1
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Shortill SP, Frier MS, Wongsangaroonsri P, Davey M, Conibear E. The VINE complex is an endosomal VPS9-domain GEF and SNX-BAR coat. eLife 2022; 11:77035. [PMID: 35938928 PMCID: PMC9507130 DOI: 10.7554/elife.77035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 08/05/2022] [Indexed: 11/18/2022] Open
Abstract
Membrane trafficking pathways perform important roles in establishing and maintaining the endosomal network. Retrograde protein sorting from the endosome is promoted by conserved SNX-BAR-containing coat complexes including retromer which enrich cargo at tubular microdomains and generate transport carriers. In metazoans, retromer cooperates with VARP, a conserved VPS9-domain GEF, to direct an endosomal recycling pathway. The function of the yeast VARP homolog Vrl1 has been overlooked due to an inactivating mutation found in commonly studied strains. Here, we demonstrate that Vrl1 has features of a SNX-BAR coat protein and forms an obligate complex with Vin1, the paralog of the retromer SNX-BAR protein Vps5. Unique features in the Vin1 N-terminus allow Vrl1 to distinguish it from Vps5, thereby forming a complex that we have named VINE. The VINE complex occupies endosomal tubules and redistributes a conserved mannose 6-phosphate receptor-like protein from endosomes. We also find that membrane recruitment by Vin1 is essential for Vrl1 GEF activity, suggesting that VINE is a multifunctional coat complex that regulates trafficking and signaling events at the endosome. All healthy cells have a highly organized interior: different compartments with specialized roles are in different places, and in order to do their jobs properly, proteins need to be in the right place. Endosomes are membrane-bound compartments that act as transport hubs where proteins are sorted into small vesicles and delivered to other parts of the cell. Two groups of proteins regulate this transport: the first group, known as VPS9 GEFs, switches on the enzymes that recruit the second group of proteins, called the sorting nexins. This second group is responsible for forming the transport vesicles via which proteins are distributed all over the cell. Defects in protein sorting can lead to various diseases, including neurodegenerative conditions such as Parkinson’s disease and juvenile amyotrophic lateral sclerosis. Scientists often use budding yeast cells to study protein sorting, because these cells are similar to human cells, but easier to grow in large numbers and examine in the laboratory. Previous work showed that a yeast protein called Vrl1 is equivalent to a VPS9 GEF from humans called VARP. However, Vrl1 only exists in wild forms of budding yeast, and not in laboratory strains of the organism. Therefore, researchers had not studied Vrl1 in detail, and its roles remained unclear. To learn more about Vrl1, Shortill et al. started by re-introducing the protein into laboratory strains of budding yeast and observing what happened to protein sorting in these cells. Like VARP, Vrl1 was found in the endosomes of budding yeast. However, biochemical experiments revealed that, while human VARP binds to a protein called retromer, Vrl1 does not bind to the equivalent protein in yeast. Instead, Vrl1 itself has features of both the VPS9 GEFs and the sorting nexins. Shortill et al. also found that Vrl1 interacted with a different protein in the sorting nexin family called Vin1. In the absence of Vrl1, Vin1 was found floating around the cell, but once Vrl1 was re-introduced into the budding yeast, Vin1 relocated to the endosomes. Vrl1 uses its VPS9 GEF part to move itself to the endosome membrane, and Vin1 controls this movement, highlighting the interdependence between the two proteins. Once they are at the endosome together, Vrl1 and Vin1 help redistribute proteins to other parts of the cell. This study suggests that, like VARP, Vrl1 cooperates with sorting nexins to transport proteins. Since many previous experiments about protein sorting were carried out in yeast cells lacking Vrl1, it is possible that this process was overlooked despite its potential importance. These new findings could also help other researchers investigating how endosomes and protein sorting work, or do not work, in the context of neurodegenerative diseases.
