1
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Mahalingan KK, Grotjahn DA, Li Y, Lander GC, Zehr EA, Roll-Mecak A. Structural basis for α-tubulin-specific and modification state-dependent glutamylation. Nat Chem Biol 2024:10.1038/s41589-024-01599-0. [PMID: 38658656 DOI: 10.1038/s41589-024-01599-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 03/06/2024] [Indexed: 04/26/2024]
Abstract
Microtubules have spatiotemporally complex posttranslational modification patterns. Tubulin tyrosine ligase-like (TTLL) enzymes introduce the most prevalent modifications on α-tubulin and β-tubulin. How TTLLs specialize for specific substrate recognition and ultimately modification-pattern generation is largely unknown. TTLL6, a glutamylase implicated in ciliopathies, preferentially modifies tubulin α-tails in microtubules. Cryo-electron microscopy, kinetic analysis and single-molecule biochemistry reveal an unprecedented quadrivalent recognition that ensures simultaneous readout of microtubule geometry and posttranslational modification status. By binding to a β-tubulin subunit, TTLL6 modifies the α-tail of the longitudinally adjacent tubulin dimer. Spanning two tubulin dimers along and across protofilaments (PFs) ensures fidelity of recognition of both the α-tail and the microtubule. Moreover, TTLL6 reads out and is stimulated by glutamylation of the β-tail of the laterally adjacent tubulin dimer, mediating crosstalk between α-tail and β-tail. This positive feedback loop can generate localized microtubule glutamylation patterns. Our work uncovers general principles that generate tubulin chemical and topographic complexity.
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Affiliation(s)
- Kishore K Mahalingan
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Danielle A Grotjahn
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute La Jolla, La Jolla, CA, USA
| | - Yan Li
- Proteomics Core Facility, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute La Jolla, La Jolla, CA, USA
| | - Elena A Zehr
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Antonina Roll-Mecak
- Cell Biology and Biophysics Unit, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
- Biochemistry & Biophysics Center, National Heart, Lung and Blood Institute, Bethesda, MD, USA.
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2
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Muir KW, Batters C, Dendooven T, Yang J, Zhang Z, Burt A, Barford D. Structural mechanism of outer kinetochore Dam1-Ndc80 complex assembly on microtubules. Science 2023; 382:1184-1190. [PMID: 38060647 PMCID: PMC7615550 DOI: 10.1126/science.adj8736] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/25/2023] [Indexed: 12/18/2023]
Abstract
Kinetochores couple chromosomes to the mitotic spindle to segregate the genome during cell division. An error correction mechanism drives the turnover of kinetochore-microtubule attachments until biorientation is achieved. The structural basis for how kinetochore-mediated chromosome segregation is accomplished and regulated remains an outstanding question. In this work, we describe the cryo-electron microscopy structure of the budding yeast outer kinetochore Ndc80 and Dam1 ring complexes assembled onto microtubules. Complex assembly occurs through multiple interfaces, and a staple within Dam1 aids ring assembly. Perturbation of key interfaces suppresses yeast viability. Force-rupture assays indicated that this is a consequence of impaired kinetochore-microtubule attachment. The presence of error correction phosphorylation sites at Ndc80-Dam1 ring complex interfaces and the Dam1 staple explains how kinetochore-microtubule attachments are destabilized and reset.
