51
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Di Fiore B, Davey NE, Hagting A, Izawa D, Mansfeld J, Gibson TJ, Pines J. The ABBA motif binds APC/C activators and is shared by APC/C substrates and regulators. Dev Cell 2015; 32:358-372. [PMID: 25669885 PMCID: PMC4713905 DOI: 10.1016/j.devcel.2015.01.003] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Revised: 09/03/2014] [Accepted: 01/05/2015] [Indexed: 11/30/2022]
Abstract
The anaphase-promoting complex or cyclosome (APC/C) is the ubiquitin ligase that regulates mitosis by targeting specific proteins for degradation at specific times under the control of the spindle assembly checkpoint (SAC). How the APC/C recognizes its different substrates is a key problem in the control of cell division. Here, we have identified the ABBA motif in cyclin A, BUBR1, BUB1, and Acm1, and we show that it binds to the APC/C coactivator CDC20. The ABBA motif in cyclin A is required for its proper degradation in prometaphase through competing with BUBR1 for the same site on CDC20. Moreover, the ABBA motifs in BUBR1 and BUB1 are necessary for the SAC to work at full strength and to recruit CDC20 to kinetochores. Thus, we have identified a conserved motif integral to the proper control of mitosis that connects APC/C substrate recognition with the SAC.
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Affiliation(s)
- Barbara Di Fiore
- The Gurdon Institute and Department of Zoology, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Norman E. Davey
- Department of Physiology and Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Baden-Württemberg 69117, Germany
| | - Anja Hagting
- The Gurdon Institute and Department of Zoology, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Daisuke Izawa
- The Gurdon Institute and Department of Zoology, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Jörg Mansfeld
- Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Toby J. Gibson
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Baden-Württemberg 69117, Germany
| | - Jonathon Pines
- The Gurdon Institute and Department of Zoology, University of Cambridge, Cambridge, CB2 1QN, UK
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52
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Zhang C, Zhang F. The Multifunctions of WD40 Proteins in Genome Integrity and Cell Cycle Progression. J Genomics 2015; 3:40-50. [PMID: 25653723 PMCID: PMC4316180 DOI: 10.7150/jgen.11015] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Eukaryotic genome encodes numerous WD40 repeat proteins, which generally function as platforms of protein-protein interactions and are involved in numerous biological process, such as signal transduction, gene transcriptional regulation, protein modifications, cytoskeleton assembly, vesicular trafficking, DNA damage and repair, cell death and cell cycle progression. Among these diverse functions, genome integrity maintenance and cell cycle progression are extremely important as deregulation of them is clinically linked to uncontrolled proliferative diseases such as cancer. Thus, we mainly summarize and discuss the recent understanding of WD40 proteins and their molecular mechanisms linked to genome stability and cell cycle progression in this review, thereby demonstrating their pervasiveness and importance in cellular networks.
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Affiliation(s)
- Caiguo Zhang
- 1. Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Fan Zhang
- 2. Orthopedics Department, Changhai Hospital Affiliated to Second Military Medical University, Shanghai, 200433, China
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53
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Izawa D, Pines J. The mitotic checkpoint complex binds a second CDC20 to inhibit active APC/C. Nature 2015; 517:631-4. [PMID: 25383541 PMCID: PMC4312099 DOI: 10.1038/nature13911] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 10/02/2014] [Indexed: 12/23/2022]
Abstract
The spindle assembly checkpoint (SAC) maintains genomic stability by delaying chromosome segregation until the last chromosome has attached to the mitotic spindle. The SAC prevents the anaphase promoting complex/cyclosome (APC/C) ubiquitin ligase from recognizing cyclin B and securin by catalysing the incorporation of the APC/C co-activator, CDC20, into a complex called the mitotic checkpoint complex (MCC). The SAC works through unattached kinetochores generating a diffusible 'wait anaphase' signal that inhibits the APC/C in the cytoplasm, but the nature of this signal remains a key unsolved problem. Moreover, the SAC and the APC/C are highly responsive to each other: the APC/C quickly targets cyclin B and securin once all the chromosomes attach in metaphase, but is rapidly inhibited should kinetochore attachment be perturbed. How this is achieved is also unknown. Here, we show that the MCC can inhibit a second CDC20 that has already bound and activated the APC/C. We show how the MCC inhibits active APC/C and that this is essential for the SAC. Moreover, this mechanism can prevent anaphase in the absence of kinetochore signalling. Thus, we propose that the diffusible 'wait anaphase' signal could be the MCC itself, and explain how reactivating the SAC can rapidly inhibit active APC/C.
