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Le Tallec B, Barrault MB, Guérois R, Carré T, Peyroche A. Hsm3/S5b participates in the assembly pathway of the 19S regulatory particle of the proteasome. Mol Cell 2009; 33:389-99. [PMID: 19217412 DOI: 10.1016/j.molcel.2009.01.010] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2008] [Revised: 10/03/2008] [Accepted: 01/09/2009] [Indexed: 11/19/2022]
Abstract
The 26S proteasome, the central enzyme of the ubiquitin-proteasome system, is comprised of the 20S catalytic core particle (CP) and the 19S regulatory particle (RP), itself composed of two subcomplexes, the base and the lid. 20S proteasome assembly is assisted by several chaperones. Integral subunits of the RP participate in its assembly, but no external factors have been identified so far. Here we characterize the yeast Hsm3 protein, which displays unique features regarding 19S assembly. Hsm3 associates with 19S subcomplexes via a carboxy-terminal domain of the Rpt1 base subunit but is missing in the final 26S proteasome. Moreover, Hsm3 is specifically required for the base subcomplex assembly. Finally, we identify the putative species-specific 19S subunit S5b as a functional homolog of the Hsm3 chaperone in mammals. These findings shed light on chaperone-assisted proteasome assembly in eukaryotes.
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Affiliation(s)
- Benoît Le Tallec
- Laboratoire du Métabolisme de l'ADN et Réponses aux Génotoxiques, SBIGeM, CEA, iBiTecS, Gif-sur-Yvette, F-91191, France
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52
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Faza MB, Kemmler S, Jimeno S, González-Aguilera C, Aguilera A, Hurt E, Panse VG. Sem1 is a functional component of the nuclear pore complex-associated messenger RNA export machinery. ACTA ACUST UNITED AC 2009; 184:833-46. [PMID: 19289793 PMCID: PMC2699155 DOI: 10.1083/jcb.200810059] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The evolutionarily conserved protein Sem1/Dss1 is a subunit of the regulatory particle (RP) of the proteasome, and, in mammalian cells, binds the tumor suppressor protein BRCA2. Here, we describe a new function for yeast Sem1. We show that sem1 mutants are impaired in messenger RNA (mRNA) export and transcription elongation, and induce strong transcription-associated hyper-recombination phenotypes. Importantly, Sem1, independent of the RP, is functionally linked to the mRNA export pathway. Biochemical analyses revealed that, in addition to the RP, Sem1 coenriches with components of two other multisubunit complexes: the nuclear pore complex (NPC)-associated TREX-2 complex that is required for transcription-coupled mRNA export, and the COP9 signalosome, which is involved in deneddylation. Notably, targeting of Thp1, a TREX-2 component, to the NPC is perturbed in a sem1 mutant. These findings reveal an unexpected nonproteasomal function of Sem1 in mRNA export and in prevention of transcription-associated genome instability. Thus, Sem1 is a versatile protein that might stabilize multiple protein complexes involved in diverse pathways.
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53
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Motegi A, Murakawa Y, Takeda S. The vital link between the ubiquitin-proteasome pathway and DNA repair: impact on cancer therapy. Cancer Lett 2009; 283:1-9. [PMID: 19201084 DOI: 10.1016/j.canlet.2008.12.030] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Revised: 12/23/2008] [Accepted: 12/27/2008] [Indexed: 01/05/2023]
Abstract
Proteasome-dependent protein degradation is involved in a variety of biological processes, including cell-cycle regulation, apoptosis, and stress-responses. Growing evidence from translational research and clinical trials proved the effectiveness of proteasome inhibitors (PIs) in treating several types of hematological malignancies. Although various key molecules in ubiquitin-dependent cellular processes have been proposed as relevant targets of therapeutic proteasome inhibition, our current understanding is far from complete. Recent rapid progress in DNA repair research has unveiled a crucial role of the ubiquitin-proteasome pathway (UPP) in regulating DNA repair. These findings thus bring up the idea that DNA repair pathways could be effective targets of PIs in mediating their cytotoxicity and enhancing the effect of radiotherapy and some DNA-damaging chemotherapeutic agents, such as cisplatin and camptothecin. In this review, we present the current perspective on the UPP-dependent regulatory mechanisms of DNA repair and discuss their therapeutic potential in the application of PIs to a broad spectrum of human cancers.
