1
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Neiman AM. Membrane and organelle rearrangement during ascospore formation in budding yeast. Microbiol Mol Biol Rev 2024:e0001324. [PMID: 38899894 DOI: 10.1128/mmbr.00013-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024] Open
Abstract
SUMMARYIn ascomycete fungi, sexual spores, termed ascospores, are formed after meiosis. Ascospore formation is an unusual cell division in which daughter cells are created within the cytoplasm of the mother cell by de novo generation of membranes that encapsulate each of the haploid chromosome sets created by meiosis. This review describes the molecular events underlying the creation, expansion, and closure of these membranes in the budding yeast, Saccharomyces cerevisiae. Recent advances in our understanding of the regulation of gene expression and the dynamic behavior of different membrane-bound organelles during this process are detailed. While less is known about ascospore formation in other systems, comparison to the distantly related fission yeast suggests that the molecular events will be broadly similar throughout the ascomycetes.
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Affiliation(s)
- Aaron M Neiman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
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2
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Feathers JR, Vignogna RC, Fromme JC. Structural basis for Rab6 activation by the Ric1-Rgp1 complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.06.592747. [PMID: 38766083 PMCID: PMC11100747 DOI: 10.1101/2024.05.06.592747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Rab GTPases act as molecular switches to regulate organelle homeostasis and membrane trafficking. Rab6 plays a central role in regulating cargo flux through the Golgi and is activated via nucleotide exchange by the Ric1-Rgp1 protein complex. Ric1-Rgp1 is conserved throughout eukaryotes but the structural and mechanistic basis for its function has not been established. Here we report the cryoEM structure of a Ric1-Rgp1-Rab6 complex representing a key intermediate of the nucleotide exchange reaction. This structure reveals the overall architecture of the complex and enabled us to identify interactions critical for proper recognition and activation of Rab6 on the Golgi membrane surface. Ric1-Rgp1 interacts with the nucleotide-binding domain of Rab6 using an uncharacterized helical domain, which we establish as a novel RabGEF domain by identifying residues required for Rab6 nucleotide exchange. Unexpectedly, the complex uses an arrestin fold to interact with the Rab6 hypervariable domain, indicating that interactions with the unstructured C-terminal regions of Rab GTPases may be a common specificity mechanism used by their activators. Collectively, our findings provide a detailed mechanistic understanding of regulated Rab6 activation at the Golgi.
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Affiliation(s)
- J. Ryan Feathers
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850 USA
- Current address: 201 Schultz Laboratory, Princeton University, Princeton, NJ 08544 USA
| | - Ryan C. Vignogna
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850 USA
| | - J. Christopher Fromme
- Department of Molecular Biology & Genetics and Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14850 USA
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3
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Wilmes S, Kümmel D. Insights into the role of the membranes in Rab GTPase regulation. Curr Opin Cell Biol 2023; 83:102177. [PMID: 37327649 DOI: 10.1016/j.ceb.2023.102177] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/15/2023] [Accepted: 05/19/2023] [Indexed: 06/18/2023]
Abstract
Rab GTPases are molecular switches with essential roles in mediating vesicular trafficking and establishing organelle identity. The conversion from the inactive, cytosolic to the membrane-bound, active species and back is tightly controlled by regulatory proteins. Recently, the roles of membrane properties and lipid composition of different target organelles in determining the activity state of Rabs have come to light. The investigation of several Rab guanine nucleotide exchange factors (GEFs) has revealed principles of how the recruitment via lipid interactions and the spatial confinement on the membrane surface contribute to spatiotemporal specificity in the Rab GTPase network. This paints an intricate picture of the control mechanisms in Rab activation and highlights the importance of the membrane lipid code in the organization of the endomembrane system.
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Affiliation(s)
- Stephan Wilmes
- University of Münster, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany
| | - Daniel Kümmel
- University of Münster, Institute of Biochemistry, Corrensstraße 36, 48149 Münster, Germany.
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4
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Li X, Liu D, Griffis E, Novick P. Exploring the consequences of redirecting an exocytic Rab onto endocytic vesicles. Mol Biol Cell 2023; 34:ar38. [PMID: 36857153 PMCID: PMC10162416 DOI: 10.1091/mbc.e23-01-0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Bidirectional vesicular traffic links compartments along the exocytic and endocytic pathways. Rab GTPases have been implicated in specifying the direction of vesicular transport. To explore this possibility, we sought to redirect an exocytic Rab, Sec4, onto endocytic vesicles by fusing the catalytic domain of the Sec4 GEF, Sec2, onto the CUE localization domain of Vps9, a GEF for the endocytic Rab Ypt51. The Sec2GEF-GFP-CUE construct localized to bright puncta predominantly near sites of polarized growth, and this localization was dependent on the ability of the CUE domain to bind to the ubiquitin moieties added to the cytoplasmic tails of proteins destined for endocytic internalization. Sec4 and Sec4 effectors were recruited to these puncta with various efficiencies. Cells expressing Sec2GEF-GFP-CUE grew surprisingly well and secreted protein at near-normal efficiency, implying that Golgi-derived secretory vesicles were delivered to polarized sites of cell growth despite the misdirection of Sec4 and its effectors. A low efficiency mechanism for localization of Sec2 to secretory vesicles that is independent of known cues might be responsible. In total, the results suggest that while Rabs may play a critical role in specifying the direction of vesicular transport, cells are remarkably tolerant of Rab misdirection.
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Affiliation(s)
- Xia Li
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0644
| | - Dongmei Liu
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0644
| | - Eric Griffis
- Nikon Imaging Center, University of California, San Diego, La Jolla, CA 92093-0694
| | - Peter Novick
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0644
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5
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Li X, Liu D, Griffis E, Novick P. Exploring the consequences of redirecting an exocytic Rab onto endocytic vesicles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527811. [PMID: 36798320 PMCID: PMC9934678 DOI: 10.1101/2023.02.09.527811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Bidirectional vesicular traffic links compartments along the exocytic and endocytic pathways. Rab GTPases have been implicated in specifying the direction of vesicular transport because anterograde vesicles are marked with a different Rab than retrograde vesicles. To explore this proposal, we sought to redirect an exocytic Rab, Sec4, onto endocytic vesicles by fusing the catalytic domain of the Sec4 GEF, Sec2, onto the CUE localization domain of Vps9, a GEF for the endocytic Rab, Ypt51. The Sec2GEF-GFP-CUE construct was found to localize to bright puncta predominantly near sites of polarized growth and this localization was strongly dependent upon the ability of the CUE domain to bind to the ubiquitin moieties added to the cytoplasmic tails of proteins destined for endocytic internalization. Sec4 and Sec4 effectors were recruited to these puncta with varying efficiency. The puncta appeared to consist of clusters of 80 nm vesicles and although the puncta are largely static, FRAP analysis suggests that traffic into and out of these clusters continues. Cells expressing Sec2GEF-GFP-CUE grew surprisingly well and secreted protein at near normal efficiency, implying that Golgi derived secretory vesicles were delivered to polarized sites of cell growth, where they tethered and fused with the plasma membrane despite the misdirection of Sec4 and its effectors. In total, the results suggest that while Rabs play a critical role in regulating vesicular transport, cells are remarkably tolerant of Rab misdirection.
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Affiliation(s)
- Xia Li
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California, United States
| | - Dongmei Liu
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California, United States
| | - Eric Griffis
- Nikon Imaging Center, University of California at San Diego, La Jolla, California, United States
| | - Peter Novick
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California, United States
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6
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Felline A, Raimondi F, Gentile S, Fanelli F. Structural communication between the GTPase Sec4p and its activator Sec2p: Determinants of GEF activity and early deformations to nucleotide release. Comput Struct Biotechnol J 2022; 20:5162-5180. [PMID: 36187918 PMCID: PMC9508438 DOI: 10.1016/j.csbj.2022.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/08/2022] [Accepted: 09/08/2022] [Indexed: 11/29/2022] Open
Abstract
Ras GTPases are molecular switches that cycle between OFF and ON states depending on the bound nucleotide (i.e. GDP-bound and GTP-bound, respectively). The Rab GTPase, Sec4p, plays regulatory roles in multiple steps of intracellular vesicle trafficking. Nucleotide release is catalyzed by the Guanine Nucleotide Exchange Factor (GEF) Sec2p. Here, the integration of structural information with molecular dynamics (MD) simulations addressed a number of questions concerning the intrinsic and stimulated dynamics of Sec2p and Sec4p as well as the chain of structural deformations leading to GEF-assisted activation of the Rab GTPase. Sec2p holds an intrinsic ability to adopt the conformation found in the crystallographic complexes with Sec4p, thus suggesting that the latter selects and shifts the conformational equilibrium towards a pre-existing bound-like conformation of Sec2p. The anchoring of Sec4p to a suitable conformation of Sec2p favors the Sec2p-assisted pulling on itself of the α1/switch 1 (SWI) loop and of SWI, which loose any contact with GDP. Those deformations of Sec4p would occur earlier. Formation of the final Sec2p-Sec4p hydrophobic interface, accomplishes later. Disruption of the nucleotide cage would cause firstly loss of interactions with the guanine ring and secondly loss of interactions with the phosphates. The ease in sampling the energy landscape and adopting a bound-like conformation likely favors the catalyzing ability of GEFs for Ras GTPases.
