1
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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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2
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Som S, Paul R. Mechanistic model for nuclear migration in hyphae during mitosis. Phys Rev E 2023; 108:014401. [PMID: 37583222 DOI: 10.1103/physreve.108.014401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/13/2023] [Indexed: 08/17/2023]
Abstract
Saccharomyces cerevisiae and Candida albicans, the two well-known human pathogens, can be found in all three morphologies, i.e., yeast, pseudohyphae, and true hyphae. The cylindrical daughter-bud (germ tube) grows very long for true hyphae, and the cell cycle is delayed compared to the other two morphologies. The place of the nuclear division is specific for true hyphae determined by the position of the septin ring. However, the septin ring can localize anywhere inside the germ tube, unlike the mother-bud junction in budding yeast. Since the nucleus often migrates a long path in the hyphae, the underlying mechanism must be robust for executing mitosis in a timely manner. We explore the mechanism of nuclear migration through hyphae in light of mechanical interactions between astral microtubules and the cell cortex. We report that proper migration through constricted hyphae requires a large dynein pull applied on the astral microtubules from the hyphal cortex. This is achieved when the microtubules frequently slide along the hyphal cortex so that a large population of dyneins actively participate, pulling on them. Simulation shows timely migration when the dyneins from the mother cortex do not participate in pulling on the microtubules. These findings are robust for long migration and positioning of the nucleus in the germ tube at the septin ring.
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Affiliation(s)
- Subhendu Som
- Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Raja Paul
- Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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3
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Virant D, Vojnovic I, Winkelmeier J, Endesfelder M, Turkowyd B, Lando D, Endesfelder U. Unraveling the kinetochore nanostructure in Schizosaccharomyces pombe using multi-color SMLM imaging. J Cell Biol 2023; 222:213836. [PMID: 36705602 PMCID: PMC9930162 DOI: 10.1083/jcb.202209096] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 01/28/2023] Open
Abstract
The key to ensuring proper chromosome segregation during mitosis is the kinetochore (KT), a tightly regulated multiprotein complex that links the centromeric chromatin to the spindle microtubules and as such leads the segregation process. Understanding its architecture, function, and regulation is therefore essential. However, due to its complexity and dynamics, only its individual subcomplexes could be studied in structural detail so far. In this study, we construct a nanometer-precise in situ map of the human-like regional KT of Schizosaccharomyces pombe using multi-color single-molecule localization microscopy. We measure each protein of interest (POI) in conjunction with two references, cnp1CENP-A at the centromere and sad1 at the spindle pole. This allows us to determine cell cycle and mitotic plane, and to visualize individual centromere regions separately. We determine protein distances within the complex using Bayesian inference, establish the stoichiometry of each POI and, consequently, build an in situ KT model with unprecedented precision, providing new insights into the architecture.
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Affiliation(s)
- David Virant
- https://ror.org/05r7n9c40Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiologyand LOEWE Center for Synthetic Microbiology, Marburg, Germany
| | - Ilijana Vojnovic
- https://ror.org/05r7n9c40Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiologyand LOEWE Center for Synthetic Microbiology, Marburg, Germany,Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA,Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Jannik Winkelmeier
- https://ror.org/05r7n9c40Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiologyand LOEWE Center for Synthetic Microbiology, Marburg, Germany,Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA,Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Marc Endesfelder
- https://ror.org/05591te55Institute for Assyriology and Hittitology, Ludwig-Maximilians-Universität München, München, Germany
| | - Bartosz Turkowyd
- https://ror.org/05r7n9c40Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiologyand LOEWE Center for Synthetic Microbiology, Marburg, Germany,Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA,Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - David Lando
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Ulrike Endesfelder
- https://ror.org/05r7n9c40Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiologyand LOEWE Center for Synthetic Microbiology, Marburg, Germany,Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA,Institute for Microbiology and Biotechnology, Rheinische-Friedrich-Wilhelms-Universität Bonn, Bonn, Germany,Correspondence to Ulrike Endesfelder:
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4
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Cieslinski K, Wu YL, Nechyporenko L, Hörner SJ, Conti D, Skruzny M, Ries J. Nanoscale structural organization and stoichiometry of the budding yeast kinetochore. J Cell Biol 2023; 222:213833. [PMID: 36705601 PMCID: PMC9929930 DOI: 10.1083/jcb.202209094] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/16/2022] [Accepted: 12/27/2022] [Indexed: 01/28/2023] Open
Abstract
Proper chromosome segregation is crucial for cell division. In eukaryotes, this is achieved by the kinetochore, an evolutionarily conserved multiprotein complex that physically links the DNA to spindle microtubules and takes an active role in monitoring and correcting erroneous spindle-chromosome attachments. Our mechanistic understanding of these functions and how they ensure an error-free outcome of mitosis is still limited, partly because we lack a complete understanding of the kinetochore structure in the cell. In this study, we use single-molecule localization microscopy to visualize individual kinetochore complexes in situ in budding yeast. For major kinetochore proteins, we measured their abundance and position within the metaphase kinetochore. Based on this comprehensive dataset, we propose a quantitative model of the budding yeast kinetochore. While confirming many aspects of previous reports based on bulk imaging, our results present a unifying nanoscale model of the kinetochore in budding yeast.
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Affiliation(s)
- Konstanty Cieslinski
- https://ror.org/03mstc592Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany,Translational Radiation Oncology Unit, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Yu-Le Wu
- https://ror.org/03mstc592Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany,Faculty of Biosciences, Collaboration for Joint PhD Degree Between European Molecular Biology Laboratory and Heidelberg University, Heidelberg, Germany
| | - Lisa Nechyporenko
- https://ror.org/03mstc592Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany,Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Heidelberg, Germany
| | - Sarah Janice Hörner
- https://ror.org/03mstc592Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany,https://ror.org/04p61dj41Institute of Molecular and Cell Biology, Mannheim University of Applied Sciences, Mannheim, Germany,Interdisciplinary Center for Neuroscience, Heidelberg University, Heidelberg, Germany
| | - Duccio Conti
- https://ror.org/03vpj4s62Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Michal Skruzny
- https://ror.org/03mstc592Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jonas Ries
- https://ror.org/03mstc592Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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5
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Lawrimore J, de Larminat SC, Cook D, Friedman B, Doshi A, Yeh E, Bloom K. Polymer models reveal how chromatin modification can modulate force at the kinetochore. Mol Biol Cell 2022; 33:ar97. [PMID: 35704466 DOI: 10.1091/mbc.e22-02-0041] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
A key feature of chromosome segregation is the ability to sense tension between sister kinetochores. DNA between sister kinetochores must be packaged in a way that sustains tension propagation from one kinetochore to its sister, approximately 1 micron away. A molecular bottlebrush consisting of a primary axis populated with a crowded array of side chains provides a means to build tension over length scales considerably larger than the stiffness of the individual elements, that is, DNA polymer. Evidence for the bottlebrush organization of chromatin between sister kinetochores comes from genetic, cell biological, and polymer modeling of the budding yeast centromere. In this study, we have used polymer dynamic simulations of the bottlebrush to recapitulate experimental observations of kinetochore structure. Several aspects of the spatial distribution of kinetochore proteins and their response to perturbation lack a mechanistic understanding. Changes in physical parameters of bottlebrush, DNA stiffness, and DNA loops directly impact the architecture of the inner kinetochore. This study reveals that the bottlebrush is an active participant in building tension between sister kinetochores and proposes a mechanism for chromatin feedback to the kinetochore.
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Affiliation(s)
- Josh Lawrimore
- Biology Department, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Solenn C de Larminat
- Biology Department, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Diana Cook
- Biology Department, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Brandon Friedman
- Biology Department, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Ayush Doshi
- Biology Department, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Elaine Yeh
- Biology Department, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Kerry Bloom
- Biology Department, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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6
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Mishra PK, Wood H, Stanton J, Au WC, Eisenstatt JR, Boeckmann L, Sclafani RA, Weinreich M, Bloom KS, Thorpe PH, Basrai MA. Cdc7-mediated phosphorylation of Cse4 regulates high-fidelity chromosome segregation in budding yeast. Mol Biol Cell 2021; 32:ar15. [PMID: 34432494 PMCID: PMC8693968 DOI: 10.1091/mbc.e21-06-0323] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 08/11/2021] [Accepted: 08/18/2021] [Indexed: 12/21/2022] Open
Abstract
Faithful chromosome segregation maintains chromosomal stability as errors in this process contribute to chromosomal instability (CIN), which has been observed in many diseases including cancer. Epigenetic regulation of kinetochore proteins such as Cse4 (CENP-A in humans) plays a critical role in high-fidelity chromosome segregation. Here we show that Cse4 is a substrate of evolutionarily conserved Cdc7 kinase, and that Cdc7-mediated phosphorylation of Cse4 prevents CIN. We determined that Cdc7 phosphorylates Cse4 in vitro and interacts with Cse4 in vivo in a cell cycle-dependent manner. Cdc7 is required for kinetochore integrity as reduced levels of CEN-associated Cse4, a faster exchange of Cse4 at the metaphase kinetochores, and defects in chromosome segregation, are observed in a cdc7-7 strain. Phosphorylation of Cse4 by Cdc7 is important for cell survival as constitutive association of a kinase-dead variant of Cdc7 (cdc7-kd) with Cse4 at the kinetochore leads to growth defects. Moreover, phospho-deficient mutations of Cse4 for consensus Cdc7 target sites contribute to CIN phenotype. In summary, our results have defined a role for Cdc7-mediated phosphorylation of Cse4 in faithful chromosome segregation.
