1
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Kim D, Cianfrocco MA, Verhey KJ, Smith GA. The HSV-1 pUL37 protein promotes cell invasion by regulating the kinesin-1 motor. Proc Natl Acad Sci U S A 2024; 121:e2401341121. [PMID: 38696466 PMCID: PMC11087751 DOI: 10.1073/pnas.2401341121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/17/2024] [Indexed: 05/04/2024] Open
Abstract
Neurotropic alphaherpesviruses, including herpes simplex virus type 1 (HSV-1), recruit microtubule motor proteins to invade cells. The incoming viral particle traffics to nuclei in a two-step process. First, the particle uses the dynein-dynactin motor to sustain transport to the centrosome. In neurons, this step is responsible for long-distance retrograde axonal transport and is an important component of the neuroinvasive property shared by these viruses. Second, a kinesin-dependent mechanism redirects the particle from the centrosome to the nucleus. We have reported that the kinesin motor used during the second step of invasion is assimilated into nascent virions during the previous round of infection. Here, we report that the HSV-1 pUL37 tegument protein suppresses the assimilated kinesin-1 motor during retrograde axonal transport. Region 2 (R2) of pUL37 was required for suppression and functioned independently of the autoinhibitory mechanism native to kinesin-1. Furthermore, the motor domain and proximal coiled coil of kinesin-1 were sufficient for HSV-1 assimilation, pUL37 suppression, and nuclear trafficking. pUL37 localized to the centrosome, the site of assimilated kinesin-1 activation during infection, when expressed in cells in the absence of other viral proteins; however, pUL37 did not suppress kinesin-1 in this context. These results indicate that the pUL37 tegument protein spatially and temporally regulates kinesin-1 via the amino-terminal motor region in the context of the incoming viral particle.
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Affiliation(s)
- DongHo Kim
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| | - Michael A. Cianfrocco
- Life Sciences Institute, Department of Biological Chemistry, University of Michigan, Ann Arbor, MI48109
| | - Kristen J. Verhey
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI48109
| | - Gregory A. Smith
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL60611
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2
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Waas B, Carpenter BS, Franks NE, Merchant OQ, Verhey KJ, Allen BL. Dual and opposing roles for the kinesin-2 motor, KIF17, in Hedgehog-dependent cerebellar development. Sci Adv 2024; 10:eade1650. [PMID: 38669326 PMCID: PMC11051677 DOI: 10.1126/sciadv.ade1650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 03/26/2024] [Indexed: 04/28/2024]
Abstract
While the kinesin-2 motors KIF3A and KIF3B have essential roles in ciliogenesis and Hedgehog (HH) signal transduction, potential role(s) for another kinesin-2 motor, KIF17, in HH signaling have yet to be explored. Here, we investigated the contribution of KIF17 to HH-dependent cerebellar development, where Kif17 is expressed in both HH-producing Purkinje cells and HH-responding cerebellar granule neuron progenitors (CGNPs). Germline Kif17 deletion in mice results in cerebellar hypoplasia due to reduced CGNP proliferation, a consequence of decreased HH pathway activity mediated through decreased Sonic HH (SHH) protein. Notably, Purkinje cell-specific Kif17 deletion partially phenocopies Kif17 germline mutants. Unexpectedly, CGNP-specific Kif17 deletion results in the opposite phenotype-increased CGNP proliferation and HH target gene expression due to altered GLI transcription factor processing. Together, these data identify KIF17 as a key regulator of HH-dependent cerebellar development, with dual and opposing roles in HH-producing Purkinje cells and HH-responding CGNPs.
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Affiliation(s)
- Bridget Waas
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Brandon S. Carpenter
- Department of Molecular and Cellular Biology, College of Science and Mathematics, Kennesaw State University, Kennesaw, GA, 30061, USA
| | - Nicole E. Franks
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Olivia Q. Merchant
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kristen J. Verhey
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Benjamin L. Allen
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA
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3
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Takagishi M, Yue Y, Gray RS, Verhey KJ, Wallingford JB. Motor protein Kif6 regulates cilia motility and polarity in brain ependymal cells. Dis Model Mech 2024; 17:dmm050137. [PMID: 38235522 PMCID: PMC10924229 DOI: 10.1242/dmm.050137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 12/21/2023] [Indexed: 01/19/2024] Open
Abstract
Motile cilia on ependymal cells that line brain ventricular walls beat in concert to generate a flow of laminar cerebrospinal fluid (CSF). Dyneins and kinesins are ATPase microtubule motor proteins that promote the rhythmic beating of cilia axonemes. Despite common consensus about the importance of axonemal dynein motor proteins, little is known about how kinesin motors contribute to cilia motility. Here, we show that Kif6 is a slow processive motor (12.2±2.0 nm/s) on microtubules in vitro and localizes to both the apical cytoplasm and the axoneme in ependymal cells, although it does not display processive movement in vivo. Using a mouse mutant that models a human Kif6 mutation in a proband displaying macrocephaly, hypotonia and seizures, we found that loss of Kif6 function causes decreased ependymal cilia motility and, subsequently, decreases fluid flow on the surface of brain ventricular walls. Disruption of Kif6 also disrupts orientation of cilia, formation of robust apical actin networks and stabilization of basal bodies at the apical surface. This suggests a role for the Kif6 motor protein in the maintenance of ciliary homeostasis within ependymal cells.
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Affiliation(s)
- Maki Takagishi
- Department of Molecular Biosciences, Patterson Labs, The University of Texas at Austin, TX 78712, USA
| | - Yang Yue
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ryan S. Gray
- Departments of Nutrition and Pediatrics, Dell Pediatric Research Institute, The University of Texas at Austin, Dell Medical School, Austin, TX 78712, USA
| | - Kristen J. Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - John B. Wallingford
- Department of Molecular Biosciences, Patterson Labs, The University of Texas at Austin, TX 78712, USA
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4
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Tan Z, Yue Y, Leprevost F, Haynes S, Basrur V, Nesvizhskii AI, Verhey KJ, Cianfrocco MA. Autoinhibited kinesin-1 adopts a hierarchical folding pattern. eLife 2023; 12:RP86776. [PMID: 37910016 PMCID: PMC10619981 DOI: 10.7554/elife.86776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Conventional kinesin-1 is the primary anterograde motor in cells for transporting cellular cargo. While there is a consensus that the C-terminal tail of kinesin-1 inhibits motility, the molecular architecture of a full-length autoinhibited kinesin-1 remains unknown. Here, we combine crosslinking mass spectrometry (XL-MS), electron microscopy (EM), and AlphaFold structure prediction to determine the architecture of the full-length autoinhibited kinesin-1 homodimer (kinesin-1 heavy chain [KHC]) and kinesin-1 heterotetramer (KHC bound to kinesin light chain 1 [KLC1]). Our integrative analysis shows that kinesin-1 forms a compact, bent conformation through a break in coiled-coil 3. Moreover, our XL-MS analysis demonstrates that kinesin light chains stabilize the folded inhibited state rather than inducing a new structural state. Using our structural model, we show that disruption of multiple interactions between the motor, stalk, and tail domains is required to activate the full-length kinesin-1. Our work offers a conceptual framework for understanding how cargo adaptors and microtubule-associated proteins relieve autoinhibition to promote activation.
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Affiliation(s)
- Zhenyu Tan
- Department of Biophysics, University of MichiganAnn ArborUnited States
- Life Sciences Institute, University of MichiganAnn ArborUnited States
| | - Yang Yue
- Department of Cell & Developmental Biology, University of MichiganAnn ArborUnited States
| | - Felipe Leprevost
- Department of Pathology, University of MichiganAnn ArborUnited States
| | - Sarah Haynes
- Department of Pathology, University of MichiganAnn ArborUnited States
| | - Venkatesha Basrur
- Department of Pathology, University of MichiganAnn ArborUnited States
| | - Alexey I Nesvizhskii
- Department of Pathology, University of MichiganAnn ArborUnited States
- Department of Computational Medicine and Bioinformatics, University of MichiganAnn ArborUnited States
| | - Kristen J Verhey
- Department of Cell & Developmental Biology, University of MichiganAnn ArborUnited States
| | - Michael A Cianfrocco
- Life Sciences Institute, University of MichiganAnn ArborUnited States
- Department of Biological Chemistry, University of MichiganAnn ArborUnited States
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5
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Geng Q, Keya JJ, Hotta T, Verhey KJ. KIF1C, an RNA transporting kinesin-3, undergoes liquid-liquid phase separation through its C-terminal disordered domain. bioRxiv 2023:2023.10.23.563538. [PMID: 37961614 PMCID: PMC10634753 DOI: 10.1101/2023.10.23.563538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
The spatial distribution of mRNA is critical for local control of protein production. Recent studies have identified the kinesin-3 family member KIF1C as an RNA transporter. However, it is not clear how KIF1C interacts with RNA molecules. Here, we show that KIF1C's C-terminal tail domain is an intrinsically disordered region (IDR) containing a prion-like domain (PLD) that is unique compared to the C-terminal tails of other kinesin family members. In cells, KIF1C constructs undergo reversible formation of dynamic puncta that display physical properties of liquid condensates and incorporate RNA molecules in a sequence-selective manner. The IDR is necessary and sufficient for driving liquid-liquid phase separation (LLPS) but the condensate properties can be modulated by adjacent coiled-coil segments. The purified KIF1C IDR domain undergoes LLPS in vitro at near-endogenous nM concentrations in a salt-dependent manner. Deletion of the IDR abolished the ability of KIF1C to undergo LLPS and disrupted the distribution of mRNA cargoes to the cell periphery. Our work thus uncovers an intrinsic correlation between the LLPS activity of KIF1C and its role as an RNA transporter. In addition, as the first kinesin motor reported to undergo LLPS, our work reveals a previously uncharacterized mode of motor-cargo interaction that extends our understanding of the behavior of cytoskeletal motor proteins.
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Affiliation(s)
- Qi Geng
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jakia Jannat Keya
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Takashi Hotta
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
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6
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Yue Y, Hotta T, Higaki T, Verhey KJ, Ohi R. Microtubule detyrosination by VASH1/SVBP is regulated by the conformational state of tubulin in the lattice. Curr Biol 2023; 33:4111-4123.e7. [PMID: 37716348 PMCID: PMC10592207 DOI: 10.1016/j.cub.2023.07.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 09/18/2023]
Abstract
Tubulin, a heterodimer of α- and β-tubulin, is a GTPase that assembles into microtubule (MT) polymers whose dynamic properties are intimately coupled to nucleotide hydrolysis. In cells, the organization and dynamics of MTs are further tuned by post-translational modifications (PTMs), which control the ability of MT-associated proteins (MAPs) and molecular motors to engage MTs. Detyrosination is a PTM of α-tubulin, wherein its C-terminal tyrosine residue is enzymatically removed by either the vasohibin (VASH) or MT-associated tyrosine carboxypeptidase (MATCAP) peptidases. How these enzymes generate specific patterns of MT detyrosination in cells is not known. Here, we use a novel antibody-based probe to visualize the formation of detyrosinated MTs in real time and employ single-molecule imaging of VASH1 bound to its regulatory partner small-vasohibin binding protein (SVBP) to understand the process of MT detyrosination in vitro and in cells. We demonstrate that the activity, but not binding, of VASH1/SVBP is much greater on mimics of guanosine triphosphate (GTP)-MTs than on guanosine diphosphate (GDP)-MTs. Given emerging data showing that tubulin subunits in GTP-MTs are in expanded conformation relative to tubulin subunits in GDP-MTs, we reasoned that the lattice conformation of MTs is a key factor that gates the activity of VASH1/SVBP. We show that Taxol, a drug known to expand the MT lattice, promotes MT detyrosination and that CAMSAP2 and CAMSAP3 are two MAPs that spatially regulate detyrosination in cells. Collectively, our work shows that VASH1/SVBP detyrosination is regulated by the conformational state of tubulin in the MT lattice and that this is spatially determined in cells by the activity of MAPs.
