1
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Ng HY, Adly AN, Whelpley DH, Suhandynata RT, Zhou H, Morgan DO. Phosphate-binding pocket on cyclin B governs CDK substrate phosphorylation and mitotic timing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582599. [PMID: 38464173 PMCID: PMC10925351 DOI: 10.1101/2024.02.28.582599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Cell cycle progression is governed by complexes of the cyclin-dependent kinases (CDKs) and their regulatory subunits cyclin and Cks1. CDKs phosphorylate hundreds of substrates, often at multiple sites. Multisite phosphorylation depends on Cks1, which binds initial priming phosphorylation sites to promote secondary phosphorylation at other sites. Here, we describe a similar role for a recently discovered phosphate-binding pocket (PP) on B-type cyclins. Mutation of the PP in Clb2, the major mitotic cyclin of budding yeast, alters bud morphology and delays the onset of anaphase. Using phosphoproteomics in vivo and kinase reactions in vitro, we find that mutation of the PP reduces phosphorylation of several CDK substrates, including the Bud6 subunit of the polarisome and the Cdc16 and Cdc27 subunits of the anaphase-promoting complex/cyclosome. We conclude that the cyclin PP, like Cks1, controls the timing of multisite phosphorylation on CDK substrates, thereby helping to establish the robust timing of cell-cycle events.
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Affiliation(s)
- Henry Y. Ng
- Department of Physiology, University of California San Francisco, San Francisco CA
| | - Armin N. Adly
- Department of Physiology, University of California San Francisco, San Francisco CA
| | - Devon H. Whelpley
- Department of Physiology, University of California San Francisco, San Francisco CA
| | - Raymond T. Suhandynata
- School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla CA
- Department of Pathology, University of California San Diego, La Jolla CA
| | - Huilin Zhou
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla CA
| | - David O. Morgan
- Department of Physiology, University of California San Francisco, San Francisco CA
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2
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Sorensen Turpin CG, Sloan D, LaForest M, Klebanow LU, Mitchell D, Severson AF, Bembenek JN. Securin Regulates the Spatiotemporal Dynamics of Separase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571338. [PMID: 38168402 PMCID: PMC10760073 DOI: 10.1101/2023.12.12.571338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Separase is a key regulator of the metaphase to anaphase transition with multiple functions. Separase cleaves cohesin to allow chromosome segregation and localizes to vesicles to promote exocytosis in mid-anaphase. The anaphase promoting complex/cyclosome (APC/C) activates separase by ubiquitinating its inhibitory chaperone, securin, triggering its degradation. How this pathway controls the exocytic function of separase has not been investigated. During meiosis I, securin is degraded over several minutes, while separase rapidly relocalizes from kinetochore structures at the spindle and cortex to sites of action on chromosomes and vesicles at anaphase onset. The loss of cohesin coincides with the relocalization of separase to the chromosome midbivalent at anaphase onset. APC/C depletion prevents separase relocalization, while securin depletion causes precocious separase relocalization. Expression of non-degradable securin inhibits chromosome segregation, exocytosis, and separase localization to vesicles but not to the anaphase spindle. We conclude that APC/C mediated securin degradation controls separase localization. This spatiotemporal regulation will impact the effective local concentration of separase for more precise targeting of substrates in anaphase.
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Affiliation(s)
- Christopher G. Sorensen Turpin
- Current Address: Department of Obstetrics and Gynecology, C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Dillon Sloan
- Current Address: Department of Biology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Marian LaForest
- Current Address: Columbia University, Herbert Irving Comprehensive Cancer Center, NYC, New York, United States of America
| | | | - Diana Mitchell
- Current Address: Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Aaron F. Severson
- Current Address: Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, Ohio, United States of America
| | - Joshua N. Bembenek
- Current Address: Department of Obstetrics and Gynecology, C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, Detroit, Michigan, United States of America
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3
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HN1 Is Enriched in the S-Phase, Phosphorylated in Mitosis, and Contributes to Cyclin B1 Degradation in Prostate Cancer Cells. BIOLOGY 2023; 12:biology12020189. [PMID: 36829467 PMCID: PMC9952942 DOI: 10.3390/biology12020189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/18/2023] [Accepted: 01/24/2023] [Indexed: 01/28/2023]
Abstract
HN1 has previously been shown as overexpressed in various cancers. In Prostate cancer, it regulates AR signaling and centrosome-related functions. Previously, in two different studies, HN1 expression has been observed as inversely correlated with Cyclin B1. However, HN1 interacting partners and the role of HN1 interactions in cell cycle pathways have not been completely elucidated. Therefore, we used Prostate cancer cell lines again and utilized both transient and stable inducible overexpression systems to delineate the role of HN1 in the cell cycle. HN1 characterization was performed using treatments of kinase inhibitors, western blotting, flow cytometry, immunofluorescence, cellular fractionation, and immunoprecipitation approaches. Our findings suggest that HN1 overexpression before mitosis (post-G2), using both transient and stable expression systems, leads to S-phase accumulation and causes early mitotic exit after post-G2 overexpression. Mechanistically, HN1 interacted with Cyclin B1 and increased its degradation via ubiquitination through stabilized Cdh1, which is a co-factor of the APC/C complex. Stably HN1-expressing cells exhibited a reduced Cdt1 loading onto chromatin, demonstrating an exit from a G1 to S phenotype. We found HN1 and Cdh1 interaction as a new regulator of the Cyclin B1/CDK1 axis in mitotic regulation which can be explored further to dissect the roles of HN1 in the cell cycle.
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4
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Hartooni N, Sung J, Jain A, Morgan DO. Single-molecule analysis of specificity and multivalency in binding of short linear substrate motifs to the APC/C. Nat Commun 2022; 13:341. [PMID: 35039540 PMCID: PMC8764033 DOI: 10.1038/s41467-022-28031-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/05/2022] [Indexed: 11/09/2022] Open
Abstract
Robust regulatory signals in the cell often depend on interactions between short linear motifs (SLiMs) and globular proteins. Many of these interactions are poorly characterized because the binding proteins cannot be produced in the amounts needed for traditional methods. To address this problem, we developed a single-molecule off-rate (SMOR) assay based on microscopy of fluorescent ligand binding to immobilized protein partners. We used it to characterize substrate binding to the Anaphase-Promoting Complex/Cyclosome (APC/C), a ubiquitin ligase that triggers chromosome segregation. We find that SLiMs in APC/C substrates (the D box and KEN box) display distinct affinities and specificities for the substrate-binding subunits of the APC/C, and we show that multiple SLiMs in a substrate generate a high-affinity multivalent interaction. The remarkably adaptable substrate-binding mechanisms of the APC/C have the potential to govern the order of substrate destruction in mitosis.
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Affiliation(s)
- Nairi Hartooni
- Department of Physiology, University of California, San Francisco, CA, 94143, USA.,Tetrad Graduate Program, University of California, San Francisco, CA, 94143, USA
| | - Jongmin Sung
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, 94143, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA, 94143, USA.,Roche Sequencing Solutions, Santa Clara, CA, 95050, USA
| | - Ankur Jain
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA, 94143, USA.,Howard Hughes Medical Institute, University of California, San Francisco, CA, 94143, USA.,Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
| | - David O Morgan
- Department of Physiology, University of California, San Francisco, CA, 94143, USA. .,Tetrad Graduate Program, University of California, San Francisco, CA, 94143, USA.
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5
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Lara-Gonzalez P, Pines J, Desai A. Spindle assembly checkpoint activation and silencing at kinetochores. Semin Cell Dev Biol 2021; 117:86-98. [PMID: 34210579 PMCID: PMC8406419 DOI: 10.1016/j.semcdb.2021.06.009] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/17/2021] [Accepted: 06/17/2021] [Indexed: 01/01/2023]
Abstract
The spindle assembly checkpoint (SAC) is a surveillance mechanism that promotes accurate chromosome segregation in mitosis. The checkpoint senses the attachment state of kinetochores, the proteinaceous structures that assemble onto chromosomes in mitosis in order to mediate their interaction with spindle microtubules. When unattached, kinetochores generate a diffusible inhibitor that blocks the activity of the anaphase-promoting complex/cyclosome (APC/C), an E3 ubiquitin ligase required for sister chromatid separation and exit from mitosis. Work from the past decade has greatly illuminated our understanding of the mechanisms by which the diffusible inhibitor is assembled and how it inhibits the APC/C. However, less is understood about how SAC proteins are recruited to kinetochores in the absence of microtubule attachment, how the kinetochore catalyzes formation of the diffusible inhibitor, and how attachments silence the SAC at the kinetochore. Here, we summarize current understanding of the mechanisms that activate and silence the SAC at kinetochores and highlight open questions for future investigation.
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Affiliation(s)
- Pablo Lara-Gonzalez
- Ludwig Institute for Cancer Research, USA; Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA.
| | | | - Arshad Desai
- Ludwig Institute for Cancer Research, USA; Department of Cellular & Molecular Medicine, University of California San Diego, La Jolla, CA 92093, USA.
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6
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Thomas C, Wetherall B, Levasseur MD, Harris RJ, Kerridge ST, Higgins JMG, Davies OR, Madgwick S. A prometaphase mechanism of securin destruction is essential for meiotic progression in mouse oocytes. Nat Commun 2021; 12:4322. [PMID: 34262048 PMCID: PMC8280194 DOI: 10.1038/s41467-021-24554-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 06/24/2021] [Indexed: 11/10/2022] Open
Abstract
Successful cell division relies on the timely removal of key cell cycle proteins such as securin. Securin inhibits separase, which cleaves the cohesin rings holding chromosomes together. Securin must be depleted before anaphase to ensure chromosome segregation occurs with anaphase. Here we find that in meiosis I, mouse oocytes contain an excess of securin over separase. We reveal a mechanism that promotes excess securin destruction in prometaphase I. Importantly, this mechanism relies on two phenylalanine residues within the separase-interacting segment (SIS) of securin that are only exposed when securin is not bound to separase. We suggest that these residues facilitate the removal of non-separase-bound securin ahead of metaphase, as inhibiting this period of destruction by mutating both residues causes the majority of oocytes to arrest in meiosis I. We further propose that cellular securin levels exceed the amount an oocyte is capable of removing in metaphase alone, such that the prometaphase destruction mechanism identified here is essential for correct meiotic progression in mouse oocytes.
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Affiliation(s)
- Christopher Thomas
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK. .,Max Planck Institute for Biophysical Chemistry, Gottingen, Germany.
| | - Benjamin Wetherall
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Mark D Levasseur
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Rebecca J Harris
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Scott T Kerridge
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Jonathan M G Higgins
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Owen R Davies
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.,Institute of Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh, UK
| | - Suzanne Madgwick
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK.
