1
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Shukla S, Bhattacharya A, Sehrawat P, Agarwal P, Shobhawat R, Malik N, Duraisamy K, Rangan NS, Hosur RV, Kumar A. Disorder in CENP-A Cse4 tail-chaperone interaction facilitates binding with Ame1/Okp1 at the kinetochore. Structure 2024; 32:690-705.e6. [PMID: 38565139 DOI: 10.1016/j.str.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 11/16/2023] [Accepted: 03/06/2024] [Indexed: 04/04/2024]
Abstract
The centromere is epigenetically marked by a histone H3 variant-CENP-A. The budding yeast CENP-A called Cse4, consists of an unusually long N-terminus that is known to be involved in kinetochore assembly. Its disordered chaperone, Scm3 is responsible for the centromeric deposition of Cse4 as well as in the maintenance of a segregation-competent kinetochore. In this study, we show that the Cse4 N-terminus is intrinsically disordered and interacts with Scm3 at multiple sites, and the complex does not gain any substantial structure. Additionally, the complex forms a synergistic association with an essential inner kinetochore component (Ctf19-Mcm21-Okp1-Ame1), and a model has been suggested to this effect. Thus, our study provides mechanistic insights into the Cse4 N-terminus-chaperone interaction and also illustrates how intrinsically disordered proteins mediate assembly of complex multiprotein networks, in general.
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Affiliation(s)
- Shivangi Shukla
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | | | - Parveen Sehrawat
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Prakhar Agarwal
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Rahul Shobhawat
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Nikita Malik
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Kalaiyarasi Duraisamy
- Centre for Advanced Protein Studies, Syngene International Limited, Bangalore, India
| | | | - Ramakrishna V Hosur
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India
| | - Ashutosh Kumar
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Mumbai, India.
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2
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Kshirsagar R, Munhoven A, Tran Nguyen TM, Ehrenhofer-Murray AE. A role for β-1,6- and β-1,3-glucans in kinetochore function in Saccharomyces cerevisiae. Genetics 2024; 226:iyad195. [PMID: 37950911 PMCID: PMC11221361 DOI: 10.1093/genetics/iyad195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/13/2023] Open
Abstract
Chromosome segregation is crucial for the faithful inheritance of DNA to the daughter cells after DNA replication. For this, the kinetochore, a megadalton protein complex, assembles on centromeric chromatin containing the histone H3 variant CENP-A, and provides a physical connection to the microtubules. Here, we report an unanticipated role for enzymes required for β-1,6- and β-1,3-glucan biosynthesis in regulating kinetochore function in Saccharomyces cerevisiae. These carbohydrates are the major constituents of the yeast cell wall. We found that the deletion of KRE6, which encodes a glycosylhydrolase/ transglycosidase required for β-1,6-glucan synthesis, suppressed the centromeric defect of mutations in components of the kinetochore, foremost the NDC80 components Spc24, Spc25, the MIND component Nsl1, and Okp1, a constitutive centromere-associated network protein. Similarly, the absence of Fks1, a β-1,3-glucan synthase, and Kre11/Trs65, a TRAPPII component, suppressed a mutation in SPC25. Genetic analysis indicates that the reduction of intracellular β-1,6- and β-1,3-glucans, rather than the cell wall glucan content, regulates kinetochore function. Furthermore, we found a physical interaction between Kre6 and CENP-A/Cse4 in yeast, suggesting a potential function for Kre6 in glycosylating CENP-A/Cse4 or another kinetochore protein. This work shows a moonlighting function for selected cell wall synthesis proteins in regulating kinetochore assembly, which may provide a mechanism to connect the nutritional status of the cell to cell-cycle progression and chromosome segregation.
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Affiliation(s)
- Rucha Kshirsagar
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstr. 13, Rhoda-Erdmann-Haus, 10099 Berlin, Germany
| | - Arno Munhoven
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstr. 13, Rhoda-Erdmann-Haus, 10099 Berlin, Germany
| | - Tra My Tran Nguyen
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstr. 13, Rhoda-Erdmann-Haus, 10099 Berlin, Germany
| | - Ann E Ehrenhofer-Murray
- Institut für Biologie, Humboldt-Universität zu Berlin, Philippstr. 13, Rhoda-Erdmann-Haus, 10099 Berlin, Germany
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3
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Deng S, Cai J, Harrison SC, Zhou H, Hinshaw SM. Recognition of centromere-specific histone Cse4 by the inner kinetochore Okp1-Ame1 complex. EMBO Rep 2023; 24:e57702. [PMID: 37983946 PMCID: PMC10702835 DOI: 10.15252/embr.202357702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/30/2023] [Accepted: 11/02/2023] [Indexed: 11/22/2023] Open
Abstract
Successful mitosis depends on the timely establishment of correct chromosomal attachments to microtubules. The kinetochore, a modular multiprotein complex, mediates this connection by recognizing specialized chromatin containing a histone H3 variant called Cse4 in budding yeast and CENP-A in vertebrates. Structural features of the kinetochore that enable discrimination between Cse4/CENP-A and H3 have been identified in several species. How and when these contribute to centromere recognition and how they relate to the overall structure of the inner kinetochore are unsettled questions. More generally, this molecular recognition ensures that only one kinetochore is built on each chromatid and that this happens at the right place on the chromatin fiber. We have determined the crystal structure of a Cse4 peptide bound to the essential inner kinetochore Okp1-Ame1 heterodimer from budding yeast. The structure and related experiments show in detail an essential point of Cse4 contact and provide information about the arrangement of the inner kinetochore.