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Affiliation(s)
- Yang Yue
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Takashi Hotta
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Takumi Higaki
- Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan; International Research Organization in Advanced Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Ryoma Ohi
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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7
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Tan Z, Yue Y, da Veiga Leprevost F, Haynes SE, Basrur V, Nesvizhskii AI, Verhey KJ, Cianfrocco MA. Autoinhibited kinesin-1 adopts a hierarchical folding pattern. bioRxiv 2023:2023.01.26.525761. [PMID: 36747757 PMCID: PMC9901034 DOI: 10.1101/2023.01.26.525761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Conventional kinesin-1 is the primary anterograde motor in cells for transporting cellular cargo. While there is a consensus that the C-terminal tail of kinesin-1 inhibits motility, the molecular architecture of a full-length autoinhibited kinesin-1 remains unknown. Here, we combine cross-linking mass spectrometry (XL-MS), electron microscopy (EM), and AlphaFold structure prediction to determine the architecture of the full-length autoinhibited kinesin-1 homodimer [kinesin-1 heavy chain (KHC)] and kinesin-1 heterotetramer [KHC bound to kinesin light chain 1 (KLC1)]. Our integrative analysis shows that kinesin-1 forms a compact, bent conformation through a break in coiled coil 3. Moreover, our XL-MS analysis demonstrates that kinesin light chains stabilize the folded inhibited state rather than inducing a new structural state. Using our structural model, we show that disruption of multiple interactions between the motor, stalk, and tail domains is required to activate the full-length kinesin-1. Our work offers a conceptual framework for understanding how cargo adaptors and microtubule-associated proteins relieve autoinhibition to promote activation.
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Affiliation(s)
- Zhenyu Tan
- Department of Biophysics, University of Michigan
- Life Sciences Institute, University of Michigan
| | - Yang Yue
- Department of Cell & Developmental Biology, University of Michigan
| | | | | | | | - Alexey I. Nesvizhskii
- Department of Pathology, University of Michigan
- Department of Computational Medicine and Bioinformatics, University of Michigan
| | | | - Michael A. Cianfrocco
- Life Sciences Institute, University of Michigan
- Department of Biological Chemistry, University of Michigan
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8
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Birk MA, Liscovitch-Brauer N, Dominguez MJ, McNeme S, Yue Y, Hoff JD, Twersky I, Verhey KJ, Sutton RB, Eisenberg E, Rosenthal JJC. Temperature-dependent RNA editing in octopus extensively recodes the neural proteome. Cell 2023; 186:2544-2555.e13. [PMID: 37295402 PMCID: PMC10445230 DOI: 10.1016/j.cell.2023.05.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/24/2023] [Accepted: 05/04/2023] [Indexed: 06/12/2023]
Abstract
In poikilotherms, temperature changes challenge the integration of physiological function. Within the complex nervous systems of the behaviorally sophisticated coleoid cephalopods, these problems are substantial. RNA editing by adenosine deamination is a well-positioned mechanism for environmental acclimation. We report that the neural proteome of Octopus bimaculoides undergoes massive reconfigurations via RNA editing following a temperature challenge. Over 13,000 codons are affected, and many alter proteins that are vital for neural processes. For two highly temperature-sensitive examples, recoding tunes protein function. For synaptotagmin, a key component of Ca2+-dependent neurotransmitter release, crystal structures and supporting experiments show that editing alters Ca2+ binding. For kinesin-1, a motor protein driving axonal transport, editing regulates transport velocity down microtubules. Seasonal sampling of wild-caught specimens indicates that temperature-dependent editing occurs in the field as well. These data show that A-to-I editing tunes neurophysiological function in response to temperature in octopus and most likely other coleoids.
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Affiliation(s)
- Matthew A Birk
- Bell Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA; Department of Biology, Saint Francis University, Loretto, PA 15940, USA
| | | | - Matthew J Dominguez
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79410, USA
| | - Sean McNeme
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77550, USA
| | - Yang Yue
- Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - J Damon Hoff
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Itamar Twersky
- The Nano Center, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Kristen J Verhey
- Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - R Bryan Sutton
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79410, USA
| | - Eli Eisenberg
- School of Physics and Astronomy, Tel Aviv University, Tel Aviv 69978, Israel.
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9
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Konjikusic MJ, Lee C, Yue Y, Shrestha BD, Nguimtsop AM, Horani A, Brody S, Prakash VN, Gray RS, Verhey KJ, Wallingford JB. Kif9 is an active kinesin motor required for ciliary beating and proximodistal patterning of motile axonemes. J Cell Sci 2023; 136:jcs259535. [PMID: 35531639 PMCID: PMC9357393 DOI: 10.1242/jcs.259535] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 04/27/2022] [Indexed: 03/19/2024] Open
Abstract
Most motile cilia have a stereotyped structure of nine microtubule outer doublets and a single central pair of microtubules. The central pair of microtubules are surrounded by a set of proteins, termed the central pair apparatus. A specific kinesin, Klp1 projects from the central pair and contributes to ciliary motility in Chlamydomonas. The vertebrate ortholog, Kif9, is required for beating in mouse sperm flagella, but the mechanism of Kif9/Klp1 function remains poorly defined. Here, using Xenopus epidermal multiciliated cells, we show that Kif9 is necessary for ciliary motility and the proper distal localization of not only central pair proteins, but also radial spokes and dynein arms. In addition, single-molecule assays in vitro reveal that Xenopus Kif9 is a long-range processive motor, although it does not mediate long-range movement in ciliary axonemes in vivo. Together, our data suggest that Kif9 is integral for ciliary beating and is necessary for proper axonemal distal end integrity.
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Affiliation(s)
- Mia J. Konjikusic
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
- Department of Pediatrics, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd, The University of Texas at Austin, Dell Medical School, Austin, TX 78712, USA
- Department of Nutritional Sciences, 200 W 24th Street, The University of Texas at Austin, Austin, TX 78712, USA
| | - Chanjae Lee
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Yang Yue
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | - Ange M. Nguimtsop
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Amjad Horani
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63130, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Steven Brody
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Vivek N. Prakash
- Department of Physics, University of Miami, Coral Gables, FL 33146, USA
- Department of Biology and Department of Marine Biology and Ecology, University of Miami, Coral Gables, FL 33146,USA
| | - Ryan S. Gray
- Department of Pediatrics, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd, The University of Texas at Austin, Dell Medical School, Austin, TX 78712, USA
- Department of Nutritional Sciences, 200 W 24th Street, The University of Texas at Austin, Austin, TX 78712, USA
| | - Kristen J. Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - John B. Wallingford
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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10
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Abstract
Microtubules are critical for a variety of important functions in eukaryotic cells. During intracellular trafficking, molecular motor proteins of the kinesin superfamily drive the transport of cellular cargoes by stepping processively along the microtubule surface. Traditionally, the microtubule has been viewed as simply a track for kinesin motility. New work is challenging this classic view by showing that kinesin-1 and kinesin-4 proteins can induce conformational changes in tubulin subunits while they are stepping. These conformational changes appear to propagate along the microtubule such that the kinesins can work allosterically through the lattice to influence other proteins on the same track. Thus, the microtubule is a plastic medium through which motors and other microtubule-associated proteins (MAPs) can communicate. Furthermore, stepping kinesin-1 can damage the microtubule lattice. Damage can be repaired by the incorporation of new tubulin subunits, but too much damage leads to microtubule breakage and disassembly. Thus, the addition and loss of tubulin subunits are not restricted to the ends of the microtubule filament but rather, the lattice itself undergoes continuous repair and remodeling. This work leads to a new understanding of how kinesin motors and their microtubule tracks engage in allosteric interactions that are critical for normal cell physiology.
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Affiliation(s)
- Kristen J. Verhey
- Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Author for correspondence ()
| | - Ryoma Ohi
- Department of Cell & Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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11
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Takagishi M, Yue Y, Gray RS, Verhey KJ, Wallingford JB. Kif6 regulates cilia motility and polarity in brain ependymal cells. bioRxiv 2023:2023.02.15.528715. [PMID: 36824804 PMCID: PMC9948966 DOI: 10.1101/2023.02.15.528715] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Ependymal cells, lining brain ventricular walls, display tufts of cilia that beat in concert promoting laminar Cerebrospinal fluid (CSF) flow within brain ventricles. The ciliary axonemes of multiciliated ependymal cells display a 9+2 microtubule array common to motile cilia. Dyneins and kinesins are ATPase microtubule motor proteins that promote the rhythmic beating of cilia axonemes. Despite common consensus about the importance of axonemal dynein motor proteins, little is known about how Kinesin motors contribute to cilia motility. Here, we define the function of Kinesin family member 6 (Kif6) using a mutation that lacks a highly conserved C-terminal tail domain ( Kif6 p.G555fs ) and which displays progressive hydrocephalus in mice. An analogous mutation was isolated in a proband displaying macrocephaly, hypotonia, and seizures implicating an evolutionarily conserved function for Kif6 in neurodevelopment. We find that loss of Kif6 function caused decreased ependymal cilia motility and subsequently decreased fluid flow on the surface of brain ventricular walls. Kif6 protein was localized at ependymal cilia and displayed processive motor movement (676 nm/s) on microtubules in vitro . Loss of the Kif6 C-terminal tail domain did not affect the initial ciliogenesis in vivo , but did result in defects in cilia orientation, the formation of robust apical actin networks, and stabilization of basal bodies at the apical surface. This suggests a novel role for the Kif6 motor in maintenance of ciliary homeostasis of ependymal cells. Summary statement We found that Kif6 is localized to the axonemes of ependymal cells. In vitro analysis shows that Kif6 moves on microtubules and that its loss mice decrease cilia motility and cilia-driven flow, resulting in hydrocephalus.
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12
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Poulos A, Budaitis BG, Verhey KJ. Single-motor and multi-motor motility properties of kinesin-6 family members. Biol Open 2022; 11:276958. [PMID: 36178151 PMCID: PMC9581516 DOI: 10.1242/bio.059533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/22/2022] [Indexed: 12/31/2022] Open
Abstract
Kinesin motor proteins are responsible for orchestrating a variety of microtubule-based processes including intracellular transport, cell division, cytoskeletal organization, and cilium function. Members of the kinesin-6 family play critical roles in anaphase and cytokinesis during cell division as well as in cargo transport and microtubule organization during interphase, however little is known about their motility properties. We find that truncated versions of MKLP1 (HsKIF23), MKLP2 (HsKIF20A), and HsKIF20B largely interact statically with microtubules as single molecules but can also undergo slow, processive motility, most prominently for MKLP2. In multi-motor assays, all kinesin-6 proteins were able to drive microtubule gliding and MKLP1 and KIF20B were also able to drive robust transport of both peroxisomes, a low-load cargo, and Golgi, a high-load cargo, in cells. In contrast, MKLP2 showed minimal transport of peroxisomes and was unable to drive Golgi dispersion. These results indicate that the three mammalian kinesin-6 motor proteins can undergo processive motility but differ in their ability to generate forces needed to drive cargo transport and microtubule organization in cells.
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Affiliation(s)
- Andrew Poulos
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Breane G. Budaitis
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA,Authors for correspondence (; )
| | - Kristen J. Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA,Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA,Authors for correspondence (; )
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13
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Hotta T, McAlear TS, Yue Y, Higaki T, Haynes SE, Nesvizhskii AI, Sept D, Verhey KJ, Bechstedt S, Ohi R. EML2-S constitutes a new class of proteins that recognizes and regulates the dynamics of tyrosinated microtubules. Curr Biol 2022; 32:3898-3910.e14. [PMID: 35963242 PMCID: PMC9530018 DOI: 10.1016/j.cub.2022.07.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 06/13/2022] [Accepted: 07/13/2022] [Indexed: 02/01/2023]
Abstract
Tubulin post-translational modifications (PTMs) alter microtubule properties by affecting the binding of microtubule-associated proteins (MAPs). Microtubule detyrosination, which occurs by proteolytic removal of the C-terminal tyrosine from ɑ-tubulin, generates the oldest known tubulin PTM, but we lack comprehensive knowledge of MAPs that are regulated by this PTM. We developed a screening pipeline to identify proteins that discriminate between Y- and ΔY-microtubules and found that echinoderm microtubule-associated protein-like 2 (EML2) preferentially interacts with Y-microtubules. This activity depends on a Y-microtubule interaction motif built from WD40 repeats. We show that EML2 tracks the tips of shortening microtubules, a behavior not previously seen among human MAPs in vivo, and influences dynamics to increase microtubule stability. Our screening pipeline is readily adapted to identify proteins that specifically recognize a wide range of microtubule PTMs.
