1
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Gopaldass N, Chen KE, Collins B, Mayer A. Assembly and fission of tubular carriers mediating protein sorting in endosomes. Nat Rev Mol Cell Biol 2024; 25:765-783. [PMID: 38886588 DOI: 10.1038/s41580-024-00746-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2024] [Indexed: 06/20/2024]
Abstract
Endosomes are central protein-sorting stations at the crossroads of numerous membrane trafficking pathways in all eukaryotes. They have a key role in protein homeostasis and cellular signalling and are involved in the pathogenesis of numerous diseases. Endosome-associated protein assemblies or coats collect transmembrane cargo proteins and concentrate them into retrieval domains. These domains can extend into tubular carriers, which then pinch off from the endosomal membrane and deliver the cargoes to appropriate subcellular compartments. Here we discuss novel insights into the structure of a number of tubular membrane coats that mediate the recruitment of cargoes into these carriers, focusing on sorting nexin-based coats such as Retromer, Commander and ESCPE-1. We summarize current and emerging views of how selective tubular endosomal carriers form and detach from endosomes by fission, highlighting structural aspects, conceptual challenges and open questions.
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Affiliation(s)
- Navin Gopaldass
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland.
| | - Kai-En Chen
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Brett Collins
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Andreas Mayer
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland.
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2
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Butkovič R, Walker AP, Healy MD, McNally KE, Liu M, Veenendaal T, Kato K, Liv N, Klumperman J, Collins BM, Cullen PJ. Mechanism and regulation of cargo entry into the Commander endosomal recycling pathway. Nat Commun 2024; 15:7180. [PMID: 39168982 PMCID: PMC11339278 DOI: 10.1038/s41467-024-50971-0] [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: 12/21/2023] [Accepted: 07/25/2024] [Indexed: 08/23/2024] Open
Abstract
Commander is a multiprotein complex that orchestrates endosomal recycling of integral cargo proteins and is essential for normal development. While the structure of this complex has recently been described, how cargo proteins are selected for Commander-mediated recycling remains unclear. Here we identify the mechanism through which the unstructured carboxy-terminal tail of the cargo adaptor sorting nexin-17 (SNX17) directly binds to the Retriever sub-complex of Commander. SNX17 adopts an autoinhibited conformation where its carboxy-terminal tail occupies the cargo binding groove. Competitive cargo binding overcomes this autoinhibition, promoting SNX17 endosomal residency and the release of the tail for Retriever association. Furthermore, our study establishes the central importance of SNX17-Retriever association in the handover of integrin and lipoprotein receptor cargoes into pre-existing endosomal retrieval sub-domains. In describing the principal mechanism of cargo entry into the Commander recycling pathway we provide key insight into the function and regulation of this evolutionary conserved sorting pathway.
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Affiliation(s)
- Rebeka Butkovič
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol, UK.
| | - Alexander P Walker
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol, UK
| | - Michael D Healy
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Biosciences, The University of Queensland, SLCA, Australia
| | - Kerrie E McNally
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol, UK
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Meihan Liu
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Biosciences, The University of Queensland, SLCA, Australia
| | - Tineke Veenendaal
- Center for Molecular Medicine, University Medical Center Utrecht, Institute of Biomembranes, Utrecht University, Utrecht, The Netherlands
| | - Kohji Kato
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol, UK
| | - Nalan Liv
- Center for Molecular Medicine, University Medical Center Utrecht, Institute of Biomembranes, Utrecht University, Utrecht, The Netherlands
| | - Judith Klumperman
- Center for Molecular Medicine, University Medical Center Utrecht, Institute of Biomembranes, Utrecht University, Utrecht, The Netherlands
| | - Brett M Collins
- Centre for Cell Biology of Chronic Disease, Institute for Molecular Biosciences, The University of Queensland, SLCA, Australia.
| | - Peter J Cullen
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol, UK.
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3
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Chandra M, Kendall AK, Ford MGJ, Jackson LP. VARP binds SNX27 to promote endosomal supercomplex formation on membranes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.603126. [PMID: 39026782 PMCID: PMC11257539 DOI: 10.1101/2024.07.11.603126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Multiple essential membrane trafficking pathways converge at endosomes to maintain cellular homeostasis by sorting critical transmembrane cargo proteins to the plasma membrane or the trans-Golgi network (TGN). The Retromer heterotrimer (VPS26/VPS35/VPS29 subunits) binds multiple sorting nexin (SNX) proteins on endosomal membranes, but molecular mechanisms regarding formation and regulation of metazoan SNX/Retromer complexes have been elusive. Here, we combine biochemical and biophysical approaches with AlphaFold2 Multimer modeling to identify a direct interaction between the VARP N-terminus and SNX27 PDZ domain. VARP and SNX27 interact with high nanomolar affinity using the binding pocket established for PDZ binding motif (PDZbm) cargo. Specific point mutations in VARP abrogate the interaction in vitro. We further establish a full biochemical reconstitution system using purified mammalian proteins to directly and systematically test whether multiple endosomal coat complexes are recruited to membranes to generate tubules. We successfully use purified coat components to demonstrate which combinations of Retromer with SNX27, ESCPE-1 (SNX2/SNX6), or both complexes can remodel membranes containing physiological cargo motifs and phospholipid composition. SNX27, alone and with Retromer, induces tubule formation in the presence of PI(3)P and PDZ cargo motifs. ESCPE-1 deforms membranes enriched with Folch I and CI-MPR cargo motifs, but surprisingly does not recruit Retromer. Finally, we find VARP is required to reconstitute a proposed endosomal "supercomplex" containing SNX27, ESCPE-1, and Retromer on PI(3)P-enriched membranes. These data suggest VARP functions as a key regulator in metazoans to promote cargo sorting out of endosomes.