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Affiliation(s)
- Daisuke Izawa
- The Gurdon Institute and Department of Zoology, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Jonathon Pines
- The Gurdon Institute and Department of Zoology, Tennis Court Road, Cambridge CB2 1QN, UK
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54
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Rahimi H, Negahdari B, Shokrgozar M, Madadkar-Sobhani A, Mahdian R, Foroumadi A, Amin MK, Karimipoor M. A structural model of the anaphase promoting complex co-activator (Cdh1) and in silico design of inhibitory compounds. Res Pharm Sci 2015; 10:59-67. [PMID: 26430458 PMCID: PMC4578213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Anaphase promoting complex (APC) controls cell cycle and chromosome segregation. The APC activation occurs after binding of co-activators, cdh1 and cdc20. Cdh1 plays a role in cancer pathogenesis and is known as a potential drug target. The main aim of this study was prediction of 3D structure of cdh1 and designing the inhibitory compounds based on the structural model. First, 3D structure of cdh1 was predicted by means of homology modelling and molecular dynamics tools, MODELLER and Gromacs package, respectively. Then, inhibitory compounds were designed using virtual screening and molecular docking by means AutoDock package. The overall structure of cdh1 is propeller like and each DW40 repeat contains four anti-parallel beta-sheets. Moreover, binding pocket of the inhibitory compounds was determined. The results might be helpful in finding a suitable cdh1 inhibitor for the treatment of cancer.
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Affiliation(s)
- H. Rahimi
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, I.R. Iran
| | - B. Negahdari
- Department of Medical Biotechnology, Advanced Medical Science School, Tehran University of Medical Sciences, Tehran, I.R. Iran
| | - M.A. Shokrgozar
- National Cell Bank of Iran, Pasteur Institute of Iran, Tehran, I.R. Iran
| | - A. Madadkar-Sobhani
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain,Department of Bioinformatics, Institute of Biophysics and Biochemistry (IBB), University of Tehran, Tehran, I.R. Iran
| | - R. Mahdian
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, I.R. Iran
| | - A. Foroumadi
- Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Tehran University of Medical Sciences, Tehran, I.R. Iran
| | - M. Kafshdouzi Amin
- Faculty of Paramedical Sciences, Qazvin University of Medical Sciences, Qazvin, I.R. Iran
| | - M. Karimipoor
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, I.R. Iran,Corresponding author: M. Karimipoor Tel: 0098 9122806133, Fax: 00982166480780
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55
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Edgerton H, Paolillo V, Oakley BR. Spatial regulation of the spindle assembly checkpoint and anaphase-promoting complex in Aspergillus nidulans. Mol Microbiol 2014; 95:442-57. [PMID: 25417844 DOI: 10.1111/mmi.12871] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2014] [Indexed: 11/29/2022]
Abstract
The spindle assembly checkpoint (SAC) plays a critical role in preventing mitotic errors by inhibiting anaphase until all kinetochores are correctly attached to spindle microtubules. In spite of the economic and medical importance of filamentous fungi, relatively little is known about the behavior of SAC proteins in these organisms. In our efforts to understand the role of γ-tubulin in cell cycle regulation, we have created functional fluorescent protein fusions of four SAC proteins in Aspergillus nidulans, the homologs of Mad2, Mps1, Bub1/BubR1 and Bub3. Time-lapse imaging reveals that SAC proteins are in distinct compartments of the cell until early mitosis when they co-localize at the spindle pole body. SAC activity is, thus, spatially regulated in A. nidulans. Likewise, Cdc20, an activator of the anaphase-promoting complex/cyclosome, is excluded from interphase nuclei, but enters nuclei at mitotic onset and accumulates to a higher level in mitotic nuclei than in the surrounding nucleoplasm before leaving in anaphase/telophase. The activity of this critical cell cycle regulatory complex is likely regulated by the location of Cdc20. Finally, the γ-tubulin mutation mipAD159 causes a nuclear-specific failure of nuclear localization of Mps1 and Bub1/R1 but not of Cdc20, Bub3 or Mad2.
