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Ekal L, Alqahtani AMS, Schuldiner M, Zalckvar E, Hettema EH, Ayscough KR. Spindle Position Checkpoint Kinase Kin4 Regulates Organelle Transport in Saccharomyces cerevisiae. Biomolecules 2023; 13:1098. [PMID: 37509134 PMCID: PMC10377308 DOI: 10.3390/biom13071098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/29/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
Membrane-bound organelles play important, frequently essential, roles in cellular metabolism in eukaryotes. Hence, cells have evolved molecular mechanisms to closely monitor organelle dynamics and maintenance. The actin cytoskeleton plays a vital role in organelle transport and positioning across all eukaryotes. Studies in the budding yeast Saccharomyces cerevisiae (S. cerevisiae) revealed that a block in actomyosin-dependent transport affects organelle inheritance to daughter cells. Indeed, class V Myosins, Myo2, and Myo4, and many of their organelle receptors, have been identified as key factors in organelle inheritance. However, the spatiotemporal regulation of yeast organelle transport remains poorly understood. Using peroxisome inheritance as a proxy to study actomyosin-based organelle transport, we performed an automated genome-wide genetic screen in S. cerevisiae. We report that the spindle position checkpoint (SPOC) kinase Kin4 and, to a lesser extent, its paralog Frk1, regulates peroxisome transport, independent of their role in the SPOC. We show that Kin4 requires its kinase activity to function and that both Kin4 and Frk1 protect Inp2, the peroxisomal Myo2 receptor, from degradation in mother cells. In addition, vacuole inheritance is also affected in kin4/frk1-deficient cells, suggesting a common regulatory mechanism for actin-based transport for these two organelles in yeast. More broadly our findings have implications for understanding actomyosin-based transport in cells.
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Affiliation(s)
- Lakhan Ekal
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Abdulaziz M S Alqahtani
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- Department of Biology, Faculty of Science, University of Bisha, P.O. Box 551, Bisha 61922, Saudi Arabia
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ewald H Hettema
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
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Niu F, Liu Y, Sun K, Xu S, Dong J, Yu C, Yan K, Wei Z. Autoinhibition and activation mechanisms revealed by the triangular-shaped structure of myosin Va. SCIENCE ADVANCES 2022; 8:eadd4187. [PMID: 36490350 PMCID: PMC9733927 DOI: 10.1126/sciadv.add4187] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
As the prototype of unconventional myosin motor family, myosin Va (MyoVa) transport cellular cargos along actin filaments in diverse cellular processes. The off-duty MyoVa adopts a closed and autoinhibited state, which can be relieved by cargo binding. The molecular mechanisms governing the autoinhibition and activation of MyoVa remain unclear. Here, we report the cryo-electron microscopy structure of the two full-length, closed MyoVa heavy chains in complex with 12 calmodulin light chains at 4.78-Å resolution. The MyoVa adopts a triangular structure with multiple intra- and interpolypeptide chain interactions in establishing the closed state with cargo binding and adenosine triphosphatase activity inhibited. Structural, biochemical, and cellular analyses uncover an asymmetric autoinhibition mechanism, in which the cargo-binding sites in the two MyoVa heavy chains are differently protected. Thus, specific and efficient MyoVa activation requires coincident binding of multiple cargo adaptors, revealing an intricate and elegant activity regulation of the motor in response to cargos.