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Affiliation(s)
- Mintu Chandra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Amy K Kendall
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Marijn G J Ford
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Lauren P Jackson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
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4
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Wang D, Zhao X, Wang P, Liu JJ. SNX32 Regulates Sorting and Trafficking of Activated EGFR to the Lysosomal Degradation Pathway. Traffic 2024; 25:e12952. [PMID: 39073202 DOI: 10.1111/tra.12952] [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: 12/05/2023] [Revised: 07/07/2024] [Accepted: 07/08/2024] [Indexed: 07/30/2024]
Abstract
SNX32 is a member of the evolutionarily conserved Phox (PX) homology domain- and Bin/Amphiphysin/Rvs (BAR) domain- containing sorting nexin (SNX-BAR) family of proteins, which play important roles in sorting and membrane trafficking of endosomal cargoes. Although SNX32 shares the highest amino acid sequence homology with SNX6, and has been believed to function redundantly with SNX5 and SNX6 in retrieval of the cation-independent mannose-6-phosphate receptor (CI-MPR) from endosomes to the trans-Golgi network (TGN), its role(s) in intracellular protein trafficking remains largely unexplored. Here, we report that it functions in parallel with SNX1 in mediating epidermal growth factor (EGF)-stimulated postendocytic trafficking of the epidermal growth factor receptor (EGFR). Moreover, SNX32 interacts directly with EGFR, and recruits SNX5 to promote sorting of EGF-EGFR into multivesicular bodies (MVBs) for lysosomal degradation. Thus, SNX32 functions distinctively from other SNX-BAR proteins to mediate signaling-coupled endolysosomal trafficking of EGFR.
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Affiliation(s)
- Dou Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xia Zhao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, Yunnan University, Kunming, China
| | - Panpan Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jia-Jia Liu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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5
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Li S, Williamson ZL, Christofferson MA, Jeevanandam A, Campos SK. A peptide derived from sorting nexin 1 inhibits HPV16 entry, retrograde trafficking, and L2 membrane spanning. Tumour Virus Res 2024; 18:200287. [PMID: 38909779 PMCID: PMC11255958 DOI: 10.1016/j.tvr.2024.200287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/16/2024] [Accepted: 06/16/2024] [Indexed: 06/25/2024] Open
Abstract
High risk human papillomavirus (HPV) infection is responsible for 99 % of cervical cancers and 5 % of all human cancers worldwide. HPV infection requires the viral genome (vDNA) to gain access to nuclei of basal keratinocytes of epithelium. After virion endocytosis, the minor capsid protein L2 dictates the subcellular retrograde trafficking and nuclear localization of the vDNA during mitosis. Prior work identified a cell-permeable peptide termed SNX1.3, derived from the BAR domain of sorting nexin 1 (SNX1), that potently blocks the retrograde and nuclear trafficking of EGFR in triple negative breast cancer cells. Given the importance of EGFR and retrograde trafficking pathways in HPV16 infection, we set forth to study the effects of SNX1.3 within this context. SNX1.3 inhibited HPV16 infection by both delaying virion endocytosis, as well as potently blocking virion retrograde trafficking and Golgi localization. SNX1.3 had no effect on cell proliferation, nor did it affect post-Golgi trafficking of HPV16. Looking more directly at L2 function, SNX1.3 was found to impair membrane spanning of the minor capsid protein. Future work will focus on mechanistic studies of SNX1.3 inhibition, and the role of EGFR signaling and SNX1-mediated endosomal tubulation, cargo sorting, and retrograde trafficking in HPV infection.
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Affiliation(s)
- Shuaizhi Li
- Department of Immunobiology, University of Arizona, Tucson, AZ, USA
| | - Zachary L Williamson
- Biochemistry and Molecular & Cellular Biology Graduate Program, University of Arizona, Tucson, AZ, USA
| | | | | | - Samuel K Campos
- Department of Immunobiology, University of Arizona, Tucson, AZ, USA; Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ, USA; Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ, USA; BIO5 Institute, University of Arizona, Tucson, AZ, USA.