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7
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Bodrug T, Welsh KA, Hinkle M, Emanuele MJ, Brown NG. Intricate Regulatory Mechanisms of the Anaphase-Promoting Complex/Cyclosome and Its Role in Chromatin Regulation. Front Cell Dev Biol 2021; 9:687515. [PMID: 34109183 PMCID: PMC8182066 DOI: 10.3389/fcell.2021.687515] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/26/2021] [Indexed: 02/04/2023] Open
Abstract
The ubiquitin (Ub)-proteasome system is vital to nearly every biological process in eukaryotes. Specifically, the conjugation of Ub to target proteins by Ub ligases, such as the Anaphase-Promoting Complex/Cyclosome (APC/C), is paramount for cell cycle transitions as it leads to the irreversible destruction of cell cycle regulators by the proteasome. Through this activity, the RING Ub ligase APC/C governs mitosis, G1, and numerous aspects of neurobiology. Pioneering cryo-EM, biochemical reconstitution, and cell-based studies have illuminated many aspects of the conformational dynamics of this large, multi-subunit complex and the sophisticated regulation of APC/C function. More recent studies have revealed new mechanisms that selectively dictate APC/C activity and explore additional pathways that are controlled by APC/C-mediated ubiquitination, including an intimate relationship with chromatin regulation. These tasks go beyond the traditional cell cycle role historically ascribed to the APC/C. Here, we review these novel findings, examine the mechanistic implications of APC/C regulation, and discuss the role of the APC/C in previously unappreciated signaling pathways.
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Affiliation(s)
- Tatyana Bodrug
- Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kaeli A Welsh
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Megan Hinkle
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Michael J Emanuele
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Nicholas G Brown
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, United States
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8
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Function analysis and molecular characterization of cyclin A in ovary development of oriental river prawn, Macrobrachium nipponense. Gene 2021; 788:145583. [PMID: 33753150 DOI: 10.1016/j.gene.2021.145583] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 11/26/2020] [Accepted: 03/12/2021] [Indexed: 11/24/2022]
Abstract
Macrobrachium nipponense has the characteristics of fast ovarian development cycle, which leads to the coexistence of multiple generations, the reduction of commodity specifications and the low economic benefit. Therefore, the study on the mechanism of ovarian development is of great significance to the development of industry. Cyclin A (CycA)is a key gene regulating ovarian development in vertebrates, but little information was available for its function in crustaceans. In this study, the full-length cDNA of Mn-CycA was obtained from the ovary. The full-length cDNA (2033 bp) with an open reading frame of 1368 bp, encoded a 456-amino acid protein. qRT-PCR revealed tissue-specific expression pattern of Mn-CycA, with abundant expression in the ovary. Results in different developmental stages of ovary indicated that Mn-CycA expression is positively correlated with ovarian maturation. qRT-PCR In different developmental stages, the expression of Mn-CycA mRNA gradually increased during the embryonic stage and decreased significantly on the first day of the hatching stage. At the 25th day of the metamorphosis stage, the expression level of Mn-CycAmRNA in female shrimp was 3.5 times higher than that in male shrimp, which may be related to the proliferation of oogonia and the formation of oocytes. In situ hybridization (ISH) of ovary showed Mn-CycA was examined in all stages and was mainly located in oogonia and oocytes. Compared with the control group, the obvious change of gonad somatic index (GSI) proved that injection of Mn-CycA dsRNA could delay the ovarian development cycle, which provided strong evidence for the involvement of Mn-CycA in ovarian maturation and oogenesis, and expanded a new perspective for studying the fast ovarian development cycle in M. nipponense.
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9
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Faustova I, Bulatovic L, Matiyevskaya F, Valk E, Örd M, Loog M. A new linear cyclin docking motif that mediates exclusively S-phase CDK-specific signaling. EMBO J 2020; 40:e105839. [PMID: 33210757 PMCID: PMC7809796 DOI: 10.15252/embj.2020105839] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/23/2020] [Accepted: 10/13/2020] [Indexed: 01/20/2023] Open
Abstract
Cyclin‐dependent kinases (CDKs), the master regulators of cell division, are activated by different cyclins at different cell cycle stages. In addition to being activators of CDKs, cyclins recognize various linear motifs to target CDK activity to specific proteins. We uncovered a cyclin docking motif, NLxxxL, that contributes to phosphorylation‐dependent degradation of the CDK inhibitor Far1 at the G1/S stage in the yeast Saccharomyces cerevisiae. This motif is recognized exclusively by S‐phase CDK (S‐CDK) Clb5/6‐Cdc28 and is considerably more potent than the conventional RxL docking motif. The NLxxxL and RxL motifs were found to overlap in some target proteins, suggesting that cyclin docking motifs can evolve to switch from one to another for fine‐tuning of cell cycle events. Using time‐lapse fluorescence microscopy, we show how different docking connections temporally control phosphorylation‐driven target degradation. This also revealed a differential function of the phosphoadaptor protein Cks1, as Cks1 docking potentiated degron phosphorylation of RxL‐containing but not of NLxxxL‐containing substrates. The NLxxxL motif was found to govern S‐cyclin‐specificity in multiple yeast CDK targets including Fin1, Lif1, and Slx4, suggesting its wider importance.
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Affiliation(s)
- Ilona Faustova
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Luka Bulatovic
- Institute of Technology, University of Tartu, Tartu, Estonia
| | | | - Ervin Valk
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Mihkel Örd
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Mart Loog
- Institute of Technology, University of Tartu, Tartu, Estonia
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10
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Tsunematsu T, Arakaki R, Kawai H, Ruppert J, Tsuneyama K, Ishimaru N, Earnshaw WC, Pagano M, Kudo Y. APC/C Cdh1 is required for the termination of chromosomal passenger complex activity upon mitotic exit. J Cell Sci 2020; 133:133/18/jcs251314. [PMID: 32934012 PMCID: PMC7520452 DOI: 10.1242/jcs.251314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 07/13/2020] [Indexed: 01/31/2023] Open
Abstract
During mitosis, the chromosomal passenger complex (CPC) ensures the faithful transmission of the genome. The CPC is composed of the enzymatic component Aurora B (AURKB) and the three regulatory and targeting components borealin, INCENP, and survivin (also known as BIRC5). Although the CPC is known to be involved in diverse mitotic events, it is still unclear how CPC function terminates after mitosis. Here we show that borealin is ubiquitylated by the anaphase promoting complex/cyclosome (APC/C) and its cofactor Cdh1 (also known as FZR1) and is subsequently degraded in G1 phase. Cdh1 binds to regions within the N terminus of borealin that act as a non-canonical degron. Aurora B has also been shown previously to be degraded by the APC/CCdh1 from late mitosis to G1. Indeed, Cdh1 depletion sustains an Aurora B activity with stable levels of borealin and Aurora B throughout the cell cycle, and causes reduced efficiency of DNA replication after release from serum starvation. Notably, inhibition of Aurora B kinase activity improves the efficiency of DNA replication in Cdh1-depleted cells. We thus propose that APC/CCdh1 terminates CPC activity upon mitotic exit and thereby contributes to proper control of DNA replication. Summary: APC/CCdh1 ubiquitylates both borealin, via a non-canonical degron motif, and Aurora B to terminate activity of the CPC in G1 phase. Disruption of this ubiquitylation reduces the efficiency of DNA replication.
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Affiliation(s)
- Takaaki Tsunematsu
- Department of Oral Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8504, Japan
| | - Rieko Arakaki
- Department of Oral Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8504, Japan
| | - Hidehiko Kawai
- Department of Nucleic Acids Biochemistry, Hiroshima University Graduate School of Biomedical & Health Sciences, Hiroshima 734-8553, Japan
| | - Jan Ruppert
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
| | - Koichi Tsuneyama
- Department of Pathology and Laboratory Medicine, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8504, Japan
| | - Naozumi Ishimaru
- Department of Oral Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8504, Japan
| | - William C Earnshaw
- Wellcome Centre for Cell Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, Scotland, UK
| | - Michele Pagano
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.,NYU Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA.,Howard Hughes Medical Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Yasusei Kudo
- Department of Oral Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8504, Japan .,Department of Oral Bioscience, Tokushima University Graduate School of Biomedical Sciences, Tokushima 770-8504, Japan
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11
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Holder J, Mohammed S, Barr FA. Ordered dephosphorylation initiated by the selective proteolysis of cyclin B drives mitotic exit. eLife 2020; 9:e59885. [PMID: 32869743 PMCID: PMC7529458 DOI: 10.7554/elife.59885] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/31/2020] [Indexed: 12/13/2022] Open
Abstract
APC/C-mediated proteolysis of cyclin B and securin promotes anaphase entry, inactivating CDK1 and permitting chromosome segregation, respectively. Reduction of CDK1 activity relieves inhibition of the CDK1-counteracting phosphatases PP1 and PP2A-B55, allowing wide-spread dephosphorylation of substrates. Meanwhile, continued APC/C activity promotes proteolysis of other mitotic regulators. Together, these activities orchestrate a complex series of events during mitotic exit. However, the relative importance of regulated proteolysis and dephosphorylation in dictating the order and timing of these events remains unclear. Using high temporal-resolution proteomics, we compare the relative extent of proteolysis and protein dephosphorylation. This reveals highly-selective rapid proteolysis of cyclin B, securin and geminin at the metaphase-anaphase transition, followed by slow proteolysis of other substrates. Dephosphorylation requires APC/C-dependent destruction of cyclin B and was resolved into PP1-dependent categories with unique sequence motifs. We conclude that dephosphorylation initiated by selective proteolysis of cyclin B drives the bulk of changes observed during mitotic exit.
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Affiliation(s)
- James Holder
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | - Shabaz Mohammed
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | - Francis A Barr
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
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12
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Jackman M, Marcozzi C, Barbiero M, Pardo M, Yu L, Tyson AL, Choudhary JS, Pines J. Cyclin B1-Cdk1 facilitates MAD1 release from the nuclear pore to ensure a robust spindle checkpoint. J Cell Biol 2020; 219:e201907082. [PMID: 32236513 PMCID: PMC7265330 DOI: 10.1083/jcb.201907082] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 02/05/2020] [Accepted: 03/06/2020] [Indexed: 11/22/2022] Open
Abstract
How the cell rapidly and completely reorganizes its architecture when it divides is a problem that has fascinated researchers for almost 150 yr. We now know that the core regulatory machinery is highly conserved in eukaryotes, but how these multiple protein kinases, protein phosphatases, and ubiquitin ligases are coordinated in space and time to remodel the cell in a matter of minutes remains a major question. Cyclin B1-Cdk is the primary kinase that drives mitotic remodeling; here we show that it is targeted to the nuclear pore complex (NPC) by binding an acidic face of the kinetochore checkpoint protein, MAD1, where it coordinates NPC disassembly with kinetochore assembly. Localized cyclin B1-Cdk1 is needed for the proper release of MAD1 from the embrace of TPR at the nuclear pore so that it can be recruited to kinetochores before nuclear envelope breakdown to maintain genomic stability.
