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Cloutier G, Seltana A, Fallah S, Beaulieu JF. Integrin α7β1 represses intestinal absorptive cell differentiation. Exp Cell Res 2023; 430:113723. [PMID: 37499931 DOI: 10.1016/j.yexcr.2023.113723] [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: 03/28/2023] [Revised: 07/14/2023] [Accepted: 07/22/2023] [Indexed: 07/29/2023]
Abstract
Intestinal epithelial cell differentiation is a highly controlled and orderly process occurring in the crypt so that cells migrating out to cover the villi are already fully functional. Absorptive cell precursors, which originate from the stem cell population located in the lower third of the crypt, are subject to several cycles of amplification in the transit amplifying (TA) zone, before reaching the terminal differentiation compartment located in the upper third. There is a large body of evidence that absorptive cell differentiation is halted in the TA zone through various epigenetic, transcriptional and intracellular signalling events or mechanisms allowing the transient expansion of this cell population but how these mechanisms are themself regulated remains obscure. One clue can be found in the epithelial cell-matrix microenvironment located all along the crypt-villus axis. Indeed, a previous study from our group revealed that α5-subunit containing laminins such as lamimin-511 and 512 inhibit early stages of differentiation in Caco-2/15 cells. Among potential receptors for laminin 511/512 is the integrin α7β1, which has previously been reported to be expressed in the human intestinal crypts and in early stages of Caco-2/15 cell differentiation. In this study, the effects of knocking down ITGA7 in Caco-2/15 cells were studied using shRNA and CRISPR/Cas9 strategies. Abolition of the α7 integrin subunit resulted in a significant increase in the level of differentiation and polarization markers as well as the morphological features of intestinal cells. Activities of focal adhesion kinase and Src kinase were both reduced in α7-knockdown cells while the three major intestinal pro-differentiation factors CDX2, HNFα1 and HNF4α were overexpressed. Two epigenetic events associated with intestinal differentiation, the reduction of tri-methylated lysine 27 on histone H3 and the increase of acetylation of histone H4 were also observed in α7-knockdown cells. On the other hand, the ablation of α7 had no effect on cell proliferation. In conclusion, these data indicate that integrin α7β1 acts as a major repressor of absorptive cell terminal differentiation in the Caco-2/15 cell model and suggest that the laminin-α7β1 integrin interaction occurring in the transit amplifying zone of the adult intestine is involved in the transient halting of absorptive cell terminal differentiation.
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Affiliation(s)
- Gabriel Cloutier
- Laboratory of Intestinal Physiopathology, Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada
| | - Amira Seltana
- Laboratory of Intestinal Physiopathology, Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada
| | - Sepideh Fallah
- Laboratory of Intestinal Physiopathology, Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada
| | - Jean-François Beaulieu
- Laboratory of Intestinal Physiopathology, Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada.
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2
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Oh S, Lee CM, Kwon SH. Extracellular Vesicle MicroRNA in the Kidney. Compr Physiol 2023; 13:4833-4850. [PMID: 37358511 DOI: 10.1002/cphy.c220023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2023]
Abstract
Most cells in our body release membrane-bound, nano-sized particles into the extracellular milieu through cellular metabolic processes. Various types of macromolecules, reflecting the physiological and pathological status of the producing cells, are packaged into such so-called extracellular vesicles (EVs), which can travel over a distance to target cells, thereby transmitting donor cell information. The short, noncoding ribonucleic acid (RNA) called microRNA (miRNA) takes a crucial part in EV-resident macromolecules. Notably, EVs transferring miRNAs can induce alterations in the gene expression profiles of the recipient cells, through genetically instructed, base-pairing interaction between the miRNAs and their target cell messenger RNAs (mRNAs), resulting in either nucleolytic decay or translational halt of the engaged mRNAs. As in other body fluids, EVs released in urine, termed urinary EVs (uEVs), carry specific sets of miRNA molecules, which indicate either normal or diseased states of the kidney, the principal source of uEVs. Studies have therefore been directed to elucidate the contents and biological roles of miRNAs in uEVs and moreover to utilize the gene regulatory properties of miRNA cargos in ameliorating kidney diseases through their delivery via engineered EVs. We here review the fundamental principles of the biology of EVs and miRNA as well as our current understanding of the biological roles and applications of EV-loaded miRNAs in the kidney. We further discuss the limitations of contemporary research approaches, suggesting future directions to overcome the difficulties to advance both the basic biological understanding of miRNAs in EVs and their clinical applications in treating kidney diseases. © 2023 American Physiological Society. Compr Physiol 13:4833-4850, 2023.
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Affiliation(s)
- Sekyung Oh
- Department of Medical Science, Catholic Kwandong University College of Medicine, Incheon, South Korea
| | - Chang M Lee
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Sang-H Kwon
- Department of Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
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3
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Wilson B, Flett C, Gemperle J, Lawless C, Hartshorn M, Hinde E, Harrison T, Chastney M, Taylor S, Allen J, Norman JC, Zacharchenko T, Caswell PT. Proximity labelling identifies pro-migratory endocytic recycling cargo and machinery of the Rab4 and Rab11 families. J Cell Sci 2023; 136:jcs260468. [PMID: 37232246 PMCID: PMC10323252 DOI: 10.1242/jcs.260468] [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: 07/28/2022] [Accepted: 05/18/2023] [Indexed: 05/27/2023] Open
Abstract
Endocytic recycling controls the return of internalised cargoes to the plasma membrane to coordinate their positioning, availability and downstream signalling. The Rab4 and Rab11 small GTPase families regulate distinct recycling routes, broadly classified as fast recycling from early endosomes (Rab4) and slow recycling from perinuclear recycling endosomes (Rab11), and both routes handle a broad range of overlapping cargoes to regulate cell behaviour. We adopted a proximity labelling approach, BioID, to identify and compare the protein complexes recruited by Rab4a, Rab11a and Rab25 (a Rab11 family member implicated in cancer aggressiveness), revealing statistically robust protein-protein interaction networks of both new and well-characterised cargoes and trafficking machinery in migratory cancer cells. Gene ontological analysis of these interconnected networks revealed that these endocytic recycling pathways are intrinsically connected to cell motility and cell adhesion. Using a knock-sideways relocalisation approach, we were further able to confirm novel links between Rab11, Rab25 and the ESCPE-1 and retromer multiprotein sorting complexes, and identify new endocytic recycling machinery associated with Rab4, Rab11 and Rab25 that regulates cancer cell migration in the 3D matrix.
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Affiliation(s)
- Beverley Wilson
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
| | - Chloe Flett
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
| | - Jakub Gemperle
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
| | - Craig Lawless
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
| | - Matthew Hartshorn
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
| | - Eleanor Hinde
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
| | - Tess Harrison
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
| | - Megan Chastney
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
| | - Sarah Taylor
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
| | - Jennifer Allen
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
| | - Jim C. Norman
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK
| | - Thomas Zacharchenko
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
| | - Patrick T. Caswell
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, M13 9PT, UK
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4
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Pei Y, Lv S, Shi Y, Jia J, Ma M, Han H, Zhang R, Tan J, Zhang X. RAB21 controls autophagy and cellular energy homeostasis by regulating retromer-mediated recycling of SLC2A1/GLUT1. Autophagy 2023; 19:1070-1086. [PMID: 35993307 PMCID: PMC10012929 DOI: 10.1080/15548627.2022.2114271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 08/08/2022] [Accepted: 08/15/2022] [Indexed: 12/09/2022] Open
Abstract
The endosomal system maintains cellular homeostasis by coordinating multiple vesicular trafficking events, and the retromer complex plays a critical role in endosomal cargo recognition and sorting. Here, we demonstrate an essential role for the small GTPase RAB21 in regulating retromer-mediated recycling of the glucose transporter SLC2A1/GLUT1 and macroautophagy/autophagy. RAB21 depletion mis-sorts SLC2A1 to lysosomes and affects glucose uptake, thereby activating the AMPK-ULK1 pathway to increase autophagic flux. RAB21 depletion also increases lysosome function. Notably, RAB21 depletion does not overtly affect retrograde transport of IGF2R/CI-M6PR or WLS from endosomes to the trans-Golgi network. We speculate that RAB21 regulates fission of retromer-decorated endosomal tubules, as RAB21 depletion causes accumulation of the SNX27-containing retromer complex on enlarged endosomes at the perinuclear region. Functionally, RAB21 depletion sensitizes cancer cells to energy stress and inhibits tumor growth in vivo, suggesting an oncogenic role for RAB21. Overall, our study illuminates the role of RAB21 in regulating endosomal dynamics and maintaining cellular energy homeostasis and suggests RAB21 as a potential metabolic target for cancer therapy.