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Affiliation(s)
- Akira Motegi
- Department of Radiation Genetics, Kyoto University Graduate School of Medicine, Yoshida Konoe, Sakyo-ku, Kyoto 606-8501, Japan
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54
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Murata S, Yashiroda H, Tanaka K. Molecular mechanisms of proteasome assembly. Nat Rev Mol Cell Biol 2009; 10:104-15. [DOI: 10.1038/nrm2630] [Citation(s) in RCA: 400] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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55
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Wilmes GM, Bergkessel M, Bandyopadhyay S, Shales M, Braberg H, Cagney G, Collins SR, Whitworth GB, Kress TL, Weissman JS, Ideker T, Guthrie C, Krogan NJ. A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Mol Cell 2009; 32:735-46. [PMID: 19061648 DOI: 10.1016/j.molcel.2008.11.012] [Citation(s) in RCA: 204] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Revised: 10/20/2008] [Accepted: 11/13/2008] [Indexed: 01/11/2023]
Abstract
We used a quantitative, high-density genetic interaction map, or E-MAP (Epistatic MiniArray Profile), to interrogate the relationships within and between RNA-processing pathways. Due to their complexity and the essential roles of many of the components, these pathways have been difficult to functionally dissect. Here, we report the results for 107,155 individual interactions involving 552 mutations, 166 of which are hypomorphic alleles of essential genes. Our data enabled the discovery of links between components of the mRNA export and splicing machineries and Sem1/Dss1, a component of the 19S proteasome. In particular, we demonstrate that Sem1 has a proteasome-independent role in mRNA export as a functional component of the Sac3-Thp1 complex. Sem1 also interacts with Csn12, a component of the COP9 signalosome. Finally, we show that Csn12 plays a role in pre-mRNA splicing, which is independent of other signalosome components. Thus, Sem1 is involved in three separate and functionally distinct complexes.
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Affiliation(s)
- Gwendolyn M Wilmes
- Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94143-2200, USA
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56
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Matiuhin Y, Kirkpatrick DS, Ziv I, Kim W, Dakshinamurthy A, Kleifeld O, Gygi SP, Reis N, Glickman MH. Extraproteasomal Rpn10 restricts access of the polyubiquitin-binding protein Dsk2 to proteasome. Mol Cell 2008; 32:415-25. [PMID: 18995839 PMCID: PMC2643056 DOI: 10.1016/j.molcel.2008.10.011] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2007] [Revised: 06/01/2008] [Accepted: 10/10/2008] [Indexed: 10/21/2022]
Abstract
Polyubiquitin is a diverse signal both in terms of chain length and linkage type. Lysine 48-linked ubiquitin is essential for marking targets for proteasomal degradation, but the significance and relative abundance of different linkages remain ambiguous. Here we dissect the relationship of two proteasome-associated polyubiquitin-binding proteins, Rpn10 and Dsk2, and demonstrate how Rpn10 filters Dsk2 interactions, maintaining proper function of the ubiquitin-proteasome system. Using quantitative mass spectrometry of ubiquitin, we found that in S. cerevisiae under normal growth conditions the majority of conjugated ubiquitin was linked via lysine 48 and lysine 63. In contrast, upon DSK2 induction, conjugates accumulated primarily in the form of lysine 48 linkages correlating with impaired proteolysis and cytotoxicity. By restricting Dsk2 access to the proteasome, extraproteasomal Rpn10 was essential for alleviating the cellular stress associated with Dsk2. This work highlights the importance of polyubiquitin shuttles such as Rpn10 and Dsk2 in controlling the ubiquitin landscape.
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Affiliation(s)
- Yulia Matiuhin
- Department of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
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57
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Kusmierczyk AR, Hochstrasser M. Some assembly required: dedicated chaperones in eukaryotic proteasome biogenesis. Biol Chem 2008; 389:1143-51. [PMID: 18713001 DOI: 10.1515/bc.2008.130] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The 26S proteasome is the key eukaryotic protease responsible for the degradation of intracellular proteins. Protein degradation by the 26S proteasome plays important roles in numerous cellular processes, including the cell cycle, differentiation, apoptosis, and the removal of damaged or misfolded proteins. How this 2.5-MDa complex, composed of at least 32 different polypeptides, is assembled in the first place is not well understood. However, it has become evident that this complicated task is facilitated by a framework of protein factors that chaperone the nascent proteasome through its various stages of assembly. We review here the known proteasome-specific assembly factors, most only recently discovered, and describe their potential roles in proteasome assembly, with an emphasis on the many remaining unanswered questions about this intricate process of assisted self-assembly.
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Affiliation(s)
- Andrew R Kusmierczyk
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
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58
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Wei SJ, Williams JG, Dang H, Darden TA, Betz BL, Humble MM, Chang FM, Trempus CS, Johnson K, Cannon RE, Tennant RW. Identification of a specific motif of the DSS1 protein required for proteasome interaction and p53 protein degradation. J Mol Biol 2008; 383:693-712. [PMID: 18775730 DOI: 10.1016/j.jmb.2008.08.044] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2008] [Revised: 07/16/2008] [Accepted: 08/19/2008] [Indexed: 10/21/2022]
Abstract
Deleted in Split hand/Split foot 1 (DSS1) was previously identified as a novel 12-O-tetradecanoylphorbol-13-acetate (TPA)-inducible gene with possible involvement in early event of mouse skin carcinogenesis. The mechanisms by which human DSS1 (HsDSS1) exerts its biological effects via regulation of the ubiquitin-proteasome system (UPS) are currently unknown. Here, we demonstrated that HsDSS1 regulates the human proteasome by associating with it in the cytosol and nucleus via the RPN3/S3 subunit of the 19S regulatory particle (RP). Molecular anatomy of HsDSS1 revealed an RPN3/S3-interacting motif (R3IM), located at amino acid residues 15 to 21 of the NH(2) terminus. Importantly, negative charges of the R3IM motif were demonstrated to be required for proteasome interaction and binding to poly-ubiquitinated substrates. Indeed, the R3IM motif of HsDSS1 protein alone was sufficient to replace the ability of intact HsDSS1 protein to pull down proteasome complexes and protein substrates with high-molecular mass ubiquitin conjugates. Interestingly, this interaction is highly conserved throughout evolution from humans to nematodes. Functional study, lowering the levels of the endogenous HsDSS1 using siRNA, indicates that the R3IM/proteasome complex binds and targets p53 for ubiquitin-mediated degradation via gankyrin-MDM2/HDM2 pathway. Most significantly, this work indicates that the R3IM motif of HsDSS1, in conjunction with the complexes of 19S RP and 20S core particle (CP), regulates proteasome interaction through RPN3/S3 molecule, and utilizes a specific subset of poly-ubiquitinated p53 as a substrate.
