Replication protein A (RPA), the major single-stranded DNA-binding protein in eukaryotic cells, is required for processing of single-stranded DNA (ssDNA) intermediates found in replication, repair, and recombination. Recent studies have shown that RPA binding to ssDNA is highly dynamic and that more than high-affinity binding is needed for function. Analysis of DNA binding mutants identified forms of RPA with reduced affinity for ssDNA that are fully active, and other mutants with higher affinity that are inactive. Single molecule studies showed that while RPA binds ssDNA with high affinity, the RPA complex can rapidly diffuse along ssDNA and be displaced by other proteins that act on ssDNA. Finally, dynamic DNA binding allows RPA to prevent error-prone repair of double-stranded breaks and promote error-free repair. Together, these findings suggest a new paradigm where RPA acts as a first responder at sites with ssDNA, thereby actively coordinating DNA repair and DNA synthesis.
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Affiliation(s)
- Ran Chen
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
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229
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Gao J, Wang H, Wong AHH, Zeng G, Huang Z, Wang Y, Sang J, Wang Y. Regulation of Rfa2 phosphorylation in response to genotoxic stress in Candida albicans. Mol Microbiol 2014; 94:141-55. [PMID: 25109320 DOI: 10.1111/mmi.12749] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2014] [Indexed: 01/10/2023]
Abstract
Successful pathogens must be able to swiftly respond to and repair DNA damages inflicted by the host defence. The replication protein A (RPA) complex plays multiple roles in DNA damage response and is regulated by phosphorylation. However, the regulators of RPA phosphorylation remain unclear. Here, we investigated Rfa2 phosphorylation in the pathogenic fungus Candida albicans. Rfa2, a RFA subunit, is phosphorylated when DNA replication is inhibited by hydroxyurea and dephosphorylated during the recovery. By screening a phosphatase mutant library, we found that Pph3 associates with different regulatory subunits to differentially control Rfa2 dephosphorylation in stressed and unstressed cells. Site-directed mutagenesis revealed T11, S18, S29, and S30 being critical for Rfa2 phosphorylation in response to genotoxic insult. We obtained evidence that the genome integrity checkpoint kinase Mec1 and the cyclin-dependent kinase Clb2-Cdc28 mediate Rfa2 phosphorylation. Although cells expressing either a phosphomimetic or a non-phosphorylatable version of Rfa2 had defects, the latter exhibited greater sensitivity to genotoxic challenge, failure to repair DNA damages and to deactivate Rad53-mediated checkpoint pathways in a dosage-dependent manner. These mutants were also less virulent in mice. Our results provide important new insights into the regulatory mechanism and biological significance of Rfa2 phosphorylation in C. albicans.
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Affiliation(s)
- Jiaxin Gao
- Key Laboratory of Cell Proliferation and Regulation Biology, College of Life Sciences, Beijing Normal University, Beijing, China; Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
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230
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Eschbach V, Kobbe D. Different replication protein A complexes of Arabidopsis thaliana have different DNA-binding properties as a function of heterotrimer composition. PLANT & CELL PHYSIOLOGY 2014; 55:1460-1472. [PMID: 24880780 DOI: 10.1093/pcp/pcu076] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The heterotrimeric RPA (replication protein A) protein complex has single-stranded DNA-binding functions that are important for all DNA processing pathways in eukaryotic cells. In Arabidopsis thaliana, which has five homologs of the RPA1 subunit and two homologs each of RPA2 and RPA3, in theory 20 RPA complexes could form. Using Escherichia coli as a heterologous expression system and analysing the results of the co-purification of the different subunits, we conclude that AtRPA1a interacts with the AtRPA2b subunit, and AtRPA1b interacts with AtRPA2a. Additionally either AtRPA3a or AtRPA3b is part of the complexes. As shown by electrophoretic mobility shift assays, all of the purified AtRPA complexes bind single-stranded DNA, but differences in DNA binding, especially with respect to modified DNA, could be revealed for all four of the analyzed RPA complexes. Thus, the RPA3 subunits influence the DNA-binding properties of the complexes differently despite their high degree of similarity of 82%. The data support the idea that in plants a subfunctionalization of RPA homologs has occurred and that different complexes act preferentially in different pathways.
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Affiliation(s)
- Verena Eschbach
- Botanical Institute II, Karlsruhe Institute of Technology (KIT), D-76131 Karlsruhe, Germany
| | - Daniela Kobbe
- Botanical Institute II, Karlsruhe Institute of Technology (KIT), D-76131 Karlsruhe, Germany
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231
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Nguyen B, Sokoloski J, Galletto R, Elson EL, Wold MS, Lohman TM. Diffusion of human replication protein A along single-stranded DNA. J Mol Biol 2014; 426:3246-3261. [PMID: 25058683 DOI: 10.1016/j.jmb.2014.07.014] [Citation(s) in RCA: 106] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 06/30/2014] [Accepted: 07/08/2014] [Indexed: 10/25/2022]
Abstract
Replication protein A (RPA) is a eukaryotic single-stranded DNA (ssDNA) binding protein that plays critical roles in most aspects of genome maintenance, including replication, recombination and repair. RPA binds ssDNA with high affinity, destabilizes DNA secondary structure and facilitates binding of other proteins to ssDNA. However, RPA must be removed from or redistributed along ssDNA during these processes. To probe the dynamics of RPA-DNA interactions, we combined ensemble and single-molecule fluorescence approaches to examine human RPA (hRPA) diffusion along ssDNA and find that an hRPA heterotrimer can diffuse rapidly along ssDNA. Diffusion of hRPA is functional in that it provides the mechanism by which hRPA can transiently disrupt DNA hairpins by diffusing in from ssDNA regions adjacent to the DNA hairpin. hRPA diffusion was also monitored by the fluctuations in fluorescence intensity of a Cy3 fluorophore attached to the end of ssDNA. Using a novel method to calibrate the Cy3 fluorescence intensity as a function of hRPA position on the ssDNA, we estimate a one-dimensional diffusion coefficient of hRPA on ssDNA of D1~5000nt(2) s(-1) at 37°C. Diffusion of hRPA while bound to ssDNA enables it to be readily repositioned to allow other proteins access to ssDNA.