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13
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A masked initiation region in retinoblastoma protein regulates its proteasomal degradation. Nat Commun 2020; 11:2019. [PMID: 32332747 PMCID: PMC7181824 DOI: 10.1038/s41467-020-16003-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 04/01/2020] [Indexed: 12/03/2022] Open
Abstract
Retinoblastoma protein (Rb) is a tumor suppressor that binds and represses E2F transcription factors. In cervical cancer cells, human papilloma virus (HPV) protein E7 binds to Rb, releasing it from E2F to promote cell cycle progression, and inducing ubiquitination of Rb. E7-mediated proteasomal degradation of Rb requires action by another protease, calpain, which cleaves Rb after Lys 810. However, it is not clear why cleavage is required for Rb degradation. Here, we report that the proteasome cannot initiate degradation efficiently on full-length Rb. Calpain cleavage exposes a region that is recognized by the proteasome, leading to rapid proteolysis of Rb. These findings identify a mechanism for regulating protein stability by controlling initiation and provide a better understanding of the molecular mechanism underlying transformation by HPV. Human papilloma virus (HPV) E7 protein destabilizes the retinoblastoma protein (Rb) by inducing its ubiquitination in cervical cancer cells, however proteasomal degradation requires cleavage of Rb after Lys 810 and so far it has been unclear how Rb cleavage contributes to its degradation. Here, the authors combine cell based and in vitro assays and show that calpain cleavage exposes a region in Rb that is recognized by the proteasome, leading to rapid proteolysis of Rb, whereas the proteasome cannot initiate degradation efficiently on full-length Rb.
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14
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PP2A Functions during Mitosis and Cytokinesis in Yeasts. Int J Mol Sci 2019; 21:ijms21010264. [PMID: 31906018 PMCID: PMC6981662 DOI: 10.3390/ijms21010264] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 12/13/2022] Open
Abstract
Protein phosphorylation is a common mechanism for the regulation of cell cycle progression. The opposing functions of cell cycle kinases and phosphatases are crucial for accurate chromosome segregation and exit from mitosis. Protein phosphatases 2A are heterotrimeric complexes that play essential roles in cell growth, proliferation, and regulation of the cell cycle. Here, we review the function of the protein phosphatase 2A family as the counteracting force for the mitotic kinases. We focus on recent findings in the regulation of mitotic exit and cytokinesis by PP2A phosphatases in S. cerevisiae and other fungal species.
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15
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Bansal S, Tiwari S. Mechanisms for the temporal regulation of substrate ubiquitination by the anaphase-promoting complex/cyclosome. Cell Div 2019; 14:14. [PMID: 31889987 PMCID: PMC6927175 DOI: 10.1186/s13008-019-0057-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 12/04/2019] [Indexed: 12/16/2022] Open
Abstract
The anaphase-promoting complex/cyclosome (APC/C) is a multi-subunit, multifunctional ubiquitin ligase that controls the temporal degradation of numerous cell cycle regulatory proteins to direct the unidirectional cell cycle phases. Several different mechanisms contribute to ensure the correct order of substrate modification by the APC/C complex. Recent advances in biochemical, biophysical and structural studies of APC/C have provided a deep mechanistic insight into the working of this complex ubiquitin ligase. This complex displays remarkable conformational flexibility in response to various binding partners and post-translational modifications, which together regulate substrate selection and catalysis of APC/C. Apart from this, various features and modifications of the substrates also influence their recognition and affinity to APC/C complex. Ultimately, temporal degradation of substrates depends on the kind of ubiquitin modification received, the processivity of APC/C, and other extrinsic mechanisms. This review discusses our current understanding of various intrinsic and extrinsic mechanisms responsible for ‘substrate ordering’ by the APC/C complex.
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Affiliation(s)
- Shivangee Bansal
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
| | - Swati Tiwari
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067 India
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16
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Mizrak A, Morgan DO. Polyanions provide selective control of APC/C interactions with the activator subunit. Nat Commun 2019; 10:5807. [PMID: 31862931 PMCID: PMC6925294 DOI: 10.1038/s41467-019-13864-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 12/04/2019] [Indexed: 01/18/2023] Open
Abstract
Transient interactions between the anaphase-promoting complex/cyclosome (APC/C) and its activator subunit Cdc20 or Cdh1 generate oscillations in ubiquitylation activity necessary to maintain the order of cell cycle events. Activator binds the APC/C with high affinity and exhibits negligible dissociation kinetics in vitro, and it is not clear how the rapid turnover of APC/C-activator complexes is achieved in vivo. Here, we describe a mechanism that controls APC/C-activator interactions based on the availability of substrates. We find that APC/C-activator dissociation is stimulated by abundant cellular polyanions such as nucleic acids and polyphosphate. Polyanions also interfere with substrate ubiquitylation. However, engagement with high-affinity substrate blocks the inhibitory effects of polyanions on activator binding and APC/C activity. We propose that this mechanism amplifies the effects of substrate affinity on APC/C function, stimulating processive ubiquitylation of high-affinity substrates and suppressing ubiquitylation of low-affinity substrates.
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Affiliation(s)
- Arda Mizrak
- Department of Physiology, University of California, San Francisco, CA, 94143, USA
| | - David O Morgan
- Department of Physiology, University of California, San Francisco, CA, 94143, USA.
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17
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Zhang S, Tischer T, Barford D. Cyclin A2 degradation during the spindle assembly checkpoint requires multiple binding modes to the APC/C. Nat Commun 2019; 10:3863. [PMID: 31455778 PMCID: PMC6712056 DOI: 10.1038/s41467-019-11833-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 07/29/2019] [Indexed: 12/19/2022] Open
Abstract
The anaphase-promoting complex/cyclosome (APC/C) orchestrates cell cycle progression by controlling the temporal degradation of specific cell cycle regulators. Although cyclin A2 and cyclin B1 are both targeted for degradation by the APC/C, during the spindle assembly checkpoint (SAC), the mitotic checkpoint complex (MCC) represses APC/C's activity towards cyclin B1, but not cyclin A2. Through structural, biochemical and in vivo analysis, we identify a non-canonical D box (D2) that is critical for cyclin A2 ubiquitination in vitro and degradation in vivo. During the SAC, cyclin A2 is ubiquitinated by the repressed APC/C-MCC, mediated by the cooperative engagement of its KEN and D2 boxes, ABBA motif, and the cofactor Cks. Once the SAC is satisfied, cyclin A2 binds APC/C-Cdc20 through two mutually exclusive binding modes, resulting in differential ubiquitination efficiency. Our findings reveal that a single substrate can engage an E3 ligase through multiple binding modes, affecting its degradation timing and efficiency.
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Affiliation(s)
- Suyang Zhang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- Max Planck Institute for Biophysical Chemistry, Göttingen, 37077, Germany
| | - Thomas Tischer
- 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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18
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Eldeeb MA, Siva-Piragasam R, Ragheb MA, Esmaili M, Salla M, Fahlman RP. A molecular toolbox for studying protein degradation in mammalian cells. J Neurochem 2019; 151:520-533. [PMID: 31357232 DOI: 10.1111/jnc.14838] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/03/2019] [Accepted: 07/24/2019] [Indexed: 12/14/2022]
Abstract
Protein degradation is a crucial regulatory process in maintaining cellular proteostasis. The selective degradation of intracellular proteins controls diverse cellular and biochemical processes in all kingdoms of life. Targeted protein degradation is implicated in controlling the levels of regulatory proteins as well as eliminating misfolded and any otherwise abnormal proteins. Deregulation of protein degradation is concomitant with the progression of various neurodegenerative disorders such as Parkinson's and Alzheimer's diseases. Thus, methods of measuring metabolic half-lives of proteins greatly influence our understanding of the diverse functions of proteins in mammalian cells including neuronal cells. Historically, protein degradation rates have been studied via exploiting methods that estimate overall protein degradation or focus on few individual proteins. Notably, with the recent technical advances and developments in proteomic and imaging techniques, it is now possible to measure degradation rates of a large repertoire of defined proteins and analyze the degradation profile in a detailed spatio-temporal manner, with the aim of determining proteome-wide protein stabilities upon different physiological conditions. Herein, we discuss some of the classical and novel methods for determining protein degradation rates highlighting the crucial role of some state of art approaches in deciphering the global impact of dynamic nature of targeted degradation of cellular proteins. This article is part of the Special Issue "Proteomics".
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Affiliation(s)
- Mohamed A Eldeeb
- Department of Chemistry (Biochemistry Division), Faculty of Science, Cairo University, Giza, Egypt.,Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | | | - Mohamed A Ragheb
- Department of Chemistry (Biochemistry Division), Faculty of Science, Cairo University, Giza, Egypt
| | - Mansoore Esmaili
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Mohamed Salla
- Department of Biological Sciences, Lebanese International University, Bekaa, Lebanon
| | - Richard P Fahlman
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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19
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Interplay between Phosphatases and the Anaphase-Promoting Complex/Cyclosome in Mitosis. Cells 2019; 8:cells8080814. [PMID: 31382469 PMCID: PMC6721574 DOI: 10.3390/cells8080814] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 07/25/2019] [Accepted: 08/01/2019] [Indexed: 12/14/2022] Open
Abstract
Accurate division of cells into two daughters is a process that is vital to propagation of life. Protein phosphorylation and selective degradation have emerged as two important mechanisms safeguarding the delicate choreography of mitosis. Protein phosphatases catalyze dephosphorylation of thousands of sites on proteins, steering the cells through establishment of the mitotic phase and exit from it. A large E3 ubiquitin ligase, the anaphase-promoting complex/cyclosome (APC/C) becomes active during latter stages of mitosis through G1 and marks hundreds of proteins for destruction. Recent studies have revealed the complex interregulation between these two classes of enzymes. In this review, we highlight the direct and indirect mechanisms by which phosphatases and the APC/C mutually influence each other to ensure accurate spatiotemporal and orderly progression through mitosis, with a particular focus on recent insights and conceptual advances.