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Affiliation(s)
- Kyle W. Muir
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Christopher Batters
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Tom Dendooven
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Jing Yang
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Ziguo Zhang
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Alister Burt
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - David Barford
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
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3
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Sankaranarayanan SR, Polisetty SD, Das K, Dumbrepatil A, Medina-Pritchard B, Singleton M, Jeyaprakash AA, Sanyal K. Functional plasticity in chromosome-microtubule coupling on the evolutionary time scale. Life Sci Alliance 2023; 6:e202201720. [PMID: 37793775 PMCID: PMC10551642 DOI: 10.26508/lsa.202201720] [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: 09/12/2022] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 10/06/2023] Open
Abstract
The Dam1 complex is essential for mitotic progression across evolutionarily divergent fungi. Upon analyzing amino acid (aa) sequences of Dad2, a Dam1 complex subunit, we identified a conserved 10-aa-long Dad2 signature sequence (DSS). An arginine residue (R126) in the DSS is essential for viability in Saccharomyces cerevisiae that possesses point centromeres. The corresponding arginine residues are functionally important but not essential for viability in Candida albicans and Cryptococcus neoformans; both carry several kilobases long regional centromeres. The purified recombinant Dam1 complex containing either Dad2ΔDSS or Dad2R126A failed to bind microtubules (MTs) or form any visible rings like the WT complex. Intriguingly, functional analysis revealed that the requirement of the conserved arginine residue for chromosome biorientation and mitotic progression reduced with increasing centromere length. We propose that plasticity of the invariant arginine of Dad2 in organisms with regional centromeres is achieved by conditional elevation of the kinetochore protein(s) to enable multiple kinetochore MTs to bind to each chromosome. The capacity of a chromosome to bind multiple kinetochore MTs may mask the deleterious effects of such lethal mutations.
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Affiliation(s)
- Sundar Ram Sankaranarayanan
- https://ror.org/0538gdx71 Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Satya Dev Polisetty
- https://ror.org/0538gdx71 Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Kuladeep Das
- https://ror.org/0538gdx71 Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Arti Dumbrepatil
- https://ror.org/0538gdx71 Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Bethan Medina-Pritchard
- https://ror.org/01nrxwf90 Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Martin Singleton
- https://ror.org/01nrxwf90 Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - A Arockia Jeyaprakash
- https://ror.org/01nrxwf90 Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
- Gene Center and Department of Biochemistry, Ludwig-Maximilian-Universität, Munich, Germany
| | - Kaustuv Sanyal
- https://ror.org/0538gdx71 Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
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4
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Zahm JA, Jenni S, Harrison SC. Structure of the Ndc80 complex and its interactions at the yeast kinetochore-microtubule interface. Open Biol 2023; 13:220378. [PMID: 36883282 PMCID: PMC9993044 DOI: 10.1098/rsob.220378] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
Abstract
The conserved Ndc80 kinetochore complex, Ndc80c, is the principal link between mitotic spindle microtubules and centromere-associated proteins. We used AlphaFold 2 (AF2) to obtain predictions of the Ndc80 'loop' structure and of the Ndc80 : Nuf2 globular head domains that interact with the Dam1 subunit of the heterodecameric DASH/Dam1 complex (Dam1c). The predictions guided design of crystallizable constructs, with structures close to the predicted ones. The Ndc80 'loop' is a stiff, α-helical 'switchback' structure; AF2 predictions and positions of preferential cleavage sites indicate that flexibility within the long Ndc80c rod occurs instead at a hinge closer to the globular head. Conserved stretches of the Dam1 C terminus bind Ndc80c such that phosphorylation of Dam1 serine residues 257, 265 and 292 by the mitotic kinase Ipl1/Aurora B can release this contact during error correction of mis-attached kinetochores. We integrate the structural results presented here into our current molecular model of the kinetochore-microtubule interface. The model illustrates how multiple interactions between Ndc80c, DASH/Dam1c and the microtubule lattice stabilize kinetochore attachments.