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Affiliation(s)
- Binh Nguyen
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Joshua Sokoloski
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Roberto Galletto
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Elliot L Elson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Marc S Wold
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Timothy M Lohman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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232
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Xie S, Lu Y, Jakoncic J, Sun H, Xia J, Qian C. Structure of RPA32 bound to the N-terminus of SMARCAL1 redefines the binding interface between RPA32 and its interacting proteins. FEBS J 2014; 281:3382-96. [PMID: 24910198 DOI: 10.1111/febs.12867] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 05/16/2014] [Accepted: 06/05/2014] [Indexed: 11/28/2022]
Abstract
UNLABELLED Replication protein A subunit RPA32 contains a C-terminal domain that interacts with a variety of DNA damage response proteins including SMARCAL1, Tipin, UNG2 and XPA. We have solved the high-resolution crystal structure of RPA32 C-terminal domain (RPA32C) in complex with a 26-amino-acid peptide derived from the N-terminus of SMARCAL1 (SMARCAL1N). The RPA32C-SMARCAL1N structure reveals a 1 : 1 binding stoichiometry and displays a well-ordered binding interface. SMARCAL1N adopts a long α-helical conformation with the highly conserved 11 residues aligned on one face of the α-helix showing extensive interactions with the RPA32C domain. Extensive mutagenesis experiments were performed to corroborate the interactions observed in crystal structure. Moreover, the α1/α2 loop of the RPA32C domain undergoes a conformational rearrangement upon SMARCAL1N binding. NMR study has further confirmed that the RPA32C-SMARCAL1N interaction induces conformational changes in RPA32C. Isothermal titration calorimetry studies have also demonstrated that the conserved α-helical motif defined in the current study is required for sufficient binding of RPA32C. Taken together, our study has provided convincing structural information that redefines the common recognition pattern shared by RPA32C interacting proteins. DATABASE The atomic coordinates of RPA32C in complex with 26-aa SMARCAL1 (SMARCAL1N) peptide have been deposited at the Protein Data Bank with accession code 4MQV. STRUCTURED DIGITAL ABSTRACT RPA32 and SMARCAL1 bind by isothermal titration calorimetry(1, 2, 3, 4, 5, 6, 7, 8, 9) RPA32 and SMARCAL1 bind by molecular sieving (View interaction) RPA32 and SMARCAL1 bind by x-ray crystallography (View interaction) Tipin and RPA32 bind by isothermal titration calorimetry (1, 2) RPA32 and UNG2 bind by isothermal titration calorimetry (1, 2, 3) SMARCAL1 and RPA32 bind by nuclear magnetic resonance (View interaction) UNG2 and RPA32 bind by nuclear magnetic resonance (View interaction) Tipin and RPA32 bind by nuclear magnetic resonance (View interaction).
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Affiliation(s)
- Si Xie
- Department of Biochemistry, the University of Hong Kong, China
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233
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Feldkamp MD, Mason AC, Eichman BF, Chazin WJ. Structural analysis of replication protein A recruitment of the DNA damage response protein SMARCAL1. Biochemistry 2014; 53:3052-61. [PMID: 24730652 PMCID: PMC4020579 DOI: 10.1021/bi500252w] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
![]()
SWI/SNF-related,
matrix-associated, actin-dependent regulator of
chromatin, subfamily A-like1 (SMARCAL1) is a recently identified DNA
damage response protein involved in remodeling stalled replication
forks. The eukaryotic single-strand DNA binding protein replication
protein A (RPA) recruits SMARCAL1 to stalled forks in vivo and facilitates regression of forks containing leading strand gaps.
Both activities are mediated by a direct interaction between an RPA
binding motif (RBM) at the N-terminus of SMARCAL1 and the C-terminal
winged-helix domain of the RPA 32 kDa subunit (RPA32C). Here we report
a biophysical and structural characterization of the SMARCAL1–RPA
interaction. Isothermal titration calorimetry and circular dichroism
spectroscopy revealed that RPA32C binds SMARCAL1-RBM with a Kd of 2.5 μM and induces a disorder-to-helix
transition. The crystal structure of RPA32C was refined to 1.4 Å
resolution, and the SMARCAL1-RBM binding site was mapped on the structure
on the basis of nuclear magnetic resonance chemical shift perturbations.
Conservation of the interaction surface to other RBM-containing proteins
allowed construction of a model for the RPA32C/SMARCAL1-RBM complex.