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Affiliation(s)
- Sung-Jen Wei
- Laboratory of Molecular Toxicology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.
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59
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Pispa J, Palmén S, Holmberg CI, Jäntti J. C. elegans dss-1 is functionally conserved and required for oogenesis and larval growth. BMC DEVELOPMENTAL BIOLOGY 2008; 8:51. [PMID: 18471277 PMCID: PMC2409312 DOI: 10.1186/1471-213x-8-51] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2007] [Accepted: 05/09/2008] [Indexed: 11/10/2022]
Abstract
Background Dss1 (or Rpn15) is a recently identified subunit of the 26S proteasome regulatory particle. In addition to its function in the protein degradation machinery, it has been linked to BRCA2 (breast cancer susceptibility gene 2 product) and homologous DNA recombination, mRNA export, and exocytosis. While the fungal orthologues of Dss1 are not essential for viability, the significance of Dss1 in metazoans has remained unknown due to a lack of knockout animal models. Results In the current study deletion of dss-1 was studied in Caenorhabditis elegans with a dss-1 loss-of-function mutant and dss-1 directed RNAi. The analysis revealed an essential role for dss-1 in oogenesis. In addition, dss-1 RNAi caused embryonic lethality and larval arrest, presumably due to loss of the dss-1 mRNA maternal contribution. DSS-1::GFP fusion protein localised primarily in the nucleus. No apparent effect on proteasome function was found in dss-1 RNAi treated worms. However, expression of the C. elegans dss-1 in yeast cells deleted for its orthologue SEM1 rescued their temperature-sensitive growth phenotype, and partially rescued the accumulation of polyubiquitinated proteins in these cells. Conclusion The first knockout animal model for the gene encoding the proteasome subunit DSS-1/Rpn15/Sem1 is characterised in this study. In contrast to unicellular eukaryotes, the C. elegans dss-1 encodes an essential protein, which is required for embryogenesis, larval growth, and oogenesis, and which is functionally conserved with its yeast and human homologues.
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Affiliation(s)
- Johanna Pispa
- Cellular Biotechnology Research Program, Institute of Biotechnology, University of Helsinki, Finland.
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60
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Hoyt MA, McDonough S, Pimpl SA, Scheel H, Hofmann K, Coffino P. A genetic screen forSaccharomyces cerevisiae mutants affecting proteasome function, using a ubiquitin-independent substrate. Yeast 2008; 25:199-217. [DOI: 10.1002/yea.1579] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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61
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Murakawa Y, Sonoda E, Barber LJ, Zeng W, Yokomori K, Kimura H, Niimi A, Lehmann A, Zhao GY, Hochegger H, Boulton SJ, Takeda S. Inhibitors of the Proteasome Suppress Homologous DNA Recombination in Mammalian Cells. Cancer Res 2007; 67:8536-43. [PMID: 17875693 DOI: 10.1158/0008-5472.can-07-1166] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Proteasome inhibitors are novel antitumor agents against multiple myeloma and other malignancies. Despite the increasing clinical application, the molecular basis of their antitumor effect has been poorly understood due to the involvement of the ubiquitin-proteasome pathway in multiple cellular metabolisms. Here, we show that treatment of cells with proteasome inhibitors has no significant effect on nonhomologous end joining but suppresses homologous recombination (HR), which plays a key role in DNA double-strand break (DSB) repair. In this study, we treat human cells with proteasome inhibitors and show that the inhibition of the proteasome reduces the efficiency of HR-dependent repair of an artificial HR substrate. We further show that inhibition of the proteasome interferes with the activation of Rad51, a key factor for HR, although it does not affect the activation of ATM, gammaH2AX, or Mre11. These data show that the proteasome-mediated destruction is required for the promotion of HR at an early step. We suggest that the defect in HR-mediated DNA repair caused by proteasome inhibitors contributes to antitumor effect, as HR plays an essential role in cellular proliferation. Moreover, because HR plays key roles in the repair of DSBs caused by chemotherapeutic agents such as cisplatin and by radiotherapy, proteasome inhibitors may enhance the efficacy of these treatments through the suppression of HR-mediated DNA repair pathways.