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7
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Borchers AC, Langemeyer L, Ungermann C. Who's in control? Principles of Rab GTPase activation in endolysosomal membrane trafficking and beyond. J Cell Biol 2021; 220:212549. [PMID: 34383013 PMCID: PMC8366711 DOI: 10.1083/jcb.202105120] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/08/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022] Open
Abstract
The eukaryotic endomembrane system consists of multiple interconnected organelles. Rab GTPases are organelle-specific markers that give identity to these membranes by recruiting transport and trafficking proteins. During transport processes or along organelle maturation, one Rab is replaced by another, a process termed Rab cascade, which requires at its center a Rab-specific guanine nucleotide exchange factor (GEF). The endolysosomal system serves here as a prime example for a Rab cascade. Along with endosomal maturation, the endosomal Rab5 recruits and activates the Rab7-specific GEF Mon1-Ccz1, resulting in Rab7 activation on endosomes and subsequent fusion of endosomes with lysosomes. In this review, we focus on the current idea of Mon1-Ccz1 recruitment and activation in the endolysosomal and autophagic pathway. We compare identified principles to other GTPase cascades on endomembranes, highlight the importance of regulation, and evaluate in this context the strength and relevance of recent developments in in vitro analyses to understand the underlying foundation of organelle biogenesis and maturation.
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Affiliation(s)
- Ann-Christin Borchers
- Department of Biology/Chemistry, Biochemistry Section, Osnabrück University, Osnabrück, Germany
| | - Lars Langemeyer
- Department of Biology/Chemistry, Biochemistry Section, Osnabrück University, Osnabrück, Germany
| | - Christian Ungermann
- Department of Biology/Chemistry, Biochemistry Section, Osnabrück University, Osnabrück, Germany.,Center of Cellular Nanoanalytics Osnabrück (CellNanOs), Osnabrück University, Osnabrück, Germany
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8
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Chandrakumar AA, Coyaud É, Marshall CB, Ikura M, Raught B, Rottapel R. Tankyrase regulates epithelial lumen formation via suppression of Rab11 GEFs. J Cell Biol 2021; 220:212384. [PMID: 34128958 PMCID: PMC8221736 DOI: 10.1083/jcb.202008037] [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: 08/12/2020] [Revised: 02/24/2021] [Accepted: 03/05/2021] [Indexed: 01/08/2023] Open
Abstract
Rab11 GTPase proteins are required for cytokinesis, ciliogenesis, and lumenogenesis. Rab11a is critical for apical delivery of podocalyxin (PODXL) during lumen formation in epithelial cells. SH3BP5 and SH3BP5L are guanine nucleotide exchange factors (GEFs) for Rab11. We show that SH3BP5 and SH3BP5L are required for activation of Rab11a and cyst lumen formation. Using proximity-dependent biotin identification (BioID) interaction proteomics, we have identified SH3BP5 and its paralogue SH3BP5L as new substrates of the poly-ADP-ribose polymerase Tankyrase and the E3 ligase RNF146. We provide data demonstrating that epithelial polarity via cyst lumen formation is governed by Tankyrase, which inhibits Rab11a activation through the suppression of SH3BP5 and SH3BP5L. RNF146 reduces Tankyrase protein abundance and restores Rab11a activation and lumen formation. Thus, Rab11a activation is controlled by a signaling pathway composed of the sequential inhibition of SH3BP5 paralogues by Tankyrase, which is itself suppressed by RNF146.
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Affiliation(s)
- Arun A Chandrakumar
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Étienne Coyaud
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | | | - Mitsuhiko Ikura
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Brian Raught
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Robert Rottapel
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.,Department of Immunology, University of Toronto, Toronto, Ontario, Canada.,Division of Rheumatology, St. Michael's Hospital, Toronto, Ontario, Canada
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9
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Joiner AMN, Phillips BP, Yugandhar K, Sanford EJ, Smolka MB, Yu H, Miller EA, Fromme JC. Structural basis of TRAPPIII-mediated Rab1 activation. EMBO J 2021; 40:e107607. [PMID: 34018207 PMCID: PMC8204860 DOI: 10.15252/embj.2020107607] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/07/2021] [Accepted: 04/11/2021] [Indexed: 12/17/2022] Open
Abstract
The GTPase Rab1 is a master regulator of the early secretory pathway and is critical for autophagy. Rab1 activation is controlled by its guanine nucleotide exchange factor, the multisubunit TRAPPIII complex. Here, we report the 3.7 Å cryo-EM structure of the Saccharomyces cerevisiae TRAPPIII complex bound to its substrate Rab1/Ypt1. The structure reveals the binding site for the Rab1/Ypt1 hypervariable domain, leading to a model for how the complex interacts with membranes during the activation reaction. We determined that stable membrane binding by the TRAPPIII complex is required for robust activation of Rab1/Ypt1 in vitro and in vivo, and is mediated by a conserved amphipathic α-helix within the regulatory Trs85 subunit. Our results show that the Trs85 subunit serves as a membrane anchor, via its amphipathic helix, for the entire TRAPPIII complex. These findings provide a structural understanding of Rab activation on organelle and vesicle membranes.
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Affiliation(s)
- Aaron MN Joiner
- Department of Molecular Biology and Genetics/Weill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | | | - Kumar Yugandhar
- Department of Computational Biology/Weill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Ethan J Sanford
- Department of Molecular Biology and Genetics/Weill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics/Weill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | - Haiyuan Yu
- Department of Computational Biology/Weill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
| | | | - J Christopher Fromme
- Department of Molecular Biology and Genetics/Weill Institute for Cell and Molecular BiologyCornell UniversityIthacaNYUSA
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10
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Yuan H, Novick P. Testing the Phenotypic Effects of a Rab Chimera that Resolves Exchange Factor Specificity from Effector Specificity. Methods Mol Biol 2021; 2293:57-67. [PMID: 34453710 DOI: 10.1007/978-1-0716-1346-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Rab GTPases play key roles in defining the identity of the various compartments that comprise the secretory and endocytic pathways. Recruitment of a Rab to a specific compartment requires its localized activation by a guanine nucleotide exchange factor (GEF). This in turn results in the recruitment of a distinct set of Rab effectors that directs the recognition of the appropriate target compartment by a carrier vesicle and their subsequent fusion. A chimeric Rab protein, Ypt1-SW1Sec4, was found to separate GEF specificity from effector specificity (Grosshans BL, et al. Proc Natl Acad Sci U S A 103(32):11821-11827, 2006), but early studies did not observe strong effects of this allele on growth or membrane traffic (Brennwald P, Novick P. Nature 362(6420):560-563, 1993). To resolve this apparent conundrum, yeast strains expressing the chimeric Rab were subjected to a more extensive battery of phenotypic tests. These tests demonstrated that changing the specificity of the GEF interaction does lead to a change in Rab localization and can lead to the ectopic recruitment of an effector, creating trafficking defects that are dependent upon the level of expression (Grosshans BL, et al. Proc Natl Acad Sci U S A 103(32):11821-11827, 2006). Here we describe the methods used in this analysis. Specifically we describe the following: 1. An assay used to quantify the efficiency of export of a cell wall protein Bgl2, 2. The use of thin section electron microscopy to address the morphology of the secretory machinery, 3. The use of a fluorescently tagged vesicle SNARE protein, GFP-Snc1, to follow plasma membrane recycling and. 4. The use of fluorescently tagged Ypt1 effectors, Cog3-GFP, Uso1-GFP, and Sec7-GFP to follow their recruitment by Ypt1-SW1Sec4.
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Affiliation(s)
- Hua Yuan
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Peter Novick
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA.
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11
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Ford LK, Fioriti L. Coiled-Coil Motifs of RNA-Binding Proteins: Dynamicity in RNA Regulation. Front Cell Dev Biol 2020; 8:607947. [PMID: 33330512 PMCID: PMC7710910 DOI: 10.3389/fcell.2020.607947] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 10/30/2020] [Indexed: 01/29/2023] Open
Abstract
Neuronal granules are biomolecular condensates that concentrate high quantities of RNAs and RNA-related proteins within neurons. These dense packets of information are trafficked from the soma to distal sites rich in polysomes, where local protein synthesis can occur. Movement of neuronal granules to distal sites, and local protein synthesis, play a critical role in synaptic plasticity. The formation of neuronal granules is intriguing; these granules lack a membrane and instead phase separate due to protein and RNA interactions. Low complexity motifs and RNA binding domains are highly prevalent in these proteins. Here, we introduce the role that coiled-coil motifs play in neuronal granule proteins, and investigate the structure-function relationship of coiled-coil proteins in RNA regulation. Interestingly, low complexity domains and coiled-coil motifs are highly dynamic, allowing for increased functional response to environmental influences. Finally, biomolecular condensates have been suggested to drive the formation of toxic, neurodegenerative proteins such as TDP-43 and tau. Here, we review the conversion of coiled-coil motifs to amyloid structures, and speculate a role that neuronal granules play in coiled-coil to amyloid conversions of neurodegenerative proteins.