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Affiliation(s)
- Jacob A. Zahm
- Department of Biological Chemistry and Molecular Pharmacology, and
| | - Simon Jenni
- Department of Biological Chemistry and Molecular Pharmacology, and
| | - Stephen C. Harrison
- Department of Biological Chemistry and Molecular Pharmacology, and
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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5
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Rafiei A, Cruz Tetlalmatzi S, Edrington CH, Lee L, Crowder DA, Saltzberg DJ, Sali A, Brouhard G, Schriemer DC. Doublecortin engages the microtubule lattice through a cooperative binding mode involving its C-terminal domain. eLife 2022; 11:66975. [PMID: 35485925 PMCID: PMC9122500 DOI: 10.7554/elife.66975] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/07/2022] [Indexed: 11/17/2022] Open
Abstract
Doublecortin (DCX) is a microtubule (MT)-associated protein that regulates MT structure and function during neuronal development and mutations in DCX lead to a spectrum of neurological disorders. The structural properties of MT-bound DCX that explain these disorders are incompletely determined. Here, we describe the molecular architecture of the DCX–MT complex through an integrative modeling approach that combines data from X-ray crystallography, cryo-electron microscopy, and a high-fidelity chemical crosslinking method. We demonstrate that DCX interacts with MTs through its N-terminal domain and induces a lattice-dependent self-association involving the C-terminal structured domain and its disordered tail, in a conformation that favors an open, domain-swapped state. The networked state can accommodate multiple different attachment points on the MT lattice, all of which orient the C-terminal tails away from the lattice. As numerous disease mutations cluster in the C-terminus, and regulatory phosphorylations cluster in its tail, our study shows that lattice-driven self-assembly is an important property of DCX.
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Affiliation(s)
- Atefeh Rafiei
- Department of Chemistry, University of Calgary, Calgary, Canada
| | | | | | - Linda Lee
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - D Alex Crowder
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
| | - Daniel J Saltzberg
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
| | - Gary Brouhard
- Department of Biology, McGill University, Montreal, Canada
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Canada
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6
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Rafiei A, Schriemer DC. A Crosslinking Mass Spectrometry Protocol for the Structural Analysis of Microtubule-Associated Proteins. Methods Mol Biol 2022; 2456:211-222. [PMID: 35612744 DOI: 10.1007/978-1-0716-2124-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Microtubule-associated proteins (MAPs) engage microtubules (MTs) to regulate both the MT state and wide variety of cytoskeletal functions. A comprehensive understanding of MAPs function requires the structural characterization of physical contacts MAPs make with other proteins, particularly when engaged with the microtubule (MT) lattice. Most of the interaction between MAPs and MTs evade classical structural determination techniques, as the interactions can be both heterogenous and sub-stoichiometric. Crosslinking mass spectrometry (XL-MS) can aid in MAP-MT structure analysis by providing a wealth of residue-based distance restraints. This protocol provides an XL-MS workflow for accurate and unbiased sampling of an equilibrated MAP-MT interaction, involving modifications to the preparation and validation of a MAP-MT construct suitable for crosslinking with fast-sampling heterobifunctional crosslinkers. The distance restrains obtained by this protocol can be used to generate accurate models assembled with an integrative structural modeling approach.
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Affiliation(s)
- Atefeh Rafiei
- Department of Chemistry, University of Calgary, Calgary, AB, Canada
| | - David C Schriemer
- Department of Chemistry, University of Calgary, Calgary, AB, Canada.
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada.
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7
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Dudziak A, Engelhard L, Bourque C, Klink BU, Rombaut P, Kornakov N, Jänen K, Herzog F, Gatsogiannis C, Westermann S. Phospho-regulated Bim1/EB1 interactions trigger Dam1c ring assembly at the budding yeast outer kinetochore. EMBO J 2021; 40:e108004. [PMID: 34313341 PMCID: PMC8441410 DOI: 10.15252/embj.2021108004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 07/01/2021] [Accepted: 07/07/2021] [Indexed: 11/16/2022] Open
Abstract
Kinetochores form the link between chromosomes and microtubules of the mitotic spindle. The heterodecameric Dam1 complex (Dam1c) is a major component of the Saccharomyces cerevisiae outer kinetochore, assembling into 3 MDa‐sized microtubule‐embracing rings, but how ring assembly is specifically initiated in vivo remains to be understood. Here, we describe a molecular pathway that provides local control of ring assembly during the establishment of sister kinetochore bi‐orientation. We show that Dam1c and the general microtubule plus end‐associated protein (+TIP) Bim1/EB1 form a stable complex depending on a conserved motif in the Duo1 subunit of Dam1c. EM analyses reveal that Bim1 crosslinks protrusion domains of adjacent Dam1c heterodecamers and promotes the formation of oligomers with defined curvature. Disruption of the Dam1c‐Bim1 interaction impairs kinetochore localization of Dam1c in metaphase and delays mitosis. Phosphorylation promotes Dam1c‐Bim1 binding by relieving an intramolecular inhibition of the Dam1 C‐terminus. In addition, Bim1 recruits Bik1/CLIP‐170 to Dam1c and induces formation of full rings even in the absence of microtubules. Our data help to explain how new kinetochore end‐on attachments are formed during the process of attachment error correction.