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20
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Krystkowiak I, Davey NE. SLiMSearch: a framework for proteome-wide discovery and annotation of functional modules in intrinsically disordered regions. Nucleic Acids Res 2019; 45:W464-W469. [PMID: 28387819 PMCID: PMC5570202 DOI: 10.1093/nar/gkx238] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 04/05/2017] [Indexed: 12/12/2022] Open
Abstract
The extensive intrinsically disordered regions of higher eukaryotic proteomes contain vast numbers of functional interaction modules known as short linear motifs (SLiMs). Here, we present SLiMSearch, a motif discovery tool that scans a motif consensus, representing the specificity determinants of a motif-binding domain, against a proteome to discover putative novel motif instances. SLiMSearch applies several distinct and complementary approaches exploiting the common properties of SLiMs to predict novel motifs. Consensus matches are annotated with overlapping sequence annotation, including feature information describing protein modular architecture, post-translational modification, structure, sequence variation and experimental characterisation of functional regions. Discriminatory motif attributes such as conservation and accessibility are also calculated. In addition, SLiMSearch provides functional enrichment and evolutionary analysis tools. The enrichment tool analyses GO terms, keywords and interacting partner enrichment to indicate possible motif function. The evolutionary tool evaluates motif taxonomic range and the conservation of motif sequence context. Consensus matches can be filtered based on motif attributes such as accessibility and taxonomic range; or by the localisation, interacting partners or ontology annotation of the peptide-containing protein. SLiMSearch supports a range of species of experimental and therapeutic relevance and is available online at http://slim.ucd.ie/slimsearch/.
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Affiliation(s)
- Izabella Krystkowiak
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.,UCD School of Medicine & Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Norman E Davey
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland.,UCD School of Medicine & Medical Science, University College Dublin, Belfield, Dublin 4, Ireland
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21
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Wang JH, Li Y, Deng SL, Liu YX, Lian ZX, Yu K. Recent Research Advances in Mitosis during Mammalian Gametogenesis. Cells 2019; 8:cells8060567. [PMID: 31185583 PMCID: PMC6628140 DOI: 10.3390/cells8060567] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/02/2019] [Accepted: 06/06/2019] [Indexed: 12/13/2022] Open
Abstract
Mitosis is a highly sophisticated and well-regulated process during the development and differentiation of mammalian gametogenesis. The regulation of mitosis plays an essential role in keeping the formulation in oogenesis and gametogenesis. In the past few years, substantial research progress has been made by showing that cyclins/cyclin-dependent kinase (CDK) have roles in the regulation of meiosis. In addition, more functional signaling molecules have been discovered in mitosis. Growing evidence has also indicated that miRNAs influence cell cycling. In this review, we focus on specific genes, cyclins/Cdk, signaling pathways/molecules, and miRNAs to discuss the latest achievements in understanding their roles in mitosis during gametogenesis. Further elucidation of mitosis during gametogenesis may facilitate delineating all processes of mammalian reproduction and the development of disease treatments.
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Affiliation(s)
- Jia-Hao Wang
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Yan Li
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Shou-Long Deng
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yi-Xun Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Zheng-Xing Lian
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Kun Yu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
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22
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The mammalian kinetochore-microtubule interface: robust mechanics and computation with many microtubules. Curr Opin Cell Biol 2019; 60:60-67. [PMID: 31132675 DOI: 10.1016/j.ceb.2019.04.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/10/2019] [Accepted: 04/15/2019] [Indexed: 12/31/2022]
Abstract
The kinetochore drives chromosome segregation at cell division. It acts as a physical link between chromosomes and dynamic microtubules, and as a signaling hub detecting and processing microtubule attachments to control anaphase onset. The mammalian kinetochore is a large macromolecular machine that forms a dynamic interface with the many microtubules that it binds. While we know most of the kinetochore's component parts, how they work together to give rise to its robust functions remains poorly understood. Here we highlight recent findings that shed light on this question, driven by an expanding physical and molecular toolkit. We present emerging principles that underlie the kinetochore's robust microtubule grip, such as redundancy, specialization, and dynamicity, and present signal processing principles that connect this microtubule grip to robust computation. Throughout, we identify open questions, and define simple engineering concepts that provide insight into kinetochore function.
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23
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Mukherjee S, Sandri BJ, Tank D, McClellan M, Harasymiw LA, Yang Q, Parker LL, Gardner MK. A Gradient in Metaphase Tension Leads to a Scaled Cellular Response in Mitosis. Dev Cell 2019; 49:63-76.e10. [PMID: 30799228 PMCID: PMC6535804 DOI: 10.1016/j.devcel.2019.01.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 11/20/2018] [Accepted: 01/21/2019] [Indexed: 12/27/2022]
Abstract
During mitosis, motor proteins associate with microtubules to exert pushing forces that establish a mitotic spindle. These pushing forces generate opposing tension in the chromatin that connects oppositely attached sister chromatids, which may then act as a mechanical signal to ensure the fidelity of chromosome segregation during mitosis. However, the role of tension in mitotic cellular signaling remains controversial. In this study, we generated a gradient in tension over multiple isogenic budding yeast cell lines by genetically altering the magnitude of motor-based spindle forces. We found that a decreasing gradient in tension led to an increasing gradient in the rates of kinetochore detachment and anaphase chromosome mis-segregration, and in metaphase time. Simulations and experiments indicated that these tension responses originate from a tension-dependent kinetochore phosphorylation gradient. We conclude that the cell is exquisitely tuned to the magnitude of tension as a signal to detect potential chromosome segregation errors during mitosis.
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Affiliation(s)
- Soumya Mukherjee
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Brian J Sandri
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Damien Tank
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mark McClellan
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Lauren A Harasymiw
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Qing Yang
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA
| | - Laurie L Parker
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Melissa K Gardner
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN 55455, USA.
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24
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Yang Y, Zhou H, Shu H, Zhong D, Zhang M, Xia JH. Effect of fasting and subsequent refeeding on the transcriptional profiles of brain in juvenile Spinibarbus hollandi. PLoS One 2019; 14:e0214589. [PMID: 30921420 PMCID: PMC6438469 DOI: 10.1371/journal.pone.0214589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 03/17/2019] [Indexed: 11/18/2022] Open
Abstract
Starvation is a common stress in fish. The underlying molecular mechanisms associated with growth depression caused by feeding restriction and compensatory growth are not well understood. We investigated the effect of fasting and refeeding on the transcriptome profiles of brain in juvenile S. hollandi using RNA-seq. A total of 4.73 × 108 raw reads were obtained from nine brain samples. De novo transcriptome assembly identified 387,085 unigenes with 2.1×109 nucleotides. A total of 936 annotated unigenes showed significantly differential expression among the control, fasting, and fasting-refeeding groups. The down-regulated differentially expressed genes (DEGs) during fasting were mainly associated with cell cycle, DNA replication, and mitosis. The up-regulated DEGs were mainly related to glucose and lipid metabolism, material transportation, and transcription factors. Most decreased DEGs during fasting were restored to normal levels after refeeding. Comparing with the control group, genes associated with protein synthesis, stimulus response, and carbohydrate metabolism were significantly over-expressed and pro-opio melanocortin (POMC) was down-regulated during the refeeding period. In conclusion, fish mobilized stored energetic materials and reduced energy consumption to prolong survival during fasting. After refeeding, the down-regulation of DEGs, e.g., POMC may be associated with compensatory growth. Up-regulation of DEGs related to ribosomal protein, stimulus response, and carbohydrate metabolism may contribute to eliminate negative effect of starvation on brain. This study provided the first transcriptome data related with impact of short-time starvation and refeeding in S. hollandi brains.
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Affiliation(s)
- Yang Yang
- School of Life Science, Guangzhou University, Guangzhou, China
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
| | - Huiqiang Zhou
- School of Life Science, Guangzhou University, Guangzhou, China
| | - Hu Shu
- School of Life Science, Guangzhou University, Guangzhou, China
- * E-mail: (JHX); (HS)
| | - Dongming Zhong
- School of Life Science, Guangzhou University, Guangzhou, China
| | - Mingqing Zhang
- School of Life Science, Guangzhou University, Guangzhou, China
| | - Jun Hong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou, PR China
- * E-mail: (JHX); (HS)
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25
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Münzner U, Klipp E, Krantz M. A comprehensive, mechanistically detailed, and executable model of the cell division cycle in Saccharomyces cerevisiae. Nat Commun 2019; 10:1308. [PMID: 30899000 PMCID: PMC6428898 DOI: 10.1038/s41467-019-08903-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 01/24/2019] [Indexed: 01/31/2023] Open
Abstract
Understanding how cellular functions emerge from the underlying molecular mechanisms is a key challenge in biology. This will require computational models, whose predictive power is expected to increase with coverage and precision of formulation. Genome-scale models revolutionised the metabolic field and made the first whole-cell model possible. However, the lack of genome-scale models of signalling networks blocks the development of eukaryotic whole-cell models. Here, we present a comprehensive mechanistic model of the molecular network that controls the cell division cycle in Saccharomyces cerevisiae. We use rxncon, the reaction-contingency language, to neutralise the scalability issues preventing formulation, visualisation and simulation of signalling networks at the genome-scale. We use parameter-free modelling to validate the network and to predict genotype-to-phenotype relationships down to residue resolution. This mechanistic genome-scale model offers a new perspective on eukaryotic cell cycle control, and opens up for similar models-and eventually whole-cell models-of human cells.
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Affiliation(s)
- Ulrike Münzner
- Humboldt-Universität zu Berlin, Institute of Biology, Theoretical Biophysics, Berlin, 10099, Germany
- Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, 611-0011, Japan
| | - Edda Klipp
- Humboldt-Universität zu Berlin, Institute of Biology, Theoretical Biophysics, Berlin, 10099, Germany
| | - Marcus Krantz
- Humboldt-Universität zu Berlin, Institute of Biology, Theoretical Biophysics, Berlin, 10099, Germany.
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26
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Control of Eukaryotic DNA Replication Initiation-Mechanisms to Ensure Smooth Transitions. Genes (Basel) 2019; 10:genes10020099. [PMID: 30700044 PMCID: PMC6409694 DOI: 10.3390/genes10020099] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 01/25/2019] [Accepted: 01/25/2019] [Indexed: 02/06/2023] Open
Abstract
DNA replication differs from most other processes in biology in that any error will irreversibly change the nature of the cellular progeny. DNA replication initiation, therefore, is exquisitely controlled. Deregulation of this control can result in over-replication characterized by repeated initiation events at the same replication origin. Over-replication induces DNA damage and causes genomic instability. The principal mechanism counteracting over-replication in eukaryotes is a division of replication initiation into two steps—licensing and firing—which are temporally separated and occur at distinct cell cycle phases. Here, we review this temporal replication control with a specific focus on mechanisms ensuring the faultless transition between licensing and firing phases.