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Affiliation(s)
- Lenzie K Ford
- Department of Neuroscience, Zuckerman Institute, Columbia University, New York, NY, United States
| | - Luana Fioriti
- Laboratory of Molecular Mechanisms of Polyglutamine Disorders, Department of Neuroscience, Dulbecco Telethon Institute, Istituto di Ricerche Farmacologiche Mario Negri (IRCCS), Milan, Italy
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12
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Kalman ZE, Mészáros B, Gáspári Z, Dobson L. Distribution of disease-causing germline mutations in coiled-coils implies an important role of their N-terminal region. Sci Rep 2020; 10:17333. [PMID: 33060664 PMCID: PMC7562717 DOI: 10.1038/s41598-020-74354-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/21/2020] [Indexed: 11/08/2022] Open
Abstract
Next-generation sequencing resulted in the identification of a huge number of naturally occurring variations in human proteins. The correct interpretation of the functional effects of these variations necessitates the understanding of how they modulate protein structure. Coiled-coils are α-helical structures responsible for a diverse range of functions, but most importantly, they facilitate the structural organization of macromolecular scaffolds via oligomerization. In this study, we analyzed a comprehensive set of disease-associated germline mutations in coiled-coil structures. Our results suggest an important role of residues near the N-terminal part of coiled-coil regions, possibly critical for superhelix assembly and folding in some cases. We also show that coiled-coils of different oligomerization states exhibit characteristically distinct patterns of disease-causing mutations. Our study provides structural and functional explanations on how disease emerges through the mutation of these structural motifs.
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Affiliation(s)
- Zsofia E Kalman
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, 1083, Budapest, Hungary
- 3in-PPCU Research Group, 2500, Esztergom, Hungary
| | - Bálint Mészáros
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Zoltán Gáspári
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, 1083, Budapest, Hungary.
| | - Laszlo Dobson
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, 1083, Budapest, Hungary.
- Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, 1117, Budapest, Hungary.
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13
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The Role of Secretory Pathways in Candida albicans Pathogenesis. J Fungi (Basel) 2020; 6:jof6010026. [PMID: 32102426 PMCID: PMC7151058 DOI: 10.3390/jof6010026] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 02/19/2020] [Accepted: 02/20/2020] [Indexed: 12/17/2022] Open
Abstract
Candida albicans is a fungus that is a commensal organism and a member of the normal human microbiota. It has the ability to transition into an opportunistic invasive pathogen. Attributes that support pathogenesis include secretion of virulence-associated proteins, hyphal formation, and biofilm formation. These processes are supported by secretion, as defined in the broad context of membrane trafficking. In this review, we examine the role of secretory pathways in Candida virulence, with a focus on the model opportunistic fungal pathogen, Candida albicans.
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14
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Structural Insights into the Regulation Mechanism of Small GTPases by GEFs. Molecules 2019; 24:molecules24183308. [PMID: 31514408 PMCID: PMC6767298 DOI: 10.3390/molecules24183308] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/09/2019] [Accepted: 09/10/2019] [Indexed: 12/12/2022] Open
Abstract
Small GTPases are key regulators of cellular events, and their dysfunction causes many types of cancer. They serve as molecular switches by cycling between inactive guanosine diphosphate (GDP)-bound and active guanosine triphosphate (GTP)-bound states. GTPases are deactivated by GTPase-activating proteins (GAPs) and are activated by guanine-nucleotide exchange factors (GEFs). The intrinsic GTP hydrolysis activity of small GTPases is generally low and is accelerated by GAPs. GEFs promote GDP dissociation from small GTPases to allow for GTP binding, which results in a conformational change of two highly flexible segments, called switch I and switch II, that enables binding of the gamma phosphate and allows small GTPases to interact with downstream effectors. For several decades, crystal structures of many GEFs and GAPs have been reported and have shown tremendous structural diversity. In this review, we focus on the latest structural studies of GEFs. Detailed pictures of the variety of GEF mechanisms at atomic resolution can provide insights into new approaches for drug discovery.
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15
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Lamber EP, Siedenburg AC, Barr FA. Rab regulation by GEFs and GAPs during membrane traffic. Curr Opin Cell Biol 2019; 59:34-39. [PMID: 30981180 DOI: 10.1016/j.ceb.2019.03.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 03/06/2019] [Indexed: 01/05/2023]
Abstract
Rab GTPases and their regulatory proteins play a crucial role in vesicle-mediated membrane trafficking. During vesicle membrane tethering Rab GTPases are activated by GEFs (guanine nucleotide exchange factors) and then inactivated by GAPs (GTPase activating proteins). Recent evidence shows that in addition to activating and inactivating Rab GTPases, both Rab GEFs and GAPs directly contribute to membrane tethering events during vesicle traffic. Other studies have extended the range of processes, in which Rabs function, and revealed roles for Rabs and their GAPs in the regulation of autophagy. Here, we will discuss these advances and the emerging relationship between the domain architectures of Rab GEFs and vesicle coat protein complexes linked with GTPases of the Sar, ARF and Arl families in animal cells.
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Affiliation(s)
- Ekaterina P Lamber
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | | | - Francis A Barr
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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16
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Goto-Ito S, Morooka N, Yamagata A, Sato Y, Sato K, Fukai S. Structural basis of guanine nucleotide exchange for Rab11 by SH3BP5. Life Sci Alliance 2019; 2:2/2/e201900297. [PMID: 30872413 PMCID: PMC6419104 DOI: 10.26508/lsa.201900297] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/07/2019] [Accepted: 03/08/2019] [Indexed: 01/30/2023] Open
Abstract
The Rab GTPase family is a major regulator of membrane traffic in eukaryotic cells. The Rab11 subfamily plays important roles in specific trafficking events such as exocytosis, endosomal recycling, and cytokinesis. SH3BP5 and SH3BP5-like (SH3BP5L) proteins have recently been found to serve as guanine nucleotide exchange factors (GEF) for Rab11. Here, we report the crystal structures of the SH3BP5 GEF domain alone and its complex with Rab11a. SH3BP5 exhibits a V-shaped structure comprising two coiled coils. The coiled coil composed of α1, and α4 is solely responsible for the Rab11a binding and GEF activity. SH3BP5 pulls out and deforms switch I of Rab11a so as to facilitate the GDP release from Rab11a. SH3BP5 interacts with the N-terminal region, switch I, interswitch, and switch II of Rab11a. SH3BP5 and SH3BP5L localize to Rab11-positive recycling endosomes and show GEF activity for all of the Rab11 family but not for Rab14. Fluorescence-based GEF assays combined with site-directed mutagenesis reveal the essential interactions between SH3BP5 and Rab11 family proteins for the GEF reaction on recycling endosomes.
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Affiliation(s)
- Sakurako Goto-Ito
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, Japan
| | - Nobukatsu Morooka
- Laboratory of Molecular Traffic, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Atsushi Yamagata
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Yusuke Sato
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Ken Sato
- Laboratory of Molecular Traffic, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Shuya Fukai
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan .,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
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17
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Thomas LL, van der Vegt SA, Fromme JC. A Steric Gating Mechanism Dictates the Substrate Specificity of a Rab-GEF. Dev Cell 2018; 48:100-114.e9. [PMID: 30528786 DOI: 10.1016/j.devcel.2018.11.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/23/2018] [Accepted: 11/07/2018] [Indexed: 10/27/2022]
Abstract
Correct localization of Rab GTPases in cells is critical for proper function in membrane trafficking, yet the mechanisms that target Rabs to specific subcellular compartments remain controversial. Guanine nucleotide exchange factors (GEFs) activate and consequently stabilize Rab substrates on membranes, thus implicating GEFs as the primary determinants of Rab localization. A competing hypothesis is that the Rab C-terminal hypervariable domain (HVD) serves as a subcellular targeting signal. In this study, we present a unifying mechanism in which the HVD controls targeting of certain Rabs by mediating interaction with their GEFs. We demonstrate that the TRAPP complexes, two related GEFs that use the same catalytic site to activate distinct Rabs, distinguish between Ypt1 (Rab1) and Ypt31/32 (Rab11) via their divergent HVDs. Remarkably, we find that HVD length gates Rab access to the TRAPPII complex by constraining the distance between the nucleotide-binding domain and the membrane surface.
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Affiliation(s)
- Laura L Thomas
- Department of Molecular Biology and Genetics/Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Solveig A van der Vegt
- Department of Molecular Biology and Genetics/Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - J Christopher Fromme
- Department of Molecular Biology and Genetics/Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA.
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18
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Structural determinants of Rab11 activation by the guanine nucleotide exchange factor SH3BP5. Nat Commun 2018; 9:3772. [PMID: 30217979 PMCID: PMC6138693 DOI: 10.1038/s41467-018-06196-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/14/2018] [Indexed: 12/18/2022] Open
Abstract
The GTPase Rab11 plays key roles in receptor recycling, oogenesis, autophagosome formation, and ciliogenesis. However, investigating Rab11 regulation has been hindered by limited molecular detail describing activation by cognate guanine nucleotide exchange factors (GEFs). Here, we present the structure of Rab11 bound to the GEF SH3BP5, along with detailed characterization of Rab-GEF specificity. The structure of SH3BP5 shows a coiled-coil architecture that mediates exchange through a unique Rab-GEF interaction. Furthermore, it reveals a rearrangement of the switch I region of Rab11 compared with solved Rab-GEF structures, with a constrained conformation when bound to SH3BP5. Mutation of switch I provides insights into the molecular determinants that allow for Rab11 selectivity over evolutionarily similar Rab GTPases present on Rab11-positive organelles. Moreover, we show that GEF-deficient mutants of SH3BP5 show greatly decreased Rab11 activation in cellular assays of active Rab11. Overall, our results give molecular insight into Rab11 regulation, and how Rab-GEF specificity is achieved.