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Affiliation(s)
- Takashi Hotta
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Thomas S McAlear
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
| | - Yang Yue
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Takumi Higaki
- Faculty of Advanced Science and Technology (FAST), Kumamoto University, Kumamoto, Japan; International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, Kumamoto, Japan
| | - Sarah E Haynes
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - David Sept
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Susanne Bechstedt
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
| | - Ryoma Ohi
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
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14
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Balseiro-Gómez S, Park J, Yue Y, Ding C, Shao L, Ҫetinkaya S, Kuzoian C, Hammarlund M, Verhey KJ, Yogev S. Neurexin and frizzled intercept axonal transport at microtubule minus ends to control synapse formation. Dev Cell 2022; 57:1802-1816.e4. [PMID: 35809561 PMCID: PMC9378695 DOI: 10.1016/j.devcel.2022.06.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 02/01/2022] [Accepted: 06/13/2022] [Indexed: 01/29/2023]
Abstract
Synapse formation is locally determined by transmembrane proteins, yet synaptic material is synthesized remotely and undergoes processive transport in axons. How local synaptogenic signals intercept synaptic cargo in transport to promote its delivery and synapse formation is unknown. We found that the control of synaptic cargo delivery at microtubule (MT) minus ends mediates pro- and anti-synaptogenic activities of presynaptic neurexin and frizzled in C. elegans and identified the atypical kinesin VAB-8/KIF26 as a key molecule in this process. VAB-8/KIF26 levels at synaptic MT minus ends are controlled by frizzled and neurexin; loss of VAB-8 mimics neurexin mutants or frizzled hyperactivation, and its overexpression can rescue synapse loss in these backgrounds. VAB-8/KIF26 is required for the synaptic localization of other minus-end proteins and promotes the pausing of retrograde transport to allow delivery to synapses. Consistently, reducing retrograde transport rescues synapse loss in vab-8 and neurexin mutants. These results uncover a mechanistic link between synaptogenic signaling and axonal transport.
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Affiliation(s)
- Santiago Balseiro-Gómez
- Department of Neuroscience, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, USA
| | - Junhyun Park
- Department of Neuroscience, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, USA
| | - Yang Yue
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chen Ding
- Department of Neuroscience, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, USA; Department of Genetics, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, USA
| | - Lin Shao
- Department of Neuroscience, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, USA
| | - Selim Ҫetinkaya
- Department of Neuroscience, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, USA
| | - Caroline Kuzoian
- Department of Neuroscience, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, USA
| | - Marc Hammarlund
- Department of Neuroscience, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, USA; Department of Genetics, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shaul Yogev
- Department of Neuroscience, Yale School of Medicine, 295 Congress Avenue, New Haven, CT 06510, USA.
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15
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Budaitis BG, Badieyan S, Yue Y, Blasius TL, Reinemann DN, Lang MJ, Cianfrocco MA, Verhey KJ. A kinesin-1 variant reveals motor-induced microtubule damage in cells. Curr Biol 2022; 32:2416-2429.e6. [PMID: 35504282 PMCID: PMC9993403 DOI: 10.1016/j.cub.2022.04.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 03/11/2022] [Accepted: 04/08/2022] [Indexed: 12/16/2022]
Abstract
Kinesins drive the transport of cellular cargoes as they walk along microtubule tracks; however, recent work has suggested that the physical act of kinesins walking along microtubules can stress the microtubule lattice. Here, we describe a kinesin-1 KIF5C mutant with an increased ability to generate damage sites in the microtubule lattice as compared with the wild-type motor. The expression of the mutant motor in cultured cells resulted in microtubule breakage and fragmentation, suggesting that kinesin-1 variants with increased damage activity would have been selected against during evolution. The increased ability to damage microtubules is not due to the enhanced motility properties of the mutant motor, as the expression of the kinesin-3 motor KIF1A, which has similar single-motor motility properties, also caused increased microtubule pausing, bending, and buckling but not breakage. In cells, motor-induced microtubule breakage could not be prevented by increased α-tubulin K40 acetylation, a post-translational modification known to increase microtubule flexibility. In vitro, lattice damage induced by wild-type KIF5C was repaired by soluble tubulin and resulted in increased rescues and overall microtubule growth, whereas lattice damage induced by the KIF5C mutant resulted in larger repair sites that made the microtubule vulnerable to breakage and fragmentation when under mechanical stress. These results demonstrate that kinesin-1 motility causes defects in and damage to the microtubule lattice in cells. While cells have the capacity to repair lattice damage, conditions that exceed this capacity result in microtubule breakage and fragmentation and may contribute to human disease.
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Affiliation(s)
- Breane G Budaitis
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA; Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Somayesadat Badieyan
- Department of Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yang Yue
- Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - T Lynne Blasius
- Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dana N Reinemann
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37240, USA
| | - Matthew J Lang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN 37240, USA
| | - Michael A Cianfrocco
- Department of Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kristen J Verhey
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA; Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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16
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Yue Y, Engelke MF, Blasius TL, Verhey KJ. Hedgehog-induced ciliary trafficking of kinesin-4 motor KIF7 requires intraflagellar transport but not KIF7's microtubule binding. Mol Biol Cell 2021; 33:br1. [PMID: 34705483 PMCID: PMC8886809 DOI: 10.1091/mbc.e21-04-0215] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The kinesin-4 motor KIF7 is a conserved regulator of the Hedgehog signaling pathway. In vertebrates, Hedgehog signaling requires the primary cilium, and KIF7 and Gli transcription factors accumulate at the cilium tip in response to Hedgehog activation. Unlike conventional kinesins, KIF7 is an immotile kinesin and its mechanism of ciliary accumulation is unknown. We generated KIF7 variants with altered microtubule binding or motility. We demonstrate that microtubule binding of KIF7 is not required for the increase in KIF7 or Gli localization at the cilium tip in response to Hedgehog signaling. In addition, we show that the immotile behavior of KIF7 is required to prevent ciliary localization of Gli transcription factors in the absence of Hedgehog signaling. Using an engineered kinesin-2 motor that enables acute inhibition of intraflagellar transport, we demonstrate that kinesin-2 KIF3A/KIF3B/KAP mediates the translocation of KIF7 to the cilium tip in response to Hedgehog pathway activation. Together, these results suggest that KIF7’s role at the tip of the cilium is unrelated to its ability to bind to microtubules.
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Affiliation(s)
- Yang Yue
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Martin F Engelke
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - T Lynne Blasius
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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17
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Koenning M, Wang X, Karki M, Jangid RK, Kearns S, Tripathi DN, Cianfrocco M, Verhey KJ, Jung SY, Coarfa C, Ward CS, Kalish BT, Grimm SL, Rathmell WK, Mostany R, Dere R, Rasband MN, Walker CL, Park IY. Neuronal SETD2 activity links microtubule methylation to an anxiety-like phenotype in mice. Brain 2021; 144:2527-2540. [PMID: 34014281 PMCID: PMC8418347 DOI: 10.1093/brain/awab200] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/22/2021] [Accepted: 05/02/2021] [Indexed: 02/07/2023] Open
Abstract
Gene discovery efforts in autism spectrum disorder have identified heterozygous defects in chromatin remodeller genes, the 'readers, writers and erasers' of methyl marks on chromatin, as major contributors to this disease. Despite this advance, a convergent aetiology between these defects and aberrant chromatin architecture or gene expression has remained elusive. Recently, data have begun to emerge that chromatin remodellers also function directly on the cytoskeleton. Strongly associated with autism spectrum disorder, the SETD2 histone methyltransferase for example, has now been shown to directly methylate microtubules of the mitotic spindle. However, whether microtubule methylation occurs in post-mitotic cells, for example on the neuronal cytoskeleton, is not known. We found the SETD2 α-tubulin lysine 40 trimethyl mark occurs on microtubules in the brain and in primary neurons in culture, and that the SETD2 C-terminal SRI domain is required for binding and methylation of α-tubulin. A CRISPR knock-in of a pathogenic SRI domain mutation (Setd2SRI) that disables microtubule methylation revealed at least one wild-type allele was required in mice for survival, and while viable, heterozygous Setd2SRI/wtmice exhibited an anxiety-like phenotype. Finally, whereas RNA-sequencing (RNA-seq) and chromatin immunoprecipitation-sequencing (ChIP-seq) showed no concomitant changes in chromatin methylation or gene expression in Setd2SRI/wtmice, primary neurons exhibited structural deficits in axon length and dendritic arborization. These data provide the first demonstration that microtubules of neurons are methylated, and reveals a heterozygous chromatin remodeller defect that specifically disables microtubule methylation is sufficient to drive an autism-associated phenotype.
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Affiliation(s)
- Matthias Koenning
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xianlong Wang
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Menuka Karki
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rahul Kumar Jangid
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah Kearns
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Durga Nand Tripathi
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael Cianfrocco
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sung Yun Jung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cristian Coarfa
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christopher Scott Ward
- Molecular Physiology and Biophysics, Mouse Metabolic and Phenotyping Core, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Sandra L Grimm
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - W Kimryn Rathmell
- Vanderbilt-Ingram Cancer Center, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Ricardo Mostany
- Department of Pharmacology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Ruhee Dere
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Cheryl Lyn Walker
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - In Young Park
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
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18
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Blasius TL, Yue Y, Prasad R, Liu X, Gennerich A, Verhey KJ. Sequences in the stalk domain regulate auto-inhibition and ciliary tip localization of the immotile kinesin-4 KIF7. J Cell Sci 2021; 134:269104. [PMID: 34114033 DOI: 10.1242/jcs.258464] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/27/2021] [Indexed: 12/31/2022] Open
Abstract
The kinesin-4 member KIF7 plays critical roles in Hedgehog signaling in vertebrate cells. KIF7 is an atypical kinesin as it binds to microtubules but is immotile. We demonstrate that, like conventional kinesins, KIF7 is regulated by auto-inhibition, as the full-length protein is inactive for microtubule binding in cells. We identify a segment, the inhibitory coiled coil (inhCC), that is required for auto-inhibition of KIF7, whereas the adjacent regulatory coiled coil (rCC) that contributes to auto-inhibition of the motile kinesin-4s KIF21A and KIF21B is not sufficient for KIF7 auto-inhibition. Disease-associated mutations in the inhCC relieve auto-inhibition and result in strong microtubule binding. Surprisingly, uninhibited KIF7 proteins did not bind preferentially to or track the plus ends of growing microtubules in cells, as suggested by previous in vitro work, but rather bound along cytosolic and axonemal microtubules. Localization to the tip of the primary cilium also required the inhCC, and could be increased by disease-associated mutations regardless of the auto-inhibition state of the protein. These findings suggest that loss of KIF7 auto-inhibition and/or altered cilium tip localization can contribute to the pathogenesis of human disease.
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Affiliation(s)
- T Lynne Blasius
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Yang Yue
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - RaghuRam Prasad
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Xinglei Liu
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Arne Gennerich
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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19
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Karki M, Jangid R, Anish R, Seervai RN, Bertocchio JP, Hotta T, Msaouel P, Jung SY, Grimm SL, Coarfa C, Weissman BE, Ohi R, Verhey KJ, Hodges CH, Dere R, Park IY, Prasad BVV, Rathmell WK, Walker CL, Tripathi DN. Abstract 2042: A cytoskeletal function for PBRM1: reading methylated microtubules to maintain genomic stability. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The chromatin modifier SETD2 often mutated in clear cell renal cell carcinoma (ccRCC), was recently shown to be a dual-function methyltransferase that “writes” methyl marks on both chromatin and microtubules, revealing α-tubulin methylation as a new posttranslational modification of the mitotic spindle. Here, we report that the polybromo protein PBRM1, the 2nd most mutated gene in ccRCC, is a “reader” for this SETD2-dependent methyl mark on α-tubulin. PBRM1 is a component of the PBAF (Polybromo BRG1 associated factor) chromatin remodeler complex. Our western and immunocytochemistry data in multiple kidney-derived cell lines, including HEK293T, HKC and 786-O, revealed that PBRM1 binds to methylated α-tubulin and localizes to the mitotic spindle and spindle pole during cell division. PBRM1 has six bromo domains, two bromo-associated homology (BAH) domains and one HMG domain. While PBRM1 is known to bind acetylated histones via its bromo domains, our GST pull down assays showed that PBRM1 binds methylated α-tubulin via its two BAH domains. Additional western and immunocytochemical experiments following knockout or re-expression of PBRM1 revealed that PBRM1 recruits other PBAF components to the mitotic spindle to maintain genomic stability. Two clinically established ccRCC mutations (P1048R and C1233W) in PBRM1 BAH domains result in loss of microtubule binding, mislocalization of PBAF, and the inability of PBRM1 to maintain genomic stability, as assessed by increased lagging chromosomes, chromosome bridges, multipolar spindles and micronuclei count. A third pathogenic ccRCC mutation (T1202K) in the PBRM1 BAH domain did not affect microtubule binding and consequently was not associated with mitotic spindle defects or genomic instability. Mass spectrometry and RNASeq confirmed BAH domain mutant PBRM1 still assembled a transcriptionally competent PBAF complex, clearly distinguishing the cytoskeletal from the chromatin impact of these mutations. These data reveal a previously unknown function of PBRM1 beyond reading acetylated histones, and expand the repertoire of chromatin remodelers acting on the cytoskeleton to maintain genomic stability.
