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Pottier C, Küçükali F, Baker M, Batzler A, Jenkins GD, van Blitterswijk M, Vicente CT, De Coster W, Wynants S, Van de Walle P, Ross OA, Murray ME, Faura J, Haggarty SJ, van Rooij JG, Mol MO, Hsiung GYR, Graff C, Öijerstedt L, Neumann M, Asmann Y, McDonnell SK, Baheti S, Josephs KA, Whitwell JL, Bieniek KF, Forsberg L, Heuer H, Lago AL, Geier EG, Yokoyama JS, Oddi AP, Flanagan M, Mao Q, Hodges JR, Kwok JB, Domoto-Reilly K, Synofzik M, Wilke C, Onyike C, Dickerson BC, Evers BM, Dugger BN, Munoz DG, Keith J, Zinman L, Rogaeva E, Suh E, Gefen T, Geula C, Weintraub S, Diehl-Schmid J, Farlow MR, Edbauer D, Woodruff BK, Caselli RJ, Donker Kaat LL, Huey ED, Reiman EM, Mead S, King A, Roeber S, Nana AL, Ertekin-Taner N, Knopman DS, Petersen RC, Petrucelli L, Uitti RJ, Wszolek ZK, Ramos EM, Grinberg LT, Gorno Tempini ML, Rosen HJ, Spina S, Piguet O, Grossman M, Trojanowski JQ, Keene DC, Lee-Way J, Prudlo J, Geschwind DH, Rissman RA, Cruchaga C, Ghetti B, Halliday GM, Beach TG, Serrano GE, Arzberger T, Herms J, Boxer AL, Honig LS, Vonsattel JP, Lopez OL, Kofler J, White CL, Gearing M, Glass J, Rohrer JD, Irwin DJ, Lee EB, Van Deerlin V, Castellani R, Mesulam MM, Tartaglia MC, Finger EC, Troakes C, Al-Sarraj S, Miller BL, Seelaar H, Graff-Radford NR, Boeve BF, Mackenzie IR, van Swieten JC, Seeley WW, Sleegers K, Dickson DW, Biernacka JM, Rademakers R. Deciphering Distinct Genetic Risk Factors for FTLD-TDP Pathological Subtypes via Whole-Genome Sequencing. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.24.24309088. [PMID: 38978643 PMCID: PMC11230325 DOI: 10.1101/2024.06.24.24309088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Frontotemporal lobar degeneration with neuronal inclusions of the TAR DNA-binding protein 43 (FTLD-TDP) is a fatal neurodegenerative disorder with only a limited number of risk loci identified. We report our comprehensive genome-wide association study as part of the International FTLD-TDP Whole-Genome Sequencing Consortium, including 985 cases and 3,153 controls, and meta-analysis with the Dementia-seq cohort, compiled from 26 institutions/brain banks in the United States, Europe and Australia. We confirm UNC13A as the strongest overall FTLD-TDP risk factor and identify TNIP1 as a novel FTLD-TDP risk factor. In subgroup analyses, we further identify for the first time genome-wide significant loci specific to each of the three main FTLD-TDP pathological subtypes (A, B and C), as well as enrichment of risk loci in distinct tissues, brain regions, and neuronal subtypes, suggesting distinct disease aetiologies in each of the subtypes. Rare variant analysis confirmed TBK1 and identified VIPR1 , RBPJL , and L3MBTL1 as novel subtype specific FTLD-TDP risk genes, further highlighting the role of innate and adaptive immunity and notch signalling pathway in FTLD-TDP, with potential diagnostic and novel therapeutic implications.
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Grosjean N, Le Jean M, Ory J, Blaudez D. Yeast Deletomics to Uncover Gadolinium Toxicity Targets and Resistance Mechanisms. Microorganisms 2023; 11:2113. [PMID: 37630673 PMCID: PMC10459663 DOI: 10.3390/microorganisms11082113] [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: 06/30/2023] [Revised: 08/01/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Among the rare earth elements (REEs), a crucial group of metals for high-technologies. Gadolinium (Gd) is the only REE intentionally injected to human patients. The use of Gd-based contrasting agents for magnetic resonance imaging (MRI) is the primary route for Gd direct exposure and accumulation in humans. Consequently, aquatic environments are increasingly exposed to Gd due to its excretion through the urinary tract of patients following an MRI examination. The increasing number of reports mentioning Gd toxicity, notably originating from medical applications of Gd, necessitates an improved risk-benefit assessment of Gd utilizations. To go beyond toxicological studies, unravelling the mechanistic impact of Gd on humans and the ecosystem requires the use of genome-wide approaches. We used functional deletomics, a robust method relying on the screening of a knock-out mutant library of Saccharomyces cerevisiae exposed to toxic concentrations of Gd. The analysis of Gd-resistant and -sensitive mutants highlighted the cell wall, endosomes and the vacuolar compartment as cellular hotspots involved in the Gd response. Furthermore, we identified endocytosis and vesicular trafficking pathways (ESCRT) as well as sphingolipids homeostasis as playing pivotal roles mediating Gd toxicity. Finally, tens of yeast genes with human orthologs linked to renal dysfunction were identified as Gd-responsive. Therefore, the molecular and cellular pathways involved in Gd toxicity and detoxification uncovered in this study underline the pleotropic consequences of the increasing exposure to this strategic metal.
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Affiliation(s)
- Nicolas Grosjean
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA;
| | - Marie Le Jean
- Université de Lorraine, CNRS, LIEC, F-57000 Metz, France;
| | - Jordan Ory
- Université de Lorraine, CNRS, LIEC, F-54000 Nancy, France;
| | - Damien Blaudez
- Université de Lorraine, CNRS, LIEC, F-54000 Nancy, France;
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3
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Khakurel A, Lupashin VV. Role of GARP Vesicle Tethering Complex in Golgi Physiology. Int J Mol Sci 2023; 24:6069. [PMID: 37047041 PMCID: PMC10094427 DOI: 10.3390/ijms24076069] [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] [Received: 02/22/2023] [Revised: 03/17/2023] [Accepted: 03/19/2023] [Indexed: 04/14/2023] Open
Abstract
The Golgi associated retrograde protein complex (GARP) is an evolutionarily conserved component of Golgi membrane trafficking machinery that belongs to the Complexes Associated with Tethering Containing Helical Rods (CATCHR) family. Like other multisubunit tethering complexes such as COG, Dsl1, and Exocyst, the GARP is believed to function by tethering and promoting fusion of the endosome-derived small trafficking intermediate. However, even twenty years after its discovery, the exact structure and the functions of GARP are still an enigma. Recent studies revealed novel roles for GARP in Golgi physiology and identified human patients with mutations in GARP subunits. In this review, we summarized our knowledge of the structure of the GARP complex, its protein partners, GARP functions related to Golgi physiology, as well as cellular defects associated with the dysfunction of GARP subunits.
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Affiliation(s)
| | - Vladimir V. Lupashin
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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4
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Khakurel A, Kudlyk T, Lupashin VV. Generation and Analysis of hTERT-RPE1 VPS54 Knock-Out and Rescued Cell Lines. Methods Mol Biol 2023; 2557:349-364. [PMID: 36512226 PMCID: PMC10026839 DOI: 10.1007/978-1-0716-2639-9_22] [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: 12/15/2022]
Abstract
The Golgi-associated retrograde protein (GARP) complex is proposed to tether endosome-derived transport vesicles, but the exact function and mechanism of GARP action are not completely understood. To uncover the GARP function in human cells, we employ CRISPR/Cas9 strategy and knock out (KO) the unique VPS54 subunit of the GARP complex. In this chapter, we describe the detailed method of generating CRISPR/Cas9-mediated VPS54-KO in hTERT-RPE1 cells, rescue of resulting KO cells with stable near-endogenous expression of myc-tagged VPS54, and validation of KO and rescued (KO-R) cells using Western blot and immunofluorescence approaches. This approach is helpful in uncovering new functions of the GARP and other vesicle tethering complexes.
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Affiliation(s)
- Amrita Khakurel
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Tetyana Kudlyk
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Vladimir V Lupashin
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
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5
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Khakurel A, Kudlyk T, Pokrovskaya I, D’Souza Z, Lupashin VV. GARP dysfunction results in COPI displacement, depletion of Golgi v-SNAREs and calcium homeostasis proteins. Front Cell Dev Biol 2022; 10:1066504. [PMID: 36578782 PMCID: PMC9791199 DOI: 10.3389/fcell.2022.1066504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
Golgi-associated retrograde protein (GARP) is an evolutionary conserved heterotetrameric protein complex that tethers endosome-derived vesicles and is vital for Golgi glycosylation. Microscopy and proteomic approaches were employed to investigate defects in Golgi physiology in RPE1 cells depleted for the GARP complex. Both cis and trans-Golgi compartments were significantly enlarged in GARP-knock-out (KO) cells. Proteomic analysis of Golgi-enriched membranes revealed significant depletion of a subset of Golgi residents, including Ca2+ binding proteins, enzymes, and SNAREs. Validation of proteomics studies revealed that SDF4 and ATP2C1, related to Golgi calcium homeostasis, as well as intra-Golgi v-SNAREs GOSR1 and BET1L, were significantly depleted in GARP-KO cells. Finding that GARP-KO is more deleterious to Golgi physiology than deletion of GARP-sensitive v-SNAREs, prompted a detailed investigation of COPI trafficking machinery. We discovered that in GARP-KO cells COPI is significantly displaced from the Golgi and partially relocalized to the ER-Golgi intermediate compartment (ERGIC). Moreover, COPI accessory proteins GOLPH3, ARFGAP1, GBF1, and BIG1 are also relocated to off-Golgi compartments. We propose that the dysregulation of COPI machinery, along with the depletion of Golgi v-SNAREs and alteration of Golgi Ca2+ homeostasis, are the major driving factors for the depletion of Golgi resident proteins, structural alterations, and glycosylation defects in GARP deficient cells.
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6
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Csizmadia T, Dósa A, Farkas E, Csikos BV, Kriska EA, Juhász G, Lőw P. Developmental program-independent secretory granule degradation in larval salivary gland cells of Drosophila. Traffic 2022; 23:568-586. [PMID: 36353974 PMCID: PMC10099382 DOI: 10.1111/tra.12871] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/26/2022] [Accepted: 11/03/2022] [Indexed: 11/11/2022]
Abstract
Both constitutive and regulated secretion require cell organelles that are able to store and release the secretory cargo. During development, the larval salivary gland of Drosophila initially produces high amount of glue-containing small immature secretory granules, which then fuse with each other and reach their normal 3-3.5 μm in size. Following the burst of secretion, obsolete glue granules directly fuse with late endosomes or lysosomes by a process called crinophagy, which leads to fast degradation and recycling of the secretory cargo. However, hindering of endosome-to-TGN retrograde transport in these cells causes abnormally small glue granules which are not able to fuse with each other. Here, we show that loss of function of the SNARE genes Syntaxin 16 (Syx16) and Synaptobrevin (Syb), the small GTPase Rab6 and the GARP tethering complex members Vps53 and Scattered (Vps54) all involved in retrograde transport cause intense early degradation of immature glue granules via crinophagy independently of the developmental program. Moreover, silencing of these genes also provokes secretory failure and accelerated crinophagy during larval development. Our results provide a better understanding of the relations among secretion, secretory granule maturation and degradation and paves the way for further investigation of these connections in other metazoans.
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Affiliation(s)
- Tamás Csizmadia
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Anna Dósa
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Erika Farkas
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Belián Valentin Csikos
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Eszter Adél Kriska
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Gábor Juhász
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary.,Institute of Genetics, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Péter Lőw
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
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Hossain S, Robbins N, Cowen LE. The GARP complex is required for filamentation in Candida albicans. Genetics 2022; 222:iyac152. [PMID: 36226807 PMCID: PMC9713427 DOI: 10.1093/genetics/iyac152] [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] [Received: 08/10/2022] [Accepted: 09/29/2022] [Indexed: 12/13/2022] Open
Abstract
Candida albicans is an opportunistic fungal pathogen that causes superficial infections in immunocompetent individuals, as well as life-threatening systemic disease in immunocompromised patients. A key virulence trait of this pathogen is its ability to transition between yeast and filamentous morphologies. A functional genomic screen to identify novel regulators of filamentation previously revealed VPS53 as being important for morphogenesis. Vps53 belongs to the Golgi-associated retrograde protein (GARP) complex, which mediates retrograde trafficking from the endosome to the trans-Golgi network. Here, we explored the role of the entire GARP complex in regulating morphogenesis. Deletion of any of the four genes encoding GARP complex subunits severely impaired filamentation in response to diverse filament-inducing cues, including upon internalization by macrophages. Genetic pathway analysis revealed that while hyperactivation of protein kinase A (PKA) signaling is insufficient to drive filamentation in GARP complex mutants, these strains are capable of filamentation upon overexpression of transcriptional activators or upon deletion of transcriptional repressors of hyphal morphogenesis. Finally, compromise of the GARP complex induced lipotoxicity, and pharmacological inhibition of sphingolipid biosynthesis phenocopied genetic compromise of the GARP complex by impairing filamentation. Together, this work identifies the GARP complex as an important mediator of filamentation in response to multiple inducing cues, maps genetic circuitry important for filamentation upon compromise of GARP function, and supports a model whereby GARP deficiency impairs lipid homeostasis, which is important for supporting filamentous growth in C. albicans.