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Affiliation(s)
- Yasuhiro Murakawa
- Department of Radiation Genetics, Horizontal Medical Research Organization, Kyoto University Graduate School of Medicine, Kyoto, Japan
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62
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Gudmundsdottir K, Lord CJ, Ashworth A. The proteasome is involved in determining differential utilization of double-strand break repair pathways. Oncogene 2007; 26:7601-6. [PMID: 17563742 DOI: 10.1038/sj.onc.1210579] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The DSS1 protein interacts with the breast cancer susceptibility protein BRCA2 that plays an integral role in the repair of DNA double-strand breaks (DSBs). DSS1 has also been shown to interact with components of the 26S proteasome in Saccharomyces cerevisiae and in human tumour cells. This raises the possibility of functional interplay between the DNA repair machinery and the proteasome. We show here that human DSS1 interacts with the RPN3 and RPN7 proteasome subunits and define regions of DSS1 important for the interactions with RPN3, RPN7 and BRCA2. We also show that BRCA2 interacts with RPN3 and RPN7 and that the BRCA2/RPN7 interaction is independent of DSS1. Finally, and most significantly, we demonstrate that the proteolytic activity of the proteasome is a determinant of the choice of DSB repair pathway; inhibition of proteasome proteolytic activity results in an increase in the utilization of potentially mutagenic single-strand annealing at the expense of a reduction in the level of error-free gene conversion. This confirms a functional link between DSB repair and proteasomal activity.
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Affiliation(s)
- K Gudmundsdottir
- Gene Function Laboratory, The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
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63
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Syrjäkoski K, Jäntti J, Kallioniemi A, Karhu R. Mutations in the BRCA2 interacting DSS1 are not a risk factor for male breast cancer. Int J Cancer 2007; 120:444-6. [PMID: 17066443 DOI: 10.1002/ijc.22163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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64
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Isono E, Nishihara K, Saeki Y, Yashiroda H, Kamata N, Ge L, Ueda T, Kikuchi Y, Tanaka K, Nakano A, Toh-e A. The assembly pathway of the 19S regulatory particle of the yeast 26S proteasome. Mol Biol Cell 2007; 18:569-80. [PMID: 17135287 PMCID: PMC1783769 DOI: 10.1091/mbc.e06-07-0635] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2006] [Revised: 11/13/2006] [Accepted: 11/20/2006] [Indexed: 12/13/2022] Open
Abstract
The 26S proteasome consists of the 20S proteasome (core particle) and the 19S regulatory particle made of the base and lid substructures, and it is mainly localized in the nucleus in yeast. To examine how and where this huge enzyme complex is assembled, we performed biochemical and microscopic characterization of proteasomes produced in two lid mutants, rpn5-1 and rpn7-3, and a base mutant DeltaN rpn2, of the yeast Saccharomyces cerevisiae. We found that, although lid formation was abolished in rpn5-1 mutant cells at the restrictive temperature, an apparently intact base was produced and localized in the nucleus. In contrast, in DeltaN rpn2 cells, a free lid was formed and localized in the nucleus even at the restrictive temperature. These results indicate that the modules of the 26S proteasome, namely, the core particle, base, and lid, can be formed and imported into the nucleus independently of each other. Based on these observations, we propose a model for the assembly process of the yeast 26S proteasome.
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Affiliation(s)
- Erika Isono
- *Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan
- Entwicklungsgenetik, ZMBP, University of Tübingen, D-72076 Tübingen, Germany
| | - Kiyoshi Nishihara
- *Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan
| | - Yasushi Saeki
- *Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan
| | - Hideki Yashiroda
- Tokyo Metropolitan Institute of Medical Science, Tokyo 113-8613, Japan; and
| | - Naoko Kamata
- *Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan
| | - Liying Ge
- *Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan
| | - Takashi Ueda
- *Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan
| | - Yoshiko Kikuchi
- *Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan
| | - Keiji Tanaka
- Tokyo Metropolitan Institute of Medical Science, Tokyo 113-8613, Japan; and
| | - Akihiko Nakano
- *Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan
- RIKEN Discovery Research Institute, Saitama 351-0198, Japan
| | - Akio Toh-e
- *Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-0033, Japan
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65
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Abstract
The known molecular players in cell-cycle control are much studied, not only to learn more about this intricate system, but also to understand the molecular features of oncogenic transformation. Infrequently, new players are discovered that change the interpretation of cell-cycle control. Gankyrin is one such player and was discovered in yeast two-hybrid screens as a new proteasomal subunit that interacts specifically with the S6b (rpt3) AAA (ATPase associated with various cellular activities) ATPase, which, with five other AAAs, are present in the so-called base of the 19 S regulator of the 26 S proteasome. Gankyrin is also the first liver oncogene. Gankyrin is found in other complexes that contain Rb (retinoblastoma protein) and the ubiquitin protein ligase Mdm2 (murine double minute 2). Gankyrin increases the hyperphosphorylation of Rb and therefore activates E2F-dependent transcription of DNA synthesis genes. Additionally, gankyrin, by binding to Mdm2, increases the ubiquitylation and degradation of p53 and prevents apoptosis. Gankyrin controls the functions of two major tumour suppressors and, when overexpressed, causes hepatocellular carcinoma.
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Affiliation(s)
- R J Mayer
- School of Biomedical Sciences, University of Nottingham Medical School, Queen's Medical Centre, Nottingham NG7 2UH, UK.