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Affiliation(s)
- Yifei Pei
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Shuning Lv
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yong Shi
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jingwen Jia
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Mengru Ma
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Hailong Han
- Department of Neuroscience, Postdoctoral Station for Basic Medicine, Hengyang School of Medicine, University of South China, Hengyang, China
| | - Rongying Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jieqiong Tan
- Centre for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Xinjun Zhang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
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5
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Shikanai M, Ito S, Nishimura YV, Akagawa R, Fukuda M, Yuzaki M, Nabeshima Y, Kawauchi T. Rab21 regulates caveolin-1-mediated endocytic trafficking to promote immature neurite pruning. EMBO Rep 2023; 24:e54701. [PMID: 36683567 PMCID: PMC9986827 DOI: 10.15252/embr.202254701] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 12/09/2022] [Accepted: 12/21/2022] [Indexed: 01/24/2023] Open
Abstract
Transmembrane proteins are internalized by clathrin- and caveolin-dependent endocytosis. Both pathways converge on early endosomes and are thought to share the small GTPase Rab5 as common regulator. In contrast to this notion, we show here that the clathrin- and caveolin-mediated endocytic pathways are differentially regulated. Rab5 and Rab21 localize to distinct populations of early endosomes in cortical neurons and preferentially regulate clathrin- and caveolin-mediated pathways, respectively, suggesting heterogeneity in the early endosomes, rather than a converging point. Suppression of Rab21, but not Rab5, results in decreased plasma membrane localization and total protein levels of caveolin-1, which perturbs immature neurite pruning of cortical neurons, an in vivo-specific step of neuronal maturation. Taken together, our data indicate that clathrin- and caveolin-mediated endocytic pathways run in parallel in early endosomes, which show different molecular regulation and physiological function.
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Affiliation(s)
- Mima Shikanai
- Department of PhysiologyKeio University School of MedicineTokyoJapan
| | - Shiho Ito
- Department of Aging Science and Medicine, Graduate School of MedicineKyoto UniversityKyotoJapan
- Laboratory of Molecular Life ScienceInstitute of Biomedical Research and Innovation, FBRI, CLIK‐5FKobeJapan
| | - Yoshiaki V Nishimura
- Division of Neuroscience, Faculty of MedicineTohoku Medical and Pharmaceutical UniversitySendaiJapan
| | - Remi Akagawa
- Laboratory of Molecular Life ScienceInstitute of Biomedical Research and Innovation, FBRI, CLIK‐5FKobeJapan
| | - Mitsunori Fukuda
- Laboratory of Membrane Trafficking Mechanisms, Department of Integrative Life Sciences, Graduate School of Life SciencesTohoku UniversitySendaiJapan
| | - Michisuke Yuzaki
- Department of PhysiologyKeio University School of MedicineTokyoJapan
| | - Yo‐ichi Nabeshima
- Department of Aging Science and Medicine, Graduate School of MedicineKyoto UniversityKyotoJapan
- Laboratory of Molecular Life ScienceInstitute of Biomedical Research and Innovation, FBRI, CLIK‐5FKobeJapan
| | - Takeshi Kawauchi
- Department of PhysiologyKeio University School of MedicineTokyoJapan
- Department of Aging Science and Medicine, Graduate School of MedicineKyoto UniversityKyotoJapan
- Laboratory of Molecular Life ScienceInstitute of Biomedical Research and Innovation, FBRI, CLIK‐5FKobeJapan
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6
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Golas S, Chory EJ. Proximity labeling of endogenous protein interactions enabled by directed evolution. Trends Biotechnol 2023; 41:301-303. [PMID: 36710130 DOI: 10.1016/j.tibtech.2023.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/29/2023]
Abstract
Enhanced ascorbate peroxidase 2 (APEX2) is a protein generated with directed evolution by Lam et al. that has transformed our understanding of subcellular entities and phenomena. The rapid kinetics of this engineered protein highlights the power of directed evolution to expand the molecular toolkit for biologists.
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Affiliation(s)
- Stefan Golas
- Media Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Emma J Chory
- Media Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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7
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Johnson JL, Meneses-Salas E, Ramadass M, Monfregola J, Rahman F, Carvalho Gontijo R, Kiosses WB, Pestonjamasp K, Allen D, Zhang J, Osborne DG, Zhu YP, Wineinger N, Askari K, Chen D, Yu J, Henderson SC, Hedrick CC, Ursini MV, Grinstein S, Billadeau DD, Catz SD. Differential dysregulation of granule subsets in WASH-deficient neutrophil leukocytes resulting in inflammation. Nat Commun 2022; 13:5529. [PMID: 36130971 PMCID: PMC9492659 DOI: 10.1038/s41467-022-33230-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 09/08/2022] [Indexed: 11/09/2022] Open
Abstract
Dysregulated secretion in neutrophil leukocytes associates with human inflammatory disease. The exocytosis response to triggering stimuli is sequential; gelatinase granules modulate the initiation of the innate immune response, followed by the release of pro-inflammatory azurophilic granules, requiring stronger stimulation. Exocytosis requires actin depolymerization which is actively counteracted under non-stimulatory conditions. Here we show that the actin nucleator, WASH, is necessary to maintain azurophilic granules in their refractory state by granule actin entrapment and interference with the Rab27a-JFC1 exocytic machinery. On the contrary, gelatinase granules of WASH-deficient neutrophil leukocytes are characterized by decreased Rac1, shortened granule-associated actin comets and impaired exocytosis. Rac1 activation restores exocytosis of these granules. In vivo, WASH deficiency induces exacerbated azurophilic granule exocytosis, inflammation, and decreased survival. WASH deficiency thus differentially impacts neutrophil granule subtypes, impairing exocytosis of granules that mediate the initiation of the neutrophil innate response while exacerbating pro-inflammatory granule secretion.
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Affiliation(s)
- Jennifer L Johnson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Elsa Meneses-Salas
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Mahalakshmi Ramadass
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Jlenia Monfregola
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy
| | - Farhana Rahman
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | | | - William B Kiosses
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Kersi Pestonjamasp
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Dale Allen
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Jinzhong Zhang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Douglas G Osborne
- The Division of Oncology Research, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Yanfang Peipei Zhu
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Nathan Wineinger
- Research Translational Institute, Statistics, The Scripps Research Institute, La Jolla, CA, USA
| | - Kasra Askari
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Danni Chen
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Juan Yu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Scott C Henderson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | - Catherine C Hedrick
- Division of Inflammation Biology, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Sergio Grinstein
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Daniel D Billadeau
- The Division of Oncology Research, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Sergio D Catz
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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8
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Proteomic mapping and optogenetic manipulation of membrane contact sites. Biochem J 2022; 479:1857-1875. [PMID: 36111979 PMCID: PMC9555801 DOI: 10.1042/bcj20220382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022]
Abstract
Membrane contact sites (MCSs) mediate crucial physiological processes in eukaryotic cells, including ion signaling, lipid metabolism, and autophagy. Dysregulation of MCSs is closely related to various diseases, such as type 2 diabetes mellitus (T2DM), neurodegenerative diseases, and cancers. Visualization, proteomic mapping and manipulation of MCSs may help the dissection of the physiology and pathology MCSs. Recent technical advances have enabled better understanding of the dynamics and functions of MCSs. Here we present a summary of currently known functions of MCSs, with a focus on optical approaches to visualize and manipulate MCSs, as well as proteomic mapping within MCSs.