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Affiliation(s)
- Sunbin Deng
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical School, and Howard Hughes Medical InstituteBostonMAUSA
| | - Jiaxi Cai
- Department of BioengineeringJacobs School of Engineering, UCSDSan DiegoCAUSA
| | - Stephen C Harrison
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical School, and Howard Hughes Medical InstituteBostonMAUSA
| | - Huilin Zhou
- Department of BioengineeringJacobs School of Engineering, UCSDSan DiegoCAUSA
- Department of Cellular and Molecular Medicine, School of MedicineMoores Cancer Center, UCSDSan DiegoCAUSA
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4
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Mishra PK, Au WC, Castineira PG, Ali N, Stanton J, Boeckmann L, Takahashi Y, Costanzo M, Boone C, Bloom KS, Thorpe PH, Basrai MA. Misregulation of cell cycle-dependent methylation of budding yeast CENP-A contributes to chromosomal instability. Mol Biol Cell 2023; 34:ar99. [PMID: 37436802 PMCID: PMC10551700 DOI: 10.1091/mbc.e23-03-0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/15/2023] [Accepted: 07/06/2023] [Indexed: 07/13/2023] Open
Abstract
Centromere (CEN) identity is specified epigenetically by specialized nucleosomes containing evolutionarily conserved CEN-specific histone H3 variant CENP-A (Cse4 in Saccharomyces cerevisiae, CENP-A in humans), which is essential for faithful chromosome segregation. However, the epigenetic mechanisms that regulate Cse4 function have not been fully defined. In this study, we show that cell cycle-dependent methylation of Cse4-R37 regulates kinetochore function and high-fidelity chromosome segregation. We generated a custom antibody that specifically recognizes methylated Cse4-R37 and showed that methylation of Cse4 is cell cycle regulated with maximum levels of methylated Cse4-R37 and its enrichment at the CEN chromatin occur in the mitotic cells. Methyl-mimic cse4-R37F mutant exhibits synthetic lethality with kinetochore mutants, reduced levels of CEN-associated kinetochore proteins and chromosome instability (CIN), suggesting that mimicking the methylation of Cse4-R37 throughout the cell cycle is detrimental to faithful chromosome segregation. Our results showed that SPOUT methyltransferase Upa1 contributes to methylation of Cse4-R37 and overexpression of UPA1 leads to CIN phenotype. In summary, our studies have defined a role for cell cycle-regulated methylation of Cse4 in high-fidelity chromosome segregation and highlight an important role of epigenetic modifications such as methylation of kinetochore proteins in preventing CIN, an important hallmark of human cancers.
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Affiliation(s)
- Prashant K. Mishra
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Wei-Chun Au
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Pedro G. Castineira
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Nazrin Ali
- Queen Mary University of London, E1 4NS, UK
| | - John Stanton
- University of North Carolina, Chapel Hill, NC 27599
| | - Lars Boeckmann
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Yoshimitsu Takahashi
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Michael Costanzo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Charles Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | | | | | - Munira A. Basrai
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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Yatskevich S, Barford D, Muir KW. Conserved and divergent mechanisms of inner kinetochore assembly onto centromeric chromatin. Curr Opin Struct Biol 2023; 81:102638. [PMID: 37343495 DOI: 10.1016/j.sbi.2023.102638] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/03/2023] [Accepted: 05/23/2023] [Indexed: 06/23/2023]
Abstract
Kinetochores are large protein complexes built on centromeric chromatin that mediate chromosome segregation. The inner kinetochore, or constitutive centromere-associated network (CCAN), assembles onto centromeres defined by centromere protein A (CENP-A) nucleosomes (CENP-ANuc), and acts as a platform for the regulated assembly of the microtubule-binding outer kinetochore. Recent cryo-EM work revealed structural conservation of CCAN, from the repeating human regional centromeres to the point centromere of budding yeast. Centromere recognition is determined mainly through engagement of duplex DNA proximal to the CENP-A nucleosome by a DNA-binding CENP-LN channel located at the core of CCAN. Additional DNA interactions formed by other CCAN modules create an enclosed DNA-binding chamber. This configuration explains how kinetochores maintain their tight grip on centromeric DNA to withstand the forces of chromosome segregation. Defining the higher-order architecture of complete kinetochore assemblies with implications for understanding the 3D organisation of regional centromeres and mechanisms of kinetochore dynamics, including how kinetochores sense and respond to tension, are important future directions.
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Affiliation(s)
- Stanislau Yatskevich
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, United Kingdom. https://twitter.com/StanislauY
| | - David Barford
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, United Kingdom.
| | - Kyle W Muir
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, United Kingdom. https://twitter.com/centromuir
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6
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Dendooven T, Zhang Z, Yang J, McLaughlin SH, Schwab J, Scheres SHW, Yatskevich S, Barford D. Cryo-EM structure of the complete inner kinetochore of the budding yeast point centromere. SCIENCE ADVANCES 2023; 9:eadg7480. [PMID: 37506202 PMCID: PMC10381965 DOI: 10.1126/sciadv.adg7480] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023]
Abstract
The point centromere of budding yeast specifies assembly of the large kinetochore complex to mediate chromatid segregation. Kinetochores comprise the centromere-associated inner kinetochore (CCAN) complex and the microtubule-binding outer kinetochore KNL1-MIS12-NDC80 (KMN) network. The budding yeast inner kinetochore also contains the DNA binding centromere-binding factor 1 (CBF1) and CBF3 complexes. We determined the cryo-electron microscopy structure of the yeast inner kinetochore assembled onto the centromere-specific centromere protein A nucleosomes (CENP-ANuc). This revealed a central CENP-ANuc with extensively unwrapped DNA ends. These free DNA duplexes bind two CCAN protomers, one of which entraps DNA topologically, positioned on the centromere DNA element I (CDEI) motif by CBF1. The two CCAN protomers are linked through CBF3 forming an arch-like configuration. With a structural mechanism for how CENP-ANuc can also be linked to KMN involving only CENP-QU, we present a model for inner kinetochore assembly onto a point centromere and how it organizes the outer kinetochore for chromosome attachment to the mitotic spindle.