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Affiliation(s)
- Fengfeng Niu
- Brain Research Center, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yong Liu
- Brain Research Center, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
- SUSTech-HIT Joint PhD Program, Harbin Institute of Technology, Harbin, Heilongjiang, China
| | - Kang Sun
- Brain Research Center, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Shun Xu
- Brain Research Center, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Jiayuan Dong
- Brain Research Center, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Cong Yu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research and Shenzhen Key Laboratory of Cell Microenvironment, Shenzhen, Guangdong, China
| | - Kaige Yan
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Zhiyi Wei
- Brain Research Center, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
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Liu Y, Li L, Yu C, Zeng F, Niu F, Wei Z. Cargo Recognition Mechanisms of Yeast Myo2 Revealed by AlphaFold2-Powered Protein Complex Prediction. Biomolecules 2022; 12:biom12081032. [PMID: 35892342 PMCID: PMC9330073 DOI: 10.3390/biom12081032] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/17/2022] [Accepted: 07/20/2022] [Indexed: 02/01/2023] Open
Abstract
Myo2, a yeast class V myosin, transports a broad range of organelles and plays important roles in various cellular processes, including cell division in budding yeast. Despite the fact that several structures of Myo2/cargo adaptor complexes have been determined, the understanding of the versatile cargo-binding modes of Myo2 is still very limited, given the large number of cargo adaptors identified for Myo2. Here, we used ColabFold, an AlphaFold2-powered and easy-to-use tool, to predict the complex structures of Myo2-GTD and its several cargo adaptors. After benchmarking the prediction strategy with three Myo2/cargo adaptor complexes that have been determined previously, we successfully predicted the atomic structures of Myo2-GTD in complex with another three cargo adaptors, Vac17, Kar9 and Pea2, which were confirmed by our biochemical characterizations. By systematically comparing the interaction details of the six complexes of Myo2 and its cargo adaptors, we summarized the cargo-binding modes on the three conserved sites of Myo2-GTD, providing an overall picture of the versatile cargo-recognition mechanisms of Myo2. In addition, our study demonstrates an efficient and effective solution to study protein-protein interactions in the future via the AlphaFold2-powered prediction.
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Affiliation(s)
- Yong Liu
- SUSTech-HIT Joint PhD Program, Harbin Institute of Technology, Harbin 150001, China;
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; (L.L.); (C.Y.); (F.Z.)
- Brain Research Center, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Lingxuan Li
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; (L.L.); (C.Y.); (F.Z.)
- Brain Research Center, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Cong Yu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; (L.L.); (C.Y.); (F.Z.)
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, Shenzhen 518055, China
- Shenzhen Key Laboratory of Cell Microenvironment, Southern University of Science and Technology, Shenzhen 518055, China
| | - Fuxing Zeng
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; (L.L.); (C.Y.); (F.Z.)
| | - Fengfeng Niu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; (L.L.); (C.Y.); (F.Z.)
- Brain Research Center, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- Correspondence: (F.N.); (Z.W.)
| | - Zhiyi Wei
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China; (L.L.); (C.Y.); (F.Z.)
- Brain Research Center, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- Correspondence: (F.N.); (Z.W.)
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Chao JT, Pina F, Niwa M. Regulation of the early stages of endoplasmic reticulum inheritance during ER stress. Mol Biol Cell 2021; 32:109-119. [PMID: 33448894 PMCID: PMC8120693 DOI: 10.1091/mbc.e20-08-0558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The endoplasmic reticulum (ER) is one of the largest cytoplasmic organelles in eukaryotic cells and plays a role in many cellular processes, such as the production and quality control of secretory protein, lipid synthesis, and calcium homeostasis. The ER cannot be generated de novo, and thus its proper inheritance during cell division is paramount to the health and survival of the daughter cells. Although previous work has uncovered the cytoskeletal components involved, we still lack a comprehensive understanding of the intricate steps of and the cytoplasmic and membrane-bound components involved in ER inheritance. To directly address these issues, we utilized microfluidics and genetic analyses to show that before nuclear migration, early ER inheritance can be further divided into three distinctive steps. Moreover, we demonstrated that perturbing each of these steps affects the cell's ability to mitigate ER stress. Thus, proper ER inheritance is essential to ensuring a healthy, functional cell.
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Affiliation(s)
- Jesse T Chao
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, La Jolla, CA 92093-0377.,Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Francisco Pina
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, La Jolla, CA 92093-0377.,Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada V6T 1Z3
| | - Maho Niwa
- Division of Biological Sciences, Section of Molecular Biology, University of California, San Diego, La Jolla, CA 92093-0377
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Dünkler A, Leda M, Kromer JM, Neller J, Gronemeyer T, Goryachev AB, Johnsson N. Type V myosin focuses the polarisome and shapes the tip of yeast cells. J Cell Biol 2021; 220:211845. [PMID: 33656555 PMCID: PMC7933982 DOI: 10.1083/jcb.202006193] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 01/25/2021] [Accepted: 02/04/2021] [Indexed: 11/22/2022] Open
Abstract
The polarisome is a cortical proteinaceous microcompartment that organizes the growth of actin filaments and the fusion of secretory vesicles in yeasts and filamentous fungi. Polarisomes are compact, spotlike structures at the growing tips of their respective cells. The molecular forces that control the form and size of this microcompartment are not known. Here we identify a complex between the polarisome subunit Pea2 and the type V Myosin Myo2 that anchors Myo2 at the cortex of yeast cells. We discovered a point mutation in the cargo-binding domain of Myo2 that impairs the interaction with Pea2 and consequently the formation and focused localization of the polarisome. Cells carrying this mutation grow round instead of elongated buds. Further experiments and biophysical modeling suggest that the interactions between polarisome-bound Myo2 motors and dynamic actin filaments spatially focus the polarisome and sustain its compact shape.