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Affiliation(s)
- Saif Hossain
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Nicole Robbins
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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8
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O’Brien CE, Younger SH, Jan LY, Jan YN. The GARP complex prevents sterol accumulation at the trans-Golgi network during dendrite remodeling. J Biophys Biochem Cytol 2022; 222:213548. [PMID: 36239632 PMCID: PMC9577387 DOI: 10.1083/jcb.202112108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 08/11/2022] [Accepted: 09/20/2022] [Indexed: 11/29/2022] Open
Abstract
Membrane trafficking is essential for sculpting neuronal morphology. The GARP and EARP complexes are conserved tethers that regulate vesicle trafficking in the secretory and endolysosomal pathways, respectively. Both complexes contain the Vps51, Vps52, and Vps53 proteins, and a complex-specific protein: Vps54 in GARP and Vps50 in EARP. In Drosophila, we find that both complexes are required for dendrite morphogenesis during developmental remodeling of multidendritic class IV da (c4da) neurons. Having found that sterol accumulates at the trans-Golgi network (TGN) in Vps54KO/KO neurons, we investigated genes that regulate sterols and related lipids at the TGN. Overexpression of oxysterol binding protein (Osbp) or knockdown of the PI4K four wheel drive (fwd) exacerbates the Vps54KO/KO phenotype, whereas eliminating one allele of Osbp rescues it, suggesting that excess sterol accumulation at the TGN is, in part, responsible for inhibiting dendrite regrowth. These findings distinguish the GARP and EARP complexes in neurodevelopment and implicate vesicle trafficking and lipid transfer pathways in dendrite morphogenesis.
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Affiliation(s)
- Caitlin E. O’Brien
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA,Department of Physiology, University of California at San Francisco, San Francisco, CA
| | - Susan H. Younger
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA,Department of Physiology, University of California at San Francisco, San Francisco, CA
| | - Lily Yeh Jan
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA,Department of Physiology, University of California at San Francisco, San Francisco, CA,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA
| | - Yuh Nung Jan
- Howard Hughes Medical Institute, University of California at San Francisco, San Francisco, CA,Department of Physiology, University of California at San Francisco, San Francisco, CA,Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, CA
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9
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Hassing B, Candy A, Eaton CJ, Fernandes TR, Mesarich CH, Di Pietro A, Scott B. Localisation of phosphoinositides in the grass endophyte Epichloë festucae and genetic and functional analysis of key components of their biosynthetic pathway in E. festucae symbiosis and Fusarium oxysporum pathogenesis. Fungal Genet Biol 2022; 159:103669. [PMID: 35114379 DOI: 10.1016/j.fgb.2022.103669] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/15/2022] [Accepted: 01/27/2022] [Indexed: 11/24/2022]
Abstract
Phosphoinositides (PI) are essential components of eukaryotic membranes and function in a large number of signaling processes. While lipid second messengers are well studied in mammals and yeast, their role in filamentous fungi is poorly understood. We used fluorescent PI-binding molecular probes to localize the phosphorylated phosphatidylinositol species PI[3]P, PI[3,5]P2, PI[4]P and PI[4,5]P2 in hyphae of the endophyte Epichloë festucae in axenic culture and during interaction with its grass host Lolium perenne. We also analysed the roles of the phosphatidylinositol-4-phosphate 5-kinase MssD and the predicted phosphatidylinositol-3,4,5-triphosphate 3-phosphatase TepA, a homolog of the mammalian tumour suppressor protein PTEN. Deletion of tepA in E. festucae and in the root-infecting tomato pathogen Fusarium oxysporum had no impact on growth in culture or the host interaction phenotype. However, this mutation did enable the detection of PI[3,4,5]P3 in septa and mycelium of E. festucae and showed that TepA is required for chemotropism in F. oxysporum. The identification of PI[3,4,5]P3 in ΔtepA strains suggests that filamentous fungi are able to generate PI[3,4,5]P3 and that fungal PTEN homologs are functional lipid phosphatases. The F. oxysporum chemotropism defect suggests a conserved role of PTEN homologs in chemotaxis across protists, fungi and mammals.
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Affiliation(s)
- Berit Hassing
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand; Bio-Protection Research Centre, New Zealand
| | - Alyesha Candy
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand; Bio-Protection Research Centre, New Zealand
| | - Carla J Eaton
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand; Bio-Protection Research Centre, New Zealand
| | - Tania R Fernandes
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba, Spain
| | - Carl H Mesarich
- Bio-Protection Research Centre, New Zealand; School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Antonio Di Pietro
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario ceiA3, Universidad de Córdoba, Córdoba, Spain
| | - Barry Scott
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand; Bio-Protection Research Centre, New Zealand.
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10
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D’Souza Z, Sumya FT, Khakurel A, Lupashin V. Getting Sugar Coating Right! The Role of the Golgi Trafficking Machinery in Glycosylation. Cells 2021; 10:cells10123275. [PMID: 34943782 PMCID: PMC8699264 DOI: 10.3390/cells10123275] [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: 10/15/2021] [Revised: 11/17/2021] [Accepted: 11/19/2021] [Indexed: 12/18/2022] Open
Abstract
The Golgi is the central organelle of the secretory pathway and it houses the majority of the glycosylation machinery, which includes glycosylation enzymes and sugar transporters. Correct compartmentalization of the glycosylation machinery is achieved by retrograde vesicular trafficking as the secretory cargo moves forward by cisternal maturation. The vesicular trafficking machinery which includes vesicular coats, small GTPases, tethers and SNAREs, play a major role in coordinating the Golgi trafficking thereby achieving Golgi homeostasis. Glycosylation is a template-independent process, so its fidelity heavily relies on appropriate localization of the glycosylation machinery and Golgi homeostasis. Mutations in the glycosylation enzymes, sugar transporters, Golgi ion channels and several vesicle tethering factors cause congenital disorders of glycosylation (CDG) which encompass a group of multisystem disorders with varying severities. Here, we focus on the Golgi vesicle tethering and fusion machinery, namely, multisubunit tethering complexes and SNAREs and their role in Golgi trafficking and glycosylation. This review is a comprehensive summary of all the identified CDG causing mutations of the Golgi trafficking machinery in humans.
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Wilkinson EC, Starke EL, Barbee SA. Vps54 Regulates Lifespan and Locomotor Behavior in Adult Drosophila melanogaster. Front Genet 2021; 12:762012. [PMID: 34712272 PMCID: PMC8546322 DOI: 10.3389/fgene.2021.762012] [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: 08/20/2021] [Accepted: 09/28/2021] [Indexed: 11/13/2022] Open
Abstract
Vps54 is an integral subunit of the Golgi-associated retrograde protein (GARP) complex, which is involved in tethering endosome-derived vesicles to the trans-Golgi network (TGN). A destabilizing missense mutation in Vps54 causes the age-progressive motor neuron (MN) degeneration, muscle weakness, and muscle atrophy observed in the wobbler mouse, an established animal model for human MN disease. It is currently unclear how the disruption of Vps54, and thereby the GARP complex, leads to MN and muscle phenotypes. To develop a new tool to address this question, we have created an analogous model in Drosophila by generating novel loss-of-function alleles of the fly Vps54 ortholog (scattered/scat). We find that null scat mutant adults are viable but have a significantly shortened lifespan. Like phenotypes observed in the wobbler mouse, we show that scat mutant adults are male sterile and have significantly reduced body size and muscle area. Moreover, we demonstrate that scat mutant adults have significant age-progressive defects in locomotor function. Interestingly, we see sexually dimorphic effects, with scat mutant adult females exhibiting significantly stronger phenotypes. Finally, we show that scat interacts genetically with rab11 in MNs to control age-progressive muscle atrophy in adults. Together, these data suggest that scat mutant flies share mutant phenotypes with the wobbler mouse and may serve as a new genetic model system to study the cellular and molecular mechanisms underlying MN disease.
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Affiliation(s)
- Emily C Wilkinson
- Department of Biological Sciences, University of Denver, Denver, CO, United States
| | - Emily L Starke
- Department of Biological Sciences, University of Denver, Denver, CO, United States
| | - Scott A Barbee
- Department of Biological Sciences, University of Denver, Denver, CO, United States.,Molecular and Cellular Biophysics Program, University of Denver, Denver, CO, United States
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12
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Homma Y, Fukuda M. Knockout analysis of Rab6 effector proteins revealed the role of VPS52 in the secretory pathway. Biochem Biophys Res Commun 2021; 561:151-157. [PMID: 34023780 DOI: 10.1016/j.bbrc.2021.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 05/05/2021] [Indexed: 10/21/2022]
Abstract
Rab small GTPases regulate intracellular membrane trafficking by interacting with specific binding proteins called Rab effectors. Although Rab6 is implicated in basement membrane formation and secretory cargo trafficking, its precise regulatory mechanisms have remained largely unknown. In the present study we established five knockout cell lines for candidate Rab6 effectors and discovered that knockout of VPS52, a subunit of the GARP complex, resulted in attenuated secretion and lysosomal accumulation of secretory cargos, the same as Rab6-knockout does. We also evaluated the functional importance of the previously uncharacterized C-terminal region of VPS52 for restoring these phenotypes, as well as for the sorting of lysosomal proteins. Our findings suggest that VPS52 is an effector protein that is responsible for the Rab6-dependent secretory cargo trafficking.
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Affiliation(s)
- Yuta Homma
- Laboratory of Membrane Trafficking Mechanisms, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai, Miyagi, 980-8578, Japan.
| | - Mitsunori Fukuda
- Laboratory of Membrane Trafficking Mechanisms, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai, Miyagi, 980-8578, Japan.
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13
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Pinar M, Peñalva MA. The fungal RABOME: RAB GTPases acting in the endocytic and exocytic pathways of Aspergillus nidulans (with excursions to other filamentous fungi). Mol Microbiol 2021; 116:53-70. [PMID: 33724562 DOI: 10.1111/mmi.14716] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/04/2021] [Accepted: 03/11/2021] [Indexed: 10/21/2022]
Abstract
RAB GTPases are major determinants of membrane identity that have been exploited as highly specific reporters to study intracellular traffic in vivo. A score of fungal papers have considered individual RABs, but systematic, integrated studies on the localization and physiological role of these regulators and their effectors have been performed only with Aspergillus nidulans. These studies have influenced the intracellular trafficking field beyond fungal specialists, leading to findings such as the maturation of trans-Golgi (TGN) cisternae into post-Golgi RAB11 secretory vesicles, the concept that these RAB11 secretory carriers are loaded with three molecular nanomotors, the understanding of the role of endocytic recycling mediated by RAB6 and RAB11 in determining the hyphal mode of life, the discovery that early endosome maturation and the ESCRT pathway are essential, the identification of specific adaptors of dynein-dynactin to RAB5 endosomes, the exquisite dependence that autophagy displays on RAB1 activity, the role of TRAPPII as a GEF for RAB11, or the conclusion that the RAB1-to-RAB11 transition is not mediated by TRAPP maturation. A remarkable finding was that the A. nidulans Spitzenkörper contains four RABs: RAB11, Sec4, RAB6, and RAB1. How these RABs cooperate during exocytosis represents an as yet outstanding question.