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Affiliation(s)
| | | | - Jing Yang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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Sridhar S, Fukagawa T. Kinetochore Architecture Employs Diverse Linker Strategies Across Evolution. Front Cell Dev Biol 2022; 10:862637. [PMID: 35800888 PMCID: PMC9252888 DOI: 10.3389/fcell.2022.862637] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/23/2022] [Indexed: 01/09/2023] Open
Abstract
The assembly of a functional kinetochore on centromeric chromatin is necessary to connect chromosomes to the mitotic spindle, ensuring accurate chromosome segregation. This connecting function of the kinetochore presents multiple internal and external structural challenges. A microtubule interacting outer kinetochore and centromeric chromatin interacting inner kinetochore effectively confront forces from the external spindle and centromere, respectively. While internally, special inner kinetochore proteins, defined as “linkers,” simultaneously interact with centromeric chromatin and the outer kinetochore to enable association with the mitotic spindle. With the ability to simultaneously interact with outer kinetochore components and centromeric chromatin, linker proteins such as centromere protein (CENP)-C or CENP-T in vertebrates and, additionally CENP-QOkp1-UAme1 in yeasts, also perform the function of force propagation within the kinetochore. Recent efforts have revealed an array of linker pathways strategies to effectively recruit the largely conserved outer kinetochore. In this review, we examine these linkages used to propagate force and recruit the outer kinetochore across evolution. Further, we look at their known regulatory pathways and implications on kinetochore structural diversity and plasticity.
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8
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Shukla S, Agarwal P, Kumar A. Disordered regions tune order in chromatin organization and function. Biophys Chem 2022; 281:106716. [PMID: 34844028 DOI: 10.1016/j.bpc.2021.106716] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/10/2021] [Accepted: 11/10/2021] [Indexed: 12/29/2022]
Abstract
Intrinsically disordered proteins or hybrid proteins with ordered domains and disordered regions (both collectively designated as IDP(R)s) defy the well-established structure-function paradigm due to their ability to perform multiple biological functions even in the absence of a well-defined 3D structure. IDP(R)s have a unique ability to exist as a functional heterogeneous ensemble, where they adopt multiple thermodynamically stable conformations with low energy barriers between states. The resultant structural plasticity or conformational adaptability provides them with a high functional diversity and ease of regulation. Hence, IDP(R)s are highly efficient biological machinery to mediate intricate cellular functions such as signaling, gene expression, and assembly of complex structures. One such structure is the nucleoprotein complex known as Chromatin. Interestingly, the proteins involved in shaping up the structure and function of chromatin are abundant in disordered regions, which serve more than just as mere flexible linkers. The disordered regions are involved in crucial processes such as gene expression regulation, chromatin architecture maintenance, and liquid-liquid phase separation initiation. This review is an attempt to explore the advantages and the functional and regulatory roles of intrinsic disorder in several Chromatin Associated Proteins from a mechanistic standpoint.
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Affiliation(s)
- Shivangi Shukla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Prakhar Agarwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Ashutosh Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
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9
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Böhm M, Killinger K, Dudziak A, Pant P, Jänen K, Hohoff S, Mechtler K, Örd M, Loog M, Sanchez-Garcia E, Westermann S. Cdc4 phospho-degrons allow differential regulation of Ame1 CENP-U protein stability across the cell cycle. eLife 2021; 10:67390. [PMID: 34308839 PMCID: PMC8341979 DOI: 10.7554/elife.67390] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 07/24/2021] [Indexed: 02/05/2023] Open
Abstract
Kinetochores are multi-subunit protein assemblies that link chromosomes to microtubules of the mitotic and meiotic spindle. It is still poorly understood how efficient, centromere-dependent kinetochore assembly is accomplished from hundreds of individual protein building blocks in a cell cycle-dependent manner. Here, by combining comprehensive phosphorylation analysis of native Ctf19CCAN subunits with biochemical and functional assays in the model system budding yeast, we demonstrate that Cdk1 phosphorylation activates phospho-degrons on the essential subunit Ame1CENP-U, which are recognized by the E3 ubiquitin ligase complex SCF-Cdc4. Gradual phosphorylation of degron motifs culminates in M-phase and targets the protein for degradation. Binding of the Mtw1Mis12 complex shields the proximal phospho-degron, protecting kinetochore-bound Ame1 from the degradation machinery. Artificially increasing degron strength partially suppresses the temperature sensitivity of a cdc4 mutant, while overexpression of Ame1-Okp1 is toxic in SCF mutants, demonstrating the physiological importance of this mechanism. We propose that phospho-regulated clearance of excess CCAN subunits facilitates efficient centromere-dependent kinetochore assembly. Our results suggest a novel strategy for how phospho-degrons can be used to regulate the assembly of multi-subunit complexes.
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Affiliation(s)
- Miriam Böhm
- Department of Molecular Genetics I, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Kerstin Killinger
- Department of Molecular Genetics I, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Alexander Dudziak
- Department of Molecular Genetics I, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Pradeep Pant
- Department of Computational Biochemistry, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Karolin Jänen
- Department of Molecular Genetics I, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Simone Hohoff
- Department of Molecular Genetics I, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Karl Mechtler
- IMP - Research Institute of Molecular Pathology, Vienna, Austria.,Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria.,Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Mihkel Örd
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Mart Loog
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Elsa Sanchez-Garcia
- Department of Computational Biochemistry, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Stefan Westermann
- Department of Molecular Genetics I, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
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10
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Cao B, Zhao C, Zhang Y, Wang X, Ye J, Hu L, He X. The novel interaction mode among centromere sub-complex CENP-O/P/U/Q/R. J Mol Recognit 2021; 34:e2892. [PMID: 33660361 DOI: 10.1002/jmr.2892] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 01/22/2021] [Accepted: 01/28/2021] [Indexed: 01/31/2023]
Abstract
The kinetochore is essential for the accurate segregation of sister chromosome in the eukaryote cell. Among the kinetochore subunits, five proteins CENP-O/P/U/Q/R form a stable complex, referred to as CENP-O class, and are required for proper kinetochore function. Although the function and structure of yeast COMA complex (CENP-O/P/U/Q homologs) have been revealed extensively, the assembly mechanism and detail interactions among human CENP-O class are significantly different and remain largely unclear. Here, we identified the fragment (residues 241-360) of CENP-U and the C-terminal half of CENP-Q are essential to form a hetero-complex and interact with CENP-O/P sub-complex in vitro. We for the first time showed that CENP-R does not directly interact with CENP-O/P in vitro, but indeed interact with CENP-U and CENP-Q. Furthermore, both the N- and C-terminus of CENP-R are required for the interaction with CENP-U and CENP-Q. Our research pinpointed a novel interaction pattern that might shed light on the assembly mechanism of vertebrate CENP-O class.