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Affiliation(s)
- Shawn P Shortill
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
| | - Mia S Frier
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
| | | | - Michael Davey
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
| | - Elizabeth Conibear
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
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2
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Li S, Cerri M, Strazzer P, Li Y, Spelt C, Bliek M, Vandenbussche M, Martínez-Calvó E, Lai B, Reale L, Koes R, Quattrocchio FM. An ancient RAB5 governs the formation of additional vacuoles and cell shape in petunia petals. Cell Rep 2021; 36:109749. [PMID: 34592147 DOI: 10.1016/j.celrep.2021.109749] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 06/11/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022] Open
Abstract
Homologous ("canonical") RAB5 proteins regulate endosomal trafficking to lysosomes in animals and to the central vacuole in plants. Epidermal petal cells contain small vacuoles (vacuolinos) that serve as intermediate stations for proteins on their way to the central vacuole. Here, we show that transcription factors required for vacuolino formation in petunia induce expression of RAB5a. RAB5a defines a previously unrecognized clade of canonical RAB5s that is evolutionarily and functionally distinct from ARA7-type RAB5s, which act in trafficking to the vacuole. Loss of RAB5a reduces cell height and abolishes vacuolino formation, which cannot be rescued by the ARA7 homologs, whereas constitutive RAB5a (over)expression alters the conical cell shape and promotes homotypic vacuolino fusion, resulting in oversized vacuolinos. These findings provide a rare example of how gene duplication and neofunctionalization increased the complexity of membrane trafficking during evolution and suggest a mechanism by which cells may form multiple vacuoles with distinct content and function.
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Affiliation(s)
- Shuangjiang Li
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Martina Cerri
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - Pamela Strazzer
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Yanbang Li
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Cornelis Spelt
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Mattijs Bliek
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Michiel Vandenbussche
- Laboratoire Reproduction et Développement des Plantes (RDP), ENS de Lyon/CNRS/INRA/UCBL, 46 Allée d'Italie, 69364 Lyon, France
| | - Enric Martínez-Calvó
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Biao Lai
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Lara Reale
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
| | - Ronald Koes
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands.
| | - Francesca M Quattrocchio
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
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3
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Pipaliya SV, Santos R, Salas-Leiva D, Balmer EA, Wirdnam CD, Roger AJ, Hehl AB, Faso C, Dacks JB. Unexpected organellar locations of ESCRT machinery in Giardia intestinalis and complex evolutionary dynamics spanning the transition to parasitism in the lineage Fornicata. BMC Biol 2021; 19:167. [PMID: 34446013 PMCID: PMC8394649 DOI: 10.1186/s12915-021-01077-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/23/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Comparing a parasitic lineage to its free-living relatives is a powerful way to understand how that evolutionary transition to parasitism occurred. Giardia intestinalis (Fornicata) is a leading cause of gastrointestinal disease world-wide and is famous for its unusual complement of cellular compartments, such as having peripheral vacuoles instead of typical endosomal compartments. Endocytosis plays an important role in Giardia's pathogenesis. Endosomal sorting complexes required for transport (ESCRT) are membrane-deforming proteins associated with the late endosome/multivesicular body (MVB). MVBs are ill-defined in G. intestinalis, and roles for identified ESCRT-related proteins are not fully understood in the context of its unique endocytic system. Furthermore, components thought to be required for full ESCRT functionality have not yet been documented in this species. RESULTS We used genomic and transcriptomic data from several Fornicata species to clarify the evolutionary genome streamlining observed in Giardia, as well as to detect any divergent orthologs of the Fornicata ESCRT subunits. We observed differences in the ESCRT machinery complement between Giardia strains. Microscopy-based investigations of key components of ESCRT machinery such as GiVPS36 and GiVPS25 link them to peripheral vacuoles, highlighting these organelles as simplified MVB equivalents. Unexpectedly, we show ESCRT components associated with the endoplasmic reticulum and, for the first time, mitosomes. Finally, we identified the rare ESCRT component CHMP7 in several fornicate representatives, including Giardia and show that contrary to current understanding, CHMP7 evolved from a gene fusion of VPS25 and SNF7 domains, prior to the last eukaryotic common ancestor, over 1.5 billion years ago. CONCLUSIONS Our findings show that ESCRT machinery in G. intestinalis is far more varied and complete than previously thought, associates to multiple cellular locations, and presents changes in ESCRT complement which pre-date adoption of a parasitic lifestyle.