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27
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Abstract
The separation of sister chromatids at anaphase, which is regulated by an E3 ubiquitin ligase called the anaphase-promoting complex/cyclosome (APC/C), is arguably the most important irrevocable event during the cell cycle. The APC/C and cyclin-dependent kinase 1 (Cdk1) are just two of the many significant cell cycle regulators and exert control through ubiquitylation and phosphorylation, respectively. The temporal and spatial regulation of the APC/C is achieved by multiple mechanisms, including phosphorylation, interaction with the structurally related co-activators Cdc20 and Cdh1, loading of distinct E2 ubiquitin-conjugating enzymes, binding with inhibitors and differential affinities for various substrates. Since the discovery of APC/C 25 years ago, intensive studies have uncovered many aspects of APC/C regulation, but we are still far from a full understanding of this important cellular machinery. Recent high-resolution cryogenic electron microscopy analysis and reconstitution of the APC/C have greatly advanced our understanding of molecular mechanisms underpinning the enzymatic properties of APC/C. In this review, we will examine the historical background and current understanding of APC/C regulation.
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Affiliation(s)
- Hiroyuki Yamano
- Cell Cycle Control Group, UCL Cancer Institute, University College London, Paul O’Gorman Building, 72 Huntley Street, London, WC1E 6DD, UK
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28
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Hernández-Carralero E, Cabrera E, Alonso-de Vega I, Hernández-Pérez S, Smits VAJ, Freire R. Control of DNA Replication Initiation by Ubiquitin. Cells 2018; 7:E146. [PMID: 30241373 PMCID: PMC6211026 DOI: 10.3390/cells7100146] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 09/18/2018] [Accepted: 09/19/2018] [Indexed: 01/07/2023] Open
Abstract
Eukaryotic cells divide by accomplishing a program of events in which the replication of the genome is a fundamental part. To ensure all cells have an accurate copy of the genome, DNA replication occurs only once per cell cycle and is controlled by numerous pathways. A key step in this process is the initiation of DNA replication in which certain regions of DNA are marked as competent to replicate. Moreover, initiation of DNA replication needs to be coordinated with other cell cycle processes. At the molecular level, initiation of DNA replication relies, among other mechanisms, upon post-translational modifications, including the conjugation and hydrolysis of ubiquitin. An example is the precise control of the levels of the DNA replication initiation protein Cdt1 and its inhibitor Geminin by ubiquitin-mediated proteasomal degradation. This control ensures that DNA replication occurs with the right timing during the cell cycle, thereby avoiding re-replication events. Here, we review the events that involve ubiquitin signalling during DNA replication initiation, and how they are linked to human disease.
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Affiliation(s)
- Esperanza Hernández-Carralero
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, Ofra s/n, 38320 La Laguna, Tenerife, Spain.
| | - Elisa Cabrera
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, Ofra s/n, 38320 La Laguna, Tenerife, Spain.
| | - Ignacio Alonso-de Vega
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, Ofra s/n, 38320 La Laguna, Tenerife, Spain.
| | - Santiago Hernández-Pérez
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, Ofra s/n, 38320 La Laguna, Tenerife, Spain.
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
| | - Veronique A J Smits
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, Ofra s/n, 38320 La Laguna, Tenerife, Spain.
| | - Raimundo Freire
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, Ofra s/n, 38320 La Laguna, Tenerife, Spain.
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29
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Bonacci T, Suzuki A, Grant GD, Stanley N, Cook JG, Brown NG, Emanuele MJ. Cezanne/OTUD7B is a cell cycle-regulated deubiquitinase that antagonizes the degradation of APC/C substrates. EMBO J 2018; 37:embj.201798701. [PMID: 29973362 DOI: 10.15252/embj.201798701] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 06/14/2018] [Accepted: 06/15/2018] [Indexed: 11/09/2022] Open
Abstract
The anaphase-promoting complex/cyclosome (APC/C) is an E3 ubiquitin ligase and key regulator of cell cycle progression. Since APC/C promotes the degradation of mitotic cyclins, it controls cell cycle-dependent oscillations in cyclin-dependent kinase (CDK) activity. Both CDKs and APC/C control a large number of substrates and are regulated by analogous mechanisms, including cofactor-dependent activation. However, whereas substrate dephosphorylation is known to counteract CDK, it remains largely unknown whether deubiquitinating enzymes (DUBs) antagonize APC/C substrate ubiquitination during mitosis. Here, we demonstrate that Cezanne/OTUD7B is a cell cycle-regulated DUB that opposes the ubiquitination of APC/C targets. Cezanne is remarkably specific for K11-linked ubiquitin chains, which are formed by APC/C in mitosis. Accordingly, Cezanne binds established APC/C substrates and reverses their APC/C-mediated ubiquitination. Cezanne depletion accelerates APC/C substrate degradation and causes errors in mitotic progression and formation of micronuclei. These data highlight the importance of tempered APC/C substrate destruction in maintaining chromosome stability. Furthermore, Cezanne is recurrently amplified and overexpressed in numerous malignancies, suggesting a potential role in genome maintenance and cancer cell proliferation.
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Affiliation(s)
- Thomas Bonacci
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aussie Suzuki
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Gavin D Grant
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Natalie Stanley
- Curriculum in Bioinformatics and Computational Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jeanette G Cook
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nicholas G Brown
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael J Emanuele
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA .,Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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30
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Taming the Beast: Control of APC/C Cdc20-Dependent Destruction. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2017; 82:111-121. [PMID: 29133301 DOI: 10.1101/sqb.2017.82.033712] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The anaphase-promoting complex/cyclosome (APC/C) is a large multisubunit ubiquitin ligase that triggers the metaphase-to-anaphase transition in the cell cycle by targeting the substrates cyclin B and securin for destruction. APC/C activity toward these two key substrates requires the coactivator Cdc20. To ensure that cells enter mitosis and partition their duplicated genome with high accuracy, APC/CCdc20 activity must be tightly controlled. Here, we discuss the mechanisms that regulate APC/CCdc20 activity both before and during mitosis. We focus our discussion primarily on the chromosomal pathways that both accelerate and delay APC/C activation by targeting Cdc20 to opposing fates. The findings discussed provide an overview of how cells control the activation of this major cell cycle regulator to ensure both accurate and timely cell division.
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31
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Oh JH, Chen SJ, Varshavsky A. A reference-based protein degradation assay without global translation inhibitors. J Biol Chem 2017; 292:21457-21465. [PMID: 29122887 DOI: 10.1074/jbc.m117.814236] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/05/2017] [Indexed: 11/06/2022] Open
Abstract
Although it is widely appreciated that the use of global translation inhibitors, such as cycloheximide, in protein degradation assays may result in artefacts, these inhibitors continue to be employed, owing to the absence of robust alternatives. We describe here the promoter reference technique (PRT), an assay for protein degradation with two advantageous features: a reference protein and a gene-specific inhibition of translation. In PRT assays, one measures, during a chase, the ratio of a test protein to a long-lived reference protein, a dihydrofolate reductase (DHFR). The test protein and DHFR are coexpressed, in the yeast Saccharomyces cerevisiae, on a low-copy plasmid from two identical P TDH3 promoters containing additional, previously developed DNA elements. Once transcribed, these elements form 5'-RNA aptamers that bind to the added tetracycline, which represses translation of aptamer-containing mRNAs. The selectivity of repression avoids a global inhibition of translation. This selectivity is particularly important if a component of a relevant proteolytic pathway (e.g. a specific ubiquitin ligase) is itself short-lived. We applied PRT to the Pro/N-end rule pathway, whose substrates include the short-lived Mdh2 malate dehydrogenase. Mdh2 is targeted for degradation by the Gid4 subunit of the GID ubiquitin ligase. Gid4 is also a metabolically unstable protein. Through analyses of short-lived Mdh2 as a target of short-lived Gid4, we illustrate the advantages of PRT over degradation assays that lack a reference and/or involve cycloheximide. In sum, PRT avoids the use of global translation inhibitors during a chase and also provides a "built-in" reference protein.
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Affiliation(s)
- Jang-Hyun Oh
- From the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Shun-Jia Chen
- From the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
| | - Alexander Varshavsky
- From the Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125
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32
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Alfieri C, Zhang S, Barford D. Visualizing the complex functions and mechanisms of the anaphase promoting complex/cyclosome (APC/C). Open Biol 2017; 7:170204. [PMID: 29167309 PMCID: PMC5717348 DOI: 10.1098/rsob.170204] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/10/2017] [Indexed: 12/17/2022] Open
Abstract
The anaphase promoting complex or cyclosome (APC/C) is a large multi-subunit E3 ubiquitin ligase that orchestrates cell cycle progression by mediating the degradation of important cell cycle regulators. During the two decades since its discovery, much has been learnt concerning its role in recognizing and ubiquitinating specific proteins in a cell-cycle-dependent manner, the mechanisms governing substrate specificity, the catalytic process of assembling polyubiquitin chains on its target proteins, and its regulation by phosphorylation and the spindle assembly checkpoint. The past few years have witnessed significant progress in understanding the quantitative mechanisms underlying these varied APC/C functions. This review integrates the overall functions and properties of the APC/C with mechanistic insights gained from recent cryo-electron microscopy (cryo-EM) studies of reconstituted human APC/C complexes.