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Affiliation(s)
- Beibei Cao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Congcong Zhao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyu Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jingjing Ye
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Liqiao Hu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaojing He
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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11
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The Proteomic Landscape of Centromeric Chromatin Reveals an Essential Role for the Ctf19 CCAN Complex in Meiotic Kinetochore Assembly. Curr Biol 2021; 31:283-296.e7. [PMID: 33157029 PMCID: PMC7846277 DOI: 10.1016/j.cub.2020.10.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/10/2020] [Accepted: 10/08/2020] [Indexed: 11/23/2022]
Abstract
Kinetochores direct chromosome segregation in mitosis and meiosis. Faithful gamete formation through meiosis requires that kinetochores take on new functions that impact homolog pairing, recombination, and the orientation of kinetochore attachment to microtubules in meiosis I. Using an unbiased proteomics pipeline, we determined the composition of centromeric chromatin and kinetochores at distinct cell-cycle stages, revealing extensive reorganization of kinetochores during meiosis. The data uncover a network of meiotic chromosome axis and recombination proteins that bind to centromeres in the absence of the microtubule-binding outer kinetochore sub-complexes during meiotic prophase. We show that the Ctf19cCCAN inner kinetochore complex is essential for kinetochore organization in meiosis. Our functional analyses identify a Ctf19cCCAN-dependent kinetochore assembly pathway that is dispensable for mitotic growth but becomes critical upon meiotic entry. Therefore, changes in kinetochore composition and a distinct assembly pathway specialize meiotic kinetochores for successful gametogenesis. The composition of meiotic centromeres and kinetochores is revealed Kinetochores undergo extensive changes between meiotic prophase I and metaphase I The Ctf19CCAN orchestrates meiotic kinetochore specialization A Ctf19CCAN-directed kinetochore assembly pathway is uniquely critical in meiosis
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12
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Abstract
The kinetochore is a complex structure whose function is absolutely essential. Unlike the centromere, the kinetochore at first appeared remarkably well conserved from yeast to humans, especially the microtubule-binding outer kinetochore. However, recent efforts towards biochemical reconstitution of diverse kinetochores challenge the notion of a similarly conserved architecture for the constitutively centromere-associated network of the inner kinetochore. This review briefly summarizes the evidence from comparative genomics for interspecific variability in inner kinetochore composition and focuses on novel biochemical evidence indicating that even homologous inner kinetochore protein complexes are put to different uses in different organisms.
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Affiliation(s)
- G E Hamilton
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - T N Davis
- Department of Biochemistry, University of Washington, Seattle, WA, USA
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13
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Zhang Z, Bellini D, Barford D. Crystal structure of the Cenp-HIKHead-TW sub-module of the inner kinetochore CCAN complex. Nucleic Acids Res 2020; 48:11172-11184. [PMID: 32976599 PMCID: PMC7641736 DOI: 10.1093/nar/gkaa772] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/31/2020] [Accepted: 09/11/2020] [Indexed: 11/12/2022] Open
Abstract
Kinetochores are large multi-subunit complexes that attach centromeric chromatin to microtubules of the mitotic spindle, enabling sister chromatid segregation in mitosis. The inner kinetochore constitutive centromere associated network (CCAN) complex assembles onto the centromere-specific Cenp-A nucleosome (Cenp-ANuc), thereby coupling the centromere to the microtubule-binding outer kinetochore. CCAN is a conserved 14-16 subunit complex composed of discrete modules. Here, we determined the crystal structure of the Saccharomyces cerevisiae Cenp-HIKHead-TW sub-module, revealing how Cenp-HIK and Cenp-TW interact at the conserved Cenp-HIKHead-Cenp-TW interface. A major interface is formed by the C-terminal anti-parallel α-helices of the histone fold extension (HFE) of the Cenp-T histone fold domain (HFD) combining with α-helix H3 of Cenp-K to create a compact three α-helical bundle. We fitted the Cenp-HIKHead-TW sub-module to the previously determined cryo-EM map of the S. cerevisiae CCAN-Cenp-ANuc complex. This showed that the HEAT repeat domain of Cenp-IHead and C-terminal HFD of Cenp-T of the Cenp-HIKHead-TW sub-module interact with the nucleosome DNA gyre at a site close to the Cenp-ANuc dyad axis. Our structure provides a framework for understanding how Cenp-T links centromeric Cenp-ANuc to the outer kinetochore through its HFD and N-terminal Ndc80-binding motif, respectively.