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Affiliation(s)
- Mario Pinar
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
| | - Miguel A Peñalva
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas Margarita Salas, CSIC, Madrid, Spain
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14
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Simon-Vecsei Z, Sőth Á, Lőrincz P, Rubics A, Tálas A, Kulcsár PI, Juhász G. Identification of New Interactions between Endolysosomal Tethering Factors. J Mol Biol 2021; 433:166965. [PMID: 33781757 DOI: 10.1016/j.jmb.2021.166965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 02/28/2021] [Accepted: 03/22/2021] [Indexed: 10/21/2022]
Abstract
Proper functioning of the precisely controlled endolysosomal system is essential for maintaining the homeostasis of the entire cell. Tethering factors play pivotal roles in mediating the fusion of different transport vesicles, such as endosomes or autophagosomes with each other or with lysosomes. In this work, we uncover several new interactions between the endolysosomal tethering factors Rabenosyn-5 (Rbsn) and the HOPS and CORVET complexes. We find that Rbsn binds to the HOPS/CORVET complexes mainly via their shared subunit Vps18 and we mapped this interaction to the 773-854 region of Vps18. Based on genetic rescue experiments, the binding between Rbsn and Vps18 is required for endosomal transport and is dispensable for autophagy. Moreover, Vps18 seems to be important for β1 integrin recycling by binding to Rbsn and its known partner Vps45.
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Affiliation(s)
- Zsófia Simon-Vecsei
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary.
| | - Ármin Sőth
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - Péter Lőrincz
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary; Premium Postdoctoral Research Program, Eötvös Loránd Research Network, Budapest, Hungary
| | - András Rubics
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary
| | - András Tálas
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Péter István Kulcsár
- Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Gábor Juhász
- Department of Anatomy, Cell and Developmental Biology, Eötvös Loránd University, Budapest, Hungary; Institute of Genetics, Biological Research Centre, Szeged, Hungary.
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15
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Gauthier KD, Rocheleau CE. Golgi localization of the LIN-2/7/10 complex points to a role in basolateral secretion of LET-23 EGFR in the Caenorhabditiselegans vulval precursor cells. Development 2021; 148:dev194167. [PMID: 33526581 PMCID: PMC10692275 DOI: 10.1242/dev.194167] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 01/25/2021] [Indexed: 12/28/2022]
Abstract
The evolutionarily conserved LIN-2 (CASK)/LIN-7 (Lin7A-C)/LIN-10 (APBA1) complex plays an important role in regulating spatial organization of membrane proteins and signaling components. In Caenorhabditiselegans, the complex is essential for the development of the vulva by promoting the localization of the sole Epidermal growth factor receptor (EGFR) ortholog LET-23 to the basolateral membrane of the vulva precursor cells where it can specify the vulval cell fate. To understand how the LIN-2/7/10 complex regulates receptor localization, we determined its expression and localization during vulva development. We found that LIN-7 colocalizes with LET-23 EGFR at the basolateral membrane, whereas the LIN-2/7/10 complex colocalizes with LET-23 EGFR at cytoplasmic punctae that mostly overlap with the Golgi. Furthermore, LIN-10 recruits LIN-2, which in turn recruits LIN-7. We demonstrate that the complex forms in vivo with a particularly strong interaction and colocalization between LIN-2 and LIN-7, consistent with them forming a subcomplex. Thus, the LIN-2/7/10 complex forms on the Golgi on which it likely targets LET-23 EGFR trafficking to the basolateral membrane rather than functioning as a tether.
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Affiliation(s)
- Kimberley D Gauthier
- Division of Endocrinology and Metabolism, Department of Medicine, and Department of Anatomy and Cell Biology, McGill University; and the Metabolic Disorders and Complications Program, Centre for Translational Biology, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
| | - Christian E Rocheleau
- Division of Endocrinology and Metabolism, Department of Medicine, and Department of Anatomy and Cell Biology, McGill University; and the Metabolic Disorders and Complications Program, Centre for Translational Biology, Research Institute of the McGill University Health Centre, Montreal, QC H4A 3J1, Canada
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16
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Ueda S, Tamura N, Mima J. Membrane Tethering Potency of Rab-Family Small GTPases Is Defined by the C-Terminal Hypervariable Regions. Front Cell Dev Biol 2020; 8:577342. [PMID: 33102484 PMCID: PMC7554592 DOI: 10.3389/fcell.2020.577342] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022] Open
Abstract
Membrane tethering is a crucial step to determine the spatiotemporal specificity of secretory and endocytic trafficking pathways in all eukaryotic endomembrane systems. Recent biochemical studies by a chemically-defined reconstitution approach reveal that, in addition to the structurally-diverse classic tethering factors such as coiled-coil tethering proteins and multisubunit tethering complexes, Rab-family small GTPases also retain the inherent membrane tethering functions to directly and physically bridge two distinct lipid bilayers by themselves. Although Rab-mediated membrane tethering reactions are fairly efficient and specific in the physiological context, its mechanistic basis is yet to be understood. Here, to explore whether and how the intrinsic tethering potency of Rab GTPases is controlled by their C-terminal hypervariable region (HVR) domains that link the conserved small GTPase domains (G-domains) to membrane anchors at the C-terminus, we quantitatively compared tethering activities of two representative Rab isoforms in humans (Rab5a, Rab4a) and their HVR-deleted mutant forms. Strikingly, deletion of the HVR linker domains enabled both Rab5a and Rab4a isoforms to enhance their intrinsic tethering potency, exhibiting 5- to 50-fold higher initial velocities of tethering for the HVR-deleted mutants than those for the full-length, wild-type Rabs. Furthermore, we revealed that the tethering activity of full-length Rab5a was significantly reduced by the omission of anionic lipids and cholesterol from membrane lipids and, however, membrane tethering driven by HVR-deleted Rab5a mutant was completely insensitive to the headgroup composition of lipids. Reconstituted membrane tethering assays with the C-terminally-truncated mutants of Rab4a further uncovered that the N-terminal residues in the HVR linker, located adjacent to the G-domain, are critical for regulating the intrinsic tethering activity. In conclusion, our current findings establish that the non-conserved, flexible C-terminal HVR linker domains define membrane tethering potency of Rab-family small GTPases through controlling the close attachment of the globular G-domains to membrane surfaces, which confers the active tethering-competent state of the G-domains on lipid bilayers.
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Affiliation(s)
- Sanae Ueda
- Institute for Protein Research, Osaka University, Suita, Japan
| | - Naoki Tamura
- Institute for Protein Research, Osaka University, Suita, Japan
| | - Joji Mima
- Institute for Protein Research, Osaka University, Suita, Japan
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17
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Patel PH, Wilkinson EC, Starke EL, McGimsey MR, Blankenship JT, Barbee SA. Vps54 regulates Drosophila neuromuscular junction development and interacts genetically with Rab7 to control composition of the postsynaptic density. Biol Open 2020; 9:bio053421. [PMID: 32747448 PMCID: PMC7473652 DOI: 10.1242/bio.053421] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/22/2020] [Indexed: 01/04/2023] Open
Abstract
Vps54 is a subunit of the Golgi-associated retrograde protein (GARP) complex, which is involved in tethering endosome-derived vesicles to the trans-Golgi network (TGN). In the wobbler mouse, a model for human motor neuron (MN) disease, reduction in the levels of Vps54 causes neurodegeneration. However, it is unclear how disruption of the GARP complex leads to MN dysfunction. To better understand the role of Vps54 in MNs, we have disrupted expression of the Vps54 ortholog in Drosophila and examined the impact on the larval neuromuscular junction (NMJ). Surprisingly, we show that both null mutants and MN-specific knockdown of Vps54 leads to NMJ overgrowth. Reduction of Vps54 partially disrupts localization of the t-SNARE, Syntaxin-16, to the TGN but has no visible impact on endosomal pools. MN-specific knockdown of Vps54 in MNs combined with overexpression of the small GTPases Rab5, Rab7, or Rab11 suppresses the Vps54 NMJ phenotype. Conversely, knockdown of Vps54 combined with overexpression of dominant negative Rab7 causes NMJ and behavioral abnormalities including a decrease in postsynaptic Dlg and GluRIIB levels without any effect on GluRIIA. Taken together, these data suggest that Vps54 controls larval MN axon development and postsynaptic density composition through a mechanism that requires Rab7.
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Affiliation(s)
- Prajal H Patel
- Department of Biological Sciences, University of Denver, Denver, CO 80210, USA
| | - Emily C Wilkinson
- Department of Biological Sciences, University of Denver, Denver, CO 80210, USA
| | - Emily L Starke
- Department of Biological Sciences, University of Denver, Denver, CO 80210, USA
| | - Malea R McGimsey
- Department of Biological Sciences, University of Denver, Denver, CO 80210, USA
| | - J Todd Blankenship
- Department of Biological Sciences, University of Denver, Denver, CO 80210, USA
- Molecular and Cellular Biophysics Program, University of Denver, Denver, CO 80210, USA
| | - Scott A Barbee
- Department of Biological Sciences, University of Denver, Denver, CO 80210, USA
- Molecular and Cellular Biophysics Program, University of Denver, Denver, CO 80210, USA
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18
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Eisemann TJ, Allen F, Lau K, Shimamura GR, Jeffrey PD, Hughson FM. The Sec1/Munc18 protein Vps45 holds the Qa-SNARE Tlg2 in an open conformation. eLife 2020; 9:e60724. [PMID: 32804076 PMCID: PMC7470827 DOI: 10.7554/elife.60724] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 08/15/2020] [Indexed: 01/17/2023] Open
Abstract
Fusion of intracellular trafficking vesicles is mediated by the assembly of SNARE proteins into membrane-bridging complexes. SNARE-mediated membrane fusion requires Sec1/Munc18-family (SM) proteins, SNARE chaperones that can function as templates to catalyze SNARE complex assembly. Paradoxically, the SM protein Munc18-1 traps the Qa-SNARE protein syntaxin-1 in an autoinhibited closed conformation. Here we present the structure of a second SM-Qa-SNARE complex, Vps45-Tlg2. Strikingly, Vps45 holds Tlg2 in an open conformation, with its SNARE motif disengaged from its Habc domain and its linker region unfolded. The domain 3a helical hairpin of Vps45 is unfurled, exposing the presumptive R-SNARE binding site to allow template complex formation. Although Tlg2 has a pronounced tendency to form homo-tetramers, Vps45 can rescue Tlg2 tetramers into stoichiometric Vps45-Tlg2 complexes. Our findings demonstrate that SM proteins can engage Qa-SNAREs using at least two different modes, one in which the SNARE is closed and one in which it is open.
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Affiliation(s)
- Travis J Eisemann
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Frederick Allen
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | - Kelly Lau
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
| | | | - Philip D Jeffrey
- Department of Molecular Biology, Princeton UniversityPrincetonUnited States
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19
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On the discovery of an endomembrane compartment in plants. Proc Natl Acad Sci U S A 2020; 117:10623-10624. [PMID: 32376631 DOI: 10.1073/pnas.2006766117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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20
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MTV proteins unveil ER- and microtubule-associated compartments in the plant vacuolar trafficking pathway. Proc Natl Acad Sci U S A 2020; 117:9884-9895. [PMID: 32321832 DOI: 10.1073/pnas.1919820117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The factors and mechanisms involved in vacuolar transport in plants, and in particular those directing vesicles to their target endomembrane compartment, remain largely unknown. To identify components of the vacuolar trafficking machinery, we searched for Arabidopsis modified transport to the vacuole (mtv) mutants that abnormally secrete the synthetic vacuolar cargo VAC2. We report here on the identification of 17 mtv mutations, corresponding to mutant alleles of MTV2/VSR4, MTV3/PTEN2A MTV7/EREL1, MTV8/ARFC1, MTV9/PUF2, MTV10/VPS3, MTV11/VPS15, MTV12/GRV2, MTV14/GFS10, MTV15/BET11, MTV16/VPS51, MTV17/VPS54, and MTV18/VSR1 Eight of the MTV proteins localize at the interface between the trans-Golgi network (TGN) and the multivesicular bodies (MVBs), supporting that the trafficking step between these compartments is essential for segregating vacuolar proteins from those destined for secretion. Importantly, the GARP tethering complex subunits MTV16/VPS51 and MTV17/VPS54 were found at endoplasmic reticulum (ER)- and microtubule-associated compartments (EMACs). Moreover, MTV16/VPS51 interacts with the motor domain of kinesins, suggesting that, in addition to tethering vesicles, the GARP complex may regulate the motors that transport them. Our findings unveil a previously uncharacterized compartment of the plant vacuolar trafficking pathway and support a role for microtubules and kinesins in GARP-dependent transport of soluble vacuolar cargo in plants.