Citation Format: Menuka Karki, Rahul Jangid, Ramakrishnan Anish, Riyad N. Seervai, Jean-Philippe Bertocchio, Takashi Hotta, Pavlos Msaouel, Sung Y. Jung, Sandra L. Grimm, Cristian Coarfa, Bernard E. Weissman, Ryoma Ohi, Kristen J. Verhey, Courtney H. Hodges, Ruhee Dere, In Young Park, B. V. Venkataram Prasad, W. Kimryn Rathmell, Cheryl L. Walker, Durga N. Tripathi. A cytoskeletal function for PBRM1: reading methylated microtubules to maintain genomic stability [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2042.
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Affiliation(s)
| | | | | | | | | | - Takashi Hotta
- 3University of Michigan Medical School, Ann Arbor, MI
| | | | | | | | | | | | - Ryoma Ohi
- 3University of Michigan Medical School, Ann Arbor, MI
| | | | | | - Ruhee Dere
- 1Baylor College of Medicine, Houston, TX
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20
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Kearns S, Mason FM, Rathmell WK, Park IY, Walker C, Verhey KJ, Cianfrocco MA. Molecular determinants for α-tubulin methylation by SETD2. J Biol Chem 2021; 297:100898. [PMID: 34157286 PMCID: PMC8294582 DOI: 10.1016/j.jbc.2021.100898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 05/28/2021] [Accepted: 06/18/2021] [Indexed: 12/16/2022] Open
Abstract
Post-translational modifications to tubulin are important for many microtubule-based functions inside cells. It was recently shown that methylation of tubulin by the histone methyltransferase SETD2 occurs on mitotic spindle microtubules during cell division, with its absence resulting in mitotic defects. However, the catalytic mechanism of methyl addition to tubulin is unclear. We used a truncated version of human wild type SETD2 (tSETD2) containing the catalytic SET and C-terminal Set2-Rpb1-interacting (SRI) domains to investigate the biochemical mechanism of tubulin methylation. We found that recombinant tSETD2 had a higher activity toward tubulin dimers than polymerized microtubules. Using recombinant single-isotype tubulin, we demonstrated that methylation was restricted to lysine 40 of α-tubulin. We then introduced pathogenic mutations into tSETD2 to probe the recognition of histone and tubulin substrates. A mutation in the catalytic domain (R1625C) allowed tSETD2 to bind to tubulin but not methylate it, whereas a mutation in the SRI domain (R2510H) caused loss of both tubulin binding and methylation. Further investigation of the role of the SRI domain in substrate binding found that mutations within this region had differential effects on the ability of tSETD2 to bind to tubulin versus the binding partner RNA polymerase II for methylating histones in vivo, suggesting distinct mechanisms for tubulin and histone methylation by SETD2. Finally, we found that substrate recognition also requires the negatively charged C-terminal tail of α-tubulin. Together, this study provides a framework for understanding how SETD2 serves as a dual methyltransferase for both histone and tubulin methylation.
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Affiliation(s)
- Sarah Kearns
- Program of Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA; Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Frank M Mason
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Genetics, Vanderbilt University, Nashville, Tennessee, USA
| | - W Kimryn Rathmell
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, Tennessee, USA; Department of Genetics, Vanderbilt University, Nashville, Tennessee, USA
| | - In Young Park
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, USA
| | - Cheryl Walker
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, Texas, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael A Cianfrocco
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
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21
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Karki M, Jangid RK, Anish R, Seervai RNH, Bertocchio JP, Hotta T, Msaouel P, Jung SY, Grimm SL, Coarfa C, Weissman BE, Ohi R, Verhey KJ, Hodges HC, Burggren W, Dere R, Park IY, Prasad BVV, Rathmell WK, Walker CL, Tripathi DN. A cytoskeletal function for PBRM1 reading methylated microtubules. Sci Adv 2021; 7:eabf2866. [PMID: 33811077 PMCID: PMC11059954 DOI: 10.1126/sciadv.abf2866] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/12/2021] [Indexed: 06/12/2023]
Abstract
Epigenetic effectors "read" marks "written" on chromatin to regulate function and fidelity of the genome. Here, we show that this coordinated read-write activity of the epigenetic machinery extends to the cytoskeleton, with PBRM1 in the PBAF chromatin remodeling complex reading microtubule methyl marks written by the SETD2 histone methyltransferase. PBRM1 binds SETD2 methyl marks via BAH domains, recruiting PBAF components to the mitotic spindle. This read-write activity was required for normal mitosis: Loss of SETD2 methylation or pathogenic BAH domain mutations disrupt PBRM1 microtubule binding and PBAF recruitment and cause genomic instability. These data reveal PBRM1 functions beyond chromatin remodeling with domains that allow it to integrate chromatin and cytoskeletal activity via its acetyl-binding BD and methyl-binding BAH domains, respectively. Conserved coordinated activity of the epigenetic machinery on the cytoskeleton opens a previously unknown window into how chromatin remodeler defects can drive disease via both epigenetic and cytoskeletal dysfunction.
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Affiliation(s)
- Menuka Karki
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rahul K Jangid
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ramakrishnan Anish
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Riyad N H Seervai
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jean-Philippe Bertocchio
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Genitourinary Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Takashi Hotta
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Pavlos Msaouel
- Department of Genitourinary Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sung Yun Jung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sandra L Grimm
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cristian Coarfa
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bernard E Weissman
- Department of Pathology and Laboratory Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Ryoma Ohi
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - H Courtney Hodges
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Warren Burggren
- Department of Biological Sciences, University of North Texas, Denton, TX 76201, USA
| | - Ruhee Dere
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - In Young Park
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - W Kimryn Rathmell
- Vanderbilt-Ingram Cancer Center, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Cheryl L Walker
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Durga N Tripathi
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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22
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Varela PF, Chenon M, Velours C, Verhey KJ, Ménétrey J, Gigant B. Structural snapshots of the kinesin-2 OSM-3 along its nucleotide cycle: implications for the ATP hydrolysis mechanism. FEBS Open Bio 2021; 11:564-577. [PMID: 33513284 PMCID: PMC7931232 DOI: 10.1002/2211-5463.13101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 01/27/2021] [Indexed: 11/09/2022] Open
Abstract
Motile kinesins are motor proteins that translocate along microtubules as they hydrolyze ATP. They share a conserved motor domain which harbors both ATPase and microtubule-binding activities. An ATP hydrolysis mechanism involving two water molecules has been proposed based on the structure of the kinesin-5 Eg5 bound to an ATP analog. Whether this mechanism is general in the kinesin superfamily remains uncertain. Here, we present structural snapshots of the motor domain of OSM-3 along its nucleotide cycle. OSM-3 belongs to the homodimeric kinesin-2 subfamily and is the Caenorhabditis elegans homologue of human KIF17. OSM-3 bound to ADP or devoid of a nucleotide shows features of ADP-kinesins with a docked neck linker. When bound to an ATP analog, OSM-3 adopts a conformation similar to those of several ATP-like kinesins, either isolated or bound to tubulin. Moreover, the OSM-3 nucleotide-binding site is virtually identical to that of ATP-like Eg5, demonstrating a shared ATPase mechanism. Therefore, our data extend to kinesin-2 the two-water ATP hydrolysis mechanism and further suggest that it is universal within the kinesin superfamily. PROTEIN DATABASE ENTRIES: 7A3Z, 7A40, 7A5E.
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Affiliation(s)
- Paloma F Varela
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Mélanie Chenon
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Christophe Velours
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Julie Ménétrey
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Benoît Gigant
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
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23
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Spriggs CC, Badieyan S, Verhey KJ, Cianfrocco MA, Tsai B. Golgi-associated BICD adaptors couple ER membrane penetration and disassembly of a viral cargo. J Cell Biol 2021; 219:151622. [PMID: 32259203 PMCID: PMC7199864 DOI: 10.1083/jcb.201908099] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 12/04/2019] [Accepted: 02/21/2020] [Indexed: 12/22/2022] Open
Abstract
During entry, viruses must navigate through the host endomembrane system, penetrate cellular membranes, and undergo capsid disassembly to reach an intracellular destination that supports infection. How these events are coordinated is unclear. Here, we reveal an unexpected function of a cellular motor adaptor that coordinates virus membrane penetration and disassembly. Polyomavirus SV40 traffics to the endoplasmic reticulum (ER) and penetrates a virus-induced structure in the ER membrane called “focus” to reach the cytosol, where it disassembles before nuclear entry to promote infection. We now demonstrate that the ER focus is constructed proximal to the Golgi-associated BICD2 and BICDR1 dynein motor adaptors; this juxtaposition enables the adaptors to directly bind to and disassemble SV40 upon arrival to the cytosol. Our findings demonstrate that positioning of the virus membrane penetration site couples two decisive infection events, cytosol arrival and disassembly, and suggest cargo remodeling as a novel function of dynein adaptors.
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Affiliation(s)
- Chelsey C Spriggs
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
| | - Somayesadat Badieyan
- Department of Biological Chemistry and the Life Sciences Institute, University of Michigan, Ann Arbor, MI
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
| | - Michael A Cianfrocco
- Department of Biological Chemistry and the Life Sciences Institute, University of Michigan, Ann Arbor, MI
| | - Billy Tsai
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
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24
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Budaitis BG, Jariwala S, Rao L, Yue Y, Sept D, Verhey KJ, Gennerich A. Pathogenic mutations in the kinesin-3 motor KIF1A diminish force generation and movement through allosteric mechanisms. J Cell Biol 2021; 220:211720. [PMID: 33496723 PMCID: PMC7844421 DOI: 10.1083/jcb.202004227] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/27/2020] [Accepted: 12/30/2020] [Indexed: 02/07/2023] Open
Abstract
The kinesin-3 motor KIF1A functions in neurons, where its fast and superprocessive motility facilitates long-distance transport, but little is known about its force-generating properties. Using optical tweezers, we demonstrate that KIF1A stalls at an opposing load of ~3 pN but more frequently detaches at lower forces. KIF1A rapidly reattaches to the microtubule to resume motion due to its class-specific K-loop, resulting in a unique clustering of force generation events. To test the importance of neck linker docking in KIF1A force generation, we introduced mutations linked to human neurodevelopmental disorders. Molecular dynamics simulations predict that V8M and Y89D mutations impair neck linker docking. Indeed, both mutations dramatically reduce the force generation of KIF1A but not the motor’s ability to rapidly reattach to the microtubule. Although both mutations relieve autoinhibition of the full-length motor, the mutant motors display decreased velocities, run lengths, and landing rates and delayed cargo transport in cells. These results advance our understanding of how mutations in KIF1A can manifest in disease.