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Affiliation(s)
- Prashant K. Mishra
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Henry Wood
- Queen Mary University of London, London E1 4NS, UK
| | - John Stanton
- University of North Carolina, Chapel Hill, NC 27599
| | - Wei-Chun Au
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Jessica R. Eisenstatt
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Lars Boeckmann
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | | | | | | | | | - Munira A. Basrai
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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7
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Mishra PK, Chakraborty A, Yeh E, Feng W, Bloom KS, Basrai MA. R-loops at centromeric chromatin contribute to defects in kinetochore integrity and chromosomal instability in budding yeast. Mol Biol Cell 2020; 32:74-89. [PMID: 33147102 PMCID: PMC8098821 DOI: 10.1091/mbc.e20-06-0379] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
R-loops, the byproduct of DNA–RNA hybridization and the displaced single-stranded DNA (ssDNA), have been identified in bacteria, yeasts, and other eukaryotic organisms. The persistent presence of R-loops contributes to defects in DNA replication and repair, gene expression, and genomic integrity. R-loops have not been detected at centromeric (CEN) chromatin in wild-type budding yeast. Here we used an hpr1∆ strain that accumulates R-loops to investigate the consequences of R-loops at CEN chromatin and chromosome segregation. We show that Hpr1 interacts with the CEN-histone H3 variant, Cse4, and prevents the accumulation of R-loops at CEN chromatin for chromosomal stability. DNA–RNA immunoprecipitation (DRIP) analysis showed an accumulation of R-loops at CEN chromatin that was reduced by overexpression of RNH1 in hpr1∆ strains. Increased levels of ssDNA, reduced levels of Cse4 and its assembly factor Scm3, and mislocalization of histone H3 at CEN chromatin were observed in hpr1∆ strains. We determined that accumulation of R-loops at CEN chromatin contributes to defects in kinetochore biorientation and chromosomal instability (CIN) and these phenotypes are suppressed by RNH1 overexpression in hpr1∆ strains. In summary, our studies provide mechanistic insights into how accumulation of R-loops at CEN contributes to defects in kinetochore integrity and CIN.
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Affiliation(s)
- Prashant K Mishra
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | | | - Elaine Yeh
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Wenyi Feng
- SUNY Upstate Medical University, Syracuse, NY 13210
| | - Kerry S Bloom
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Munira A Basrai
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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8
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Guin K, Sreekumar L, Sanyal K. Implications of the Evolutionary Trajectory of Centromeres in the Fungal Kingdom. Annu Rev Microbiol 2020; 74:835-853. [PMID: 32706633 DOI: 10.1146/annurev-micro-011720-122512] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Chromosome segregation during the cell cycle is an evolutionarily conserved, fundamental biological process. Dynamic interaction between spindle microtubules and the kinetochore complex that assembles on centromere DNA is required for faithful chromosome segregation. The first artificial minichromosome was constructed by cloning the centromere DNA of the budding yeast Saccharomyces cerevisiae. Since then, centromeres have been identified in >60 fungal species. The DNA sequence and organization of the sequence elements are highly diverse across these fungal centromeres. In this article, we provide a comprehensive view of the evolution of fungal centromeres. Studies of this process facilitated the identification of factors influencing centromere specification, maintenance, and propagation through many generations. Additionally, we discuss the unique features and plasticity of centromeric chromatin and the involvement of centromeres in karyotype evolution. Finally, we discuss the implications of recurrent loss of RNA interference (RNAi) and/or heterochromatin components on the trajectory of the evolution of fungal centromeres and propose the centromere structure of the last common ancestor of three major fungal phyla-Ascomycota, Basidiomycota, and Mucoromycota.
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Affiliation(s)
- Krishnendu Guin
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka 560064, India; , ,
| | - Lakshmi Sreekumar
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka 560064, India; , ,
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, Karnataka 560064, India; , ,
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9
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ImageJ for Partially and Fully Automated Analysis of Trypanosome Micrographs. Methods Mol Biol 2020. [PMID: 32221933 DOI: 10.1007/978-1-0716-0294-2_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Trypanosomes and related parasites such as Leishmania are unicellular parasites with a precise internal structure. This makes light microscopy a powerful tool for interrogating their biology-whether considering advance techniques for visualizing the precise localization of proteins within the cell or simply measuring parasite cell shape. Methods to partially or fully automate analysis and interpretation are extremely powerful and provide easier access to microscope images as a source of quantitative data. This chapter provides an introduction to these methods using ImageJ/FIJI, free and open source software for scientific image analysis. It provides an overview of how ImageJ handles images and introduces the ImageJ macro/scripting language for automated images, starting at a basic level and assuming no previous programming/scripting experience. It then outlines three methods using ImageJ for automated analysis of trypanosome micrographs: Semiautomated cropping and setting image contrast for presentation, automated analysis of cell properties from a light micrograph field of view, and example semiautomated tools for quantitative analysis of protein localization. These are not presented as strict methods, but are instead described in detail with the intention of furnishing the reader with the ability to "hack" the scripts for their own needs or write their own scripts for partially and fully automated quantitation of trypanosomes from light micrographs. Most of the methods described here are transferrable to other types of microscope image and other cell types.
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10
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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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11
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Chen CF, Pohl TJ, Chan A, Slocum JS, Zakian VA. Saccharomyces cerevisiae Centromere RNA Is Negatively Regulated by Cbf1 and Its Unscheduled Synthesis Impacts CenH3 Binding. Genetics 2019; 213:465-479. [PMID: 31391265 PMCID: PMC6781895 DOI: 10.1534/genetics.119.302528] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 07/19/2019] [Indexed: 12/12/2022] Open
Abstract
Two common features of centromeres are their transcription into noncoding centromere RNAs (cen-RNAs) and their assembly into nucleosomes that contain a centromere-specific histone H3 (cenH3). Here, we show that Saccharomyces cerevisiae cen-RNA was present in low amounts in wild-type (WT) cells, and that its appearance was tightly cell cycle-regulated, appearing and disappearing in a narrow window in S phase after centromere replication. In cells lacking Cbf1, a centromere-binding protein, cen-RNA was 5-12 times more abundant throughout the cell cycle. In WT cells, cen-RNA appearance occurred at the same time as loss of Cbf1's centromere binding, arguing that the physical presence of Cbf1 inhibits cen-RNA production. Binding of the Pif1 DNA helicase, which happens in mid-late S phase, occurred at about the same time as Cbf1 loss from the centromere, suggesting that Pif1 may facilitate this loss by its known ability to displace proteins from DNA. Cen-RNAs were more abundant in rnh1Δ cells but only in mid-late S phase. However, fork pausing at centromeres was not elevated in rnh1Δ cells but rather was due to centromere-binding proteins, including Cbf1 Strains with increased cen-RNA lost centromere plasmids at elevated rates. In cbf1Δ cells, where both the levels and the cell cycle-regulated appearance of cen-RNA were disrupted, the timing and levels of cenH3 centromere binding were perturbed. Thus, cen-RNAs are highly regulated, and disruption of this regulation correlates with changes in centromere structure and function.
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Affiliation(s)
- Chi-Fu Chen
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, New Jersey 08544
| | - Thomas J Pohl
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, New Jersey 08544
| | - Angela Chan
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, New Jersey 08544
| | - Joshua S Slocum
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, New Jersey 08544
| | - Virginia A Zakian
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, New Jersey 08544
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12
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Lawrimore J, Bloom K. The regulation of chromosome segregation via centromere loops. Crit Rev Biochem Mol Biol 2019; 54:352-370. [PMID: 31573359 PMCID: PMC6856439 DOI: 10.1080/10409238.2019.1670130] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/02/2019] [Accepted: 09/17/2019] [Indexed: 12/14/2022]
Abstract
Biophysical studies of the yeast centromere have shown that the organization of the centromeric chromatin plays a crucial role in maintaining proper tension between sister kinetochores during mitosis. While centromeric chromatin has traditionally been considered a simple spring, recent work reveals the centromere as a multifaceted, tunable shock absorber. Centromeres can differ from other regions of the genome in their heterochromatin state, supercoiling state, and enrichment of structural maintenance of chromosomes (SMC) protein complexes. Each of these differences can be utilized to alter the effective stiffness of centromeric chromatin. In budding yeast, the SMC protein complexes condensin and cohesin stiffen chromatin by forming and cross-linking chromatin loops, respectively, into a fibrous structure resembling a bottlebrush. The high density of the loops compacts chromatin while spatially isolating the tension from spindle pulling forces to a subset of the chromatin. Paradoxically, the molecular crowding of chromatin via cohesin and condensin also causes an outward/poleward force. The structure allows the centromere to act as a shock absorber that buffers the variable forces generated by dynamic spindle microtubules. Based on the distribution of SMCs from bacteria to human and the conserved distance between sister kinetochores in a wide variety of organisms (0.4 to 1 micron), we propose that the bottlebrush mechanism is the foundational principle for centromere function in eukaryotes.
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Affiliation(s)
- Josh Lawrimore
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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13
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Sreekumar L, Jaitly P, Chen Y, Thimmappa BC, Sanyal A, Sanyal K. Cis- and Trans-chromosomal Interactions Define Pericentric Boundaries in the Absence of Conventional Heterochromatin. Genetics 2019; 212:1121-1132. [PMID: 31142612 PMCID: PMC6707466 DOI: 10.1534/genetics.119.302179] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 05/22/2019] [Indexed: 01/28/2023] Open
Abstract
The diploid budding yeast Candida albicans harbors unique CENPA-rich 3- to 5-kb regions that form the centromere (CEN) core on each of its eight chromosomes. The epigenetic nature of these CENs does not permit the stabilization of a functional kinetochore on an exogenously introduced CEN plasmid. The flexible nature of such centromeric chromatin is exemplified by the reversible silencing of a transgene upon its integration into the CENPA-bound region. The lack of a conventional heterochromatin machinery and the absence of defined boundaries of CENPA chromatin makes the process of CEN specification in this organism elusive. Additionally, upon native CEN deletion, C. albicans can efficiently activate neocentromeres proximal to the native CEN locus, hinting at the importance of CEN-proximal regions. In this study, we examine this CEN-proximity effect and identify factors for CEN specification in C. albicans We exploit a counterselection assay to isolate cells that can silence a transgene when integrated into the CEN-flanking regions. We show that the frequency of reversible silencing of the transgene decreases from the central core of CEN7 to its peripheral regions. Using publicly available C. albicans high-throughput chromosome conformation capture data, we identify a 25-kb region centering on the CENPA-bound core that acts as CEN-flanking compact chromatin (CFCC). Cis- and trans-chromosomal interactions associated with the CFCC spatially segregates it from bulk chromatin. We further show that neocentromere activation on chromosome 7 occurs within this specified region. Hence, this study identifies a specialized CEN-proximal domain that specifies and restricts the centromeric activity to a unique region.