The implications of our results are discussed with respect to the
recruitment of SMARCAL1 and other DNA damage response and repair proteins
to stalled replication forks.
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Affiliation(s)
- Michael D Feldkamp
- Department of Biochemistry, ‡Department of Biological Sciences, §Department of Chemistry, and ∥Center for Structural Biology, Vanderbilt University , Nashville, Tennessee 37232, United States
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234
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Kovvuru P, Mancilla PE, Shirode AB, Murray TM, Begley TJ, Reliene R. Oral ingestion of silver nanoparticles induces genomic instability and DNA damage in multiple tissues. Nanotoxicology 2014; 9:162-71. [DOI: 10.3109/17435390.2014.902520] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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235
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Frank A, Vangamudi B, Feldkamp MD, Souza-Fagundes E, Luzwick JW, Cortez D, Olejniczak E, Waterson AG, Rossanese O, Chazin WJ, Fesik SW. Discovery of a potent stapled helix peptide that binds to the 70N domain of replication protein A. J Med Chem 2014; 57:2455-61. [PMID: 24491171 PMCID: PMC3969094 DOI: 10.1021/jm401730y] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Indexed: 01/07/2023]
Abstract
Stapled helix peptides can serve as useful tools for inhibiting protein-protein interactions but can be difficult to optimize for affinity. Here we describe the discovery and optimization of a stapled helix peptide that binds to the N-terminal domain of the 70 kDa subunit of replication protein A (RPA70N). In addition to applying traditional optimization strategies, we employed a novel approach for efficiently designing peptides containing unnatural amino acids. We discovered hot spots in the target protein using a fragment-based screen, identified the amino acid that binds to the hot spot, and selected an unnatural amino acid to incorporate, based on the structure-activity relationships of small molecules that bind to this site. The resulting stapled helix peptide potently and selectively binds to RPA70N, does not disrupt ssDNA binding, and penetrates cells. This peptide may serve as a probe to explore the therapeutic potential of RPA70N inhibition in cancer.
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Affiliation(s)
- Andreas
O. Frank
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232-0146, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232-8725, United States
| | - Bhavatarini Vangamudi
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232-0146, United States
| | - Michael D. Feldkamp
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232-0146, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232-8725, United States
| | - Elaine
M. Souza-Fagundes
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232-0146, United States
| | - Jessica W. Luzwick
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232-0146, United States
| | - David Cortez
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232-0146, United States
| | - Edward
T. Olejniczak
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232-0146, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232-8725, United States
| | - Alex G. Waterson
- Department
of Pharmacology, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232-6600, United States
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37232-1822, United States
| | - Olivia
W. Rossanese
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232-0146, United States
| | - Walter J. Chazin
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232-0146, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232-8725, United States
- Department
of Pharmacology, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232-6600, United States
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37232-1822, United States
| | - Stephen W. Fesik
- Department
of Biochemistry, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232-0146, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232-8725, United States
- Department
of Pharmacology, Vanderbilt University School
of Medicine, Nashville, Tennessee 37232-6600, United States
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37232-1822, United States
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236
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Ren W, Chen H, Sun Q, Tang X, Lim SC, Huang J, Song H. Structural basis of SOSS1 complex assembly and recognition of ssDNA. Cell Rep 2014; 6:982-991. [PMID: 24630995 DOI: 10.1016/j.celrep.2014.02.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Revised: 02/06/2014] [Accepted: 02/14/2014] [Indexed: 01/03/2023] Open
Abstract
The SOSS1 complex comprising SOSSA, SOSSB1, and SOSSC senses single-stranded DNA (ssDNA) and promotes repair of DNA double-strand breaks (DSBs). But how SOSS1 is assembled and recognizes ssDNA remains elusive. The crystal structure of the N-terminal half of SOSSA (SOSSAN) in complex with SOSSB1 and SOSSC showed that SOSSAN serves as a scaffold to bind both SOSSB1 and SOSSC for assembly of the SOSS1 complex. The structures of SOSSAN/B1 in complex with a 12 nt ssDNA and SOSSAN/B1/C in complex with a 35 nt ssDNA showed that SOSSB1 interacts with both SOSSAN and ssDNA via two distinct surfaces. Recognition of ssDNA with a length of up to nine nucleotides is mediated solely by SOSSB1, whereas neither SOSSC nor SOSSAN are critical for ssDNA binding. These results reveal the structural basis of SOSS1 assembly and provide a framework for further study of the mechanism governing longer ssDNA recognition by the SOSS1 complex during DSB repair.
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Affiliation(s)
- Wendan Ren
- Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China; Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Hongxia Chen
- Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China
| | - Qiangzu Sun
- Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China
| | - Xuhua Tang
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Siew Choo Lim
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Jun Huang
- Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China.
| | - Haiwei Song
- Life Sciences Institute, Zhejiang University, 388 Yuhangtang Road, Hangzhou 310058, China; Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore; Department of Biochemistry, National University of Singapore, 14 Science Drive, Singapore 117543, Singapore.