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Affiliation(s)
- Breane G Budaitis
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI
| | - Shashank Jariwala
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI
| | - Lu Rao
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, New York, NY
| | - Yang Yue
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - David Sept
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI
| | - Kristen J Verhey
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI.,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Arne Gennerich
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, New York, NY
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25
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Hotta T, Haynes SE, Blasius TL, Gebbie M, Eberhardt EL, Sept D, Cianfrocco M, Verhey KJ, Nesvizhskii AI, Ohi R. Parthenolide Destabilizes Microtubules by Covalently Modifying Tubulin. Curr Biol 2021; 31:900-907.e6. [PMID: 33482110 DOI: 10.1016/j.cub.2020.11.055] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/02/2020] [Accepted: 11/19/2020] [Indexed: 12/28/2022]
Abstract
Detyrosination of the α-tubulin C-terminal tail is a post-translational modification (PTM) of microtubules that is key for many biological processes.1 Although detyrosination is the oldest known microtubule PTM,2-7 the carboxypeptidase responsible for this modification, VASH1/2-SVBP, was identified only 3 years ago,8,9 precluding genetic approaches to prevent detyrosination. Studies examining the cellular functions of detyrosination have therefore relied on a natural product, parthenolide, which is widely believed to block detyrosination of α-tubulin in cells, presumably by inhibiting the activity of the relevant carboxypeptidase(s).10 Parthenolide is a sesquiterpene lactone that forms covalent linkages predominantly with exposed thiol groups; e.g., on cysteine residues.11-13 Using mass spectrometry, we show that parthenolide forms adducts on both cysteine and histidine residues on tubulin itself, in vitro and in cells. Parthenolide causes tubulin protein aggregation and prevents the formation of microtubules. In contrast to epoY, an epoxide inhibitor of VASH1/2-SVBP,9 parthenolide does not block VASH1-SVBP activity in vitro. Lastly, we show that epoY is an efficacious inhibitor of microtubule detyrosination in cells, providing an alternative chemical means to block detyrosination. Collectively, our work supports the notion that parthenolide is a promiscuous inhibitor of many cellular processes and suggests that its ability to block detyrosination may be an indirect consequence of reducing the polymerization-competent pool of tubulin in cells.
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Affiliation(s)
- Takashi Hotta
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Sarah E Haynes
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Teresa L Blasius
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Margo Gebbie
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Emily L Eberhardt
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - David Sept
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Michael Cianfrocco
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Ryoma Ohi
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA.
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26
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Seervai RNH, Jangid RK, Karki M, Tripathi DN, Jung SY, Kearns SE, Verhey KJ, Cianfrocco MA, Millis BA, Tyska MJ, Mason FM, Rathmell WK, Park IY, Dere R, Walker CL. The Huntingtin-interacting protein SETD2/HYPB is an actin lysine methyltransferase. Sci Adv 2020; 6:6/40/eabb7854. [PMID: 33008892 PMCID: PMC7852384 DOI: 10.1126/sciadv.abb7854] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 08/07/2020] [Indexed: 05/05/2023]
Abstract
The methyltransferase SET domain-containing 2 (SETD2) was originally identified as Huntingtin (HTT) yeast partner B. However, a SETD2 function associated with the HTT scaffolding protein has not been elucidated, and no linkage between HTT and methylation has yet been uncovered. Here, we show that SETD2 is an actin methyltransferase that trimethylates lysine-68 (ActK68me3) in cells via its interaction with HTT and the actin-binding adapter HIP1R. ActK68me3 localizes primarily to the insoluble F-actin cytoskeleton in cells and regulates actin polymerization/depolymerization dynamics. Disruption of the SETD2-HTT-HIP1R axis inhibits actin methylation, causes defects in actin polymerization, and impairs cell migration. Together, these data identify SETD2 as a previously unknown HTT effector regulating methylation and polymerization of actin filaments and provide new avenues for understanding how defects in SETD2 and HTT drive disease via aberrant cytoskeletal methylation.
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Affiliation(s)
- Riyad N H Seervai
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rahul K Jangid
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Menuka Karki
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Durga Nand Tripathi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sung Yun Jung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sarah E Kearns
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Michael A Cianfrocco
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Bryan A Millis
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
- Vanderbilt Biophotonics Center, Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37240, USA
| | - Matthew J Tyska
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Frank M Mason
- Vanderbilt-Ingram Cancer Center, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - W Kimryn Rathmell
- Vanderbilt-Ingram Cancer Center, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - In Young Park
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Ruhee Dere
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Cheryl Lyn Walker
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
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27
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Kaur S, Van Bergen NJ, Verhey KJ, Nowell CJ, Budaitis B, Yue Y, Ellaway C, Brunetti‐Pierri N, Cappuccio G, Bruno I, Boyle L, Nigro V, Torella A, Roscioli T, Cowley MJ, Massey S, Sonawane R, Burton MD, Schonewolf‐Greulich B, Tümer Z, Chung WK, Gold WA, Christodoulou J. Cover, Volume 41, Issue 10. Hum Mutat 2020. [DOI: 10.1002/humu.24115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Simranpreet Kaur
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute Royal Children's Hospital Melbourne Victoria Australia
- Department of Paediatrics University of Melbourne Melbourne Victoria Australia
| | - Nicole J. Van Bergen
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute Royal Children's Hospital Melbourne Victoria Australia
- Department of Paediatrics University of Melbourne Melbourne Victoria Australia
| | - Kristen J. Verhey
- Department of Cell and Developmental Biology University of Michigan Medical School Ann Arbor Michigan
| | - Cameron J. Nowell
- Drug Discover Biology, Monash Institute of Pharmaceutical Sciences Monash University Melbourne Victoria Australia
| | - Breane Budaitis
- Cellular and Molecular Biology Program University of Michigan Medical School Ann Arbor Michigan
| | - Yang Yue
- Department of Cell and Developmental Biology University of Michigan Medical School Ann Arbor Michigan
| | - Carolyn Ellaway
- Discipline of Genomic Medicine, School of Medical Sciences, Faculty of Medicine and Health University of Sydney Sydney New South Wales Australia
- Western Sydney Genetics Program Children's Hospital at Westmead Westmead New South Wales Australia
| | - Nicola Brunetti‐Pierri
- Department of Translational Medicine University of Naples “Federico II” Naples Italy
- Telethon Institute of Genetics and Medicine Pozzuoli Italy
| | - Gerarda Cappuccio
- Department of Translational Medicine University of Naples “Federico II” Naples Italy
- Telethon Institute of Genetics and Medicine Pozzuoli Italy
| | - Irene Bruno
- Department of Precision Medicine University of Campania “Luigi Vanvitelli” Naples Italy
| | - Lia Boyle
- Division of Molecular Genetics Columbia University Irving Medical Center New York New York
| | - Vincenzo Nigro
- Department of Precision Medicine University of Campania “Luigi Vanvitelli” Naples Italy
| | - Annalaura Torella
- Department of Precision Medicine University of Campania “Luigi Vanvitelli” Naples Italy
| | - Tony Roscioli
- New South Wales Health Pathology Randwick New South Wales Australia
- Neuroscience Research Australia University of New South Wales Sydney New South Wales Australia
| | - Mark J. Cowley
- Kinghorn Centre for Clinical Genomics Garvan Institute of Medical Research Sydney New South Wales Australia
- St Vincent's Clinical School UNSW Sydney Sydney New South Wales Australia
- Children's Cancer Institute, Lowy Cancer Research Centre UNSW Sydney New South Wales Australia
| | - Sean Massey
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute Royal Children's Hospital Melbourne Victoria Australia
| | - Rhea Sonawane
- Faculty of Science, Engineering and Built Environment Deakin University Melbourne Australia
| | - Matthew D. Burton
- Flow Cytometry and Imaging Facility, Murdoch Children's Research Institute Royal Children's Hospital Melbourne Victoria Australia
| | - Bitten Schonewolf‐Greulich
- Department of Clinical Genetics, Kennedy Center Copenhagen University Hospital, Rigshospitalet Glostrup Denmark
| | - Zeynep Tümer
- Department of Clinical Genetics, Kennedy Center Copenhagen University Hospital, Rigshospitalet Glostrup Denmark
| | - Wendy K. Chung
- Departments of Paediatrics and Medicine Columbia University Medical Center New York New York
| | - Wendy A. Gold
- Molecular Neurobiology Research Laboratory, Kids Research Children's Hospital at Westmead, and The Children's Medical Research Institute Westmead New South Wales Australia
- Kids Neuroscience Centre, Kids Research Children's Hospital at Westmead Westmead New South Wales Australia
- School of Medical Sciences and Discipline of Child and Adolescent Health, Faculty of Medicine and Health The University of Sydney Sydney New South Wales Australia
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute Royal Children's Hospital Melbourne Victoria Australia
- Department of Paediatrics University of Melbourne Melbourne Victoria Australia
- Discipline of Genomic Medicine, School of Medical Sciences, Faculty of Medicine and Health University of Sydney Sydney New South Wales Australia
- Victorian Clinical Genetics Services Royal Children's Hospital Melbourne Victoria Australia
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28
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Kaur S, Van Bergen NJ, Verhey KJ, Nowell CJ, Budaitis B, Yue Y, Ellaway C, Brunetti-Pierri N, Cappuccio G, Bruno I, Boyle L, Nigro V, Torella A, Roscioli T, Cowley MJ, Massey S, Sonawane R, Burton MD, Schonewolf-Greulich B, Tümer Z, Chung WK, Gold WA, Christodoulou J. Expansion of the phenotypic spectrum of de novo missense variants in kinesin family member 1A (KIF1A). Hum Mutat 2020; 41:1761-1774. [PMID: 32652677 DOI: 10.1002/humu.24079] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022]
Abstract
Defects in the motor domain of kinesin family member 1A (KIF1A), a neuron-specific ATP-dependent anterograde axonal transporter of synaptic cargo, are well-recognized to cause a spectrum of neurological conditions, commonly known as KIF1A-associated neurological disorders (KAND). Here, we report one mutation-negative female with classic Rett syndrome (RTT) harboring a de novo heterozygous novel variant [NP_001230937.1:p.(Asp248Glu)] in the highly conserved motor domain of KIF1A. In addition, three individuals with severe neurodevelopmental disorder along with clinical features overlapping with KAND are also reported carrying de novo heterozygous novel [NP_001230937.1:p.(Cys92Arg) and p.(Pro305Leu)] or previously reported [NP_001230937.1:p.(Thr99Met)] variants in KIF1A. In silico tools predicted these variants to be likely pathogenic, and 3D molecular modeling predicted defective ATP hydrolysis and/or microtubule binding. Using the neurite tip accumulation assay, we demonstrated that all novel KIF1A variants significantly reduced the ability of the motor domain of KIF1A to accumulate along the neurite lengths of differentiated SH-SY5Y cells. In vitro microtubule gliding assays showed significantly reduced velocities for the variant p.(Asp248Glu) and reduced microtubule binding for the p.(Cys92Arg) and p.(Pro305Leu) variants, suggesting a decreased ability of KIF1A to move along microtubules. Thus, this study further expanded the phenotypic characteristics of KAND individuals with pathogenic variants in the KIF1A motor domain to include clinical features commonly seen in RTT individuals.
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Affiliation(s)
- Simranpreet Kaur
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Nicole J Van Bergen
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Cameron J Nowell
- Drug Discover Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria, Australia
| | - Breane Budaitis
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, Michigan
| | - Yang Yue
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Carolyn Ellaway
- Discipline of Genomic Medicine, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia.,Western Sydney Genetics Program, Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Nicola Brunetti-Pierri
- Department of Translational Medicine, University of Naples "Federico II", Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Gerarda Cappuccio
- Department of Translational Medicine, University of Naples "Federico II", Naples, Italy.,Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Irene Bruno
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Lia Boyle
- Division of Molecular Genetics, Columbia University Irving Medical Center, New York, New York
| | - Vincenzo Nigro
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Annalaura Torella
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Tony Roscioli
- New South Wales Health Pathology, Randwick, New South Wales, Australia.,Neuroscience Research Australia, University of New South Wales, Sydney, New South Wales, Australia
| | - Mark J Cowley
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,St Vincent's Clinical School, UNSW Sydney, Sydney, New South Wales, Australia.,Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, New South Wales, Australia
| | - Sean Massey
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Rhea Sonawane
- Faculty of Science, Engineering and Built Environment, Deakin University, Melbourne, Australia
| | - Matthew D Burton
- Flow Cytometry and Imaging Facility, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia
| | - Bitten Schonewolf-Greulich
- Department of Clinical Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Zeynep Tümer
- Department of Clinical Genetics, Kennedy Center, Copenhagen University Hospital, Rigshospitalet, Glostrup, Denmark
| | - Wendy K Chung
- Departments of Paediatrics and Medicine, Columbia University Medical Center, New York, New York
| | - Wendy A Gold
- Molecular Neurobiology Research Laboratory, Kids Research, Children's Hospital at Westmead, and The Children's Medical Research Institute, Westmead, New South Wales, Australia.,Kids Neuroscience Centre, Kids Research, Children's Hospital at Westmead, Westmead, New South Wales, Australia.,School of Medical Sciences and Discipline of Child and Adolescent Health, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Discipline of Genomic Medicine, School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, Sydney, New South Wales, Australia.,Victorian Clinical Genetics Services, Royal Children's Hospital, Melbourne, Victoria, Australia
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29
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Abstract
Cilia are microtubule-based organelles that protrude from the surface of eukaryotic cells to generate motility and to sense and respond to environmental cues. In order to carry out these functions, the complement of proteins in the cilium must be specific for the organelle. Regulation of protein entry into primary cilia has been shown to utilize mechanisms and components of nuclear gating, including nucleoporins of the nuclear pore complex (NPC). We show that nucleoporins also localize to the base of motile cilia on the surface of trachea epithelial cells. How nucleoporins are anchored at the cilium base has been unclear as transmembrane nucleoporins, which anchor nucleoporins at the nuclear envelope, have not been found to localize at the cilium. Here we use the directed yeast two-hybrid assay to identify direct interactions between nucleoporins and nephronophthisis proteins (NPHPs) which localize to the cilium base and contribute to cilium assembly and identity. We validate NPHP-nucleoporin interactions in mammalian cells using the knocksideways assay and demonstrate that the interactions occur at the base of the primary cilium using bimolecular fluorescence complementation. We propose that NPHP proteins anchor nucleoporins at the base of primary cilia to regulate protein entry into the organelle.