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9
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Shortill SP, Frier MS, Wongsangaroonsri P, Davey M, Conibear E. The VINE complex is an endosomal VPS9-domain GEF and SNX-BAR coat. eLife 2022; 11:77035. [PMID: 35938928 PMCID: PMC9507130 DOI: 10.7554/elife.77035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 08/05/2022] [Indexed: 11/18/2022] Open
Abstract
Membrane trafficking pathways perform important roles in establishing and maintaining the endosomal network. Retrograde protein sorting from the endosome is promoted by conserved SNX-BAR-containing coat complexes including retromer which enrich cargo at tubular microdomains and generate transport carriers. In metazoans, retromer cooperates with VARP, a conserved VPS9-domain GEF, to direct an endosomal recycling pathway. The function of the yeast VARP homolog Vrl1 has been overlooked due to an inactivating mutation found in commonly studied strains. Here, we demonstrate that Vrl1 has features of a SNX-BAR coat protein and forms an obligate complex with Vin1, the paralog of the retromer SNX-BAR protein Vps5. Unique features in the Vin1 N-terminus allow Vrl1 to distinguish it from Vps5, thereby forming a complex that we have named VINE. The VINE complex occupies endosomal tubules and redistributes a conserved mannose 6-phosphate receptor-like protein from endosomes. We also find that membrane recruitment by Vin1 is essential for Vrl1 GEF activity, suggesting that VINE is a multifunctional coat complex that regulates trafficking and signaling events at the endosome. All healthy cells have a highly organized interior: different compartments with specialized roles are in different places, and in order to do their jobs properly, proteins need to be in the right place. Endosomes are membrane-bound compartments that act as transport hubs where proteins are sorted into small vesicles and delivered to other parts of the cell. Two groups of proteins regulate this transport: the first group, known as VPS9 GEFs, switches on the enzymes that recruit the second group of proteins, called the sorting nexins. This second group is responsible for forming the transport vesicles via which proteins are distributed all over the cell. Defects in protein sorting can lead to various diseases, including neurodegenerative conditions such as Parkinson’s disease and juvenile amyotrophic lateral sclerosis. Scientists often use budding yeast cells to study protein sorting, because these cells are similar to human cells, but easier to grow in large numbers and examine in the laboratory. Previous work showed that a yeast protein called Vrl1 is equivalent to a VPS9 GEF from humans called VARP. However, Vrl1 only exists in wild forms of budding yeast, and not in laboratory strains of the organism. Therefore, researchers had not studied Vrl1 in detail, and its roles remained unclear. To learn more about Vrl1, Shortill et al. started by re-introducing the protein into laboratory strains of budding yeast and observing what happened to protein sorting in these cells. Like VARP, Vrl1 was found in the endosomes of budding yeast. However, biochemical experiments revealed that, while human VARP binds to a protein called retromer, Vrl1 does not bind to the equivalent protein in yeast. Instead, Vrl1 itself has features of both the VPS9 GEFs and the sorting nexins. Shortill et al. also found that Vrl1 interacted with a different protein in the sorting nexin family called Vin1. In the absence of Vrl1, Vin1 was found floating around the cell, but once Vrl1 was re-introduced into the budding yeast, Vin1 relocated to the endosomes. Vrl1 uses its VPS9 GEF part to move itself to the endosome membrane, and Vin1 controls this movement, highlighting the interdependence between the two proteins. Once they are at the endosome together, Vrl1 and Vin1 help redistribute proteins to other parts of the cell. This study suggests that, like VARP, Vrl1 cooperates with sorting nexins to transport proteins. Since many previous experiments about protein sorting were carried out in yeast cells lacking Vrl1, it is possible that this process was overlooked despite its potential importance. These new findings could also help other researchers investigating how endosomes and protein sorting work, or do not work, in the context of neurodegenerative diseases.
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Affiliation(s)
- Shawn P Shortill
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
| | - Mia S Frier
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
| | | | - Michael Davey
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
| | - Elizabeth Conibear
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
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10
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Shortill SP, Frier MS, Conibear E. You can go your own way: SNX-BAR coat complexes direct traffic at late endosomes. Curr Opin Cell Biol 2022; 76:102087. [DOI: 10.1016/j.ceb.2022.102087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/23/2022] [Accepted: 04/01/2022] [Indexed: 12/20/2022]
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11
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Lee BR, Lee TJ, Oh S, Li C, Song JA, Marshall B, Zhi W, Kwon S. Ascorbate peroxidase-mediated in situ labelling of proteins in secreted exosomes. J Extracell Vesicles 2022; 11:e12239. [PMID: 35716063 PMCID: PMC9206227 DOI: 10.1002/jev2.12239] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 04/27/2022] [Accepted: 06/07/2022] [Indexed: 11/12/2022] Open
Abstract
The extracellular vesicle exosome mediates intercellular communication by transporting macromolecules such as proteins and ribonucleic acids (RNAs). Determining cargo contents with high accuracy will help decipher the biological processes that exosomes mediate in various contexts. Existing methods for probing exosome cargo molecules rely on a prior exosome isolation procedure. Here we report an in situ labelling approach for exosome cargo identification, which bypasses the exosome isolation steps. In this methodology, a variant of the engineered ascorbate peroxidase APEX, fused to an exosome cargo protein such as CD63, is expressed specifically in exosome-generating vesicles in live cells or in secreted exosomes in the conditioned medium, to induce biotinylation of the proteins in the vicinity of the APEX variant for a short period of time. Mass spectrometry analysis of the proteins biotinylated by this approach in exosomes secreted by kidney proximal tubule-derived cells reveals that oxidative stress can cause ribosomal proteins to accumulate in an exosome subpopulation that contains the CD63-fused APEX variant.
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Affiliation(s)
- Byung Rho Lee
- Department of Cellular Biology and AnatomyMedical College of GeorgiaAugusta UniversityAugustaGeorgiaUSA
| | - Tae Jin Lee
- Center for Biotechnology and Genomic MedicineMedical College of GeorgiaAugusta UniversityAugustaGeorgiaUSA
| | - Sekyung Oh
- Department of Medical ScienceCatholic Kwandong University College of MedicineIncheonSouth Korea
| | - Chenglong Li
- Department of Cellular Biology and AnatomyMedical College of GeorgiaAugusta UniversityAugustaGeorgiaUSA
| | - Jin‐Hyuk A Song
- Department of Cellular Biology and AnatomyMedical College of GeorgiaAugusta UniversityAugustaGeorgiaUSA
| | - Brendan Marshall
- Department of Cellular Biology and AnatomyMedical College of GeorgiaAugusta UniversityAugustaGeorgiaUSA
| | - Wenbo Zhi
- Center for Biotechnology and Genomic MedicineMedical College of GeorgiaAugusta UniversityAugustaGeorgiaUSA
| | - Sang‐Ho Kwon
- Department of Cellular Biology and AnatomyMedical College of GeorgiaAugusta UniversityAugustaGeorgiaUSA
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12
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Abstract
Emerging zoonotic viral pathogens threaten global health, and there is an urgent need to discover host and viral determinants influencing infection. We performed a loss-of-function genome-wide CRISPR screen in a human lung cell line using HCoV-OC43, a human betacoronavirus. One candidate gene, VPS29, a component of the retromer complex, was required for infection by HCoV-OC43, SARS-CoV-2, other endemic- and pandemic-threat coronaviruses, as well as ebolavirus. Notably, we observed a heightened requirement for VPS29 by the recently described Omicron variant of SARS-CoV-2 compared to the ancestral variant. However, VPS29 deficiency had no effect on certain other viruses that enter cells via endosomes and had an opposing, enhancing effect on influenza A virus infection. Deficiency in VPS29 or other retromer components caused changes in endosome morphology and acidity and attenuated the activity of endosomal proteases. These changes in endosome properties caused incoming coronavirus, but not influenza virus particles, to become entrapped therein. Overall, these data show how host regulation of endosome characteristics can influence cellular susceptibility to viral infection and identify a host pathway that could serve as a pharmaceutical target for intervention in zoonotic viral diseases.
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13
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Lauzier A, Bossanyi MF, Larcher R, Nassari S, Ugrankar R, Henne WM, Jean S. Snazarus and its human ortholog SNX25 modulate autophagic flux. J Cell Sci 2022; 135:273525. [PMID: 34821359 DOI: 10.1242/jcs.258733] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 11/12/2021] [Indexed: 12/26/2022] Open
Abstract
Macroautophagy, the degradation and recycling of cytosolic components in the lysosome, is an important cellular mechanism. It is a membrane-mediated process that is linked to vesicular trafficking events. The sorting nexin (SNX) protein family controls the sorting of a large array of cargoes, and various SNXs impact autophagy. To improve our understanding of their functions in vivo, we screened all Drosophila SNXs using inducible RNA interference in the fat body. Significantly, depletion of Snazarus (Snz) led to decreased autophagic flux. Interestingly, we observed altered distribution of Vamp7-positive vesicles with Snz depletion, and the roles of Snz were conserved in human cells. SNX25, the closest human ortholog to Snz, regulates both VAMP8 endocytosis and lipid metabolism. Through knockout-rescue experiments, we demonstrate that these activities are dependent on specific SNX25 domains and that the autophagic defects seen upon SNX25 loss can be rescued by ethanolamine addition. We also demonstrate the presence of differentially spliced forms of SNX14 and SNX25 in cancer cells. This work identifies a conserved role for Snz/SNX25 as a regulator of autophagic flux and reveals differential isoform expression between paralogs.