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237
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Toledo LI, Altmeyer M, Rask MB, Lukas C, Larsen DH, Povlsen LK, Bekker-Jensen S, Mailand N, Bartek J, Lukas J. ATR prohibits replication catastrophe by preventing global exhaustion of RPA. Cell 2014; 155:1088-103. [PMID: 24267891 DOI: 10.1016/j.cell.2013.10.043] [Citation(s) in RCA: 634] [Impact Index Per Article: 63.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Revised: 08/19/2013] [Accepted: 10/18/2013] [Indexed: 11/26/2022]
Abstract
ATR, activated by replication stress, protects replication forks locally and suppresses origin firing globally. Here, we show that these functions of ATR are mechanistically coupled. Although initially stable, stalled forks in ATR-deficient cells undergo nucleus-wide breakage after unscheduled origin firing generates an excess of single-stranded DNA that exhausts the nuclear pool of RPA. Partial reduction of RPA accelerated fork breakage, and forced elevation of RPA was sufficient to delay such "replication catastrophe" even in the absence of ATR activity. Conversely, unscheduled origin firing induced breakage of stalled forks even in cells with active ATR. Thus, ATR-mediated suppression of dormant origins shields active forks against irreversible breakage via preventing exhaustion of nuclear RPA. This study elucidates how replicating genomes avoid destabilizing DNA damage. Because cancer cells commonly feature intrinsically high replication stress, this study also provides a molecular rationale for their hypersensitivity to ATR inhibitors.
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Affiliation(s)
- Luis Ignacio Toledo
- Chromosome Stability and Dynamics Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
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238
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Yu H, Lim HH, Tjokro NO, Sathiyanathan P, Natarajan S, Chew TW, Klonisch T, Goodman SD, Surana U, Dröge P. Chaperoning HMGA2 protein protects stalled replication forks in stem and cancer cells. Cell Rep 2014; 6:684-97. [PMID: 24508460 DOI: 10.1016/j.celrep.2014.01.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 11/26/2013] [Accepted: 01/14/2014] [Indexed: 10/25/2022] Open
Abstract
Maintaining genome integrity requires the accurate and complete replication of chromosomal DNA. This is of the utmost importance for embryonic stem cells (ESCs), which differentiate into cells of all lineages, including germ cells. However, endogenous and exogenous factors frequently induce stalling of replication forks in every cell cycle, which can trigger mutations and chromosomal instabilities. We show here that the oncofetal, nonhistone chromatin factor HMGA2 equips cells with a highly effective first-line defense mechanism against endonucleolytic collapse of stalled forks. This fork-stabilizing function most likely employs scaffold formation at branched DNA via multiple DNA-binding domains. Moreover, HMGA2 works independently of other human factors in two heterologous cell systems to prevent DNA strand breaks. This fork chaperone function seemingly evolved to preserve ESC genome integrity. It is hijacked by tumor (stem) cells to also guard their genomes against DNA-damaging agents widely used to treat cancer patients.
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Affiliation(s)
- Haojie Yu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Hong Hwa Lim
- Institute of Molecular and Cell Biology, Proteos, 61 Biopolis Drive, Singapore 138673, Singapore; Bioprocessing Technology Institute, 20 Biopolis Way, 6-01 Centros, Singapore 138668, Singapore
| | - Natalia O Tjokro
- Division of Biomedical Sciences, The Herman Ostrow School of Dentistry of the University of Southern California, Los Angeles, CA 90089, USA
| | - Padmapriya Sathiyanathan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Suchitra Natarajan
- Department of Human Anatomy and Cell Science, Faculty of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Tian Wei Chew
- Institute of Molecular and Cell Biology, Proteos, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Thomas Klonisch
- Department of Human Anatomy and Cell Science, Faculty of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; Department of Medical Microbiology and Infectious Diseases, Faculty of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; Department of Surgery, Faculty of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Steven D Goodman
- Division of Biomedical Sciences, The Herman Ostrow School of Dentistry of the University of Southern California, Los Angeles, CA 90089, USA
| | - Uttam Surana
- Institute of Molecular and Cell Biology, Proteos, 61 Biopolis Drive, Singapore 138673, Singapore
| | - Peter Dröge
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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239
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Carvalho JFS, Kanaar R. Targeting homologous recombination-mediated DNA repair in cancer. Expert Opin Ther Targets 2014; 18:427-58. [PMID: 24491188 DOI: 10.1517/14728222.2014.882900] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION DNA is the target of many traditional non-specific chemotherapeutic drugs. New drugs or therapeutic approaches with a more rational and targeted component are mandatory to improve the success of cancer therapy. The homologous recombination (HR) pathway is an attractive target for the development of inhibitors because cancer cells rely heavily on HR for repair of DNA double-strand breaks resulting from chemotherapeutic treatments. Additionally, the discovery that poly(ADP)ribose polymerase-1 inhibitors selectively kill cells with genetic defects in HR has spurned an even greater interest in inhibitors of HR. AREAS COVERED HR drives the repair of broken DNA via numerous protein-mediated sequential DNA manipulations. Due to extensive number of steps and proteins involved, the HR pathway provides a rich pool of potential drug targets. This review discusses the latest developments concerning the strategies being explored to inhibit HR. Particular attention is given to the identification of small molecule inhibitors of key HR proteins, including the BRCA proteins and RAD51. EXPERT OPINION Current HR inhibitors are providing the basis for pharmaceutical development of more potent and specific inhibitors to be applied in mono- or combinatorial therapy regimes, while novel targets will be uncovered by experiments aimed to gain a deeper mechanistic understanding of HR and its subpathways.