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Affiliation(s)
- Heather Edgerton
- Department of Molecular Biosciences, University of Kansas, 1200 Sunnyside Ave., Lawrence, KS, 66045, USA
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56
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Arnold L, Höckner S, Seufert W. Insights into the cellular mechanism of the yeast ubiquitin ligase APC/C-Cdh1 from the analysis of in vivo degrons. Mol Biol Cell 2014; 26:843-58. [PMID: 25540434 PMCID: PMC4342022 DOI: 10.1091/mbc.e14-09-1342] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The anaphase-promoting complex/cyclosome (APC/C) controls a variety of cellular processes through its ability to target numerous protein substrates for timely degradation. Substrate selection by this ubiquitin ligase depends on related activator proteins, Cdc20 and Cdh1, which bind and activate the APC/C at distinct cell cycle stages. Biochemical and structural studies revealed that Cdc20 and Cdh1 carry conserved receptor domains to recognize specific sequence motifs in substrates, such as D and KEN boxes. The mechanisms for ordered degradation of APC/C substrates, however, remain incompletely understood. Here we describe minimal degradation sequences (degrons) sufficient for rapid APC/C-Cdh1-specific in vivo degradation. The polo kinase Cdc5-derived degron contained an essential KEN motif, whereas a single RxxL-type D box was the relevant signal in the Cdc20-derived degradation domain, indicating that either motif may support specific recognition by Cdh1. In both degrons, the APC/C recognition motif was flanked by a nuclear localization sequence. Forced localization of the degron constructs revealed that proteolysis mediated by APC/C-Cdh1 is restricted to the nucleus and maximally active in the nucleoplasm. Levels of Iqg1, a cytoplasmic Cdh1 substrate, decreased detectably later than the nucleus-localized Cdh1 substrate Ase1, indicating that confinement to the nucleus may allow for temporal control of APC/C-Cdh1-mediated proteolysis.
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Affiliation(s)
- Lea Arnold
- Department of Genetics, University of Regensburg, D-93040 Regensburg, Germany
| | - Sebastian Höckner
- Department of Genetics, University of Regensburg, D-93040 Regensburg, Germany
| | - Wolfgang Seufert
- Department of Genetics, University of Regensburg, D-93040 Regensburg, Germany
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57
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Diaz-Martinez LA, Tian W, Li B, Warrington R, Jia L, Brautigam CA, Luo X, Yu H. The Cdc20-binding Phe box of the spindle checkpoint protein BubR1 maintains the mitotic checkpoint complex during mitosis. J Biol Chem 2014; 290:2431-43. [PMID: 25505175 DOI: 10.1074/jbc.m114.616490] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The spindle checkpoint ensures accurate chromosome segregation by monitoring kinetochore-microtubule attachment. Unattached or tensionless kinetochores activate the checkpoint and enhance the production of the mitotic checkpoint complex (MCC) consisting of BubR1, Bub3, Mad2, and Cdc20. MCC is a critical checkpoint inhibitor of the anaphase-promoting complex/cyclosome, a ubiquitin ligase required for anaphase onset. The N-terminal region of BubR1 binds to both Cdc20 and Mad2, thus nucleating MCC formation. The middle region of human BubR1 (BubR1M) also interacts with Cdc20, but the nature and function of this interaction are not understood. Here we identify two critical motifs within BubR1M that contribute to Cdc20 binding and anaphase-promoting complex/cyclosome inhibition: a destruction box (D box) and a phenylalanine-containing motif termed the Phe box. A BubR1 mutant lacking these motifs is defective in MCC maintenance in mitotic human cells but is capable of supporting spindle-checkpoint function. Thus, the BubR1M-Cdc20 interaction indirectly contributes to MCC homeostasis. Its apparent dispensability in the spindle checkpoint might be due to functional duality or redundant, competing mechanisms.
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Affiliation(s)
| | - Wei Tian
- From the Department of Pharmacology
| | - Bing Li
- From the Department of Pharmacology, Howard Hughes Medical Institute, Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
| | - Ross Warrington
- From the Department of Pharmacology, Howard Hughes Medical Institute, Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
| | | | | | | | - Hongtao Yu
- From the Department of Pharmacology, Howard Hughes Medical Institute, Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
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58
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The internal Cdc20 binding site in BubR1 facilitates both spindle assembly checkpoint signalling and silencing. Nat Commun 2014; 5:5563. [DOI: 10.1038/ncomms6563] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 10/13/2014] [Indexed: 11/09/2022] Open
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59
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Yamaguchi M, Yu S, Qiao R, Weissmann F, Miller DJ, VanderLinden R, Brown NG, Frye JJ, Peters JM, Schulman BA. Structure of an APC3-APC16 complex: insights into assembly of the anaphase-promoting complex/cyclosome. J Mol Biol 2014; 427:1748-64. [PMID: 25490258 DOI: 10.1016/j.jmb.2014.11.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 11/14/2014] [Accepted: 11/15/2014] [Indexed: 01/05/2023]
Abstract
The anaphase-promoting complex/cyclosome (APC/C) is a massive E3 ligase that controls mitosis by catalyzing ubiquitination of key cell cycle regulatory proteins. The APC/C assembly contains two subcomplexes: the "Platform" centers around a cullin-RING-like E3 ligase catalytic core; the "Arc Lamp" is a hub that mediates transient association with regulators and ubiquitination substrates. The Arc Lamp contains the small subunits APC16, CDC26, and APC13, and tetratricopeptide repeat (TPR) proteins (APC7, APC3, APC6, and APC8) that homodimerize and stack with quasi-2-fold symmetry. Within the APC/C complex, APC3 serves as center for regulation. APC3's TPR motifs recruit substrate-binding coactivators, CDC20 and CDH1, via their C-terminal conserved Ile-Arg (IR) tail sequences. Human APC3 also binds APC16 and APC7 and contains a >200-residue loop that is heavily phosphorylated during mitosis, although the basis for APC3 interactions and whether loop phosphorylation is required for ubiquitination are unclear. Here, we map the basis for human APC3 assembly with APC16 and APC7, report crystal structures of APC3Δloop alone and in complex with the C-terminal domain of APC16, and test roles of APC3's loop and IR tail binding surfaces in APC/C-catalyzed ubiquitination. The structures show how one APC16 binds asymmetrically to the symmetric APC3 dimer and, together with biochemistry and prior data, explain how APC16 recruits APC7 to APC3, show how APC3's C-terminal domain is rearranged in the full APC/C assembly, and visualize residues in the IR tail binding cleft important for coactivator-dependent ubiquitination. Overall, the results provide insights into assembly, regulation, and interactions of TPR proteins and the APC/C.