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6
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Yoshida S, Hasegawa T, Nakamura T, Sato K, Sugeno N, Ishiyama S, Sekiguchi K, Tobita M, Takeda A, Aoki M. Dysregulation of SNX1-retromer axis in pharmacogenetic models of Parkinson's disease. Cell Death Discov 2024; 10:290. [PMID: 38886344 PMCID: PMC11183211 DOI: 10.1038/s41420-024-02062-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/30/2024] [Accepted: 06/05/2024] [Indexed: 06/20/2024] Open
Abstract
Since the identification of vacuolar protein sorting (VPS) 35, as a causative molecule for familial Parkinson's disease (PD), retromer-mediated endosomal machinery has been a rising factor in the pathogenesis of the disease. The retromer complex cooperates with sorting nexin (SNX) dimer and DNAJC13, another causal molecule in PD, to transport cargoes from endosomes to the trans-Golgi network, and is also involved in mitochondrial dynamics and autophagy. Retromer dysfunction may induce neuronal death leading to PD via several biological cascades, including misfolded, insoluble α-synuclein (aS) accumulation and mitochondrial dysfunction; however, the detailed mechanisms remain poorly understood. In this study, we showed that the stagnation of retromer-mediated retrograde transport consistently occurs in different PD-mimetic conditions, i.e., overexpression of PD-linked mutant DNAJC13, excess aS induction, or toxin-induced mitochondrial dysfunction. Mechanistically, DNAJC13 was found to be involved in clathrin-dependent retromer transport as a functional modulator of SNX1 together with heat shock cognate 70 kDa protein (Hsc70), which was controlled by the binding and dissociation of DNAJC13 and SNX1 in an Hsc70 activity-dependent manner. In addition, excess amount of aS decreased the interaction between SNX1 and VPS35, the core component of retromer. Furthermore, R33, a pharmacological retromer chaperone, reduced insoluble aS and mitigated rotenone-induced neuronal apoptosis. These findings suggest that retrograde transport regulated by SNX1-retromer may be profoundly involved in the pathogenesis of PD and is a potential target for disease-modifying therapy for the disease.
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Grants
- 20K07896 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 23K06823 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 19K16998 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 23K14769 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 20K07862 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- 23K19557 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
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Affiliation(s)
- Shun Yoshida
- Division of Neurology, Department of Neuroscience & Sensory Organs, Tohoku University Graduate School of Medicine, Sendai, Miyagi, 980-8574, Japan
- Department of Neurology, NHO Yonezawa National Hospital, Yonezawa, Yamagata, 992-1202, Japan
| | - Takafumi Hasegawa
- Division of Neurology, Department of Neuroscience & Sensory Organs, Tohoku University Graduate School of Medicine, Sendai, Miyagi, 980-8574, Japan.
- Department of Neurology, NHO Sendai-Nishitaga Hospital, Sendai, Miyagi, 982-8555, Japan.
| | - Takaaki Nakamura
- Division of Neurology, Department of Neuroscience & Sensory Organs, Tohoku University Graduate School of Medicine, Sendai, Miyagi, 980-8574, Japan
- Department of Neurology, NHO Miyagi National Hospital, Watari, Miyagi, 989-2202, Japan
| | - Kazuki Sato
- Division of Neurology, Department of Neuroscience & Sensory Organs, Tohoku University Graduate School of Medicine, Sendai, Miyagi, 980-8574, Japan
| | - Naoto Sugeno
- Division of Neurology, Department of Neuroscience & Sensory Organs, Tohoku University Graduate School of Medicine, Sendai, Miyagi, 980-8574, Japan
| | - Shun Ishiyama
- Division of Neurology, Department of Neuroscience & Sensory Organs, Tohoku University Graduate School of Medicine, Sendai, Miyagi, 980-8574, Japan
| | - Kiyotoshi Sekiguchi
- Division of Matrixome Research and Application, Institute for Protein Research, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Muneshige Tobita
- Department of Neurology, NHO Yonezawa National Hospital, Yonezawa, Yamagata, 992-1202, Japan
| | - Atsushi Takeda
- Department of Neurology, NHO Sendai-Nishitaga Hospital, Sendai, Miyagi, 982-8555, Japan
| | - Masashi Aoki
- Division of Neurology, Department of Neuroscience & Sensory Organs, Tohoku University Graduate School of Medicine, Sendai, Miyagi, 980-8574, Japan
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7
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Li S, Williamson ZL, Christofferson MA, Jeevanandam A, Campos SK. A Peptide Derived from Sorting Nexin 1 Inhibits HPV16 Entry, Retrograde Trafficking, and L2 Membrane Spanning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.25.595865. [PMID: 38826391 PMCID: PMC11142256 DOI: 10.1101/2024.05.25.595865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
High risk human papillomavirus (HPV) infection is responsible for 99% of cervical cancers and 5% of all human cancers worldwide. HPV infection requires the viral genome (vDNA) to gain access to nuclei of basal keratinocytes of epithelium. After virion endocytosis, the minor capsid protein L2 dictates the subcellular retrograde trafficking and nuclear localization of the vDNA during mitosis. Prior work identified a cell-permeable peptide termed SNX1.3, derived from the BAR domain of sorting nexin 1 (SNX1), that potently blocks the retrograde and nuclear trafficking of EGFR in triple negative breast cancer cells. Given the importance of EGFR and retrograde trafficking pathways in HPV16 infection, we set forth to study the effects of SNX1.3 within this context. SNX1.3 inhibited HPV16 infection by both delaying virion endocytosis, as well as potently blocking virion retrograde trafficking and Golgi localization. SNX1.3 had no effect on cell proliferation, nor did it affect post-Golgi trafficking of HPV16. Looking more directly at L2 function, SNX1.3 was found to impair membrane spanning of the minor capsid protein. Future work will focus on mechanistic studies of SNX1.3 inhibition, and the role of EGFR signaling and SNX1- mediated endosomal tubulation, cargo sorting, and retrograde trafficking in HPV infection.
