201
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Recent progress in mass spectrometry proteomics for biomedical research. SCIENCE CHINA-LIFE SCIENCES 2017; 60:1093-1113. [DOI: 10.1007/s11427-017-9175-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 09/15/2017] [Indexed: 12/30/2022]
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202
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Gersch M, Gladkova C, Schubert AF, Michel MA, Maslen S, Komander D. Mechanism and regulation of the Lys6-selective deubiquitinase USP30. Nat Struct Mol Biol 2017; 24:920-930. [PMID: 28945249 PMCID: PMC5757785 DOI: 10.1038/nsmb.3475] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 08/30/2017] [Indexed: 12/24/2022]
Abstract
Damaged mitochondria undergo mitophagy, a specialized form of autophagy that is initiated by the protein kinase PINK1 and the ubiquitin E3 ligase Parkin. Ubiquitin-specific protease USP30 antagonizes Parkin-mediated ubiquitination events on mitochondria and is a key negative regulator of mitophagy. Parkin and USP30 both show a preference for assembly or disassembly, respectively, of Lys6-linked polyubiquitin, a chain type that has not been well studied. Here we report crystal structures of human USP30 bound to monoubiquitin and Lys6-linked diubiquitin, which explain how USP30 achieves Lys6-linkage preference through unique ubiquitin binding interfaces. We assess the interplay between USP30, PINK1 and Parkin and show that distally phosphorylated ubiquitin chains impair USP30 activity. Lys6-linkage-specific affimers identify numerous mitochondrial substrates for this modification, and we show that USP30 regulates Lys6-polyubiquitinated TOM20. Our work provides insights into the architecture, activity and regulation of USP30, which will aid drug design against this and related enzymes.
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Affiliation(s)
- Malte Gersch
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | | | - Martin A Michel
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Sarah Maslen
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - David Komander
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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203
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Michel MA, Swatek KN, Hospenthal MK, Komander D. Ubiquitin Linkage-Specific Affimers Reveal Insights into K6-Linked Ubiquitin Signaling. Mol Cell 2017; 68:233-246.e5. [PMID: 28943312 PMCID: PMC5640506 DOI: 10.1016/j.molcel.2017.08.020] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/13/2017] [Accepted: 08/22/2017] [Indexed: 12/30/2022]
Abstract
Several ubiquitin chain types have remained unstudied, mainly because tools and techniques to detect these posttranslational modifications are scarce. Linkage-specific antibodies have shaped our understanding of the roles and dynamics of polyubiquitin signals but are available for only five out of eight linkage types. We here characterize K6- and K33-linkage-specific "affimer" reagents as high-affinity ubiquitin interactors. Crystal structures of affimers bound to their cognate chain types reveal mechanisms of specificity and a K11 cross-reactivity in the K33 affimer. Structure-guided improvements yield superior affinity reagents suitable for western blotting, confocal fluorescence microscopy and pull-down applications. This allowed us to identify RNF144A and RNF144B as E3 ligases that assemble K6-, K11-, and K48-linked polyubiquitin in vitro. A protocol to enrich K6-ubiquitinated proteins from cells identifies HUWE1 as a main E3 ligase for this chain type, and we show that mitofusin-2 is modified with K6-linked polyubiquitin in a HUWE1-dependent manner.
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Affiliation(s)
- Martin A Michel
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kirby N Swatek
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Manuela K Hospenthal
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - David Komander
- Division of Protein and Nucleic Acid Chemistry, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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204
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Abstract
Host anti-viral innate-immune signalling pathways are regulated by a variety of post-translation modifications including ubiquitination, which is critical to regulate various signalling pathways for synthesis of anti-viral molecules. A homeostasis of host immune responses, induced due to viral infection and further ubiquitination, is maintained by the action of deubiquitinases (DUB). Infecting viruses utilize the process of deubiquitination for tricking host immune system wherein viral DUBs compete with host DUBs for inhibition of innate-immune anti-viral signalling pathways, which instead of maintaining an immune homeostasis bring about virus-mediated pathogenesis. This suggests that viruses co-evolve with their hosts to acquire similar machinery for tricking immune surveillance and establishing infection.
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Affiliation(s)
- Puja Kumari
- a Department of Biological Sciences, Laboratory of Immunology and Infectious Disease Biology , Indian Institute of Science Education and Research (IISER) Bhopal , Bhopal , India
| | - Himanshu Kumar
- a Department of Biological Sciences, Laboratory of Immunology and Infectious Disease Biology , Indian Institute of Science Education and Research (IISER) Bhopal , Bhopal , India
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205
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Galper J, Rayner SL, Hogan AL, Fifita JA, Lee A, Chung RS, Blair IP, Yang S. Cyclin F: A component of an E3 ubiquitin ligase complex with roles in neurodegeneration and cancer. Int J Biochem Cell Biol 2017; 89:216-220. [DOI: 10.1016/j.biocel.2017.06.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 06/05/2017] [Accepted: 06/22/2017] [Indexed: 12/13/2022]
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206
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He H, Wang J, Liu T. UV-Induced RPA1 Acetylation Promotes Nucleotide Excision Repair. Cell Rep 2017; 20:2010-2025. [DOI: 10.1016/j.celrep.2017.08.016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 06/21/2017] [Accepted: 07/14/2017] [Indexed: 12/31/2022] Open
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207
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Nikolova T, Kiweler N, Krämer OH. Interstrand Crosslink Repair as a Target for HDAC Inhibition. Trends Pharmacol Sci 2017; 38:822-836. [PMID: 28687272 DOI: 10.1016/j.tips.2017.05.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 05/29/2017] [Accepted: 05/31/2017] [Indexed: 12/29/2022]
Abstract
DNA interstrand crosslinks (ICLs) covalently connect complementary DNA strands. Consequently, DNA replication and transcription are hampered, DNA damage responses (DDR) are initiated, and cell death is triggered. Therefore, drugs inducing ICLs are effective against rapidly growing cancer cells. However, tumors engage a complicated enzymatic machinery to repair and survive ICLs. Several factors, including the post-translational acetylation/deacetylation of lysine residues within proteins, control this network. Histone deacetylases (HDACs) modulate the expression and functions of DNA repair proteins which remove ICLs and control the accessibility of chromatin. Accordingly, histone deacetylase inhibitors (HDACi) are small, pharmacologically and clinically relevant molecules that sensitize cancer cells to ICL inducers. We discuss the mechanism of ICL repair and targets of HDACi within this pathway.
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Affiliation(s)
- Teodora Nikolova
- Institute of Toxicology, University Medical Center, Obere Zahlbacher Strasse 67, 55131 Mainz, Germany.
| | - Nicole Kiweler
- Institute of Toxicology, University Medical Center, Obere Zahlbacher Strasse 67, 55131 Mainz, Germany
| | - Oliver H Krämer
- Institute of Toxicology, University Medical Center, Obere Zahlbacher Strasse 67, 55131 Mainz, Germany.
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208
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Tomimatsu N, Mukherjee B, Harris JL, Boffo FL, Hardebeck MC, Potts PR, Khanna KK, Burma S. DNA-damage-induced degradation of EXO1 exonuclease limits DNA end resection to ensure accurate DNA repair. J Biol Chem 2017; 292:10779-10790. [PMID: 28515316 PMCID: PMC5491765 DOI: 10.1074/jbc.m116.772475] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 05/11/2017] [Indexed: 12/22/2022] Open
Abstract
End resection of DNA double-strand breaks (DSBs) to generate 3'-single-stranded DNA facilitates DSB repair via error-free homologous recombination (HR) while stymieing repair by the error-prone non-homologous end joining (NHEJ) pathway. Activation of DNA end resection involves phosphorylation of the 5' to 3' exonuclease EXO1 by the phosphoinositide 3-kinase-like kinases ATM (ataxia telangiectasia-mutated) and ATR (ATM and Rad3-related) and by the cyclin-dependent kinases 1 and 2. After activation, EXO1 must also be restrained to prevent over-resection that is known to hamper optimal HR and trigger global genomic instability. However, mechanisms by which EXO1 is restrained are still unclear. Here, we report that EXO1 is rapidly degraded by the ubiquitin-proteasome system soon after DSB induction in human cells. ATR inhibition attenuated DNA-damage-induced EXO1 degradation, indicating that ATR-mediated phosphorylation of EXO1 targets it for degradation. In accord with these results, EXO1 became resistant to degradation when its SQ motifs required for ATR-mediated phosphorylation were mutated. We show that upon the induction of DNA damage, EXO1 is ubiquitinated by a member of the Skp1-Cullin1-F-box (SCF) family of ubiquitin ligases in a phosphorylation-dependent manner. Importantly, expression of degradation-resistant EXO1 resulted in hyper-resection, which attenuated both NHEJ and HR and severely compromised DSB repair resulting in chromosomal instability. These findings indicate that the coupling of EXO1 activation with its eventual degradation is a timing mechanism that limits the extent of DNA end resection for accurate DNA repair.
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Affiliation(s)
- Nozomi Tomimatsu
- From the Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Bipasha Mukherjee
- From the Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Janelle Louise Harris
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Francesca Ludovica Boffo
- Department of Molecular Medicine and Medical Biotechnology, Università Federico II, Napoli 80131, Italy, and
| | - Molly Catherine Hardebeck
- From the Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Patrick Ryan Potts
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Kum Kum Khanna
- Signal Transduction Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
| | - Sandeep Burma
- From the Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75390,
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209
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Affiliation(s)
- Tycho E.T. Mevissen
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - David Komander
- Medical Research Council, Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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210
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The interplay between histone deacetylases and rho kinases is important for cancer and neurodegeneration. Cytokine Growth Factor Rev 2017; 37:29-45. [PMID: 28606734 DOI: 10.1016/j.cytogfr.2017.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/18/2017] [Accepted: 05/21/2017] [Indexed: 12/24/2022]
Abstract
Rho associated coiled-coil containing kinases (ROCKs) respond to defined extra- and intracellular stimuli to control cell migration, cell proliferation, and apoptosis. Histone deacetylases (HDACs) are epigenetic modifiers that regulate nuclear and cytoplasmic signaling through the deacetylation of histones and non-histone proteins. ROCK and HDAC functions are important compounds of basic and applied research interests. Recent evidence suggests a physiologically important interplay between HDACs and ROCKs in various cells and organisms. Here we summarize the crosstalk between these enzymatic families and its implications for cancer and neurodegeneration.