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Affiliation(s)
- Alexander Dünkler
- Institute of Molecular Genetics and Cell Biology, Department of Biology, Ulm University, Ulm, Germany
| | - Marcin Leda
- Centre for Synthetic and Systems Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Jan-Michael Kromer
- Institute of Molecular Genetics and Cell Biology, Department of Biology, Ulm University, Ulm, Germany
| | - Joachim Neller
- Institute of Molecular Genetics and Cell Biology, Department of Biology, Ulm University, Ulm, Germany
| | - Thomas Gronemeyer
- Institute of Molecular Genetics and Cell Biology, Department of Biology, Ulm University, Ulm, Germany
| | - Andrew B Goryachev
- Centre for Synthetic and Systems Biology, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Nils Johnsson
- Institute of Molecular Genetics and Cell Biology, Department of Biology, Ulm University, Ulm, Germany
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Turowski VR, Ruiz DM, Nascimento AFZ, Millán C, Sammito MD, Juanhuix J, Cremonesi AS, Usón I, Giuseppe PO, Murakami MT. Structure of the class XI myosin globular tail reveals evolutionary hallmarks for cargo recognition in plants. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:522-533. [PMID: 33825712 DOI: 10.1107/s2059798321001583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 02/09/2021] [Indexed: 11/10/2022]
Abstract
The plant-specific class XI myosins (MyoXIs) play key roles at the molecular, cellular and tissue levels, engaging diverse adaptor proteins to transport cargoes along actin filaments. To recognize their cargoes, MyoXIs have a C-terminal globular tail domain (GTD) that is evolutionarily related to those of class V myosins (MyoVs) from animals and fungi. Despite recent advances in understanding the functional roles played by MyoXI in plants, the structure of its GTD, and therefore the molecular determinants for cargo selectivity and recognition, remain elusive. In this study, the first crystal structure of a MyoXI GTD, that of MyoXI-K from Arabidopsis thaliana, was elucidated at 2.35 Å resolution using a low-identity and fragment-based phasing approach in ARCIMBOLDO_SHREDDER. The results reveal that both the composition and the length of the α5-α6 loop are distinctive features of MyoXI-K, providing evidence for a structural stabilizing role for this loop, which is otherwise carried out by a molecular zipper in MyoV GTDs. The crystal structure also shows that most of the characterized cargo-binding sites in MyoVs are not conserved in plant MyoXIs, pointing to plant-specific cargo-recognition mechanisms. Notably, the main elements involved in the self-regulation mechanism of MyoVs are conserved in plant MyoXIs, indicating this to be an ancient ancestral trait.
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Affiliation(s)
- Valeria R Turowski
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas-SP 13083-100, Brazil
| | - Diego M Ruiz
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas-SP 13083-100, Brazil
| | - Andrey F Z Nascimento
- Structural Biology, Instituto de Biología Molecular de Barcelona, CSIC, Carrer de Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Claudia Millán
- Structural Biology, Instituto de Biología Molecular de Barcelona, CSIC, Carrer de Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Massimo D Sammito
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Judith Juanhuix
- XALOC Beamline, Experiments Division, ALBA Synchrotron Light Source, Cerdanyola del Vallès, 08290 Barcelona, Spain
| | - Aline Sampaio Cremonesi
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas-SP 13083-100, Brazil
| | - Isabel Usón
- Structural Biology, Instituto de Biología Molecular de Barcelona, CSIC, Carrer de Baldiri Reixac 15, 08028 Barcelona, Spain
| | - Priscila O Giuseppe
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas-SP 13083-100, Brazil
| | - Mario T Murakami
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas-SP 13083-100, Brazil
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Wong S, Weisman LS. Roles and regulation of myosin V interaction with cargo. Adv Biol Regul 2021; 79:100787. [PMID: 33541831 PMCID: PMC7920922 DOI: 10.1016/j.jbior.2021.100787] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 05/08/2023]
Abstract
A major question in cell biology is, how are organelles and large macromolecular complexes transported within a cell? Myosin V molecular motors play critical roles in the distribution of organelles, vesicles, and mRNA. Mis-localization of organelles that depend on myosin V motors underlie diseases in the skin, gut, and brain. Thus, the delivery of organelles to their proper destination is important for animal physiology and cellular function. Cargoes attach to myosin V motors via cargo specific adaptor proteins, which transiently bridge motors to their cargoes. Regulation of these adaptor proteins play key roles in the regulation of cargo transport. Emerging studies reveal that cargo adaptors play additional essential roles in the activation of myosin V, and the regulation of actin filaments. Here, we review how motor-adaptor interactions are controlled to regulate the proper loading and unloading of cargoes, as well as roles of adaptor proteins in the regulation of myosin V activity and the dynamics of actin filaments.