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21
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Ilyas M, Efthymiou S, Salpietro V, Noureen N, Zafar F, Rauf S, Mir A, Houlden H. Novel variants underlying autosomal recessive intellectual disability in Pakistani consanguineous families. BMC MEDICAL GENETICS 2020; 21:59. [PMID: 32209057 PMCID: PMC7092478 DOI: 10.1186/s12881-020-00998-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/16/2020] [Indexed: 12/24/2022]
Abstract
Background Intellectual disability (ID) is both a clinically diverse and genetically heterogeneous group of disorder, with an onset of cognitive impairment before the age of 18 years. ID is characterized by significant limitations in intellectual functioning and adaptive behaviour. The identification of genetic variants causing ID and neurodevelopmental disorders using whole-exome sequencing (WES) has proven to be successful. So far more than 1222 primary and 1127 candidate genes are associated with ID. Methods To determine pathogenic variants causative of ID in three unrelated consanguineous Pakistani families, we used a combination of WES, homozygosity-by-descent mapping, de-deoxy sequencing and bioinformatics analysis. Results Rare pathogenic single nucleotide variants identified by WES which passed our filtering strategy were confirmed by traditional Sanger sequencing and segregation analysis. Novel and deleterious variants in VPS53, GLB1, and MLC1, genes previously associated with variable neurodevelopmental anomalies, were found to segregate with the disease in the three families. Conclusions This study expands our knowledge on the molecular basis of ID as well as the clinical heterogeneity associated to different rare genetic causes of neurodevelopmental disorders. This genetic study could also provide additional knowledge to help genetic assessment as well as clinical and social management of ID in Pakistani families.
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Affiliation(s)
- Muhammad Ilyas
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan
| | - Stephanie Efthymiou
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Vincenzo Salpietro
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Nuzhat Noureen
- Department of Pediatric Neurology, Children's Hospital and Institute of Child Health, Multan, 60000, Pakistan
| | - Faisal Zafar
- Department of Pediatric Neurology, Children's Hospital and Institute of Child Health, Multan, 60000, Pakistan
| | - Sobiah Rauf
- National Center for Bioinformatics, Quaid-i-Azam University, Islamabad, Pakistan
| | - Asif Mir
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, 44000, Pakistan.
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
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22
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Topalidou I, Cattin-Ortolá J, Hummer B, Asensio CS, Ailion M. EIPR1 controls dense-core vesicle cargo retention and EARP complex localization in insulin-secreting cells. Mol Biol Cell 2019; 31:59-79. [PMID: 31721635 PMCID: PMC6938272 DOI: 10.1091/mbc.e18-07-0469] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Dense-core vesicles (DCVs) are secretory vesicles found in neurons and endocrine cells. DCVs package and release cargoes including neuropeptides, biogenic amines, and peptide hormones. We recently identified the endosome-associated recycling protein (EARP) complex and the EARP-interacting-protein EIPR-1 as proteins important for controlling levels of DCV cargoes in Caenorhabditis elegans neurons. Here we determine the role of mammalian EIPR1 in insulinoma cells. We find that in Eipr1 KO cells, there is reduced insulin secretion, and mature DCV cargoes such as insulin and carboxypeptidase E (CPE) accumulate near the trans-Golgi network and are not retained in mature DCVs in the cell periphery. In addition, we find that EIPR1 is required for the stability of the EARP complex subunits and for the localization of EARP and its association with membranes, but EIPR1 does not affect localization or function of the related Golgi-associated retrograde protein (GARP) complex. EARP is localized to two distinct compartments related to its function: an endosomal compartment and a DCV biogenesis-related compartment. We propose that EIPR1 functions with EARP to control both endocytic recycling and DCV maturation.
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Affiliation(s)
- Irini Topalidou
- Department of Biochemistry, University of Washington, Seattle, WA 98195
| | | | - Blake Hummer
- Department of Biological Sciences, University of Denver, Denver, CO 80210
| | - Cedric S Asensio
- Department of Biological Sciences, University of Denver, Denver, CO 80210
| | - Michael Ailion
- Department of Biochemistry, University of Washington, Seattle, WA 98195
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23
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Santos SM, Hartman JL. A yeast phenomic model for the influence of Warburg metabolism on genetic buffering of doxorubicin. Cancer Metab 2019; 7:9. [PMID: 31660150 PMCID: PMC6806529 DOI: 10.1186/s40170-019-0201-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 09/03/2019] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The influence of the Warburg phenomenon on chemotherapy response is unknown. Saccharomyces cerevisiae mimics the Warburg effect, repressing respiration in the presence of adequate glucose. Yeast phenomic experiments were conducted to assess potential influences of Warburg metabolism on gene-drug interaction underlying the cellular response to doxorubicin. Homologous genes from yeast phenomic and cancer pharmacogenomics data were analyzed to infer evolutionary conservation of gene-drug interaction and predict therapeutic relevance. METHODS Cell proliferation phenotypes (CPPs) of the yeast gene knockout/knockdown library were measured by quantitative high-throughput cell array phenotyping (Q-HTCP), treating with escalating doxorubicin concentrations under conditions of respiratory or glycolytic metabolism. Doxorubicin-gene interaction was quantified by departure of CPPs observed for the doxorubicin-treated mutant strain from that expected based on an interaction model. Recursive expectation-maximization clustering (REMc) and Gene Ontology (GO)-based analyses of interactions identified functional biological modules that differentially buffer or promote doxorubicin cytotoxicity with respect to Warburg metabolism. Yeast phenomic and cancer pharmacogenomics data were integrated to predict differential gene expression causally influencing doxorubicin anti-tumor efficacy. RESULTS Yeast compromised for genes functioning in chromatin organization, and several other cellular processes are more resistant to doxorubicin under glycolytic conditions. Thus, the Warburg transition appears to alleviate requirements for cellular functions that buffer doxorubicin cytotoxicity in a respiratory context. We analyzed human homologs of yeast genes exhibiting gene-doxorubicin interaction in cancer pharmacogenomics data to predict causality for differential gene expression associated with doxorubicin cytotoxicity in cancer cells. This analysis suggested conserved cellular responses to doxorubicin due to influences of homologous recombination, sphingolipid homeostasis, telomere tethering at nuclear periphery, actin cortical patch localization, and other gene functions. CONCLUSIONS Warburg status alters the genetic network required for yeast to buffer doxorubicin toxicity. Integration of yeast phenomic and cancer pharmacogenomics data suggests evolutionary conservation of gene-drug interaction networks and provides a new experimental approach to model their influence on chemotherapy response. Thus, yeast phenomic models could aid the development of precision oncology algorithms to predict efficacious cytotoxic drugs for cancer, based on genetic and metabolic profiles of individual tumors.
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Affiliation(s)
- Sean M. Santos
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL USA
| | - John L. Hartman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL USA
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24
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Ma M, Burd CG. Retrograde trafficking and plasma membrane recycling pathways of the budding yeast Saccharomyces cerevisiae. Traffic 2019; 21:45-59. [PMID: 31471931 DOI: 10.1111/tra.12693] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 08/23/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023]
Abstract
The endosomal system functions as a network of protein and lipid sorting stations that receives molecules from endocytic and secretory pathways and directs them to the lysosome for degradation, or exports them from the endosome via retrograde trafficking or plasma membrane recycling pathways. Retrograde trafficking pathways describe endosome-to-Golgi transport while plasma membrane recycling pathways describe trafficking routes that return endocytosed molecules to the plasma membrane. These pathways are crucial for lysosome biogenesis, nutrient acquisition and homeostasis and for the physiological functions of many types of specialized cells. Retrograde and recycling sorting machineries of eukaryotic cells were identified chiefly through genetic screens using the budding yeast Saccharomyces cerevisiae system and discovered to be highly conserved in structures and functions. In this review, we discuss advances regarding retrograde trafficking and recycling pathways, including new discoveries that challenge existing ideas about the organization of the endosomal system, as well as how these pathways intersect with cellular homeostasis pathways.
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Affiliation(s)
- Mengxiao Ma
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut
| | - Christopher G Burd
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut
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25
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Uwineza A, Caberg JH, Hitayezu J, Wenric S, Mutesa L, Vial Y, Drunat S, Passemard S, Verloes A, El Ghouzzi V, Bours V. VPS51 biallelic variants cause microcephaly with brain malformations: A confirmatory report. Eur J Med Genet 2019; 62:103704. [PMID: 31207318 DOI: 10.1016/j.ejmg.2019.103704] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 06/05/2019] [Accepted: 06/13/2019] [Indexed: 12/18/2022]
Abstract
Whole exome sequencing undertaken in two siblings with delayed psychomotor development, absent speech, severe intellectual disability and postnatal microcephaly, with brain malformations consisting of cerebellar atrophy in the eldest affected and hypoplastic corpus callosum in the younger sister; revealed a homozygous intragenic deletion in VPS51, which encodes the vacuolar protein sorting-associated protein, one the four subunits of the Golgi-associated retrograde protein (GARP) and endosome-associated recycling protein (EARP) complexes that promotes the fusion of endosome-derived vesicles with the trans-Golgi network (GARP) and recycling endosomes (EARP). This observation supports a pathogenic effect of VPS51 variants, which has only been reported previously once, in a single child with microcephaly. It confirms the key role of membrane trafficking in normal brain development and homeostasis.
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Affiliation(s)
- Annette Uwineza
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda.
| | - Jean-Hubert Caberg
- Center for Human Genetics, Centre Hospitalier Universitaire, University of Liege, Liege, Belgium
| | - Janvier Hitayezu
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Stephane Wenric
- GIGA-Research, Human Genetics Unit, University of Liege, Liege, Belgium
| | - Leon Mutesa
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Yoann Vial
- Department of Genetics, AP HP - Robert Debré University Hospital, Paris, France; PROTECT, INSERM UMR1141, Université de Paris, Paris, France
| | - Séverine Drunat
- Department of Genetics, AP HP - Robert Debré University Hospital, Paris, France; PROTECT, INSERM UMR1141, Université de Paris, Paris, France
| | - Sandrine Passemard
- Department of Genetics, AP HP - Robert Debré University Hospital, Paris, France; PROTECT, INSERM UMR1141, Université de Paris, Paris, France
| | - Alain Verloes
- Department of Genetics, AP HP - Robert Debré University Hospital, Paris, France; PROTECT, INSERM UMR1141, Université de Paris, Paris, France
| | | | - Vincent Bours
- Center for Human Genetics, Centre Hospitalier Universitaire, University of Liege, Liege, Belgium
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26
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Ungermann C, Kümmel D. Structure of membrane tethers and their role in fusion. Traffic 2019; 20:479-490. [DOI: 10.1111/tra.12655] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/26/2019] [Accepted: 05/03/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Christian Ungermann
- Biochemistry Section, Department of Biology/ChemistryUniversity of Osnabrück Osnabrück Germany
- Center for Cellular Nanoanalytics (CellNanOs)University of Osnabrück Osnabrück Germany
| | - Daniel Kümmel
- Biochemistry & Structural Biology Section, Institute of BiochemistryUniversity of Münster Münster Germany
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27
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Anderson NS, Barlowe C. Conserved juxtamembrane domains in the yeast golgin Coy1 drive assembly of a megadalton-sized complex and mediate binding to tethering and SNARE proteins. J Biol Chem 2019; 294:9690-9705. [PMID: 31073031 DOI: 10.1074/jbc.ra119.008107] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/26/2019] [Indexed: 12/13/2022] Open
Abstract
The architecture and organization of the Golgi complex depend on a family of coiled-coil proteins called golgins. Golgins are thought to form extended homodimers that are C-terminally anchored to Golgi membranes, whereas their N termini extend into the cytoplasm to initiate vesicle capture. Previously, we reported that the Saccharomyces cerevisiae golgin Coy1 contributes to intra-Golgi retrograde transport and binds to the conserved oligomeric Golgi (COG) complex and multiple retrograde Golgi Q-SNAREs (where SNARE is soluble NSF-attachment protein receptor). Here, using various engineered yeast strains, membrane protein extraction and fractionation methods, and in vitro binding assays, we mapped the Coy1 regions responsible for these activities. We also report that Coy1 assembles into a megadalton-size complex and that assembly of this complex depends on the most C-terminal coiled-coil and a conserved region between this coiled-coil and the transmembrane domain of Coy1. We found that this conserved region is necessary and sufficient for binding the SNARE protein Sed5 and the COG complex. Mutagenesis of conserved arginine residues within the C-terminal coiled-coil disrupted oligomerization, binding, and function of Coy1. Our findings indicate that the stable incorporation of Coy1 into a higher-order oligomer is required for its interactions and role in maintaining Golgi homeostasis. We propose that Coy1 assembles into a docking platform that directs COG-bound vesicles toward cognate SNAREs on the Golgi membrane.