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66
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Zhou Q, Kojic M, Cao Z, Lisby M, Mazloum NA, Holloman WK. Dss1 interaction with Brh2 as a regulatory mechanism for recombinational repair. Mol Cell Biol 2007; 27:2512-26. [PMID: 17261595 PMCID: PMC1899899 DOI: 10.1128/mcb.01907-06] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Brh2, the BRCA2 ortholog in Ustilago maydis, enables recombinational repair of DNA by controlling Rad51 and is in turn regulated by Dss1. Interplay with Rad51 is conducted via the BRC element located in the N-terminal region of the protein and through an unrelated domain, CRE, at the C terminus. Mutation in either BRC or CRE severely reduces functional activity, but repair deficiency of the brh2 mutant can be complemented by expressing BRC and CRE on different molecules. This intermolecular complementation is dependent upon the presence of Dss1. Brh2 molecules associate through the region overlapping with the Dss1-interacting domain to form at least dimer-sized complexes, which in turn, can be dissociated by Dss1 to monomer. We propose that cooperation between BRC and CRE domains and the Dss1-provoked dissociation of Brh2 complexes are requisite features of Brh2's molecular mechanism.
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Affiliation(s)
- Qingwen Zhou
- Department of Microbiology and Immunology, Cornell University Weill Medical College, 1300 York Avenue, New York, NY 10021, USA
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67
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Fillingham J, Keogh MC, Krogan NJ. GammaH2AX and its role in DNA double-strand break repair. Biochem Cell Biol 2007; 84:568-77. [PMID: 16936829 DOI: 10.1139/o06-072] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
One of the earliest responses to a DNA double-strand break (DSB) is the carboxy-terminal phosphorylation of budding yeast H2A (metazoan histone H2AX) to create gammaH2A (or gammaH2AX). This chromatin modification stretches more than tens of kilobases around the DSB and has been proposed to play numerous roles in break recognition and repair, although it may not be the primary signal for many of these events. Studies suggest that gammaH2A(X) has 2 more direct roles: (i) to recruit cohesin around the DSB, and (ii) to maintain a checkpoint arrest. Recent work has identified other factors, including chromatin remodelers and protein phosphatases, which target gammaH2A(X) and regulate DSB repair/recovery.
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Affiliation(s)
- Jeffrey Fillingham
- Banting and Best Dept of Medical Research, University of Toronto, Toronto, ON M5S 1A8, Canada
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68
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Kearsey SE, Stevenson AL, Toda T, Wang SW. Fission yeast Cut8 is required for the repair of DNA double-strand breaks, ribosomal DNA maintenance, and cell survival in the absence of Rqh1 helicase. Mol Cell Biol 2006; 27:1558-67. [PMID: 17178839 PMCID: PMC1820446 DOI: 10.1128/mcb.01495-06] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Schizosaccharomyces pombe Rqh1 is a member of the RecQ DNA helicase family. Members of this protein family are mutated in cancer predisposition diseases, causing Bloom's, Werner, and Rothmund-Thomson syndromes. Rqh1 forms a complex with topoisomerase III and is proposed to process or disrupt aberrant recombination structures that arise during S phase to allow proper chromosome segregation during mitosis. Intriguingly, in the absence of Rqh1, processing of these structures appears to be dependent on Rad3 (human ATR) in a manner that is distinct from its role in checkpoint control. Here, we show that rad3 rqh1 mutants are normally committed to a lethal pathway of DNA repair requiring homologous recombination, but blocking this pathway by Rhp51 inactivation restores viability. Remarkably, viability is also restored by overexpression of Cut8, a nuclear envelope protein involved in tethering and proper function of the proteasome. In keeping with a recently described function of the proteasome in the repair of DNA double-strand breaks, we found that Cut8 is also required for DNA double-strand break repair and is essential for proper chromosome segregation in the absence of Rqh1, suggesting that these proteins might function in a common pathway in homologous recombination repair to ensure accurate nuclear division in S. pombe.
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Affiliation(s)
- Stephen E Kearsey
- Department of Zoology, South Parks Road, Oxford OX1 3PS, United Kingdom.
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69
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Gudmundsdottir K, Ashworth A. The roles of BRCA1 and BRCA2 and associated proteins in the maintenance of genomic stability. Oncogene 2006; 25:5864-74. [PMID: 16998501 DOI: 10.1038/sj.onc.1209874] [Citation(s) in RCA: 427] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The BRCA1 and BRCA2 proteins are important in maintaining genomic stability by promoting efficient and precise repair of double-strand breaks. The main role of BRCA2 appears to involve regulating the function of RAD51 in the repair by homologous recombination. BRCA1 has a broader role upstream of BRCA2, participating in various cellular processes in response to DNA damage. The DNA repair defect associated with mutations in BRCA1 or BRCA2 could be exploited to develop new targeted therapeutic approaches for cancer occurring in mutation carriers.