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Affiliation(s)
- Shweta V Pipaliya
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Rui Santos
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
| | - Dayana Salas-Leiva
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Erina A Balmer
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Corina D Wirdnam
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Andrew J Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Adrian B Hehl
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
| | - Carmen Faso
- Institute of Cell Biology, University of Bern, Bern, Switzerland.
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.
| | - Joel B Dacks
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.
- Institute of Parasitology, Biology Centre, CAS, v.v.i. Branisovska 31, 370 05, Ceske Budejovice, Czech Republic.
- Centre for Life's Origin and Evolution, Department of Genetics, Evolution and Environment, University College of London, London, UK.
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4
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An interdependence between GAPVD1 gene polymorphism, expression level and response to interferon beta in patients with multiple sclerosis. J Neuroimmunol 2021; 353:577507. [PMID: 33548618 DOI: 10.1016/j.jneuroim.2021.577507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 01/02/2021] [Accepted: 01/27/2021] [Indexed: 11/21/2022]
Abstract
Interferon-β (IFN-β) is among the first drugs used for reducing the symptoms of multiple sclerosis (MS). Many studies show that the genetic predisposition of patients might modulate their response to IFN-β treatment. In this study GAPVD1 gene expression and the genotyping of rs2291858 variant were analysed in 100 responder and 100 non-responder patients with MS treated using IFN-β. Moreover, rs2291858 genotyping was performed for 200 patients with MS and 200 healthy controls. GAPVD1 expression was significantly increased in the responder patients than in non-responders and the distribution of rs2291858 polymorphism was significantly different between them. The GAPVD1 expression level in AA genotype of the responder group was higher than that in other genotypes of these two groups. The results show that the GAPVD1 expression level and rs2291858 genotype probably affect the response to IFN- β in patients with MS.
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5
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Crawley-Snowdon H, Yang JC, Zaccai NR, Davis LJ, Wartosch L, Herman EK, Bright NA, Swarbrick JS, Collins BM, Jackson LP, Seaman MNJ, Luzio JP, Dacks JB, Neuhaus D, Owen DJ. Mechanism and evolution of the Zn-fingernail required for interaction of VARP with VPS29. Nat Commun 2020; 11:5031. [PMID: 33024112 PMCID: PMC7539009 DOI: 10.1038/s41467-020-18773-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 09/08/2020] [Indexed: 01/13/2023] Open
Abstract
VARP and TBC1D5 are accessory/regulatory proteins of retromer-mediated retrograde trafficking from endosomes. Using an NMR/X-ray approach, we determined the structure of the complex between retromer subunit VPS29 and a 12 residue, four-cysteine/Zn++ microdomain, which we term a Zn-fingernail, two of which are present in VARP. Mutations that abolish VPS29:VARP binding inhibit trafficking from endosomes to the cell surface. We show that VARP and TBC1D5 bind the same site on VPS29 and can compete for binding VPS29 in vivo. The relative disposition of VPS29s in hetero-hexameric, membrane-attached, retromer arches indicates that VARP will prefer binding to assembled retromer coats through simultaneous binding of two VPS29s. The TBC1D5:VPS29 interaction is over one billion years old but the Zn-fingernail appears only in VARP homologues in the lineage directly giving rise to animals at which point the retromer/VARP/TBC1D5 regulatory network became fully established.