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Affiliation(s)
- Lakshmi Sreekumar
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Priya Jaitly
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Yao Chen
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore 637551
| | - Bhagya C Thimmappa
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
| | - Amartya Sanyal
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore 637551
| | - Kaustuv Sanyal
- Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India
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14
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Dhatchinamoorthy K, Unruh JR, Lange JJ, Levy M, Slaughter BD, Gerton JL. The stoichiometry of the outer kinetochore is modulated by microtubule-proximal regulatory factors. J Cell Biol 2019; 218:2124-2135. [PMID: 31118239 PMCID: PMC6605801 DOI: 10.1083/jcb.201810070] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 04/11/2019] [Accepted: 05/02/2019] [Indexed: 12/16/2022] Open
Abstract
Dhatchinamoorthy et al. suggest the stoichiometry of outer submodules of the budding yeast kinetochore is strongly influenced by factors at the kinetochore–microtubule interface such as Fin1 and Dam1. Outer kinetochore stoichiometry is remarkably plastic and responsive to microtubule-proximal regulation. The kinetochore is a large molecular machine that attaches chromosomes to microtubules and facilitates chromosome segregation. The kinetochore includes submodules that associate with the centromeric DNA and submodules that attach to microtubules. Additional copies of several submodules of the kinetochore are added during anaphase, including the microtubule binding module Ndc80. While the factors governing plasticity are not known, they could include regulation based on microtubule–kinetochore interactions. We report that Fin1 localizes to the microtubule-proximal edge of the kinetochore cluster during anaphase based on single-particle averaging of super-resolution images. Fin1 is required for the assembly of normal levels of Dam1 and Ndc80 submodules. Levels of Ndc80 further depend on the Dam1 microtubule binding complex. Our results suggest the stoichiometry of outer kinetochore submodules is strongly influenced by factors at the kinetochore–microtubule interface such as Fin1 and Dam1, and phosphorylation by cyclin-dependent kinase. Outer kinetochore stoichiometry is remarkably plastic and responsive to microtubule-proximal regulation.
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Affiliation(s)
- Karthik Dhatchinamoorthy
- Stowers Institute for Medical Research, Kansas City, MO.,Open University, Milton Keynes, England, UK
| | - Jay R Unruh
- Stowers Institute for Medical Research, Kansas City, MO
| | | | | | | | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, MO .,Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS
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15
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Mishra PK, Basrai MA. Protein kinases in mitotic phosphorylation of budding yeast CENP-A. Curr Genet 2019; 65:1325-1332. [PMID: 31119371 DOI: 10.1007/s00294-019-00997-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 05/16/2019] [Accepted: 05/18/2019] [Indexed: 01/24/2023]
Abstract
Centromere identity is specified epigenetically by specialized nucleosomes containing the evolutionarily conserved centromeric histone H3 variant (Cse4 in budding yeast, CENP-A in humans) which is essential for faithful chromosome segregation. However, the mechanisms of epigenetic regulation of Cse4 have not been clearly defined. We have identified two kinases, Cdc5 (Plk1 in humans) and Ipl1 (Aurora B kinase in humans) that phosphorylate Cse4 to prevent chromosomal instability (CIN). Cdc5 associates with Cse4 in mitosis and Cdc5-mediated phosphorylation of Cse4 is coincident with the centromeric enrichment of Cdc5 during metaphase. Defects in Cdc5-mediated Cse4 phosphorylation causes CIN, whereas constitutive association of Cdc5 with Cse4 results in lethality. Cse4 is also a substrate for Ipl1 and phospho-mimetic cse4 mutants suppress growth defects of ipl1 and Ipl1 kinetochore substrate mutants, namely dam1 spc34 and ndc80. Ipl1-mediated phosphorylation of Cse4 regulates kinetochore-microtubule interactions and chromosome biorientation. We propose that collaboration of Cdc5- and Ipl1-mediated phosphorylation of Cse4 modulates kinetochore structure and function, and chromosome biorientation. These findings demonstrate how phosphorylation of Cse4 regulates the integrity of the kinetochore, and acts as an epigenetic marker for mitotic control.
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Affiliation(s)
- Prashant K Mishra
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Munira A Basrai
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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16
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Mishra PK, Olafsson G, Boeckmann L, Westlake TJ, Jowhar ZM, Dittman LE, Baker RE, D’Amours D, Thorpe PH, Basrai MA. Cell cycle-dependent association of polo kinase Cdc5 with CENP-A contributes to faithful chromosome segregation in budding yeast. Mol Biol Cell 2019; 30:1020-1036. [PMID: 30726152 PMCID: PMC6589903 DOI: 10.1091/mbc.e18-09-0584] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/04/2019] [Accepted: 01/30/2019] [Indexed: 12/18/2022] Open
Abstract
Evolutionarily conserved polo-like kinase, Cdc5 (Plk1 in humans), associates with kinetochores during mitosis; however, the role of cell cycle-dependent centromeric ( CEN) association of Cdc5 and its substrates that exclusively localize to the kinetochore have not been characterized. Here we report that evolutionarily conserved CEN histone H3 variant, Cse4 (CENP-A in humans), is a substrate of Cdc5, and that the cell cycle-regulated association of Cse4 with Cdc5 is required for cell growth. Cdc5 contributes to Cse4 phosphorylation in vivo and interacts with Cse4 in mitotic cells. Mass spectrometry analysis of in vitro kinase assays showed that Cdc5 phosphorylates nine serine residues clustered within the N-terminus of Cse4. Strains with cse4-9SA exhibit increased errors in chromosome segregation, reduced levels of CEN-associated Mif2 and Mcd1/Scc1 when combined with a deletion of MCM21. Moreover, the loss of Cdc5 from the CEN chromatin contributes to defects in kinetochore integrity and reduction in CEN-associated Cse4. The cell cycle-regulated association of Cdc5 with Cse4 is essential for cell viability as constitutive association of Cdc5 with Cse4 at the kinetochore leads to growth defects. In summary, our results have defined a role for Cdc5-mediated Cse4 phosphorylation in faithful chromosome segregation.
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Affiliation(s)
- Prashant K. Mishra
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Gudjon Olafsson
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Lars Boeckmann
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Timothy J. Westlake
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Ziad M. Jowhar
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Lauren E. Dittman
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Richard E. Baker
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655
| | - Damien D’Amours
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Peter H. Thorpe
- School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Munira A. Basrai
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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17
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Mittal P, Chavan A, Trakroo D, Shah S, Ghosh SK. Outer kinetochore protein Dam1 promotes centromere clustering in parallel with Slk19 in budding yeast. Chromosoma 2019; 128:133-148. [PMID: 30903360 DOI: 10.1007/s00412-019-00694-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 01/14/2019] [Accepted: 02/11/2019] [Indexed: 12/16/2022]
Abstract
A higher order organization of the centromeres in the form of clustering of these DNA loci has been observed in many organisms. While centromere clustering is biologically significant to achieve faithful chromosome segregation, the underlying molecular mechanism is yet to be fully understood. In budding yeast, a kinetochore-associated protein Slk19 is shown to have a role in clustering in association with the microtubules whereas removal of either Slk19 or microtubules alone does not have any effect on the centromere clustering. Furthermore, Slk19 is non-essential for growth and becomes cleaved during anaphase whereas clustering being an essential event occurs throughout the cell cycle. Hence, we searched for an additional factor involved in the clustering and since the integrity of the kinetochore complex is shown to be crucial for centromere clustering, we restricted our search within the complex. We observed that the outermost kinetochore protein Dam1 promotes centromere clustering through stabilization of the kinetochore integrity. While in the absence of Dam1 we failed to detect Slk19 at the centromere, on the other hand, we found almost no Dam1 at the centromere in the absence of Slk19 and microtubules suggesting interdependency between these two pathways. Strikingly, we observed that overexpression of Dam1 or Slk19 could restore the centromere clustering largely in the cells devoid of Slk19 and microtubules or Dam1, respectively. Thus, we propose that in budding yeast, centromere clustering is achieved at least by two parallel pathways, through Dam1 and another via Slk19, in concert with the microtubules suggesting that having a dual mechanism may be crucial for ensuring microtubule capture by the point centromeres where each attaches to only one microtubule.
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Affiliation(s)
- Priyanka Mittal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Ankita Chavan
- Molecular and Cell Biology Department, University of Connecticut, Storrs, CT, 06269, USA
| | - Deepika Trakroo
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Sanket Shah
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai, 410210, India
| | - Santanu K Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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18
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Hoffmann G, Samel-Pommerencke A, Weber J, Cuomo A, Bonaldi T, Ehrenhofer-Murray AE. A role for CENP-A/Cse4 phosphorylation on serine 33 in deposition at the centromere. FEMS Yeast Res 2019; 18:4768140. [PMID: 29272409 DOI: 10.1093/femsyr/fox094] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/18/2017] [Indexed: 12/16/2022] Open
Abstract
Centromeres are the sites of assembly of the kinetochore, which connect the chromatids to the microtubules for sister chromatid segregation during cell division. Centromeres are characterized by the presence of the histone H3 variant CENP-A (termed Cse4 in Saccharomyces cerevisiae). Here, we investigated the function of serine 33 phosphorylation of Cse4 (Cse4-S33ph) in S. cerevisiae, which lies within the essential N-terminal domain (END) of the extended Cse4 N-terminus. Significantly, we identified histone H4-K5, 8, 12R to cause a temperature-sensitive growth defect with mutations in Cse4-S33 and sensitivity to nocodazole and hydroxyurea. Furthermore, the absence of Cse4-S33ph reduced the levels of Cse4 at centromeric sequences, suggesting that Cse4 deposition is defective in the absence of S33 phosphorylation. We furthermore identified synthetic genetic interactions with histone H2A-E57A and H2A-L66A, which both cause a reduced interaction with the histone chaperone FACT and reduced H2A/H2B levels in chromatin, again supporting the notion that a combined defect of H2A/H2B and Cse4 deposition causes centromeric defects. Altogether, our data highlight the importance of correct histone deposition in building a functional centromeric nucleosome and suggests a role for Cse4-S33ph in this process.