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Affiliation(s)
- K Gudmundsdottir
- The Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, Fulham Road, London, UK
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70
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Hoyt MA, Zich J, Takeuchi J, Zhang M, Govaerts C, Coffino P. Glycine-alanine repeats impair proper substrate unfolding by the proteasome. EMBO J 2006; 25:1720-9. [PMID: 16601692 PMCID: PMC1440830 DOI: 10.1038/sj.emboj.7601058] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2005] [Accepted: 03/01/2006] [Indexed: 11/09/2022] Open
Abstract
Proteasome ATPases unravel folded proteins. Introducing a sequence containing only glycine and alanine residues (GAr) into substrates can impair their digestion. We previously proposed that a GAr interferes with the unfolding capacity of the proteasome, leading to partial degradation of products. Here we tested that idea in several ways. Stabilizing or destabilizing a folded domain within substrate proteins changed GAr-mediated intermediate production in the way predicted by the model. A downstream folded domain determined the sites of terminal proteolysis. The spacing between a GAr and a folded domain was critical for intermediate production. Intermediates containing a GAr did not remain associated with proteasomes, excluding models whereby retained GAr-containing proteins halt further processing. The following model is supported: a GAr positioned within the ATPase ring reduces the efficiency of coupling between nucleotide hydrolysis and work performed on the substrate. If this impairment takes place when unfolding must be initiated, insertion pauses and proteolysis is limited to the portion of the substrate that has already entered the catalytic chamber of the proteasome.
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Affiliation(s)
- Martin A Hoyt
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Judith Zich
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Junko Takeuchi
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Mingsheng Zhang
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
| | - Cedric Govaerts
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, USA
| | - Philip Coffino
- Department of Microbiology and Immunology, University of California, San Francisco, CA, USA
- Department of Microbiology and Immunology, UCSF, 513 Parnassus Avenue, San Francisco, CA 94143-0414, USA. Tel.: +1 415 476 1783; E-mail:
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71
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Jossé L, Harley M, Pires I, Hughes D. Fission yeast Dss1 associates with the proteasome and is required for efficient ubiquitin-dependent proteolysis. Biochem J 2006; 393:303-9. [PMID: 16149916 PMCID: PMC1383689 DOI: 10.1042/bj20051238] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Human DSS1 associates with BRCA2, a tumour suppressor protein required for efficient recombinational DNA repair, but the biochemical function of DSS1 is not known. Orthologues of DSS1 are found in organisms such as budding yeast and fission yeast that do not have BRCA2-related proteins, indicating that DSS1 has a physiological role independent of BRCA2. The DSS1 orthologue in Saccharomyces cerevisiae has been shown to associate with the 26 S proteasome and, in the present paper, we report that in the distantly related fission yeast Schizosaccharomyces pombe, Dss1 associates with the 19 S RP (regulatory particle) of the 26 S proteasome. A role for S. pombe Dss1 in proteasome function is supported by three lines of evidence. First, overexpression of two components of the 19 S RP, namely Pad1/Rpn11 and Mts3/Rpn12, rescued the temperature-sensitive growth defect of the dss1 mutant. Secondly, the dss1 mutant showed phenotypes indicative of a defect in proteasome function: growth of the dss1 mutant was inhibited by low concentrations of L-canavanine, an amino acid analogue, and cells of the dss1 mutant accumulated high molecular mass poly-ubiquitylated proteins. Thirdly, synthetic growth defects were found when the dss1 mutation was combined with mutations in other proteasome subunit genes. These findings show that DSS1 has an evolutionarily conserved role as a regulator of proteasome function and suggest that DSS1 may provide a link between BRCA2 and ubiquitin-mediated proteolysis in human cells.
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Affiliation(s)
- Lyne Jossé
- Faculty of Life Sciences, University of Manchester, Jackson's Mill, P.O. Box 88, Manchester M60 1QD, U.K
| | - Margaret E. Harley
- Faculty of Life Sciences, University of Manchester, Jackson's Mill, P.O. Box 88, Manchester M60 1QD, U.K
| | - Isabel M. S. Pires
- Faculty of Life Sciences, University of Manchester, Jackson's Mill, P.O. Box 88, Manchester M60 1QD, U.K
| | - David A. Hughes
- Faculty of Life Sciences, University of Manchester, Jackson's Mill, P.O. Box 88, Manchester M60 1QD, U.K
- To whom correspondence should be addressed (email )
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72
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Dray E, Siaud N, Dubois E, Doutriaux MP. Interaction between Arabidopsis Brca2 and its partners Rad51, Dmc1, and Dss1. PLANT PHYSIOLOGY 2006; 140:1059-69. [PMID: 16415210 PMCID: PMC1400560 DOI: 10.1104/pp.105.075838] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The Arabidopsis (Arabidopsis thaliana) orthologs of Brca2, a protein whose mutations are involved in breast cancer in humans, were previously shown to be essential at meiosis. In an attempt to better understand the Brca2-interacting properties, we examined four partners of the two isoforms of Brca2 identified in Arabidopsis (AtRad51, AtDmc1, and two AtDss1 isoforms). The two Brca2 and the two Dss1 isoforms are named AtBrca2(IV), AtBrca2(V), AtDss1(I), and AtDss1(V) after their chromosomal localization. We first show that both AtBrca2 proteins can interact with either AtRad51 or AtDmc1 in vitro, and that the N-terminal region of AtBrca2 is responsible for these interactions. More specifically, the BRC motifs (so called because iterated in the Brca2 protein) in Brca2 are involved in these interactions: BRC motif number 2 (BRC2) alone can interact with AtDmc1, whereas BRC motif number 4 (BRC4) recognizes AtRad51. The human Rad51 and Dmc1 proteins themselves can interact with either the complete (HsRad51) or a shorter version of AtBrca2 (HsRad51 or HsDmc1) that comprises all four BRC motifs. We also identified two Arabidopsis isoforms of Dss1, another known partner of Brca2 in other organisms. Although all four Brca2 and Dss1 proteins are much conserved, AtBrca2(IV) interacts with only one of these AtDss1 proteins, whereas AtBrca2(V) interacts with both of them. Finally, we show for the first time that an AtBrca2 protein could bind two different partners at the same time: AtRad51 and AtDss1(I), or AtDmc1 and AtDss1(I).