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Affiliation(s)
- Alexander Dudziak
- Department of Molecular Genetics I, Center of Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Lena Engelhard
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Cole Bourque
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,Institute for Medical Physics and Biophysics and Center for Soft Nanoscience, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Björn Udo Klink
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,Institute for Medical Physics and Biophysics and Center for Soft Nanoscience, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Pascaline Rombaut
- Gene Center Munich, Ludwig Maximilian University Munich, Munich, Germany
| | - Nikolay Kornakov
- Department of Molecular Genetics I, Center of Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Karolin Jänen
- Department of Molecular Genetics I, Center of Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
| | - Franz Herzog
- Gene Center Munich, Ludwig Maximilian University Munich, Munich, Germany
| | - Christos Gatsogiannis
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,Institute for Medical Physics and Biophysics and Center for Soft Nanoscience, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Stefan Westermann
- Department of Molecular Genetics I, Center of Molecular Biotechnology, University of Duisburg-Essen, Essen, Germany
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8
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Doodhi H, Kasciukovic T, Clayton L, Tanaka TU. Aurora B switches relative strength of kinetochore-microtubule attachment modes for error correction. J Cell Biol 2021; 220:211981. [PMID: 33851957 PMCID: PMC8050843 DOI: 10.1083/jcb.202011117] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/03/2021] [Accepted: 03/17/2021] [Indexed: 11/24/2022] Open
Abstract
To establish chromosome biorientation, aberrant kinetochore–microtubule interaction must be resolved (error correction) by Aurora B kinase. Aurora B differentially regulates kinetochore attachment to the microtubule plus end and its lateral side (end-on and lateral attachment, respectively). However, it is still unclear how kinetochore–microtubule interactions are exchanged during error correction. Here, we reconstituted the budding yeast kinetochore–microtubule interface in vitro by attaching the Ndc80 complexes to nanobeads. These Ndc80C nanobeads recapitulated in vitro the lateral and end-on attachments of authentic kinetochores on dynamic microtubules loaded with the Dam1 complex. This in vitro assay enabled the direct comparison of lateral and end-on attachment strength and showed that Dam1 phosphorylation by Aurora B makes the end-on attachment weaker than the lateral attachment. Similar reconstitutions with purified kinetochore particles were used for comparison. We suggest the Dam1 phosphorylation weakens interaction with the Ndc80 complex, disrupts the end-on attachment, and promotes the exchange to a new lateral attachment, leading to error correction.
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Affiliation(s)
- Harinath Doodhi
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Taciana Kasciukovic
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Lesley Clayton
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Tomoyuki U Tanaka
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
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9
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Microtubules pull the strings: disordered sequences as efficient couplers of microtubule-generated force. Essays Biochem 2020; 64:371-382. [PMID: 32502246 DOI: 10.1042/ebc20190078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/01/2020] [Accepted: 05/14/2020] [Indexed: 11/17/2022]
Abstract
Microtubules are dynamic polymers that grow and shrink through addition or loss of tubulin subunits at their ends. Microtubule ends generate mechanical force that moves chromosomes and cellular organelles, and provides mechanical tension. Recent literature describes a number of proteins and protein complexes that couple dynamics of microtubule ends to movements of their cellular cargoes. These 'couplers' are quite diverse in their microtubule-binding domains (MTBDs), while sharing similarity in function, but a systematic understanding of the principles underlying their activity is missing. Here, I review various types of microtubule couplers, focusing on their essential activities: ability to follow microtubule ends and capture microtubule-generated force. Most of the couplers require presence of unstructured positively charged sequences and multivalency in their microtubule-binding sites to efficiently convert the microtubule-generated force into useful connection to a cargo. An overview of the microtubule features supporting end-tracking and force-coupling, and the experimental methods to assess force-coupling properties is also provided.