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19
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Zheng H, Li L, Miao P, Wu C, Chen X, Yuan M, Fang T, Norvienyeku J, Li G, Zheng W, Wang Z, Zhou J. FgSec2A, a guanine nucleotide exchange factor of FgRab8, is important for polarized growth, pathogenicity and deoxynivalenol production in Fusarium graminearum. Environ Microbiol 2018; 20:3378-3392. [PMID: 30105886 DOI: 10.1111/1462-2920.14373] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 08/03/2018] [Accepted: 08/04/2018] [Indexed: 12/20/2022]
Abstract
Sec4/Rab8 is one of the well-studied members of the Rab GTPase family, previous studies have shown that Sec4/Rab8 crucially promotes the pathogenesis of phytopathogens, but the upstream regulators of Rab8 are still unknown. Here, we have identified two Sec2 homologues FgSec2A and FgSec2B in devastating fungal pathogen Fusarium graminearum and investigated their functions and interactions with FgRab8 by live-cell imaging, genetic and functional analyses. Yeast two-hybrid assay shows that FgSec2A specifically interacts with FgRab8DN(N123I) and itself. Importantly, FgSec2A is required for growth, conidiation, DON production and virulence of F. graminearum. Live-cell imaging shows that FgSec2A and FgSec2B are both localized to the tip region of hyphae and conidia. Both N-terminal region and Sec2 domain of FgSec2A are essential for its function, but not for localization, whereas the C-terminal region is important for its polarized localization. Furthermore, constitutively active FgRab8CA(Q69L) partially rescues the defects of ΔFgsec2A. Consistently, FgSec2A is required for the polarized localization of FgRab8. Finally, FgSec2A and FgSec2B show partial functions, but FgSec2A does not interact and co-localize with FgSec2B. Taken together, these results indicate that FgSec2A acts as a FgRab8 guanine nucleotide exchange factor and is necessary for polarized growth, DON production and pathogenicity in F. graminearum.
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Affiliation(s)
- Huawei Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lingping Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Pengfei Miao
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Congxian Wu
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaomin Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Mingyue Yuan
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Tian Fang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Justice Norvienyeku
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Guangpu Li
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Wenhui Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,College of Ocean Science, Minjiang University, Fuzhou, 350108, China
| | - Jie Zhou
- Fujian Province Key Laboratory of Pathogenic Fungi and Mycotoxins, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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20
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Pylypenko O, Hammich H, Yu IM, Houdusse A. Rab GTPases and their interacting protein partners: Structural insights into Rab functional diversity. Small GTPases 2018. [PMID: 28632484 DOI: 10.1080/215412481336191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023] Open
Abstract
Rab molecular switches are key players in defining membrane identity and regulating intracellular trafficking events in eukaryotic cells. In spite of their global structural similarity, Rab-family members acquired particular features that allow them to perform specific cellular functions. The overall fold and local sequence conservations enable them to utilize a common machinery for prenylation and recycling; while individual Rab structural differences determine interactions with specific partners such as GEFs, GAPs and effector proteins. These interactions orchestrate the spatiotemporal regulation of Rab localization and their turning ON and OFF, leading to tightly controlled Rab-specific functionalities such as membrane composition modifications, recruitment of molecular motors for intracellular trafficking, or recruitment of scaffold proteins that mediate interactions with downstream partners, as well as actin cytoskeleton regulation. In this review we summarize structural information on Rab GTPases and their complexes with protein partners in the context of partner binding specificity and functional outcomes of their interactions in the cell.
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Affiliation(s)
- Olena Pylypenko
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France
| | - Hussein Hammich
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France
- b Sorbonne Universités , UPMC Univ Paris 06, Sorbonne Universités, IFD , Paris , France
| | - I-Mei Yu
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France
| | - Anne Houdusse
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France
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21
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Abstract
Fission yeast Ypt2, an orthologue of the mammalian small GTPase Rab8, is responsible for post-Golgi membrane trafficking. During meiosis, Ypt2 localizes at the spindle pole body (SPB), where it regulates de novo biogenesis of the spore plasma membrane. Recruitment of Ypt2 to the SPB is dependent on its meiosis-specific GDP/GTP exchange factor (GEF), the SPB-resident protein Spo13. Here we have examined the SPB recruitment of Ypt2 by Spo13. The GEF activity of Spo13 was required, but not essential for recruitment. Furthermore, Ypt2 recruitment was regulated in a meiosis-specific manner and partially regulated by the nuclear Dbf2-related (NDR) kinase Sid2, indicating the existence of a novel regulatory mechanism for localization of Rab GTPases during meiosis.
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Affiliation(s)
- Kazuki Imada
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka, Japan.,Department of Chemistry and Biochemistry, National Institute of Technology, Suzuka College, Suzuka, Mie, Japan
| | - Taro Nakamura
- Department of Biology, Graduate School of Science, Osaka City University, Sumiyoshi-ku, Osaka, Japan
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22
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Mayers JR, Hu T, Wang C, Cárdenas JJ, Tan Y, Pan J, Bednarek SY. SCD1 and SCD2 Form a Complex That Functions with the Exocyst and RabE1 in Exocytosis and Cytokinesis. THE PLANT CELL 2017; 29:2610-2625. [PMID: 28970336 PMCID: PMC5774579 DOI: 10.1105/tpc.17.00409] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 09/12/2017] [Accepted: 09/26/2017] [Indexed: 05/21/2023]
Abstract
Although exocytosis is critical for the proper trafficking of materials to the plasma membrane, relatively little is known about the mechanistic details of post-Golgi trafficking in plants. Here, we demonstrate that the DENN (Differentially Expressed in Normal and Neoplastic cells) domain protein STOMATAL CYTOKINESIS DEFECTIVE1 (SCD1) and SCD2 form a previously unknown protein complex, the SCD complex, that functionally interacts with subunits of the exocyst complex and the RabE1 family of GTPases in Arabidopsis thaliana Consistent with a role in post-Golgi trafficking, scd1 and scd2 mutants display defects in exocytosis and recycling of PIN2-GFP. Perturbation of exocytosis using the small molecule Endosidin2 results in growth inhibition and PIN2-GFP trafficking defects in scd1 and scd2 mutants. In addition to the exocyst, the SCD complex binds in a nucleotide state-specific manner with Sec4p/Rab8-related RabE1 GTPases and overexpression of wild-type RabE1 rescues scd1 temperature-sensitive mutants. Furthermore, SCD1 colocalizes with the exocyst subunit, SEC15B, and RabE1 at the cell plate and in distinct punctae at or near the plasma membrane. Our findings reveal a mechanism for plant exocytosis, through the identification and characterization of a protein interaction network that includes the SCD complex, RabE1, and the exocyst.
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Affiliation(s)
| | - Tianwei Hu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Chao Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jessica J Cárdenas
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Yuqi Tan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Jianwei Pan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Sebastian Y Bednarek
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
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23
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Rewiring a Rab regulatory network reveals a possible inhibitory role for the vesicle tether, Uso1. Proc Natl Acad Sci U S A 2017; 114:E8637-E8645. [PMID: 28973856 DOI: 10.1073/pnas.1708394114] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ypt1 and Sec4 are essential Rab GTPases that control the early and late stages of the yeast secretory pathway, respectively. A chimera consisting of Ypt1 with the switch I domain of Sec4, Ypt1-SW1Sec4, is efficiently activated in vitro by the Sec4 exchange factor, Sec2. This should lead to its ectopic activation in vivo and thereby disrupt membrane traffic. Nonetheless early studies found that yeast expressing Ypt1-SW1Sec4 as the sole copy of YPT1 exhibit no growth defect. To resolve this conundrum, we have analyzed yeast expressing various levels of Ypt1-SW1Sec4 We show that even normal expression of Ypt1-SW1Sec4 leads to kinetic transport defects at a late stage of the pathway, with secretory vesicles accumulating near exocytic sites. Higher levels are toxic. Toxicity is suppressed by truncation of Uso1, a vesicle tether required for endoplasmic reticulum-Golgi traffic. The globular head of Uso1 binds to Ypt1 and its coiled-coil tail binds to the Golgi-associated SNARE, Sed5. We propose that when Uso1 is inappropriately recruited to secretory vesicles by Ypt1-SW1Sec4, the extended coiled-coil tail blocks docking to the plasma membrane. This putative inhibitory function could serve to increase the fidelity of vesicle docking.
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24
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RABIF/MSS4 is a Rab-stabilizing holdase chaperone required for GLUT4 exocytosis. Proc Natl Acad Sci U S A 2017; 114:E8224-E8233. [PMID: 28894007 DOI: 10.1073/pnas.1712176114] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Rab GTPases are switched from their GDP-bound inactive conformation to a GTP-bound active state by guanine nucleotide exchange factors (GEFs). The first putative GEFs isolated for Rabs are RABIF (Rab-interacting factor)/MSS4 (mammalian suppressor of Sec4) and its yeast homolog DSS4 (dominant suppressor of Sec4). However, the biological function and molecular mechanism of these molecules remained unclear. In a genome-wide CRISPR genetic screen, we isolated RABIF as a positive regulator of exocytosis. Knockout of RABIF severely impaired insulin-stimulated GLUT4 exocytosis in adipocytes. Unexpectedly, we discovered that RABIF does not function as a GEF, as previously assumed. Instead, RABIF promotes the stability of Rab10, a key Rab in GLUT4 exocytosis. In the absence of RABIF, Rab10 can be efficiently synthesized but is rapidly degraded by the proteasome, leading to exocytosis defects. Strikingly, restoration of Rab10 expression rescues exocytosis defects, bypassing the requirement for RABIF. These findings reveal a crucial role of RABIF in vesicle transport and establish RABIF as a Rab-stabilizing holdase chaperone, a previously unrecognized mode of Rab regulation independent of its GDP-releasing activity. Besides Rab10, RABIF also regulates the stability of two other Rab GTPases, Rab8 and Rab13, suggesting that the requirement of holdase chaperones is likely a general feature of Rab GTPases.