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Affiliation(s)
- Annie Lauzier
- Faculté de Médecine et des Sciences de la Santé, Département d'immunologie et de biologie cellulaire, Université de Sherbrooke, 3201, Rue Jean Mignault, Sherbrooke, Québec, CanadaJ1E 4K8
| | - Marie-France Bossanyi
- Faculté de Médecine et des Sciences de la Santé, Département d'immunologie et de biologie cellulaire, Université de Sherbrooke, 3201, Rue Jean Mignault, Sherbrooke, Québec, CanadaJ1E 4K8
| | - Raphaëlle Larcher
- Faculté de Médecine et des Sciences de la Santé, Département d'immunologie et de biologie cellulaire, Université de Sherbrooke, 3201, Rue Jean Mignault, Sherbrooke, Québec, CanadaJ1E 4K8
| | - Sonya Nassari
- Faculté de Médecine et des Sciences de la Santé, Département d'immunologie et de biologie cellulaire, Université de Sherbrooke, 3201, Rue Jean Mignault, Sherbrooke, Québec, CanadaJ1E 4K8
| | - Rupali Ugrankar
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Hary Lines Boulevard, Dallas, TX 75390, USA
| | - W Mike Henne
- Department of Cell Biology, UT Southwestern Medical Center, 6000 Hary Lines Boulevard, Dallas, TX 75390, USA
| | - Steve Jean
- Faculté de Médecine et des Sciences de la Santé, Département d'immunologie et de biologie cellulaire, Université de Sherbrooke, 3201, Rue Jean Mignault, Sherbrooke, Québec, CanadaJ1E 4K8
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14
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Nassari S, Lacarrière-Keïta C, Lévesque D, Boisvert FM, Jean S. Rab21 in enterocytes participates in intestinal epithelium maintenance. Mol Biol Cell 2022; 33:ar32. [PMID: 35171715 PMCID: PMC9250356 DOI: 10.1091/mbc.e21-03-0139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Membrane trafficking is defined as the vesicular transport of proteins into, out of, and throughout the cell. In intestinal enterocytes, defects in endocytic/recycling pathways result in impaired function and are linked to diseases. However, how these trafficking pathways regulate intestinal tissue homeostasis is poorly understood. Using the Drosophila intestine as an in vivo system, we investigated enterocyte-specific functions for the early endosomal machinery. We focused on Rab21, which regulates specific steps in early endosomal trafficking. Depletion of Rab21 in enterocytes led to abnormalities in intestinal morphology, with deregulated cellular equilibrium associated with a gain in mitotic cells and increased cell death. Increases in apoptosis and Yorkie signaling were responsible for compensatory proliferation and tissue inflammation. Using an RNAi screen, we identified regulators of autophagy and membrane trafficking that phenocopied Rab21 knockdown. We further showed that Rab21 knockdown-induced hyperplasia was rescued by inhibition of epidermal growth factor receptor signaling. Moreover, quantitative proteomics identified proteins affected by Rab21 depletion. Of these, we validated changes in apolipoprotein ApoLpp and the trehalose transporter Tret1-1, indicating roles for enterocyte Rab21 in lipid and carbohydrate homeostasis, respectively. Our data shed light on an important role for early endosomal trafficking, and Rab21, in enterocyte-mediated intestinal epithelium maintenance. [Media: see text] [Media: see text].
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Affiliation(s)
- Sonya Nassari
- Faculté de Médecine et des Sciences de la Santé, Department of Immunology and Cell Biology, Université de Sherbrooke, 3201 Rue Jean Mignault, Sherbrooke, Québec J1E 4K8, Canada
| | - Camille Lacarrière-Keïta
- Faculté de Médecine et des Sciences de la Santé, Department of Immunology and Cell Biology, Université de Sherbrooke, 3201 Rue Jean Mignault, Sherbrooke, Québec J1E 4K8, Canada
| | - Dominique Lévesque
- Faculté de Médecine et des Sciences de la Santé, Department of Immunology and Cell Biology, Université de Sherbrooke, 3201 Rue Jean Mignault, Sherbrooke, Québec J1E 4K8, Canada
| | - François-Michel Boisvert
- Faculté de Médecine et des Sciences de la Santé, Department of Immunology and Cell Biology, Université de Sherbrooke, 3201 Rue Jean Mignault, Sherbrooke, Québec J1E 4K8, Canada
| | - Steve Jean
- Faculté de Médecine et des Sciences de la Santé, Department of Immunology and Cell Biology, Université de Sherbrooke, 3201 Rue Jean Mignault, Sherbrooke, Québec J1E 4K8, Canada
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15
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Christopher JA, Geladaki A, Dawson CS, Vennard OL, Lilley KS. Subcellular Transcriptomics and Proteomics: A Comparative Methods Review. Mol Cell Proteomics 2022; 21:100186. [PMID: 34922010 PMCID: PMC8864473 DOI: 10.1016/j.mcpro.2021.100186] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 11/16/2021] [Accepted: 12/13/2021] [Indexed: 12/23/2022] Open
Abstract
The internal environment of cells is molecularly crowded, which requires spatial organization via subcellular compartmentalization. These compartments harbor specific conditions for molecules to perform their biological functions, such as coordination of the cell cycle, cell survival, and growth. This compartmentalization is also not static, with molecules trafficking between these subcellular neighborhoods to carry out their functions. For example, some biomolecules are multifunctional, requiring an environment with differing conditions or interacting partners, and others traffic to export such molecules. Aberrant localization of proteins or RNA species has been linked to many pathological conditions, such as neurological, cancer, and pulmonary diseases. Differential expression studies in transcriptomics and proteomics are relatively common, but the majority have overlooked the importance of subcellular information. In addition, subcellular transcriptomics and proteomics data do not always colocate because of the biochemical processes that occur during and after translation, highlighting the complementary nature of these fields. In this review, we discuss and directly compare the current methods in spatial proteomics and transcriptomics, which include sequencing- and imaging-based strategies, to give the reader an overview of the current tools available. We also discuss current limitations of these strategies as well as future developments in the field of spatial -omics.
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Affiliation(s)
- Josie A Christopher
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Aikaterini Geladaki
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Department of Genetics, University of Cambridge, Cambridge, UK
| | - Charlotte S Dawson
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Owen L Vennard
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK
| | - Kathryn S Lilley
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, Cambridge, UK.
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16
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Liu P, Wu A, Li H, Zhang J, Ni J, Quan Z, Qing H. Rab21 Protein Is Degraded by Both the Ubiquitin-Proteasome Pathway and the Autophagy-Lysosome Pathway. Int J Mol Sci 2022; 23:ijms23031131. [PMID: 35163051 PMCID: PMC8835697 DOI: 10.3390/ijms23031131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/17/2022] [Accepted: 01/17/2022] [Indexed: 02/05/2023] Open
Abstract
Rab21 is a GTPase protein that is functional in intracellular trafficking and involved in the pathologies of many diseases, such as Alzheimer’s disease (AD), glioma, cancer, etc. Our previous work has reported its interaction with the catalytic subunit of gamma-secretase, PS1, and it regulates the activity of PS1 via transferring it from the early endosome to the late endosome/lysosome. However, it is still unknown how Rab21 protein itself is regulated. This work revealed that Rab21 protein, either endogenously or exogenously, can be degraded by the ubiquitin-proteasome pathway and the autophagy-lysosome pathway. It is further observed that the ubiquitinated Rab21 is increased, but the total protein is unchanged in AD model mice. We further observed that overexpression of Rab21 leads to increased expression of a series of genes involved in the autophagy-lysosome pathway. We speculated that even though the ubiquitinated Rab21 is increased due to the impaired proteasome function in the AD model, the autophagy-lysosome pathway functions in parallel to degrade Rab21 to keep its protein level in homeostasis. In conclusion, understanding the characters of Rab21 protein itself help explore its potential as a target for therapeutic strategy in diseases.
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17
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Higashi S, Makiyama T, Sakane H, Nogami S, Shirataki H. Regulation of Hook1-mediated endosomal sorting of clathrin-independent cargo by γ-taxilin. J Cell Sci 2021; 135:273710. [PMID: 34897470 DOI: 10.1242/jcs.258849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 11/30/2021] [Indexed: 11/20/2022] Open
Abstract
In clathrin-independent endocytosis, Hook1, a microtubule- and cargo-tethering protein, participates in sorting of cargo proteins such as CD98 and CD147 into recycling endosomes. However, the molecular mechanism that regulates Hook1-mediated endosomal sorting is not fully understood. Here, we found that γ-taxilin is a novel regulator of Hook1-mediated endosomal sorting. γ-Taxilin depletion promoted both CD98-positive tubular formation and CD98 recycling. Conversely, overexpression of γ-taxilin inhibited the CD98-positive tubular formation. Depletion of Hook1, or Rab10 or Rab22a (which are both involved in Hook1-mediated endosomal sorting), attenuated the effect of γ-taxilin depletion on the CD98-positive tubular formation. γ-Taxilin depletion promoted CD147-mediated spreading of HeLa cells, suggesting that γ-taxilin may be a pivotal player in various cellular functions in which Hook1-mediated cargo proteins are involved. γ-Taxilin bound to the C-terminal region of Hook1 and inhibited its interaction with CD98; the latter interaction is necessary for sorting CD98. We suggest that γ-taxilin negatively regulates the sorting of Hook1-mediated cargo proteins into recycling endosomes by interfering with the interactions between Hook1 and the cargo proteins.