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Affiliation(s)
- Claudio Alfieri
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Suyang Zhang
- 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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33
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Overlack K, Bange T, Weissmann F, Faesen AC, Maffini S, Primorac I, Müller F, Peters JM, Musacchio A. BubR1 Promotes Bub3-Dependent APC/C Inhibition during Spindle Assembly Checkpoint Signaling. Curr Biol 2017; 27:2915-2927.e7. [PMID: 28943088 PMCID: PMC5640511 DOI: 10.1016/j.cub.2017.08.033] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/16/2017] [Accepted: 08/15/2017] [Indexed: 12/25/2022]
Abstract
The spindle assembly checkpoint (SAC) prevents premature sister chromatid separation during mitosis. Phosphorylation of unattached kinetochores by the Mps1 kinase promotes recruitment of SAC machinery that catalyzes assembly of the SAC effector mitotic checkpoint complex (MCC). The SAC protein Bub3 is a phospho-amino acid adaptor that forms structurally related stable complexes with functionally distinct paralogs named Bub1 and BubR1. A short motif (“loop”) of Bub1, but not the equivalent loop of BubR1, enhances binding of Bub3 to kinetochore phospho-targets. Here, we asked whether the BubR1 loop directs Bub3 to different phospho-targets. The BubR1 loop is essential for SAC function and cannot be removed or replaced with the Bub1 loop. BubR1 loop mutants bind Bub3 and are normally incorporated in MCC in vitro but have reduced ability to inhibit the MCC target anaphase-promoting complex (APC/C), suggesting that BubR1:Bub3 recognition and inhibition of APC/C requires phosphorylation. Thus, small sequence differences in Bub1 and BubR1 direct Bub3 to different phosphorylated targets in the SAC signaling cascade. The molecular basis of kinetochore recruitment of Bub1 and BubR1 is dissected Bub1 and BubR1 modulate the ability of Bub3 to recognize phosphorylated targets A newly identified BubR1 motif targets Bub3 to the anaphase-promoting complex The newly identified motif of BubR1 is required for checkpoint signaling
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Affiliation(s)
- Katharina Overlack
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Tanja Bange
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Florian Weissmann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Alex C Faesen
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Stefano Maffini
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Ivana Primorac
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Franziska Müller
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Andrea Musacchio
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany; Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Universitätsstrasse, 45141 Essen, Germany.
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34
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Seoane AI, Morgan DO. Firing of Replication Origins Frees Dbf4-Cdc7 to Target Eco1 for Destruction. Curr Biol 2017; 27:2849-2855.e2. [PMID: 28918948 DOI: 10.1016/j.cub.2017.07.070] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 07/12/2017] [Accepted: 07/31/2017] [Indexed: 12/14/2022]
Abstract
Robust progression through the cell-division cycle depends on the precisely ordered phosphorylation of hundreds of different proteins by cyclin-dependent kinases (CDKs) and other kinases. The order of CDK substrate phosphorylation depends on rising CDK activity, coupled with variations in substrate affinities for different CDK-cyclin complexes and the opposing phosphatases [1-4]. Here, we address the ordering of substrate phosphorylation by a second major cell-cycle kinase, Cdc7-Dbf4 or Dbf4-dependent kinase (DDK). The primary function of DDK is to initiate DNA replication by phosphorylating the Mcm2-7 replicative helicase [5-7]. DDK also phosphorylates the cohesin acetyltransferase Eco1 [8]. Sequential phosphorylations of Eco1 by CDK, DDK, and Mck1 create a phosphodegron that is recognized by the ubiquitin ligase SCFCdc4. DDK, despite being activated in early S phase, does not phosphorylate Eco1 to trigger its degradation until late S phase [8]. DDK associates with docking sites on loaded Mcm double hexamers at unfired replication origins [9, 10]. We hypothesized that these docking interactions sequester limiting amounts of DDK, delaying Eco1 phosphorylation by DDK until replication is complete. Consistent with this hypothesis, we find that overproduction of DDK leads to premature Eco1 degradation. Eco1 degradation also occurs prematurely if Mcm complex loading at origins is prevented by depletion of Cdc6, and Eco1 is stabilized if loaded Mcm complexes are prevented from firing by a Cdc45 mutant. We propose that the timing of Eco1 phosphorylation, and potentially that of other DDK substrates, is determined in part by sequestration of DDK at unfired replication origins during S phase.
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Affiliation(s)
- Agustin I Seoane
- Departments of Physiology and Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - David O Morgan
- Departments of Physiology and Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA.
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35
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Davey NE, Morgan DO. Building a Regulatory Network with Short Linear Sequence Motifs: Lessons from the Degrons of the Anaphase-Promoting Complex. Mol Cell 2017; 64:12-23. [PMID: 27716480 DOI: 10.1016/j.molcel.2016.09.006] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The anaphase-promoting complex or cyclosome (APC/C) is a ubiquitin ligase that polyubiquitinates specific substrates at precise times in the cell cycle, thereby triggering the events of late mitosis in a strict order. The robust substrate specificity of the APC/C prevents the potentially deleterious degradation of non-APC/C substrates and also averts the cell-cycle errors and genomic instability that could result from mistimed degradation of APC/C targets. The APC/C recognizes short linear sequence motifs, or degrons, on its substrates. The specific and timely modification and degradation of APC/C substrates is likely to be modulated by variations in degron sequence and context. We discuss the extensive affinity, specificity, and selectivity determinants encoded in APC/C degrons, and we describe some of the extrinsic mechanisms that control APC/C-substrate recognition. As an archetype for protein motif-driven regulation of cell function, the APC/C-substrate interaction provides insights into the general properties of post-translational regulatory systems.
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Affiliation(s)
- Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland.
| | - David O Morgan
- Departments of Physiology and Biochemistry & Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA.
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36
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Gilberto S, Peter M. Dynamic ubiquitin signaling in cell cycle regulation. J Cell Biol 2017; 216:2259-2271. [PMID: 28684425 PMCID: PMC5551716 DOI: 10.1083/jcb.201703170] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 05/11/2017] [Accepted: 05/25/2017] [Indexed: 12/16/2022] Open
Abstract
Gilberto and Peter discuss the role of ubiquitylation in the regulation of DNA replication and mitosis. The cell division cycle is driven by a collection of enzymes that coordinate DNA duplication and separation, ensuring that genomic information is faithfully and perpetually maintained. The activity of the effector proteins that perform and coordinate these biological processes oscillates by regulated expression and/or posttranslational modifications. Ubiquitylation is a cardinal cellular modification and is long known for driving cell cycle transitions. In this review, we emphasize emerging concepts of how ubiquitylation brings the necessary dynamicity and plasticity that underlie the processes of DNA replication and mitosis. New studies, often focusing on the regulation of chromosomal proteins like DNA polymerases or kinetochore kinases, are demonstrating that ubiquitylation is a versatile modification that can be used to fine-tune these cell cycle events, frequently through processes that do not involve proteasomal degradation. Understanding how the increasing variety of identified ubiquitin signals are transduced will allow us to develop a deeper mechanistic perception of how the multiple factors come together to faithfully propagate genomic information. Here, we discuss these and additional conceptual challenges that are currently under study toward understanding how ubiquitin governs cell cycle regulation.
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Affiliation(s)
- Samuel Gilberto
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology, Zurich, Switzerland.,Molecular Life Science PhD Program, Life Science Zurich Graduate School, Zurich, Switzerland
| | - Matthias Peter
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology, Zurich, Switzerland
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37
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Abstract
The ubiquitin proteasome system controls the concentrations of regulatory proteins and removes damaged and misfolded proteins from cells. Proteins are targeted to the protease at the center of this system, the proteasome, by ubiquitin tags, but ubiquitin is also used as a signal in other cellular processes. Specificity is conferred by the size and structure of the ubiquitin tags, which are recognized by receptors associated with the different cellular processes. However, the ubiquitin code remains ambiguous, and the same ubiquitin tag can target different proteins to different fates. After binding substrate protein at the ubiquitin tag, the proteasome initiates degradation at a disordered region in the substrate. The proteasome has pronounced preferences for the initiation site, and its recognition represents a second component of the degradation signal.
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Affiliation(s)
- Houqing Yu
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712;
| | - Andreas Matouschek
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712;
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38
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Cdc20: At the Crossroads between Chromosome Segregation and Mitotic Exit. Trends Biochem Sci 2017; 42:193-205. [PMID: 28202332 DOI: 10.1016/j.tibs.2016.12.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 11/13/2016] [Accepted: 12/06/2016] [Indexed: 11/21/2022]
Abstract
Cell-division cycle protein 20 homologue (Cdc20) has important functions in chromosome segregation and mitotic exit. Cdc20 is the target of the spindle assembly checkpoint (SAC) and a key cofactor of the anaphase-promoting complex or cyclosome (APC/C) E3 ubiquitin ligase, thus regulating APC/C ubiquitin activity on specific substrates for their subsequent degradation by the proteasome. Here we discuss the roles of Cdc20 in SAC signalling and mitotic exit, describe how the integration of traditional approaches with emerging technologies has revealed new details of Cdc20 functions, comment about the potential of Cdc20 as a therapeutic target for the treatment of human malignancies, and discuss recent advances and controversies in the mechanistic understanding of the control of chromosome segregation during cell division.
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39
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Matson JP, Cook JG. Cell cycle proliferation decisions: the impact of single cell analyses. FEBS J 2017; 284:362-375. [PMID: 27634578 PMCID: PMC5296213 DOI: 10.1111/febs.13898] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/23/2016] [Accepted: 09/13/2016] [Indexed: 12/16/2022]
Abstract
Cell proliferation is a fundamental requirement for organismal development and homeostasis. The mammalian cell division cycle is tightly controlled to ensure complete and precise genome duplication and segregation of replicated chromosomes to daughter cells. The onset of DNA replication marks an irreversible commitment to cell division, and the accumulated efforts of many decades of molecular and cellular studies have probed this cellular decision, commonly called the restriction point. Despite a long-standing conceptual framework of the restriction point for progression through G1 phase into S phase or exit from G1 phase to quiescence (G0), recent technical advances in quantitative single cell analysis of mammalian cells have provided new insights. Significant intercellular heterogeneity revealed by single cell studies and the discovery of discrete subpopulations in proliferating cultures suggests the need for an even more nuanced understanding of cell proliferation decisions. In this review, we describe some of the recent developments in the cell cycle field made possible by quantitative single cell experimental approaches.