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Affiliation(s)
- T. Lynne Blasius
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Daisuke Takao
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Kristen J. Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- * E-mail:
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30
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Budaitis BG, Jariwala S, Reinemann DN, Schimert KI, Scarabelli G, Grant BJ, Sept D, Lang MJ, Verhey KJ. Neck linker docking is critical for Kinesin-1 force generation in cells but at a cost to motor speed and processivity. eLife 2019; 8:44146. [PMID: 31084716 PMCID: PMC6533058 DOI: 10.7554/elife.44146] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 05/09/2019] [Indexed: 12/12/2022] Open
Abstract
Kinesin force generation involves ATP-induced docking of the neck linker (NL) along the motor core. However, the roles of the proposed steps of NL docking, cover-neck bundle (CNB) and asparagine latch (N-latch) formation, during force generation are unclear. Furthermore, the necessity of NL docking for transport of membrane-bound cargo in cells has not been tested. We generated kinesin-1 motors impaired in CNB and/or N-latch formation based on molecular dynamics simulations. The mutant motors displayed reduced force output and inability to stall in optical trap assays but exhibited increased speeds, run lengths, and landing rates under unloaded conditions. NL docking thus enhances force production but at a cost to speed and processivity. In cells, teams of mutant motors were hindered in their ability to drive transport of Golgi elements (high-load cargo) but not peroxisomes (low-load cargo). These results demonstrate that the NL serves as a mechanical element for kinesin-1 transport under physiological conditions.
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Affiliation(s)
- Breane G Budaitis
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, United States
| | - Shashank Jariwala
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States
| | - Dana N Reinemann
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, United States
| | | | - Guido Scarabelli
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States
| | - Barry J Grant
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, San Diego, United States
| | - David Sept
- Biophysics Program, University of Michigan, Ann Arbor, United States.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, United States.,Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, United States
| | - Matthew J Lang
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, United States.,Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, United States
| | - Kristen J Verhey
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, United States.,Biophysics Program, University of Michigan, Ann Arbor, United States.,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, United States
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31
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Engelke MF, Waas B, Kearns SE, Suber A, Boss A, Allen BL, Verhey KJ. Acute Inhibition of Heterotrimeric Kinesin-2 Function Reveals Mechanisms of Intraflagellar Transport in Mammalian Cilia. Curr Biol 2019; 29:1137-1148.e4. [PMID: 30905605 PMCID: PMC6445692 DOI: 10.1016/j.cub.2019.02.043] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 01/02/2019] [Accepted: 02/18/2019] [Indexed: 10/27/2022]
Abstract
The trafficking of components within cilia, called intraflagellar transport (IFT), is powered by kinesin-2 and dynein-2 motors. Loss of function in any subunit of the heterotrimeric KIF3A/KIF3B/KAP kinesin-2 motor prevents ciliogenesis in mammalian cells and has hindered an understanding of how kinesin-2 motors function in cilium assembly and IFT. We used a chemical-genetic approach to generate an inhibitable KIF3A/KIF3B/KAP kinesin-2 motor (i3A/i3B) that is capable of rescuing wild-type (WT) motor function for cilium assembly and Hedgehog signaling in Kif3a/Kif3b double-knockout cells. We demonstrate that KIF3A/KIF3B function is required not just for cilium assembly but also for cilium maintenance, as inhibition of i3A/i3B blocks IFT within 2 min and leads to a complete loss of primary cilia within 8 h. In contrast, inhibition of dynein-2 has no effect on cilium maintenance within the same time frame. The kinetics of cilia loss indicate that two processes contribute to ciliary disassembly in response to cessation of anterograde IFT: a slow shortening that is steady over time and a rapid deciliation that occurs with stochastic onset. We also demonstrate that the kinesin-2 family members KIF3A/KIF3C and KIF17 cannot rescue ciliogenesis in Kif3a/Kif3b double-knockout cells or delay the loss of assembled cilia upon i3A/i3B inhibition. These results demonstrate that KIF3A/KIF3B/KAP is the sole and essential motor for cilium assembly and maintenance in mammalian cells. These findings highlight differences in how kinesin-2 motors were adapted for cilium assembly and IFT function across species.
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Affiliation(s)
- Martin F Engelke
- Department of Cell & Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA.
| | - Bridget Waas
- Department of Cell & Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Sarah E Kearns
- Department of Cell & Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA; Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ayana Suber
- Department of Cell & Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Allison Boss
- Department of Cell & Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Benjamin L Allen
- Department of Cell & Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Kristen J Verhey
- Department of Cell & Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA.
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32
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Arpağ G, Norris SR, Mousavi SI, Soppina V, Verhey KJ, Hancock WO, Tüzel E. Motor Dynamics Underlying Cargo Transport by Pairs of Kinesin-1 and Kinesin-3 Motors. Biophys J 2019; 116:1115-1126. [PMID: 30824116 PMCID: PMC6428962 DOI: 10.1016/j.bpj.2019.01.036] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 05/25/2018] [Accepted: 01/03/2019] [Indexed: 01/01/2023] Open
Abstract
Intracellular cargo transport by kinesin family motor proteins is crucial for many cellular processes, particularly vesicle transport in axons and dendrites. In a number of cases, the transport of specific cargo is carried out by two classes of kinesins that move at different speeds and thus compete during transport. Despite advances in single-molecule characterization and modeling approaches, many questions remain regarding the effect of intermotor tension on motor attachment/reattachment rates during cooperative multimotor transport. To understand the motor dynamics underlying multimotor transport, we analyzed the complexes of kinesin-1 and kinesin-3 motors attached through protein scaffolds moving on immobilized microtubules in vitro. To interpret the observed behavior, simulations were carried out using a model that incorporated motor stepping, attachment/detachment rates, and intermotor force generation. In single-molecule experiments, isolated kinesin-3 motors moved twofold faster and had threefold higher landing rates than kinesin-1. When the positively charged loop 12 of kinesin-3 was swapped with that of kinesin-1, the landing rates reversed, indicating that this "K-loop" is a key determinant of the motor reattachment rate. In contrast, swapping loop 12 had negligible effects on motor velocities. Two-motor complexes containing one kinesin-1 and one kinesin-3 moved at different speeds depending on the identity of their loop 12, indicating the importance of the motor reattachment rate on the cotransport speed. Simulations of these loop-swapped motors using experimentally derived motor parameters were able to reproduce the experimental results and identify best fit parameters for the motor reattachment rates for this geometry. Simulation results also supported previous work, suggesting that kinesin-3 microtubule detachment is very sensitive to load. Overall, the simulations demonstrate that the transport behavior of cargo carried by pairs of kinesin-1 and -3 motors are determined by three properties that differ between these two families: the unloaded velocity, the load dependence of detachment, and the motor reattachment rate.
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Affiliation(s)
- Göker Arpağ
- Department of Physics, Worcester Polytechnic Institute, Worcester, Massachusetts
| | - Stephen R Norris
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan; Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - S Iman Mousavi
- Department of Physics, Worcester Polytechnic Institute, Worcester, Massachusetts
| | | | - Kristen J Verhey
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan; Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - William O Hancock
- Department of Biomedical Engineering, Pennsylvania State University, State College, Pennsylvania.
| | - Erkan Tüzel
- Department of Physics, Worcester Polytechnic Institute, Worcester, Massachusetts.
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33
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Lessard DV, Zinder OJ, Hotta T, Verhey KJ, Ohi R, Berger CL. Polyglutamylation of tubulin's C-terminal tail controls pausing and motility of kinesin-3 family member KIF1A. J Biol Chem 2019; 294:6353-6363. [PMID: 30770469 DOI: 10.1074/jbc.ra118.005765] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 02/11/2019] [Indexed: 01/06/2023] Open
Abstract
The kinesin-3 family member KIF1A plays a critical role in site-specific neuronal cargo delivery during axonal transport. KIF1A cargo is mislocalized in many neurodegenerative diseases, indicating that KIF1A's highly efficient, superprocessive motility along axonal microtubules needs to be tightly regulated. One potential regulatory mechanism may be through posttranslational modifications (PTMs) of axonal microtubules. These PTMs often occur on the C-terminal tails of the microtubule tracks, act as molecular "traffic signals" helping to direct kinesin motor cargo delivery, and include C-terminal tail polyglutamylation important for KIF1A cargo transport. KIF1A initially interacts with microtubule C-terminal tails through its K-loop, a positively charged surface loop of the KIF1A motor domain. However, the role of the K-loop in KIF1A motility and response to perturbations in C-terminal tail polyglutamylation is underexplored. Using single-molecule imaging, we present evidence that KIF1A pauses on different microtubule lattice structures, linking multiple processive segments together and contributing to KIF1A's characteristic superprocessive run length. Furthermore, modifications of the KIF1A K-loop or tubulin C-terminal tail polyglutamylation reduced KIF1A pausing and overall run length. These results suggest a new mechanism to regulate KIF1A motility via pauses mediated by K-loop/polyglutamylated C-terminal tail interactions, providing further insight into KIF1A's role in axonal transport.
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Affiliation(s)
- Dominique V Lessard
- From the Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, Vermont 05405 and
| | - Oraya J Zinder
- From the Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, Vermont 05405 and
| | - Takashi Hotta
- the Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Kristen J Verhey
- the Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Ryoma Ohi
- the Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Christopher L Berger
- From the Department of Molecular Physiology and Biophysics, University of Vermont, Burlington, Vermont 05405 and
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34
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Ohi R, Verhey KJ. Promoting Diversity in the Cytoskeleton through STEM-Structural Transitions and Energetics of Microtubule Subunits. Dev Cell 2018; 47:137-139. [PMID: 30352173 DOI: 10.1016/j.devcel.2018.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
All microtubules assemble from tubulin subunits, but the functional impact of tubulin isotypes has been unclear. Reporting in Developmental Cell, Chaaban et al. (2018) and Ti et al. (2018) show that tubulin isotypes differ in their conformational flexibility, which alters microtubule dynamics and architecture, yet maintain "lock-and-key" interactions with neighbors.
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Affiliation(s)
- Ryoma Ohi
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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35
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Tymanskyj SR, Yang BH, Verhey KJ, Ma L. MAP7 regulates axon morphogenesis by recruiting kinesin-1 to microtubules and modulating organelle transport. eLife 2018; 7:36374. [PMID: 30132755 PMCID: PMC6133550 DOI: 10.7554/elife.36374] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 08/21/2018] [Indexed: 12/14/2022] Open
Abstract
Neuronal cell morphogenesis depends on proper regulation of microtubule-based transport, but the underlying mechanisms are not well understood. Here, we report our study of MAP7, a unique microtubule-associated protein that interacts with both microtubules and the motor protein kinesin-1. Structure-function analysis in rat embryonic sensory neurons shows that the kinesin-1 interacting domain in MAP7 is required for axon and branch growth but not for branch formation. Also, two unique microtubule binding sites are found in MAP7 that have distinct dissociation kinetics and are both required for branch formation. Furthermore, MAP7 recruits kinesin-1 dynamically to microtubules, leading to alterations in organelle transport behaviors, particularly pause/speed switching. As MAP7 is localized to branch sites, our results suggest a novel mechanism mediated by the dual interactions of MAP7 with microtubules and kinesin-1 in the precise control of microtubule-based transport during axon morphogenesis.