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Affiliation(s)
- Sara Wong
- Cell and Molecular Biology, University of Michigan, Ann Arbor, United States; Life Sciences Institute, University of Michigan, Ann Arbor, United States
| | - Lois S Weisman
- Cell and Developmental Biology, University of Michigan, Ann Arbor, United States; Life Sciences Institute, University of Michigan, Ann Arbor, United States.
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Gingras RM, Lwin KM, Miller AM, Bretscher A. Yeast Rgd3 is a phospho-regulated F-BAR-containing RhoGAP involved in the regulation of Rho3 distribution and cell morphology. Mol Biol Cell 2020; 31:2570-2582. [PMID: 32941095 PMCID: PMC7851877 DOI: 10.1091/mbc.e20-05-0288] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Polarized growth requires the integration of polarity pathways with the delivery of exocytic vesicles for cell expansion and counterbalancing endocytic uptake. In budding yeast, the myosin-V Myo2 is aided by the kinesin-related protein Smy1 in carrying out the essential Sec4-dependent transport of secretory vesicles to sites of polarized growth. Overexpression suppressors of a conditional myo2 smy1 mutant identified a novel F-BAR (Fes/CIP4 homology-Bin-Amphiphysin-Rvs protein)-containing RhoGAP, Rgd3, that has activity primarily on Rho3, but also Cdc42. Internally tagged Rho3 is restricted to the plasma membrane in a gradient corresponding to cell polarity that is altered upon Rgd3 overexpression. Rgd3 itself is localized to dynamic polarized vesicles that, while distinct from constitutive secretory vesicles, are dependent on actin and Myo2 function. In vitro Rgd3 associates with liposomes in a PIP2-enhanced manner. Further, the Rgd3 C-terminal region contains several phosphorylatable residues within a reported SH3-binding motif. An unphosphorylated mimetic construct is active and highly polarized, while the phospho-mimetic form is not. Rgd3 is capable of activating Myo2, dependent on its phospho state, and Rgd3 overexpression rescues aberrant Rho3 localization and cell morphologies seen at the restrictive temperature in the myo2 smy1 mutant. We propose a model where Rgd3 functions to modulate and maintain Rho3 polarity during growth.
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Affiliation(s)
- Robert M Gingras
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Kyaw Myo Lwin
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Abigail M Miller
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
| | - Anthony Bretscher
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853
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Klecker T, Westermann B. Asymmetric inheritance of mitochondria in yeast. Biol Chem 2020; 401:779-791. [DOI: 10.1515/hsz-2019-0439] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 01/15/2020] [Indexed: 01/27/2023]
Abstract
AbstractMitochondria are essential organelles of virtually all eukaryotic organisms. As they cannot be made de novo, they have to be inherited during cell division. In this review, we provide an overview on mitochondrial inheritance in Saccharomyces cerevisiae, a powerful model organism to study asymmetric cell division. Several processes have to be coordinated during mitochondrial inheritance: mitochondrial transport along the actin cytoskeleton into the emerging bud is powered by a myosin motor protein; cell cortex anchors retain a critical fraction of mitochondria in the mother cell and bud to ensure proper partitioning; and the quantity of mitochondria inherited by the bud is controlled during cell cycle progression. Asymmetric division of yeast cells produces rejuvenated daughter cells and aging mother cells that die after a finite number of cell divisions. We highlight the critical role of mitochondria in this process and discuss how asymmetric mitochondrial partitioning and cellular aging are connected.
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Affiliation(s)
- Till Klecker
- Institut für Zellbiologie, Universität Bayreuth, 95440 Bayreuth, Germany
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