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Affiliation(s)
- Nadine S Anderson
- From the Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755
| | - Charles Barlowe
- From the Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755
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28
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Gershlick DC, Ishida M, Jones JR, Bellomo A, Bonifacino JS, Everman DB. A neurodevelopmental disorder caused by mutations in the VPS51 subunit of the GARP and EARP complexes. Hum Mol Genet 2019; 28:1548-1560. [PMID: 30624672 PMCID: PMC6489419 DOI: 10.1093/hmg/ddy423] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 11/27/2018] [Accepted: 12/02/2018] [Indexed: 11/12/2022] Open
Abstract
Golgi-associated retrograde protein (GARP) and endosome-associated recycling protein (EARP) are related heterotetrameric complexes that associate with the cytosolic face of the trans-Golgi network and recycling endosomes, respectively. At these locations, GARP and EARP function to promote the fusion of endosome-derived transport carriers with their corresponding compartments. GARP and EARP share three subunits, VPS51, VPS52 and VPS53, and each has an additional complex-specific subunit, VPS54 or VPS50, respectively. The role of these complexes in human physiology, however, remains poorly understood. By exome sequencing, we have identified compound heterozygous mutations in the gene encoding the shared GARP/EARP subunit VPS51 in a 6-year-old patient with severe global developmental delay, microcephaly, hypotonia, epilepsy, cortical vision impairment, pontocerebellar abnormalities, failure to thrive, liver dysfunction, lower extremity edema and dysmorphic features. The mutation in one allele causes a frameshift that produces a longer but highly unstable protein that is degraded by the proteasome. In contrast, the other mutant allele produces a protein with a single amino acid substitution that is stable but assembles less efficiently with the other GARP/EARP subunits. Consequently, skin fibroblasts from the patient have reduced levels of fully assembled GARP and EARP complexes. Likely because of this deficiency, the patient's fibroblasts display altered distribution of the cation-independent mannose 6-phosphate receptor, which normally sorts acid hydrolases to lysosomes. Furthermore, a fraction of the patient's fibroblasts exhibits swelling of lysosomes. These findings thus identify a novel genetic locus for a neurodevelopmental disorder and highlight the critical importance of GARP/EARP function in cellular and organismal physiology.
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Affiliation(s)
- David C Gershlick
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Morié Ishida
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Juan S Bonifacino
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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29
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Shi Z, Chen S, Han X, Peng R, Luo J, Yang L, Zheng Y, Wang H. The rare mutation in the endosome-associated recycling protein gene VPS50 is associated with human neural tube defects. Mol Cytogenet 2019; 12:8. [PMID: 30828385 PMCID: PMC6381738 DOI: 10.1186/s13039-019-0421-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 02/04/2019] [Indexed: 12/22/2022] Open
Abstract
Background Tight control of endosome trafficking is essential for the generation of a normally patterned embryo. Recent studies have found that VPS50 is a key ingredient in EARP which is required for recycling of internalized TfRs to the cell surface and dense-core vesicle maturation. However, the role of VPS50 in embryogenesis and human physiology are poorly understood. Results We identified a rare missense heterozygous VPS50 mutation (p. Gly169Val) in NTDs by high-throughput sequencing. In vitro functional analysis demonstrated that the p. Gly169Val was a loss-of-function mutation, delaying transferrin recycling and altering its interaction with VPS53. Using WISH during zebrafish embryogenesis, we demonstrated that vps50 gene was expressed throughout the early embryo, especially in the head. Abnormal body axis phenotypes were observed in those vps50 knock-down zebrafishes. Further rescue study in zebrafish suggested that the mutation displayed loss-of-function effects comparing with wild-type VPS50. Conclusions These findings thus demonstrated that the functional mutations in VPS50 might contribute to neurodevelopmental disorder and highlighted the critical importance of VPS50 function in cellular and organismal physiology. Electronic supplementary material The online version of this article (10.1186/s13039-019-0421-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhiwen Shi
- 1Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Reproduction and Development, Fudan University, Shanghai, 200011 China.,2Key Laboratory of Reproduction Regulation of NPFPC, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200032 China
| | - Shuxia Chen
- 1Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Reproduction and Development, Fudan University, Shanghai, 200011 China.,2Key Laboratory of Reproduction Regulation of NPFPC, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200032 China
| | - Xiao Han
- 1Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Reproduction and Development, Fudan University, Shanghai, 200011 China.,2Key Laboratory of Reproduction Regulation of NPFPC, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200032 China
| | - Rui Peng
- 1Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Reproduction and Development, Fudan University, Shanghai, 200011 China.,2Key Laboratory of Reproduction Regulation of NPFPC, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200032 China
| | - Jin Luo
- 1Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Reproduction and Development, Fudan University, Shanghai, 200011 China.,2Key Laboratory of Reproduction Regulation of NPFPC, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200032 China
| | - Luming Yang
- 2Key Laboratory of Reproduction Regulation of NPFPC, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200032 China
| | - Yufang Zheng
- 2Key Laboratory of Reproduction Regulation of NPFPC, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200032 China.,1Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Reproduction and Development, Fudan University, Shanghai, 200011 China.,3Institute of Developmental Biology & Molecular Medicine, Fudan University, Shanghai, 200433 China
| | - Hongyan Wang
- 2Key Laboratory of Reproduction Regulation of NPFPC, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, 200032 China.,1Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Reproduction and Development, Fudan University, Shanghai, 200011 China.,4Children's Hospital and Institutes of Biomedical Sciences of Fudan University, 399 Wanyuan Road, Shanghai, 201102 China
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30
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Chen YT, Wang IH, Wang YH, Chiu WY, Hu JH, Chen WH, Lee FJS. Action of Arl1 GTPase and golgin Imh1 in Ypt6-independent retrograde transport from endosomes to the trans-Golgi network. Mol Biol Cell 2019; 30:1008-1019. [PMID: 30726160 PMCID: PMC6589904 DOI: 10.1091/mbc.e18-09-0579] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The Arf and Rab/Ypt GTPases coordinately regulate membrane traffic and organelle structure by regulating vesicle formation and fusion. Ample evidence has indicated that proteins in these two families may function in parallel or complementarily; however, the manner in which Arf and Rab/Ypt proteins perform interchangeable functions remains unclear. In this study, we report that a Golgi-localized Arf, Arl1, could suppress Ypt6 dysfunction via its effector golgin, Imh1, but not via the lipid flippase Drs2. Ypt6 is critical for the retrograde transport of vesicles from endosomes to the trans-Golgi network (TGN), and its mutation leads to severe protein mislocalization and growth defects. We first overexpress the components of the Arl3-Syt1-Arl1-Imh1 cascade and show that only Arl1 and Imh1 can restore endosome-to-TGN trafficking in ypt6-deleted cells. Interestingly, increased abundance of Arl1 or Imh1 restores localization of the tethering factor Golgi associated retrograde–protein (GARP) complex to the TGN in the absence of Ypt6. We further show that the N-terminal domain of Imh1 is critical for restoring GARP localization and endosome-to-TGN transport in ypt6-deleted cells. Together, our results reveal the mechanism by which Arl1-Imh1 facilitates the recruitment of GARP to the TGN and compensates for the endosome-to-TGN trafficking defects in dysfunctional Ypt6 conditions.
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Affiliation(s)
- Yan-Ting Chen
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - I-Hao Wang
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Yi-Hsun Wang
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Wan-Yun Chiu
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Jen-Hao Hu
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Wen-Hui Chen
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
| | - Fang-Jen S Lee
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan.,Department of Medical Research, National Taiwan University Hospital, Taipei 100, Taiwan.,Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei 10002, Taiwan
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31
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Eising S, Thiele L, Fröhlich F. A systematic approach to identify recycling endocytic cargo depending on the GARP complex. eLife 2019; 8:42837. [PMID: 30694181 PMCID: PMC6374077 DOI: 10.7554/elife.42837] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 01/29/2019] [Indexed: 12/14/2022] Open
Abstract
Proteins and lipids of the plasma membrane underlie constant remodeling via a combination of the secretory- and the endocytic pathway. In the yeast endocytic pathway, cargo is sorted for recycling to the plasma membrane or degradation in vacuoles. Previously we have shown a role for the GARP complex in sphingolipid sorting and homeostasis (Fröhlich et al. 2015). However, the majority of cargo sorted in a GARP dependent process remain largely unknown. Here we use auxin induced degradation of GARP combined with mass spectrometry based vacuolar proteomics and lipidomics to show that recycling of two specific groups of proteins, the amino-phospholipid flippases and cell wall synthesis proteins depends on a functional GARP complex. Our results suggest that mis-sorting of flippases and remodeling of the lipid composition are the first occurring defects in GARP mutants. Our assay can be adapted to systematically map cargo of the entire endocytic pathway.
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Affiliation(s)
- Sebastian Eising
- Department of Biology/Chemistry, Molecular Membrane Biology Group, University of Osnabrück, Osnabrück, Germany.,Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
| | - Lisa Thiele
- Department of Biology/Chemistry, Molecular Membrane Biology Group, University of Osnabrück, Osnabrück, Germany.,Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
| | - Florian Fröhlich
- Center of Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany
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32
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Ganesan S, Sosa Ponce ML, Tavassoli M, Shabits BN, Mahadeo M, Prenner EJ, Terebiznik MR, Zaremberg V. Metabolic control of cytosolic-facing pools of diacylglycerol in budding yeast. Traffic 2019; 20:226-245. [PMID: 30569465 DOI: 10.1111/tra.12632] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 12/18/2018] [Accepted: 12/18/2018] [Indexed: 12/12/2022]
Abstract
Diacylglycerol (DAG) is a key signaling lipid and intermediate in lipid metabolism. Our knowledge of DAG distribution and dynamics in cell membranes is limited. Using live-cell fluorescence microscopy we investigated the localization of yeast cytosolic-facing pools of DAG in response to conditions where lipid homeostasis and DAG levels were known to be altered. Two main pools were monitored over time using DAG sensors. One pool was associated with vacuolar membranes and the other localized to sites of polarized growth. Dynamic changes in DAG distribution were observed during resumption of growth from stationary phase, when DAG is used to support phospholipid synthesis for membrane proliferation. Vacuolar membranes experienced constant morphological changes displaying DAG enriched microdomains coexisting with liquid-disordered areas demarcated by Vph1. Formation of these domains was dependent on triacylglycerol (TAG) lipolysis. DAG domains and puncta were closely connected to lipid droplets. Lack of conversion of DAG to phosphatidate in growth conditions dependent on TAG mobilization, led to the accumulation of DAG in a vacuolar-associated compartment, impacting the polarized distribution of DAG at budding sites. DAG polarization was also regulated by phosphatidylserine synthesis/traffic and sphingolipid synthesis in the Golgi.
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Affiliation(s)
| | - Maria L Sosa Ponce
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Marjan Tavassoli
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Brittney N Shabits
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Mark Mahadeo
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Elmar J Prenner
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Mauricio R Terebiznik
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada.,Department of Cell and System Biology, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Vanina Zaremberg
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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33
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Wang K, Zhao S, Zhang Q, Yuan J, Liu J, Ding X, Song X, Lin J, Du R, Zhou Y, Sugimoto M, Chen W, Yuan B, Liu J, Yan Z, Liu B, Zhang Y, Li X, Niu Y, Long B, Shen Y, Zhang S, Abe K, Su J, Wu Z, Wu N, Liu P, Yang X. Whole-exome sequencing reveals known and novel variants in a cohort of intracranial vertebral-basilar artery dissection (IVAD). J Hum Genet 2018; 63:1119-1128. [PMID: 30115950 DOI: 10.1038/s10038-018-0496-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 07/09/2018] [Accepted: 07/20/2018] [Indexed: 01/25/2023]
Abstract
Intracranial vertebral-basilar artery dissection (IVAD) is an arterial disorder leading to life-threatening consequences. Genetic factors are known to be causative to certain syndromic forms of IVAD. However, systematic study of the molecular basis of sporadic and isolated IVAD is lacking. To identify genetic variants contributing to the etiology of IVAD, we enrolled a cohort of 44 unrelated cases with a clinical diagnosis of isolated IVAD and performed whole-exome sequencing (WES) for all the participants; a trio exome sequencing approach was used when samples from both parents were available. Four previously reported disease-causing heterozygous variants (three in COL3A1 and one in FBN1) and seven novel heterozygous variants in IVAD-related genes were identified. In addition, six variants in novel IVAD genes including two de novo heterozygous nonsynonymous variants (each in VPS52 and CDK18), two stop-gain variants (each in MYH9 and LYL1), and two heterozygous biallelic variants in TNXB were considered to be possibly contributing to the phenotype, with unknown significance according to the existing knowledge. A significantly higher mutational rate of IVAD candidate genes was observed in patients versus our in-house controls (P = 0.002) (DISCO study, http://www.discostudy.org/ , n = 2248). Our study provided a mutational landscape for patients with isolated IVAD.