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Affiliation(s)
- Stephen R Tymanskyj
- Jefferson Synaptic Biology Center, Vickie and Jack Farber Institute for Neuroscience, Thomas Jefferson University, Philadelphia, United States.,Department of Neuroscience, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, United States
| | - Benjamin H Yang
- Jefferson Synaptic Biology Center, Vickie and Jack Farber Institute for Neuroscience, Thomas Jefferson University, Philadelphia, United States.,Department of Neuroscience, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, United States
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, United States
| | - Le Ma
- Jefferson Synaptic Biology Center, Vickie and Jack Farber Institute for Neuroscience, Thomas Jefferson University, Philadelphia, United States.,Department of Neuroscience, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, United States
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36
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Kelliher MT, Yue Y, Ng A, Kamiyama D, Huang B, Verhey KJ, Wildonger J. Autoinhibition of kinesin-1 is essential to the dendrite-specific localization of Golgi outposts. J Cell Biol 2018; 217:2531-2547. [PMID: 29728423 PMCID: PMC6028532 DOI: 10.1083/jcb.201708096] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 03/01/2018] [Accepted: 04/16/2018] [Indexed: 12/20/2022] Open
Abstract
Neuronal polarity relies on the axon- or dendrite-specific localization of cargo by molecular motors such as kinesin-1. This study shows how autoinhibition regulates both kinesin-1 activity and localization to keep dendritic Golgi outposts from entering axons. Neuronal polarity relies on the selective localization of cargo to axons or dendrites. The molecular motor kinesin-1 moves cargo into axons but is also active in dendrites. This raises the question of how kinesin-1 activity is regulated to maintain the compartment-specific localization of cargo. Our in vivo structure–function analysis of endogenous Drosophila melanogaster kinesin-1 reveals a novel role for autoinhibition in enabling the dendrite-specific localization of Golgi outposts. Mutations that disrupt kinesin-1 autoinhibition result in the axonal mislocalization of Golgi outposts. Autoinhibition also regulates kinesin-1 localization. Uninhibited kinesin-1 accumulates in axons and is depleted from dendrites, correlating with the change in outpost distribution and dendrite growth defects. Genetic interaction tests show that a balance of kinesin-1 inhibition and dynein activity is necessary to localize Golgi outposts to dendrites and keep them from entering axons. Our data indicate that kinesin-1 activity is precisely regulated by autoinhibition to achieve the selective localization of dendritic cargo.
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Affiliation(s)
- Michael T Kelliher
- Integrated Program in Biochemistry, University of Wisconsin-Madison, Madison, WI.,Biochemistry Department, University of Wisconsin-Madison, Madison, WI
| | - Yang Yue
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Ashley Ng
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI.,Biochemistry Scholars Program, University of Wisconsin-Madison, Madison, WI
| | - Daichi Kamiyama
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI
| | - Jill Wildonger
- Biochemistry Department, University of Wisconsin-Madison, Madison, WI
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37
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Yue Y, Blasius TL, Zhang S, Jariwala S, Walker B, Grant BJ, Cochran JC, Verhey KJ. Altered chemomechanical coupling causes impaired motility of the kinesin-4 motors KIF27 and KIF7. J Cell Biol 2018; 217:1319-1334. [PMID: 29351996 PMCID: PMC5881503 DOI: 10.1083/jcb.201708179] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 11/28/2017] [Accepted: 01/02/2018] [Indexed: 01/08/2023] Open
Abstract
Despite their shared ability to regulate microtubule polymerization dynamics, kinesin-4 motors display dramatically different motility properties ranging from fast processive motility to no movement. Yue et al. demonstrate that for KIF7 and KIF27, altered chemomechanical coupling results in immotile behavior and slow processive movement, respectively. Kinesin-4 motors play important roles in cell division, microtubule organization, and signaling. Understanding how motors perform their functions requires an understanding of their mechanochemical and motility properties. We demonstrate that KIF27 can influence microtubule dynamics, suggesting a conserved function in microtubule organization across the kinesin-4 family. However, kinesin-4 motors display dramatically different motility characteristics: KIF4 and KIF21 motors are fast and processive, KIF7 and its Drosophila melanogaster homologue Costal2 (Cos2) are immotile, and KIF27 is slow and processive. Neither KIF7 nor KIF27 can cooperate for fast processive transport when working in teams. The mechanistic basis of immotile KIF7 behavior arises from an inability to release adenosine diphosphate in response to microtubule binding, whereas slow processive KIF27 behavior arises from a slow adenosine triphosphatase rate and a high affinity for both adenosine triphosphate and microtubules. We suggest that evolutionarily selected sequence differences enable immotile KIF7 and Cos2 motors to function not as transporters but as microtubule-based tethers of signaling complexes.
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Affiliation(s)
- Yang Yue
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
| | - T Lynne Blasius
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
| | - Stephanie Zhang
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN
| | - Shashank Jariwala
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Benjamin Walker
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN
| | - Barry J Grant
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Jared C Cochran
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI
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38
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Luo W, Ruba A, Takao D, Zweifel LP, Lim RYH, Verhey KJ, Yang W. Axonemal Lumen Dominates Cytosolic Protein Diffusion inside the Primary Cilium. Sci Rep 2017; 7:15793. [PMID: 29150645 PMCID: PMC5693955 DOI: 10.1038/s41598-017-16103-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 11/03/2017] [Indexed: 12/02/2022] Open
Abstract
Transport of membrane and cytosolic proteins in primary cilia is thought to depend on intraflagellar transport (IFT) and diffusion. However, the relative contribution and spatial routes of each transport mechanism are largely unknown. Although challenging to decipher, the details of these routes are essential for our understanding of protein transport in primary cilia, a critically affected process in many genetic diseases. By using a high-speed virtual 3D super-resolution microscopy, we have mapped the 3D spatial locations of transport routes for various cytosolic proteins in the 250-nm-wide shaft of live primary cilia with a spatiotemporal resolution of 2 ms and <16 nm. Our data reveal two spatially distinguishable transport routes for cytosolic proteins: an IFT-dependent path along the axoneme, and a passive-diffusion route in the axonemal lumen that escaped previous studies. While all cytosolic proteins tested primarily utilize the IFT path in the anterograde direction, differences are observed in the retrograde direction where IFT20 only utilizes IFT, and approximately half of KIF17 and one third of α–tubulin utilizes diffusion besides IFT.
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Affiliation(s)
- Wangxi Luo
- Department of Biology, Temple University, Philadelphia, Pennsylvania, 19122, USA
| | - Andrew Ruba
- Department of Biology, Temple University, Philadelphia, Pennsylvania, 19122, USA
| | - Daisuke Takao
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Ludovit P Zweifel
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Roderick Y H Lim
- Biozentrum and the Swiss Nanoscience Institute, University of Basel, Basel, Switzerland
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, Pennsylvania, 19122, USA.
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39
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Takao D, Wang L, Boss A, Verhey KJ. Protein Interaction Analysis Provides a Map of the Spatial and Temporal Organization of the Ciliary Gating Zone. Curr Biol 2017; 27:2296-2306.e3. [PMID: 28736169 DOI: 10.1016/j.cub.2017.06.044] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/09/2017] [Accepted: 06/16/2017] [Indexed: 11/19/2022]
Abstract
The motility and signaling functions of the primary cilium require a unique protein and lipid composition that is determined by gating mechanisms localized at the base of the cilium. Several protein complexes localize to the gating zone and may regulate ciliary protein composition; however, the mechanisms of ciliary gating and the dynamics of the gating components are largely unknown. Here, we used the BiFC (bimolecular fluorescence complementation) assay and report for the first time on the protein-protein interactions that occur between ciliary gating components and transiting cargoes during ciliary entry. We find that the nucleoporin Nup62 and the C termini of the nephronophthisis (NPHP) proteins NPHP4 and NPHP5 interact with the axoneme-associated kinesin-2 motor KIF17 and thus spatially map to the inner region of the ciliary gating zone. Nup62 and NPHP4 exhibit rapid turnover at the transition zone and thus define dynamic components of the gate. We find that B9D1, AHI1, and the N termini of NPHP4 and NPHP5 interact with the transmembrane protein SSTR3 and thus spatially map to the outer region of the ciliary gating zone. B9D1, AHI1, and NPHP5 exhibit little to no turnover at the transition zone and thus define components of a stable gating structure. These data provide the first comprehensive map of the molecular orientations of gating zone components along the inner-to-outer axis of the ciliary gating zone. These results advance our understanding of the functional roles of gating zone components in regulating ciliary protein composition.
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Affiliation(s)
- Daisuke Takao
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Liang Wang
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA; The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, School of Life Science, Jiangsu Normal University, 101 Shanghai Road, Tongshan District, Xuzhou 221116, China
| | - Allison Boss
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA.
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40
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Ravindran MS, Engelke MF, Verhey KJ, Tsai B. Exploiting the kinesin-1 molecular motor to generate a virus membrane penetration site. Nat Commun 2017; 8:15496. [PMID: 28537258 PMCID: PMC5458101 DOI: 10.1038/ncomms15496] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 03/30/2017] [Indexed: 02/06/2023] Open
Abstract
Viruses exploit cellular machineries to penetrate a host membrane and cause infection, a process that remains enigmatic for non-enveloped viruses. Here we probe how the non-enveloped polyomavirus SV40 penetrates the endoplasmic reticulum (ER) membrane to reach the cytosol, a crucial infection step. We find that the microtubule-based motor kinesin-1 is recruited to the ER membrane by binding to the transmembrane J-protein B14. Strikingly, this motor facilitates SV40 ER-to-cytosol transport by constructing a penetration site on the ER membrane called a ‘focus'. Neither kinesin-2, kinesin-3 nor kinesin-5 promotes foci formation or infection. The specific use of kinesin-1 is due to its unique ability to select posttranslationally modified microtubules for cargo transport and thereby spatially restrict focus formation to the perinucleus. These findings support the idea of a ‘tubulin code' for motor-dependent trafficking and establish a distinct kinesin-1 function in which a motor is exploited to create a viral membrane penetration site. How non-enveloped viruses cross host membranes is incompletely understood. Here, Ravindran et al. show that polyomavirus SV40 recruits kinesin-1 to construct a penetration site on the ER membrane.
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Affiliation(s)
- Madhu Sudhan Ravindran
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, 3043 BSRB, Ann Arbor, Michigan 48109, USA
| | - Martin F Engelke
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, 3043 BSRB, Ann Arbor, Michigan 48109, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, 3043 BSRB, Ann Arbor, Michigan 48109, USA
| | - Billy Tsai
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, 3043 BSRB, Ann Arbor, Michigan 48109, USA
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Breznau EB, Murt M, Blasius TL, Verhey KJ, Miller AL. The MgcRacGAP SxIP motif tethers Centralspindlin to microtubule plus ends in Xenopus laevis. J Cell Sci 2017; 130:1809-1821. [PMID: 28389580 DOI: 10.1242/jcs.195891] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 04/04/2017] [Indexed: 12/27/2022] Open
Abstract
Centralspindlin, a complex of the kinesin-6-family member MKLP1 and MgcRacGAP (also known as Kif23 and Racgap1, respectively), is required for cytokinesis and cell-cell junctions. During anaphase, Centralspindlin accumulates at overlapping central spindle microtubules and directs contractile ring formation by recruiting the GEF Ect2 to the cell equator to activate RhoA. We found that MgcRacGAP localized to the plus ends of equatorial astral microtubules during cytokinesis in Xenopus laevis embryos. How MgcRacGAP is stabilized at microtubule plus ends is unknown. We identified an SxIP motif in X. laevis MgcRacGAP that is conserved with other proteins that bind to EB1 (also known as Mapre1), a microtubule plus-end tracking protein. Mutation of the SxIP motif in MgcRacGAP resulted in loss of MgcRacGAP tracking with EB3 (also known as Mapre3) on growing microtubule plus ends, abnormal astral microtubule organization, redistribution of MgcRacGAP from the contractile ring to the polar cell cortex, and mislocalization of RhoA and its downstream targets, which together contributed to severe cytokinesis defects. Furthermore, mutation of the MgcRacGAP SxIP motif perturbed adherens junctions. We propose that the MgcRacGAP SxIP motif is functionally important both for its role in regulating adherens junction structure during interphase and for regulating Rho GTPase activity during cytokinesis.