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10
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Structural view of the yeast Dam1 complex, a ring-shaped molecular coupler for the dynamic microtubule end. Essays Biochem 2020; 64:359-370. [PMID: 32579171 DOI: 10.1042/ebc20190079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 11/17/2022]
Abstract
In a dividing eukaryotic cell, proper chromosome segregation requires the dynamic yet persistent attachment of kinetochores to spindle microtubules. In the budding yeast Saccharomyces cerevisiae, this function is especially crucial because each kinetochore is attached to a single microtubule; consequently, loss of attachment could lead to unrecoverable chromosome loss. The highly specialized heterodecameric Dam1 protein complex achieves this coupling by assembling into a microtubule-encircling ring that glides near the end of the dynamic microtubule to mediate chromosome motion. In recent years, we have learned a great deal about the structural properties of the Dam1 heterodecamer, its mechanism of self-assembly into rings, and its tethering to the kinetochore by the elongated Ndc80 complex. The most remarkable progress has resulted from defining the fine structures of helical bundles within Dam1 heterodecamer. In this review, we critically analyze structural observations collected by diverse approaches with the goal of obtaining a unified view of Dam1 ring architecture. A considerable consistency between different studies supports a coherent model of the circular core of the Dam1 ring. However, there are persistent uncertainties about the composition of ring protrusions and flexible extensions, as well as their roles in mediating ring core assembly and interactions with the Ndc80 complex and microtubule.
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11
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Rafiei A, Schriemer DC. A microtubule crosslinking protocol for integrative structural modeling activities. Anal Biochem 2019; 586:113416. [PMID: 31499019 DOI: 10.1016/j.ab.2019.113416] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/30/2019] [Accepted: 09/05/2019] [Indexed: 11/15/2022]
Abstract
Microtubules (MTs) are key components in the cytoskeleton of the eukaryotic cell, and play roles in processes such as intracellular transport and cell division. An improved understanding MT regulation requires structural analysis of the extensive interactions between the MT lattice and its regulatory proteins, but MT interactions are challenging for even the most advanced structural methods to characterize. Integrative methods involving crosslinking mass spectrometry (XL-MS) can extend structural analysis to many interaction classes, but the representation of MTs in crosslinking data-sets has been surprisingly low. Here, we explore the basis for the underrepresentation of the MT lattice and present an enhanced method for mapping MT structural features using an optimized set of reagents, together with fluorescence detection to ensure MT structural integrity. Through the application of stringent identification criteria, 91 unique crosslinks were identified, 78 of which were uniquely matched to 7 distinct structural features of the MT lattice. Of note, 4 crosslinks were detected for the lattice-A protofilament organization. The lattice-A structure defines a "seam" or discontinuity in MTs and is an emerging site of interest for MT regulation. Our methodology should be broadly applicable to integrative structural studies involving any MT-protein interaction.
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Affiliation(s)
- Atefeh Rafiei
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada
| | - David C Schriemer
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada; Department of Biochemistry and Molecular Biology, University of Calgary, Alberta, Canada.
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12
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Hamilton G, Dimitrova Y, Davis TN. Seeing is believing: our evolving view of kinetochore structure, composition, and assembly. Curr Opin Cell Biol 2019; 60:44-52. [PMID: 31078123 DOI: 10.1016/j.ceb.2019.03.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/20/2019] [Accepted: 03/28/2019] [Indexed: 11/26/2022]
Abstract
This review highlights three recent trends in the field of kinetochore biology: the proliferation of structural data for kinetochore protein complexes (including CBF3, Dam1c, Mis12cMIND, and CENP-NLChl4/Iml3); the growing consensus that the kinetochore is a dynamic structure whose composition changes as the cell cycle progresses; and the mounting evidence of multiple pathways whereby the microtubule-binding elements of the outer kinetochore may be recruited by inner kinetochore proteins. Our focus is on the two best-studied systems in the field: human and budding yeast kinetochores. This review will demonstrate the remarkable similarity of these two systems, as well as their intriguing differences.