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Affiliation(s)
- Kun Wang
- Department of Interventional Neuroradiology, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Sen Zhao
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China.,Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Qianqian Zhang
- Department of Interventional Neuroradiology, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jian Yuan
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Jiaqi Liu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China.,Department of Breast Surgical Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinghuan Ding
- Department of Interventional Neuroradiology, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xiaofei Song
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jiachen Lin
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Renqian Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yangzhong Zhou
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China.,Department of Internal Medicine, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Michihiko Sugimoto
- Technology and Development Team for Mammalian Cellular Dynamics, RIKEN BioResource Center, Tsukuba, Japan
| | - Weisheng Chen
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China.,Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Bo Yuan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jian Liu
- Department of Interventional Neuroradiology, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Zihui Yan
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China.,Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Bowen Liu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China.,Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yisen Zhang
- Department of Interventional Neuroradiology, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xiaoxin Li
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yuchen Niu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Bo Long
- Department of Central Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yiping Shen
- Division of Genetics and Genomics, Boston Childrens Hospital, Department of Neurology, Harvard Medical School, Boston, MA, USA.,Birth Defect Prevention Research Institute, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Shuyang Zhang
- Department of Cardiology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Kuniya Abe
- Technology and Development Team for Mammalian Cellular Dynamics, RIKEN BioResource Center, Tsukuba, Japan
| | - Jianzhong Su
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Zhihong Wu
- Department of Interventional Neuroradiology, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China.,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China
| | - Nan Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China. .,Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing, China. .,Department of Orthopedic Surgery, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China.
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Xinjian Yang
- Department of Interventional Neuroradiology, Beijing Neurosurgical Institute and Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
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34
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Wei J, Zhang YY, Luo J, Wang JQ, Zhou YX, Miao HH, Shi XJ, Qu YX, Xu J, Li BL, Song BL. The GARP Complex Is Involved in Intracellular Cholesterol Transport via Targeting NPC2 to Lysosomes. Cell Rep 2018; 19:2823-2835. [PMID: 28658628 DOI: 10.1016/j.celrep.2017.06.012] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 05/07/2017] [Accepted: 05/31/2017] [Indexed: 10/19/2022] Open
Abstract
Proper intracellular cholesterol trafficking is critical for cellular function. Two lysosome-resident proteins, NPC1 and NPC2, mediate the egress of low-density lipoprotein-derived cholesterol from lysosomes. However, other proteins involved in this process remain largely unknown. Through amphotericin B-based selection, we isolated two cholesterol transport-defective cell lines. Subsequent whole-transcriptome-sequencing analysis revealed two cell lines bearing the same mutation in the vacuolar protein sorting 53 (Vps53) gene. Depletion of VPS53 or other subunits of the Golgi-associated retrograde protein (GARP) complex impaired NPC2 sorting to lysosomes and caused cholesterol accumulation. GARP deficiency blocked the retrieval of the cation-independent mannose 6-phosphate receptor (CI-MPR) to the trans-Golgi network. Further, Vps54 mutant mice displayed reduced cellular NPC2 protein levels and increased cholesterol accumulation, underscoring the physiological role of the GARP complex in cholesterol transport. We conclude that the GARP complex contributes to intracellular cholesterol transport by targeting NPC2 to lysosomes in a CI-MPR-dependent manner.
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Affiliation(s)
- Jian Wei
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, the Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Ying-Yu Zhang
- The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jie Luo
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, the Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Ju-Qiong Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, the Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Yu-Xia Zhou
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, the Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Hong-Hua Miao
- The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiong-Jie Shi
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, the Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Yu-Xiu Qu
- The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jie Xu
- The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bo-Liang Li
- The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bao-Liang Song
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, the Institute for Advanced Studies, Wuhan University, Wuhan 430072, China.
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35
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Hernández-González M, Bravo-Plaza I, Pinar M, de los Ríos V, Arst HN, Peñalva MA. Endocytic recycling via the TGN underlies the polarized hyphal mode of life. PLoS Genet 2018; 14:e1007291. [PMID: 29608571 PMCID: PMC5880334 DOI: 10.1371/journal.pgen.1007291] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/06/2018] [Indexed: 12/13/2022] Open
Abstract
Intracellular traffic in Aspergillus nidulans hyphae must cope with the challenges that the high rates of apical extension (1μm/min) and the long intracellular distances (>100 μm) impose. Understanding the ways in which the hyphal tip cell coordinates traffic to meet these challenges is of basic importance, but is also of considerable applied interest, as fungal invasiveness of animals and plants depends critically upon maintaining these high rates of growth. Rapid apical extension requires localization of cell-wall-modifying enzymes to hyphal tips. By combining genetic blocks in different trafficking steps with multidimensional epifluorescence microscopy and quantitative image analyses we demonstrate that polarization of the essential chitin-synthase ChsB occurs by indirect endocytic recycling, involving delivery/exocytosis to apices followed by internalization by the sub-apical endocytic collar of actin patches and subsequent trafficking to TGN cisternae, where it accumulates for ~1 min before being re-delivered to the apex by a RAB11/TRAPPII-dependent pathway. Accordingly, ChsB is stranded at the TGN by Sec7 inactivation but re-polarizes to the apical dome if the block is bypassed by a mutation in geaAgea1 that restores growth in the absence of Sec7. That polarization is independent of RAB5, that ChsB predominates at apex-proximal cisternae, and that upon dynein impairment ChsB is stalled at the tips in an aggregated endosome indicate that endocytosed ChsB traffics to the TGN via sorting endosomes functionally located upstream of the RAB5 domain and that this step requires dynein-mediated basipetal transport. It also requires RAB6 and its effector GARP (Vps51/Vps52/Vps53/Vps54), whose composition we determined by MS/MS following affinity chromatography purification. Ablation of any GARP component diverts ChsB to vacuoles and impairs growth and morphology markedly, emphasizing the important physiological role played by this pathway that, we propose, is central to the hyphal mode of growth. Filamentous fungi form long tubular cells, called hyphae, which grow rapidly by apical extension, enabling these sessile organisms to explore substrates and facilitating tissue invasion in the case of pathogenic species. Because the shape of the hyphae is determined by an external cell wall, hyphal growth requires that cell-wall sculpting enzymes polarize to the tips. Endocytosis is essential for hyphal growth, and it was suspected that this results from its participation in a recycling pathway that takes up cell-wall enzymes from the plasma membrane and re-delivers them to the apex. Here we track the trafficking of a chitin synthase (a cell-wall modifying enzyme) to demonstrate that it is polarized by endocytic recycling. This chitin synthase is delivered by exocytosis to the apex, but diffuses away until being captured by a subapical collar of actin patches (sites of endocytosis) from where it reaches a sorting endosome before undergoing transport to the nearest trans-Golgi cisternae and incorporating into secretory vesicles that re-deliver the enzyme to the apex. Because impairing transit across this pathway compromises apical extension markedly and results in severe morphological defects, the pathway could be manipulated to prevent fungal pathogenicity of plants and humans, an enormous burden on human welfare.
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Affiliation(s)
- Miguel Hernández-González
- Department of Cellular and Molecular Biology and Intradepartmental WhiteBiotech Unit, Centro de Investigaciones Biológicas del Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, Madrid, Spain
| | - Ignacio Bravo-Plaza
- Department of Cellular and Molecular Biology and Intradepartmental WhiteBiotech Unit, Centro de Investigaciones Biológicas del Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, Madrid, Spain
| | - Mario Pinar
- Department of Cellular and Molecular Biology and Intradepartmental WhiteBiotech Unit, Centro de Investigaciones Biológicas del Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, Madrid, Spain
| | - Vivian de los Ríos
- Proteomics Facility, Centro de Investigaciones Biológicas del Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, Madrid, Spain
| | - Herbert N. Arst
- Section of Microbiology, Imperial College London, Flowers Building, Armstrong Road, London, United Kingdom
| | - Miguel A. Peñalva
- Department of Cellular and Molecular Biology and Intradepartmental WhiteBiotech Unit, Centro de Investigaciones Biológicas del Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu, Madrid, Spain
- * E-mail:
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Hovsepian J, Albanèse V, Becuwe M, Ivashov V, Teis D, Léon S. The yeast arrestin-related protein Bul1 is a novel actor of glucose-induced endocytosis. Mol Biol Cell 2018. [PMID: 29514933 PMCID: PMC5921569 DOI: 10.1091/mbc.e17-07-0466] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Yeast cells have a remarkable ability to adapt to nutritional changes in their environment. During adaptation, nutrient-signaling pathways drive the selective endocytosis of nutrient transporters present at the cell surface. A current challenge is to understand the mechanistic basis of this regulation. Transporter endocytosis is triggered by their ubiquitylation, which involves the ubiquitin ligase Rsp5 and its adaptors of the arrestin-related family (ART). This step is highly regulated by nutrient availability. For instance, the monocarboxylate transporter Jen1 is ubiquitylated, endocytosed, and degraded upon exposure to glucose. The ART protein Rod1 is required for this overall process; yet Rod1 rather controls Jen1 trafficking later in the endocytic pathway and is almost dispensable for Jen1 internalization. Thus, how glucose triggers Jen1 internalization remains unclear. We report that another ART named Bul1, but not its paralogue Bul2, contributes to Jen1 internalization. Bul1 responds to glucose availability, and preferentially acts at the plasma membrane for Jen1 internalization. Thus, multiple ARTs can act sequentially along the endocytic pathway to control transporter homeostasis. Moreover, Bul1 is in charge of Jen1 endocytosis after cycloheximide treatment, suggesting that the functional redundancy of ARTs may be explained by their ability to interact with multiple cargoes in various conditions.
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Affiliation(s)
- Junie Hovsepian
- Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75205 Paris, France
| | - Véronique Albanèse
- Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75205 Paris, France
| | - Michel Becuwe
- Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75205 Paris, France
| | - Vasyl Ivashov
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - David Teis
- Division of Cell Biology, Biocenter, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Sébastien Léon
- Institut Jacques Monod, UMR 7592 Centre National de la Recherche Scientifique/Université Paris-Diderot, Sorbonne Paris Cité, 75205 Paris, France
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Dharwada ST, Dalton LE, Bean BDM, Padmanabhan N, Choi C, Schluter C, Davey M, Conibear E. The chaperone Chs7 forms a stable complex with Chs3 and promotes its activity at the cell surface. Traffic 2018; 19:285-295. [DOI: 10.1111/tra.12553] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 01/29/2018] [Accepted: 01/31/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Sai T. Dharwada
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute; University of British Columbia; Vancouver Canada
| | - Lauren E. Dalton
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute; University of British Columbia; Vancouver Canada
| | - Björn D. M. Bean
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute; University of British Columbia; Vancouver Canada
| | - Nirmala Padmanabhan
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute; University of British Columbia; Vancouver Canada
| | - Catherine Choi
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute; University of British Columbia; Vancouver Canada
| | - Cayetana Schluter
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute; University of British Columbia; Vancouver Canada
| | - Michael Davey
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute; University of British Columbia; Vancouver Canada
| | - Elizabeth Conibear
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute; University of British Columbia; Vancouver Canada
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Navarro Negredo P, Edgar JR, Manna PT, Antrobus R, Robinson MS. The WDR11 complex facilitates the tethering of AP-1-derived vesicles. Nat Commun 2018; 9:596. [PMID: 29426865 PMCID: PMC5807400 DOI: 10.1038/s41467-018-02919-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/02/2018] [Indexed: 12/14/2022] Open
Abstract
Vesicluar transport of proteins from endosomes to the trans-Golgi network (TGN) is an essential cellular pathway, but much of its machinery is still unknown. A screen for genes involved in endosome-to-TGN trafficking produced two hits, the adaptor protein-1 (AP-1 complex), which facilitates vesicle budding, and WDR11. Here we demonstrate that WDR11 forms a stable complex with two other proteins, which localises to the TGN region and does not appear to be associated with AP-1, suggesting it may act downstream from budding. In a vesicle tethering assay, capture of vesicles by golgin-245 was substantially reduced in WDR11-knockout cells. Moreover, structured illumination microscopy and relocation assays indicate that the WDR11 complex is initially recruited onto vesicles rather than the TGN, where it may in turn recruit the golgin binding partner TBC1D23. We propose that the complex acts together with TBC1D23 to facilitate the golgin-mediated capture of vesicles that were generated using AP-1. Trafficking from endosomes to the trans-Golgi network requires recognition of vesicle tethers during membrane docking. Here, the authors identify a complex localised to AP-1 generated vesicles containing WDR11, C17orf75 and FAM91A, which together with TBC1D23 facilitates vesicle capture on Golgi membranes
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Affiliation(s)
- Paloma Navarro Negredo
- Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - James R Edgar
- Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - Paul T Manna
- Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - Robin Antrobus
- Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK
| | - Margaret S Robinson
- Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY, UK.