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Affiliation(s)
- Gesine Hoffmann
- Institut für Biologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | | | - Jan Weber
- Biozentrum Köln, Universität zu Köln, 50674 Köln, Germany
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology, 20139 Milano, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology, 20139 Milano, Italy
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19
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Malik N, Dantu SC, Shukla S, Kombrabail M, Ghosh SK, Krishnamoorthy G, Kumar A. Conformational flexibility of histone variant CENP-A Cse4 is regulated by histone H4: A mechanism to stabilize soluble Cse4. J Biol Chem 2018; 293:20273-20284. [PMID: 30381395 PMCID: PMC6311523 DOI: 10.1074/jbc.ra118.004141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 10/23/2018] [Indexed: 11/06/2022] Open
Abstract
The histone variant CENP-ACse4 is a core component of the specialized nucleosome at the centromere in budding yeast and is required for genomic integrity. Accordingly, the levels of Cse4 in cells are tightly regulated, primarily by ubiquitin-mediated proteolysis. However, structural transitions in Cse4 that regulate its centromeric localization and interaction with regulatory components are poorly understood. Using time-resolved fluorescence, NMR, and molecular dynamics simulations, we show here that soluble Cse4 can exist in a "closed" conformation, inaccessible to various regulatory components. We further determined that binding of its obligate partner, histone H4, alters the interdomain interaction within Cse4, enabling an "open" state that is susceptible to proteolysis. This dynamic model allows kinetochore formation only in the presence of H4, as the Cse4 N terminus, which is required for interaction with other centromeric components, is unavailable in the absence of H4. The specific requirement of H4 binding for the conformational regulation of Cse4 suggests a structure-based regulatory mechanism for Cse4 localization. Our data suggested a novel structural transition-based mechanism where conformational flexibility of the Cse4 N terminus can control Cse4 levels in the yeast cell and prevent Cse4 from interacting with kinetochore components at ectopic locations for formation of premature kinetochore assembly.
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Affiliation(s)
- Nikita Malik
- From the Departments of Biosciences and Bioengineering and
| | | | | | - Mamta Kombrabail
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | | | - Guruswamy Krishnamoorthy
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India; Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India and.
| | - Ashutosh Kumar
- From the Departments of Biosciences and Bioengineering and.
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20
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Suzuki A, Gupta A, Long SK, Evans R, Badger BL, Salmon ED, Biggins S, Bloom K. A Kinesin-5, Cin8, Recruits Protein Phosphatase 1 to Kinetochores and Regulates Chromosome Segregation. Curr Biol 2018; 28:2697-2704.e3. [PMID: 30174190 DOI: 10.1016/j.cub.2018.08.038] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 08/02/2018] [Accepted: 08/16/2018] [Indexed: 01/03/2023]
Abstract
Kinesin-5 is a highly conserved homo-tetrameric protein complex responsible for crosslinking microtubules and pushing spindle poles apart. The budding yeast Kinesin-5, Cin8, is highly concentrated at kinetochores in mitosis before anaphase, but its functions there are largely unsolved. Here, we show that Cin8 localizes to kinetochores in a cell-cycle-dependent manner and concentrates near the microtubule binding domains of Ndc80 at metaphase. Cin8's kinetochore localization depends on the Ndc80 complex, kinetochore microtubules, and the Dam1 complex. Consistent with its kinetochore localization, a Cin8 deletion induces a loss of tension at the Ndc80 microtubule binding domains and a major delay in mitotic progression. Cin8 associates with Protein Phosphatase 1 (PP1), and mutants that inhibit its PP1 binding also induce a loss of tension at the Ndc80 microtubule binding domains and delay mitotic progression. Taken together, our results suggest that Cin8-PP1 plays a critical role at kinetochores to promote accurate chromosome segregation by controlling Ndc80 attachment to microtubules.
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Affiliation(s)
- Aussie Suzuki
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; McArdle Laboratory for Cancer Research, Department of Oncology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA.
| | - Amitabha Gupta
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Sarah K Long
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Rena Evans
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Benjamin L Badger
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Edward D Salmon
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sue Biggins
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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21
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22
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Samel A, Nguyen TKL, Ehrenhofer-Murray AE. Defects in methylation of arginine 37 on CENP-A/Cse4 are compensated by the ubiquitin ligase complex Ubr2/Mub1. FEMS Yeast Res 2018; 17:2966861. [PMID: 28158539 DOI: 10.1093/femsyr/fox009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 02/01/2017] [Indexed: 12/11/2022] Open
Abstract
The kinetochore, a supramolecular protein complex, provides the physical connection between chromatin and the microtubule and ensures correct chromosome segregation during mitosis. Centromeric regions are marked by the presence of the histone H3 variant CENP-A. Cse4, the CENP-A homologue from Saccharomyces cerevisiae, is methylated on arginine 37 in its N-terminus (R37), and the absence of methylation (cse4-R37A) causes synthetic genetic defects in combination with mutations or deletions in genes encoding components of the Ctf19/CCAN complex and with the CDEI binding protein Cbf1. Here, we report that the absence of the E3 ubiquitin ligase Ubr2 as well as its adaptor protein Mub1 suppresses the defects caused by the absence of Cse4-R37 methylation. Ubr2 is known to regulate the levels of the MIND complex component Dsn1 via ubiquitination and proteasome-mediated degradation. Accordingly, we found that overexpression of DSN1 also led to suppression of Cse4 methylation defects. Altogether, our data indicate that the absence of R37 methylation reduces the recruitment of kinetochore proteins to centromeric chromatin, and that this can be compensated for by stabilising the outer kinetochore protein Dsn1.
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23
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Haase KP, Fox JC, Byrnes AE, Adikes RC, Speed SK, Haase J, Friedman B, Cook DM, Bloom K, Rusan NM, Slep KC. Stu2 uses a 15-nm parallel coiled coil for kinetochore localization and concomitant regulation of the mitotic spindle. Mol Biol Cell 2018; 29:285-294. [PMID: 29187574 PMCID: PMC5996958 DOI: 10.1091/mbc.e17-01-0057] [Citation(s) in RCA: 5] [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: 01/23/2017] [Revised: 10/10/2017] [Accepted: 11/22/2017] [Indexed: 11/23/2022] Open
Abstract
XMAP215/Dis1 family proteins are potent microtubule polymerases, critical for mitotic spindle structure and dynamics. While microtubule polymerase activity is driven by an N-terminal tumor overexpressed gene (TOG) domain array, proper cellular localization is a requisite for full activity and is mediated by a C-terminal domain. Structural insight into the C-terminal domain's architecture and localization mechanism remain outstanding. We present the crystal structure of the Saccharomyces cerevisiae Stu2 C-terminal domain, revealing a 15-nm parallel homodimeric coiled coil. The parallel architecture of the coiled coil has mechanistic implications for the arrangement of the homodimer's N-terminal TOG domains during microtubule polymerization. The coiled coil has two spatially distinct conserved regions: CRI and CRII. Mutations in CRI and CRII perturb the distribution and localization of Stu2 along the mitotic spindle and yield defects in spindle morphology including increased frequencies of mispositioned and fragmented spindles. Collectively, these data highlight roles for the Stu2 dimerization domain as a scaffold for factor binding that optimally positions Stu2 on the mitotic spindle to promote proper spindle structure and dynamics.
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Affiliation(s)
- Karen P Haase
- Molecular and Cellular Biophysics Program, University of North Carolina, Chapel Hill, NC 27599
- Cell Biology and Physiology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
- Cell Biology and Physiology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Jaime C Fox
- Molecular and Cellular Biophysics Program, University of North Carolina, Chapel Hill, NC 27599
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599
| | - Amy E Byrnes
- Cell Biology and Physiology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599
| | - Rebecca C Adikes
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Sarah K Speed
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Julian Haase
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Brandon Friedman
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Diana M Cook
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Kerry Bloom
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Nasser M Rusan
- Cell Biology and Physiology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Kevin C Slep
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
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24
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Bloom K, Costanzo V. Centromere Structure and Function. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2017; 56:515-539. [PMID: 28840251 DOI: 10.1007/978-3-319-58592-5_21] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The centromere is the genetic locus that specifies the site of kinetochore assembly, where the chromosome will attach to the kinetochore microtubule. The pericentromere is the physical region responsible for the geometry of bi-oriented sister kinetochores in metaphase. In budding yeast the 125 bp point centromere is sufficient to specify kinetochore assembly. The flanking region is enriched (3X) in cohesin and condensin relative to the remaining chromosome arms. The enrichment spans about 30-50 kb around each centromere. We refer to the flanking chromatin as the pericentromere in yeast. In mammals, a 5-10 Mb region dictates where the kinetochore is built. The kinetochore interacts with a very small fraction of DNA on the surface of the centromeric region. The remainder of the centromere lies between the sister kinetochores. This is typically called centromere chromatin. The chromatin sites that directly interface to microtubules cannot be identified due to the repeated sequence within the mammalian centromere. However in both yeast and mammals, the total amount of DNA between the sites of microtubule attachment in metaphase is highly conserved. In yeast the 16 chromosomes are clustered into a 250 nm diameter region, and 800 kb (16 × 50 kb) or ~1 Mb of DNA lies between sister kinetochores. In mammals, 5-10 Mb lies between sister kinetochores. In both organisms the sister kinetochores are separated by about 1 μm. Thus, centromeres of different organisms differ in how they specify kinetochore assembly, but there may be important centromere chromatin functions that are conserved throughout phylogeny. Recently, centromeric chromatin has been reconstituted in vitro using alpha satellite DNA revealing unexpected features of centromeric DNA organization, replication, and response to stress. We will focus on the conserved features of centromere in this review.