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Affiliation(s)
- Grace Hamilton
- Department of Biochemistry, University of Washington Box 357350, 1705 NE Pacific St., Seattle, WA 98195-7350, USA
| | - Yoana Dimitrova
- Genentech, Inc., 1 DNA Way, MS: 27, South San Francisco, CA 94080, USA
| | - Trisha N Davis
- Department of Biochemistry, University of Washington Box 357350, 1705 NE Pacific St., Seattle, WA 98195-7350, USA.
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13
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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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14
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Shah H, Rawat K, Ashar H, Patkar R, Manjrekar J. Dual role for fungal-specific outer kinetochore proteins during cell cycle and development in Magnaporthe oryzae. J Cell Sci 2019; 132:jcs.224147. [DOI: 10.1242/jcs.224147] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Accepted: 05/07/2019] [Indexed: 01/02/2023] Open
Abstract
The outer kinetochore DAM/DASH complex ensures proper spindle structure and chromosome segregation. While DASH complex protein requirement diverges among different yeasts, its role in filamentous fungi has not been investigated so far. We studied the dynamics and role of middle (Mis12) and outer (Dam1 and Ask1) kinetochore proteins in the filamentous fungal pathogen, Magnaporthe oryzae, which undergoes multiple cell cycle linked developmental transitions. While Mis12 was constitutively present in the nucleus, Dam1 and Ask1 were recruited only during mitosis. Although Dam1 was not required for viability, loss of its function (dam1Δ) delayed mitotic progression, resulting in impaired conidial and hyphal development. Both Dam1 and Ask1 also localised to the hyphal tips, in the form of punctae oscillating back and forth from the growing ends, suggesting that Magnaporthe DASH complex proteins may play a non-canonical role in polarised growth during interphase, in addition to their function in nuclear segregation during mitosis. Impaired appressorial (infection structure) development and host penetration in the dam1Δ mutant suggest that fungus-specific Dam1 complex proteins could be an attractive target for a novel anti-fungal strategy.
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Affiliation(s)
- Hiral Shah
- Bharat Chattoo Genome Research Centre, Department of Microbiology and Biotechnology Centre, The Maharaja Sayajirao University of Baroda, Vadodara 390002, Gujarat, India
| | - Kanika Rawat
- Bharat Chattoo Genome Research Centre, Department of Microbiology and Biotechnology Centre, The Maharaja Sayajirao University of Baroda, Vadodara 390002, Gujarat, India
- Present affiliation: Centre for Ecological Sciences, Indian Institute of Science, Bengaluru-560012, Karnataka, India
| | - Harsh Ashar
- Bharat Chattoo Genome Research Centre, Department of Microbiology and Biotechnology Centre, The Maharaja Sayajirao University of Baroda, Vadodara 390002, Gujarat, India
- Present affiliation: Stem Cell Biology Group, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, Maharashtra, India
| | - Rajesh Patkar
- Bharat Chattoo Genome Research Centre, Department of Microbiology and Biotechnology Centre, The Maharaja Sayajirao University of Baroda, Vadodara 390002, Gujarat, India
| | - Johannes Manjrekar
- Biotechnology Programme, Department of Microbiology and Biotechnology Centre, The Maharaja Sayajirao University of Baroda, Vadodara 390002, Gujarat, India
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15