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Affiliation(s)
- Masaya Yamaguchi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shanshan Yu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Renping Qiao
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Florian Weissmann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ryan VanderLinden
- Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, TN 38105 USA
| | - Nicholas G Brown
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jeremiah J Frye
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Brenda A Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, TN 38105 USA.
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60
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Chang L, Barford D. Insights into the anaphase-promoting complex: a molecular machine that regulates mitosis. Curr Opin Struct Biol 2014; 29:1-9. [PMID: 25174288 DOI: 10.1016/j.sbi.2014.08.003] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 08/01/2014] [Accepted: 08/05/2014] [Indexed: 12/13/2022]
Abstract
The anaphase-promoting complex/cyclosome (APC/C) is a large multimeric complex that functions as a RING domain E3 ubiquitin ligase to regulate ordered transitions through the cell cycle. It does so by controlling the ubiquitin-mediated proteolysis of cell cycle proteins, notably cyclins and securins, whose degradation triggers sister chromatid disjunction and mitotic exit. Regulation of APC/C activity and modulation of its substrate specificity are subject to intricate cell cycle checkpoints and control mechanisms involving the switching of substrate-specifying cofactors, association of regulatory protein complexes and post-translational modifications. This review discusses the recent progress towards understanding the overall architecture of the APC/C, the molecular basis for degron recognition and ubiquitin chain synthesis, and how these activities are regulated.
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Affiliation(s)
- Leifu Chang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - David Barford
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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61
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Structure-biological function relationship extended to mitotic arrest-deficient 2-like protein Mad2 native and mutants-new opportunity for genetic disorder control. Int J Mol Sci 2014; 15:21381-400. [PMID: 25411801 PMCID: PMC4264231 DOI: 10.3390/ijms151121381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/07/2014] [Accepted: 11/07/2014] [Indexed: 02/07/2023] Open
Abstract
Overexpression of mitotic arrest-deficient proteins Mad1 and Mad2, two components of spindle assembly checkpoint, is a risk factor for chromosomal instability (CIN) and a trigger of many genetic disorders. Mad2 transition from inactive open (O-Mad2) to active closed (C-Mad2) conformations or Mad2 binding to specific partners (cell-division cycle protein 20 (Cdc20) or Mad1) were targets of previous pharmacogenomics studies. Here, Mad2 binding to Cdc20 and the interconversion rate from open to closed Mad2 were predicted and the molecular features with a critical contribution to these processes were determined by extending the quantitative structure-activity relationship (QSAR) method to large-size proteins such as Mad2. QSAR models were built based on available published data on 23 Mad2 mutants inducing CIN-related functional changes. The most relevant descriptors identified for predicting Mad2 native and mutants action mechanism and their involvement in genetic disorders are the steric (van der Waals area and solvent accessible area and their subdivided) and energetic van der Waals energy descriptors. The reliability of our QSAR models is indicated by significant values of statistical coefficients: Cross-validated correlation q2 (0.53–0.65) and fitted correlation r2 (0.82–0.90). Moreover, based on established QSAR equations, we rationally design and analyze nine de novo Mad2 mutants as possible promoters of CIN.