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211
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Nicholson J, Jevons SJ, Groselj B, Ellermann S, Konietzny R, Kerr M, Kessler BM, Kiltie AE. E3 Ligase cIAP2 Mediates Downregulation of MRE11 and Radiosensitization in Response to HDAC Inhibition in Bladder Cancer. Cancer Res 2017; 77:3027-3039. [PMID: 28363998 DOI: 10.1158/0008-5472.can-16-3232] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/10/2017] [Accepted: 03/27/2017] [Indexed: 11/16/2022]
Abstract
The MRE11/RAD50/NBS1 (MRN) complex mediates DNA repair pathways, including double-strand breaks induced by radiotherapy. Meiotic recombination 11 homolog (MRE11) is downregulated by histone deacetylase inhibition (HDACi), resulting in reduced levels of DNA repair in bladder cancer cells and radiosensitization. In this study, we show that the mechanism of this downregulation is posttranslational and identify a C-terminally truncated MRE11, which is formed after HDAC inhibition as full-length MRE11 is downregulated. Truncated MRE11 was stabilized by proteasome inhibition, exhibited a decreased half-life after treatment with panobinostat, and therefore represents a newly identified intermediate induced and degraded in response to HDAC inhibition. The E3 ligase cellular inhibitor of apoptosis protein 2 (cIAP2) was upregulated in response to HDAC inhibition and was validated as a new MRE11 binding partner whose upregulation had similar effects to HDAC inhibition. cIAP2 overexpression resulted in downregulation and altered ubiquitination patterns of MRE11 and mediated radiosensitization in response to HDAC inhibition. These results highlight cIAP2 as a player in the DNA damage response as a posttranscriptional regulator of MRE11 and identify cIAP2 as a potential target for biomarker discovery or chemoradiation strategies in bladder cancer. Cancer Res; 77(11); 3027-39. ©2017 AACR.
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Affiliation(s)
- Judith Nicholson
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom.
| | - Sarah J Jevons
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | - Blaz Groselj
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | - Sophie Ellermann
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | - Rebecca Konietzny
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Martin Kerr
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom
| | - Benedikt M Kessler
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Anne E Kiltie
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Oxford, United Kingdom.
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212
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Schwertman P, Bekker-Jensen S, Mailand N. Regulation of DNA double-strand break repair by ubiquitin and ubiquitin-like modifiers. Nat Rev Mol Cell Biol 2017; 17:379-94. [PMID: 27211488 DOI: 10.1038/nrm.2016.58] [Citation(s) in RCA: 257] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
DNA double-strand breaks (DSBs) are highly cytotoxic DNA lesions. The swift recognition and faithful repair of such damage is crucial for the maintenance of genomic stability, as well as for cell and organismal fitness. Signalling by ubiquitin, SUMO and other ubiquitin-like modifiers (UBLs) orchestrates and regulates cellular responses to DSBs at multiple levels, often involving extensive crosstalk between these modifications. Recent findings have revealed compelling insights into the complex mechanisms by which ubiquitin and UBLs regulate protein interactions with DSB sites to promote accurate lesion repair and protection of genome integrity in mammalian cells. These advances offer new therapeutic opportunities for diseases linked to genetic instability.
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Affiliation(s)
- Petra Schwertman
- Ubiquitin Signaling Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Simon Bekker-Jensen
- Ubiquitin Signaling Group, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Niels Mailand
- Ubiquitin Signaling Group, The 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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213
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Xu H, Zhou J, Lin S, Deng W, Zhang Y, Xue Y. PLMD: An updated data resource of protein lysine modifications. J Genet Genomics 2017; 44:243-250. [DOI: 10.1016/j.jgg.2017.03.007] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 01/26/2017] [Accepted: 03/30/2017] [Indexed: 01/08/2023]
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214
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Awwad SW, Abu-Zhayia ER, Guttmann-Raviv N, Ayoub N. NELF-E is recruited to DNA double-strand break sites to promote transcriptional repression and repair. EMBO Rep 2017; 18:745-764. [PMID: 28336775 PMCID: PMC5412775 DOI: 10.15252/embr.201643191] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 02/07/2017] [Accepted: 02/08/2017] [Indexed: 01/12/2023] Open
Abstract
Double-strand breaks (DSBs) trigger rapid and transient transcription pause to prevent collisions between repair and transcription machineries at damage sites. Little is known about the mechanisms that ensure transcriptional block after DNA damage. Here, we reveal a novel role of the negative elongation factor NELF in blocking transcription activity nearby DSBs. We show that NELF-E and NELF-A are rapidly recruited to DSB sites. Furthermore, NELF-E recruitment and its repressive activity are both required for switching off transcription at DSBs. Remarkably, using I-SceI endonuclease and CRISPR-Cas9 systems, we observe that NELF-E is preferentially recruited, in a PARP1-dependent manner, to DSBs induced upstream of transcriptionally active rather than inactive genes. Moreover, the presence of RNA polymerase II is a prerequisite for the preferential recruitment of NELF-E to DNA break sites. Additionally, we demonstrate that NELF-E is required for intact repair of DSBs. Altogether, our data identify the NELF complex as a new component in the DNA damage response.
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Affiliation(s)
- Samah W Awwad
- Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Enas R Abu-Zhayia
- Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Noga Guttmann-Raviv
- Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Nabieh Ayoub
- Department of Biology, Technion - Israel Institute of Technology, Haifa, Israel
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215
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Hänzelmann P, Schindelin H. The Interplay of Cofactor Interactions and Post-translational Modifications in the Regulation of the AAA+ ATPase p97. Front Mol Biosci 2017; 4:21. [PMID: 28451587 PMCID: PMC5389986 DOI: 10.3389/fmolb.2017.00021] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 03/24/2017] [Indexed: 12/18/2022] Open
Abstract
The hexameric type II AAA ATPase (ATPase associated with various activities) p97 (also referred to as VCP, Cdc48, and Ter94) is critically involved in a variety of cellular activities including pathways such as DNA replication and repair which both involve chromatin remodeling, and is a key player in various protein quality control pathways mediated by the ubiquitin proteasome system as well as autophagy. Correspondingly, p97 has been linked to various pathophysiological states including cancer, neurodegeneration, and premature aging. p97 encompasses an N-terminal domain, two highly conserved ATPase domains and an unstructured C-terminal tail. This enzyme hydrolyzes ATP and utilizes the resulting energy to extract or disassemble protein targets modified with ubiquitin from stable protein assemblies, chromatin and membranes. p97 participates in highly diverse cellular processes and hence its activity is tightly controlled. This is achieved by multiple regulatory cofactors, which either associate with the N-terminal domain or interact with the extreme C-terminus via distinct binding elements and target p97 to specific cellular pathways, sometimes requiring the simultaneous association with more than one cofactor. Most cofactors are recruited to p97 through conserved binding motifs/domains and assist in substrate recognition or processing by providing additional molecular properties. A tight control of p97 cofactor specificity and diversity as well as the assembly of higher-order p97-cofactor complexes is accomplished by various regulatory mechanisms, which include bipartite binding, binding site competition, changes in oligomeric assemblies, and nucleotide-induced conformational changes. Furthermore, post-translational modifications (PTMs) like acetylation, palmitoylation, phosphorylation, SUMOylation, and ubiquitylation of p97 have been reported which further modulate its diverse molecular activities. In this review, we will describe the molecular basis of p97-cofactor specificity/diversity and will discuss how PTMs can modulate p97-cofactor interactions and affect the physiological and patho-physiological functions of p97.
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Affiliation(s)
- Petra Hänzelmann
- Rudolf Virchow Center for Experimental Biomedicine, University of WürzburgWürzburg, Germany
| | - Hermann Schindelin
- Rudolf Virchow Center for Experimental Biomedicine, University of WürzburgWürzburg, Germany
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216
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Murray HC, Dun MD, Verrills NM. Harnessing the power of proteomics for identification of oncogenic, druggable signalling pathways in cancer. Expert Opin Drug Discov 2017; 12:431-447. [PMID: 28286965 DOI: 10.1080/17460441.2017.1304377] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Genomic and transcriptomic profiling of tumours has revolutionised our understanding of cancer. However, the majority of tumours possess multiple mutations, and determining which oncogene, or even which pathway, to target is difficult. Proteomics is emerging as a powerful approach to identify the functionally important pathways driving these cancers, and how they can be targeted therapeutically. Areas covered: The authors provide a technical overview of mass spectrometry based approaches for proteomic profiling, and review the current and emerging strategies available for the identification of dysregulated networks, pathways, and drug targets in cancer cells, with a key focus on the ability to profile cancer kinomes. The potential applications of mass spectrometry in the clinic are also highlighted. Expert opinion: The addition of proteomic information to genomic platforms - 'proteogenomics' - is providing unparalleled insight in cancer cell biology. Application of improved mass spectrometry technology and methodology, in particular the ability to analyse post-translational modifications (the PTMome), is providing a more complete picture of the dysregulated networks in cancer, and uncovering novel therapeutic targets. While the application of proteomics to discovery research will continue to rise, improved workflow standardisation and reproducibility is required before mass spectrometry can enter routine clinical use.
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Affiliation(s)
- Heather C Murray
- a School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, Priority Research Centre for Cancer Research, Innovation and Translation , University of Newcastle , Callaghan , NSW , Australia.,b Cancer Research Program , Hunter Medical Research Institute , Newcastle , NSW , Australia
| | - Matthew D Dun
- a School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, Priority Research Centre for Cancer Research, Innovation and Translation , University of Newcastle , Callaghan , NSW , Australia.,b Cancer Research Program , Hunter Medical Research Institute , Newcastle , NSW , Australia
| | - Nicole M Verrills
- a School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, Priority Research Centre for Cancer Research, Innovation and Translation , University of Newcastle , Callaghan , NSW , Australia.,b Cancer Research Program , Hunter Medical Research Institute , Newcastle , NSW , Australia
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217
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Zhang X, Smits AH, van Tilburg GBA, Jansen PWTC, Makowski MM, Ovaa H, Vermeulen M. An Interaction Landscape of Ubiquitin Signaling. Mol Cell 2017; 65:941-955.e8. [PMID: 28190767 DOI: 10.1016/j.molcel.2017.01.004] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 12/06/2016] [Accepted: 01/05/2017] [Indexed: 02/07/2023]
Abstract
Intracellular signaling via the covalent attachment of different ubiquitin linkages to protein substrates is fundamental to many cellular processes. Although linkage-selective ubiquitin interactors have been studied on a case-by-case basis, proteome-wide analyses have not been conducted yet. Here, we present ubiquitin interactor affinity enrichment-mass spectrometry (UbIA-MS), a quantitative interaction proteomics method that makes use of chemically synthesized diubiquitin to enrich and identify ubiquitin linkage interactors from crude cell lysates. UbIA-MS reveals linkage-selective diubiquitin interactions in multiple cell types. For example, we identify TAB2 and TAB3 as novel K6 diubiquitin interactors and characterize UCHL3 as a K27-linkage selective interactor that regulates K27 polyubiquitin chain formation in cells. Additionally, we show a class of monoubiquitin and K6 diubiquitin interactors whose binding is induced by DNA damage. We expect that our proteome-wide diubiquitin interaction landscape and established workflows will have broad applications in the ongoing efforts to decipher the complex language of ubiquitin signaling.