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Affiliation(s)
- Jacob P. Matson
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill. Chapel Hill, North Carolina 27599
| | - Jeanette G. Cook
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill. Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill. Chapel Hill, North Carolina 27599
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40
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Xu L, Fan S, Zhao J, Zhou P, Chu S, Luo J, Wen Q, Chen L, Wen S, Wang L, Shi L. Increased expression of Cks1 protein is associated with lymph node metastasis and poor prognosis in nasopharyngeal carcinoma. Diagn Pathol 2017; 12:2. [PMID: 28061788 PMCID: PMC5219755 DOI: 10.1186/s13000-016-0589-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 12/06/2016] [Indexed: 12/12/2022] Open
Abstract
Background The Cks1 protein is an essential factor in regulating cell cycle by mediating the ubiquitination of CDK inhibitor p27kip1. It has been reported that aberrant expression of Cks1 and p27kip1 proteins was found in various tumors and related to initiation and progression of carcinomas. However, the potential roles which Cks1 and p27KIP1 proteins play in NPC remain unclear. This study aims to examine the expression status of Cks1 and p27kip1 and their possible prognostic significance in NPC. Methods Paraffin-embedded specimens with NPC (n = 168) and non-tumor nasopharyngeal tissues (n = 49) were analyzed by IHC. Results Expression of Cks1 increased in NPC tissues compared with non-tumor nasopharyngeal tissues (P < 0.05), whereas p27kip1 protein frequently expressed in non-tumor nasopharyngeal tissues compared with NPC tissues (P < 0.05). There was a significant reverse correlation between Cks1 and p27kip1 protein expression in NPC (r = −0.189, P < 0.05).In addition, Kaplan-Meier survival curve showed that there was a significant tendency of shorter overall survival (OS) in NPC patients with Cks1 positive expression compared to negative ones, especially in patients with lymph node metastasis (P < 0.001, respectively). But there was no significance between p27kip1 expression and survival viability of NPC patients. Multivariate Cox regression analysis further identified increased expression of Cks1 was the independent poor prognostic factor for NPC (p = 0.13). Conclusion Our research found expression of Cks1 increased and was inverse to the expression of p27KIP1. High expression of Cks1 was significantly associated with lymph node metastasis and survival status in NPC. In addition, the abnormally high level of Cks1 protein was proved to be an independent poor prognostic factor in NPC. These results may provide novel clue for NPC therapy method. Electronic supplementary material The online version of this article (doi:10.1186/s13000-016-0589-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lina Xu
- Department of Pathology, The Second Xiangya Hospital of Central South University, Renmin Road 139, Changsha, Hunan, 410000, China
| | - Songqing Fan
- Department of Pathology, The Second Xiangya Hospital of Central South University, Renmin Road 139, Changsha, Hunan, 410000, China
| | - Jin Zhao
- Department of Clinical Laboratory, Hunan Cancer Hospital, Changsha, Hunan, China
| | - Peng Zhou
- Department of Pathology, The Second Xiangya Hospital of Central South University, Renmin Road 139, Changsha, Hunan, 410000, China
| | - Shuzhou Chu
- Department of Pathology, The Second Xiangya Hospital of Central South University, Renmin Road 139, Changsha, Hunan, 410000, China
| | - Jiadi Luo
- Department of Pathology, The Second Xiangya Hospital of Central South University, Renmin Road 139, Changsha, Hunan, 410000, China
| | - Qiuyuan Wen
- Department of Pathology, The Second Xiangya Hospital of Central South University, Renmin Road 139, Changsha, Hunan, 410000, China
| | - Lingjiao Chen
- Department of Pathology, The Second Xiangya Hospital of Central South University, Renmin Road 139, Changsha, Hunan, 410000, China
| | - Sailan Wen
- Department of Pathology, The Second Xiangya Hospital of Central South University, Renmin Road 139, Changsha, Hunan, 410000, China
| | - Li Wang
- Department of Chest Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Lei Shi
- Department of Pathology, The Second Xiangya Hospital of Central South University, Renmin Road 139, Changsha, Hunan, 410000, China.
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41
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Kamenz J, Hauf S. Time To Split Up: Dynamics of Chromosome Separation. Trends Cell Biol 2017; 27:42-54. [DOI: 10.1016/j.tcb.2016.07.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/14/2016] [Accepted: 07/29/2016] [Indexed: 11/16/2022]
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42
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Brown NG, VanderLinden R, Watson ER, Weissmann F, Ordureau A, Wu KP, Zhang W, Yu S, Mercredi PY, Harrison JS, Davidson IF, Qiao R, Lu Y, Dube P, Brunner MR, Grace CRR, Miller DJ, Haselbach D, Jarvis MA, Yamaguchi M, Yanishevski D, Petzold G, Sidhu SS, Kuhlman B, Kirschner MW, Harper JW, Peters JM, Stark H, Schulman BA. Dual RING E3 Architectures Regulate Multiubiquitination and Ubiquitin Chain Elongation by APC/C. Cell 2016; 165:1440-1453. [PMID: 27259151 DOI: 10.1016/j.cell.2016.05.037] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 04/16/2016] [Accepted: 05/09/2016] [Indexed: 11/25/2022]
Abstract
Protein ubiquitination involves E1, E2, and E3 trienzyme cascades. E2 and RING E3 enzymes often collaborate to first prime a substrate with a single ubiquitin (UB) and then achieve different forms of polyubiquitination: multiubiquitination of several sites and elongation of linkage-specific UB chains. Here, cryo-EM and biochemistry show that the human E3 anaphase-promoting complex/cyclosome (APC/C) and its two partner E2s, UBE2C (aka UBCH10) and UBE2S, adopt specialized catalytic architectures for these two distinct forms of polyubiquitination. The APC/C RING constrains UBE2C proximal to a substrate and simultaneously binds a substrate-linked UB to drive processive multiubiquitination. Alternatively, during UB chain elongation, the RING does not bind UBE2S but rather lures an evolving substrate-linked UB to UBE2S positioned through a cullin interaction to generate a Lys11-linked chain. Our findings define mechanisms of APC/C regulation, and establish principles by which specialized E3-E2-substrate-UB architectures control different forms of polyubiquitination.
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Affiliation(s)
- Nicholas G Brown
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ryan VanderLinden
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, Memphis, TN 38105, USA
| | - Edmond R Watson
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Florian Weissmann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Kuen-Phon Wu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Wei Zhang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Shanshan Yu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Peter Y Mercredi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Joseph S Harrison
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Iain F Davidson
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Renping Qiao
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Ying Lu
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Prakash Dube
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Michael R Brunner
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Christy R R Grace
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David Haselbach
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Marc A Jarvis
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Masaya Yamaguchi
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - David Yanishevski
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Georg Petzold
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Sachdev S Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - J Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jan-Michael Peters
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria.
| | - Holger Stark
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
| | - Brenda A Schulman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, Memphis, TN 38105, USA.
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Ondracka A, Robbins JA, Cross FR. An APC/C-Cdh1 Biosensor Reveals the Dynamics of Cdh1 Inactivation at the G1/S Transition. PLoS One 2016; 11:e0159166. [PMID: 27410035 PMCID: PMC4943722 DOI: 10.1371/journal.pone.0159166] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 06/28/2016] [Indexed: 12/31/2022] Open
Abstract
B-type cyclin-dependent kinase activity must be turned off for mitotic exit and G1 stabilization. B-type cyclin degradation is mediated by the anaphase-promoting complex/cyclosome (APC/C); during and after mitotic exit, APC/C is dependent on Cdh1. Cdh1 is in turn phosphorylated and inactivated by cyclin-CDK at the Start transition of the new cell cycle. We developed a biosensor to assess the cell cycle dynamics of APC/C-Cdh1. Nuclear exit of the G1 transcriptional repressor Whi5 is a known marker of Start; APC/C-Cdh1 is inactivated 12 min after Whi5 nuclear exit with little measurable cell-to-cell timing variability. Multiple phosphorylation sites on Cdh1 act in a redundant manner to repress its activity. Reducing the number of phosphorylation sites on Cdh1 can to some extent be tolerated for cell viability, but it increases variability in timing of APC/C-Cdh1 inactivation. Mutants with minimal subsets of phosphorylation sites required for viability exhibit striking stochasticity in multiple responses including budding, nuclear division, and APC/C-Cdh1 activity itself. Multiple cyclin-CDK complexes, as well as the stoichiometric inhibitor Acm1, contribute to APC/C-Cdh1 inactivation; this redundant control is likely to promote rapid and reliable APC/C-Cdh1 inactivation immediately following the Start transition.
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Affiliation(s)
- Andrej Ondracka
- Laboratory of Cell Cycle Genetics, The Rockefeller University, New York, NY 10065, United States of America
| | - Jonathan A. Robbins
- Laboratory of Cell Cycle Genetics, The Rockefeller University, New York, NY 10065, United States of America
| | - Frederick R. Cross
- Laboratory of Cell Cycle Genetics, The Rockefeller University, New York, NY 10065, United States of America
- * E-mail:
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Qin L, Guimarães DSPSF, Melesse M, Hall MC. Substrate Recognition by the Cdh1 Destruction Box Receptor Is a General Requirement for APC/CCdh1-mediated Proteolysis. J Biol Chem 2016; 291:15564-74. [PMID: 27226622 DOI: 10.1074/jbc.m116.731190] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Indexed: 11/06/2022] Open
Abstract
The anaphase-promoting complex, or cyclosome (APC/C), is a ubiquitin ligase that selectively targets proteins for degradation in mitosis and the G1 phase and is an important component of the eukaryotic cell cycle control system. How the APC/C specifically recognizes its substrates is not fully understood. Although well characterized degron motifs such as the destruction box (D-box) and KEN-box are commonly found in APC/C substrates, many substrates apparently lack these motifs. A variety of alternative APC/C degrons have been reported, suggesting either that multiple modes of substrate recognition are possible or that our definitions of degron structure are incomplete. We used an in vivo yeast assay to compare the G1 degradation rate of 15 known substrates of the APC/C co-activator Cdh1 under normal conditions and conditions that impair binding of D-box, KEN-box, and the recently identified ABBA motif degrons to Cdh1. The D-box receptor was required for efficient proteolysis of all Cdh1 substrates, despite the absence of canonical D-boxes in many. In contrast, the KEN-box receptor was only required for normal proteolysis of a subset of substrates and the ABBA motif receptor for a single substrate in our system. Our results suggest that binding to the D-box receptor may be a shared requirement for recognition and processing of all Cdh1 substrates.
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Affiliation(s)
- Liang Qin
- From the Department of Biochemistry and Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907
| | | | - Michael Melesse
- From the Department of Biochemistry and Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907
| | - Mark C Hall
- From the Department of Biochemistry and Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907
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Jia L, Li B, Yu H. The Bub1-Plk1 kinase complex promotes spindle checkpoint signalling through Cdc20 phosphorylation. Nat Commun 2016; 7:10818. [PMID: 26912231 PMCID: PMC4773433 DOI: 10.1038/ncomms10818] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 01/25/2016] [Indexed: 12/15/2022] Open
Abstract
The spindle checkpoint senses unattached kinetochores and inhibits the Cdc20-bound anaphase-promoting complex or cyclosome (APC/C), to delay anaphase, thereby preventing aneuploidy. A critical checkpoint inhibitor of APC/C(Cdc20) is the mitotic checkpoint complex (MCC). It is unclear whether MCC suffices to inhibit all cellular APC/C. Here we show that human checkpoint kinase Bub1 not only directly phosphorylates Cdc20, but also scaffolds Plk1-mediated phosphorylation of Cdc20. Phosphorylation of Cdc20 by Bub1-Plk1 inhibits APC/C(Cdc20) in vitro and is required for checkpoint signalling in human cells. Bub1-Plk1-dependent Cdc20 phosphorylation is regulated by upstream checkpoint signals and is dispensable for MCC assembly. A phospho-mimicking Cdc20 mutant restores nocodazole-induced mitotic arrest in cells depleted of Mad2 or BubR1. Thus, Bub1-Plk1-mediated phosphorylation of Cdc20 constitutes an APC/C-inhibitory mechanism that is parallel, but not redundant, to MCC formation. Both mechanisms are required to sustain mitotic arrest in response to spindle defects.