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62
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Lee H. How chromosome mis-segregation leads to cancer: lessons from BubR1 mouse models. Mol Cells 2014; 37:713-8. [PMID: 25256220 PMCID: PMC4213761 DOI: 10.14348/molcells.2014.0233] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 08/25/2014] [Indexed: 12/12/2022] Open
Abstract
Alteration in chromosome numbers and structures instigate and foster massive genetic instability. As Boveri has seen a hundred years ago (Boveri, 1914; 2008), aneuploidy is hallmark of many cancers. However, whether aneuploidy is the cause or the result of cancer is still at debate. The molecular mechanism behind aneuploidy includes the chromo-some mis-segregation in mitosis by the compromise of spindle assembly checkpoint (SAC). SAC is an elaborate network of proteins, which monitor that all chromosomes are bipolarly attached with the spindles. Therefore, the weakening of the SAC is the major reason for chromosome number instability, while complete compromise of SAC results in detrimental death, exemplified in natural abortion in embryonic stage. Here, I will review on the recent progress on the understanding of chromosome mis-segregation and cancer, based on the comparison of different mouse models of BubR1, the core component of SAC.
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Affiliation(s)
- Hyunsook Lee
- Department of Biological Sciences and the Institute of Molecular Biology and Genetics, Seoul National University, Seoul 151-742,
Korea
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63
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Kelly A, Wickliffe KE, Song L, Fedrigo I, Rape M. Ubiquitin chain elongation requires E3-dependent tracking of the emerging conjugate. Mol Cell 2014; 56:232-245. [PMID: 25306918 DOI: 10.1016/j.molcel.2014.09.010] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Revised: 08/27/2014] [Accepted: 09/03/2014] [Indexed: 12/22/2022]
Abstract
Protein modification with ubiquitin chains is an essential signaling event catalyzed by E3 ubiquitin ligases. Most human E3s contain a signature RING domain that recruits a ubiquitin-charged E2 and a separate domain for substrate recognition. How RING-E3s can build polymeric ubiquitin chains while binding substrates and E2s at defined interfaces remains poorly understood. Here, we show that the RING-E3 APC/C catalyzes chain elongation by strongly increasing the affinity of its E2 for the distal acceptor ubiquitin in a growing conjugate. This function of the APC/C requires its coactivator as well as conserved residues of the E2 and ubiquitin. APC/C's ability to track the tip of an emerging conjugate is required for APC/C-substrate degradation and accurate cell division. Our results suggest that RING-E3s tether the distal ubiquitin of a growing chain in proximity to the active site of their E2s, allowing them to assemble polymeric conjugates without altering their binding to substrate or E2.
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Affiliation(s)
- Aileen Kelly
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Katherine E Wickliffe
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Ling Song
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Indro Fedrigo
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA
| | - Michael Rape
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA.
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64
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Chang LF, Zhang Z, Yang J, McLaughlin SH, Barford D. Molecular architecture and mechanism of the anaphase-promoting complex. Nature 2014; 513:388-393. [PMID: 25043029 PMCID: PMC4456660 DOI: 10.1038/nature13543] [Citation(s) in RCA: 162] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 05/28/2014] [Indexed: 12/12/2022]
Abstract
The ubiquitination of cell cycle regulatory proteins by the anaphase-promoting complex/cyclosome (APC/C) controls sister chromatid segregation, cytokinesis and the establishment of the G1 phase of the cell cycle. The APC/C is an unusually large multimeric cullin-RING ligase. Its activity is strictly dependent on regulatory coactivator subunits that promote APC/C-substrate interactions and stimulate its catalytic reaction. Because the structures of many APC/C subunits and their organization within the assembly are unknown, the molecular basis for these processes is poorly understood. Here, from a cryo-electron microscopy reconstruction of a human APC/C-coactivator-substrate complex at 7.4 Å resolution, we have determined the complete secondary structural architecture of the complex. With this information we identified protein folds for structurally uncharacterized subunits, and the definitive location of all 20 APC/C subunits within the 1.2 MDa assembly. Comparison with apo APC/C shows that the coactivator promotes a profound allosteric transition involving displacement of the cullin-RING catalytic subunits relative to the degron-recognition module of coactivator and APC10. This transition is accompanied by increased flexibility of the cullin-RING subunits and enhanced affinity for UBCH10-ubiquitin, changes which may contribute to coactivator-mediated stimulation of APC/C E3 ligase activity.