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Affiliation(s)
- Xiaofei Zhang
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen 6525, the Netherlands.
| | - Arne H Smits
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen 6525, the Netherlands
| | - Gabrielle B A van Tilburg
- Division of Cell Biology II, Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, the Netherlands; Department of Chemical Immunology, Leiden University Medical Center, Albinusdreef 2, Leiden 2333ZA, the Netherlands
| | - Pascal W T C Jansen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen 6525, the Netherlands
| | - Matthew M Makowski
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen 6525, the Netherlands
| | - Huib Ovaa
- Division of Cell Biology II, Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam 1066CX, the Netherlands; Department of Chemical Immunology, Leiden University Medical Center, Albinusdreef 2, Leiden 2333ZA, the Netherlands.
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen 6525, the Netherlands.
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218
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Dwane L, Gallagher WM, Ní Chonghaile T, O'Connor DP. The Emerging Role of Non-traditional Ubiquitination in Oncogenic Pathways. J Biol Chem 2017; 292:3543-3551. [PMID: 28154183 DOI: 10.1074/jbc.r116.755694] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The addition of ubiquitin to a target protein has long been implicated in the process of degradation and is the primary mediator of protein turnover in the cell. Recently, however, many non-proteolytic functions of ubiquitination have emerged as key regulators of cellular homeostasis. In this review, we will describe the various non-traditional functions of ubiquitination, with particular focus on how they can be used as signaling entities in cancer formation and progression. Elaboration of this topic can lead to a better understanding of oncogenic mechanisms, as well as the discovery of novel druggable proteins within the ubiquitin pathway.
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Affiliation(s)
- Lisa Dwane
- From Molecular and Cellular Therapeutics and
| | - William M Gallagher
- the Cancer Biology and Therapeutics Laboratory, UCD School of Biomolecular and Biomedical Science, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland
| | - Tríona Ní Chonghaile
- the Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin 2, Ireland and
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219
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von Stechow L, Olsen JV. Proteomics insights into DNA damage response and translating this knowledge to clinical strategies. Proteomics 2017; 17:1600018. [PMID: 27682984 PMCID: PMC5333460 DOI: 10.1002/pmic.201600018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/07/2016] [Accepted: 09/26/2016] [Indexed: 12/31/2022]
Abstract
Genomic instability is a critical driver in the process of cancer formation. At the same time, inducing DNA damage by irradiation or genotoxic compounds constitutes a key therapeutic strategy to kill fast-dividing cancer cells. Sensing of DNA lesions initiates a complex set of signalling pathways, collectively known as the DNA damage response (DDR). Deciphering DDR signalling pathways with high-throughput technologies could provide insights into oncogenic transformation, metastasis formation and therapy responses, and could build a basis for better therapeutic interventions in cancer treatment. Mass spectrometry (MS)-based proteomics emerged as a method of choice for global studies of proteins and their posttranslational modifications (PTMs). MS-based studies of the DDR have aided in delineating DNA damage-induced signalling responses. Those studies identified changes in abundance, interactions and modification of proteins in the context of genotoxic stress. Here we review ground-breaking MS-based proteomics studies, which analysed changes in protein abundance, protein-protein and protein-DNA interactions, phosphorylation, acetylation, ubiquitylation, SUMOylation and Poly(ADP-ribose)ylation (PARylation) in the DDR. Finally, we provide an outlook on how proteomics studies of the DDR could aid clinical developments on multiple levels.
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Affiliation(s)
- Louise von Stechow
- Proteomics ProgramNovo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Jesper V. Olsen
- Proteomics ProgramNovo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
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220
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Martinez-Val A, Garcia F, Ximénez-Embún P, Martínez Teresa-Calleja A, Ibarz N, Ruppen I, Munoz J. Urea Artifacts Interfere with Immuno-Purification of Lysine Acetylation. J Proteome Res 2017; 16:1061-1068. [DOI: 10.1021/acs.jproteome.6b00463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ana Martinez-Val
- ProteoRed-ISCIII, Proteomics
Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Fernando Garcia
- ProteoRed-ISCIII, Proteomics
Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Pilar Ximénez-Embún
- ProteoRed-ISCIII, Proteomics
Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | | | - Nuria Ibarz
- ProteoRed-ISCIII, Proteomics
Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Isabel Ruppen
- ProteoRed-ISCIII, Proteomics
Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Javier Munoz
- ProteoRed-ISCIII, Proteomics
Unit, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
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221
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Hall J, Jeggo PA, West C, Gomolka M, Quintens R, Badie C, Laurent O, Aerts A, Anastasov N, Azimzadeh O, Azizova T, Baatout S, Baselet B, Benotmane MA, Blanchardon E, Guéguen Y, Haghdoost S, Harms-Ringhdahl M, Hess J, Kreuzer M, Laurier D, Macaeva E, Manning G, Pernot E, Ravanat JL, Sabatier L, Tack K, Tapio S, Zitzelsberger H, Cardis E. Ionizing radiation biomarkers in epidemiological studies - An update. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2017; 771:59-84. [PMID: 28342453 DOI: 10.1016/j.mrrev.2017.01.001] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 01/09/2017] [Indexed: 01/13/2023]
Abstract
Recent epidemiology studies highlighted the detrimental health effects of exposure to low dose and low dose rate ionizing radiation (IR): nuclear industry workers studies have shown increased leukaemia and solid tumour risks following cumulative doses of <100mSv and dose rates of <10mGy per year; paediatric patients studies have reported increased leukaemia and brain tumours risks after doses of 30-60mGy from computed tomography scans. Questions arise, however, about the impact of even lower doses and dose rates where classical epidemiological studies have limited power but where subsets within the large cohorts are expected to have an increased risk. Further progress requires integration of biomarkers or bioassays of individual exposure, effects and susceptibility to IR. The European DoReMi (Low Dose Research towards Multidisciplinary Integration) consortium previously reviewed biomarkers for potential use in IR epidemiological studies. Given the increased mechanistic understanding of responses to low dose radiation the current review provides an update covering technical advances and recent studies. A key issue identified is deciding which biomarkers to progress. A roadmap is provided for biomarker development from discovery to implementation and used to summarise the current status of proposed biomarkers for epidemiological studies. Most potential biomarkers remain at the discovery stage and for some there is sufficient evidence that further development is not warranted. One biomarker identified in the final stages of development and as a priority for further research is radiation specific mRNA transcript profiles.
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Affiliation(s)
- Janet Hall
- Centre de Recherche en Cancérologie de Lyon, INSERM 1052, CNRS 5286, Univ Lyon, Université Claude Bernard, Lyon 1, Lyon, F-69424, France.
| | - Penny A Jeggo
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, United Kingdom
| | - Catharine West
- Translational Radiobiology Group, Institute of Cancer Sciences, The University of Manchester, Manchester Academic Health Science Centre, Christie Hospital, Manchester, M20 4BX, United Kingdom
| | - Maria Gomolka
- Federal Office for Radiation Protection, Department of Radiation Protection and Health, D-85764 Neuherberg, Germany
| | - Roel Quintens
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK·CEN, B-2400 Mol, Belgium
| | - Christophe Badie
- Cancer Mechanisms and Biomarkers group, Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, United Kingdom
| | - Olivier Laurent
- Institut de Radioprotection et de Sûreté Nucléaire, F-92260 Fontenay-aux-Roses, France
| | - An Aerts
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK·CEN, B-2400 Mol, Belgium
| | - Nataša Anastasov
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute of Radiation Biology, D-85764 Neuherberg, Germany
| | - Omid Azimzadeh
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute of Radiation Biology, D-85764 Neuherberg, Germany
| | - Tamara Azizova
- Southern Urals Biophysics Institute, Clinical Department, Ozyorsk, Russia
| | - Sarah Baatout
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK·CEN, B-2400 Mol, Belgium; Cell Systems and Imaging Research Group, Department of Molecular Biotechnology, Ghent University, B-9000 Ghent, Belgium
| | - Bjorn Baselet
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK·CEN, B-2400 Mol, Belgium; Pole of Pharmacology, Institut de Recherche Expérimentale et Clinique, Université catholique de Louvain, B-1200 Brussels, Belgium
| | - Mohammed A Benotmane
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK·CEN, B-2400 Mol, Belgium
| | - Eric Blanchardon
- Institut de Radioprotection et de Sûreté Nucléaire, F-92260 Fontenay-aux-Roses, France
| | - Yann Guéguen
- Institut de Radioprotection et de Sûreté Nucléaire, F-92260 Fontenay-aux-Roses, France
| | - Siamak Haghdoost
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE 106 91 Stockholm, Sweden
| | - Mats Harms-Ringhdahl
- Centre for Radiation Protection Research, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, SE 106 91 Stockholm, Sweden
| | - Julia Hess
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute of Radiation Biology, D-85764 Neuherberg, Germany
| | - Michaela Kreuzer
- Federal Office for Radiation Protection, Department of Radiation Protection and Health, D-85764 Neuherberg, Germany
| | - Dominique Laurier
- Institut de Radioprotection et de Sûreté Nucléaire, F-92260 Fontenay-aux-Roses, France
| | - Ellina Macaeva
- Radiobiology Unit, Belgian Nuclear Research Centre, SCK·CEN, B-2400 Mol, Belgium; Cell Systems and Imaging Research Group, Department of Molecular Biotechnology, Ghent University, B-9000 Ghent, Belgium
| | - Grainne Manning
- Cancer Mechanisms and Biomarkers group, Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, United Kingdom
| | - Eileen Pernot
- INSERM U897, Université de Bordeaux, F-33076 Bordeaux cedex, France
| | - Jean-Luc Ravanat
- Laboratoire des Lésions des Acides Nucléiques, Univ. Grenoble Alpes, INAC-SCIB, F-38000 Grenoble, France; Commissariat à l'Énergie Atomique, INAC-SyMMES, F-38000 Grenoble, France
| | - Laure Sabatier
- Commissariat à l'Énergie Atomique, BP6, F-92265 Fontenay-aux-Roses, France
| | - Karine Tack
- Institut de Radioprotection et de Sûreté Nucléaire, F-92260 Fontenay-aux-Roses, France
| | - Soile Tapio
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute of Radiation Biology, D-85764 Neuherberg, Germany
| | - Horst Zitzelsberger
- Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Institute of Radiation Biology, D-85764 Neuherberg, Germany
| | - Elisabeth Cardis
- Barcelona Institute of Global Health (ISGlobal), Centre for Research in Environmental Epidemiology, Radiation Programme, Barcelona Biomedical Research Park, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF) (MTD formerly), Barcelona, Spain; CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain.