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Glucose Signaling Is Connected to Chromosome Segregation Through Protein Kinase A Phosphorylation of the Dam1 Kinetochore Subunit in Saccharomyces cerevisiae. Genetics 2018; 211:531-547. [PMID: 30546002 DOI: 10.1534/genetics.118.301727] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/10/2018] [Indexed: 11/18/2022] Open
Abstract
The Dam1 complex is an essential component of the outer kinetochore that mediates attachments between spindle microtubules and chromosomes. Dam1p, a subunit of the Dam1 complex, binds to microtubules and is regulated by Aurora B/Ipl1p phosphorylation. We find that overexpression of cAMP-dependent protein kinase (PKA) catalytic subunits (i.e., TPK1, TPK2, TPK3) is lethal in DAM1 mutants and increases the rate of chromosome loss in wild-type cells. Replacing an evolutionarily conserved PKA site (S31) in Dam1p with a nonphosphorylatable alanine suppressed the high-copy PKA dosage lethality in dam1-1 Consistent with Dam1p as a target of PKA, we find that in vitro PKA can directly phosphorylate S31 in Dam1p and we observed phosphorylation of S31 in Dam1p purified from asynchronously growing yeast cells. Cells carrying high-copy TPK2 or a Dam1p phospho-mimetic S31D mutant displayed a reduction in Dam1p localization at the kinetochore, suggesting that PKA phosphorylation plays a role in assembly and/or stability of the Dam1 complex. Furthermore, we observed spindle defects associated with S31 phosphorylation. Finally, we find that phosphorylation of Dam1p on S31 is reduced when glucose is limiting as well as during α-factor arrest, conditions that inhibit PKA activity. These observations suggest that the PKA site of Dam1p participates in regulating kinetochore activity. While PKA is a well-established effector of glucose signaling, our work shows for the first time that glucose-dependent PKA activity has an important function in chromosome segregation.
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16
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Ng CT, Deng L, Chen C, Lim HH, Shi J, Surana U, Gan L. Electron cryotomography analysis of Dam1C/DASH at the kinetochore-spindle interface in situ. J Cell Biol 2018; 218:455-473. [PMID: 30504246 PMCID: PMC6363454 DOI: 10.1083/jcb.201809088] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/25/2018] [Accepted: 10/31/2018] [Indexed: 01/01/2023] Open
Abstract
In dividing cells, depolymerizing spindle microtubules move chromosomes by pulling at their kinetochores. While kinetochore subcomplexes have been studied extensively in vitro, little is known about their in vivo structure and interactions with microtubules or their response to spindle damage. Here we combine electron cryotomography of serial cryosections with genetic and pharmacological perturbation to study the yeast chromosome segregation machinery in vivo. Each kinetochore microtubule has one (rarely, two) Dam1C/DASH outer kinetochore assemblies. Dam1C/DASH contacts the microtubule walls and does so with its flexible "bridges"; there are no contacts with the protofilaments' curved tips. In metaphase, ∼40% of the Dam1C/DASH assemblies are complete rings; the rest are partial rings. Ring completeness and binding position along the microtubule are sensitive to kinetochore attachment and tension, respectively. Our study and those of others support a model in which each kinetochore must undergo cycles of conformational change to couple microtubule depolymerization to chromosome movement.