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25
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Pylypenko O, Hammich H, Yu IM, Houdusse A. Rab GTPases and their interacting protein partners: Structural insights into Rab functional diversity. Small GTPases 2017. [PMID: 28632484 PMCID: PMC5902227 DOI: 10.1080/21541248.2017.1336191] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Rab molecular switches are key players in defining membrane identity and regulating intracellular trafficking events in eukaryotic cells. In spite of their global structural similarity, Rab-family members acquired particular features that allow them to perform specific cellular functions. The overall fold and local sequence conservations enable them to utilize a common machinery for prenylation and recycling; while individual Rab structural differences determine interactions with specific partners such as GEFs, GAPs and effector proteins. These interactions orchestrate the spatiotemporal regulation of Rab localization and their turning ON and OFF, leading to tightly controlled Rab-specific functionalities such as membrane composition modifications, recruitment of molecular motors for intracellular trafficking, or recruitment of scaffold proteins that mediate interactions with downstream partners, as well as actin cytoskeleton regulation. In this review we summarize structural information on Rab GTPases and their complexes with protein partners in the context of partner binding specificity and functional outcomes of their interactions in the cell.
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Affiliation(s)
- Olena Pylypenko
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France
| | - Hussein Hammich
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France.,b Sorbonne Universités , UPMC Univ Paris 06, Sorbonne Universités, IFD , Paris , France
| | - I-Mei Yu
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France
| | - Anne Houdusse
- a Structural Motility, Institut Curie , PSL Research University, CNRS, UMR 144 , Paris , France
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26
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Abstract
Rab proteins are the major regulators of vesicular trafficking in eukaryotic cells. Their activity can be tightly controlled within cells: Regulated by guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs), they switch between an active GTP-bound state and an inactive GDP-bound state, interacting with downstream effector proteins only in the active state. Additionally, they can bind to membranes via C-terminal prenylated cysteine residues and they can be solubilized and shuttled between membranes by chaperone-like molecules called GDP dissociation inhibitors (GDIs). In this review we give an overview of Rab proteins with a focus on the current understanding of their regulation by GEFs, GAPs and GDI.
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Affiliation(s)
- Matthias P Müller
- a Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Dortmund , Germany
| | - Roger S Goody
- a Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Dortmund , Germany
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27
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Architecture and mechanism of the late endosomal Rab7-like Ypt7 guanine nucleotide exchange factor complex Mon1-Ccz1. Nat Commun 2017; 8:14034. [PMID: 28051187 PMCID: PMC5216073 DOI: 10.1038/ncomms14034] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 11/23/2016] [Indexed: 01/21/2023] Open
Abstract
The Mon1–Ccz1 complex (MC1) is the guanine nucleotide exchange factor (GEF) for the Rab GTPase Ypt7/Rab7 and is required for endosomal maturation and fusion at the vacuole/lysosome. Here we present the overall architecture of MC1 from Chaetomium thermophilum, and in combining biochemical studies and mutational analysis in yeast, we identify the domains required for catalytic activity, complex assembly and localization of MC1. The crystal structure of a catalytic MC1 core complex bound to Ypt7 provides mechanistic insight into its function. We pinpoint the determinants that allow for a discrimination of the Rab7-like Ypt7 over the Rab5-like Vps21, which are both located on the same membrane. MC1 shares structural similarities with the TRAPP complex, but employs a novel mechanism to promote nucleotide exchange that utilizes a conserved lysine residue of Ypt7, which is inserted upon MC1 binding into the nucleotide-binding pocket of Ypt7 and contributes to specificity. The Mon1-Ccz1 (MC1) complex is a Rab guanine nucleotide exchange factor (RabGEF) for Ypt7/Rab7 important for endosomal maturation. Here the authors present the biochemical and structural characterization of MC1, elucidating its catalytic mechanism and showing that MC1 represents novel class of RabGEFs.
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28
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Abstract
Coiled‐coils are found in proteins throughout all three kingdoms of life. Coiled‐coil domains of some proteins are almost invariant in sequence and length, betraying a structural and functional role for amino acids along the entire length of the coiled‐coil. Other coiled‐coils are divergent in sequence, but conserved in length, thereby functioning as molecular spacers. In this capacity, coiled‐coil proteins influence the architecture of organelles such as centrioles and the Golgi, as well as permit the tethering of transport vesicles. Specialized coiled‐coils, such as those found in motor proteins, are capable of propagating conformational changes along their length that regulate cargo binding and motor processivity. Coiled‐coil domains have also been identified in enzymes, where they function as molecular rulers, positioning catalytic activities at fixed distances. Finally, while coiled‐coils have been extensively discussed for their potential to nucleate and scaffold large macromolecular complexes, structural evidence to substantiate this claim is relatively scarce.
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Affiliation(s)
- Linda Truebestein
- Department of Structural and Computational Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), Vienna, Austria
| | - Thomas A Leonard
- Department of Structural and Computational Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), Vienna, Austria.,Department of Medical Biochemistry, Medical University of Vienna, Vienna, Austria
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29
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Abstract
ASBTRACT Rab GTPases serve as master regulators of membrane traffic, each typically controlling several different aspects of a specific stage of membrane traffic by recruiting diverse effector proteins such as cytoskeletal motors, vesicle tethering proteins and regulators of SNARE complex assembly. Rabs, in turn, are regulated by specific guanine nucleotide exchange factors (GEFs), which catalyze the displacement of GDP and binding of GTP, as well as GTPase activating proteins (GAPs) that stimulate the slow intrinsic rate of GTP hydrolysis. Here I review our studies on the final stages of the yeast secretory pathway that have led us to propose that adjacent Rabs on a pathway are networked to one another through their regulators; specifically we have shown that the Rab, Ypt32, in its GTP-bound form recruits both Sec2, the GEF that activates the downstream Rab, Sec4, as well as Gyp1, the GAP that inactivates the upstream Rab, Ypt1. The postulated effect of these counter-current cascades is a programmed series of abrupt Rab transitions that lead to critical changes in the functional identity of the membrane as it flows along the exocytic pathway. Phosphoinositides also play key roles in the temporal and spatial regulation of membrane traffic. The Golgi pool of phosphatidylinositol 4-phosphate (PI(4)P) works in concert with Ypt32 to initially recruit Sec2, yet a subsequent drop in PI(4)P levels directs a regulatory switch in Sec2 function in which it binds to the Sec4 effector Sec15 generating a positive feedback loop. PI(4)P distribution together with Sec2 phosphorylation by a casein kinase determines when and where each regulatory circuit is used.
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Affiliation(s)
- Peter Novick
- a Department of Cellular and Molecular Medicine , University of California San Diego , La Jolla , CA , USA
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30
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Ishida M, E Oguchi M, Fukuda M. Multiple Types of Guanine Nucleotide Exchange Factors (GEFs) for Rab Small GTPases. Cell Struct Funct 2016; 41:61-79. [PMID: 27246931 DOI: 10.1247/csf.16008] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Rab small GTPases are highly conserved master regulators of membrane traffic in all eukaryotes. The same as the activation and inactivation of other small GTPases, the activation and inactivation of Rabs are tightly controlled by specific GEFs (guanine nucleotide exchange factors) and GAPs (GTPase-activating proteins), respectively. Although almost all Rab-GAPs reported thus far have a TBC (Tre-2/Bub2/Cdc16)/Rab-GAP domain in common, recent accumulating evidence has indicated the existence of a number of structurally unrelated types of Rab-GEFs, including DENN proteins, VPS9 proteins, Sec2 proteins, TRAPP complexes, heterodimer GEFs (Mon1-Ccz1, HPS1-HPS4 (BLOC-3 complex), Ric1-Rgp1 and Rab3GAP1/2), and other GEFs (e.g., REI-1 and RPGR). In this review article we provide an up-to-date overview of the structures and functions of all putative Rab-GEFs in mammals, with a special focus on their substrate Rabs, interacting proteins, associations with genetic diseases, and intracellular localizations.
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Affiliation(s)
- Morié Ishida
- Laboratory of Membrane Trafficking Mechanisms, Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University
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31
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Koch D, Rai A, Ali I, Bleimling N, Friese T, Brockmeyer A, Janning P, Goud B, Itzen A, Müller MP, Goody RS. A pull-down procedure for the identification of unknown GEFs for small GTPases. Small GTPases 2016; 7:93-106. [PMID: 26918858 PMCID: PMC4905258 DOI: 10.1080/21541248.2016.1156803] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Members of the family of small GTPases regulate a variety of important cellular functions. In order to accomplish this, tight temporal and spatial regulation is absolutely necessary. The two most important factors for this regulation are GTPase activating proteins (GAPs) and guanine nucleotide exchange factors (GEFs), the latter being responsible for the activation of the GTPase downstream pathways at the correct location and time. Although a large number of exchange factors have been identified, it is likely that a similarly large number remains unidentified. We have therefore developed a procedure to specifically enrich GEF proteins from biological samples making use of the high affinity binding of GEFs to nucleotide-free GTPases. In order to verify the results of these pull-down experiments, we have additionally developed two simple validation procedures: An in vitro transcription/translation system coupled with a GEF activity assay and a yeast two-hybrid screen for detection of GEFs. Although the procedures were established and tested using the Rab protein Sec4, the similar basic principle of action of all nucleotide exchange factors will allow the method to be used for identification of unknown GEFs of small GTPases in general.