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Affiliation(s)
- João F S Carvalho
- Erasmus MC Cancer Institute, Department of Genetics, Department of Radiation Oncology, Cancer Genomics Netherlands , PO Box 2040, 3000 CA Rotterdam , The Netherlands
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240
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Gibb B, Ye LF, Gergoudis SC, Kwon Y, Niu H, Sung P, Greene EC. Concentration-dependent exchange of replication protein A on single-stranded DNA revealed by single-molecule imaging. PLoS One 2014; 9:e87922. [PMID: 24498402 PMCID: PMC3912175 DOI: 10.1371/journal.pone.0087922] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 12/31/2013] [Indexed: 11/18/2022] Open
Abstract
Replication protein A (RPA) is a ubiquitous eukaryotic single-stranded DNA (ssDNA) binding protein necessary for all aspects of DNA metabolism involving an ssDNA intermediate, including DNA replication, repair, recombination, DNA damage response and checkpoint activation, and telomere maintenance [1], [2], [3]. The role of RPA in most of these reactions is to protect the ssDNA until it can be delivered to downstream enzymes. Therefore a crucial feature of RPA is that it must bind very tightly to ssDNA, but must also be easily displaced from ssDNA to allow other proteins to gain access to the substrate. Here we use total internal reflection fluorescence microscopy and nanofabricated DNA curtains to visualize the behavior of Saccharomyces cerevisiae RPA on individual strands of ssDNA in real-time. Our results show that RPA remains bound to ssDNA for long periods of time when free protein is absent from solution. In contrast, RPA rapidly dissociates from ssDNA when free RPA is present in solution allowing rapid exchange between the free and bound states. In addition, the S. cerevisiae DNA recombinase Rad51 and E. coli single-stranded binding protein (SSB) also promote removal of RPA from ssDNA. These results reveal an unanticipated exchange between bound and free RPA suggesting a binding mechanism that can confer exceptionally slow off rates, yet also enables rapid displacement through a direct exchange mechanism that is reliant upon the presence of free ssDNA-binding proteins in solution. Our results indicate that RPA undergoes constant microscopic dissociation under all conditions, but this is only manifested as macroscopic dissociation (i.e. exchange) when free proteins are present in solution, and this effect is due to mass action. We propose that the dissociation of RPA from ssDNA involves a partially dissociated intermediate, which exposes a small section of ssDNA allowing other proteins to access to the DNA.
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Affiliation(s)
- Bryan Gibb
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
| | - Ling F. Ye
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Stephanie C. Gergoudis
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - YoungHo Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Hengyao Niu
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Eric C. Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
- Howard Hughes Medical Institute, Columbia University, New York, New York, United States of America
- * E-mail:
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241
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Dickey TH, Altschuler SE, Wuttke DS. Single-stranded DNA-binding proteins: multiple domains for multiple functions. Structure 2014; 21:1074-84. [PMID: 23823326 DOI: 10.1016/j.str.2013.05.013] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 05/15/2013] [Accepted: 05/20/2013] [Indexed: 10/26/2022]
Abstract
The recognition of single-stranded DNA (ssDNA) is integral to myriad cellular functions. In eukaryotes, ssDNA is present stably at the ends of chromosomes and at some promoter elements. Furthermore, it is formed transiently by several cellular processes including telomere synthesis, transcription, and DNA replication, recombination, and repair. To coordinate these diverse activities, a variety of proteins have evolved to bind ssDNA in a manner specific to their function. Here, we review the recognition of ssDNA through the analysis of high-resolution structures of proteins in complex with ssDNA. This functionally diverse set of proteins arises from a limited set of structural motifs that can be modified and arranged to achieve distinct activities, including a range of ligand specificities. We also investigate the ways in which these domains interact in the context of large multidomain proteins/complexes. These comparisons reveal the structural features that define the range of functions exhibited by these proteins.
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Affiliation(s)
- Thayne H Dickey
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
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242
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Tsaalbi-Shtylik A, Moser J, Mullenders LHF, Jansen JG, de Wind N. Persistently stalled replication forks inhibit nucleotide excision repair in trans by sequestering Replication protein A. Nucleic Acids Res 2014; 42:4406-13. [PMID: 24464993 PMCID: PMC3985633 DOI: 10.1093/nar/gkt1412] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Rev3, the catalytic subunit of DNA polymerase ζ, is essential for translesion synthesis of cytotoxic DNA photolesions, whereas the Rev1 protein plays a noncatalytic role in translesion synthesis. Here, we reveal that mammalian Rev3(-/-) and Rev1(-/-) cell lines additionally display a nucleotide excision repair (NER) defect, specifically during S phase. This defect is correlated with the normal recruitment but protracted persistence at DNA damage sites of factors involved in an early stage of NER, while repair synthesis is affected. Remarkably, the NER defect becomes apparent only at 2 h post-irradiation indicating that Rev3 affects repair synthesis only indirectly, rather than performing an enzymatic role in NER. We provide evidence that the NER defect is caused by scarceness of Replication protein A (Rpa) available to NER, resulting from its sequestration at stalled replication forks. Also the induction of replicative stress using hydroxyurea precludes the accumulation of Rpa at photolesion sites, both in Rev3(-/-) and in wild-type cells. These data support a model in which the limited Rpa pool coordinates replicative stress and NER, resulting in increased cytotoxicity of ultraviolet light when replicative stress exceeds a threshold.