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Affiliation(s)
- Shuaizhi Li
- Department of Immunobiology, University of Arizona, Tucson, AZ USA
- Current Address: Microbiologics, Inc. Saint Cloud, MN USA
| | - Zachary L Williamson
- Department of Immunobiology, University of Arizona, Tucson, AZ USA
- Current Address: Microbiologics, Inc. Saint Cloud, MN USA
- Biochemistry and Molecular & Cellular Biology Graduate Program, University of Arizona, Tucson, AZ USA
- Current Address: Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC Canada
- Current Address: Department of Immunobiology, Yale University, New Haven, CT USA
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ USA
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ USA
- BIO5 Institute, University of Arizona, Tucson, AZ USA, HPV16
| | - Matthew A Christofferson
- Department of Immunobiology, University of Arizona, Tucson, AZ USA
- Current Address: Department of Microbiology & Immunology, University of British Columbia, Vancouver, BC Canada
| | - Advait Jeevanandam
- Department of Immunobiology, University of Arizona, Tucson, AZ USA
- Current Address: Department of Immunobiology, Yale University, New Haven, CT USA
| | - Samuel K Campos
- Department of Immunobiology, University of Arizona, Tucson, AZ USA
- Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ USA
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona, Tucson, AZ USA
- BIO5 Institute, University of Arizona, Tucson, AZ USA, HPV16
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8
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Shortill SP, Frier MS, Davey M, Conibear E. N-terminal signals in the SNX-BAR paralogs Vps5 and Vin1 guide endosomal coat complex formation. Mol Biol Cell 2024; 35:ar76. [PMID: 38598303 PMCID: PMC11238075 DOI: 10.1091/mbc.e24-01-0043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/03/2024] [Accepted: 04/05/2024] [Indexed: 04/12/2024] Open
Abstract
Endosomal coats incorporate membrane-binding subunits such as sorting nexin (SNX) proteins. The Saccharomyces cerevisiae SNX-BAR paralogs Vin1 and Vps5 are respective subunits of the endosomal VINE and retromer complexes whose dimerizing BAR domains are required for complex assembly and membrane association. However, a degree of promiscuity is predicted for yeast BAR-BAR pairings, and recent work has implicated the unstructured N-terminal domains of Vin1 and Vps5 in coat formation. Here, we map N-terminal signals in both SNX-BAR paralogs that contribute to the assembly and function of two distinct endosomal coats in vivo. Whereas Vin1 leverages a polybasic region and adjacent hydrophobic motif to bind Vrl1 and form VINE, the N-terminus of Vps5 interacts with the retromer subunit Vps29 at two sites, including a conserved hydrophobic pocket in Vps29 that engages other accessory proteins in humans. We also examined the sole isoform of Vps5 from the milk yeast Kluyveromyces lactis and found that ancestral yeasts may have used a nested N-terminal signal to form both VINE and retromer. Our results suggest that the specific assembly of Vps5-family SNX-BAR coats depends on inputs from unique N-terminal sequence features in addition to BAR domain coupling, expanding our understanding of endosomal coat biology.