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Affiliation(s)
- Eloïse Dray
- Institut de Biotechnologie des Plantes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8618, Université Paris XI, Orsay, France
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73
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Maupin-Furlow JA, Humbard MA, Kirkland PA, Li W, Reuter CJ, Wright AJ, Zhou G. Proteasomes from Structure to Function: Perspectives from Archaea. Curr Top Dev Biol 2006; 75:125-69. [PMID: 16984812 DOI: 10.1016/s0070-2153(06)75005-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Insight into the world of proteolysis has expanded considerably over the past decade. Energy-dependent proteases, such as the proteasome, are no longer viewed as nonspecific degradative enzymes associated solely with protein catabolism but are intimately involved in controlling biological processes that span life to death. The proteasome maintains this exquisite control by catalyzing the precisely timed and rapid turnover of key regulatory proteins. Proteasomes also interplay with chaperones to ensure protein quality and to readjust the composition of the proteome following stress. Archaea encode proteasomes that are highly related to those of eukaryotes in basic structure and function. Investigations of archaeal proteasomes coupled with those of eukaryotes has greatly facilitated our understanding of the molecular mechanisms that govern regulated protein degradation by this elaborate nanocompartmentalized machine.
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Affiliation(s)
- Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida Gainesville, Florida 32611, USA
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74
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Baillat D, Hakimi MA, Näär AM, Shilatifard A, Cooch N, Shiekhattar R. Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II. Cell 2005; 123:265-76. [PMID: 16239144 DOI: 10.1016/j.cell.2005.08.019] [Citation(s) in RCA: 372] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2005] [Revised: 06/06/2005] [Accepted: 08/10/2005] [Indexed: 12/13/2022]
Abstract
The C-terminal domain (CTD) of RNA polymerase II (RNAPII) is an essential component of transcriptional regulation and RNA processing of protein-coding genes. A large body of data also implicates the CTD in the transcription and processing of RNAPII-mediated small nuclear RNAs (snRNAs). However, the identity of the complex (or complexes) that associates with the CTD and mediates the processing of snRNAs has remained elusive. Here, we describe an RNA polymerase II complex that contains at least 12 novel subunits, termed the Integrator, in addition to core RNAPII subunits. Two of the Integrator subunits display similarities to the subunits of the cleavage and polyadenylation specificity factor (CPSF) complex. We show that Integrator is recruited to the U1 and U2 snRNA genes and mediates the snRNAs' 3' end processing. The Integrator complex is evolutionarily conserved in metazoans and directly interacts with the C-terminal domain of the RNA polymerase II largest subunit.
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MESH Headings
- Amino Acid Sequence
- Amino Acid Substitution
- Binding Sites
- Blotting, Western
- Carrier Proteins/chemistry
- Carrier Proteins/metabolism
- Cell Line
- Chromatin Immunoprecipitation
- Conserved Sequence
- Endoribonucleases
- Escherichia coli/genetics
- Evolution, Molecular
- Glyceraldehyde-3-Phosphate Dehydrogenases/analysis
- Glyceraldehyde-3-Phosphate Dehydrogenases/metabolism
- HeLa Cells
- Humans
- Models, Biological
- Molecular Sequence Data
- Protein Structure, Tertiary
- Protein Subunits/chemistry
- RNA/biosynthesis
- RNA Polymerase II/chemistry
- RNA Polymerase II/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Messenger/analysis
- RNA, Messenger/metabolism
- RNA, Small Interfering/metabolism
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- Recombinant Fusion Proteins/isolation & purification
- Recombinant Fusion Proteins/metabolism
- Sequence Homology, Amino Acid
- Transcription, Genetic
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Affiliation(s)
- David Baillat
- The Wistar Institute, 3601 Spruce Street, Philadelphia, Pennsylvania 19104, USA
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75
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Schmidt M, Hanna J, Elsasser S, Finley D. Proteasome-associated proteins: regulation of a proteolytic machine. Biol Chem 2005; 386:725-37. [PMID: 16201867 DOI: 10.1515/bc.2005.085] [Citation(s) in RCA: 137] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The proteasome is a compartmentalized, ATP-dependent protease composed of more than 30 subunits that recognizes and degrades polyubiquitinated substrates. Despite its physiological importance, many aspects of the proteasome's structural organization and regulation remain poorly understood. In addition to the proteins that form the proteasome holocomplex, there is increasing evidence that proteasomal function is affected by a wide variety of associating proteins. A group of ubiquitin-binding proteins assist in delivery of substrates to the proteasome, whereas proteasome-associated ubiquitin ligases and deubiquitinating enzymes may alter the dynamics of ubiquitin chains already associated with the proteasome. Some proteins appear to influence the overall stability of the complex, and still others have the capacity to activate or inhibit the hydrolytic activity of the core particle. The increasing number of interacting proteins identified suggests that proteasomes, as they exist in the cell, are larger and more diverse in composition than previously assumed. Thus, the study of proteasome-associated proteins will lead to new perspectives on the dynamics of this uniquely complex proteolytic machine.