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222
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Couturier AM, Fleury H, Patenaude AM, Bentley VL, Rodrigue A, Coulombe Y, Niraj J, Pauty J, Berman JN, Dellaire G, Di Noia JM, Mes-Masson AM, Masson JY. Roles for APRIN (PDS5B) in homologous recombination and in ovarian cancer prediction. Nucleic Acids Res 2016; 44:10879-10897. [PMID: 27924011 PMCID: PMC5159559 DOI: 10.1093/nar/gkw921] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 09/11/2016] [Accepted: 10/22/2016] [Indexed: 12/28/2022] Open
Abstract
APRIN (PDS5 cohesin associated factor B) interacts with both the cohesin complex and the BRCA2 tumor suppressor. How APRIN influences cohesion and DNA repair processes is not well understood. Here, we show that APRIN is recruited to DNA damage sites. We find that APRIN interacts directly with RAD51, PALB2 and BRCA2. APRIN stimulates RAD51-mediated DNA strand invasion. APRIN also binds DNA with an affinity for D-loop structures and single-strand (ss) DNA. APRIN is a new homologous recombination (HR) mediator as it counteracts the RPA inhibitory effect on RAD51 loading to ssDNA. We show that APRIN strongly improves the annealing of complementary-strand DNA and that it can stimulate this process in synergy with BRCA2. Unlike cohesin constituents, its depletion has no impact on class switch recombination, supporting a specific role for this protein in HR. Furthermore, we show that low APRIN expression levels correlate with a better survival in ovarian cancer patients and that APRIN depletion sensitizes cells to the PARP inhibitor Olaparib in xenografted zebrafish. Our findings establish APRIN as an important and specific actor of HR, with cohesin-independent functions.
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Affiliation(s)
- Anthony M Couturier
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Axis, 9 McMahon, Québec City, QC G1R 2J6, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Québec City, QC G1V 0A6, Canada
| | - Hubert Fleury
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montréal, Canada; Institut du cancer de Montréal, Montréal, QC H2X 0A9, Canada.,Department of Medicine, Université de Montréal, Montréal, QC H2X 0A9, Canada
| | - Anne-Marie Patenaude
- Institut de Recherches Cliniques de Montréal and Department of Medicine, Université de Montréal, Montréal, Québec H2W 1R7, Canada
| | - Victoria L Bentley
- Dalhousie University, Faculty of Medicine, Department of Pathology, Halifax, NS B3H 4R2, Canada
| | - Amélie Rodrigue
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Axis, 9 McMahon, Québec City, QC G1R 2J6, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Québec City, QC G1V 0A6, Canada
| | - Yan Coulombe
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Axis, 9 McMahon, Québec City, QC G1R 2J6, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Québec City, QC G1V 0A6, Canada
| | - Joshi Niraj
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Axis, 9 McMahon, Québec City, QC G1R 2J6, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Québec City, QC G1V 0A6, Canada
| | - Joris Pauty
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Axis, 9 McMahon, Québec City, QC G1R 2J6, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Québec City, QC G1V 0A6, Canada
| | - Jason N Berman
- Dalhousie University, Faculty of Medicine, Departments of Microbiology and Immunology, Pediatrics and Pathology, Halifax, NS B3H 4R2, Canada
| | - Graham Dellaire
- Dalhousie University, Faculty of Medicine, Department of Pathology, Halifax, NS B3H 4R2, Canada
| | - Javier M Di Noia
- Institut de Recherches Cliniques de Montréal and Department of Medicine, Université de Montréal, Montréal, Québec H2W 1R7, Canada
| | - Anne-Marie Mes-Masson
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM), Montréal, Canada; Institut du cancer de Montréal, Montréal, QC H2X 0A9, Canada.,Department of Medicine, Université de Montréal, Montréal, QC H2X 0A9, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Axis, 9 McMahon, Québec City, QC G1R 2J6, Canada .,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Québec City, QC G1V 0A6, Canada
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223
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Dankert JF, Rona G, Clijsters L, Geter P, Skaar JR, Bermudez-Hernandez K, Sassani E, Fenyö D, Ueberheide B, Schneider R, Pagano M. Cyclin F-Mediated Degradation of SLBP Limits H2A.X Accumulation and Apoptosis upon Genotoxic Stress in G2. Mol Cell 2016; 64:507-519. [PMID: 27773672 DOI: 10.1016/j.molcel.2016.09.010] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 08/01/2016] [Accepted: 09/08/2016] [Indexed: 10/20/2022]
Abstract
SLBP (stem-loop binding protein) is a highly conserved factor necessary for the processing, translation, and degradation of H2AFX and canonical histone mRNAs. We identified the F-box protein cyclin F, a substrate recognition subunit of an SCF (Skp1-Cul1-F-box protein) complex, as the G2 ubiquitin ligase for SLBP. SLBP interacts with cyclin F via an atypical CY motif, and mutation of this motif prevents SLBP degradation in G2. Expression of an SLBP stable mutant results in increased loading of H2AFX mRNA onto polyribosomes, resulting in increased expression of H2A.X (encoded by H2AFX). Upon genotoxic stress in G2, high levels of H2A.X lead to persistent γH2A.X signaling, high levels of H2A.X phosphorylated on Tyr142, high levels of p53, and induction of apoptosis. We propose that cyclin F co-evolved with the appearance of stem-loops in vertebrate H2AFX mRNA to mediate SLBP degradation, thereby limiting H2A.X synthesis and cell death upon genotoxic stress.
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Affiliation(s)
- John F Dankert
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Perlmutter NYU Cancer Center, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA
| | - Gergely Rona
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Perlmutter NYU Cancer Center, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA
| | - Linda Clijsters
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Perlmutter NYU Cancer Center, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA
| | - Phillip Geter
- Department of Microbiology, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA
| | - Jeffrey R Skaar
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Perlmutter NYU Cancer Center, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA
| | - Keria Bermudez-Hernandez
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Institute for System Genetics, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA
| | - Elizabeth Sassani
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Perlmutter NYU Cancer Center, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA
| | - David Fenyö
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Institute for System Genetics, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA
| | - Beatrix Ueberheide
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Proteomics Resource Center, Office of Collaborative Science, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA
| | - Robert Schneider
- Department of Microbiology, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Department of Radiation Oncology, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Perlmutter NYU Cancer Center, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, NY 10016, USA; Howard Hughes Medical Institute, 522 First Avenue, SRB 1107, New York, NY 10016, USA.
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224
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Choudhury R, Bonacci T, Arceci A, Lahiri D, Mills CA, Kernan JL, Branigan TB, DeCaprio JA, Burke DJ, Emanuele MJ. APC/C and SCF(cyclin F) Constitute a Reciprocal Feedback Circuit Controlling S-Phase Entry. Cell Rep 2016; 16:3359-3372. [PMID: 27653696 PMCID: PMC5111906 DOI: 10.1016/j.celrep.2016.08.058] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/12/2016] [Accepted: 08/17/2016] [Indexed: 02/07/2023] Open
Abstract
The anaphase promoting complex/cyclosome (APC/C) is an ubiquitin ligase and core component of the cell-cycle oscillator. During G1 phase, APC/C binds to its substrate receptor Cdh1 and APC/C(Cdh1) plays an important role in restricting S-phase entry and maintaining genome integrity. We describe a reciprocal feedback circuit between APC/C and a second ubiquitin ligase, the SCF (Skp1-Cul1-F box). We show that cyclin F, a cell-cycle-regulated substrate receptor (F-box protein) for the SCF, is targeted for degradation by APC/C. Furthermore, we establish that Cdh1 is itself a substrate of SCF(cyclin F). Cyclin F loss impairs Cdh1 degradation and delays S-phase entry, and this delay is reversed by simultaneous removal of Cdh1. These data indicate that the coordinated, temporal ordering of cyclin F and Cdh1 degradation, organized in a double-negative feedback loop, represents a fundamental aspect of cell-cycle control. This mutual antagonism could be a feature of other oscillating systems.
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Affiliation(s)
- Rajarshi Choudhury
- Lineberger Comprehensive Cancer Center and Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Thomas Bonacci
- Lineberger Comprehensive Cancer Center and Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Anthony Arceci
- Lineberger Comprehensive Cancer Center and Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Debojyoti Lahiri
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Christine A Mills
- Lineberger Comprehensive Cancer Center and Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jennifer L Kernan
- Lineberger Comprehensive Cancer Center and Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Timothy B Branigan
- Department of Medical Oncology, Dana-Farber Cancer Institute, and Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, and Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Daniel J Burke
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Michael J Emanuele
- Lineberger Comprehensive Cancer Center and Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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225
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BMI1-UBR5 axis regulates transcriptional repression at damaged chromatin. Proc Natl Acad Sci U S A 2016; 113:11243-11248. [PMID: 27647897 DOI: 10.1073/pnas.1610735113] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
BMI1 is a component of the Polycomb Repressive Complex 1 (PRC1), which plays a key role in maintaining epigenetic silencing during development. BMI1 also participates in gene silencing during DNA damage response, but the precise downstream function of BMI1 in gene silencing is unclear. Here we identified the UBR5 E3 ligase as a downstream factor of BMI1. We found that UBR5 forms damage-inducible nuclear foci in a manner dependent on the PRC1 components BMI1, RNF1 (RING1a), and RNF2 (RING1b). Whereas transcription is repressed at UV-induced lesions on chromatin, depletion of the PRC1 members or UBR5 alone derepressed transcription elongation at these sites, suggesting that UBR5 functions in a linear pathway with PRC1 in inducing gene silencing at lesions. Mass spectrometry (MS) analysis revealed that UBR5 associates with BMI1 as well as FACT components SPT16 and SSRP1. We found that UBR5 localizes to the UV-induced lesions along with SPT16. We show that UBR5 ubiquitinates SPT16, and depletion of UBR5 or BMI1 leads to an enlargement of SPT16 foci size at UV lesions, suggesting that UBR5 and BMI1 repress SPT16 enrichment at the damaged sites. Consistently, depletion of the FACT components effectively reversed the transcriptional derepression incurred in the UBR5 and BMI1 KO cells. Finally, UBR5 and BMI1 KO cells are hypersensitive to UV, which supports the notion that faulty RNA synthesis at damaged sites is harmful to the cell fitness. Altogether, these results suggest that BMI1 and UBR5 repress the polymerase II (Pol II)-mediated transcription at damaged sites, by negatively regulating the FACT-dependent Pol II elongation.