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Affiliation(s)
- Ziguo Zhang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Dom Bellini
- 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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14
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Ghodgaonkar-Steger M, Potocnjak M, Zimniak T, Fischböck-Halwachs J, Solis-Mezarino V, Singh S, Speljko T, Hagemann G, Drexler DJ, Witte G, Herzog F. C-Terminal Motifs of the MTW1 Complex Cooperatively Stabilize Outer Kinetochore Assembly in Budding Yeast. Cell Rep 2020; 32:108190. [PMID: 32997987 DOI: 10.1016/j.celrep.2020.108190] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 07/18/2020] [Accepted: 09/01/2020] [Indexed: 12/01/2022] Open
Abstract
Kinetochores are macromolecular protein assemblies at centromeres that mediate accurate chromosome segregation during cell division. The outer kinetochore KNL1SPC105, MIS12MTW1, and NDC80NDC80 complexes assemble the KMN network, which harbors the sites of microtubule binding and spindle assembly checkpoint signaling. The buildup of the KMN network that transmits microtubule pulling forces to budding yeast point centromeres is poorly understood. Here, we identify 225 inter-protein crosslinks by mass spectrometry on KMN complexes isolated from Saccharomyces cerevisiae that delineate the KMN subunit connectivity for outer kinetochore assembly. C-Terminal motifs of Nsl1 and Mtw1 recruit the SPC105 complex through Kre28, and both motifs aid tethering of the NDC80 complex by the previously reported Dsn1 C terminus. We show that a hub of three C-terminal MTW1 subunit motifs mediates the cooperative stabilization of the KMN network, which is augmented by a direct NDC80-SPC105 association.
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Affiliation(s)
- Medini Ghodgaonkar-Steger
- Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Mia Potocnjak
- Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Tomasz Zimniak
- Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Josef Fischböck-Halwachs
- Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Victor Solis-Mezarino
- Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Sylvia Singh
- Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Tea Speljko
- Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Götz Hagemann
- Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - David Jan Drexler
- Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Gregor Witte
- Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Franz Herzog
- Gene Center Munich and Department of Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Str. 25, 81377 Munich, Germany.
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15
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Hinshaw SM, Harrison SC. The Structural Basis for Kinetochore Stabilization by Cnn1/CENP-T. Curr Biol 2020; 30:3425-3431.e3. [DOI: 10.1016/j.cub.2020.06.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 12/22/2022]
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16
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Petty EL, Pillus L. Cell cycle roles for GCN5 revealed through genetic suppression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194625. [PMID: 32798737 DOI: 10.1016/j.bbagrm.2020.194625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 08/11/2020] [Accepted: 08/11/2020] [Indexed: 11/17/2022]
Abstract
The conserved acetyltransferase Gcn5 is a member of several complexes in eukaryotic cells, playing roles in regulating chromatin organization, gene expression, metabolism, and cell growth and differentiation via acetylation of both nuclear and cytoplasmic proteins. Distinct functions of Gcn5 have been revealed through a combination of biochemical and genetic approaches in many in vitro studies and model organisms. In this review, we focus on the unique insights that have been gleaned from suppressor studies of gcn5 phenotypes in the budding yeast Saccharomyces cerevisiae. Such studies were fundamental in the early understanding of the balance of counteracting chromatin activities in regulating transcription. Most recently, suppressor screens have revealed roles for Gcn5 in early cell cycle (G1 to S) gene expression and regulation of chromosome segregation during mitosis. Much has been learned, but many questions remain which will be informed by focused analysis of additional genetic and physical interactions.
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Affiliation(s)
- Emily L Petty
- University of California, San Diego, Division of Biological Sciences, Section of Molecular Biology, UCSD Moores Cancer Center, United States of America.
| | - Lorraine Pillus
- University of California, San Diego, Division of Biological Sciences, Section of Molecular Biology, UCSD Moores Cancer Center, United States of America.
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17
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Ólafsson G, Thorpe PH. Polo kinase recruitment via the constitutive centromere-associated network at the kinetochore elevates centromeric RNA. PLoS Genet 2020; 16:e1008990. [PMID: 32810142 PMCID: PMC7455000 DOI: 10.1371/journal.pgen.1008990] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 08/28/2020] [Accepted: 07/13/2020] [Indexed: 12/23/2022] Open
Abstract
The kinetochore, a multi-protein complex assembled on centromeres, is essential to segregate chromosomes during cell division. Deficiencies in kinetochore function can lead to chromosomal instability and aneuploidy-a hallmark of cancer cells. Kinetochore function is controlled by recruitment of regulatory proteins, many of which have been documented, however their function often remains uncharacterized and many are yet to be identified. To identify candidates of kinetochore regulation we used a proteome-wide protein association strategy in budding yeast and detected many proteins that are involved in post-translational modifications such as kinases, phosphatases and histone modifiers. We focused on the Polo-like kinase, Cdc5, and interrogated which cellular components were sensitive to constitutive Cdc5 localization. The kinetochore is particularly sensitive to constitutive Cdc5 kinase activity. Targeting Cdc5 to different kinetochore subcomplexes produced diverse phenotypes, consistent with multiple distinct functions at the kinetochore. We show that targeting Cdc5 to the inner kinetochore, the constitutive centromere-associated network (CCAN), increases the levels of centromeric RNA via an SPT4 dependent mechanism.
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Affiliation(s)
- Guðjón Ólafsson
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, United Kingdom
| | - Peter H. Thorpe
- School of Biological and Chemical Sciences, Queen Mary, University of London, London, United Kingdom
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18
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Killinger K, Böhm M, Steinbach P, Hagemann G, Blüggel M, Jänen K, Hohoff S, Bayer P, Herzog F, Westermann S. Auto-inhibition of Mif2/CENP-C ensures centromere-dependent kinetochore assembly in budding yeast. EMBO J 2020; 39:e102938. [PMID: 32515113 PMCID: PMC7360964 DOI: 10.15252/embj.2019102938] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 04/27/2020] [Accepted: 05/12/2020] [Indexed: 11/28/2022] Open
Abstract
Kinetochores are chromatin‐bound multi‐protein complexes that allow high‐fidelity chromosome segregation during mitosis and meiosis. Kinetochore assembly is exclusively initiated at chromatin containing Cse4/CENP‐A nucleosomes. The molecular mechanisms ensuring that subcomplexes assemble efficiently into kinetochores only at centromeres, but not anywhere else, are incompletely understood. Here, we combine biochemical and genetic experiments to demonstrate that auto‐inhibition of the conserved kinetochore subunit Mif2/CENP‐C contributes to preventing unscheduled kinetochore assembly in budding yeast cells. We show that wild‐type Mif2 is attenuated in its ability to bind a key downstream component in the assembly pathway, the Mtw1 complex, and that addition of Cse4 nucleosomes overcomes this inhibition. By exchanging the N‐terminus of Mif2 with its functional counterpart from Ame1/CENP‐U, we have created a Mif2 mutant which bypasses the Cse4 requirement for Mtw1 binding in vitro, thereby shortcutting kinetochore assembly. Expression of this Mif2 mutant in cells leads to mis‐localization of the Mtw1 complex and causes pronounced chromosome segregation defects. We propose that auto‐inhibition of Mif2/CENP‐C constitutes a key concept underlying the molecular logic of kinetochore assembly.