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Affiliation(s)
- Cai Tong Ng
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore
| | - Li Deng
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore
| | - Chen Chen
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore
| | - Hong Hwa Lim
- Institute of Molecular and Cell Biology Agency for Science Technology and Research, Singapore.,Bioprocessing Technology Institute, Agency for Science Technology and Research, Singapore
| | - Jian Shi
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore
| | - Uttam Surana
- Institute of Molecular and Cell Biology Agency for Science Technology and Research, Singapore.,Bioprocessing Technology Institute, Agency for Science Technology and Research, Singapore.,Department of Pharmacology, National University of Singapore, Singapore
| | - Lu Gan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore
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17
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Klykov O, Steigenberger B, Pektaş S, Fasci D, Heck AJR, Scheltema RA. Efficient and robust proteome-wide approaches for cross-linking mass spectrometry. Nat Protoc 2018; 13:2964-2990. [DOI: 10.1038/s41596-018-0074-x] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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18
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Jenni S, Harrison SC. Structure of the DASH/Dam1 complex shows its role at the yeast kinetochore-microtubule interface. Science 2018; 360:552-558. [PMID: 29724956 DOI: 10.1126/science.aar6436] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 03/15/2018] [Indexed: 12/13/2022]
Abstract
Kinetochores connect mitotic-spindle microtubules with chromosomes, allowing microtubule depolymerization to pull chromosomes apart during anaphase while resisting detachment as the microtubule shortens. The heterodecameric DASH/Dam1 complex (DASH/Dam1c), an essential component of yeast kinetochores, assembles into a microtubule-encircling ring. The ring associates with rodlike Ndc80 complexes to organize the kinetochore-microtubule interface. We report the cryo-electron microscopy structure (at ~4.5-angstrom resolution) of a DASH/Dam1c ring and a molecular model of its ordered components, validated by evolutionary direct-coupling analysis. Integrating this structure with that of the Ndc80 complex and with published interaction data yields a molecular picture of kinetochore-microtubule attachment, including how flexible, C-terminal extensions of DASH/Dam1c subunits project and contact widely separated sites on the Ndc80 complex rod and how phosphorylation at previously identified sites might regulate kinetochore assembly.
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Affiliation(s)
- Simon Jenni
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA
| | - Stephen C Harrison
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA. .,Howard Hughes Medical Institute, Harvard University, 250 Longwood Avenue, Boston, MA 02115, USA
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19
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Fischer L, Rappsilber J. False discovery rate estimation and heterobifunctional cross-linkers. PLoS One 2018; 13:e0196672. [PMID: 29746514 PMCID: PMC5944926 DOI: 10.1371/journal.pone.0196672] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 04/17/2018] [Indexed: 11/18/2022] Open
Abstract
False discovery rate (FDR) estimation is a cornerstone of proteomics that has recently been adapted to cross-linking/mass spectrometry. Here we demonstrate that heterobifunctional cross-linkers, while theoretically different from homobifunctional cross-linkers, need not be considered separately in practice. We develop and then evaluate the impact of applying a correct FDR formula for use of heterobifunctional cross-linkers and conclude that there are minimal practical advantages. Hence a single formula can be applied to data generated from the many different non-cleavable cross-linkers.
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Affiliation(s)
- Lutz Fischer
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
- * E-mail:
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20
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Musacchio A, Desai A. A Molecular View of Kinetochore Assembly and Function. BIOLOGY 2017; 6:E5. [PMID: 28125021 PMCID: PMC5371998 DOI: 10.3390/biology6010005] [Citation(s) in RCA: 310] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 01/16/2017] [Accepted: 01/17/2017] [Indexed: 12/15/2022]
Abstract
Kinetochores are large protein assemblies that connect chromosomes to microtubules of the mitotic and meiotic spindles in order to distribute the replicated genome from a mother cell to its daughters. Kinetochores also control feedback mechanisms responsible for the correction of incorrect microtubule attachments, and for the coordination of chromosome attachment with cell cycle progression. Finally, kinetochores contribute to their own preservation, across generations, at the specific chromosomal loci devoted to host them, the centromeres. They achieve this in most species by exploiting an epigenetic, DNA-sequence-independent mechanism; notable exceptions are budding yeasts where a specific sequence is associated with centromere function. In the last 15 years, extensive progress in the elucidation of the composition of the kinetochore and the identification of various physical and functional modules within its substructure has led to a much deeper molecular understanding of kinetochore organization and the origins of its functional output. Here, we provide a broad summary of this progress, focusing primarily on kinetochores of humans and budding yeast, while highlighting work from other models, and present important unresolved questions for future studies.
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Affiliation(s)
- Andrea Musacchio
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn Straße 11, Dortmund 44227, Germany.
- Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen 45117, Germany.
| | - Arshad Desai
- Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA.
- Department of Cellular & Molecular Medicine, 9500 Gilman Dr., La Jolla, CA 92093, USA.
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