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Affiliation(s)
- Harriet Crawley-Snowdon
- MRC Laboratory of Molecular Biology Cambridge Biomedical Campus, Francis Crick Ave, Cambridge, CB2 0QH, UK
| | - Ji-Chun Yang
- MRC Laboratory of Molecular Biology Cambridge Biomedical Campus, Francis Crick Ave, Cambridge, CB2 0QH, UK
| | - Nathan R Zaccai
- CIMR, The Keith Peters Building, Hills Road, Cambridge, CB2 0QQ, UK
| | - Luther J Davis
- CIMR, The Keith Peters Building, Hills Road, Cambridge, CB2 0QQ, UK
| | - Lena Wartosch
- CIMR, The Keith Peters Building, Hills Road, Cambridge, CB2 0QQ, UK
| | - Emily K Herman
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Canada, T6G 2G3
| | | | - James S Swarbrick
- Pharmacology and Therapeutics, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Brett M Collins
- The University of Queensland, Institute for Molecular Bioscience, St Lucia, QLD, 4072, Australia
| | - Lauren P Jackson
- CIMR, The Keith Peters Building, Hills Road, Cambridge, CB2 0QQ, UK
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
| | | | - J Paul Luzio
- CIMR, The Keith Peters Building, Hills Road, Cambridge, CB2 0QQ, UK.
| | - Joel B Dacks
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Canada, T6G 2G3.
| | - David Neuhaus
- MRC Laboratory of Molecular Biology Cambridge Biomedical Campus, Francis Crick Ave, Cambridge, CB2 0QH, UK.
| | - David J Owen
- CIMR, The Keith Peters Building, Hills Road, Cambridge, CB2 0QQ, UK.
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6
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Ono S, Otomo A, Murakoshi S, Mitsui S, Sato K, Fukuda M, Hadano S. ALS2, the small GTPase Rab17-interacting protein, regulates maturation and sorting of Rab17-associated endosomes. Biochem Biophys Res Commun 2020; 523:908-915. [PMID: 31959474 DOI: 10.1016/j.bbrc.2019.12.122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 12/22/2019] [Indexed: 12/11/2022]
Abstract
Small GTPase Rab17 has been shown to regulate a wide range of physiological processes including cell migration in tumor cells and dendrite morphogenesis in neurons. However, molecular mechanism underlying Rab17-mediated intracellular trafficking is still unclear. To address this issue, we focused on Rab17-interacting protein ALS2, which was also known as a guanine nucleotide exchange factor (GEF) for Rab5, and investigated how ALS2 contributed to Rab17-associated membrane trafficking in cells. Rab17 was primarily localized to endosomal compartments, particularly to recycling endosomes, which was dependent on Rab11 expression. Upon Rac1 activation, Rab17 along with ALS2 was recruited to membrane ruffles and early endosomes in a Rab5 activity-independent manner. While RABGEF1, another Rab17-interacting Rab5 GEF, functioned as a GEF for Rab17, ALS2 did not possess such catalytic activity but merely interacted with Rab17. Importantly, ALS2 acted downstream of RABGEF1, regulating the maturation of Rab17-residing nascent endosomes to early endosome antigen 1 (EEA1)-positive early endosomes. Further, these Rab17-residing nascent endosomes were arisen via clathrin-independent endocytosis (CIE). Collectively, ALS2 plays a crucial role in the regulation of Rab17-associated endosomal trafficking and maturation, probably through their physical interaction, in cells.
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Affiliation(s)
- Suzuka Ono
- Molecular Neuropathobiology Laboratory, Department of Molecular Life Sciences, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Asako Otomo
- Molecular Neuropathobiology Laboratory, Department of Molecular Life Sciences, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan; Micro/Nano Technology Center, Tokai University, Hiratsuka, Kanagawa, 259-1292, Japan
| | - Shuji Murakoshi
- Molecular Neuropathobiology Laboratory, Department of Molecular Life Sciences, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Shun Mitsui
- Molecular Neuropathobiology Laboratory, Department of Molecular Life Sciences, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Kai Sato
- Molecular Neuropathobiology Laboratory, Department of Molecular Life Sciences, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Mitsunori Fukuda
- Laboratory of Membrane Trafficking Mechanisms, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8578, Japan
| | - Shinji Hadano
- Molecular Neuropathobiology Laboratory, Department of Molecular Life Sciences, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan; Micro/Nano Technology Center, Tokai University, Hiratsuka, Kanagawa, 259-1292, Japan; The Institute of Medical Sciences, Tokai University, Isehara, Kanagawa, 259-1193, Japan.