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Affiliation(s)
- Anastasia Tsaalbi-Shtylik
- Department of Toxicogenetics, Leiden University Medical Center, PO box 9600, 2300 RC Leiden, The Netherlands
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243
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Kubota S, Fukumoto Y, Ishibashi K, Soeda S, Kubota S, Yuki R, Nakayama Y, Aoyama K, Yamaguchi N, Yamaguchi N. Activation of the prereplication complex is blocked by mimosine through reactive oxygen species-activated ataxia telangiectasia mutated (ATM) protein without DNA damage. J Biol Chem 2014; 289:5730-46. [PMID: 24421316 DOI: 10.1074/jbc.m113.546655] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mimosine is an effective cell synchronization reagent used for arresting cells in late G1 phase. However, the mechanism underlying mimosine-induced G1 cell cycle arrest remains unclear. Using highly synchronous cell populations, we show here that mimosine blocks S phase entry through ATM activation. HeLa S3 cells are exposed to thymidine for 15 h, released for 9 h by washing out the thymidine, and subsequently treated with 1 mM mimosine for a further 15 h (thymidine → mimosine). In contrast to thymidine-induced S phase arrest, mimosine treatment synchronizes >90% of cells at the G1-S phase boundary by inhibiting the transition of the prereplication complex to the preinitiation complex. Mimosine treatment activates ataxia telangiectasia mutated (ATM)/ataxia telangiectasia and Rad3-related (ATR)-mediated checkpoint signaling without inducing DNA damage. Inhibition of ATM activity is found to induce mimosine-arrested cells to enter S phase. In addition, ATM activation by mimosine treatment is mediated by reactive oxygen species (ROS). These results suggest that, upon mimosine treatment, ATM blocks S phase entry in response to ROS, which prevents replication fork stalling-induced DNA damage.
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Affiliation(s)
- Shoichi Kubota
- From the Department of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan
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244
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Petruseva I, Evdokimov AN, Lavrik OI. Molecular mechanism of global genome nucleotide excision repair. Acta Naturae 2014; 6:23-34. [PMID: 24772324 PMCID: PMC3999463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Nucleotide excision repair (NER) is a multistep process that recognizes and eliminates a wide spectrum of damage causing significant distortions in the DNA structure, such as UV-induced damage and bulky chemical adducts. The consequences of defective NER are apparent in the clinical symptoms of individuals affected by three disorders associated with reduced NER capacities: xeroderma pigmentosum (XP), Cockayne syndrome (CS), and trichothiodystrophy (TTD). These disorders have in common increased sensitivity to UV irradiation, greatly elevated cancer incidence (XP), and multi-system immunological and neurological disorders. The eucaryotic NER system eliminates DNA damage by the excision of 24-32 nt single-strand oligonucleotides from a damaged strand, followed by restoration of an intact double helix by DNA repair synthesis and DNA ligation. About 30 core polypeptides are involved in the entire repair process. NER consists of two pathways distinct in initial damage sensor proteins: transcription-coupled repair (TC-NER) and global genome repair (GG-NER). The article reviews current knowledge on the molecular mechanisms underlying damage recognition and its elimination from mammalian DNA.
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Affiliation(s)
- I.O. Petruseva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, prosp. Akad. Lavrentyeva, 8, 630090, Novosibirsk, Russia
| | - A. N. Evdokimov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, prosp. Akad. Lavrentyeva, 8, 630090, Novosibirsk, Russia
- Altai State University, Ministry of Education and Science of the Russian Federation, prosp. Lenina, 61, 656049, Barnaul, Russia
| | - O. I. Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, prosp. Akad. Lavrentyeva, 8, 630090, Novosibirsk, Russia
- Altai State University, Ministry of Education and Science of the Russian Federation, prosp. Lenina, 61, 656049, Barnaul, Russia
- Novosibirsk State University, Ministry of Education and Science of the Russian Federation, Pirogova Str., 2, 630090, Novosibirsk, Russia
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245
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Zhang J, Zhou R, Inoue J, Mikawa T, Ha T. Single molecule analysis of Thermus thermophilus SSB protein dynamics on single-stranded DNA. Nucleic Acids Res 2013; 42:3821-32. [PMID: 24371279 PMCID: PMC3973332 DOI: 10.1093/nar/gkt1316] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Single-stranded (ss) DNA binding (SSB) proteins play central roles in DNA replication, recombination and repair in all organisms. We previously showed that Escherichia coli (Eco) SSB, a homotetrameric bacterial SSB, undergoes not only rapid ssDNA-binding mode transitions but also one-dimensional diffusion (or migration) while remaining bound to ssDNA. Whereas the majority of bacterial SSB family members function as homotetramers, dimeric SSB proteins were recently discovered in a distinct bacterial lineage of extremophiles, the Thermus–Deinococcus group. Here we show, using single-molecule fluorescence resonance energy transfer (FRET), that homodimeric bacterial SSB from Thermus thermophilus (Tth) is able to diffuse spontaneously along ssDNA over a wide range of salt concentrations (20–500 mM NaCl), and that TthSSB diffusion can help transiently melt the DNA hairpin structures. Furthermore, we show that two TthSSB molecules undergo transitions among different DNA-binding modes while remaining bound to ssDNA. Our results extend our previous observations on homotetrameric SSBs to homodimeric SSBs, indicating that the dynamic features may be shared among different types of SSB proteins. These dynamic features of SSBs may facilitate SSB redistribution and removal on/from ssDNA, and help recruit other SSB-interacting proteins onto ssDNA for subsequent DNA processing in DNA replication, recombination and repair.