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Affiliation(s)
- Lei-Fu Chang
- Division of Structural Biology, Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Ziguo Zhang
- Division of Structural Biology, Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Jing Yang
- Division of Structural Biology, Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | | | - David Barford
- Division of Structural Biology, Institute of Cancer Research, 237 Fulham Road, London, SW3 6JB, UK
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
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65
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Synergistic blockade of mitotic exit by two chemical inhibitors of the APC/C. Nature 2014; 514:646-9. [PMID: 25156254 DOI: 10.1038/nature13660] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 07/04/2014] [Indexed: 02/07/2023]
Abstract
Protein machines are multi-subunit protein complexes that orchestrate highly regulated biochemical tasks. An example is the anaphase-promoting complex/cyclosome (APC/C), a 13-subunit ubiquitin ligase that initiates the metaphase-anaphase transition and mitotic exit by targeting proteins such as securin and cyclin B1 for ubiquitin-dependent destruction by the proteasome. Because blocking mitotic exit is an effective approach for inducing tumour cell death, the APC/C represents a potential novel target for cancer therapy. APC/C activation in mitosis requires binding of Cdc20 (ref. 5), which forms a co-receptor with the APC/C to recognize substrates containing a destruction box (D-box). Here we demonstrate that we can synergistically inhibit APC/C-dependent proteolysis and mitotic exit by simultaneously disrupting two protein-protein interactions within the APC/C-Cdc20-substrate ternary complex. We identify a small molecule, called apcin (APC inhibitor), which binds to Cdc20 and competitively inhibits the ubiquitylation of D-box-containing substrates. Analysis of the crystal structure of the apcin-Cdc20 complex suggests that apcin occupies the D-box-binding pocket on the side face of the WD40-domain. The ability of apcin to block mitotic exit is synergistically amplified by co-addition of tosyl-l-arginine methyl ester, a small molecule that blocks the APC/C-Cdc20 interaction. This work suggests that simultaneous disruption of multiple, weak protein-protein interactions is an effective approach for inactivating a protein machine.
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The zinc-binding region (ZBR) fragment of Emi2 can inhibit APC/C by targeting its association with the coactivator Cdc20 and UBE2C-mediated ubiquitylation. FEBS Open Bio 2014; 4:689-703. [PMID: 25161877 PMCID: PMC4141206 DOI: 10.1016/j.fob.2014.06.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 06/16/2014] [Accepted: 06/30/2014] [Indexed: 01/21/2023] Open
Abstract
Overexpression of the ZBR fragment of Emi2, but not of Emi1, induces abnormal cell division. The Emi2 ZBR fragment impairs the association of the coactivator Cdc20 with APC/C. The Emi2 ZBR fragment inhibits ubiquitylation by the cullin-RING of APC/C and E2C. The Emi2 ZBR-specific residues for APC/C inhibitory activity have been identified.
Anaphase-promoting complex or cyclosome (APC/C) is a multisubunit ubiquitin ligase E3 that targets cell-cycle regulators. Cdc20 is required for full activation of APC/C in M phase, and mediates substrate recognition. In vertebrates, Emi2/Erp1/FBXO43 inhibits APC/C-Cdc20, and functions as a cytostatic factor that causes long-term M phase arrest of mature oocytes. In this study, we found that a fragment corresponding to the zinc-binding region (ZBR) domain of Emi2 inhibits cell-cycle progression, and impairs the association of Cdc20 with the APC/C core complex in HEK293T cells. Furthermore, we revealed that the ZBR fragment of Emi2 inhibits in vitro ubiquitin chain elongation catalyzed by the APC/C cullin-RING ligase module, the ANAPC2–ANAPC11 subcomplex, in combination with the ubiquitin chain-initiating E2, E2C/UBE2C/UbcH10. Structural analyses revealed that the Emi2 ZBR domain uses different faces for the two mechanisms. Thus, the double-faced ZBR domain of Emi2 antagonizes the APC/C function by inhibiting both the binding with the coactivator Cdc20 and ubiquitylation mediated by the cullin-RING ligase module and E2C. In addition, the tail region between the ZBR domain and the C-terminal RL residues [the post-ZBR (PZ) region] interacts with the cullin subunit, ANAPC2. In the case of the ZBR fragment of the somatic paralogue of Emi2, Emi1/FBXO5, these inhibitory activities against cell division and ubiquitylation were not observed. Finally, we identified two sets of key residues in the Emi2 ZBR domain that selectively exert each of the dual Emi2-specific modes of APC/C inhibition, by their mutation in the Emi2 ZBR domain and their transplantation into the Emi1 ZBR domain.
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Song L, Craney A, Rape M. Microtubule-dependent regulation of mitotic protein degradation. Mol Cell 2014; 53:179-92. [PMID: 24462202 DOI: 10.1016/j.molcel.2013.12.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 10/18/2013] [Accepted: 12/20/2013] [Indexed: 01/10/2023]
Abstract
Accurate cell division depends on tightly regulated ubiquitylation events catalyzed by the anaphase-promoting complex (APC/C). Among its many substrates, the APC/C triggers the degradation of proteins that stabilize the mitotic spindle, and loss or accumulation of such spindle assembly factors can result in aneuploidy and cancer. Although critical for cell division, it has remained poorly understood how the timing of spindle assembly factor degradation is established during mitosis. Here, we report that active spindle assembly factors are protected from APC/C-dependent degradation by microtubules. In contrast, those molecules that are not bound to microtubules are highly susceptible to proteolysis and turned over immediately after APC/C activation. The correct timing of spindle assembly factor degradation, as achieved by this regulatory circuit, is required for accurate spindle structure and function. We propose that the localized stabilization of APC/C substrates provides a mechanism for the selective disposal of cell-cycle regulators that have fulfilled their mitotic roles.