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Affiliation(s)
- Kerstin Killinger
- Department of Molecular Genetics, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Miriam Böhm
- Department of Molecular Genetics, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Philine Steinbach
- Department of Molecular Genetics, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Götz Hagemann
- Department of Biochemistry, Gene Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Mike Blüggel
- Structural and Medicinal Biochemistry, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Karolin Jänen
- Department of Molecular Genetics, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Simone Hohoff
- Department of Molecular Genetics, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Peter Bayer
- Structural and Medicinal Biochemistry, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Franz Herzog
- Department of Biochemistry, Gene Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Stefan Westermann
- Department of Molecular Genetics, Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen, Germany
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19
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Hamilton GE, Helgeson LA, Noland CL, Asbury CL, Dimitrova YN, Davis TN. Reconstitution reveals two paths of force transmission through the kinetochore. eLife 2020; 9:56582. [PMID: 32406818 PMCID: PMC7367685 DOI: 10.7554/elife.56582] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/13/2020] [Indexed: 01/23/2023] Open
Abstract
Partitioning duplicated chromosomes equally between daughter cells is a microtubule-mediated process essential to eukaryotic life. A multi-protein machine, the kinetochore, drives chromosome segregation by coupling the chromosomes to dynamic microtubule tips, even as the tips grow and shrink through the gain and loss of subunits. The kinetochore must harness, transmit, and sense mitotic forces, as a lack of tension signals incorrect chromosome-microtubule attachment and precipitates error correction mechanisms. But though the field has arrived at a ‘parts list’ of dozens of kinetochore proteins organized into subcomplexes, the path of force transmission through these components has remained unclear. Here we report reconstitution of functional Saccharomyces cerevisiae kinetochore assemblies from recombinantly expressed proteins. The reconstituted kinetochores are capable of self-assembling in vitro, coupling centromeric nucleosomes to dynamic microtubules, and withstanding mitotically relevant forces. They reveal two distinct pathways of force transmission and Ndc80c recruitment.
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Affiliation(s)
- Grace E Hamilton
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Luke A Helgeson
- Department of Biochemistry, University of Washington, Seattle, United States
| | - Cameron L Noland
- Department of Structural Biology, Genentech Inc, South San Francisco, United States
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, United States
| | - Yoana N Dimitrova
- Department of Structural Biology, Genentech Inc, South San Francisco, United States
| | - Trisha N Davis
- Department of Biochemistry, University of Washington, Seattle, United States
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20
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Migl D, Kschonsak M, Arthur CP, Khin Y, Harrison SC, Ciferri C, Dimitrova YN. Cryoelectron Microscopy Structure of a Yeast Centromeric Nucleosome at 2.7 Å Resolution. Structure 2020; 28:363-370.e3. [PMID: 32004465 PMCID: PMC7166091 DOI: 10.1016/j.str.2019.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 10/17/2019] [Accepted: 12/02/2019] [Indexed: 12/21/2022]
Abstract
Kinetochores mediate chromosome segregation during cell division. They assemble on centromeric nucleosomes and capture spindle microtubules. In budding yeast, a kinetochore links a single nucleosome, containing the histone variant Cse4CENP-A instead of H3, with a single microtubule. Conservation of most kinetochore components from yeast to metazoans suggests that the yeast kinetochore represents a module of the more complex metazoan arrangements. We describe here a streamlined protocol for reconstituting a yeast centromeric nucleosome and a systematic exploration of cryo-grid preparation. These developments allowed us to obtain a high-resolution cryoelectron microscopy reconstruction. As suggested by previous work, fewer base pairs are in tight association with the histone octamer than there are in canonical nucleosomes. Weak binding of the end DNA sequences may contribute to specific recognition by other inner kinetochore components. The centromeric nucleosome structure and the strategies we describe will facilitate studies of many other aspects of kinetochore assembly and chromatin biochemistry.
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Affiliation(s)
- David Migl
- Harvard Medical School, Boston, MA 02115, USA; Biophysics Program, Harvard University, Boston, MA 02115, USA
| | - Marc Kschonsak
- Structural Biology, Genentech, South San Francisco, CA, USA
| | | | - Yadana Khin
- Harvard Medical School, Boston, MA 02115, USA
| | - Stephen C Harrison
- Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA.
| | - Claudio Ciferri
- Structural Biology, Genentech, South San Francisco, CA, USA.