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Affiliation(s)
- Daniel Koch
- a Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Dortmund , Germany
| | - Amrita Rai
- a Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Dortmund , Germany
| | - Imtiaz Ali
- a Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Dortmund , Germany
| | - Nathalie Bleimling
- a Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Dortmund , Germany
| | - Timon Friese
- a Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Dortmund , Germany
| | - Andreas Brockmeyer
- b Department of Chemical Biology , Max Planck Institute of Molecular Physiology , Dortmund , Germany
| | - Petra Janning
- b Department of Chemical Biology , Max Planck Institute of Molecular Physiology , Dortmund , Germany
| | - Bruno Goud
- c Institut Curie, PSL Research University, CNRS UMR 144 , Paris , France
| | - Aymelt Itzen
- d Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technische Universität München , Garching , Germany
| | - Matthias P Müller
- a Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Dortmund , Germany
| | - Roger S Goody
- a Department of Structural Biochemistry , Max Planck Institute of Molecular Physiology , Dortmund , Germany
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Sakaguchi A, Sato M, Sato K, Gengyo-Ando K, Yorimitsu T, Nakai J, Hara T, Sato K, Sato K. REI-1 Is a Guanine Nucleotide Exchange Factor Regulating RAB-11 Localization and Function in C. elegans Embryos. Dev Cell 2016; 35:211-21. [PMID: 26506309 DOI: 10.1016/j.devcel.2015.09.013] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 08/18/2015] [Accepted: 09/18/2015] [Indexed: 11/29/2022]
Abstract
The small GTPase Rab11 dynamically changes its location to regulate various cellular processes such as endocytic recycling, secretion, and cytokinesis. However, our knowledge of its upstream regulators is still limited. Here, we identify the RAB-11-interacting protein-1 (REI-1) as a unique family of guanine nucleotide exchange factors (GEFs) for RAB-11 in Caenorhabditis elegans. Although REI-1 and its human homolog SH3-binding protein 5 do not contain any known Rab-GEF domains, they exhibited strong GEF activity toward Rab11 in vitro. In C. elegans, REI-1 is expressed in the germline and co-localizes with RAB-11 on the late-Golgi membranes. The loss of REI-1 specifically impaired the targeting of RAB-11 to the late-Golgi compartment and the recycling endosomes in embryos and further reduced the RAB-11 distribution to the cleavage furrow, which resulted in cytokinesis delay. These results suggest that REI-1 is a GEF specifically regulating the RAB-11 localization and functions in early embryos.
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Affiliation(s)
- Aisa Sakaguchi
- Laboratory of Molecular Traffic, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma 371-8512, Japan
| | - Miyuki Sato
- Laboratory of Molecular Membrane Biology, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma 371-8512, Japan
| | - Katsuya Sato
- Laboratory of Molecular Membrane Biology, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma 371-8512, Japan
| | - Keiko Gengyo-Ando
- Brain Science Institute, Saitama University, Saitama, Saitama 338-8570, Japan
| | - Tomohiro Yorimitsu
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Junichi Nakai
- Brain Science Institute, Saitama University, Saitama, Saitama 338-8570, Japan
| | - Taichi Hara
- Laboratory of Molecular Traffic, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma 371-8512, Japan
| | - Ken Sato
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Ken Sato
- Laboratory of Molecular Traffic, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma 371-8512, Japan.
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Rinaldi FC, Packer M, Collins R. New insights into the molecular mechanism of the Rab GTPase Sec4p activation. BMC STRUCTURAL BIOLOGY 2015; 15:14. [PMID: 26263895 PMCID: PMC4531439 DOI: 10.1186/s12900-015-0041-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 07/08/2015] [Indexed: 11/14/2022]
Abstract
Background Sec4p is a small monomeric Ras-related GTP-binding protein (23 kDa) that regulates polarized exocytosis in S. cerevisiae. In this study we examine the structural effects of a conserved serine residue in the P-loop corresponding to G12 in Ras. Results We show that the Sec4p residue serine 29 forms a hydrogen bond with the nucleotide. Mutations of this residue have a different impact than equivalent mutations in Ras and can form stable associations with the exchange factor allowing us to elucidate the structure of a complex of Sec4p bound to the exchange factor Sec2p representing an early stage of the exchange reaction. Conclusions Our structural investigation of the Sec4p-Sec2p complex reveals the role of the Sec2p coiled-coil domain in facilitating the fast kinetics of the exchange reaction. For Ras-family GTPases, single point mutations that impact the signaling state of the molecule have been well described however less structural information is available for equivalent mutations in the case of Rab proteins. Understanding the structural properties of mutants such as the one described here, provides useful insights into unique aspects of Rab GTPase function.
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Affiliation(s)
- Fabio C Rinaldi
- Department of Molecular Medicine, Cornell University, Ithaca, NY, 14853, USA.
| | - Michael Packer
- Honors Program in Undergraduate Studies, Cornell University, Ithaca, NY, 14853, USA.
| | - Ruth Collins
- Department of Molecular Medicine, Cornell University, Ithaca, NY, 14853, USA.
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Ma Y, Dai X, Xu Y, Luo W, Zheng X, Zeng D, Pan Y, Lin X, Liu H, Zhang D, Xiao J, Guo X, Xu S, Niu Y, Jin J, Zhang H, Xu X, Li L, Wang W, Qian Q, Ge S, Chong K. COLD1 Confers Chilling Tolerance in Rice. Cell 2015; 160:1209-21. [DOI: 10.1016/j.cell.2015.01.046] [Citation(s) in RCA: 377] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 12/31/2014] [Accepted: 01/14/2015] [Indexed: 01/19/2023]
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35
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Cabrera M, Nordmann M, Perz A, Schmedt D, Gerondopoulos A, Barr F, Piehler J, Engelbrecht-Vandré S, Ungermann C. The Mon1-Ccz1 GEF activates the Rab7 GTPase Ypt7 via a longin-fold-Rab interface and association with PI3P-positive membranes. J Cell Sci 2014; 127:1043-51. [PMID: 24413168 DOI: 10.1242/jcs.140921] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
To function in fusion and signaling, Rab GTPases need to be converted into their active GTP form. We previously identified the conserved Mon1-Ccz1 complex as the guanine nucleotide exchange factor (GEF) of the yeast Rab7 GTPase Ypt7. To address the possible GEF mechanism, we generated a homology model of the predicted longin domains of Mon1 and Ccz1 using the Rab-binding surface of the TRAPP complex as a template. On the basis of this, we identified mutations in both yeast Mon1 and Ccz1 that block Ypt7 activation, without affecting heterodimer formation and intracellular localization of Mon1 and Ccz1 at endosomes. Strikingly, the activity of the isolated Mon1-Ccz1 complex for Ypt7 is highly stimulated on membranes, and is promoted by the same anionic phospholipids such as phosphatidylinositol-3-phosphate (PI3P), which also support membrane association of the GEF complex. Our data imply that the GEF activity of the Mon1-Ccz1 complex towards Rab7/Ypt7 requires the interface formed by their longin domains and profits strongly from its association with the organelle surface.
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Affiliation(s)
- Margarita Cabrera
- University of Osnabrück, Department of Biology/Chemistry, Biochemistry section, Barbarastrasse 13, 49076 Osnabrück, Germany
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Phosphorylation of the Rab exchange factor Sec2p directs a switch in regulatory binding partners. Proc Natl Acad Sci U S A 2013; 110:19995-20002. [PMID: 24248333 DOI: 10.1073/pnas.1320029110] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Sec2p is a guanine nucleotide exchange factor that promotes exocytosis by activating the Rab GTPase Sec4p. Sec2p is highly phosphorylated, and we have explored the role of phosphorylation in the regulation of its function. We have identified three phosphosites and demonstrate that phosphorylation regulates the interaction of Sec2p with its binding partners Ypt32p, Sec15p, and phosphatidyl-inositol-4-phosphate. In its nonphosphorylated form, Sec2p binds preferentially to the upstream Rab, Ypt32p-GTP, thus forming a Rab guanine nucleotide exchange factor cascade that leads to the activation of the downstream Rab, Sec4p. The nonphosphorylated form of Sec2p also binds to the Golgi-associated phosphatidyl-inositol-4-phosphate, which works in concert with Ypt32p-GTP to recruit Sec2p to Golgi-derived secretory vesicles. In contrast, the phosphorylated form of Sec2p binds preferentially to Sec15p, a downstream effector of Sec4p and a component of the exocyst tethering complex, thus forming a positive-feedback loop that prepares the secretory vesicle for fusion with the plasma membrane. Our results suggest that the phosphorylation state of Sec2p can direct a switch in its regulatory binding partners that facilitates maturation of the secretory vesicle and helps to promote the directionality of vesicular transport.