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Affiliation(s)
- Shawn P. Shortill
- Department of Medical Genetics, University of British Columbia, Vancouver, BC VH6 3N1, Canada
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Mia S. Frier
- Department of Medical Genetics, University of British Columbia, Vancouver, BC VH6 3N1, Canada
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Michael Davey
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Elizabeth Conibear
- Department of Medical Genetics, University of British Columbia, Vancouver, BC VH6 3N1, Canada
- Centre for Molecular Medicine and Therapeutics, British Columbia Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
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9
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Tziouvara O, Petsana M, Kourounis D, Papadaki A, Basdra E, Braliou GG, Boleti H. Characterization of the First Secreted Sorting Nexin Identified in the Leishmania Protists. Int J Mol Sci 2024; 25:4095. [PMID: 38612903 PMCID: PMC11012638 DOI: 10.3390/ijms25074095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/19/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024] Open
Abstract
Proteins of the sorting nexin (SNX) family present a modular structural architecture with a phox homology (PX) phosphoinositide (PI)-binding domain and additional PX structural domains, conferring to them a wide variety of vital eukaryotic cell's functions, from signal transduction to membrane deformation and cargo binding. Although SNXs are well studied in human and yeasts, they are poorly investigated in protists. Herein, is presented the characterization of the first SNX identified in Leishmania protozoan parasites encoded by the LdBPK_352470 gene. In silico secondary and tertiary structure prediction revealed a PX domain on the N-terminal half and a Bin/amphiphysin/Rvs (BAR) domain on the C-terminal half of this protein, with these features classifying it in the SNX-BAR subfamily of SNXs. We named the LdBPK_352470.1 gene product LdSNXi, as it is the first SNX identified in Leishmania (L.) donovani. Its expression was confirmed in L. donovani promastigotes under different cell cycle phases, and it was shown to be secreted in the extracellular medium. Using an in vitro lipid binding assay, it was demonstrated that recombinant (r) LdSNXi (rGST-LdSNXi) tagged with glutathione-S-transferase (GST) binds to the PtdIns3P and PtdIns4P PIs. Using a specific a-LdSNXi antibody and immunofluorescence confocal microscopy, the intracellular localization of endogenous LdSNXi was analyzed in L. donovani promastigotes and axenic amastigotes. Additionally, rLdSNXi tagged with enhanced green fluorescent protein (rLdSNXi-EGFP) was heterologously expressed in transfected HeLa cells and its localization was examined. All observed localizations suggest functions compatible with the postulated SNX identity of LdSNXi. Sequence, structure, and evolutionary analysis revealed high homology between LdSNXi and the human SNX2, while the investigation of protein-protein interactions based on STRING (v.11.5) predicted putative molecular partners of LdSNXi in Leishmania.
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Affiliation(s)
- Olympia Tziouvara
- Intracellular Parasitism Group, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (O.T.); (M.P.); (D.K.); (A.P.)
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Marina Petsana
- Intracellular Parasitism Group, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (O.T.); (M.P.); (D.K.); (A.P.)
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 2–4 Papasiopoulou Str., 35131 Lamia, Greece;
| | - Drosos Kourounis
- Intracellular Parasitism Group, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (O.T.); (M.P.); (D.K.); (A.P.)
| | - Amalia Papadaki
- Intracellular Parasitism Group, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (O.T.); (M.P.); (D.K.); (A.P.)
| | - Efthimia Basdra
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Georgia G. Braliou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 2–4 Papasiopoulou Str., 35131 Lamia, Greece;
| | - Haralabia Boleti
- Intracellular Parasitism Group, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (O.T.); (M.P.); (D.K.); (A.P.)
- Bioimaging Unit, Hellenic Pasteur Institute, 11521 Athens, Greece
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10
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Overduin M, Bhat R. Recognition and remodeling of endosomal zones by sorting nexins. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184305. [PMID: 38408696 DOI: 10.1016/j.bbamem.2024.184305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 02/05/2024] [Accepted: 02/18/2024] [Indexed: 02/28/2024]
Abstract
The proteolipid code determines how cytosolic proteins find and remodel membrane surfaces. Here, we investigate how this process works with sorting nexins Snx1 and Snx3. Both proteins form sorting machines by recognizing membrane zones enriched in phosphatidylinositol 3-phosphate (PI3P), phosphatidylserine (PS) and cholesterol. This co-localized combination forms a unique "lipid codon" or lipidon that we propose is responsible for endosomal targeting, as revealed by structures and interactions of their PX domain-based readers. We outline a membrane recognition and remodeling mechanism for Snx1 and Snx3 involving this code element alongside transmembrane pH gradients, dipole moment-guided docking and specific protein-protein interactions. This generates an initial membrane-protein assembly (memtein) that then recruits retromer and additional PX proteins to recruit cell surface receptors for sorting to the trans-Golgi network (TGN), lysosome and plasma membranes. Post-translational modification (PTM) networks appear to regulate how the sorting machines form and operate at each level. The commonalities and differences between these sorting nexins show how the proteolipid code orchestrates parallel flows of molecular information from ribosome emergence to organelle genesis, and illuminates a universally applicable model of the membrane.