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Affiliation(s)
- Ling Song
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Allison Craney
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michael Rape
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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Singh SA, Winter D, Kirchner M, Chauhan R, Ahmed S, Ozlu N, Tzur A, Steen JA, Steen H. Co-regulation proteomics reveals substrates and mechanisms of APC/C-dependent degradation. EMBO J 2014; 33:385-99. [PMID: 24510915 DOI: 10.1002/embj.201385876] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Using multiplexed quantitative proteomics, we analyzed cell cycle-dependent changes of the human proteome. We identified >4,400 proteins, each with a six-point abundance profile across the cell cycle. Hypothesizing that proteins with similar abundance profiles are co-regulated, we clustered the proteins with abundance profiles most similar to known Anaphase-Promoting Complex/Cyclosome (APC/C) substrates to identify additional putative APC/C substrates. This protein profile similarity screening (PPSS) analysis resulted in a shortlist enriched in kinases and kinesins. Biochemical studies on the kinesins confirmed KIFC1, KIF18A, KIF2C, and KIF4A as APC/C substrates. Furthermore, we showed that the APC/C(CDH1)-dependent degradation of KIFC1 regulates the bipolar spindle formation and proper cell division. A targeted quantitative proteomics experiment showed that KIFC1 degradation is modulated by a stabilizing CDK1-dependent phosphorylation site within the degradation motif of KIFC1. The regulation of KIFC1 (de-)phosphorylation and degradation provides insights into the fidelity and proper ordering of substrate degradation by the APC/C during mitosis.
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Affiliation(s)
- Sasha A Singh
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
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69
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Chen Z, Zhou Y, Song J, Zhang Z. hCKSAAP_UbSite: Improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1461-7. [DOI: 10.1016/j.bbapap.2013.04.006] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Revised: 03/28/2013] [Accepted: 04/09/2013] [Indexed: 11/26/2022]
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Craney A, Rape M. Dynamic regulation of ubiquitin-dependent cell cycle control. Curr Opin Cell Biol 2013; 25:704-10. [PMID: 23890701 DOI: 10.1016/j.ceb.2013.07.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Revised: 06/29/2013] [Accepted: 07/04/2013] [Indexed: 12/13/2022]
Abstract
Recent work revealed that cullin-RING ligases and the anaphase-promoting complex, two classes of ubiquitin ligases that are essential for cell division in all eukaryotes, are regulated in a highly dynamic manner. Here, we describe mechanisms that establish the dynamic regulation of these crucial ubiquitylation enzymes and discuss the functional consequences for cell division control.
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Affiliation(s)
- Allison Craney
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
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Abstract
The anaphase-promoting complex or cyclosome (APC/C) is a conserved, multisubunit E3 ubiquitin (Ub) ligase that is active both in dividing and in postmitotic cells. Its contributions to life are especially well studied in the domain of cell division, in which the APC/C lies at the epicenter of a regulatory network that controls the directionality and timing of cell cycle events. Biochemical and structural work is shedding light on the overall organization of APC/C subunits and on the mechanism of substrate recognition and Ub chain initiation and extension as well as on the molecular mechanisms of a checkpoint that seizes control of APC/C activity during mitosis. Here, we review how these recent advancements are modifying our understanding of the APC/C.
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Affiliation(s)
- Ivana Primorac
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
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Abstract
In this issue of Molecular Cell, He and colleagues (2013) unveil a high-resolution structure of a key regulatory interface in cell-cycle control: the destruction box sequence bound to the anaphase-promoting complex.
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Affiliation(s)
- David O Morgan
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158, USA.