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Affiliation(s)
- Jichuan Zhang
- Department of Physics and Center for the Physics of Living Cells, University of Illinois, Urbana, IL 61801, USA, Department of Materials Science and Engineering, University of Illinois, Urbana, IL 61801, USA, RIKEN, Cellular and Molecular Biology Unit, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan and Howard Hughes Medical Institute, University of Illinois, Urbana, IL 61801, USA
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246
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Aklilu BB, Soderquist RS, Culligan KM. 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 2013; 42:3104-18. [PMID: 24335281 PMCID: PMC3950690 DOI: 10.1093/nar/gkt1292] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Replication Protein A (RPA) is a heterotrimeric protein complex that binds single-stranded DNA. In plants, multiple genes encode the three RPA subunits (RPA1, RPA2 and RPA3), including five RPA1-like genes in Arabidopsis. Phylogenetic analysis suggests two distinct groups composed of RPA1A, RPA1C, RPA1E (ACE group) and RPA1B, RPA1D (BD group). ACE-group members are transcriptionally induced by ionizing radiation, while BD-group members show higher basal transcription and are not induced by ionizing radiation. Analysis of rpa1 T-DNA insertion mutants demonstrates that although each mutant line is likely null, all mutant lines are viable and display normal vegetative growth. The rpa1c and rpa1e single mutants however display hypersensitivity to ionizing radiation, and combination of rpa1c and rpa1e results in additive hypersensitivity to a variety of DNA damaging agents. Combination of the partially sterile rpa1a with rpa1c results in complete sterility, incomplete synapsis and meiotic chromosome fragmentation, suggesting an early role for RPA1C in promoting homologous recombination. Combination of either rpa1c and/or rpa1e with atr revealed additive hypersensitivity phenotypes consistent with each functioning in unique repair pathways. In contrast, rpa1b rpa1d double mutant plants display slow growth and developmental defects under non-damaging conditions. We show these defects in the rpa1b rpa1d mutant are likely the result of defective DNA replication leading to reduction in cell division.
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Affiliation(s)
- Behailu B Aklilu
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA and Program in Genetics, University of New Hampshire, Durham NH 03824, USA
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247
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Frank AO, Feldkamp MD, Kennedy JP, Waterson AG, Pelz NF, Patrone JD, Vangamudi B, Camper DV, Rossanese OW, Chazin WJ, Fesik SW. Discovery of a potent inhibitor of replication protein a protein-protein interactions using a fragment-linking approach. J Med Chem 2013; 56:9242-50. [PMID: 24147804 DOI: 10.1021/jm401333u] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Replication protein A (RPA), the major eukaryotic single-stranded DNA (ssDNA)-binding protein, is involved in nearly all cellular DNA transactions. The RPA N-terminal domain (RPA70N) is a recruitment site for proteins involved in DNA-damage response and repair. Selective inhibition of these protein-protein interactions has the potential to inhibit the DNA-damage response and to sensitize cancer cells to DNA-damaging agents without affecting other functions of RPA. To discover a potent, selective inhibitor of the RPA70N protein-protein interactions to test this hypothesis, we used NMR spectroscopy to identify fragment hits that bind to two adjacent sites in the basic cleft of RPA70N. High-resolution X-ray crystal structures of RPA70N-ligand complexes revealed how these fragments bind to RPA and guided the design of linked compounds that simultaneously occupy both sites. We have synthesized linked molecules that bind to RPA70N with submicromolar affinity and minimal disruption of RPA's interaction with ssDNA.
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Affiliation(s)
- Andreas O Frank
- Department of Biochemistry, Vanderbilt University School of Medicine , Nashville, Tennessee 37232-0146, United States
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248
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Wan L, Lou J, Xia Y, Su B, Liu T, Cui J, Sun Y, Lou H, Huang J. hPrimpol1/CCDC111 is a human DNA primase-polymerase required for the maintenance of genome integrity. EMBO Rep 2013; 14:1104-12. [PMID: 24126761 DOI: 10.1038/embor.2013.159] [Citation(s) in RCA: 144] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Revised: 09/17/2013] [Accepted: 09/17/2013] [Indexed: 11/09/2022] Open
Abstract
Prim-pol is a recently identified DNA primase-polymerase belonging to the archaeao-eukaryotic primase (AEP) superfamily. Here, we characterize a previously unrecognized prim-pol in human cells, which we designate hPrimpol1 (human primase-polymerase 1). hPrimpol1 possesses primase and DNA polymerase activities in vitro, interacts directly with RPA1 and is recruited to sites of DNA damage and stalled replication forks in an RPA1-dependent manner. Cells depleted of hPrimpol1 display increased spontaneous DNA damage and defects in the restart of stalled replication forks. Both RPA1 binding and the primase activity of hPrimpol1 are required for its cellular function during DNA replication. Our results indicate that hPrimpol1 is a novel factor involved in the response to DNA replication stress.