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Herman E, Siegesmund MA, Bottery MJ, van Aerle R, Shather MM, Caler E, Dacks JB, van der Giezen M. Membrane Trafficking Modulation during Entamoeba Encystation. Sci Rep 2017; 7:12854. [PMID: 28993644 PMCID: PMC5634486 DOI: 10.1038/s41598-017-12875-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 09/11/2017] [Indexed: 12/15/2022] Open
Abstract
Entamoeba histolytica is an intestinal parasite that infects 50-100 million people and causes up to 55,000 deaths annually. The transmissive form of E. histolytica is the cyst, with a single infected individual passing up to 45 million cysts per day, making cyst production an attractive target for infection control. Lectins and chitin are secreted to form the cyst wall, although little is known about the underlying membrane trafficking processes supporting encystation. As E. histolytica does not readily form cysts in vitro, we assessed membrane trafficking gene expression during encystation in the closely related model Entamoeba invadens. Genes involved in secretion are up-regulated during cyst formation, as are some trans-Golgi network-to-endosome trafficking genes. Furthermore, endocytic and general trafficking genes are up-regulated in the mature cyst, potentially preserved as mRNA in preparation for excystation. Two divergent dynamin-related proteins found in Entamoeba are predominantly expressed during cyst formation. Phylogenetic analyses indicate that they are paralogous to, but quite distinct from, classical dynamins found in human, suggesting that they may be potential drug targets to block encystation. The membrane-trafficking machinery is clearly regulated during encystation, providing an additional facet to understanding this crucial parasitic process.
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Affiliation(s)
- Emily Herman
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, T6G 2H7, Edmonton, Alberta, Canada
| | | | - Michael J Bottery
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Ronny van Aerle
- Biosciences, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
- Centre for Environment, Fisheries, and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, Dorset, DT4 8UB, UK
| | | | - Elisabet Caler
- J. Craig Venter Institute, 9714 Medical Center Drive, Rockville, MD, 20850, USA
- National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), 6701, Rockledge Drive, Room 9144, Bethesda, MD, 20892-7950, USA
| | - Joel B Dacks
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, T6G 2H7, Edmonton, Alberta, Canada.
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VPS52 induces apoptosis via cathepsin D in gastric cancer. J Mol Med (Berl) 2017; 95:1107-1116. [PMID: 28791438 DOI: 10.1007/s00109-017-1572-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/17/2017] [Accepted: 07/28/2017] [Indexed: 02/07/2023]
Abstract
Vacuolar protein sorting (VPS) genes encode a class of proteins involved in vesicular trafficking. Growing evidence suggests that VPS proteins play roles in tumor biology. Vacuolar protein sorting 52 (VPS52) is involved in retrograde transport of endosomes, and its roles in cancers have not been explored. This study investigated the genetic alterations, protein changes, biological role, and molecular mechanism of VPS52 in gastric cancer. Loss of heterozygosity of VPS52 was detected in 52.9% (9/17) of gastric cancer samples. Twenty-five percent (5/20) gastric cancer samples contained somatic stop-gain mutation of VPS52, two of which also had simultaneous loss of heterozygosity. Lack of VPS52 protein expression in gastric cancer tissue was found compared with pericancerous tissue and was significantly correlated with more advanced TNM staging and shorter 3-year overall survival. Overexpression of VPS52 significantly reduced viability and increased apoptosis in gastric cancer cells in vitro and reduced tumor volume and tumor weight in xenograft model in vivo. Activation of the cathepsin D/Bax/cytochrome C/caspase 9/caspase 3 pathway was detected in gastric cancer cells overexpressing VPS52. Collectively, VPS52 is a tumor suppressor gene in gastric cancer and could be used as a biomarker. VPS52 adenovirus could be a novel anti-tumor reagent for future gene therapy. KEY MESSAGES Loss of heterozygosity and stop-gain mutation of VPS52 were found in gastric cancer. Negative expression of VPS52 significantly correlated with poor prognosis. VPS52 inhibited viability and induced apoptosis of gastric cancer cells in vitro. VPS52 reduced tumor volume and tumor weight in vivo. VPS52 activated the apoptotic pathway through cathepsin D in gastric cancer cells.
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41
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Dalton LE, Bean BDM, Davey M, Conibear E. Quantitative high-content imaging identifies novel regulators of Neo1 trafficking at endosomes. Mol Biol Cell 2017; 28:1539-1550. [PMID: 28404745 PMCID: PMC5449152 DOI: 10.1091/mbc.e16-11-0772] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 04/05/2017] [Accepted: 04/06/2017] [Indexed: 12/21/2022] Open
Abstract
P4-ATPases are a family of putative phospholipid flippases that regulate lipid membrane asymmetry, which is important for vesicle formation. Two yeast flippases, Drs2 and Neo1, have nonredundant functions in the recycling of the synaptobrevin-like v-SNARE Snc1 from early endosomes. Drs2 activity is needed to form vesicles and regulate its own trafficking, suggesting that flippase activity and localization are linked. However, the role of Neo1 in endosomal recycling is not well characterized. To identify novel regulators of Neo1 trafficking and activity at endosomes, we first identified mutants with impaired recycling of a Snc1-based reporter and subsequently used high-content microscopy to classify these mutants based on the localization of Neo1 or its binding partners, Mon2 and Dop1. This analysis identified a role for Arl1 in stabilizing the Mon2/Dop1 complex and uncovered a new function for Vps13 in early endosome recycling and Neo1 localization. We further showed that the cargo-selective sorting nexin Snx3 is required for Neo1 trafficking and identified an Snx3 sorting motif in the Neo1 N-terminus. Of importance, the Snx3-dependent sorting of Neo1 was required for the correct sorting of another Snx3 cargo protein, suggesting that the incorporation of Neo1 into recycling tubules may influence their formation.
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Affiliation(s)
- Lauren E Dalton
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Björn D M Bean
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Michael Davey
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Elizabeth Conibear
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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42
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Siddiqah IM, Manandhar SP, Cocca SM, Hsueh T, Cervantes V, Gharakhanian E. Yeast ENV9 encodes a conserved lipid droplet (LD) short-chain dehydrogenase involved in LD morphology. Curr Genet 2017; 63:1053-1072. [PMID: 28540421 DOI: 10.1007/s00294-017-0702-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 04/24/2017] [Accepted: 05/05/2017] [Indexed: 12/31/2022]
Abstract
Lipid droplets (LDs) have emerged as dynamic and interactive organelles with important roles in lipid metabolism and membrane biogenesis. Here, we report that Saccharomyces cerevisiae Env9 is a novel conserved oxidoreductase involved in LD morphology. Microscopic and biochemical studies confirm localization of tagged Env9 to LDs and implicate its C-terminal hydrophobic domain (aa241-265) in its membrane association and stability. Confocal studies reveal a role for Env9 in LD morphology. Env9 positively affects both formation of large LDs upon overexpression and LD proliferation under poor carbon source. In silico bioinformatic and modeling approaches establish that ENV9 is a widely conserved member of the short-chain dehydrogenase (SDR) superfamily. Bayesian phylogenetic studies strongly support ENV9 as an ortholog of human SDR retinol dehydrogenase 12 (RDH12). Dehydrogenase activity of Env9 was confirmed by in vitro oxidoreductase assays. RDH12 mutations have been linked to Leber Congenital Amaurosis. Similar site-directed point mutations in the predicted Env9 oxidoreductase active site (N146L) or cofactor-binding site (G23-24A) abolished its reductase activity in vitro, consistent with those reported in other retinol dehydrogenases. The same residues were essential for affecting LD size and number in vivo. Taken together, our results implicate oxidoreductase activity of Env9 in its cellular role in LD morphology.
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Affiliation(s)
- Ikha M Siddiqah
- Department of Biological Sciences, California State University Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840, USA
| | - Surya P Manandhar
- Department of Biological Sciences, California State University Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840, USA
| | - Stephanie M Cocca
- Department of Biological Sciences, California State University Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840, USA
| | - Teli Hsueh
- Department of Biological Sciences, California State University Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840, USA
| | - Vanessa Cervantes
- Department of Biological Sciences, California State University Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840, USA
| | - Editte Gharakhanian
- Department of Biological Sciences, California State University Long Beach, 1250 Bellflower Blvd., Long Beach, CA, 90840, USA.
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RNF41 interacts with the VPS52 subunit of the GARP and EARP complexes. PLoS One 2017; 12:e0178132. [PMID: 28542518 PMCID: PMC5439944 DOI: 10.1371/journal.pone.0178132] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/12/2017] [Indexed: 11/19/2022] Open
Abstract
RNF41 (Ring Finger Protein 41) is an E3 ubiquitin ligase involved in the intracellular sorting and function of a diverse set of substrates. Next to BRUCE and Parkin, RNF41 can directly ubiquitinate ErbB3, IL-3, EPO and RARα receptors or downstream signaling molecules such as Myd88, TBK1 and USP8. In this way it can regulate receptor signaling and routing. To further elucidate the molecular mechanism behind the role of RNF41 in intracellular transport we performed an Array MAPPIT (Mammalian Protein-Protein Interaction Trap) screen using an extensive set of proteins derived from the human ORFeome collection. This paper describes the identification of VPS52, a subunit of the GARP (Golgi-Associated Retrograde Protein) and the EARP (Endosome-Associated Recycling Protein) complexes, as a novel interaction partner of RNF41. Through interaction via their coiled coil domains, RNF41 ubiquitinates and relocates VPS52 away from VPS53, a common subunit of the GARP and EARP complexes, towards RNF41 bodies.
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44
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Romanov N, Hollenstein DM, Janschitz M, Ammerer G, Anrather D, Reiter W. Identifying protein kinase-specific effectors of the osmostress response in yeast. Sci Signal 2017; 10:10/469/eaag2435. [PMID: 28270554 DOI: 10.1126/scisignal.aag2435] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The budding yeast Saccharomyces cerevisiae reacts to increased external osmolarity by modifying many cellular processes. Adaptive signaling relies primarily on the high-osmolarity glycerol (HOG) pathway, which is closely related to the mammalian p38 mitogen-activated protein kinase (MAPK) pathway in core architecture. To identify target proteins of the MAPK Hog1, we designed a mass spectrometry-based high-throughput experiment to measure the impact of Hog1 activation or inhibition on the Scerevisiae phosphoproteome. In addition, we analyzed how deletion of RCK2, which encodes a known effector protein kinase target of Hog1, modulated osmotic stress-induced phosphorylation. Our results not only provide an overview of the diversity of cellular functions that are directly and indirectly affected by the activity of the HOG pathway but also enabled an assessment of the Hog1-independent events that occur under osmotic stress conditions. We extended the number of putative Hog1 direct targets by analyzing the modulation of motifs consisting of serine or threonine followed by a proline (S/T-P motif) and subsequently validated these with an in vivo interaction assay. Rck2 appears to act as a central hub for many Hog1-mediated secondary phosphorylation events. This study clarifies many of the direct and indirect effects of HOG signaling and its stress-adaptive functions.
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Affiliation(s)
- Natalie Romanov
- Department for Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - David Maria Hollenstein
- Department for Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Marion Janschitz
- Department for Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Gustav Ammerer
- Department for Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Dorothea Anrather
- Mass Spectrometry Facility, Max F. Perutz Laboratories, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Wolfgang Reiter
- Department for Biochemistry, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria.
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Rodriguez PA, Escudero-Martinez C, Bos JIB. An Aphid Effector Targets Trafficking Protein VPS52 in a Host-Specific Manner to Promote Virulence. PLANT PHYSIOLOGY 2017; 173:1892-1903. [PMID: 28100451 PMCID: PMC5338666 DOI: 10.1104/pp.16.01458] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 01/16/2017] [Indexed: 05/20/2023]
Abstract
Plant- and animal-feeding insects secrete saliva inside their hosts, containing effectors, which may promote nutrient release and suppress immunity. Although for plant pathogenic microbes it is well established that effectors target host proteins to modulate host cell processes and promote disease, the host cell targets of herbivorous insects remain elusive. Here, we show that the existing plant pathogenic microbe effector paradigm can be extended to herbivorous insects in that effector-target interactions inside host cells modify critical host processes to promote plant susceptibility. We showed that the effector Mp1 from Myzus persicae associates with the host Vacuolar Protein Sorting Associated Protein52 (VPS52). Using natural variants, we provide a strong link between effector virulence activity and association with VPS52, and show that the association is highly specific to Mpersicae-host interactions. Also, coexpression of Mp1, but not Mp1-like variants, specifically with host VPS52s resulted in effector relocalization to vesicle-like structures that associate with prevacuolar compartments. We show that high VPS52 levels negatively impact virulence, and that aphids are able to reduce VPS52 levels during infestation, indicating that VPS52 is an important virulence target. Our work is an important step forward in understanding, at the molecular level, how a major agricultural pest promotes susceptibility during infestation of crop plants. We give evidence that an herbivorous insect employs effectors that interact with host proteins as part of an effective virulence strategy, and that these effectors likely function in a species-specific manner.