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Affiliation(s)
- Kerry Bloom
- Department of Biology, University of North Carolina at Chapel Hill, 623 Fordham Hall CB#3280, Chapel Hill, NC, 27599-3280, USA.
| | - Vincenzo Costanzo
- DNA Metabolism Laboratory, IFOM, The FIRC Institute of Molecular Oncology, Vai Adamello 16, 21139, Milan, Italy
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25
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Stankovic A, Jansen LET. Quantitative Microscopy Reveals Centromeric Chromatin Stability, Size, and Cell Cycle Mechanisms to Maintain Centromere Homeostasis. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2017; 56:139-162. [PMID: 28840236 DOI: 10.1007/978-3-319-58592-5_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Centromeres are chromatin domains specified by nucleosomes containing the histone H3 variant, CENP-A. This unique centromeric structure is at the heart of a strong self-templating epigenetic mechanism that renders centromeres heritable. We review how specific quantitative microscopy approaches have contributed to the determination of the copy number, architecture, size, and dynamics of centromeric chromatin and its associated centromere complex and kinetochore. These efforts revealed that the key to long-term centromere maintenance is the slow turnover of CENP-A nucleosomes, a critical size of the chromatin domain and its cell cycle-coupled replication. These features come together to maintain homeostasis of a chromatin locus that directs its own epigenetic inheritance and facilitates the assembly of the mitotic kinetochore.
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Affiliation(s)
- Ana Stankovic
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
| | - Lars E T Jansen
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal.
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Mishra PK, Ciftci-Yilmaz S, Reynolds D, Au WC, Boeckmann L, Dittman LE, Jowhar Z, Pachpor T, Yeh E, Baker RE, Hoyt MA, D'Amours D, Bloom K, Basrai MA. Polo kinase Cdc5 associates with centromeres to facilitate the removal of centromeric cohesin during mitosis. Mol Biol Cell 2016; 27:2286-300. [PMID: 27226485 PMCID: PMC4945145 DOI: 10.1091/mbc.e16-01-0004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 04/27/2016] [Accepted: 05/19/2016] [Indexed: 12/20/2022] Open
Abstract
Sister chromatid cohesion is essential for tension-sensing mechanisms that monitor bipolar attachment of replicated chromatids in metaphase. Cohesion is mediated by the association of cohesins along the length of sister chromatid arms. In contrast, centromeric cohesin generates intrastrand cohesion and sister centromeres, while highly cohesin enriched, are separated by >800 nm at metaphase in yeast. Removal of cohesin is necessary for sister chromatid separation during anaphase, and this is regulated by evolutionarily conserved polo-like kinase (Cdc5 in yeast, Plk1 in humans). Here we address how high levels of cohesins at centromeric chromatin are removed. Cdc5 associates with centromeric chromatin and cohesin-associated regions. Maximum enrichment of Cdc5 in centromeric chromatin occurs during the metaphase-to-anaphase transition and coincides with the removal of chromosome-associated cohesin. Cdc5 interacts with cohesin in vivo, and cohesin is required for association of Cdc5 at centromeric chromatin. Cohesin removal from centromeric chromatin requires Cdc5 but removal at distal chromosomal arm sites does not. Our results define a novel role for Cdc5 in regulating removal of centromeric cohesins and faithful chromosome segregation.
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Affiliation(s)
- Prashant K Mishra
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Sultan Ciftci-Yilmaz
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - David Reynolds
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Wei-Chun Au
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Lars Boeckmann
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Lauren E Dittman
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Ziad Jowhar
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Tejaswini Pachpor
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Elaine Yeh
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Richard E Baker
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655
| | - M Andrew Hoyt
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218
| | - Damien D'Amours
- Institute for Research in Immunology and Cancer and Département de Pathologie et Biologie Cellulaire, Université de Montréal, Montreal, QC H3C 3J7, Canada
| | - Kerry Bloom
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Munira A Basrai
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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Freire-Benéitez V, Price RJ, Buscaino A. The Chromatin of Candida albicans Pericentromeres Bears Features of Both Euchromatin and Heterochromatin. Front Microbiol 2016; 7:759. [PMID: 27242771 PMCID: PMC4871872 DOI: 10.3389/fmicb.2016.00759] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/05/2016] [Indexed: 01/06/2023] Open
Abstract
Centromeres, sites of kinetochore assembly, are important for chromosome stability and integrity. Most eukaryotes have regional centromeres epigenetically specified by the presence of the histone H3 variant CENP-A. CENP-A chromatin is often surrounded by pericentromeric regions packaged into transcriptionally silent heterochromatin. Candida albicans, the most common human fungal pathogen, possesses small regional centromeres assembled into CENP-A chromatin. The chromatin state of C. albicans pericentromeric regions is unknown. Here, for the first time, we address this question. We find that C. albicans pericentromeres are assembled into an intermediate chromatin state bearing features of both euchromatin and heterochromatin. Pericentromeric chromatin is associated with nucleosomes that are highly acetylated, as found in euchromatic regions of the genome; and hypomethylated on H3K4, as found in heterochromatin. This intermediate chromatin state is inhibitory to transcription and partially represses expression of proximal genes and inserted marker genes. Our analysis identifies a new chromatin state associated with pericentromeric regions.
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Affiliation(s)
| | - R Jordan Price
- School of Biosciences Canterbury Kent, University of Kent Canterbury, UK
| | - Alessia Buscaino
- School of Biosciences Canterbury Kent, University of Kent Canterbury, UK
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Wynne DJ, Funabiki H. Heterogeneous architecture of vertebrate kinetochores revealed by three-dimensional superresolution fluorescence microscopy. Mol Biol Cell 2016; 27:3395-3404. [PMID: 27170176 PMCID: PMC5221576 DOI: 10.1091/mbc.e16-02-0130] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/04/2016] [Indexed: 11/11/2022] Open
Abstract
Superresolution fluorescence microscopy of vertebrate kinetochore proteins reveals that outer kinetochore components assume diverse distribution patterns, including a ring-like configuration encircling the CENP-A–marked centromeric chromatin on the metaphase spindle in Xenopus egg extracts. The kinetochore is often depicted as having a disk-like architecture in which the outer layer of proteins, which engage microtubules and control checkpoint signaling, are built on a static inner layer directly linked to CENP-A chromatin. Here, applying three-dimensional (3D) structural illumination microscopy (SIM) and stochastic optical reconstruction microscopy (STORM) to Xenopus egg extracts and tissue culture cells, we report various distribution patterns of inner and outer kinetochore proteins. In egg extracts, a configuration in which outer kinetochore proteins surround the periphery of CENP-A chromatin is common, forming an ∼200-nm ring-like organization that may engage a bundle of microtubule ends. Similar rings are observed in Xenopus tissue culture cells at a lower frequency but are enriched in conditions in which the spindle is disorganized. Although rings are rare in human cells, the distribution of both inner and outer kinetochore proteins elongates in the absence of microtubule attachment in a manner dependent on Aurora B. We propose a model in which the 3D organization of both the outer and inner kinetochore regions respond to the progression from lateral to end-on microtubule attachments by coalescing into a tight disk from less uniform distributions early in prometaphase.
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Affiliation(s)
- David J Wynne
- Laboratory of Chromosome and Cell Biology, Rockefeller University, New York, NY 10065.,Department of Biology, College of New Jersey, Ewing, NJ 08628
| | - Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, Rockefeller University, New York, NY 10065
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How the kinetochore couples microtubule force and centromere stretch to move chromosomes. Nat Cell Biol 2016; 18:382-92. [PMID: 26974660 PMCID: PMC4814359 DOI: 10.1038/ncb3323] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 02/04/2016] [Indexed: 02/07/2023]
Abstract
The Ndc80 complex (Ndc80, Nuf2, Spc24 and Spc25) is a highly conserved kinetochore protein essential for end-on anchorage to spindle microtubule plus ends and for force generation coupled to plus-end polymerization and depolymerization. Spc24/Spc25 at one end of the Ndc80 complex binds the kinetochore. The N-terminal tail and CH domains of Ndc80 bind microtubules, and an internal domain binds microtubule-associated proteins (MAPs) such as the Dam1 complex. To determine how the microtubule- and MAP-binding domains of Ndc80 contribute to force production at the kinetochore in budding yeast, we have inserted a FRET tension sensor into the Ndc80 protein about halfway between its microtubule-binding and internal loop domains. The data support a mechanical model of force generation at metaphase where the position of the kinetochore relative to the microtubule plus end reflects the relative strengths of microtubule depolymerization, centromere stretch and microtubule-binding interactions with the Ndc80 and Dam1 complexes.
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Herrero E, Thorpe PH. Synergistic Control of Kinetochore Protein Levels by Psh1 and Ubr2. PLoS Genet 2016; 12:e1005855. [PMID: 26891228 PMCID: PMC4758618 DOI: 10.1371/journal.pgen.1005855] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 01/19/2016] [Indexed: 12/02/2022] Open
Abstract
The accurate segregation of chromosomes during cell division is achieved by attachment of chromosomes to the mitotic spindle via the kinetochore, a large multi-protein complex that assembles on centromeres. The budding yeast kinetochore comprises more than 60 different proteins. Although the structure and function of many of these proteins has been investigated, we have little understanding of the steady state regulation of kinetochores. The primary model of kinetochore homeostasis suggests that kinetochores assemble hierarchically from the centromeric DNA via the inclusion of a centromere-specific histone into chromatin. We tested this model by trying to perturb kinetochore protein levels by overexpressing an outer kinetochore gene, MTW1. This increase in protein failed to change protein recruitment, consistent with the hierarchical assembly model. However, we find that deletion of Psh1, a key ubiquitin ligase that is known to restrict inner kinetochore protein loading, does not increase levels of outer kinetochore proteins, thus breaking the normal kinetochore stoichiometry. This perturbation leads to chromosome segregation defects, which can be partially suppressed by mutation of Ubr2, a second ubiquitin ligase that normally restricts protein levels at the outer kinetochore. Together these data show that Psh1 and Ubr2 synergistically control the amount of proteins at the kinetochore.