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He J, Chao W, Zhang Z, Yang J, Cronin N, Barford D. Insights into degron recognition by APC/C coactivators from the structure of an Acm1-Cdh1 complex. Mol Cell 2013; 50:649-60. [PMID: 23707760 PMCID: PMC3690534 DOI: 10.1016/j.molcel.2013.04.024] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 03/05/2013] [Accepted: 04/15/2013] [Indexed: 12/14/2022]
Abstract
The anaphase-promoting complex/cyclosome (APC/C) regulates sister chromatid segregation and the exit from mitosis. Selection of most APC/C substrates is controlled by coactivator subunits (either Cdc20 or Cdh1) that interact with substrate destruction motifs--predominantly the destruction (D) box and KEN box degrons. How coactivators recognize D box degrons and how this is inhibited by APC/C regulatory proteins is not defined at the atomic level. Here, from the crystal structure of S. cerevisiae Cdh1 in complex with its specific inhibitor Acm1, which incorporates D and KEN box pseudosubstrate motifs, we describe the molecular basis for D box recognition. Additional interactions between Acm1 and Cdh1 identify a third protein-binding site on Cdh1 that is likely to confer coactivator-specific protein functions including substrate association. We provide a structural rationalization for D box and KEN box recognition by coactivators and demonstrate that many noncanonical APC/C degrons bind APC/C coactivators at the D box coreceptor.
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Affiliation(s)
- Jun He
- Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK
| | - William C.H. Chao
- Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK
| | - Ziguo Zhang
- Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK
| | - Jing Yang
- Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK
| | - Nora Cronin
- Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK
| | - David Barford
- Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK
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Electron microscopy structure of human APC/C(CDH1)-EMI1 reveals multimodal mechanism of E3 ligase shutdown. Nat Struct Mol Biol 2013; 20:827-35. [PMID: 23708605 PMCID: PMC3742808 DOI: 10.1038/nsmb.2593] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Accepted: 04/09/2013] [Indexed: 12/20/2022]
Abstract
The Anaphase Promoting Complex/Cyclosome (APC/C) is a ~1.5 MDa multiprotein E3 ligase enzyme that regulates cell division by promoting timely ubiquitin-mediated proteolysis of key cell cycle regulatory proteins. Inhibition of human APC/CCDH1 during interphase by Early Mitotic Inhibitor 1 (EMI1) is essential for accurate coordination of DNA synthesis and mitosis. Here, we report a hybrid structural approach involving NMR, electron microscopy, and enzymology, which reveal that EMI1’s 143-residue C-terminal domain inhibits multiple APC/CCDH1 functions. The intrinsically disordered D-box, Linker, and Tail elements, together with a structured zinc-binding domain, bind distinct regions of APC/CCDH1 to synergistically both block the substrate-binding site and inhibit ubiquitin chain elongation. The functional importance of intrinsic structural disorder is explained by enabling a small inhibitory domain to bind multiple sites to shut down multiple functions of a “molecular machine” nearly 100 times its size.
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Tracking spindle checkpoint signals from kinetochores to APC/C. Trends Biochem Sci 2013; 38:302-11. [PMID: 23598156 DOI: 10.1016/j.tibs.2013.03.004] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 03/11/2013] [Accepted: 03/19/2013] [Indexed: 12/13/2022]
Abstract
Accurate chromosome segregation during mitosis is critical for maintaining genomic stability. The kinetochore--a large protein assembly on centromeric chromatin--functions as the docking site for spindle microtubules and a signaling hub for the spindle checkpoint. At metaphase, spindle microtubules from opposing spindle poles capture each pair of sister kinetochores, exert pulling forces, and create tension across sister kinetochores. The spindle checkpoint detects improper kinetochore-microtubule attachments and translates these defects into biochemical activities that inhibit the anaphase-promoting complex or cyclosome (APC/C) throughout the cell to delay anaphase onset. A deficient spindle checkpoint leads to premature sister-chromatid separation and aneuploidy. Here, we review recent progress on the generation, propagation, transmission, and silencing of the spindle checkpoint signals from kinetochores to APC/C.
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Karess RE, Wassmann K, Rahmani Z. New insights into the role of BubR1 in mitosis and beyond. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2013; 306:223-73. [PMID: 24016527 DOI: 10.1016/b978-0-12-407694-5.00006-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
BubR1 is a critical component of the spindle assembly checkpoint, the surveillance mechanism that helps maintain the high fidelity of mitotic chromosome segregation by preventing cells from initiating anaphase if one or more kinetochores are not attached to the spindle. BubR1 also helps promote the establishment of stable kinetochore-microtubule attachments during prometaphase. In this chapter, we review the structure, functions, and regulation of BubR1 in these "classical roles" at the kinetochore. We discuss its recruitment to kinetochores, its assembly into the inhibitor of anaphase progression, and the importance of its posttranslational modifications. We also consider the evidence for its participation in other roles beyond mitosis, such as the meiosis-specific processes of recombination and prophase arrest of the first meiotic division, the cellular response to DNA damage, and in the regulation of centrosome and basal body function. Finally, studies are presented linking BubR1 dysfunction or misregulation to aging and human disease, particularly cancer.
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Affiliation(s)
- Roger E Karess
- Institut Jacques Monod, UMR 7592 CNRS, Université Paris Diderot-Paris 7, Paris, France.
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