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Affiliation(s)
- Elaina B Breznau
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Megan Murt
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - T Lynne Blasius
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ann L Miller
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI 48109, USA .,Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
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Chen S, Blasius TL, Engelke MF, Verhey KJ. Engineering Inhibitable Kinesin-3 Motors by a Novel Chemical-Genetic Approach. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.1429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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43
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Budaitis BG, Schimert KI, Scarabelli G, Grant BJ, Verhey KJ. The Role of the Cover-Neck Bundle in Multi-Motor Transport against Load in Cells. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.1427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Scarabelli G, Soppina V, Yao XQ, Atherton J, Moores CA, Verhey KJ, Grant BJ. Mapping the Processivity Determinants of the Kinesin-3 Motor Domain. Biophys J 2016; 109:1537-40. [PMID: 26488644 PMCID: PMC4624112 DOI: 10.1016/j.bpj.2015.08.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 08/17/2015] [Accepted: 08/20/2015] [Indexed: 12/27/2022] Open
Abstract
Kinesin superfamily members play important roles in many diverse cellular processes, including cell motility, cell division, intracellular transport, and regulation of the microtubule cytoskeleton. How the properties of the family-defining motor domain of distinct kinesins are tailored to their different cellular roles remains largely unknown. Here, we employed molecular-dynamics simulations coupled with energetic calculations to infer the family-specific interactions of kinesin-1 and kinesin-3 motor domains with microtubules in different nucleotide states. We then used experimental mutagenesis and single-molecule motility assays to further assess the predicted residue-wise determinants of distinct kinesin-microtubule binding properties. Collectively, our results identify residues in the L8, L11, and α6 regions that contribute to family-specific microtubule interactions and whose mutation affects motor-microtubule complex stability and processive motility (the ability of an individual motor to take multiple steps along its microtubule filament). In particular, substitutions of prominent kinesin-3 residues with those found in kinesin-1, namely, R167S/H171D, K266D, and R346M, were found to decrease kinesin-3 processivity 10-fold and thus approach kinesin-1 levels.
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Affiliation(s)
- Guido Scarabelli
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Virupakshi Soppina
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Xin-Qiu Yao
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan
| | - Joseph Atherton
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Carolyn A Moores
- Institute of Structural and Molecular Biology, Birkbeck College, University of London, London, United Kingdom
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan.
| | - Barry J Grant
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan.
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Verhey KJ, Yang W. Permeability barriers for generating a unique ciliary protein and lipid composition. Curr Opin Cell Biol 2016; 41:109-16. [PMID: 27232950 DOI: 10.1016/j.ceb.2016.05.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 05/04/2016] [Accepted: 05/10/2016] [Indexed: 01/08/2023]
Abstract
Cilia (and flagella) are microtubule-based protrusions that are found in single or multiple copies on the surface of most eukaryotic cells. Defects in cilia formation and/or function have now been correlated with an expanding spectrum of human genetic diseases termed ciliopathies. Recent work indicates that cilia are indeed a bona fide organelle with a unique protein and lipid content that enables specific cellular functions. Despite the physiological and clinical relevance of cilia, our understanding of how a unique protein and lipid composition is generated for this organelle remains poor. Here we review recent work on the mechanisms that determine the protein and lipid content, and thus the functional outputs, of this unique organelle.
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Affiliation(s)
- Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
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Engelke MF, Winding M, Yue Y, Shastry S, Teloni F, Reddy S, Blasius TL, Soppina P, Hancock WO, Gelfand VI, Verhey KJ. Engineered kinesin motor proteins amenable to small-molecule inhibition. Nat Commun 2016; 7:11159. [PMID: 27045608 PMCID: PMC4822052 DOI: 10.1038/ncomms11159] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 02/26/2016] [Indexed: 12/17/2022] Open
Abstract
The human genome encodes 45 kinesin motor proteins that drive cell division, cell motility, intracellular trafficking and ciliary function. Determining the cellular function of each kinesin would benefit from specific small-molecule inhibitors. However, screens have yielded only a few specific inhibitors. Here we present a novel chemical-genetic approach to engineer kinesin motors that can carry out the function of the wild-type motor yet can also be efficiently inhibited by small, cell-permeable molecules. Using kinesin-1 as a prototype, we develop two independent strategies to generate inhibitable motors, and characterize the resulting inhibition in single-molecule assays and in cells. We further apply these two strategies to create analogously inhibitable kinesin-3 motors. These inhibitable motors will be of great utility to study the functions of specific kinesins in a dynamic manner in cells and animals. Furthermore, these strategies can be used to generate inhibitable versions of any motor protein of interest.
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Affiliation(s)
- Martin F. Engelke
- Department of Cell and Developmental Biology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109, USA
| | - Michael Winding
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Yang Yue
- Department of Cell and Developmental Biology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109, USA
| | - Shankar Shastry
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, USA
| | - Federico Teloni
- Department of Cell and Developmental Biology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109, USA
| | - Sanjay Reddy
- Department of Cell and Developmental Biology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109, USA
| | - T. Lynne Blasius
- Department of Cell and Developmental Biology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109, USA
| | - Pushpanjali Soppina
- Department of Cell and Developmental Biology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109, USA
| | - William O. Hancock
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania 16802, USA
| | - Vladimir I. Gelfand
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Kristen J. Verhey
- Department of Cell and Developmental Biology, University of Michigan, 109 Zina Pitcher Place, Ann Arbor, Michigan 48109, USA
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47
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Padzik A, Deshpande P, Hollos P, Franker M, Rannikko EH, Cai D, Prus P, Mågård M, Westerlund N, Verhey KJ, James P, Hoogenraad CC, Coffey ET. KIF5C S176 Phosphorylation Regulates Microtubule Binding and Transport Efficiency in Mammalian Neurons. Front Cell Neurosci 2016; 10:57. [PMID: 27013971 PMCID: PMC4791394 DOI: 10.3389/fncel.2016.00057] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 02/24/2016] [Indexed: 12/15/2022] Open
Abstract
Increased phosphorylation of the KIF5 anterograde motor is associated with impaired axonal transport and neurodegeneration, but paradoxically also with normal transport, though the details are not fully defined. JNK phosphorylates KIF5C on S176 in the motor domain; a site that we show is phosphorylated in brain. Microtubule pelleting assays demonstrate that phosphomimetic KIF5C(1-560)(S176D) associates weakly with microtubules compared to KIF5C(1-560)(WT). Consistent with this, 50% of KIF5C(1-560)(S176D) shows diffuse movement in neurons. However, the remaining 50% remains microtubule bound and displays decreased pausing and increased bidirectional movement. The same directionality switching is observed with KIF5C(1-560)(WT) in the presence of an active JNK chimera, MKK7-JNK. Yet, in cargo trafficking assays where peroxisome cargo is bound, KIF5C(1-560)(S176D)-GFP-FRB transports normally to microtubule plus ends. We also find that JNK increases the ATP hydrolysis of KIF5C in vitro. These data suggest that phosphorylation of KIF5C-S176 primes the motor to either disengage entirely from microtubule tracks as previously observed in response to stress, or to display improved efficiency. The final outcome may depend on cargo load and motor ensembles.
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Affiliation(s)
- Artur Padzik
- Turku Centre for Biotechnology, Åbo Akademi University and University of Turku Turku, Finland
| | - Prasannakumar Deshpande
- Turku Centre for Biotechnology, Åbo Akademi University and University of Turku Turku, Finland
| | - Patrik Hollos
- Turku Centre for Biotechnology, Åbo Akademi University and University of Turku Turku, Finland
| | - Mariella Franker
- Cell Biology, Faculty of Science, Utrecht University Utrecht, Netherlands
| | - Emmy H Rannikko
- Turku Centre for Biotechnology, Åbo Akademi University and University of Turku Turku, Finland
| | - Dawen Cai
- Department of Cell and Developmental Biology, University of Michigan Ann Arbor, MI, USA
| | - Piotr Prus
- Department of Biochemistry, University of Oulu Oulu, Finland
| | - Mats Mågård
- Department of Immunotechnology, Lund University Medicon, Lund, Sweden
| | - Nina Westerlund
- Turku Centre for Biotechnology, Åbo Akademi University and University of Turku Turku, Finland
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Ann Arbor, MI, USA
| | - Peter James
- Department of Immunotechnology, Lund University Medicon, Lund, Sweden
| | | | - Eleanor T Coffey
- Turku Centre for Biotechnology, Åbo Akademi University and University of Turku Turku, Finland
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48
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Norris SR, Núñez MF, Verhey KJ. Influence of fluorescent tag on the motility properties of kinesin-1 in single-molecule assays. Biophys J 2016; 108:1133-43. [PMID: 25762325 DOI: 10.1016/j.bpj.2015.01.031] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 01/15/2015] [Accepted: 01/28/2015] [Indexed: 12/26/2022] Open
Abstract
Molecular motors such as kinesin and dynein use the energy derived from ATP hydrolysis to walk processively along microtubule tracks and transport various cargoes inside the cell. Recent advancements in fluorescent protein (FP) research enable motors to be fluorescently labeled such that single molecules can be visualized inside cells in multiple colors. The performance of these fluorescent tags can vary depending on their spectral properties and a natural tendency for oligomerization. Here we present a survey of different fluorescent tags fused to kinesin-1 and studied by single-molecule motility assays of mammalian cell lysates. We tested eight different FP tags and found that seven of them display sufficient fluorescence intensity and photostability to visualize motility events. Although none of the FP tags interfere with the enzymatic properties of the motor, four of the tags (EGFP, monomeric EGFP, tagRFPt, and mApple) cause aberrantly long motor run lengths. This behavior is unlikely to be due to electrostatic interactions and is probably caused by tag-dependent oligomerization events that appear to be facilitated by fusion to the dimeric kinesin-1. We also compared the single-molecule performance of various fluorescent SNAP and HALO ligands. We found that although both green and red SNAP ligands provide sufficient fluorescent signal, only the tetramethyl rhodamine (TMR) HALO ligand provides sufficient signal for detection in these assays. This study will serve as a valuable reference for choosing fluorescent labels for single-molecule motility assays.
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Affiliation(s)
- Stephen R Norris
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan; Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan
| | - Marcos F Núñez
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan
| | - Kristen J Verhey
- Department of Biophysics, University of Michigan, Ann Arbor, Michigan; Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan.
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Abstract
Cilia and flagella play important roles in cell motility and cell signaling. These functions require that the cilium establishes and maintains a unique lipid and protein composition. Recent work indicates that a specialized region at the base of the cilium, the transition zone, serves as both a barrier to entry and a gate for passage of select components. For at least some cytosolic proteins, the barrier and gate functions are provided by a ciliary pore complex (CPC) that shares molecular and mechanistic properties with nuclear gating. Specifically, nucleoporins of the CPC limit the diffusional entry of cytosolic proteins in a size-dependent manner and enable the active transport of large molecules and complexes via targeting signals, importins, and the small G protein Ran. For membrane proteins, the septin protein SEPT2 is part of the barrier to entry whereas the gating function is carried out and/or regulated by proteins associated with ciliary diseases (ciliopathies) such as nephronophthisis, Meckel–Gruber syndrome and Joubert syndrome. Here, we discuss the evidence behind these models of ciliary gating as well as the similarities to and differences from nuclear gating.
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Affiliation(s)
- Daisuke Takao
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Pl, Ann Arbor, MI 48109 USA
| | - Kristen J. Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Pl, Ann Arbor, MI 48109 USA
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50
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Abstract
Cilia and flagella are microtubule-based organelles that play important roles in human health by contributing to cellular motility as well as sensing and responding to environmental cues. Defects in cilia formation and function cause a broad class of human genetic diseases called ciliopathies. To carry out their specialized functions, cilia contain a unique complement of proteins that must be imported into the ciliary compartment. In this chapter, we describe methods to measure the permeability barrier of the ciliary gate by microinjection of fluorescent proteins and dextrans of different sizes into ciliated cells. We also describe a fluorescence recovery after photobleaching (FRAP) assay to measure the entry of ciliary proteins into the ciliary compartment. These assays can be used to determine the molecular mechanisms that regulate the formation and function of cilia in mammalian cells.
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Affiliation(s)
- Daisuke Takao
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI, 48109, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI, 48109, USA.
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