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Affiliation(s)
- Satoru Higashi
- Department of Molecular and Cell Biology, Graduate School of Medicine, Dokkyo Medical University, 880 Kitakobayashi, Mibu-machi, Tochigi 321-0293, Japan
| | - Tomohiko Makiyama
- Department of Molecular and Cell Biology, Graduate School of Medicine, Dokkyo Medical University, 880 Kitakobayashi, Mibu-machi, Tochigi 321-0293, Japan
| | - Hiroshi Sakane
- Department of Molecular and Cell Biology, Graduate School of Medicine, Dokkyo Medical University, 880 Kitakobayashi, Mibu-machi, Tochigi 321-0293, Japan
| | - Satoru Nogami
- Department of Molecular and Cell Biology, Graduate School of Medicine, Dokkyo Medical University, 880 Kitakobayashi, Mibu-machi, Tochigi 321-0293, Japan
| | - Hiromichi Shirataki
- Department of Molecular and Cell Biology, Graduate School of Medicine, Dokkyo Medical University, 880 Kitakobayashi, Mibu-machi, Tochigi 321-0293, Japan
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18
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Moreno-Layseca P, Jäntti NZ, Godbole R, Sommer C, Jacquemet G, Al-Akhrass H, Conway JRW, Kronqvist P, Kallionpää RE, Oliveira-Ferrer L, Cervero P, Linder S, Aepfelbacher M, Zauber H, Rae J, Parton RG, Disanza A, Scita G, Mayor S, Selbach M, Veltel S, Ivaska J. Cargo-specific recruitment in clathrin- and dynamin-independent endocytosis. Nat Cell Biol 2021; 23:1073-1084. [PMID: 34616024 DOI: 10.1038/s41556-021-00767-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 09/01/2021] [Indexed: 12/12/2022]
Abstract
Spatially controlled, cargo-specific endocytosis is essential for development, tissue homeostasis and cancer invasion. Unlike cargo-specific clathrin-mediated endocytosis, the clathrin- and dynamin-independent endocytic pathway (CLIC-GEEC, CG pathway) is considered a bulk internalization route for the fluid phase, glycosylated membrane proteins and lipids. While the core molecular players of CG-endocytosis have been recently defined, evidence of cargo-specific adaptors or selective uptake of proteins for the pathway are lacking. Here we identify the actin-binding protein Swiprosin-1 (Swip1, EFHD2) as a cargo-specific adaptor for CG-endocytosis. Swip1 couples active Rab21-associated integrins with key components of the CG-endocytic machinery-Arf1, IRSp53 and actin-and is critical for integrin endocytosis. Through this function, Swip1 supports integrin-dependent cancer-cell migration and invasion, and is a negative prognostic marker in breast cancer. Our results demonstrate a previously unknown cargo selectivity for the CG pathway and a role for specific adaptors in recruitment into this endocytic route.
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Affiliation(s)
- Paulina Moreno-Layseca
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Niklas Z Jäntti
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Rashmi Godbole
- National Centre for Biological Science (TIFR), Bangalore, India.,The University of Trans-Disciplinary Health Sciences and Technology (TDU), Bangalore, India
| | - Christian Sommer
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - Guillaume Jacquemet
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Hussein Al-Akhrass
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - James R W Conway
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Pauliina Kronqvist
- Institute of Biomedicine, Faculty of Medicine, University of Turku, Turku, Finland
| | - Roosa E Kallionpää
- Auria Biobank, Turku University Hospital and University of Turku, Turku, Finland
| | | | - Pasquale Cervero
- University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Stefan Linder
- University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | | | - Henrik Zauber
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - James Rae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Robert G Parton
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.,Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, Queensland, Australia
| | - Andrea Disanza
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare and University of Milan, Milan, Italy
| | - Giorgio Scita
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare and University of Milan, Milan, Italy
| | - Satyajit Mayor
- National Centre for Biological Science (TIFR), Bangalore, India
| | - Matthias Selbach
- Max-Delbrück-Centrum für Molekulare Medizin (MDC), Berlin, Germany
| | - Stefan Veltel
- University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany. .,Hochschule Bremen, City University of Applied Sciences, Bremen, Germany.
| | - Johanna Ivaska
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland. .,Department of Life Sciences, University of Turku, Turku, Finland. .,InFLAMES Research Flagship Center, University of Turku, Turku, Finland.
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19
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Evnouchidou I, Caillens V, Koumantou D, Saveanu L. The role of endocytic trafficking in antigen T Cell Receptor activation. Biomed J 2021; 45:310-320. [PMID: 34592497 PMCID: PMC9250096 DOI: 10.1016/j.bj.2021.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/19/2021] [Accepted: 09/22/2021] [Indexed: 12/14/2022] Open
Abstract
Antigen T cell receptors (TCR) recognize antigenic peptides displayed by the major histocompatibility complex (pMHC) and play a critical role in T cell activation. The levels of TCR complexes at the cell surface, where signaling is initiated, depend on the balance between TCR synthesis, recycling and degradation. Cell surface TCR interaction with pMHC leads to receptor clustering and formation of a tight T cell-APC contact, the immune synapse, from which the activated TCR is internalized. While TCR internalization from the immune synapse has been initially considered to arrest TCR signaling, recent evidence support the hypothesis that the internalized receptor continues to signal from specialized endosomes. Here, we review the molecular mechanisms of TCR endocytosis and recycling, both in steady state and after T cell activation. We then discuss the experimental evidence in favor of endosomal TCR signaling and its possible consequences on T cell activation.
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Affiliation(s)
- Irini Evnouchidou
- Université de Paris, Centre de Recherche sur L'inflammation, INSERM U1149, CNRS ERL8252, Paris, France; Inovarion, Paris, France.
| | - Vivien Caillens
- Université de Paris, Centre de Recherche sur L'inflammation, INSERM U1149, CNRS ERL8252, Paris, France; Inovarion, Paris, France
| | - Despoina Koumantou
- Université de Paris, Centre de Recherche sur L'inflammation, INSERM U1149, CNRS ERL8252, Paris, France; Inovarion, Paris, France
| | - Loredana Saveanu
- Université de Paris, Centre de Recherche sur L'inflammation, INSERM U1149, CNRS ERL8252, Paris, France; Inovarion, Paris, France.
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20
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Retromer dependent changes in cellular homeostasis and Parkinson's disease. Essays Biochem 2021; 65:987-998. [PMID: 34528672 PMCID: PMC8709886 DOI: 10.1042/ebc20210023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 08/12/2021] [Accepted: 08/16/2021] [Indexed: 12/18/2022]
Abstract
To date, mechanistic treatments targeting the initial cause of Parkinson's disease (PD) are limited due to the underlying biological cause(s) been unclear. Endosomes and their associated cellular homeostasis processes have emerged to have a significant role in the pathophysiology associated with PD. Several variants within retromer complex have been identified and characterised within familial PD patients. The retromer complex represents a key sorting platform within the endosomal system that regulates cargo sorting that maintains cellular homeostasis. In this review, we summarise the current understandings of how PD-associated retromer variants disrupt cellular trafficking and how the retromer complex can interact with other PD-associated genes to contribute to the disease progression.
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21
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Capitani N, Baldari CT. F-Actin Dynamics in the Regulation of Endosomal Recycling and Immune Synapse Assembly. Front Cell Dev Biol 2021; 9:670882. [PMID: 34249926 PMCID: PMC8265274 DOI: 10.3389/fcell.2021.670882] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/24/2021] [Indexed: 12/24/2022] Open
Abstract
Membrane proteins endocytosed at the cell surface as vesicular cargoes are sorted at early endosomes for delivery to lysosomes for degradation or alternatively recycled to different cellular destinations. Cargo recycling is orchestrated by multimolecular complexes that include the retromer, retriever, and the WASH complex, which promote the polymerization of new actin filaments at early endosomes. These endosomal actin pools play a key role at different steps of the recycling process, from cargo segregation to specific endosomal subdomains to the generation and mobility of tubulo-vesicular transport carriers. Local F-actin pools also participate in the complex redistribution of endomembranes and organelles that leads to the acquisition of cell polarity. Here, we will present an overview of the contribution of endosomal F-actin to T-cell polarization during assembly of the immune synapse, a specialized membrane domain that T cells form at the contact with cognate antigen-presenting cells.