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Affiliation(s)
- Luying Jia
- Department of Pharmacology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, Texas 75390, USA
| | - Bing Li
- Department of Pharmacology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, Texas 75390, USA
| | - Hongtao Yu
- Department of Pharmacology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, Texas 75390, USA
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Cedeño C, La Monaca E, Esposito M, Gutierrez GJ. Detection and Analysis of Cell Cycle-Associated APC/C-Mediated Cellular Ubiquitylation In Vitro and In Vivo. Methods Mol Biol 2016; 1449:251-265. [PMID: 27613041 DOI: 10.1007/978-1-4939-3756-1_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The anaphase-promoting complex or cyclosome (APC/C) is one of the major orchestrators of the cell division cycle in mammalian cells. The APC/C acts as a ubiquitin ligase that triggers sequential ubiquitylation of a significant number of substrates which will be eventually degraded by proteasomes during major transitions of the cell cycle. In this chapter, we present accessible methodologies to assess both in in vitro conditions and in cellular systems ubiquitylation reactions mediated by the APC/C. In addition, we also describe techniques to evidence the changes in protein stability provoked by modulation of the activity of the APC/C. Finally, specific methods to analyze interactors or posttranslational modifications of particular APC/C subunits are also discussed. Given the crucial role played by the APC/C in the regulation of the cell cycle, this review only focuses on its action and effects in actively proliferating cells.
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Affiliation(s)
- Cesyen Cedeño
- Department of Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, 1050, Belgium
| | - Esther La Monaca
- Laboratory of Pathophysiological Cell Signaling (PACS), Department of Biology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, 1050, Belgium
| | - Mara Esposito
- Laboratory of Pathophysiological Cell Signaling (PACS), Department of Biology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, 1050, Belgium
| | - Gustavo J Gutierrez
- Laboratory of Pathophysiological Cell Signaling (PACS), Department of Biology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel (VUB), Pleinlaan 2, Brussels, 1050, Belgium.
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Van Roey K, Davey NE. Motif co-regulation and co-operativity are common mechanisms in transcriptional, post-transcriptional and post-translational regulation. Cell Commun Signal 2015; 13:45. [PMID: 26626130 PMCID: PMC4666095 DOI: 10.1186/s12964-015-0123-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/24/2015] [Indexed: 01/01/2023] Open
Abstract
A substantial portion of the regulatory interactions in the higher eukaryotic cell are mediated by simple sequence motifs in the regulatory segments of genes and (pre-)mRNAs, and in the intrinsically disordered regions of proteins. Although these regulatory modules are physicochemically distinct, they share an evolutionary plasticity that has facilitated a rapid growth of their use and resulted in their ubiquity in complex organisms. The ease of motif acquisition simplifies access to basal housekeeping functions, facilitates the co-regulation of multiple biomolecules allowing them to respond in a coordinated manner to changes in the cell state, and supports the integration of multiple signals for combinatorial decision-making. Consequently, motifs are indispensable for temporal, spatial, conditional and basal regulation at the transcriptional, post-transcriptional and post-translational level. In this review, we highlight that many of the key regulatory pathways of the cell are recruited by motifs and that the ease of motif acquisition has resulted in large networks of co-regulated biomolecules. We discuss how co-operativity allows simple static motifs to perform the conditional regulation that underlies decision-making in higher eukaryotic biological systems. We observe that each gene and its products have a unique set of DNA, RNA or protein motifs that encode a regulatory program to define the logical circuitry that guides the life cycle of these biomolecules, from transcription to degradation. Finally, we contrast the regulatory properties of protein motifs and the regulatory elements of DNA and (pre-)mRNAs, advocating that co-regulation, co-operativity, and motif-driven regulatory programs are common mechanisms that emerge from the use of simple, evolutionarily plastic regulatory modules.
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Affiliation(s)
- Kim Van Roey
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany.
- Health Services Research Unit, Operational Direction Public Health and Surveillance, Scientific Institute of Public Health (WIV-ISP), 1050, Brussels, Belgium.
| | - Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland.
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Davey NE, Cyert MS, Moses AM. Short linear motifs - ex nihilo evolution of protein regulation. Cell Commun Signal 2015; 13:43. [PMID: 26589632 PMCID: PMC4654906 DOI: 10.1186/s12964-015-0120-z] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Accepted: 11/13/2015] [Indexed: 12/12/2022] Open
Abstract
Short sequence motifs are ubiquitous across the three major types of biomolecules: hundreds of classes and thousands of instances of DNA regulatory elements, RNA motifs and protein short linear motifs (SLiMs) have been characterised. The increase in complexity of transcriptional, post-transcriptional and post-translational regulation in higher Eukaryotes has coincided with a significant expansion of motif use. But how did the eukaryotic cell acquire such a vast repertoire of motifs? In this review, we curate the available literature on protein motif evolution and discuss the evidence that suggests SLiMs can be acquired by mutations, insertions and deletions in disordered regions. We propose a mechanism of ex nihilo SLiM evolution – the evolution of a novel SLiM from “nothing” – adding a functional module to a previously non-functional region of protein sequence. In our model, hundreds of motif-binding domains in higher eukaryotic proteins connect simple motif specificities with useful functions to create a large functional motif space. Accessible peptides that match the specificity of these motif-binding domains are continuously created and destroyed by mutations in rapidly evolving disordered regions, creating a dynamic supply of new interactions that may have advantageous phenotypic novelty. This provides a reservoir of diversity to modify existing interaction networks. Evolutionary pressures will act on these motifs to retain beneficial instances. However, most will be lost on an evolutionary timescale as negative selection and genetic drift act on deleterious and neutral motifs respectively. In light of the parallels between the presented model and the evolution of motifs in the regulatory segments of genes and (pre-)mRNAs, we suggest our understanding of regulatory networks would benefit from the creation of a shared model describing the evolution of transcriptional, post-transcriptional and post-translational regulation.
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Affiliation(s)
- Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland.
| | - Martha S Cyert
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.
| | - Alan M Moses
- Department of Cell & Systems Biology, University of Toronto, Toronto, Canada. .,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada.
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49
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Lu D, Girard JR, Li W, Mizrak A, Morgan DO. Quantitative framework for ordered degradation of APC/C substrates. BMC Biol 2015; 13:96. [PMID: 26573515 PMCID: PMC4647693 DOI: 10.1186/s12915-015-0205-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 10/23/2015] [Indexed: 01/07/2023] Open
Abstract
Background During cell-cycle progression, substrates of a single master regulatory enzyme can be modified in a specific order. Here, we used experimental and computational approaches to dissect the quantitative mechanisms underlying the ordered degradation of the substrates of the ubiquitin ligase APC/CCdc20, a key regulator of chromosome segregation in mitosis. Results We show experimentally that the rate of catalysis varies with different substrates of APC/CCdc20. Using a computational model based on multi-step ubiquitination, we then show how changes in the interaction between a single substrate and APC/CCdc20 can alter the timing of degradation onset relative to APC/CCdc20 activation, while ensuring a fast degradation rate. Degradation timing and dynamics depend on substrate affinity for the enzyme as well as the catalytic rate at which the substrate is modified. When two substrates share the same pool of APC/CCdc20, their relative enzyme affinities and rates of catalysis influence the partitioning of APC/CCdc20 among substrates, resulting in substrate competition. Depending on how APC/CCdc20 is partitioned among its substrates, competition can have minor or major effects on the degradation of certain substrates. We show experimentally that increased expression of the early APC/CCdc20 substrate Clb5 does not delay the degradation of the later substrate securin, arguing against a role for competition with Clb5 in establishing securin degradation timing. Conclusions The degradation timing of APC/CCdc20 substrates depends on the multi-step nature of ubiquitination, differences in substrate-APC/CCdc20 interactions, and competition among substrates. Our studies provide a conceptual framework for understanding how ordered modification can be established among substrates of the same regulatory enzyme, and facilitate our understanding of how precise temporal control is achieved by a small number of master regulators to ensure a successful cell division cycle. Electronic supplementary material The online version of this article (doi:10.1186/s12915-015-0205-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dan Lu
- Departments of Physiology and Biochemistry & Biophysics, University of California, San Francisco, CA, 94158, USA
| | - Juliet R Girard
- Departments of Physiology and Biochemistry & Biophysics, University of California, San Francisco, CA, 94158, USA
| | - Weihan Li
- Departments of Physiology and Biochemistry & Biophysics, University of California, San Francisco, CA, 94158, USA
| | - Arda Mizrak
- Departments of Physiology and Biochemistry & Biophysics, University of California, San Francisco, CA, 94158, USA
| | - David O Morgan
- Departments of Physiology and Biochemistry & Biophysics, University of California, San Francisco, CA, 94158, USA.
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50
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Kamenz J, Mihaljev T, Kubis A, Legewie S, Hauf S. Robust Ordering of Anaphase Events by Adaptive Thresholds and Competing Degradation Pathways. Mol Cell 2015; 60:446-59. [PMID: 26527280 DOI: 10.1016/j.molcel.2015.09.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 08/08/2015] [Accepted: 09/24/2015] [Indexed: 11/26/2022]
Abstract
The splitting of chromosomes in anaphase and their delivery into the daughter cells needs to be accurately executed to maintain genome stability. Chromosome splitting requires the degradation of securin, whereas the distribution of the chromosomes into the daughter cells requires the degradation of cyclin B. We show that cells encounter and tolerate variations in the abundance of securin or cyclin B. This makes the concurrent onset of securin and cyclin B degradation insufficient to guarantee that early anaphase events occur in the correct order. We uncover that the timing of chromosome splitting is not determined by reaching a fixed securin level, but that this level adapts to the securin degradation kinetics. In conjunction with securin and cyclin B competing for degradation during anaphase, this provides robustness to the temporal order of anaphase events. Our work reveals how parallel cell-cycle pathways can be temporally coordinated despite variability in protein concentrations.
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Affiliation(s)
- Julia Kamenz
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA; Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA; Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tuebingen, Germany
| | | | - Armin Kubis
- Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tuebingen, Germany
| | - Stefan Legewie
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany.
| | - Silke Hauf
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA; Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA; Friedrich Miescher Laboratory of the Max Planck Society, 72076 Tuebingen, Germany.
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