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Affiliation(s)
- Michael Overduin
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada.
| | - Rakesh Bhat
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
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11
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Liao Z, Si T, Kai JJ, Fan J. Mechanism of Membrane Curvature Induced by SNX1: Insights from Molecular Dynamics Simulations. J Phys Chem B 2024; 128:2144-2153. [PMID: 38408890 DOI: 10.1021/acs.jpcb.3c07009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
SNX proteins have been found to induce membrane remodeling to facilitate the generation of transport carriers in endosomal pathways. However, the molecular mechanism of membrane bending and the role of lipids in the bending process remain elusive. Here, we conducted coarse-grained molecular dynamics simulations to investigate the role of the three structural modules (PX, BAR, and AH) of SNX1 and the PI3P lipids in membrane deformation. We observed that the presence of all three domains is essential for SNX1 to achieve a stable membrane deformation. BAR is capable of remodeling the membrane through the charged residues on its concave surface, but it requires PX and AH to establish stable membrane binding. AH penetrates into the lipid membrane, thereby promoting the induction of membrane curvature; however, it is inadequate on its own to maintain membrane bending. PI3P lipids are also indispensable for membrane remodeling, as they play a dominant role in the interactions of lipids with the BAR domain. Our results enhance the comprehension of the molecular mechanism underlying SNX1-induced membrane curvature and help future studies of curvature-inducing proteins.
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Affiliation(s)
- Zhenyu Liao
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon 999077 Hong Kong, China
| | - Ting Si
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon 999077 Hong Kong, China
- Department of Physics, City University of Hong Kong, Kowloon 999077 Hong Kong, China
| | - Ji-Jung Kai
- Department of Mechanical Engineering, City University of Hong Kong, Kowloon 999077 Hong Kong, China
- Centre for Advanced Nuclear Safety and Sustainable Development, City University of Hong Kong, Kowloon 999077 Hong Kong, China
| | - Jun Fan
- Department of Materials Science and Engineering, City University of Hong Kong, Kowloon 999077 Hong Kong, China
- Department of Mechanical Engineering, City University of Hong Kong, Kowloon 999077 Hong Kong, China
- Centre for Advanced Nuclear Safety and Sustainable Development, City University of Hong Kong, Kowloon 999077 Hong Kong, China
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12
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Sanchez L, Lensen A, Connor MG, Hamon M, Enninga J, Valenzuela C. Shigella generates distinct IAM subpopulations during epithelial cell invasion to promote efficient intracellular niche formation. Eur J Cell Biol 2024; 103:151381. [PMID: 38183814 DOI: 10.1016/j.ejcb.2023.151381] [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: 05/22/2023] [Revised: 12/20/2023] [Accepted: 12/24/2023] [Indexed: 01/08/2024] Open
Abstract
The facultative intracellular pathogen Shigella flexneri invades non-phagocytic epithelial gut cells. Through a syringe-like apparatus called type 3 secretion system, it injects effector proteins into the host cell triggering actin rearrangements leading to its uptake within a tight vacuole, termed the bacterial-containing vacuole (BCV). Simultaneously, Shigella induces the formation of large vesicles around the entry site, which we refer to as infection-associated macropinosomes (IAMs). After entry, Shigella ruptures the BCV and escapes into the host cytosol by disassembling the BCV remnants. Previously, IAM formation has been shown to be required for efficient BCV escape, but the molecular events associated with BCV disassembly have remained unclear. To identify host components required for BCV disassembly, we performed a microscopy-based screen to monitor the recruitment of BAR domain-containing proteins, which are a family of host proteins involved in membrane shaping and sensing (e.g. endocytosis and recycling) during Shigella epithelial cell invasion. We identified endosomal recycling BAR protein Sorting Nexin-8 (SNX8) localized to IAMs in a PI(3)P-dependent manner before BCV disassembly. At least two distinct IAM subpopulations around the BCV were found, either being recycled back to cellular compartments such as the plasma membrane or transitioning to become RAB11A positive "contact-IAMs" involved in promoting BCV rupture. The IAM subpopulation duality was marked by the exclusive recruitment of either SNX8 or RAB11A. Hindering PI(3)P production at the IAMs led to an inhibition of SNX8 recruitment at these compartments and delayed both, the step of BCV rupture time and successful BCV disassembly. Finally, siRNA depletion of SNX8 accelerated BCV rupture and unpeeling of BCV remnants, indicating that SNX8 is involved in controlling the timing of the cytosolic release. Overall, our work sheds light on how Shigella establishes its intracellular niche through the subversion of a specific set of IAMs.