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Affiliation(s)
- Nagaja Capitani
- Department of Life Sciences, University of Siena, Siena, Italy
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22
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Clague MJ, Urbé S. Data mining for traffic information. Traffic 2021; 21:162-168. [PMID: 31596015 DOI: 10.1111/tra.12702] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/19/2019] [Accepted: 09/19/2019] [Indexed: 12/23/2022]
Abstract
Modern cell biology is now rich with data acquired at the whole genome and proteome level. We can add value to this data through integration and application of specialist knowledge. To illustrate, we will focus on the SNARE and RAB proteins; key regulators of intracellular fusion specificity and organelle identity. We examine published mass spectrometry data to gain an estimate of protein copy number and organelle distribution in HeLa cells for each family member. We also survey recent global CRISPR/Cas9 screens for essential genes from these families. We highlight instances of co-essentiality with other genes across a large panel of cell lines that allows for the identification of functionally coherent clusters. Examples of such correlations include RAB10 with the SNARE protein Syntaxin4 (STX4) and RAB7/RAB21 with the WASH and the CCC (COMMD/CCDC22/CCDC93) complexes, both of which are linked to endosomal recycling pathways.
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Affiliation(s)
- Michael J Clague
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Sylvie Urbé
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Liverpool, UK
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23
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Zapatero-Belinchón FJ, Carriquí-Madroñal B, Gerold G. Proximity labeling approaches to study protein complexes during virus infection. Adv Virus Res 2021; 109:63-104. [PMID: 33934830 DOI: 10.1016/bs.aivir.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Cellular compartmentalization of proteins and protein complex formation allow cells to tightly control biological processes. Therefore, understanding the subcellular localization and interactions of a specific protein is crucial to uncover its biological function. The advent of proximity labeling (PL) has reshaped cellular proteomics in infection biology. PL utilizes a genetically modified enzyme that generates a "labeling cloud" by covalently labeling proteins in close proximity to the enzyme. Fusion of a PL enzyme to a specific antibody or a "bait" protein of interest in combination with affinity enrichment mass spectrometry (AE-MS) enables the isolation and identification of the cellular proximity proteome, or proxisome. This powerful methodology has been paramount for the mapping of membrane or membraneless organelles as well as for the understanding of hard-to-purify protein complexes, such as those of transmembrane proteins. Unsurprisingly, more and more infection biology research groups have recognized the potential of PL for the identification of host-pathogen interactions. In this chapter, we introduce the enzymes commonly used for PL labeling as well as recent promising advancements and summarize the major achievements in organelle mapping and nucleic acid PL. Moreover, we comprehensively describe the research on host-pathogen interactions using PL, giving special attention to studies in the field of virology.
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Affiliation(s)
- Francisco José Zapatero-Belinchón
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany; Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden.
| | - Belén Carriquí-Madroñal
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany; Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hannover, Germany
| | - Gisa Gerold
- Department of Biochemistry & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, Hannover, Germany; Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture Between the Medical School Hannover and the Helmholtz Centre for Infection Research, Hannover, Germany; Department of Clinical Microbiology, Virology, Umeå University, Umeå, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, Umeå, Sweden.
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24
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Courtland JL, Bradshaw TWA, Waitt G, Soderblom EJ, Ho T, Rajab A, Vancini R, Kim IH, Soderling SH. Genetic disruption of WASHC4 drives endo-lysosomal dysfunction and cognitive-movement impairments in mice and humans. eLife 2021; 10:e61590. [PMID: 33749590 PMCID: PMC7984842 DOI: 10.7554/elife.61590] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 02/09/2021] [Indexed: 12/12/2022] Open
Abstract
Mutation of the Wiskott-Aldrich syndrome protein and SCAR homology (WASH) complex subunit, SWIP, is implicated in human intellectual disability, but the cellular etiology of this association is unknown. We identify the neuronal WASH complex proteome, revealing a network of endosomal proteins. To uncover how dysfunction of endosomal SWIP leads to disease, we generate a mouse model of the human WASHC4c.3056C>G mutation. Quantitative spatial proteomics analysis of SWIPP1019R mouse brain reveals that this mutation destabilizes the WASH complex and uncovers significant perturbations in both endosomal and lysosomal pathways. Cellular and histological analyses confirm that SWIPP1019R results in endo-lysosomal disruption and uncover indicators of neurodegeneration. We find that SWIPP1019R not only impacts cognition, but also causes significant progressive motor deficits in mice. A retrospective analysis of SWIPP1019R patients reveals similar movement deficits in humans. Combined, these findings support the model that WASH complex destabilization, resulting from SWIPP1019R, drives cognitive and motor impairments via endo-lysosomal dysfunction in the brain.
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Affiliation(s)
- Jamie L Courtland
- Department of Neurobiology, Duke University School of MedicineDurhamUnited States
| | - Tyler WA Bradshaw
- Department of Neurobiology, Duke University School of MedicineDurhamUnited States
| | - Greg Waitt
- Proteomics and Metabolomics Shared Resource, Duke University School of MedicineDurhamUnited States
| | - Erik J Soderblom
- Proteomics and Metabolomics Shared Resource, Duke University School of MedicineDurhamUnited States
- Department of Cell Biology, Duke University School of MedicineDurhamUnited States
| | - Tricia Ho
- Proteomics and Metabolomics Shared Resource, Duke University School of MedicineDurhamUnited States
| | - Anna Rajab
- Burjeel Hospital, VPS HealthcareMuscatOman
| | - Ricardo Vancini
- Department of Pathology, Duke University School of MedicineDurhamUnited States
| | - Il Hwan Kim
- Department of Cell Biology, Duke University School of MedicineDurhamUnited States
- Department of Anatomy and Neurobiology, University of Tennessee Heath Science CenterMemphisUnited States
| | - Scott H Soderling
- Department of Neurobiology, Duke University School of MedicineDurhamUnited States
- Department of Cell Biology, Duke University School of MedicineDurhamUnited States
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25
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Turnšek J, Brunson JK, Viedma MDPM, Deerinck TJ, Horák A, Oborník M, Bielinski VA, Allen AE. Proximity proteomics in a marine diatom reveals a putative cell surface-to-chloroplast iron trafficking pathway. eLife 2021; 10:e52770. [PMID: 33591270 PMCID: PMC7972479 DOI: 10.7554/elife.52770] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 02/15/2021] [Indexed: 12/16/2022] Open
Abstract
Iron is a biochemically critical metal cofactor in enzymes involved in photosynthesis, cellular respiration, nitrate assimilation, nitrogen fixation, and reactive oxygen species defense. Marine microeukaryotes have evolved a phytotransferrin-based iron uptake system to cope with iron scarcity, a major factor limiting primary productivity in the global ocean. Diatom phytotransferrin is endocytosed; however, proteins downstream of this environmentally ubiquitous iron receptor are unknown. We applied engineered ascorbate peroxidase APEX2-based subcellular proteomics to catalog proximal proteins of phytotransferrin in the model marine diatom Phaeodactylum tricornutum. Proteins encoded by poorly characterized iron-sensitive genes were identified including three that are expressed from a chromosomal gene cluster. Two of them showed unambiguous colocalization with phytotransferrin adjacent to the chloroplast. Further phylogenetic, domain, and biochemical analyses suggest their involvement in intracellular iron processing. Proximity proteomics holds enormous potential to glean new insights into iron acquisition pathways and beyond in these evolutionarily, ecologically, and biotechnologically important microalgae.