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Affiliation(s)
- Marion Schmidt
- Department of Cell Biology, Harvard Medical School, 240 Longwood Ave., Boston, MA 02115, USA
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76
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Lee D, Ezhkova E, Li B, Pattenden SG, Tansey WP, Workman JL. The Proteasome Regulatory Particle Alters the SAGA Coactivator to Enhance Its Interactions with Transcriptional Activators. Cell 2005; 123:423-36. [PMID: 16269334 DOI: 10.1016/j.cell.2005.08.015] [Citation(s) in RCA: 142] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2005] [Revised: 06/13/2005] [Accepted: 08/03/2005] [Indexed: 11/28/2022]
Abstract
Promoter recruitment of the Saccharomyces cerevisiae SAGA histone acetyltransferase complex is required for RNA polymerase II-dependent transcription of several genes. SAGA is targeted to promoters through interactions with sequence-specific DNA binding transcriptional activators and facilitates preinitiation-complex assembly and transcription. Here, we show that the 19S proteasome regulatory particle (19S RP) alters SAGA to stimulate its interaction with transcriptional activators. The ATPase components of the 19S RP are required for stimulation of SAGA/activator interactions and enhance SAGA recruitment to promoters. Proteasomal ATPases genetically interact with SAGA, and their inhibition reduces global histone H3 acetylation levels and SAGA recruitment to target promoters in vivo. These results indicate that the 19S RP modulates SAGA complex using its ATPase components, thereby facilitating subsequent transcription events at promoters.
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Affiliation(s)
- Daeyoup Lee
- Stowers Institute for Medical Research, 1000 East 50th Street, Kansas City, Missouri 64110, USA
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77
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Current awareness on yeast. Yeast 2005. [DOI: 10.1002/yea.1166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
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78
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Lundgren J, Masson P, Mirzaei Z, Young P. Identification and characterization of a Drosophila proteasome regulatory network. Mol Cell Biol 2005; 25:4662-75. [PMID: 15899868 PMCID: PMC1140619 DOI: 10.1128/mcb.25.11.4662-4675.2005] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Maintaining adequate proteasomal proteolytic activity is essential for eukaryotic cells. For metazoan cells, little is known about the composition of genes that are regulated in the proteasome network or the mechanisms that modulate the levels of proteasome genes. Previously, two distinct treatments have been observed to induce 26S proteasome levels in Drosophila melanogaster cell lines, RNA interference (RNAi)-mediated inhibition of the 26S proteasome subunit Rpn10/S5a and suppression of proteasome activity through treatment with active-site inhibitors. We have carried out genome array profiles from cells with decreased Rpn10/S5a levels using RNAi or from cells treated with proteasome inhibitor MG132 and have thereby identified candidate genes that are regulated as part of a metazoan proteasome network. The profiles reveal that the majority of genes that were identified to be under the control of the regulatory network consisted of 26S proteasome subunits. The 26S proteasome genes, including three new subunits, Ubp6p, Uch-L3, and Sem1p, were found to be up-regulated. A number of genes known to have proteasome-related functions, including Rad23, isopeptidase T, sequestosome, and the genes for the segregase complex TER94/VCP-Ufd1-Npl4 were also found to be up-regulated. RNAi-mediated inhibition against the segregase complex genes demonstrated pronounced stabilization of proteasome substrates throughout the Drosophila cell. Finally, transcriptional reporter assays and deletion mapping studies in Drosophila demonstrate that proteasome mRNA induction is dependent upon the 5' untranslated regions (UTRs). Transfer of the 5' UTR from the proteasome subunit Rpn1/S2 to a noninducible promoter was sufficient to confer transcriptional upregulation of the reporter mRNA after proteasome inhibition.
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Affiliation(s)
- Josefin Lundgren
- Department of Molecular Biology and Functional Genomics, Stockholm University, S-106 91 Stockholm, Sweden
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79
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Abstract
The 26S proteasome is responsible for regulated proteolysis of most intracellular proteins yet the focus of intense regulatory action itself. Proteasome abundance is responsive to cell needs or stress conditions, and dynamically localized to concentrations of substrates. Proteasomes are continually assembled and disassembled, and their subunits subject to a variety of posttranslational modifications. Furthermore, as robust and multi-tasking as this complex is, it does not function alone. A spattering of closely associating proteins enhances complex stability, fine-tunes activity, assists in substrate-binding, recycling of ubiquitin, and more. HEAT repeat caps activate proteasomes, yet share remarkable features with nuclear importins. Fascinating cross talk even occurs with ribosomes through common maturation factors. The dynamics of proteasome configurations and how they relate to diverse activities is the topic of this review.
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Affiliation(s)
- Michael H Glickman
- Department of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel
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