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Affiliation(s)
- Eva Herrero
- The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
| | - Peter H. Thorpe
- The Francis Crick Institute, Mill Hill Laboratory, London, United Kingdom
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Díaz-Ingelmo O, Martínez-García B, Segura J, Valdés A, Roca J. DNA Topology and Global Architecture of Point Centromeres. Cell Rep 2015; 13:667-677. [PMID: 26489472 DOI: 10.1016/j.celrep.2015.09.039] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 08/08/2015] [Accepted: 09/14/2015] [Indexed: 12/21/2022] Open
Abstract
DNA is wrapped in a left-handed fashion around histone octasomes containing the centromeric histone H3 variant CENP-A. However, DNA topology studies have suggested that DNA is wrapped in a right-handed manner around the CENP-A nucleosome that occupies the yeast point centromere. Here, we determine the DNA linking number difference (ΔLk) stabilized by the yeast centromere and the contribution of the centromere determining elements (CDEI, CDEII, and CDEIII). We show that the intrinsic architecture of the yeast centromere stabilizes +0.6 units of ΔLk. This topology depends on the integrity of CDEII and CDEIII, but it is independent of cbf1 binding to CDEI and of the variable length of CDEII. These findings suggest that the interaction of the CBF3 complex with CDEIII and a distal CDEII segment configures a right-handed DNA loop that excludes CDEI. This loop is then occupied by a CENP-A histone complex, which does not have to be inherently right-handed.
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Affiliation(s)
- Ofelia Díaz-Ingelmo
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona 08028, Spain
| | - Belén Martínez-García
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona 08028, Spain
| | - Joana Segura
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona 08028, Spain
| | - Antonio Valdés
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona 08028, Spain
| | - Joaquim Roca
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona 08028, Spain.
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32
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Sutradhar S, Yadav V, Sridhar S, Sreekumar L, Bhattacharyya D, Ghosh SK, Paul R, Sanyal K. A comprehensive model to predict mitotic division in budding yeasts. Mol Biol Cell 2015; 26:3954-65. [PMID: 26310442 PMCID: PMC4710229 DOI: 10.1091/mbc.e15-04-0236] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/14/2015] [Indexed: 12/26/2022] Open
Abstract
A mechanistic in silico model predicts mitotic events and effects of perturbation in budding yeasts belonging to Ascomycota and Basidiomycota. The model identifies distinct pathways based on the population of cytoplasmic microtubules and cortical dyneins as determinants of nuclear and spindle positioning in these phyla. High-fidelity chromosome segregation during cell division depends on a series of concerted interdependent interactions. Using a systems biology approach, we built a robust minimal computational model to comprehend mitotic events in dividing budding yeasts of two major phyla: Ascomycota and Basidiomycota. This model accurately reproduces experimental observations related to spindle alignment, nuclear migration, and microtubule (MT) dynamics during cell division in these yeasts. The model converges to the conclusion that biased nucleation of cytoplasmic microtubules (cMTs) is essential for directional nuclear migration. Two distinct pathways, based on the population of cMTs and cortical dyneins, differentiate nuclear migration and spindle orientation in these two phyla. In addition, the model accurately predicts the contribution of specific classes of MTs in chromosome segregation. Thus we present a model that offers a wider applicability to simulate the effects of perturbation of an event on the concerted process of the mitotic cell division.
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Affiliation(s)
- Sabyasachi Sutradhar
- Department of Solid State Physics, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Vikas Yadav
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Shreyas Sridhar
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Lakshmi Sreekumar
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
| | - Dibyendu Bhattacharyya
- Tata Memorial Centre, Advanced Centre for Treatment Research and Education in Cancer, Kharghar, Navi Mumbai 410210, India
| | - Santanu Kumar Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology, Bombay, Powai, Mumbai 400076, India
| | - Raja Paul
- Department of Solid State Physics, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore 560064, India
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Scott KC, Bloom KS. Lessons learned from counting molecules: how to lure CENP-A into the kinetochore. Open Biol 2015; 4:rsob.140191. [PMID: 25500356 PMCID: PMC4281711 DOI: 10.1098/rsob.140191] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Affiliation(s)
- Kristin C Scott
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Kerry S Bloom
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Steiner FA, Henikoff S. Diversity in the organization of centromeric chromatin. Curr Opin Genet Dev 2015; 31:28-35. [PMID: 25956076 DOI: 10.1016/j.gde.2015.03.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Revised: 03/26/2015] [Accepted: 03/28/2015] [Indexed: 01/15/2023]
Abstract
Centromeric chromatin is distinguished primarily by nucleosomes containing the histone variant cenH3, which organizes the kinetochore that links the chromosome to the spindle apparatus. Whereas budding yeast have simple 'point' centromeres with single cenH3 nucleosomes, and fission yeast have 'regional' centromeres without obvious sequence specificity, the centromeres of most organisms are embedded in highly repetitive 'satellite' DNA. Recent studies have revealed a remarkable diversity in centromere chromatin organization among different lineages, including some that have lost cenH3 altogether. We review recent progress in understanding point, regional and satellite centromeres, as well as less well-studied centromere types, such as holocentromeres. We also discuss the formation of neocentromeres, the role of pericentric heterochromatin, and the structure and composition of the cenH3 nucleosome.
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Affiliation(s)
- Florian A Steiner
- Basic Sciences Division and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Steven Henikoff
- Basic Sciences Division and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
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35
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Mishra PK, Guo J, Dittman LE, Haase J, Yeh E, Bloom K, Basrai MA. Pat1 protects centromere-specific histone H3 variant Cse4 from Psh1-mediated ubiquitination. Mol Biol Cell 2015; 26:2067-79. [PMID: 25833709 PMCID: PMC4472017 DOI: 10.1091/mbc.e14-08-1335] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 03/27/2015] [Indexed: 11/25/2022] Open
Abstract
A novel Pat1-dependent mechanism is identified for the protection of kinetochore-associated Cse4 from ubiquitination in order to ensure faithful chromosome segregation and genomic stability. Evolutionarily conserved histone H3 variant Cse4 and its homologues are essential components of specialized centromere (CEN)-specific nucleosomes and serve as an epigenetic mark for CEN identity and propagation. Cse4 is a critical determinant for the structure and function of the kinetochore and is required to ensure faithful chromosome segregation. The kinetochore protein Pat1 regulates the levels and spatial distribution of Cse4 at centromeres. Deletion of PAT1 results in altered structure of CEN chromatin and chromosome segregation errors. In this study, we show that Pat1 protects CEN-associated Cse4 from ubiquitination in order to maintain proper structure and function of the kinetochore in budding yeast. PAT1-deletion strains exhibit increased ubiquitination of Cse4 and faster turnover of Cse4 at kinetochores. Psh1, a Cse4-specific E3-ubiquitin ligase, interacts with Pat1 in vivo and contributes to the increased ubiquitination of Cse4 in pat1∆ strains. Consistent with a role of Psh1 in ubiquitination of Cse4, transient induction of PSH1 in a wild-type strain resulted in phenotypes similar to a pat1∆ strain, including a reduction in CEN-associated Cse4, increased Cse4 ubiquitination, defects in spatial distribution of Cse4 at kinetochores, and altered structure of CEN chromatin. Pat1 interacts with Scm3 and is required for its maintenance at kinetochores. In conclusion, our studies provide novel insights into mechanisms by which Pat1 affects the structure of CEN chromatin and protects Cse4 from Psh1-mediated ubiquitination for faithful chromosome segregation.
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Affiliation(s)
- Prashant K Mishra
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Jiasheng Guo
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Lauren E Dittman
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
| | - Julian Haase
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Elaine Yeh
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Kerry Bloom
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599
| | - Munira A Basrai
- Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892
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36
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Coffman VC, Wu JQ. Every laboratory with a fluorescence microscope should consider counting molecules. Mol Biol Cell 2015; 25:1545-8. [PMID: 24825827 PMCID: PMC4019486 DOI: 10.1091/mbc.e13-05-0249] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Protein numbers in cells determine rates of biological processes, influence the architecture of cellular structures, reveal the stoichiometries of protein complexes, guide in vitro biochemical reconstitutions, and provide parameter values for mathematical modeling. The purpose of this essay is to increase awareness of methods for counting protein molecules using fluorescence microscopy and encourage more cell biologists to report these numbers. We address the state of the field in terms of utility and accuracy of the numbers reported and point readers to references for details of specific techniques and applications.
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Affiliation(s)
- Valerie C Coffman
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210
| | - Jian-Qiu Wu
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210Department of Molecular and Cellular Biochemistry, The Ohio State University, Columbus, OH 43210
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38
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Westhorpe FG, Straight AF. The centromere: epigenetic control of chromosome segregation during mitosis. Cold Spring Harb Perspect Biol 2014; 7:a015818. [PMID: 25414369 DOI: 10.1101/cshperspect.a015818] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A fundamental challenge for the survival of all organisms is maintaining the integrity of the genome in all cells. Cells must therefore segregate their replicated genome equally during each cell division. Eukaryotic organisms package their genome into a number of physically distinct chromosomes, which replicate during S phase and condense during prophase of mitosis to form paired sister chromatids. During mitosis, cells form a physical connection between each sister chromatid and microtubules of the mitotic spindle, which segregate one copy of each chromatid to each new daughter cell. The centromere is the DNA locus on each chromosome that creates the site of this connection. In this review, we present a brief history of centromere research and discuss our current knowledge of centromere establishment, maintenance, composition, structure, and function in mitosis.