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Affiliation(s)
- Li Wan
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
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249
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Mohni KN, Smith S, Dee AR, Schumacher AJ, Weller SK. Herpes simplex virus type 1 single strand DNA binding protein and helicase/primase complex disable cellular ATR signaling. PLoS Pathog 2013; 9:e1003652. [PMID: 24098119 PMCID: PMC3789782 DOI: 10.1371/journal.ppat.1003652] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Accepted: 08/07/2013] [Indexed: 11/19/2022] Open
Abstract
Herpes Simplex Virus type 1 (HSV-1) has evolved to disable the cellular DNA damage response kinase, ATR. We have previously shown that HSV-1-infected cells are unable to phosphorylate the ATR substrate Chk1, even under conditions in which replication forks are stalled. Here we report that the HSV-1 single stranded DNA binding protein (ICP8), and the helicase/primase complex (UL8/UL5/UL52) form a nuclear complex in transfected cells that is necessary and sufficient to disable ATR signaling. This complex localizes to sites of DNA damage and colocalizes with ATR/ATRIP and RPA, but under these conditions, the Rad9-Rad1-Hus1 checkpoint clamp (9-1-1) do not. ATR is generally activated by substrates that contain ssDNA adjacent to dsDNA, and previous work from our laboratory has shown that ICP8 and helicase/primase also recognize this substrate. We suggest that these four viral proteins prevent ATR activation by binding to the DNA substrate and obstructing loading of the 9-1-1 checkpoint clamp. Exclusion of 9-1-1 prevents recruitment of TopBP1, the ATR kinase activator, and thus effectively disables ATR signaling. These data provide the first example of viral DNA replication proteins obscuring access to a DNA substrate that would normally trigger a DNA damage response and checkpoint signaling. This unusual mechanism used by HSV suggests that it may be possible to inhibit ATR signaling by preventing recruitment of the 9-1-1 clamp and TopBP1. DNA viruses that replicate in the nucleus have been shown to both activate and inactivate various components of the cellular DNA damage response (DDR). Previous reports from our laboratory and others have demonstrated that Herpes Simplex Virus (HSV) utilizes some aspects of the DDR while inactivating others. Paradoxically, HSV utilizes the DDR kinase ATR to complete its life cycle while at the same time disabling the kinase from activating DDR signaling. In this report we provide detail describing the mechanism of ATR inactivation. ATR is normally activated in response to single strand DNA (ssDNA), which serves as a scaffold to recruit several proteins required for complete ATR activation. In this paper we provide evidence that the HSV encoded ssDNA binding protein and helicase/primase complex function to mask the DNA substrate that recruits the ATR kinase activator. This represents the first example of viral DNA replication proteins masking a DNA substrate that could be sensed by the cell as damaged DNA and activate checkpoint signaling. It also explains how ATR can be recruited to sites of viral DNA replication in the absence of checkpoint signaling.
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Affiliation(s)
- Kareem N. Mohni
- Department of Molecular, Microbial and Structural Biology and the Molecular Biology and Biochemistry Graduate Program, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Samantha Smith
- Department of Molecular, Microbial and Structural Biology and the Molecular Biology and Biochemistry Graduate Program, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Alexander R. Dee
- Department of Molecular, Microbial and Structural Biology and the Molecular Biology and Biochemistry Graduate Program, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - April J. Schumacher
- Department of Molecular, Microbial and Structural Biology and the Molecular Biology and Biochemistry Graduate Program, University of Connecticut Health Center, Farmington, Connecticut, United States of America
| | - Sandra K. Weller
- Department of Molecular, Microbial and Structural Biology and the Molecular Biology and Biochemistry Graduate Program, University of Connecticut Health Center, Farmington, Connecticut, United States of America
- * E-mail:
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250
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MEIOB targets single-strand DNA and is necessary for meiotic recombination. PLoS Genet 2013; 9:e1003784. [PMID: 24068956 PMCID: PMC3778009 DOI: 10.1371/journal.pgen.1003784] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 07/25/2013] [Indexed: 11/19/2022] Open
Abstract
Meiotic recombination is a mandatory process for sexual reproduction. We identified a protein specifically implicated in meiotic homologous recombination that we named: meiosis specific with OB domain (MEIOB). This protein is conserved among metazoan species and contains single-strand DNA binding sites similar to those of RPA1. Our studies in vitro revealed that both recombinant and endogenous MEIOB can be retained on single-strand DNA. Those in vivo demonstrated the specific expression of Meiob in early meiotic germ cells and the co-localization of MEIOB protein with RPA on chromosome axes. MEIOB localization in Dmc1 (-/-) spermatocytes indicated that it accumulates on resected DNA. Homologous Meiob deletion in mice caused infertility in both sexes, due to a meiotic arrest at a zygotene/pachytene-like stage. DNA double strand break repair and homologous chromosome synapsis were impaired in Meiob (-/-) meiocytes. Interestingly MEIOB appeared to be dispensable for the initial loading of recombinases but was required to maintain a proper number of RAD51 and DMC1 foci beyond the zygotene stage. In light of these findings, we propose that RPA and this new single-strand DNA binding protein MEIOB, are essential to ensure the proper stabilization of recombinases which is required for successful homology search and meiotic recombination.
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