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37
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Wang J, Deretic D. Molecular complexes that direct rhodopsin transport to primary cilia. Prog Retin Eye Res 2013; 38:1-19. [PMID: 24135424 DOI: 10.1016/j.preteyeres.2013.08.004] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 08/13/2013] [Accepted: 08/19/2013] [Indexed: 11/27/2022]
Abstract
Rhodopsin is a key molecular constituent of photoreceptor cells, yet understanding of how it regulates photoreceptor membrane trafficking and biogenesis of light-sensing organelles, the rod outer segments (ROS) is only beginning to emerge. Recently identified sequence of well-orchestrated molecular interactions of rhodopsin with the functional networks of Arf and Rab GTPases at multiple stages of intracellular targeting fits well into the complex framework of the biogenesis and maintenance of primary cilia, of which the ROS is one example. This review will discuss the latest progress in dissecting the molecular complexes that coordinate rhodopsin incorporation into ciliary-targeted carriers with the recruitment and activation of membrane tethering complexes and regulators of fusion with the periciliary plasma membrane. In addition to revealing the fundamental principals of ciliary membrane renewal, recent advances also provide molecular insight into the ways by which disruptions of the exquisitely orchestrated interactions lead to cilia dysfunction and result in human retinal dystrophies and syndromic diseases that affect multiple organs, including the eyes.
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Affiliation(s)
- Jing Wang
- Department of Surgery, Division of Ophthalmology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Dusanka Deretic
- Department of Surgery, Division of Ophthalmology, University of New Mexico, Albuquerque, NM 87131, USA; Department of Cell Biology and Physiology, University of New Mexico, Albuquerque, NM 87131, USA.
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38
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Guo Z, Hou X, Goody RS, Itzen A. Intermediates in the guanine nucleotide exchange reaction of Rab8 protein catalyzed by guanine nucleotide exchange factors Rabin8 and GRAB. J Biol Chem 2013; 288:32466-32474. [PMID: 24072714 DOI: 10.1074/jbc.m113.498329] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Small G-proteins of the Ras superfamily control the temporal and spatial coordination of intracellular signaling networks by acting as molecular on/off switches. Guanine nucleotide exchange factors (GEFs) regulate the activation of these G-proteins through catalytic replacement of GDP by GTP. During nucleotide exchange, three distinct substrate·enzyme complexes occur: a ternary complex with GDP at the start of the reaction (G-protein·GEF·GDP), an intermediary nucleotide-free binary complex (G-protein·GEF), and a ternary GTP complex after productive G-protein activation (G-protein·GEF·GTP). Here, we show structural snapshots of the full nucleotide exchange reaction sequence together with the G-protein substrates and products using Rabin8/GRAB (GEF) and Rab8 (G-protein) as a model system. Together with a thorough enzymatic characterization, our data provide a detailed view into the mechanism of Rabin8/GRAB-mediated nucleotide exchange.
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Affiliation(s)
- Zhong Guo
- From the Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Xiaomin Hou
- From the Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany,; the College of Life Science, Qingdao Agricultural University, Qingdao 266109, China
| | - Roger S Goody
- From the Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany,.
| | - Aymelt Itzen
- From the Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany,; the Center for Integrated Protein Science Munich, Chemistry Department, Technische Universität München, 85747 Garching, Germany.
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Bicaudal-D uses a parallel, homodimeric coiled coil with heterotypic registry to coordinate recruitment of cargos to dynein. Genes Dev 2013; 27:1233-46. [PMID: 23723415 DOI: 10.1101/gad.212381.112] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cytoplasmic dynein is the major minus end-directed microtubule motor in eukaryotes. However, there is little structural insight into how different cargos are recognized and linked to the motor complex. Here we describe the 2.2 Å resolution crystal structure of a cargo-binding region of the dynein adaptor Bicaudal-D (BicD), which reveals a parallel coiled-coil homodimer. We identify a shared binding site for two cargo-associated proteins-Rab6 and the RNA-binding protein Egalitarian (Egl)-within a region of the BicD structure with classical, homotypic core packing. Structure-based mutagenesis in Drosophila provides evidence that occupancy of this site drives association of BicD with dynein, thereby coupling motor recruitment to cargo availability. The structure also contains a region in which, remarkably, the same residues in the polypeptide sequence have different heptad registry in each chain. In vitro and in vivo analysis of a classical Drosophila dominant mutation reveals that this heterotypic region regulates the recruitment of dynein to BicD. Our results support a model in which the heterotypic segment is part of a molecular switch that promotes release of BicD autoinhibition following cargo binding to the neighboring, homotypic coiled-coil region. Overall, our data reveal a pivotal role of a highly asymmetric coiled-coil domain in coordinating the assembly of cargo-motor complexes.
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40
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Blümer J, Rey J, Dehmelt L, Mazel T, Wu YW, Bastiaens P, Goody RS, Itzen A. RabGEFs are a major determinant for specific Rab membrane targeting. ACTA ACUST UNITED AC 2013; 200:287-300. [PMID: 23382462 PMCID: PMC3563681 DOI: 10.1083/jcb.201209113] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Analysis of three different Rab-RabGEF pairs reveals that RabGEFs contain the minimal targeting machinery for recruiting Rabs to specific membranes. Eukaryotic cells critically depend on the correct regulation of intracellular vesicular trafficking to transport biological material. The Rab subfamily of small guanosine triphosphatases controls these processes by acting as a molecular on/off switch. To fulfill their function, active Rab proteins need to localize to intracellular membranes via posttranslationally attached geranylgeranyl lipids. Each member of the manifold Rab family localizes specifically to a distinct membrane, but it is unclear how this specific membrane recruitment is achieved. Here, we demonstrate that Rab-activating guanosine diphosphate/guanosine triphosphate exchange factors (GEFs) display the minimal targeting machinery for recruiting Rabs from the cytosol to the correct membrane using the Rab-GEF pairs Rab5A–Rabex-5, Rab1A-DrrA, and Rab8-Rabin8 as model systems. Specific mistargeting of Rabex-5/DrrA/Rabin8 to mitochondria led to catalytic recruitment of Rab5A/Rab1A/Rab8A in a time-dependent manner that required the catalytic activity of the GEF. Therefore, RabGEFs are major determinants for specific Rab membrane targeting.
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Affiliation(s)
- Julia Blümer
- Department of Physical Biochemistry, Max-Planck-Institute of Molecular Physiology, 44227 Dortmund, Germany
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41
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Abstract
Small GTPases are versatile temporal and spatial regulators of virtually all cellular processes including signal transduction, cytoskeleton dynamics and membrane trafficking. They function as molecular switches, aided by a multitude of regulatory and effector proteins that link them into functional networks. A picture is beginning to emerge whereupon scaffold proteins with many functional domains perform the regulatory and effector functions, thus allowing the ordered recruitment and activation of small GTPases. This leads to the formation of scaffolding patches that coordinate cargo concentration and capture, with the recruitment and activation of the membrane tethering complexes and fusion regulators. This review will focus on the crosstalk of Arf and Rab GTPases at the Golgi complex and the scaffolds that facilitate their activation during trafficking of sensory receptors to primary cilia. The evolutionary conservation of the GTPase cascades in ciliogenesis and yeast budding will be discussed.
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Affiliation(s)
- Dusanka Deretic
- Department of Surgery, Division of Ophthalmology, University of New Mexico, Albuquerque, NM, USA.
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42
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Abstract
Small GTPases use GDP/GTP alternation to actuate a variety of functional switches that are pivotal for cell dynamics. The GTPase switch is turned on by GEFs, which stimulate dissociation of the tightly bound GDP, and turned off by GAPs, which accelerate the intrinsically sluggish hydrolysis of GTP. For Ras, Rho, and Rab GTPases, this switch incorporates a membrane/cytosol alternation regulated by GDIs and GDI-like proteins. The structures and core mechanisms of representative members of small GTPase regulators from most families have now been elucidated, illuminating their general traits combined with scores of unique features. Recent studies reveal that small GTPase regulators have themselves unexpectedly sophisticated regulatory mechanisms, by which they process cellular signals and build up specific cell responses. These mechanisms include multilayered autoinhibition with stepwise release, feedback loops mediated by the activated GTPase, feed-forward signaling flow between regulators and effectors, and a phosphorylation code for RhoGDIs. The flipside of these highly integrated functions is that they make small GTPase regulators susceptible to biochemical abnormalities that are directly correlated with diseases, notably a striking number of missense mutations in congenital diseases, and susceptible to bacterial mimics of GEFs, GAPs, and GDIs that take command of small GTPases in infections. This review presents an overview of the current knowledge of these many facets of small GTPase regulation.
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Affiliation(s)
- Jacqueline Cherfils
- Laboratoire d’Enzymologie et Biochimie Structurales, Centre National de la Recherche Scientifique, Centre deRecherche de Gif, Gif-sur-Yvette, France
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43
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Khan AR. Oligomerization of rab/effector complexes in the regulation of vesicle trafficking. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 117:579-614. [PMID: 23663983 DOI: 10.1016/b978-0-12-386931-9.00021-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Rabs comprise the largest member of the Ras superfamily of small GTPases with over 60 proteins in mammals and 11 proteins in yeast. Like all small GTPases, Rabs oscillate between an inactive GDP-bound conformation and an active GTP-bound state that is tethered to lipid membranes via a C-terminal prenylation site on conserved cysteine residues. In their active state, Rabs regulate various aspects of membrane trafficking, including vesicle formation, transport, docking, and fusion. The critical element of biological activity is the recruitment of cytosolic effector proteins to specific endomembranes by active Rabs. The importance of Rabs in cellular processes is apparent from their links to genetic disorders, immunodeficiency, cancer, and pathogen invasion. During the last decade, numerous structures of complexes have shed light on the molecular basis for Rab/effector specificity and their topological organization on subcellular membranes. Here, I review the known structures of Rab/effector complexes and their modes of oligomerization. This is followed by a brief discussion on the thermodynamics of effector recruitment, which has not been documented sufficiently in previous reviews. A summary of diseases associated with Rab/effector trafficking pathways concludes this chapter.