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Affiliation(s)
- Lisa Sanchez
- Institut Pasteur, Université Paris Cité, CNRS UMR3691, Dynamics of Host-Pathogen Interactions Unit, 75015 Paris, France
| | - Arthur Lensen
- Institut Pasteur, Université Paris Cité, CNRS UMR3691, Dynamics of Host-Pathogen Interactions Unit, 75015 Paris, France
| | - Michael G Connor
- Institut Pasteur, Université Paris Cité, Chromatin and Infection Unit, 75015 Paris, France
| | - Mélanie Hamon
- Institut Pasteur, Université Paris Cité, Chromatin and Infection Unit, 75015 Paris, France
| | - Jost Enninga
- Institut Pasteur, Université Paris Cité, CNRS UMR3691, Dynamics of Host-Pathogen Interactions Unit, 75015 Paris, France.
| | - Camila Valenzuela
- Institut Pasteur, Université Paris Cité, CNRS UMR3691, Dynamics of Host-Pathogen Interactions Unit, 75015 Paris, France.
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13
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Yu W, Hu Y, Liu Z, Guo K, Ma D, Peng M, Wang Y, Zhang J, Zhang X, Wang P, Zhang J, Liu P, Lu J. Sorting nexin 3 exacerbates doxorubicin-induced cardiomyopathy via regulation of TFRC-dependent ferroptosis. Acta Pharm Sin B 2023; 13:4875-4892. [PMID: 38045054 PMCID: PMC10692393 DOI: 10.1016/j.apsb.2023.08.016] [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: 01/17/2023] [Revised: 06/06/2023] [Accepted: 06/13/2023] [Indexed: 12/05/2023] Open
Abstract
The clinical utilization of doxorubicin (Dox) in various malignancies is restrained by its major adverse effect: irreversible cardiomyopathy. Extensive studies have been done to explore the prevention of Dox cardiomyopathy. Currently, ferroptosis has been shown to participate in the incidence and development of Dox cardiomyopathy. Sorting Nexin 3 (SNX3), the retromer-associated cargo binding protein with important physiological functions, was identified as a potent therapeutic target for cardiac hypertrophy in our previous study. However, few study has shown whether SNX3 plays a critical role in Dox-induced cardiomyopathy. In this study, a decreased level of SNX3 in Dox-induced cardiomyopathy was observed. Cardiac-specific Snx3 knockout (Snx3-cKO) significantly alleviated cardiomyopathy by downregulating Dox-induced ferroptosis significantly. SNX3 was further demonstrated to exacerbate Dox-induced cardiomyopathy via induction of ferroptosis in vivo and in vitro, and cardiac-specific Snx3 transgenic (Snx3-cTg) mice were more susceptible to Dox-induced ferroptosis and cardiomyopathy. Mechanistically, SNX3 facilitated the recycling of transferrin 1 receptor (TFRC) via direct interaction, disrupting iron homeostasis, increasing the accumulation of iron, triggering ferroptosis, and eventually exacerbating Dox-induced cardiomyopathy. Overall, these findings established a direct SNX3-TFRC-ferroptosis positive regulatory axis in Dox-induced cardiomyopathy and suggested that targeting SNX3 provided a new effective therapeutic strategy for Dox-induced cardiomyopathy through TFRC-dependent ferroptosis.
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Affiliation(s)
- Wenjing Yu
- National and Local United Engineering Lab of Druggability and New Drugs Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangdong Province Engineering Laboratory for Druggability and New Drug Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuehuai Hu
- National and Local United Engineering Lab of Druggability and New Drugs Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangdong Province Engineering Laboratory for Druggability and New Drug Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhiping Liu
- School of Pharmacy, Jinan University, Guangzhou 510632, China
| | - Kaiteng Guo
- National and Local United Engineering Lab of Druggability and New Drugs Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Dinghu Ma
- National and Local United Engineering Lab of Druggability and New Drugs Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Mingxia Peng
- National and Local United Engineering Lab of Druggability and New Drugs Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuemei Wang
- National and Local United Engineering Lab of Druggability and New Drugs Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jing Zhang
- National and Local United Engineering Lab of Druggability and New Drugs Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Xiaolei Zhang
- National and Local United Engineering Lab of Druggability and New Drugs Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Panxia Wang
- National and Local United Engineering Lab of Druggability and New Drugs Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jiguo Zhang
- School of Pharmaceutical Sciences, Shandong First Medical University & Shangdong Academy of Medical Sciences, Taian 271016, China
| | - Peiqing Liu
- National and Local United Engineering Lab of Druggability and New Drugs Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangdong Province Engineering Laboratory for Druggability and New Drug Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- School of Pharmaceutical Sciences, Shandong First Medical University & Shangdong Academy of Medical Sciences, Taian 271016, China
| | - Jing Lu
- National and Local United Engineering Lab of Druggability and New Drugs Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangdong Province Engineering Laboratory for Druggability and New Drug Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
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14
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Atwell B, Chalasani P, Schroeder J. Nuclear epidermal growth factor receptor as a therapeutic target. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:616-629. [PMID: 37720348 PMCID: PMC10501894 DOI: 10.37349/etat.2023.00156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/09/2023] [Indexed: 09/19/2023] Open
Abstract
Epidermal growth factor receptor (EGFR) is one of the most well-studied oncogenes with roles in proliferation, growth, metastasis, and therapeutic resistance. This intense study has led to the development of a range of targeted therapeutics including small-molecule tyrosine kinase inhibitors (TKIs), monoclonal antibodies, and nanobodies. These drugs are excellent at blocking the activation and kinase function of wild-type EGFR (wtEGFR) and several common EGFR mutants. These drugs have significantly improved outcomes for patients with cancers including head and neck, glioblastoma, colorectal, and non-small cell lung cancer (NSCLC). However, therapeutic resistance is often seen, resulting from acquired mutations or activation of compensatory signaling pathways. Additionally, these therapies are ineffective in tumors where EGFR is found predominantly in the nucleus, as can be found in triple negative breast cancer (TNBC). In TNBC, EGFR is subjected to alternative trafficking which drives the nuclear localization of the receptor. In the nucleus, EGFR interacts with several proteins to activate transcription, DNA repair, migration, and chemoresistance. Nuclear EGFR (nEGFR) correlates with metastatic disease and worse patient prognosis yet targeting its nuclear localization has proved difficult. This review provides an overview of current EGFR-targeted therapies and novel peptide-based therapies that block nEGFR, as well as their clinical applications and potential for use in oncology.