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226
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Guturi KKN, Bohgaki M, Bohgaki T, Srikumar T, Ng D, Kumareswaran R, El Ghamrasni S, Jeon J, Patel P, Eldin MS, Bristow R, Cheung P, Stewart GS, Raught B, Hakem A, Hakem R. RNF168 and USP10 regulate topoisomerase IIα function via opposing effects on its ubiquitylation. Nat Commun 2016; 7:12638. [PMID: 27558965 PMCID: PMC5007378 DOI: 10.1038/ncomms12638] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Accepted: 07/19/2016] [Indexed: 12/21/2022] Open
Abstract
Topoisomerase IIα (TOP2α) is essential for chromosomal condensation and segregation, as well as genomic integrity. Here we report that RNF168, an E3 ligase mutated in the human RIDDLE syndrome, interacts with TOP2α and mediates its ubiquitylation. RNF168 deficiency impairs decatenation activity of TOP2α and promotes mitotic abnormalities and defective chromosomal segregation. Our data also indicate that RNF168 deficiency, including in human breast cancer cell lines, confers resistance to the anti-cancer drug and TOP2 inhibitor etoposide. We also identify USP10 as a deubiquitylase that negatively regulates TOP2α ubiquitylation and restrains its chromatin association. These findings provide a mechanistic link between the RNF168/USP10 axis and TOP2α ubiquitylation and function, and suggest a role for RNF168 in the response to anti-cancer chemotherapeutics that target TOP2.
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Affiliation(s)
- Kiran Kumar Naidu Guturi
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Miyuki Bohgaki
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Toshiyuki Bohgaki
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Tharan Srikumar
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Deborah Ng
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Ramya Kumareswaran
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Samah El Ghamrasni
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Justin Jeon
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Parasvi Patel
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Mohamed Saad Eldin
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Rob Bristow
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Peter Cheung
- Department of Biology, York University, Toronto, Ontario, Canada M3J 1P3
| | - Grant S Stewart
- School of Cancer Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Brian Raught
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Anne Hakem
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Razqallah Hakem
- Department of Medical Biophysics, Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 1L7
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Himmels SF, Sartori AA. Controlling DNA-End Resection: An Emerging Task for Ubiquitin and SUMO. Front Genet 2016; 7:152. [PMID: 27602047 PMCID: PMC4993767 DOI: 10.3389/fgene.2016.00152] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 08/05/2016] [Indexed: 12/17/2022] Open
Abstract
DNA double-strand breaks (DSBs) are one of the most detrimental lesions, as their incorrect or incomplete repair can lead to genomic instability, a hallmark of cancer. Cells have evolved two major competing DSB repair mechanisms: Homologous recombination (HR) and non-homologous end joining (NHEJ). HR is initiated by DNA-end resection, an evolutionarily conserved process that generates stretches of single-stranded DNA tails that are no longer substrates for religation by the NHEJ machinery. Ubiquitylation and sumoylation, the covalent attachment of ubiquitin and SUMO moieties to target proteins, play multifaceted roles in DNA damage signaling and have been shown to regulate HR and NHEJ, thus ensuring appropriate DSB repair. Here, we give a comprehensive overview about the current knowledge of how ubiquitylation and sumoylation control DSB repair by modulating the DNA-end resection machinery.
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Affiliation(s)
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research, University of Zurich Zurich, Switzerland
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228
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Nicotinamide Suppresses the DNA Damage Sensitivity of Saccharomyces cerevisiae Independently of Sirtuin Deacetylases. Genetics 2016; 204:569-579. [PMID: 27527516 DOI: 10.1534/genetics.116.193524] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 08/15/2016] [Indexed: 11/18/2022] Open
Abstract
Nicotinamide is both a reaction product and an inhibitor of the conserved sirtuin family of deacetylases, which have been implicated in a broad range of cellular functions in eukaryotes from yeast to humans. Phenotypes observed following treatment with nicotinamide are most often assumed to stem from inhibition of one or more of these enzymes. Here, we used this small molecule to inhibit multiple sirtuins at once during treatment with DNA damaging agents in the Saccharomyces cerevisiae model system. Since sirtuins have been previously implicated in the DNA damage response, we were surprised to observe that nicotinamide actually increased the survival of yeast cells exposed to the DNA damage agent MMS. Remarkably, we found that enhanced resistance to MMS in the presence of nicotinamide was independent of all five yeast sirtuins. Enhanced resistance was also independent of the nicotinamide salvage pathway, which uses nicotinamide as a substrate to generate NAD+, and of a DNA damage-induced increase in the salvage enzyme Pnc1 Our data suggest a novel and unexpected function for nicotinamide that has broad implications for its use in the study of sirtuin biology across model systems.
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229
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Labonne JDJ, Graves TD, Shen Y, Jones JR, Kong IK, Layman LC, Kim HG. A microdeletion at Xq22.2 implicates a glycine receptor GLRA4 involved in intellectual disability, behavioral problems and craniofacial anomalies. BMC Neurol 2016; 16:132. [PMID: 27506666 PMCID: PMC4979147 DOI: 10.1186/s12883-016-0642-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/20/2016] [Indexed: 12/03/2022] Open
Abstract
Background Among the 21 annotated genes at Xq22.2, PLP1 is the only known gene involved in Xq22.2 microdeletion and microduplication syndromes with intellectual disability. Using an atypical microdeletion, which does not encompass PLP1, we implicate a novel gene GLRA4 involved in intellectual disability, behavioral problems and craniofacial anomalies. Case presentation We report a female patient (DGDP084) with a de novo Xq22.2 microdeletion of at least 110 kb presenting with intellectual disability, motor delay, behavioral problems and craniofacial anomalies. While her phenotypic features such as cognitive impairment and motor delay show overlap with Pelizaeus-Merzbacher disease (PMD) caused by PLP1 mutations at Xq22.2, this gene is not included in our patient’s microdeletion and is not dysregulated by a position effect. Because the microdeletion encompasses only three genes, GLRA4, MORF4L2 and TCEAL1, we investigated their expression levels in various tissues by RT-qPCR and found that all three genes were highly expressed in whole human brain, fetal brain, cerebellum and hippocampus. When we examined the transcript levels of GLRA4, MORF4L2 as well as TCEAL1 in DGDP084′s family, however, only GLRA4 transcripts were reduced in the female patient compared to her healthy mother. This suggests that GLRA4 is the plausible candidate gene for cognitive impairment, behavioral problems and craniofacial anomalies observed in DGDP084. Importantly, glycine receptors mediate inhibitory synaptic transmission in the brain stem as well as the spinal cord, and are known to be involved in syndromic intellectual disability. Conclusion We hypothesize that GLRA4 is involved in intellectual disability, behavioral problems and craniofacial anomalies as the second gene identified for X-linked syndromic intellectual disability at Xq22.2. Additional point mutations or intragenic deletions of GLRA4 as well as functional studies are needed to further validate our hypothesis. Electronic supplementary material The online version of this article (doi:10.1186/s12883-016-0642-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jonathan D J Labonne
- Department of Obstetrics & Gynecology, Section of Reproductive Endocrinology, Infertility & Genetics, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA, 30912, USA.,Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA, 30912, USA
| | - Tyler D Graves
- Department of Obstetrics & Gynecology, Section of Reproductive Endocrinology, Infertility & Genetics, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA, 30912, USA
| | - Yiping Shen
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | | | - Il-Keun Kong
- Department of Animal Science, Division of Applied Life Science (BK21plus), Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, Gyeongsangnam-do, South Korea
| | - Lawrence C Layman
- Department of Obstetrics & Gynecology, Section of Reproductive Endocrinology, Infertility & Genetics, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA, 30912, USA.,Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA, 30912, USA.,Neuroscience Program, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Hyung-Goo Kim
- Department of Obstetrics & Gynecology, Section of Reproductive Endocrinology, Infertility & Genetics, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA, 30912, USA. .,Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, 1120 15th Street, Augusta, GA, 30912, USA.
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230
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Keijzers G, Liu D, Rasmussen LJ. Exonuclease 1 and its versatile roles in DNA repair. Crit Rev Biochem Mol Biol 2016; 51:440-451. [PMID: 27494243 DOI: 10.1080/10409238.2016.1215407] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Exonuclease 1 (EXO1) is a multifunctional 5' → 3' exonuclease and a DNA structure-specific DNA endonuclease. EXO1 plays roles in DNA replication, DNA mismatch repair (MMR) and DNA double-stranded break repair (DSBR) in lower and higher eukaryotes and contributes to meiosis, immunoglobulin maturation, and micro-mediated end-joining in higher eukaryotes. In human cells, EXO1 is also thought to play a role in telomere maintenance. Mutations in the human EXO1 gene correlate with increased susceptibility to some cancers. This review summarizes recent studies on the enzymatic functions and biological roles of EXO1, its possible protective role against cancer and aging, and regulation of EXO1 by posttranslational modification.
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Affiliation(s)
- Guido Keijzers
- a Department of Cellular and Molecular Medicine , Center for Healthy Aging, University of Copenhagen , Copenhagen , Denmark
| | - Dekang Liu
- a Department of Cellular and Molecular Medicine , Center for Healthy Aging, University of Copenhagen , Copenhagen , Denmark
| | - Lene Juel Rasmussen
- a Department of Cellular and Molecular Medicine , Center for Healthy Aging, University of Copenhagen , Copenhagen , Denmark
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231
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Cukras S, Lee E, Palumbo E, Benavidez P, Moldovan GL, Kee Y. The USP1-UAF1 complex interacts with RAD51AP1 to promote homologous recombination repair. Cell Cycle 2016; 15:2636-2646. [PMID: 27463890 DOI: 10.1080/15384101.2016.1209613] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
USP1 deubiquitinating enzyme and its stoichiometric binding partner UAF1 play an essential role in promoting DNA homologous recombination (HR) repair in response to various types of DNA damaging agents. Deubiquitination of FANCD2 may be attributed to the key role of USP1-UAF1 complex in regulating HR repair, however whether USP1-UAF1 promotes HR repair independently of FANCD2 deubiquitination is not known. Here we show evidence that the USP1-UAF1 complex has a FANCD2-independent function in promoting HR repair. Proteomic search of UAF1-interacting proteins revealed that UAF1 associates with RAD51AP1, a RAD51-interacting protein implicated in HR repair. We show that UAF1 mediates the interaction between USP1 and RAD51AP1, and that depletion of USP1 or UAF1 led to a decreased stability of RAD51AP1. Protein interaction mapping analysis identified some key residues within RAD51AP1 required for interacting with the USP1-UAF1 complex. Cells expressing the UAF1 interaction-deficient mutant of RAD51AP1 show increased chromosomal aberrations in response to Mitomycin C treatment. Moreover, similar to the RAD51AP1 depleted cells, the cells expressing UAF1-interaction deficient RAD51AP1 display persistent RAD51 foci following DNA damage exposure, indicating that these factors regulate a later step during the HR repair. These data altogether suggest that the USP1-UAF1 complex promotes HR repair via multiple mechanisms: through FANCD2 deubiquitination, as well as by interacting with RAD51AP1.