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Affiliation(s)
- Amir R Khan
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
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44
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Abstract
Despite over two decades of research, the mechanism of Rab targeting to specific intracellular membranes is still not completely understood. Present evidence suggests that the original hypothesis that the message for targeting resides solely in the hypervariable C-terminus is incorrect, and a second mechanism involving a GDF [GDI (guanine-nucleotide-dissociation inhibitor) displacement factor] to disrupt stable Rab–GDI complexes has only been shown to apply in one case, despite the need for targeting over 60 human Rab proteins. Evidence for the involvement of Rab–effector interactions has only been presented for a few cases or in a very specific context. There is mounting evidence that GEFs (guanine-nucleotide-exchange factors) are essential for membrane targeting, although contributions from additional factors are likely to be of importance, at least in specific cases.
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45
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Sunitha MS, Nair AG, Charya A, Jadhav K, Mukhopadhyay S, Sowdhamini R. Structural attributes for the recognition of weak and anomalous regions in coiled-coils of myosins and other motor proteins. BMC Res Notes 2012; 5:530. [PMID: 23009691 PMCID: PMC3542152 DOI: 10.1186/1756-0500-5-530] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 08/28/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Coiled-coils are found in different proteins like transcription factors, myosin tail domain, tropomyosin, leucine zippers and kinesins. Analysis of various structures containing coiled-coils has revealed the importance of electrostatic and hydrophobic interactions. In such domains, regions of different strength of interactions need to be identified since they could be biologically relevant. FINDINGS We have updated our coiled-coil validation webserver, now called COILCHECK+, where new features were added to efficiently identify the strength of interaction at the interface region and measure the density of charged residues and hydrophobic residues. We have examined charged residues and hydrophobic ladders, using a new algorithm called CHAHO, which is incorporated within COILCHECK + server. CHAHO permits the identification of spatial charged residue patches and the continuity of hydrophobic ladder which stabilizes and destabilizes the coiled-coil structure. CONCLUSIONS The availability of such computational tools should be useful to understand the importance of spatial clustering of charged residues and the continuity of hydrophobic residues at the interface region of coiled-coil dimers. COILCHECK + is a structure based tool to validate coiled-coil stability; it can be accessed at http://caps.ncbs.res.in/coilcheckplus.
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Affiliation(s)
- Margaret S Sunitha
- National Centre for Biological Sciences (TIFR), UAS-GKVK Campus, Bellary Road, Bangalore 560 065, India
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Feng S, Knödler A, Ren J, Zhang J, Zhang X, Hong Y, Huang S, Peränen J, Guo W. A Rab8 guanine nucleotide exchange factor-effector interaction network regulates primary ciliogenesis. J Biol Chem 2012; 287:15602-9. [PMID: 22433857 DOI: 10.1074/jbc.m111.333245] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Primary cilia are microtubule-based solitary membrane projections on the cell surface that play important roles in signaling and development. Recent studies have demonstrated that polarized vesicular trafficking involving the small GTPase Rab8 and its guanine nucleotide exchange factor Rabin8 is essential for primary ciliogenesis. In this study, we show that a highly conserved region of Rabin8 is pivotal for its activation as a guanine nucleotide exchange factor for Rab8. In addition, in its activated conformation, Rabin8 interacts with Sec15, a subunit of the exocyst and downstream effector of Rab8. Expression of constitutively activated Rab8 promotes the association of Sec15 with Rabin8. Using immunofluorescence microscopy, we found that Sec15 co-localized with Rab8 along the primary cilium. Inhibition of Sec15 function in cells led to defects in primary ciliogenesis. The Rabin8-Rab8-Sec15 interaction may couple the activation of Rab8 to the recruitment of the Rab8 effector and is involved in the regulation of vesicular trafficking for primary cilium formation.
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Affiliation(s)
- Shanshan Feng
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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47
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Insights regarding guanine nucleotide exchange from the structure of a DENN-domain protein complexed with its Rab GTPase substrate. Proc Natl Acad Sci U S A 2011; 108:18672-7. [PMID: 22065758 DOI: 10.1073/pnas.1110415108] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Rab GTPases are key regulators of membrane traffic pathways within eukaryotic cells. They are specifically activated by guanine nucleotide exchange factors (GEFs), which convert them from their "inactive" GDP-bound form to the "active" GTP-bound form. In higher eukaryotes, proteins containing DENN-domains comprise a major GEF family. Here we describe at 2.1-Å resolution the first structure of a DENN-domain protein, DENND1B-S, complexed with its substrate Rab35, providing novel insights as to how DENN-domain GEFs interact with and activate Rabs. DENND1B-S is bi-lobed, and interactions with Rab35 are through conserved surfaces in both lobes. Rab35 binds via switch regions I and II, around the nucleotide-binding pocket. Positional shifts in Rab residues required for nucleotide binding may lower its affinity for bound GDP, and a conformational change in switch I, which makes the nucleotide-binding pocket more solvent accessible, likely also facilitates exchange.
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Heger CD, Wrann CD, Collins RN. Phosphorylation provides a negative mode of regulation for the yeast Rab GTPase Sec4p. PLoS One 2011; 6:e24332. [PMID: 21931684 PMCID: PMC3171412 DOI: 10.1371/journal.pone.0024332] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Accepted: 08/06/2011] [Indexed: 12/31/2022] Open
Abstract
The Rab family of Ras-related GTPases are part of a complex signaling circuitry in eukaryotic cells, yet we understand little about the mechanisms that underlie Rab protein participation in such signal transduction networks, or how these networks are integrated at the physiological level. Reversible protein phosphorylation is widely used by cells as a signaling mechanism. Several phospho-Rabs have been identified, however the functional consequences of the modification appear to be diverse and need to be evaluated on an individual basis. In this study we demonstrate a role for phosphorylation as a negative regulatory event for the action of the yeast Rab GTPase Sec4p in regulating polarized growth. Our data suggest that the phosphorylation of the Rab Sec4p prevents interactions with its effector, the exocyst component Sec15p, and that the inhibition may be relieved by a PP2A phosphatase complex containing the regulatory subunit Cdc55p.
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Affiliation(s)
- Christopher D. Heger
- Graduate Program in Pharmacology, Cornell University, Ithaca, New York, United States of America
- Department of Molecular Medicine, Cornell University, Ithaca, New York, United States of America
| | - Christiane D. Wrann
- Leadership Program for Veterinary Students, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Ruth N. Collins
- Department of Molecular Medicine, Cornell University, Ithaca, New York, United States of America
- * E-mail:
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Wixler V, Wixler L, Altenfeld A, Ludwig S, Goody RS, Itzen A. Identification and characterisation of novel Mss4-binding Rab GTPases. Biol Chem 2011; 392:239-48. [DOI: 10.1515/bc.2011.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The Mss4 (mammalian suppressor of yeast Sec4) is an evolutionarily highly conserved protein and is expressed in all mammalian tissues. Although its precise biological function is still elusive, it has been shown to associate with a subset of secretory Rab proteins (Rab1b, Rab3a, Rab8a, Rab10) and to possess a rather low guanine nucleotide exchange factor (GEF) activity towards them in vitro (Rab1, Rab3a and Rab8a). By screening a human placenta cDNA library with Mss4 as bait, we identified several Rab GTPases (Rab12, Rab13 and Rab18) as novel Mss4-binding Rab proteins. Only exocytic but no endocytic Rab GTPases were found in our search. The binding of Mss4 to Rab proteins was confirmed by direct yeast two-hybrid interaction, by co-immunoprecipitation from lysates of mammalian cells, by immunofluorescence colocalisation as well as by direct in vitro binding studies. Analysis of Mss4 catalytic activity towards different Rab substrates confirmed that it is a somewhat inefficient GEF. These data, together with our mutational analysis of Mss4-Rab binding capacity, support the already proposed idea that Mss4 functions rather as a chaperone for exocytic Rab GTPases than as a GEF.
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Abstract
Intracellular membrane traffic defines a complex network of pathways that connects many of the membrane-bound organelles of eukaryotic cells. Although each pathway is governed by its own set of factors, they all contain Rab GTPases that serve as master regulators. In this review, we discuss how Rabs can regulate virtually all steps of membrane traffic from the formation of the transport vesicle at the donor membrane to its fusion at the target membrane. Some of the many regulatory functions performed by Rabs include interacting with diverse effector proteins that select cargo, promoting vesicle movement, and verifying the correct site of fusion. We describe cascade mechanisms that may define directionality in traffic and ensure that different Rabs do not overlap in the pathways that they regulate. Throughout this review we highlight how Rab dysfunction leads to a variety of disease states ranging from infectious diseases to cancer.
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Affiliation(s)
- Alex H Hutagalung
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093, USA
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