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Affiliation(s)
- Jernej Turnšek
- Biological and Biomedical Sciences, The Graduate School of Arts and Sciences, Harvard UniversityCambridgeUnited States
- Department of Systems Biology, Harvard Medical SchoolBostonUnited States
- Wyss Institute for Biologically Inspired Engineering, Harvard UniversityBostonUnited States
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San DiegoLa JollaUnited States
- Center for Research in Biological Systems, University of California San DiegoLa JollaUnited States
- Microbial and Environmental Genomics, J. Craig Venter InstituteLa JollaUnited States
| | - John K Brunson
- Microbial and Environmental Genomics, J. Craig Venter InstituteLa JollaUnited States
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San DiegoLa JollaUnited States
| | | | - Thomas J Deerinck
- National Center for Microscopy and Imaging Research, University of California San DiegoLa JollaUnited States
| | - Aleš Horák
- Biology Centre CAS, Institute of ParasitologyČeské BudějoviceCzech Republic
- University of South Bohemia, Faculty of ScienceČeské BudějoviceCzech Republic
| | - Miroslav Oborník
- Biology Centre CAS, Institute of ParasitologyČeské BudějoviceCzech Republic
- University of South Bohemia, Faculty of ScienceČeské BudějoviceCzech Republic
| | - Vincent A Bielinski
- Synthetic Biology and Bioenergy, J. Craig Venter InstituteLa JollaUnited States
| | - Andrew Ellis Allen
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San DiegoLa JollaUnited States
- Microbial and Environmental Genomics, J. Craig Venter InstituteLa JollaUnited States
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26
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Homma Y, Hiragi S, Fukuda M. Rab family of small GTPases: an updated view on their regulation and functions. FEBS J 2021; 288:36-55. [PMID: 32542850 PMCID: PMC7818423 DOI: 10.1111/febs.15453] [Citation(s) in RCA: 212] [Impact Index Per Article: 70.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/27/2020] [Accepted: 06/11/2020] [Indexed: 12/13/2022]
Abstract
The Rab family of small GTPases regulates intracellular membrane trafficking by orchestrating the biogenesis, transport, tethering, and fusion of membrane-bound organelles and vesicles. Like other small GTPases, Rabs cycle between two states, an active (GTP-loaded) state and an inactive (GDP-loaded) state, and their cycling is catalyzed by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). Because an active form of each Rab localizes on a specific organelle (or vesicle) and recruits various effector proteins to facilitate each step of membrane trafficking, knowing when and where Rabs are activated and what effectors Rabs recruit is crucial to understand their functions. Since the discovery of Rabs, they have been regarded as one of the central hubs for membrane trafficking, and numerous biochemical and genetic studies have revealed the mechanisms of Rab functions in recent years. The results of these studies have included the identification and characterization of novel GEFs, GAPs, and effectors, as well as post-translational modifications, for example, phosphorylation, of Rabs. Rab functions beyond the simple effector-recruiting model are also emerging. Furthermore, the recently developed CRISPR/Cas technology has enabled acceleration of knockout analyses in both animals and cultured cells and revealed previously unknown physiological roles of many Rabs. In this review article, we provide the most up-to-date and comprehensive lists of GEFs, GAPs, effectors, and knockout phenotypes of mammalian Rabs and discuss recent findings in regard to their regulation and functions.
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Affiliation(s)
- Yuta Homma
- Laboratory of Membrane Trafficking MechanismsDepartment of Integrative Life SciencesGraduate School of Life SciencesTohoku UniversitySendaiJapan
| | - Shu Hiragi
- Laboratory of Membrane Trafficking MechanismsDepartment of Integrative Life SciencesGraduate School of Life SciencesTohoku UniversitySendaiJapan
| | - Mitsunori Fukuda
- Laboratory of Membrane Trafficking MechanismsDepartment of Integrative Life SciencesGraduate School of Life SciencesTohoku UniversitySendaiJapan
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27
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Iacobucci I, Monaco V, Cozzolino F, Monti M. From classical to new generation approaches: An excursus of -omics methods for investigation of protein-protein interaction networks. J Proteomics 2020; 230:103990. [PMID: 32961344 DOI: 10.1016/j.jprot.2020.103990] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/11/2020] [Accepted: 08/31/2020] [Indexed: 01/24/2023]
Abstract
Functional Proteomics aims to the identification of in vivo protein-protein interaction (PPI) in order to piece together protein complexes, and therefore, cell pathways involved in biological processes of interest. Over the years, proteomic approaches used for protein-protein interaction investigation have relied on classical biochemical protocols adapted to a global overview of protein-protein interactions, within so-called "interactomics" investigation. In particular, their coupling with advanced mass spectrometry instruments and innovative analytical methods led to make great strides in the PPIs investigation in proteomics. In this review, an overview of protein complexes purification strategies, from affinity purification approaches, including proximity-dependent labeling techniques and cross-linking strategy for the identification of transient interactions, to Blue Native Gel Electrophoresis (BN-PAGE) and Size Exclusion Chromatography (SEC) employed in the "complexome profiling", has been reported, giving a look to their developments, strengths and weakness and providing to readers several recent applications of each strategy. Moreover, a section dedicated to bioinformatic databases and platforms employed for protein networks analyses was also included.
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Affiliation(s)
- Ilaria Iacobucci
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Vittoria Monaco
- CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Flora Cozzolino
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy.
| | - Maria Monti
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy.
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28
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Bosch JA, Chen CL, Perrimon N. Proximity-dependent labeling methods for proteomic profiling in living cells: An update. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2020; 10:e392. [PMID: 32909689 DOI: 10.1002/wdev.392] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/11/2020] [Accepted: 07/01/2020] [Indexed: 12/14/2022]
Abstract
Characterizing the proteome composition of organelles and subcellular regions of living cells can facilitate the understanding of cellular organization as well as protein interactome networks. Proximity labeling-based methods coupled with mass spectrometry (MS) offer a high-throughput approach for systematic analysis of spatially restricted proteomes. Proximity labeling utilizes enzymes that generate reactive radicals to covalently tag neighboring proteins. The tagged endogenous proteins can then be isolated for further analysis by MS. To analyze protein-protein interactions or identify components that localize to discrete subcellular compartments, spatial expression is achieved by fusing the enzyme to specific proteins or signal peptides that target to particular subcellular regions. Although these technologies have only been introduced recently, they have already provided deep insights into a wide range of biological processes. Here, we provide an updated description and comparison of proximity labeling methods, as well as their applications and improvements. As each method has its own unique features, the goal of this review is to describe how different proximity labeling methods can be used to answer different biological questions. This article is categorized under: Technologies > Analysis of Proteins.
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Affiliation(s)
- Justin A Bosch
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Chiao-Lin Chen
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts, USA.,Howard Hughes Medical Institute, Boston, Massachusetts, USA
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29
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MARTINIÈRE A, MOREAU P. Complex roles of Rabs and SNAREs in the secretory pathway and plant development: a never‐ending story. J Microsc 2020; 280:140-157. [DOI: 10.1111/jmi.12952] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/22/2020] [Accepted: 07/31/2020] [Indexed: 12/14/2022]
Affiliation(s)
- A. MARTINIÈRE
- Univ Montpellier, CNRS, INRAE, Montpellier SupAgro BPMP Montpellier France
| | - P. MOREAU
- UMR 5200 Membrane Biogenesis Laboratory CNRS and University of Bordeaux, INRAE Bordeaux Villenave d'Ornon France
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30
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Ni H, Xu S, Chen H, Dai Q. Nicotine Modulates CTSS (Cathepsin S) Synthesis and Secretion Through Regulating the Autophagy-Lysosomal Machinery in Atherosclerosis. Arterioscler Thromb Vasc Biol 2020; 40:2054-2069. [PMID: 32640907 DOI: 10.1161/atvbaha.120.314053] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
OBJECTIVE Increased CTSS (cathepsin S) has been reported to play a critical role in atherosclerosis progression. Both CTSS synthesis and secretion are essential for exerting its functions. However, the underlying mechanisms contributing to CTSS synthesis and secretion in atherosclerosis remain unclear. Approach and Results: In this study, we showed that nicotine activated autophagy and upregulated CTSS expression in vascular smooth muscle cells and in atherosclerotic plaques. Western blotting and immunofluorescent staining showed that nicotine inhibited the mTORC1 (mammalian target of rapamycin complex 1) activity, promoted the nuclear translocation of TFEB (transcription factor EB), and upregulated the expression of CTSS. Chromatin immunoprecipitation-qualificative polymerase chain reaction, electrophoretic mobility shift assay, and luciferase reporter assay further demonstrated that TFEB directly bound to the CTSS promoter. mTORC1 inhibition by nicotine or rapamycin promoted lysosomal exocytosis and CTSS secretion. Live cell assays and IP-MS (immunoprecipitation-mass spectrometry) identified that the interactions involving Rab10 (Rab10, member RAS oncogene family) and mTORC1 control CTSS secretion. Nicotine promoted vascular smooth muscle cell migration by upregulating CTSS, and CTSS inhibition suppressed nicotine-induced atherosclerosis in vivo. CONCLUSIONS We concluded that nicotine mediates CTSS synthesis and secretion through regulating the autophagy-lysosomal machinery, which offers a potential therapeutic target for atherosclerosis treatment.