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Affiliation(s)
- Scott Cukras
- a Department of Cell Biology , Microbiology, and Molecular Biology, College of Arts and Sciences, University of South Florida , Tampa , FL , USA
| | - Euiho Lee
- a Department of Cell Biology , Microbiology, and Molecular Biology, College of Arts and Sciences, University of South Florida , Tampa , FL , USA
| | - Emily Palumbo
- a Department of Cell Biology , Microbiology, and Molecular Biology, College of Arts and Sciences, University of South Florida , Tampa , FL , USA
| | - Pamela Benavidez
- a Department of Cell Biology , Microbiology, and Molecular Biology, College of Arts and Sciences, University of South Florida , Tampa , FL , USA
| | - George-Lucian Moldovan
- b Department of Biochemistry and Molecular Biology , Pennsylvania State University College of Medicine , Hershey , PA , USA
| | - Younghoon Kee
- a Department of Cell Biology , Microbiology, and Molecular Biology, College of Arts and Sciences, University of South Florida , Tampa , FL , USA
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232
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Morales JC, Richard P, Patidar PL, Motea EA, Dang TT, Manley JL, Boothman DA. XRN2 Links Transcription Termination to DNA Damage and Replication Stress. PLoS Genet 2016; 12:e1006107. [PMID: 27437695 PMCID: PMC4954731 DOI: 10.1371/journal.pgen.1006107] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/14/2016] [Indexed: 11/18/2022] Open
Abstract
XRN2 is a 5’-3’ exoribonuclease implicated in transcription termination. Here we demonstrate an unexpected role for XRN2 in the DNA damage response involving resolution of R-loop structures and prevention of DNA double-strand breaks (DSBs). We show that XRN2 undergoes DNA damage-inducible nuclear re-localization, co-localizing with 53BP1 and R loops, in a transcription and R-loop-dependent process. XRN2 loss leads to increased R loops, genomic instability, replication stress, DSBs and hypersensitivity of cells to various DNA damaging agents. We demonstrate that the DSBs that arise with XRN2 loss occur at transcriptional pause sites. XRN2-deficient cells also exhibited an R-loop- and transcription-dependent delay in DSB repair after ionizing radiation, suggesting a novel role for XRN2 in R-loop resolution, suppression of replication stress, and maintenance of genomic stability. Our study highlights the importance of regulating transcription-related activities as a critical component in maintaining genetic stability. Genomic instability is one of the primary causes of disease states, in particular cancer. One major cause of genomic instability is the formation of DNA double strand breaks (DSBs), which are one of the most dangerous types of DNA lesions the cell can encounter. If not repaired in a timely manner, one DSB can lead not only to cell death. If misrepaired, one DSB can lead to a hazardous chromosomal aberration, such as a translocation, that can eventually lead to cancer. The cell encounters and repairs DSBs that arise from naturally occurring cellular processes on a daily basis. A number of studies have demonstrated that aberrant structures that form during transcription under certain circumstances, in particular RNA:DNA hybrids (R loops), can lead to DSB formation and genomic instability, especially during DNA synthesis. Thus, it is important to understand how the cell responds and repairs transcription-mediated DNA damage in general and R loop-related DNA damage in particular. This paper both demonstrates that the XRN transcription termination factor links transcription and DNA damage, but also provides a better understanding of how the cell prevents transcription-related DNA damage.
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Affiliation(s)
- Julio C. Morales
- Department of Neurosurgery, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma, United States of America
- * E-mail: (JCM); (DAB)
| | - Patricia Richard
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Praveen L. Patidar
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Edward A. Motea
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Tuyen T. Dang
- Department of Neurosurgery, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma, United States of America
| | - James L. Manley
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - David A. Boothman
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail: (JCM); (DAB)
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233
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Heidelberger JB, Wagner SA, Beli P. Mass Spectrometry-Based Proteomics for Investigating DNA Damage-Associated Protein Ubiquitylation. Front Genet 2016; 7:109. [PMID: 27379159 PMCID: PMC4905943 DOI: 10.3389/fgene.2016.00109] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 05/30/2016] [Indexed: 11/13/2022] Open
Abstract
Modification of proteins with the 76 amino acid protein ubiquitin plays essential roles in cellular signaling. Development of methods for specific enrichment of ubiquitin remnant peptides and advances in high-resolution mass spectrometry have enabled proteome-wide identification of endogenous ubiquitylation sites. Moreover, ubiquitin remnant profiling has emerged as a powerful approach for investigating changes in protein ubiquitylation in response to cellular perturbations, such as DNA damage, as well as for identification of substrates of ubiquitin-modifying enzymes. Despite these advances, interrogation of ubiquitin chain topologies on substrate proteins remains a challenging task. Here, we describe mass spectrometry-based approaches for quantitative analyses of site-specific protein ubiquitylation and highlight recent studies that employed these methods for investigation of ubiquitylation in the context of the cellular DNA damage response. Furthermore, we provide an overview of experimental strategies for probing ubiquitin chain topologies on proteins and discuss how these methods can be applied to analyze functions of ubiquitylation in the DNA damage response.
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Affiliation(s)
| | - Sebastian A Wagner
- Department of Medicine, Hematology/Oncology, Goethe University Frankfurt, Germany
| | - Petra Beli
- Institute of Molecular Biology Mainz, Germany
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234
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Identification of S-phase DNA damage-response targets in fission yeast reveals conservation of damage-response networks. Proc Natl Acad Sci U S A 2016; 113:E3676-85. [PMID: 27298342 DOI: 10.1073/pnas.1525620113] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The cellular response to DNA damage during S-phase regulates a complicated network of processes, including cell-cycle progression, gene expression, DNA replication kinetics, and DNA repair. In fission yeast, this S-phase DNA damage response (DDR) is coordinated by two protein kinases: Rad3, the ortholog of mammalian ATR, and Cds1, the ortholog of mammalian Chk2. Although several critical downstream targets of Rad3 and Cds1 have been identified, most of their presumed targets are unknown, including the targets responsible for regulating replication kinetics and coordinating replication and repair. To characterize targets of the S-phase DDR, we identified proteins phosphorylated in response to methyl methanesulfonate (MMS)-induced S-phase DNA damage in wild-type, rad3∆, and cds1∆ cells by proteome-wide mass spectrometry. We found a broad range of S-phase-specific DDR targets involved in gene expression, stress response, regulation of mitosis and cytokinesis, and DNA replication and repair. These targets are highly enriched for proteins required for viability in response to MMS, indicating their biological significance. Furthermore, the regulation of these proteins is similar in fission and budding yeast, across 300 My of evolution, demonstrating a deep conservation of S-phase DDR targets and suggesting that these targets may be critical for maintaining genome stability in response to S-phase DNA damage across eukaryotes.
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235
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Profiling DNA damage-induced phosphorylation in budding yeast reveals diverse signaling networks. Proc Natl Acad Sci U S A 2016; 113:E3667-75. [PMID: 27298372 DOI: 10.1073/pnas.1602827113] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The DNA damage response (DDR) is regulated by a protein kinase signaling cascade that orchestrates DNA repair and other processes. Identifying the substrate effectors of these kinases is critical for understanding the underlying physiology and mechanism of the response. We have used quantitative mass spectrometry to profile DDR-dependent phosphorylation in budding yeast and genetically explored the dependency of these phosphorylation events on the DDR kinases MEC1, RAD53, CHK1, and DUN1. Based on these screens, a database containing many novel DDR-regulated phosphorylation events has been established. Phosphorylation of many of these proteins has been validated by quantitative peptide phospho-immunoprecipitation and examined for functional relevance to the DDR through large-scale analysis of sensitivity to DNA damage in yeast deletion strains. We reveal a link between DDR signaling and the metabolic pathways of inositol phosphate and phosphatidyl inositol synthesis, which are required for resistance to DNA damage. We also uncover links between the DDR and TOR signaling as well as translation regulation. Taken together, these data shed new light on the organization of DDR signaling in budding yeast.
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236
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Harding SM, Greenberg RA. Choreographing the Double Strand Break Response: Ubiquitin and SUMO Control of Nuclear Architecture. Front Genet 2016; 7:103. [PMID: 27375678 PMCID: PMC4894868 DOI: 10.3389/fgene.2016.00103] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 05/24/2016] [Indexed: 12/16/2022] Open
Abstract
The cellular response to DNA double strand breaks (DSBs) is a multifaceted signaling program that centers on post-translational modifications including phosphorylation, ubiquitylation and SUMOylation. In this review we discuss how ubiquitin and SUMO orchestrate the recognition of DSBs and explore how this influences chromatin organization. We discuss functional outcomes of this response including transcriptional silencing and how pre-existing chromatin states may control the DSB response and the maintenance of genomic stability.
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Affiliation(s)
- Shane M Harding
- Departments of Cancer Biology and Pathology, Abramson Family Cancer Research Institute, Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
| | - Roger A Greenberg
- Departments of Cancer Biology and Pathology, Abramson Family Cancer Research Institute, Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
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237
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Abstract
Organism viability relies on the stable maintenance of specific chromatin landscapes, established during development, that shape cell functions and identities by driving distinct gene expression programs. Yet epigenome maintenance is challenged during transcription, replication, and repair of DNA damage, all of which elicit dynamic changes in chromatin organization. Here, we review recent advances that have shed light on the specialized mechanisms contributing to the restoration of epigenome structure and function after DNA damage in the mammalian cell nucleus. By drawing a parallel with epigenome maintenance during replication, we explore emerging concepts and highlight open issues in this rapidly growing field. In particular, we present our current knowledge of molecular players that support the coordinated maintenance of genome and epigenome integrity in response to DNA damage, and we highlight how nuclear organization impacts genome stability. Finally, we discuss possible functional implications of epigenome plasticity in response to genotoxic stress.