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Affiliation(s)
- Patricia A Rodriguez
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom (P.A.R., C.E.-M., J.I.B.B.); and
- Cell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom (C.E.-M., J.I.B.B.)
| | - Carmen Escudero-Martinez
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom (P.A.R., C.E.-M., J.I.B.B.); and
- Cell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom (C.E.-M., J.I.B.B.)
| | - Jorunn I B Bos
- Division of Plant Sciences, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom (P.A.R., C.E.-M., J.I.B.B.); and
- Cell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom (C.E.-M., J.I.B.B.)
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46
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Becker B, Schnöder T, Schmitt MJ. Yeast Reporter Assay to Identify Cellular Components of Ricin Toxin A Chain Trafficking. Toxins (Basel) 2016; 8:toxins8120366. [PMID: 27929418 PMCID: PMC5198560 DOI: 10.3390/toxins8120366] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/22/2016] [Accepted: 11/30/2016] [Indexed: 01/08/2023] Open
Abstract
RTA, the catalytic A-subunit of the ribosome inactivating A/B toxin ricin, inhibits eukaryotic protein biosynthesis by depurination of 28S rRNA. Although cell surface binding of ricin holotoxin is mainly mediated through its B-subunit (RTB), sole application of RTA is also toxic, albeit to a significantly lower extent, suggesting alternative pathways for toxin uptake and transport. Since ricin toxin trafficking in mammalian cells is still not fully understood, we developed a GFP-based reporter assay in yeast that allows rapid identification of cellular components required for RTA uptake and subsequent transport through a target cell. We hereby show that Ypt6p, Sft2p and GARP-complex components play an important role in RTA transport, while neither the retromer complex nor COPIB vesicles are part of the transport machinery. Analyses of yeast knock-out mutants with chromosomal deletion in genes whose products regulate ADP-ribosylation factor GTPases (Arf-GTPases) and/or retrograde Golgi-to-ER (endoplasmic reticulum) transport identified Sso1p, Snc1p, Rer1p, Sec22p, Erv46p, Gea1p and Glo3p as novel components in RTA transport, suggesting the developed reporter assay as a powerful tool to dissect the multistep processes of host cell intoxication in yeast.
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Affiliation(s)
- Björn Becker
- Molecular and Cell Biology, Department of Biosciences and Center of Human and Molecular Biology (ZHMB), Saarland University, Saarbrücken D-66123, Germany.
| | - Tina Schnöder
- Molecular and Cell Biology, Department of Biosciences and Center of Human and Molecular Biology (ZHMB), Saarland University, Saarbrücken D-66123, Germany.
| | - Manfred J Schmitt
- Molecular and Cell Biology, Department of Biosciences and Center of Human and Molecular Biology (ZHMB), Saarland University, Saarbrücken D-66123, Germany.
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Cui Z, Luo J, Qi C, Ruan Y, Li J, Zhang A, Yang X, He Y. Genome-wide association study (GWAS) reveals the genetic architecture of four husk traits in maize. BMC Genomics 2016; 17:946. [PMID: 27871222 PMCID: PMC5117540 DOI: 10.1186/s12864-016-3229-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 11/01/2016] [Indexed: 12/21/2022] Open
Abstract
Background Maize (Zea mays) husk referring to the leafy outer enclosing the ear, plays an important role in grain production by directly contributing photosynthate and protecting ear from pathogen infection. Although the physiological functions related to husk have been extensively studied, little is known about its morphological variation and genetic basis in natural population. Results Here we utilized a maize association panel including 508 inbred lines with tropical, subtropical and temperate backgrounds to decipher the genetic architecture attributed to four husk traits, i.e. number of layers, length, width and thickness. Evaluating the phenotypic diversity at two different environments showed that four traits exhibit broadly natural variations and moderate levels of heritability with 0.64, 0.74, 0.49 and 0.75 for number, length, width and thickness, respectively. Diversity analysis indicated that different traits have dissimilar responses to subpopulation effects. A series of significantly positive or negative correlations between husk phenotypes and other agronomic traits were identified, indicating that husk growth is coordinated with other developmental processes. Combining husk traits with about half of a million of single nucleotide polymorphisms (SNPs) via genome-wide association study revealed a total of 9 variants significantly associated with traits at P < 1.04 × 10-5, which are implicated in multiple functional categories, such as cellular trafficking, transcriptional regulation and metabolism. Conclusions These results provide instrumental information for understanding the genetic basis of husk development, and further studies on identified candidate genes facilitate to illuminate molecular pathways regulating maize husk growth. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3229-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhenhai Cui
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100094, China.,College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, 110866, China
| | - Jinhong Luo
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100094, China
| | - Chuangye Qi
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100094, China
| | - Yanye Ruan
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, 110866, China
| | - Jing Li
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100094, China
| | - Ao Zhang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100094, China.,College of Agronomy, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xiaohong Yang
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100094, China.
| | - Yan He
- National Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100094, China.
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48
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Ejzykowicz DE, Locken KM, Ruiz FJ, Manandhar SP, Olson DK, Gharakhanian E. Hygromycin B hypersensitive (hhy) mutants implicate an intact trans-Golgi and late endosome interface in efficient Tor1 vacuolar localization and TORC1 function. Curr Genet 2016; 63:531-551. [PMID: 27812735 DOI: 10.1007/s00294-016-0660-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 10/20/2016] [Accepted: 10/22/2016] [Indexed: 12/18/2022]
Abstract
Saccharomyces cerevisiae vacuoles are functionally analogous to mammalian lysosomes. Both also serve as physical platforms for Tor Complex 1 (TORC1) signal transduction, the master regulator of cellular growth and proliferation. Hygromycin B is a eukaryotic translation inhibitor. We recently reported on hygromycin B hypersensitive (hhy) mutants that fail to grow at subtranslation inhibitory concentrations of the drug and exhibit vacuolar defects (Banuelos et al. in Curr Genet 56:121-137, 2010). Here, we show that hhy phenotype is not due to increased sensitivity to translation inhibition and establish a super HHY (s-HHY) subgroup of genes comprised of ARF1, CHC1, DRS2, SAC1, VPS1, VPS34, VPS45, VPS52, and VPS54 that function exclusively or inclusively at trans-Golgi and late endosome interface. Live cell imaging of s-hhy mutants revealed that hygromycin B treatment disrupts vacuolar morphology and the localization of late endosome marker Pep12, but not that of late endosome-independent vacuolar SNARE Vam3. This, along with normal post-late endosome trafficking of the vital dye FM4-64, establishes that severe hypersensitivity to hygromycin B correlates specifically with compromised trans-Golgi and late endosome interface. We also show that Tor1p vacuolar localization and TORC1 anabolic functions, including growth promotion and phosphorylation of its direct substrate Sch9, are compromised in s-hhy mutants. Thus, an intact trans-Golgi and late endosome interface is a requisite for efficient Tor1 vacuolar localization and TORC1 function.
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Affiliation(s)
- Daniele E Ejzykowicz
- Department of Biological Sciences, California State University Long Beach, 1250 Bellflower Blvd, Long Beach, CA, 90840, USA
| | - Kristopher M Locken
- Department of Biological Sciences, California State University Long Beach, 1250 Bellflower Blvd, Long Beach, CA, 90840, USA
| | - Fiona J Ruiz
- Department of Biological Sciences, California State University Long Beach, 1250 Bellflower Blvd, Long Beach, CA, 90840, USA.,Department of Radiation Oncology, Cancer Biology Division, Washington University School of Medicine, Saint Louis, MO, 63108, USA
| | - Surya P Manandhar
- Department of Biological Sciences, California State University Long Beach, 1250 Bellflower Blvd, Long Beach, CA, 90840, USA
| | - Daniel K Olson
- Department of Biological Sciences, California State University Long Beach, 1250 Bellflower Blvd, Long Beach, CA, 90840, USA.,Inouye Center for Microbial Oceanography, Research and Education, University of Hawaii, Manoa, Honolulu, HI, 96822, USA
| | - Editte Gharakhanian
- Department of Biological Sciences, California State University Long Beach, 1250 Bellflower Blvd, Long Beach, CA, 90840, USA.
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49
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Fári K, Takács S, Ungár D, Sinka R. The role of acroblast formation during Drosophila spermatogenesis. Biol Open 2016; 5:1102-10. [PMID: 27481842 PMCID: PMC5004609 DOI: 10.1242/bio.018275] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Protein recycling is important for maintaining homeostasis of the Golgi and its cisternae. The Vps54 (Scat) protein, a subunit of the GARP tethering complex, is a central factor in retrograde transport to the trans-Golgi. We found the scat1 mutant to be male sterile in Drosophila with individualization problems occurring during spermatogenesis. Another typically observed phenotype was the abnormal nuclear structure in elongated mutant cysts. When examining the structure and function of the Golgi, a failure in acrosome formation and endosome-Golgi vesicular transport were found in the scat1 mutant. This acrosome formation defect was due to a fault in the trans-Golgi side of the acroblast ribbon. When testing a mutation in a second retrograde transport protein, Fws, a subunit of the conserved oligomeric Golgi (COG) tethering complex, the acroblast structure, was again disrupted. fwsP caused a similar, albeit milder, acrosome and sperm individualization phenotype as the scat1 mutant. In the case of fwsP the cis side of the acroblast ribbon was dispersed, in-line with the intra-Golgi retrograde function of COG. Our results highlight the importance of an intact acroblast for acrosome formation, nuclear elongation and therefore sperm maturation. Moreover, these results suggest the importance of retrograde tethering complexes in the formation of a functional Golgi ribbon. Summary: This study demonstrates that retrograde tethering complexes are necessary to form a functional acroblast, which is essential for normal nuclear elongation and acrosome formation during Drosophila spermatogenesis.
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Affiliation(s)
- Karolina Fári
- Department of Genetics, University of Szeged, Szeged 6726, Hungary
| | - Sándor Takács
- Department of Genetics, University of Szeged, Szeged 6726, Hungary
| | - Dániel Ungár
- Department of Biology, University of York, York YO10 5DD, UK
| | - Rita Sinka
- Department of Genetics, University of Szeged, Szeged 6726, Hungary
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50
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Vukašinović N, Žárský V. Tethering Complexes in the Arabidopsis Endomembrane System. Front Cell Dev Biol 2016; 4:46. [PMID: 27243010 PMCID: PMC4871884 DOI: 10.3389/fcell.2016.00046] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/02/2016] [Indexed: 12/30/2022] Open
Abstract
Targeting of endomembrane transport containers is of the utmost importance for proper land plant growth and development. Given the immobility of plant cells, localized membrane vesicle secretion and recycling are amongst the main processes guiding proper cell, tissue and whole plant morphogenesis. Cell wall biogenesis and modification are dependent on vectorial membrane traffic, not only during normal development, but also in stress responses and in plant defense against pathogens and/or symbiosis. It is surprising how little we know about these processes in plants, from small GTPase regulation to the tethering complexes that act as their effectors. Tethering factors are single proteins or protein complexes mediating first contact between the target membrane and arriving membrane vesicles. In this review we focus on the tethering complexes of the best-studied plant model—Arabidopsis thaliana. Genome-based predictions indicate the presence of all major tethering complexes in plants that are known from a hypothetical last eukaryotic common ancestor (LECA). The evolutionary multiplication of paralogs of plant tethering complex subunits has produced the massively expanded EXO70 family, indicating a subfunctionalization of the terminal exocytosis machinery in land plants. Interpretation of loss of function (LOF) mutant phenotypes has to consider that related, yet clearly functionally-specific complexes often share some common core subunits. It is therefore impossible to conclude with clarity which version of the complex is responsible for the phenotypic deviations observed. Experimental interest in the analysis of plant tethering complexes is growing and we hope to contribute with this review by attracting even more attention to this fascinating field of plant cell biology.
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Affiliation(s)
- Nemanja Vukašinović
- Laboratory of Cell Morphogenesis, Department of Experimental Plant Biology, Faculty of Science, Charles University Prague, Czech Republic
| | - Viktor Žárský
- Laboratory of Cell Morphogenesis, Department of Experimental Plant Biology, Faculty of Science, Charles University Prague, Czech Republic
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