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7
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Lauer J, Segeletz S, Cezanne A, Guaitoli G, Raimondi F, Gentzel M, Alva V, Habeck M, Kalaidzidis Y, Ueffing M, Lupas AN, Gloeckner CJ, Zerial M. Auto-regulation of Rab5 GEF activity in Rabex5 by allosteric structural changes, catalytic core dynamics and ubiquitin binding. eLife 2019; 8:46302. [PMID: 31718772 PMCID: PMC6855807 DOI: 10.7554/elife.46302] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 10/22/2019] [Indexed: 02/06/2023] Open
Abstract
Intracellular trafficking depends on the function of Rab GTPases, whose activation is regulated by guanine exchange factors (GEFs). The Rab5 GEF, Rabex5, was previously proposed to be auto-inhibited by its C-terminus. Here, we studied full-length Rabex5 and Rabaptin5 proteins as well as domain deletion Rabex5 mutants using hydrogen deuterium exchange mass spectrometry. We generated a structural model of Rabex5, using chemical cross-linking mass spectrometry and integrative modeling techniques. By correlating structural changes with nucleotide exchange activity for each construct, we uncovered new auto-regulatory roles for the ubiquitin binding domains and the Linker connecting those domains to the catalytic core of Rabex5. We further provide evidence that enhanced dynamics in the catalytic core are linked to catalysis. Our results suggest a more complex auto-regulation mechanism than previously thought and imply that ubiquitin binding serves not only to position Rabex5 but to also control its Rab5 GEF activity through allosteric structural alterations.
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Affiliation(s)
- Janelle Lauer
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Sandra Segeletz
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Alice Cezanne
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Francesco Raimondi
- Bioquant, Heidelberg University, Heidelberg, Germany.,Heidelberg University Biochemistry Centre (BZH), Heidelberg, Germany
| | - Marc Gentzel
- Molecular Analysis-Mass Spectrometry Center for Molecular and Cellular Bioengineering, Technical University Dresden, Dresden, Germany
| | - Vikram Alva
- Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Michael Habeck
- Statistical Inverse Problems in Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Felix Bernstein Institute for Mathematical Statistics in the Biosciences, University of Göttingen, Göttingen, Germany
| | - Yannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Marius Ueffing
- Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Andrei N Lupas
- Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - Christian Johannes Gloeckner
- German Center for Neurodegenerative Diseases, Tübingen, Germany.,Center for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
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8
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Pipaliya SV, Schlacht A, Klinger CM, Kahn RA, Dacks J. Ancient complement and lineage-specific evolution of the Sec7 ARF GEF proteins in eukaryotes. Mol Biol Cell 2019; 30:1846-1863. [PMID: 31141460 PMCID: PMC6727740 DOI: 10.1091/mbc.e19-01-0073] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Guanine nucleotide exchange factors (GEFs) are the initiators of signaling by every regulatory GTPase, which in turn act to regulate a wide array of essential cellular processes. To date, each family of GTPases is activated by distinct families of GEFs. Bidirectional membrane trafficking is regulated by ADP-ribosylation factor (ARF) GTPases and the development throughout eukaryotic evolution of increasingly complex systems of such traffic required the acquisition of a functionally diverse cohort of ARF GEFs to control it. We performed phylogenetic analyses of ARF GEFs in eukaryotes, defined by the presence of the Sec7 domain, and found three subfamilies (BIG, GBF1, and cytohesins) to have been present in the ancestor of all eukaryotes. The four other subfamilies (EFA6/PSD, IQSEC7/BRAG, FBX8, and TBS) are opisthokont, holozoan, metazoan, and alveolate/haptophyte specific, respectively, and each is derived from cytohesins. We also identified a cytohesin-derived subfamily, termed ankyrin repeat-containing cytohesin, that independently evolved in amoebozoans and members of the SAR and haptophyte clades. Building on evolutionary data for the ARF family GTPases and their GTPase--activating proteins allowed the generation of hypotheses about ARF GEF protein function(s) as well as a better understanding of the origins and evolution of cellular complexity in eukaryotes.