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Affiliation(s)
- Juliette Dabin
- Epigenome Integrity Group, UMR 7216 CNRS, Paris Diderot University, Sorbonne Paris Cité, 75013 Paris Cedex 13, France
| | - Anna Fortuny
- Epigenome Integrity Group, UMR 7216 CNRS, Paris Diderot University, Sorbonne Paris Cité, 75013 Paris Cedex 13, France
| | - Sophie E Polo
- Epigenome Integrity Group, UMR 7216 CNRS, Paris Diderot University, Sorbonne Paris Cité, 75013 Paris Cedex 13, France.
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238
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Boeing S, Williamson L, Encheva V, Gori I, Saunders RE, Instrell R, Aygün O, Rodriguez-Martinez M, Weems JC, Kelly GP, Conaway JW, Conaway RC, Stewart A, Howell M, Snijders AP, Svejstrup JQ. Multiomic Analysis of the UV-Induced DNA Damage Response. Cell Rep 2016; 15:1597-1610. [PMID: 27184836 PMCID: PMC4893159 DOI: 10.1016/j.celrep.2016.04.047] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 02/25/2016] [Accepted: 04/10/2016] [Indexed: 12/21/2022] Open
Abstract
In order to facilitate the identification of factors and pathways in the cellular response to UV-induced DNA damage, several descriptive proteomic screens and a functional genomics screen were performed in parallel. Numerous factors could be identified with high confidence when the screen results were superimposed and interpreted together, incorporating biological knowledge. A searchable database, bioLOGIC, which provides access to relevant information about a protein or process of interest, was established to host the results and facilitate data mining. Besides uncovering roles in the DNA damage response for numerous proteins and complexes, including Integrator, Cohesin, PHF3, ASC-1, SCAF4, SCAF8, and SCAF11, we uncovered a role for the poorly studied, melanoma-associated serine/threonine kinase 19 (STK19). Besides effectively uncovering relevant factors, the multiomic approach also provides a systems-wide overview of the diverse cellular processes connected to the transcription-related DNA damage response.
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Affiliation(s)
- Stefan Boeing
- Mechanisms of Transcription Laboratory, the Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK; Bioinformatics and Biostatistics Laboratory, the Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Laura Williamson
- Mechanisms of Transcription Laboratory, the Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Vesela Encheva
- Protein Analysis and Proteomics Laboratory, the Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Ilaria Gori
- High Throughput Screening Laboratory, the Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Rebecca E Saunders
- High Throughput Screening Laboratory, the Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Rachael Instrell
- High Throughput Screening Laboratory, the Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Ozan Aygün
- Mechanisms of Transcription Laboratory, the Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Marta Rodriguez-Martinez
- Mechanisms of Transcription Laboratory, the Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Juston C Weems
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Gavin P Kelly
- Bioinformatics and Biostatistics Laboratory, the Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Joan W Conaway
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Ronald C Conaway
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Aengus Stewart
- Bioinformatics and Biostatistics Laboratory, the Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Michael Howell
- High Throughput Screening Laboratory, the Francis Crick Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Ambrosius P Snijders
- Protein Analysis and Proteomics Laboratory, the Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK
| | - Jesper Q Svejstrup
- Mechanisms of Transcription Laboratory, the Francis Crick Institute, Clare Hall Laboratories, South Mimms EN6 3LD, UK.
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239
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Gendron JM, Webb K, Yang B, Rising L, Zuzow N, Bennett EJ. Using the Ubiquitin-modified Proteome to Monitor Distinct and Spatially Restricted Protein Homeostasis Dysfunction. Mol Cell Proteomics 2016; 15:2576-93. [PMID: 27185884 DOI: 10.1074/mcp.m116.058420] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Indexed: 01/01/2023] Open
Abstract
Protein homeostasis dysfunction has been implicated in the development and progression of aging related human pathologies. There is a need for the establishment of quantitative methods to evaluate global protein homoeostasis function. As the ubiquitin (ub) proteasome system plays a key role in regulating protein homeostasis, we applied quantitative proteomic methods to evaluate the sensitivity of site-specific ubiquitylation events as markers for protein homeostasis dysfunction. Here, we demonstrate that the ub-modified proteome can exceed the sensitivity of engineered fluorescent reporters as a marker for proteasome dysfunction and can provide unique signatures for distinct proteome challenges which is not possible with engineered reporters. We demonstrate that combining ub-proteomics with subcellular fractionation can effectively separate degradative and regulatory ubiquitylation events on distinct protein populations. Using a recently developed potent inhibitor of the critical protein homeostasis factor p97/VCP, we demonstrate that distinct insults to protein homeostasis function can elicit robust and largely unique alterations to the ub-modified proteome. Taken together, we demonstrate that proteomic approaches to monitor the ub-modified proteome can be used to evaluate global protein homeostasis and can be used to monitor distinct functional outcomes for spatially separated protein populations.
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Affiliation(s)
- Joshua M Gendron
- From the ‡Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California
| | - Kristofor Webb
- From the ‡Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California
| | - Bing Yang
- From the ‡Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California
| | - Lisa Rising
- From the ‡Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California
| | - Nathan Zuzow
- From the ‡Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California
| | - Eric J Bennett
- From the ‡Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California
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240
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Abstract
The cellular replicating machine, or "replisome," is composed of numerous different proteins. The core replication proteins in all cell types include a helicase, primase, DNA polymerases, sliding clamp, clamp loader, and single-strand binding (SSB) protein. The core eukaryotic replisome proteins evolved independently from those of bacteria and thus have distinct architectures and mechanisms of action. The core replisome proteins of the eukaryote include: an 11-subunit CMG helicase, DNA polymerase alpha-primase, leading strand DNA polymerase epsilon, lagging strand DNA polymerase delta, PCNA clamp, RFC clamp loader, and the RPA SSB protein. There are numerous other proteins that travel with eukaryotic replication forks, some of which are known to be involved in checkpoint regulation or nucleosome handling, but most have unknown functions and no bacterial analogue. Recent studies have revealed many structural and functional insights into replisome action. Also, the first structure of a replisome from any cell type has been elucidated for a eukaryote, consisting of 20 distinct proteins, with quite unexpected results. This review summarizes the current state of knowledge of the eukaryotic core replisome proteins, their structure, individual functions, and how they are organized at the replication fork as a machine.
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Affiliation(s)
- D Zhang
- The Rockefeller University, New York, NY, United States
| | - M O'Donnell
- The Rockefeller University, New York, NY, United States; Howard Hughes Medical Institute, The Rockefeller University, New York, NY, United States.
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241
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Abstract
Protein ubiquitination is a dynamic multifaceted post-translational modification involved in nearly all aspects of eukaryotic biology. Once attached to a substrate, the 76-amino acid protein ubiquitin is subjected to further modifications, creating a multitude of distinct signals with distinct cellular outcomes, referred to as the 'ubiquitin code'. Ubiquitin can be ubiquitinated on seven lysine (Lys) residues or on the N-terminus, leading to polyubiquitin chains that can encompass complex topologies. Alternatively or in addition, ubiquitin Lys residues can be modified by ubiquitin-like molecules (such as SUMO or NEDD8). Finally, ubiquitin can also be acetylated on Lys, or phosphorylated on Ser, Thr or Tyr residues, and each modification has the potential to dramatically alter the signaling outcome. While the number of distinctly modified ubiquitin species in cells is mind-boggling, much progress has been made to characterize the roles of distinct ubiquitin modifications, and many enzymes and receptors have been identified that create, recognize or remove these ubiquitin modifications. We here provide an overview of the various ubiquitin modifications present in cells, and highlight recent progress on ubiquitin chain biology. We then discuss the recent findings in the field of ubiquitin acetylation and phosphorylation, with a focus on Ser65-phosphorylation and its role in mitophagy and Parkin activation.
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Affiliation(s)
- Kirby N Swatek
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - David Komander
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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242
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Abstract
Ubiquitin plays an essential role in modulating protein functions, and deregulation of the ubiquitin system leads to the development of multiple human diseases. Owing to its molecular features, ubiquitin can form various homo- and heterotypic polymers on substrate proteins, thereby provoking distinct cellular responses. The concept of multifaceted ubiquitin chains encoding different functions has been substantiated in recent years. It has been established that all possible ubiquitin linkage types are utilized for chain assembly and propagation of specific signals in vivo. In addition, branched ubiquitin chains and phosphorylated ubiquitin molecules have been put under the spotlight recently. The development of novel technologies has provided detailed insights into the structure and function of previously poorly understood ubiquitin signals. In this Cell Science at a Glance article and accompanying poster, we provide an update on the complexity of ubiquitin chains and their physiological relevance.
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Affiliation(s)
- Masato Akutsu
- Buchmann Institute for Molecular Life Sciences, Institute of Biochemistry II, Goethe University, Max-von Laue-Str. 15, Frankfurt 60438, Germany
| | - Ivan Dikic
- Buchmann Institute for Molecular Life Sciences, Institute of Biochemistry II, Goethe University, Max-von Laue-Str. 15, Frankfurt 60438, Germany
| | - Anja Bremm
- Buchmann Institute for Molecular Life Sciences, Institute of Biochemistry II, Goethe University, Max-von Laue-Str. 15, Frankfurt 60438, Germany
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243
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Trego KS, Groesser T, Davalos AR, Parplys AC, Zhao W, Nelson MR, Hlaing A, Shih B, Rydberg B, Pluth JM, Tsai MS, Hoeijmakers JHJ, Sung P, Wiese C, Campisi J, Cooper PK. Non-catalytic Roles for XPG with BRCA1 and BRCA2 in Homologous Recombination and Genome Stability. Mol Cell 2016; 61:535-546. [PMID: 26833090 DOI: 10.1016/j.molcel.2015.12.026] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 11/13/2015] [Accepted: 12/21/2015] [Indexed: 01/01/2023]
Abstract
XPG is a structure-specific endonuclease required for nucleotide excision repair, and incision-defective XPG mutations cause the skin cancer-prone syndrome xeroderma pigmentosum. Truncating mutations instead cause the neurodevelopmental progeroid disorder Cockayne syndrome, but little is known about how XPG loss results in this devastating disease. We identify XPG as a partner of BRCA1 and BRCA2 in maintaining genomic stability through homologous recombination (HRR). XPG depletion causes DNA double-strand breaks, chromosomal abnormalities, cell-cycle delays, defective HRR, inability to overcome replication fork stalling, and replication stress. XPG directly interacts with BRCA2, RAD51, and PALB2, and XPG depletion reduces their chromatin binding and subsequent RAD51 foci formation. Upstream in HRR, XPG interacts directly with BRCA1. Its depletion causes BRCA1 hyper-phosphorylation and persistent chromatin binding. These unexpected findings establish XPG as an HRR protein with important roles in genome stability and suggest how XPG defects produce severe clinical consequences including cancer and accelerated aging.