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Affiliation(s)
- Frederick G Westhorpe
- Department of Biochemistry, Stanford University Medical School, Stanford, California 94305
| | - Aaron F Straight
- Department of Biochemistry, Stanford University Medical School, Stanford, California 94305
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39
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Hornung P, Troc P, Malvezzi F, Maier M, Demianova Z, Zimniak T, Litos G, Lampert F, Schleiffer A, Brunner M, Mechtler K, Herzog F, Marlovits TC, Westermann S. A cooperative mechanism drives budding yeast kinetochore assembly downstream of CENP-A. ACTA ACUST UNITED AC 2014; 206:509-24. [PMID: 25135934 PMCID: PMC4137059 DOI: 10.1083/jcb.201403081] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
During kinetochore assembly in budding yeast, the key steps of CENP-A recognition and outer kinetochore recruitment are executed through different yeast CCAN subunits, potentially protecting against inappropriate kinetochore assembly. Kinetochores are megadalton-sized protein complexes that mediate chromosome–microtubule interactions in eukaryotes. How kinetochore assembly is triggered specifically on centromeric chromatin is poorly understood. Here we use biochemical reconstitution experiments alongside genetic and structural analysis to delineate the contributions of centromere-associated proteins to kinetochore assembly in yeast. We show that the conserved kinetochore subunits Ame1CENP-U and Okp1CENP-Q form a DNA-binding complex that associates with the microtubule-binding KMN network via a short Mtw1 recruitment motif in the N terminus of Ame1. Point mutations in the Ame1 motif disrupt kinetochore function by preventing KMN assembly on chromatin. Ame1–Okp1 directly associates with the centromere protein C (CENP-C) homologue Mif2 to form a cooperative binding platform for outer kinetochore assembly. Our results indicate that the key assembly steps, CENP-A recognition and outer kinetochore recruitment, are executed through different yeast constitutive centromere-associated network subunits. This two-step mechanism may protect against inappropriate kinetochore assembly similar to rate-limiting nucleation steps used by cytoskeletal polymers.
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Affiliation(s)
- Peter Hornung
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Paulina Troc
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Francesca Malvezzi
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Michael Maier
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Zuzana Demianova
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Tomasz Zimniak
- Department of Biochemistry, Gene Center, Ludwig-Maximilians Universität München, 81377 Munich, Germany
| | - Gabriele Litos
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Fabienne Lampert
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Alexander Schleiffer
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria Institute of Molecular Biotechnology GmbH, Austrian Academy of Sciences, 1030 Vienna, Austria
| | - Matthias Brunner
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria Institute of Molecular Biotechnology GmbH, Austrian Academy of Sciences, 1030 Vienna, Austria Center for Structural Systems Biology, University Medical Center Eppendorf-Hamburg, 20246 Hamburg, Germany Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Karl Mechtler
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
| | - Franz Herzog
- Department of Biochemistry, Gene Center, Ludwig-Maximilians Universität München, 81377 Munich, Germany
| | - Thomas C Marlovits
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria Institute of Molecular Biotechnology GmbH, Austrian Academy of Sciences, 1030 Vienna, Austria Center for Structural Systems Biology, University Medical Center Eppendorf-Hamburg, 20246 Hamburg, Germany Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany
| | - Stefan Westermann
- Research Institute of Molecular Pathology, Vienna Biocenter, 1030 Vienna, Austria
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Ibrahim B, Henze R. Active transport can greatly enhance Cdc20:Mad2 formation. Int J Mol Sci 2014; 15:19074-91. [PMID: 25338047 PMCID: PMC4227261 DOI: 10.3390/ijms151019074] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 09/30/2014] [Accepted: 10/11/2014] [Indexed: 12/12/2022] Open
Abstract
To guarantee genomic integrity and viability, the cell must ensure proper distribution of the replicated chromosomes among the two daughter cells in mitosis. The mitotic spindle assembly checkpoint (SAC) is a central regulatory mechanism to achieve this goal. A dysfunction of this checkpoint may lead to aneuploidy and likely contributes to the development of cancer. Kinetochores of unattached or misaligned chromosomes are thought to generate a diffusible “wait-anaphase” signal, which is the basis for downstream events to inhibit the anaphase promoting complex/cyclosome (APC/C). The rate of Cdc20:C-Mad2 complex formation at the kinetochore is a key regulatory factor in the context of APC/C inhibition. Computer simulations of a quantitative SAC model show that the formation of Cdc20:C-Mad2 is too slow for checkpoint maintenance when cytosolic O-Mad2 has to encounter kinetochores by diffusion alone. Here, we show that an active transport of O-Mad2 towards the spindle mid-zone increases the efficiency of Mad2-activation. Our in-silico data indicate that this mechanism can greatly enhance the formation of Cdc20:Mad2 and furthermore gives an explanation on how the “wait-anaphase” signal can dissolve abruptly within a short time. Our results help to understand parts of the SAC mechanism that remain unclear.
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Affiliation(s)
- Bashar Ibrahim
- Al-Qunfudah University College, Umm Al-Qura University, 1109 Makkah Al-Mukarramah, Saudi Arabia.
| | - Richard Henze
- Bio Systems Analysis Group, Institute of Computer Science, Jena Center for Bioinformatics and Friedrich Schiller University, 07743 Jena, Germany.
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41
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Abstract
Centromeres are specialized domains of heterochromatin that provide the foundation for the kinetochore. Centromeric heterochromatin is characterized by specific histone modifications, a centromere-specific histone H3 variant (CENP-A), and the enrichment of cohesin, condensin, and topoisomerase II. Centromere DNA varies orders of magnitude in size from 125 bp (budding yeast) to several megabases (human). In metaphase, sister kinetochores on the surface of replicated chromosomes face away from each other, where they establish microtubule attachment and bi-orientation. Despite the disparity in centromere size, the distance between separated sister kinetochores is remarkably conserved (approximately 1 μm) throughout phylogeny. The centromere functions as a molecular spring that resists microtubule-based extensional forces in mitosis. This review explores the physical properties of DNA in order to understand how the molecular spring is built and how it contributes to the fidelity of chromosome segregation.
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Affiliation(s)
- Kerry S Bloom
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599-3280;
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42
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Hewawasam GS, Mattingly M, Venkatesh S, Zhang Y, Florens L, Workman JL, Gerton JL. Phosphorylation by casein kinase 2 facilitates Psh1 protein-assisted degradation of Cse4 protein. J Biol Chem 2014; 289:29297-309. [PMID: 25183013 PMCID: PMC4200280 DOI: 10.1074/jbc.m114.580589] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Cse4 is the centromeric histone H3 variant in budding yeast. Psh1 is an E3 ubiquitin ligase that controls Cse4 levels through proteolysis. Here we report that Psh1 is phosphorylated by the Cka2 subunit of casein kinase 2 (CK2) to promote its E3 activity for Cse4. Deletion of CKA2 significantly stabilized Cse4. Consistent with phosphorylation promoting the activity of Psh1, Cse4 was stabilized in a Psh1 phosphodepleted mutant strain in which the major phosphorylation sites were changed to alanines. Phosphorylation of Psh1 did not control Psh1-Cse4 or Psh1-Ubc3(E2) interactions. Although Cse4 was highly stabilized in a cka2Δ strain, mislocalization of Cse4 was mild, suggesting that Cse4 misincorporation was prevented by the intact Psh1-Cse4 association. Supporting this idea, Psh1 was also stabilized in a cka2Δ strain. Collectively our data suggest that phosphorylation is crucial in Psh1-assisted control of Cse4 levels and that the Psh1-Cse4 association itself functions to prevent Cse4 misincorporation.