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21
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The ATAD2/ANCCA homolog Yta7 cooperates with Scm3 HJURP to deposit Cse4 CENP-A at the centromere in yeast. Proc Natl Acad Sci U S A 2020; 117:5386-5393. [PMID: 32079723 DOI: 10.1073/pnas.1917814117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The AAA+ ATPase and bromodomain factor ATAD2/ANCCA is overexpressed in many types of cancer, but how it contributes to tumorigenesis is not understood. Here, we report that the Saccharomyces cerevisiae homolog Yta7ATAD2 is a deposition factor for the centromeric histone H3 variant Cse4CENP-A at the centromere in yeast. Yta7ATAD2 regulates the levels of centromeric Cse4CENP-A in that yta7∆ causes reduced Cse4CENP-A deposition, whereas YTA7 overexpression causes increased Cse4CENP-A deposition. Yta7ATAD2 coimmunoprecipitates with Cse4CENP-A and is associated with the centromere, arguing for a direct role of Yta7ATAD2 in Cse4CENP-A deposition. Furthermore, increasing centromeric Cse4CENP-A levels by YTA7 overexpression requires the activity of Scm3HJURP, the centromeric nucleosome assembly factor. Importantly, Yta7ATAD2 interacts in vivo with Scm3HJURP, indicating that Yta7ATAD2 is a cochaperone for Scm3HJURP The absence of Yta7 causes defects in growth and chromosome segregation with mutations in components of the inner kinetochore (CTF19/CCAN, Mif2CENP-C, Cbf1). Since Yta7ATAD2 is an AAA+ ATPase and potential hexameric unfoldase, our results suggest that it may unfold the Cse4CENP-A histone and hand it over to Scm3HJURP for subsequent deposition in the centromeric nucleosome. Furthermore, our findings suggest that ATAD2 overexpression may enhance malignant transformation in humans by misregulating centromeric CENP-A levels, thus leading to defects in kinetochore assembly and chromosome segregation.
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22
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Lawrimore J, Doshi A, Walker B, Bloom K. AI-Assisted Forward Modeling of Biological Structures. Front Cell Dev Biol 2019; 7:279. [PMID: 31799251 PMCID: PMC6868055 DOI: 10.3389/fcell.2019.00279] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/30/2019] [Indexed: 01/01/2023] Open
Abstract
The rise of machine learning and deep learning technologies have allowed researchers to automate image classification. We describe a method that incorporates automated image classification and principal component analysis to evaluate computational models of biological structures. We use a computational model of the kinetochore to demonstrate our artificial-intelligence (AI)-assisted modeling method. The kinetochore is a large protein complex that connects chromosomes to the mitotic spindle to facilitate proper cell division. The kinetochore can be divided into two regions: the inner kinetochore, including proteins that interact with DNA; and the outer kinetochore, comprised of microtubule-binding proteins. These two kinetochore regions have been shown to have different distributions during metaphase in live budding yeast and therefore act as a test case for our forward modeling technique. We find that a simple convolutional neural net (CNN) can correctly classify fluorescent images of inner and outer kinetochore proteins and show a CNN trained on simulated, fluorescent images can detect difference in experimental images. A polymer model of the ribosomal DNA locus serves as a second test for the method. The nucleolus surrounds the ribosomal DNA locus and appears amorphous in live-cell, fluorescent microscopy experiments in budding yeast, making detection of morphological changes challenging. We show a simple CNN can detect subtle differences in simulated images of the ribosomal DNA locus, demonstrating our CNN-based classification technique can be used on a variety of biological structures.
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Affiliation(s)
- Josh Lawrimore
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Ayush Doshi
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Benjamin Walker
- Department of Mathematics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Kerry Bloom
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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23
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Yan K, Yang J, Zhang Z, McLaughlin SH, Chang L, Fasci D, Ehrenhofer-Murray AE, Heck AJR, Barford D. Structure of the inner kinetochore CCAN complex assembled onto a centromeric nucleosome. Nature 2019; 574:278-282. [PMID: 31578520 PMCID: PMC6859074 DOI: 10.1038/s41586-019-1609-1] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 09/04/2019] [Indexed: 12/21/2022]
Abstract
In eukaryotes, accurate chromosome segregation in mitosis and meiosis maintains genome stability and prevents aneuploidy. Kinetochores are large protein complexes that, by assembling onto specialized Cenp-A nucleosomes1,2, function to connect centromeric chromatin to microtubules of the mitotic spindle3,4. Whereas the centromeres of vertebrate chromosomes comprise millions of DNA base pairs and attach to multiple microtubules, the simple point centromeres of budding yeast are connected to individual microtubules5,6. All 16 budding yeast chromosomes assemble complete kinetochores using a single Cenp-A nucleosome (Cenp-ANuc), each of which is perfectly centred on its cognate centromere7-9. The inner and outer kinetochore modules are responsible for interacting with centromeric chromatin and microtubules, respectively. Here we describe the cryo-electron microscopy structure of the Saccharomyces cerevisiae inner kinetochore module, the constitutive centromere associated network (CCAN) complex, assembled onto a Cenp-A nucleosome (CCAN-Cenp-ANuc). The structure explains the interdependency of the constituent subcomplexes of CCAN and shows how the Y-shaped opening of CCAN accommodates Cenp-ANuc to enable specific CCAN subunits to contact the nucleosomal DNA and histone subunits. Interactions with the unwrapped DNA duplex at the two termini of Cenp-ANuc are mediated predominantly by a DNA-binding groove in the Cenp-L-Cenp-N subcomplex. Disruption of these interactions impairs assembly of CCAN onto Cenp-ANuc. Our data indicate a mechanism of Cenp-A nucleosome recognition by CCAN and how CCAN acts as a platform for assembly of the outer kinetochore to link centromeres to the mitotic spindle for chromosome segregation.