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Affiliation(s)
- Kelly S Trego
- Biosciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Torsten Groesser
- Biosciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | - Ann C Parplys
- Biosciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Weixing Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Michael R Nelson
- Biosciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ayesu Hlaing
- Biosciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Brian Shih
- Biosciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Björn Rydberg
- Biosciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Janice M Pluth
- Biosciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Miaw-Sheue Tsai
- Biosciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jan H J Hoeijmakers
- Department of Genetics, Erasmus University Medical Center, 3000 CA Rotterdam, the Netherlands
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Claudia Wiese
- Biosciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Judith Campisi
- Biosciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; The Buck Institute for Research on Aging, Novato, CA 94945, USA
| | - Priscilla K Cooper
- Biosciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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244
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Abstract
Two studies show that the E3 ubiquitin ligase RNF138 is recruited to DNA double-strand break sites, where it ubiquitylates key repair factors to promote DNA-end resection and homologous recombination. These findings add insights into the multilayered regulatory mechanisms underlying DNA double-strand break repair pathway choice in mammalian cells.
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245
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RFWD3-Dependent Ubiquitination of RPA Regulates Repair at Stalled Replication Forks. Mol Cell 2016; 60:280-93. [PMID: 26474068 DOI: 10.1016/j.molcel.2015.09.011] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 08/02/2015] [Accepted: 09/10/2015] [Indexed: 02/07/2023]
Abstract
We have used quantitative proteomics to profile ubiquitination in the DNA damage response (DDR). We demonstrate that RPA, which functions as a protein scaffold in the replication stress response, is multiply ubiquitinated upon replication fork stalling. Ubiquitination of RPA occurs on chromatin, involves sites outside its DNA binding channel, does not cause proteasomal degradation, and increases under conditions of fork collapse, suggesting a role in repair at stalled forks. We demonstrate that the E3 ligase RFWD3 mediates RPA ubiquitination. RFWD3 is necessary for replication fork restart, normal repair kinetics during replication stress, and homologous recombination (HR) at stalled replication forks. Mutational analysis suggests that multisite ubiquitination of the entire RPA complex is responsible for repair at stalled forks. Multisite protein group sumoylation is known to promote HR in yeast. Our findings reveal a similar requirement for multisite protein group ubiquitination during HR at stalled forks in mammalian cells.
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246
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Mechanisms and Dynamics of Protein Acetylation in Mitochondria. Trends Biochem Sci 2016; 41:231-244. [PMID: 26822488 DOI: 10.1016/j.tibs.2015.12.006] [Citation(s) in RCA: 216] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 12/17/2015] [Accepted: 12/22/2015] [Indexed: 12/17/2022]
Abstract
Reversible protein acetylation is a major regulatory mechanism for controlling protein function. Through genetic manipulations, dietary perturbations, and new proteomic technologies, the diverse functions of protein acetylation are coming into focus. Protein acetylation in mitochondria has taken center stage, revealing that 63% of mitochondrially localized proteins contain lysine acetylation sites. We summarize the field and discuss salient topics that cover spurious versus targeted acetylation, the role of SIRT3 deacetylation, nonenzymatic acetylation, and molecular models for regulatory acetylations that display high and low stoichiometry.
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247
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Bensaddek D, Narayan V, Nicolas A, Murillo AB, Gartner A, Kenyon CJ, Lamond AI. Micro-proteomics with iterative data analysis: Proteome analysis in C. elegans at the single worm level. Proteomics 2016; 16:381-92. [PMID: 26552604 PMCID: PMC4819713 DOI: 10.1002/pmic.201500264] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/21/2015] [Accepted: 11/02/2015] [Indexed: 01/01/2023]
Abstract
Proteomics studies typically analyze proteins at a population level, using extracts prepared from tens of thousands to millions of cells. The resulting measurements correspond to average values across the cell population and can mask considerable variation in protein expression and function between individual cells or organisms. Here, we report the development of micro‐proteomics for the analysis of Caenorhabditis elegans, a eukaryote composed of 959 somatic cells and ∼1500 germ cells, measuring the worm proteome at a single organism level to a depth of ∼3000 proteins. This includes detection of proteins across a wide dynamic range of expression levels (>6 orders of magnitude), including many chromatin‐associated factors involved in chromosome structure and gene regulation. We apply the micro‐proteomics workflow to measure the global proteome response to heat‐shock in individual nematodes. This shows variation between individual animals in the magnitude of proteome response following heat‐shock, including variable induction of heat‐shock proteins. The micro‐proteomics pipeline thus facilitates the investigation of stochastic variation in protein expression between individuals within an isogenic population of C. elegans. All data described in this study are available online via the Encyclopedia of Proteome Dynamics (http://www.peptracker.com/epd), an open access, searchable database resource.
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Affiliation(s)
- Dalila Bensaddek
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Vikram Narayan
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom.,Department of Biochemistry and Biophysics, Genentech Hall, University of California, San Francisco, CA, USA
| | - Armel Nicolas
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Alejandro Brenes Murillo
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Anton Gartner
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
| | - Cynthia J Kenyon
- Department of Biochemistry and Biophysics, Genentech Hall, University of California, San Francisco, CA, USA
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee, United Kingdom
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248
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Eustermann S, Wu WF, Langelier MF, Yang JC, Easton LE, Riccio AA, Pascal JM, Neuhaus D. Structural Basis of Detection and Signaling of DNA Single-Strand Breaks by Human PARP-1. Mol Cell 2015; 60:742-754. [PMID: 26626479 PMCID: PMC4678113 DOI: 10.1016/j.molcel.2015.10.032] [Citation(s) in RCA: 224] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 09/26/2015] [Accepted: 10/16/2015] [Indexed: 01/10/2023]
Abstract
Poly(ADP-ribose)polymerase 1 (PARP-1) is a key eukaryotic stress sensor that responds in seconds to DNA single-strand breaks (SSBs), the most frequent genomic damage. A burst of poly(ADP-ribose) synthesis initiates DNA damage response, whereas PARP-1 inhibition kills BRCA-deficient tumor cells selectively, providing the first anti-cancer therapy based on synthetic lethality. However, the mechanism underlying PARP-1’s function remained obscure; inherent dynamics of SSBs and PARP-1’s multi-domain architecture hindered structural studies. Here we reveal the structural basis of SSB detection and how multi-domain folding underlies the allosteric switch that determines PARP-1’s signaling response. Two flexibly linked N-terminal zinc fingers recognize the extreme deformability of SSBs and drive co-operative, stepwise self-assembly of remaining PARP-1 domains to control the activity of the C-terminal catalytic domain. Automodifcation in cis explains the subsequent release of monomeric PARP-1 from DNA, allowing repair and replication to proceed. Our results provide a molecular framework for understanding PARP inhibitor action and, more generally, allosteric control of dynamic, multi-domain proteins. We identify the structural basis of DNA single-strand break detection by PARP-1 An NMR/X-ray approach reveals how multi-domain allostery underlies activity switch The molecular model of PARP-1 assembly couples damage detection to PAR signaling Automodification in cis releases enzyme so DNA repair and replication can proceed
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Affiliation(s)
- Sebastian Eustermann
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Wing-Fung Wu
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Marie-France Langelier
- Department of Molecular Biology and Biochemistry, Sidney Kimmel Cancer Center, Thomas Jefferson University, 233 South 10th Street, Bluemle Life Sciences Building, Room 804, Philadelphia, PA 19107, USA
| | - Ji-Chun Yang
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Laura E Easton
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Amanda A Riccio
- Department of Molecular Biology and Biochemistry, Sidney Kimmel Cancer Center, Thomas Jefferson University, 233 South 10th Street, Bluemle Life Sciences Building, Room 804, Philadelphia, PA 19107, USA
| | - John M Pascal
- Department of Molecular Biology and Biochemistry, Sidney Kimmel Cancer Center, Thomas Jefferson University, 233 South 10th Street, Bluemle Life Sciences Building, Room 804, Philadelphia, PA 19107, USA
| | - David Neuhaus
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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249
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Becker JR, Pons C, Nguyen HD, Costanzo M, Boone C, Myers CL, Bielinsky AK. Genetic Interactions Implicating Postreplicative Repair in Okazaki Fragment Processing. PLoS Genet 2015; 11:e1005659. [PMID: 26545110 PMCID: PMC4636136 DOI: 10.1371/journal.pgen.1005659] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 10/19/2015] [Indexed: 01/28/2023] Open
Abstract
Ubiquitination of the replication clamp proliferating cell nuclear antigen (PCNA) at the conserved residue lysine (K)164 triggers postreplicative repair (PRR) to fill single-stranded gaps that result from stalled DNA polymerases. However, it has remained elusive as to whether cells engage PRR in response to replication defects that do not directly impair DNA synthesis. To experimentally address this question, we performed synthetic genetic array (SGA) analysis with a ubiquitination-deficient K164 to arginine (K164R) mutant of PCNA against a library of S. cerevisiae temperature-sensitive alleles. The SGA signature of the K164R allele showed a striking correlation with profiles of mutants deficient in various aspects of lagging strand replication, including rad27Δ and elg1Δ. Rad27 is the primary flap endonuclease that processes 5' flaps generated during lagging strand replication, whereas Elg1 has been implicated in unloading PCNA from chromatin. We observed chronic ubiquitination of PCNA at K164 in both rad27Δ and elg1Δ mutants. Notably, only rad27Δ cells exhibited a decline in cell viability upon elimination of PRR pathways, whereas elg1Δ mutants were not affected. We further provide evidence that K164 ubiquitination suppresses replication stress resulting from defective flap processing during Okazaki fragment maturation. Accordingly, ablation of PCNA ubiquitination increased S phase checkpoint activation, indicated by hyperphosphorylation of the Rad53 kinase. Furthermore, we demonstrate that alternative flap processing by overexpression of catalytically active exonuclease 1 eliminates PCNA ubiquitination. This suggests a model in which unprocessed flaps may directly participate in PRR signaling. Our findings demonstrate that PCNA ubiquitination at K164 in response to replication stress is not limited to DNA synthesis defects but extends to DNA processing during lagging strand replication.
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Affiliation(s)
- Jordan R. Becker
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Carles Pons
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Hai Dang Nguyen
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Michael Costanzo
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Charles Boone
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Chad L. Myers
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, United States of America
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