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Affiliation(s)
- Geetha S Hewawasam
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110 and
| | - Mark Mattingly
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110 and
| | | | - Ying Zhang
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110 and
| | - Laurence Florens
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110 and
| | - Jerry L Workman
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110 and
| | - Jennifer L Gerton
- From the Stowers Institute for Medical Research, Kansas City, Missouri 64110 and Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas 66160
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43
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Bodor DL, Mata JF, Sergeev M, David AF, Salimian KJ, Panchenko T, Cleveland DW, Black BE, Shah JV, Jansen LE. The quantitative architecture of centromeric chromatin. eLife 2014; 3:e02137. [PMID: 25027692 PMCID: PMC4091408 DOI: 10.7554/elife.02137] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The centromere, responsible for chromosome segregation during mitosis, is epigenetically defined by CENP-A containing chromatin. The amount of centromeric CENP-A has direct implications for both the architecture and epigenetic inheritance of centromeres. Using complementary strategies, we determined that typical human centromeres contain ∼400 molecules of CENP-A, which is controlled by a mass-action mechanism. This number, despite representing only ∼4% of all centromeric nucleosomes, forms a ∼50-fold enrichment to the overall genome. In addition, although pre-assembled CENP-A is randomly segregated during cell division, this amount of CENP-A is sufficient to prevent stochastic loss of centromere function and identity. Finally, we produced a statistical map of CENP-A occupancy at a human neocentromere and identified nucleosome positions that feature CENP-A in a majority of cells. In summary, we present a quantitative view of the centromere that provides a mechanistic framework for both robust epigenetic inheritance of centromeres and the paucity of neocentromere formation. DOI:http://dx.doi.org/10.7554/eLife.02137.001 The genetic information in a cell is packed into structures called chromosomes. These contain strands of DNA wrapped around proteins called histones, which helps the long DNA chains to fit inside the relatively small nucleus of the cell. When a cell divides, it is important that both of the new cells contain all of the genetic information found in the parent cell. Therefore, the chromosomes duplicate during cell division, with the two copies held together at a single region of the chromosome called the centromere. The centromere then recruits and coordinates the molecular machinery that separates the two copies into different cells. Centromeres are inherited in an epigenetic manner. This means that there is no specific DNA sequence that defines the location of this structure on the chromosomes. Rather, a special type of histone, called CENP-A, is involved in defining its location. Bodor et al. use multiple techniques to show that human centromeres normally contain around 400 molecules of CENP-A, and that this number is crucial for ensuring that centromeres form in the right place. Interestingly, only a minority of the CENP-A molecules are located at centromeres; yet this is more than at any other region of the chromosome. This explains why centromeres are only formed at a single position on each chromosome. When the chromosomes separate, the CENP-A molecules at the centromere are randomly divided between the two copies. In this way memory of the centromere location is maintained. If the number of copies of CENP-A inherited by one of the chromosomes drops below a threshold value, a centromere will not form. However, Bodor et al. found that the number of CENP-A molecules in a centromere is large enough, not only to support the formation of the centromere structure, but also to keep it above the threshold value in nearly all cases. This threshold is also high enough to make it unlikely that a centromere will form in the wrong place because of a random fluctuation in the number of CENP-A molecules. Therefore, the number of CENP-A molecules is crucial for controlling both the formation and the inheritance of the centromere. DOI:http://dx.doi.org/10.7554/eLife.02137.002
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Affiliation(s)
- Dani L Bodor
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - João F Mata
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Mikhail Sergeev
- Department of Systems Biology, Harvard Medical School, Boston, United States Renal Division, Brigham and Women's Hospital, Boston, United States
| | | | - Kevan J Salimian
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Tanya Panchenko
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Don W Cleveland
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, United States Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, United States
| | - Ben E Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Jagesh V Shah
- Department of Systems Biology, Harvard Medical School, Boston, United States Renal Division, Brigham and Women's Hospital, Boston, United States
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44
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Malvezzi F, Westermann S. "Uno, nessuno e centomila": the different faces of the budding yeast kinetochore. Chromosoma 2014; 123:447-57. [PMID: 24964966 DOI: 10.1007/s00412-014-0472-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 06/10/2014] [Accepted: 06/10/2014] [Indexed: 12/28/2022]
Abstract
"One, no one and one hundred thousand" is a masterpiece of Italian literature, written by Luigi Pirandello. The central theme is that in each individual there are multiple personalities, since one's perception of one's self differs from the view of others. As a consequence, a unique identity does not exist, but rather one hundred thousand. This concept can be very well applied to the kinetochore, one of the largest macromolecular complexes conserved in eukaryotes. The kinetochore is essential during cell division and fulfills different sophisticated functions, including linking chromosomes to spindle microtubules and delaying anaphase onset in case of incorrect bi-orientation. In order to perform these tasks, the kinetochore shapes its structure by recruiting different subunits, such as the components of the spindle assembly checkpoint (SAC) or the monopolin complex during meiosis. It also modifies its internal organization by rearranging intramolecular connections and acquiring a distinct identity at different time points of cell division. In this review, we describe recent insights into the changes in composition and configuration of the kinetochore in mitosis and meiosis, focusing on the kinetochore of Saccharomyces cerevisiae.
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Affiliation(s)
- Francesca Malvezzi
- Research Institute of Molecular Pathology (IMP), Dr. Bohr Gasse 7, 1030, Vienna, Austria
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45
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Wisniewski J, Hajj B, Chen J, Mizuguchi G, Xiao H, Wei D, Dahan M, Wu C. Imaging the fate of histone Cse4 reveals de novo replacement in S phase and subsequent stable residence at centromeres. eLife 2014; 3:e02203. [PMID: 24844245 PMCID: PMC4067749 DOI: 10.7554/elife.02203] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The budding yeast centromere contains Cse4, a specialized histone H3 variant. Fluorescence pulse-chase analysis of an internally tagged Cse4 reveals that it is replaced with newly synthesized molecules in S phase, remaining stably associated with centromeres thereafter. In contrast, C-terminally-tagged Cse4 is functionally impaired, showing slow cell growth, cell lethality at elevated temperatures, and extra-centromeric nuclear accumulation. Recent studies using such strains gave conflicting findings regarding the centromeric abundance and cell cycle dynamics of Cse4. Our findings indicate that internally tagged Cse4 is a better reporter of the biology of this histone variant. Furthermore, the size of centromeric Cse4 clusters was precisely mapped with a new 3D-PALM method, revealing substantial compaction during anaphase. Cse4-specific chaperone Scm3 displays steady-state, stoichiometric co-localization with Cse4 at centromeres throughout the cell cycle, while undergoing exchange with a nuclear pool. These findings suggest that a stable Cse4 nucleosome is maintained by dynamic chaperone-in-residence Scm3.DOI: http://dx.doi.org/10.7554/eLife.02203.001.
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Affiliation(s)
- Jan Wisniewski
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Bassam Hajj
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Jiji Chen
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Gaku Mizuguchi
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Hua Xiao
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Debbie Wei
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Maxime Dahan
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Carl Wu
- Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, United States Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, United States
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46
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Abstract
Localization of the histone H3 variant Cse4 (CENP-A) at the ~125 base pair point centromere in budding yeast directs assembly of a kinetochore that binds one microtubule. Recent work suggests there is more Cse4 at point centromeres than originally thought.
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Affiliation(s)
- Thomas J Maresca
- Biology Department, University of Massachusetts Amherst, Amherst, MA 01003, USA.
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47
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Cieśliński K, Ries J. The yeast kinetochore - structural insights from optical microscopy. Curr Opin Chem Biol 2014; 20:1-8. [PMID: 24763395 DOI: 10.1016/j.cbpa.2014.03.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 03/26/2014] [Indexed: 11/19/2022]
Abstract
In eukaryotic organisms each chromosome is captured by spindle microtubules. This interaction is mediated by an evolutionarily conserved, multi-protein complex called kinetochore. The main function of the kinetochore is to maintain correct chromosome segregation during cell division by transporting each sister chromatid to the spindle pole bodies localized at the opposite sites of the yeast nucleus. The kinetochore of budding yeast (Saccharomyces cerevisiae) is often used as a model system due to its simple composition compared to higher eukaryotes. This review highlights results obtained using optical imaging that revealed relative positions and stoichiometry of the major components of the budding yeast kinetochore.
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Affiliation(s)
- Konstanty Cieśliński
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Jonas Ries
- European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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48
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Henikoff S, Ramachandran S, Krassovsky K, Bryson TD, Codomo CA, Brogaard K, Widom J, Wang JP, Henikoff JG. The budding yeast Centromere DNA Element II wraps a stable Cse4 hemisome in either orientation in vivo. eLife 2014; 3:e01861. [PMID: 24737863 PMCID: PMC3983907 DOI: 10.7554/elife.01861] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In budding yeast, a single cenH3 (Cse4) nucleosome occupies the ∼120-bp functional centromere, however conflicting structural models for the particle have been proposed. To resolve this controversy, we have applied H4S47C-anchored cleavage mapping, which reveals the precise position of histone H4 in every nucleosome in the genome. We find that cleavage patterns at centromeres are unique within the genome and are incompatible with symmetrical structures, including octameric nucleosomes and (Cse4/H4)2 tetrasomes. Centromere cleavage patterns are compatible with a precisely positioned core structure, one in which each of the 16 yeast centromeres is occupied by oppositely oriented Cse4/H4/H2A/H2B hemisomes in two rotational phases within the population. Centromere-specific hemisomes are also inferred from distances observed between closely-spaced H4 cleavages, as predicted from structural modeling. Our results indicate that the orientation and rotational position of the stable hemisome at each yeast centromere is not specified by the functional centromere sequence. DOI:http://dx.doi.org/10.7554/eLife.01861.001 DNA is tightly packaged in cells for a variety of reasons—to allow it to fit inside the nucleus, to protect it from damage, and to help control the production of proteins from genes. The basic unit of packaged DNA is called a nucleosome, which consists of DNA wrapped around a structure formed by two pairs of four different proteins. These proteins, which are called histones, have a role that extends beyond providing structural support for DNA. When cells divide, for example, pairs of ‘sister chromosomes’ are pulled apart to ensure that the two daughter cells both have the same chromosomes as the original cell. The sister chromosomes are pulled apart from a single position called a centromere, and the nucleosomes at this position contain a histone that is different from the histones found everywhere else in the cell. However, until recently it was not clear if the nucleosomes that contained these special cenH3 histones had the same structure as other nucleosomes. Now Henikoff et al. have used a method called H4S47C-anchored cleavage mapping to study every nucleosome in the genome of the yeast S. cerevisiae. This mapping technique uses DNA sequencing to measure the precise distances between fixed points on the DNA in the nucleosome. Knowing these distances tells researchers a great deal about the number and position of the histones within each nucleosome in the genome. Using this approach, Henikoff et al. found that nucleosomes at centromeres are different from other nucleosomes in histone number and arrangement. In particular, the nucleosome at each yeast centromere contains only one each of the four different histones in an asymmetrical orientation, in contrast to all other yeast nucleosomes, which contain two sets of four histones in a symmetrical arrangement. Furthermore, each nucleosome at a centromere can adopt one of two orientations: these orientations are mirror images of each other, and they occur with equal probability. It should also be possible to use the mapping technique developed by Henikoff et al. to study the larger and more complex centromeres found in other organisms, including humans. DOI:http://dx.doi.org/10.7554/eLife.01861.002
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Affiliation(s)
- Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
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49
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Abstract
Biological questions are increasingly being addressed using a wide range of quantitative analytical tools to examine protein complex composition. Knowledge of the absolute number of proteins present provides insights into organization, function, and maintenance and is used in mathematical modeling of complex cellular dynamics. In this chapter, we outline and describe three microscopy-based methods for determining absolute protein numbers--fluorescence correlation spectroscopy, stepwise photobleaching, and ratiometric comparison of fluorescence intensity to known standards. In addition, we discuss the various fluorescently labeled proteins that have been used as standards for both stepwise photobleaching and ratiometric comparison analysis. A detailed procedure for determining absolute protein number by ratiometric comparison is outlined in the second half of this chapter. Counting proteins by quantitative microscopy is a relatively simple yet very powerful analytical tool that will increase our understanding of protein complex composition.
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