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Affiliation(s)
- Kaige Yan
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Jing Yang
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Ziguo Zhang
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | - Leifu Chang
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Domenico Fasci
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
| | | | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Utrecht, The Netherlands
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24
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Fischböck-Halwachs J, Singh S, Potocnjak M, Hagemann G, Solis-Mezarino V, Woike S, Ghodgaonkar-Steger M, Weissmann F, Gallego LD, Rojas J, Andreani J, Köhler A, Herzog F. The COMA complex interacts with Cse4 and positions Sli15/Ipl1 at the budding yeast inner kinetochore. eLife 2019; 8:42879. [PMID: 31112132 PMCID: PMC6546395 DOI: 10.7554/elife.42879] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 05/20/2019] [Indexed: 01/14/2023] Open
Abstract
Kinetochores are macromolecular protein complexes at centromeres that ensure accurate chromosome segregation by attaching chromosomes to spindle microtubules and integrating safeguard mechanisms. The inner kinetochore is assembled on CENP-A nucleosomes and has been implicated in establishing a kinetochore-associated pool of Aurora B kinase, a chromosomal passenger complex (CPC) subunit, which is essential for chromosome biorientation. By performing crosslink-guided in vitro reconstitution of budding yeast kinetochore complexes we showed that the Ame1/Okp1CENP-U/Q heterodimer, which forms the COMA complex with Ctf19/Mcm21CENP-P/O, selectively bound Cse4CENP-A nucleosomes through the Cse4 N-terminus. The Sli15/Ipl1INCENP/Aurora-B core-CPC interacted with COMA in vitro through the Ctf19 C-terminus whose deletion affected chromosome segregation fidelity in Sli15 wild-type cells. Tethering Sli15 to Ame1/Okp1 rescued synthetic lethality upon Ctf19 depletion in a Sli15 centromere-targeting deficient mutant. This study shows molecular characteristics of the point-centromere kinetochore architecture and suggests a role for the Ctf19 C-terminus in mediating CPC-binding and accurate chromosome segregation.
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Affiliation(s)
- Josef Fischböck-Halwachs
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sylvia Singh
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Mia Potocnjak
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Götz Hagemann
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Victor Solis-Mezarino
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Stephan Woike
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Medini Ghodgaonkar-Steger
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Florian Weissmann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Laura D Gallego
- Max F Perutz Laboratories, Medical University of Vienna, Vienna, Austria
| | - Julie Rojas
- Laboratory of Chromosome Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jessica Andreani
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Alwin Köhler
- Max F Perutz Laboratories, Medical University of Vienna, Vienna, Austria
| | - Franz Herzog
- Gene Center Munich, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
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25
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Hara M, Fukagawa T. Where is the right path heading from the centromere to spindle microtubules? Cell Cycle 2019; 18:1199-1211. [PMID: 31075048 DOI: 10.1080/15384101.2019.1617008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
The kinetochore is a large protein complex that ensures accurate chromosome segregation during mitosis by connecting the centromere and spindle microtubules. One of the kinetochore sub-complexes, the constitutive centromere-associated network (CCAN), associates with the centromere and recruits another sub-complex, the KMN (KNL1, Mis12, and Ndc80 complexes) network (KMN), which binds to spindle microtubules. The CCAN-KMN interaction is mediated by two parallel pathways (CENP-C- and CENP-T-pathways) in the kinetochore, which bridge the centromere and microtubules. Here, we discuss dynamic protein-interaction changes in the two pathways that couple the centromere with spindle microtubules during mitotic progression.
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Affiliation(s)
- Masatoshi Hara
- a Graduate School of Frontier Biosciences , Osaka University , Suita , Japan
| | - Tatsuo Fukagawa
- a Graduate School of Frontier Biosciences , Osaka University , Suita , Japan
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26
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Hamilton G, Dimitrova Y, Davis TN. Seeing is believing: our evolving view of kinetochore structure, composition, and assembly. Curr Opin Cell Biol 2019; 60:44-52. [PMID: 31078123 DOI: 10.1016/j.ceb.2019.03.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/20/2019] [Accepted: 03/28/2019] [Indexed: 11/26/2022]
Abstract
This review highlights three recent trends in the field of kinetochore biology: the proliferation of structural data for kinetochore protein complexes (including CBF3, Dam1c, Mis12cMIND, and CENP-NLChl4/Iml3); the growing consensus that the kinetochore is a dynamic structure whose composition changes as the cell cycle progresses; and the mounting evidence of multiple pathways whereby the microtubule-binding elements of the outer kinetochore may be recruited by inner kinetochore proteins. Our focus is on the two best-studied systems in the field: human and budding yeast kinetochores. This review will demonstrate the remarkable similarity of these two systems, as well as their intriguing differences.
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Affiliation(s)
- Grace Hamilton
- Department of Biochemistry, University of Washington Box 357350, 1705 NE Pacific St., Seattle, WA 98195-7350, USA
| | - Yoana Dimitrova
- Genentech, Inc., 1 DNA Way, MS: 27, South San Francisco, CA 94080, USA
| | - Trisha N Davis
- Department of Biochemistry, University of Washington Box 357350, 1705 NE Pacific St., Seattle, WA 98195-7350, USA.
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27
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Hinshaw SM, Harrison SC. The structure of the Ctf19c/CCAN from budding yeast. eLife 2019; 8:44239. [PMID: 30762520 PMCID: PMC6407923 DOI: 10.7554/elife.44239] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 02/13/2019] [Indexed: 12/29/2022] Open
Abstract
Eukaryotic kinetochores connect spindlemicrotubules to chromosomal centromeres. A group of proteins called the Ctf19 complex (Ctf19c) in yeast and the constitutive centromere associated network (CCAN) in other organisms creates the foundation of a kinetochore. The Ctf19c/CCAN influences the timing of kinetochore assembly, sets its location by associating with a specialized nucleosome containing the histone H3 variant Cse4/CENP-A, and determines the organization of the microtubule attachment apparatus. We present here the structure of a reconstituted 13-subunit Ctf19c determined by cryo-electron microscopy at ~4 Å resolution. The structure accounts for known and inferred contacts with the Cse4 nucleosome and for an observed assembly hierarchy. We describe its implications for establishment of kinetochores and for their regulation by kinases throughout the cell cycle.
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Affiliation(s)
- Stephen M Hinshaw
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Howard Hughes Medical Institute, Boston, United States
| | - Stephen C Harrison
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Howard Hughes Medical Institute, Boston, United States
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