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Affiliation(s)
- Shweta V Pipaliya
- Department of Medicine, Division of Infectious Diseases, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2S2, Canada
| | - Alexander Schlacht
- Department of Medicine, Division of Infectious Diseases, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2S2, Canada
| | - Christen M Klinger
- Department of Medicine, Division of Infectious Diseases, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2S2, Canada
| | - Richard A Kahn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322
| | - Joel Dacks
- Department of Medicine, Division of Infectious Diseases, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2S2, Canada.,Department of Life Sciences, The Natural History Museum, London SW7 5BD, United Kingdom
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9
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Quintana JF, Pino RCD, Yamada K, Zhang N. Adaptation and Therapeutic Exploitation of the Plasma Membrane of African Trypanosomes. Genes (Basel) 2018; 9:E368. [PMID: 30037058 PMCID: PMC6071061 DOI: 10.3390/genes9070368] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 07/18/2018] [Accepted: 07/19/2018] [Indexed: 12/19/2022] Open
Abstract
African trypanosomes are highly divergent from their metazoan hosts, and as part of adaptation to a parasitic life style have developed a unique endomembrane system. The key virulence mechanism of many pathogens is successful immune evasion, to enable survival within a host, a feature that requires both genetic events and membrane transport mechanisms in African trypanosomes. Intracellular trafficking not only plays a role in immune evasion, but also in homeostasis of intracellular and extracellular compartments and interactions with the environment. Significantly, historical and recent work has unraveled some of the connections between these processes and highlighted how immune evasion mechanisms that are associated with adaptations to membrane trafficking may have, paradoxically, provided specific sensitivity to drugs. Here, we explore these advances in understanding the membrane composition of the trypanosome plasma membrane and organelles and provide a perspective for how transport could be exploited for therapeutic purposes.
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Affiliation(s)
- Juan F Quintana
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
| | | | - Kayo Yamada
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
| | - Ning Zhang
- School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK.
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10
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Herman EK, Ali M, Field MC, Dacks JB. Regulation of early endosomes across eukaryotes: Evolution and functional homology of Vps9 proteins. Traffic 2018; 19:546-563. [PMID: 29603841 PMCID: PMC6032885 DOI: 10.1111/tra.12570] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/21/2018] [Accepted: 03/27/2018] [Indexed: 12/11/2022]
Abstract
Endocytosis is a crucial process in eukaryotic cells. The GTPases Rab 5, 21 and 22 that mediate endocytosis are ancient eukaryotic features and all available evidence suggests retained conserved function. In animals and fungi, these GTPases are regulated in part by proteins possessing Vps9 domains. However, the diversity, evolution and functions of Vps9 proteins beyond animals or fungi are poorly explored. Here we report a comprehensive analysis of the Vps9 family of GTPase regulators, combining molecular evolutionary data with functional characterization in the non-opisthokont model organism Trypanosoma brucei. At least 3 subfamilies, Alsin, Varp and Rabex5 + GAPVD1, are found across eukaryotes, suggesting that all are ancient features of regulation of endocytic Rab protein function. There are examples of lineage-specific Vps9 subfamily member expansions and novel domain combinations, suggesting diversity in precise regulatory mechanisms between individual lineages. Characterization of the Rabex5 + GAPVD1 and Alsin orthologues in T. brucei demonstrates that both proteins are involved in endocytosis, and that simultaneous knockdown prevents membrane recruitment of Rab5 and Rab21, indicating conservation of function. These data demonstrate that, for the Vps9-domain family at least, modulation of Rab function is mediated by evolutionarily conserved protein-protein interactions.
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Affiliation(s)
- Emily K. Herman
- Department of Cell Biology, Faculty of Medicine and DentistryUniversity of AlbertaEdmontonCanada
| | - Moazzam Ali
- School of Life SciencesUniversity of DundeeDundeeUK
| | | | - Joel B. Dacks
- Department of Cell Biology, Faculty of Medicine and DentistryUniversity of AlbertaEdmontonCanada
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