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Affiliation(s)
- Huaner Ni
- From the Department of Cardiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Shuang Xu
- From the Department of Cardiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Hangwei Chen
- From the Department of Cardiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, China
| | - Qiuyan Dai
- From the Department of Cardiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, China
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31
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The GABARAP Co-Secretome Identified by APEX2-GABARAP Proximity Labelling of Extracellular Vesicles. Cells 2020; 9:cells9061468. [PMID: 32560054 PMCID: PMC7349886 DOI: 10.3390/cells9061468] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/05/2020] [Accepted: 06/12/2020] [Indexed: 01/07/2023] Open
Abstract
The autophagy-related ATG8 protein GABARAP has not only been shown to be involved in the cellular self-degradation process called autophagy but also fulfils functions in intracellular trafficking processes such as receptor transport to the plasma membrane. Notably, available mass spectrometry data suggest that GABARAP is also secreted into extracellular vesicles (EVs). Here, we confirm this finding by the immunoblotting of EVs isolated from cell culture supernatants and human blood serum using specific anti-GABARAP antibodies. To investigate the mechanism by which GABARAP is secreted, we applied proximity labelling, a method for studying the direct environment of a protein of interest in a confined cellular compartment. By expressing an engineered peroxidase (APEX2)-tagged variant of GABARAP—which, like endogenous GABARAP, was present in EVs prepared from HEK293 cells—we demonstrate the applicability of APEX2-based proximity labelling to EVs. The biotinylated protein pool which contains the APEX2-GABARAP co-secretome contained not only known GABARAP interaction partners but also proteins that were found in APEX2-GABARAP’s proximity inside of autophagosomes in an independent study. All in all, we not only introduce a versatile tool for co-secretome analysis in general but also uncover the first details about autophagy-based pathways as possible biogenesis mechanisms of GABARAP-containing EVs.
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32
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Nassari S, Del Olmo T, Jean S. Rabs in Signaling and Embryonic Development. Int J Mol Sci 2020; 21:E1064. [PMID: 32033485 PMCID: PMC7037298 DOI: 10.3390/ijms21031064] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 01/29/2020] [Accepted: 02/03/2020] [Indexed: 02/06/2023] Open
Abstract
Rab GTPases play key roles in various cellular processes. They are essential, among other roles, to membrane trafficking and intracellular signaling events. Both trafficking and signaling events are crucial for proper embryonic development. Indeed, embryogenesis is a complex process in which cells respond to various signals and undergo dramatic changes in their shape, position, and function. Over the last few decades, cellular studies have highlighted the novel signaling roles played by Rab GTPases, while numerous studies have shed light on the important requirements of Rab proteins at various steps of embryonic development. In this review, we aimed to generate an overview of Rab contributions during animal embryogenesis. We first briefly summarize the involvement of Rabs in signaling events. We then extensively highlight the contribution of Rabs in shaping metazoan development and conclude with new approaches that will allow investigation of Rab functions in vivo.
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Affiliation(s)
| | | | - Steve Jean
- Faculté de Médecine et des Sciences de la Santé, Department of Immunology and Cell Biology, Université de Sherbrooke, 3201 Rue Jean Mignault, Sherbrooke, QC J1E 4K8, Canada; (S.N.); (T.D.O.)
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33
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A simple method for non-denaturing purification of biotin-tagged proteins through competitive elution with free biotin. Biotechniques 2019; 68:41-44. [PMID: 31825236 DOI: 10.2144/btn-2019-0088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The use of avidin or streptavidin in the purification of biotinylated proteins has been highly restricted due to the harsh and denaturing elution conditions. Here, we use biotinylated bovine serum albumin as a working model to demonstrate a simple and rapid method for biotin-tagged protein purification under non-denaturing conditions. The biotinylated bovine serum albumin is specifically bound to the anti-biotin antibody agarose beads and competitively eluted with free biotin under near-neutral conditions. The optimized elution conditions include using 4 mg/ml biotin (pH 8.5) as the elution buffer and allowing the buffer to incubate with agarose beads for 30 min prior to elution. The elution recovery rate is over 85% without apparent protein denaturation. The method is applicable for both immunoprecipitation and column chromatography.
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Del Olmo T, Lacarrière-Keïta C, Normandin C, Jean D, Boisvert FM, Jean S. RAB21 interacts with TMED10 and modulates its localization and abundance. Biol Open 2019; 8:bio.045336. [PMID: 31455601 PMCID: PMC6777364 DOI: 10.1242/bio.045336] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Membrane trafficking controls vesicular transport of cargo between cellular compartments. Vesicular trafficking is essential for cellular homeostasis and dysfunctional trafficking is linked to several pathologies such as neurodegenerative diseases. Following endocytosis, early endosomes act as sorting stations of internalized materials, routing cargo toward various fates. One important class of membrane trafficking regulators are RAB GTPases. RAB21 has been associated with multiple functions and regulates integrin internalization, endosomal sorting of specific clathrin-independent cargo and autophagy. Although RAB21 is mostly associated with early endosomes, it has been shown to mediate a specific sorting event at the Golgi. From mass spectrometry data, we identified a GTP-favored interaction between RAB21 and TMED10 and 9, essential regulators of COPI and COPII vesicles. Using RAB21 knockout cells, we describe the role of RAB21 in modulating TMED10 Golgi localization. Taken together, our study suggests a new potential function of RAB21 in modulating TMED10 trafficking, with relevance to neurodegenerative disorders. Summary: A small early endosomal RAB GTPase is found to interact with p24 family members, with potential impacts on p24 functions.
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Affiliation(s)
- Tomas Del Olmo
- Faculté de Médecine et des Sciences de la Santé, Département d'anatomie et de biologie cellulaire, Université de Sherbrooke, 3201, Rue Jean Mignault, Sherbrooke, Québec, Canada J1E 4K8
| | - Camille Lacarrière-Keïta
- Faculté de Médecine et des Sciences de la Santé, Département d'anatomie et de biologie cellulaire, Université de Sherbrooke, 3201, Rue Jean Mignault, Sherbrooke, Québec, Canada J1E 4K8
| | - Caroline Normandin
- Faculté de Médecine et des Sciences de la Santé, Département d'anatomie et de biologie cellulaire, Université de Sherbrooke, 3201, Rue Jean Mignault, Sherbrooke, Québec, Canada J1E 4K8
| | - Dominique Jean
- Faculté de Médecine et des Sciences de la Santé, Département d'anatomie et de biologie cellulaire, Université de Sherbrooke, 3201, Rue Jean Mignault, Sherbrooke, Québec, Canada J1E 4K8
| | - François-Michel Boisvert
- Faculté de Médecine et des Sciences de la Santé, Département d'anatomie et de biologie cellulaire, Université de Sherbrooke, 3201, Rue Jean Mignault, Sherbrooke, Québec, Canada J1E 4K8
| | - Steve Jean
- Faculté de Médecine et des Sciences de la Santé, Département d'anatomie et de biologie cellulaire, Université de Sherbrooke, 3201, Rue Jean Mignault, Sherbrooke, Québec, Canada J1E 4K8
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35
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Colorectal cancer cells respond differentially to autophagy inhibition in vivo. Sci Rep 2019; 9:11316. [PMID: 31383875 PMCID: PMC6683171 DOI: 10.1038/s41598-019-47659-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 07/19/2019] [Indexed: 12/19/2022] Open
Abstract
Autophagy has both tumor-promoting and -suppressing effects in cancer, including colorectal cancer (CRC), with transformed cells often exhibiting high autophagic flux. In established tumors, autophagy inhibition can lead to opposite responses resulting in either tumor cell death or hyperproliferation. The functional mechanisms underlying these differences are poorly understood. The present study aimed to investigate the relationship between the autophagic capacities of CRC cells and their sensitivities to autophagy inhibition. All studied CRC cell lines showed high basal autophagic flux. However, only HCT116 and Caco-2/15 cells displayed regulated autophagic flux upon starvation. Knockdown of ATG5 (which disrupts autophagosome elongation) or RAB21 (which decreases autophagosome/lysosome fusion) had little effect on CRC cell proliferation in vitro. Nonetheless, inhibition of autophagy in vivo had a substantial cell line-dependent impact on tumor growth, with some cells displaying decreased (HCT116 and Caco-2/15) or increased (SW480 and LoVo) proliferation. RNA sequencing and Western blot analyses in hyperproliferative SW480 tumors revealed that the mTORC2 and AKT pathways were hyperactivated following autophagy impairment. Inhibition of either mTOR or AKT activities rescued the observed hyperproliferation in autophagy-inhibited SW480 and reduced tumor growth. These results highlight that autophagy inhibition can lead, in specific cellular contexts, to compensatory mechanisms promoting tumor growth.
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