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Affiliation(s)
- Benjamin Atwell
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Pavani Chalasani
- Department of Medicine, University of Arizona, Tucson, AZ 85721, USA
- University of Arizona Cancer Center, Tucson, AZ 85721, USA
| | - Joyce Schroeder
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA
- University of Arizona Cancer Center, Tucson, AZ 85721, USA
- Bio5 Institute, University of Arizona, Tucson, AZ 85721, USA
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15
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Lopez-Robles C, Scaramuzza S, Astorga-Simon EN, Ishida M, Williamson CD, Baños-Mateos S, Gil-Carton D, Romero-Durana M, Vidaurrazaga A, Fernandez-Recio J, Rojas AL, Bonifacino JS, Castaño-Díez D, Hierro A. Architecture of the ESCPE-1 membrane coat. Nat Struct Mol Biol 2023; 30:958-969. [PMID: 37322239 PMCID: PMC10352136 DOI: 10.1038/s41594-023-01014-7] [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: 10/13/2022] [Accepted: 05/05/2023] [Indexed: 06/17/2023]
Abstract
Recycling of membrane proteins enables the reuse of receptors, ion channels and transporters. A key component of the recycling machinery is the endosomal sorting complex for promoting exit 1 (ESCPE-1), which rescues transmembrane proteins from the endolysosomal pathway for transport to the trans-Golgi network and the plasma membrane. This rescue entails the formation of recycling tubules through ESCPE-1 recruitment, cargo capture, coat assembly and membrane sculpting by mechanisms that remain largely unknown. Herein, we show that ESCPE-1 has a single-layer coat organization and suggest how synergistic interactions between ESCPE-1 protomers, phosphoinositides and cargo molecules result in a global arrangement of amphipathic helices to drive tubule formation. Our results thus define a key process of tubule-based endosomal sorting.
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Affiliation(s)
| | | | | | - Morié Ishida
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Chad D Williamson
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | | | - David Gil-Carton
- CIC bioGUNE, Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- BREM Basque Resource for Electron Microscopy, Leioa, Spain
| | - Miguel Romero-Durana
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC-Universidad de La Rioja-Gobierno de La Rioja, Logroño, Spain
| | | | - Juan Fernandez-Recio
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
- Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC-Universidad de La Rioja-Gobierno de La Rioja, Logroño, Spain
| | | | - Juan S Bonifacino
- Neurosciences and Cellular and Structural Biology Division, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA.
| | - Daniel Castaño-Díez
- BioEM Lab, Biozentrum, University of Basel, Basel, Switzerland.
- Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, Spain.
| | - Aitor Hierro
- CIC bioGUNE, Derio, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
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16
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Carosi JM, Denton D, Kumar S, Sargeant TJ. Receptor Recycling by Retromer. Mol Cell Biol 2023; 43:317-334. [PMID: 37350516 PMCID: PMC10348044 DOI: 10.1080/10985549.2023.2222053] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/01/2023] [Indexed: 06/24/2023] Open
Abstract
The highly conserved retromer complex controls the fate of hundreds of receptors that pass through the endolysosomal system and is a central regulatory node for diverse metabolic programs. More than 20 years ago, retromer was discovered as an essential regulator of endosome-to-Golgi transport in yeast; since then, significant progress has been made to characterize how metazoan retromer components assemble to enable its engagement with endosomal membranes, where it sorts cargo receptors from endosomes to the trans-Golgi network or plasma membrane through recognition of sorting motifs in their cytoplasmic tails. In this review, we examine retromer regulation by exploring its assembled structure with an emphasis on how a range of adaptor proteins shape the process of receptor trafficking. Specifically, we focus on how retromer is recruited to endosomes, selects cargoes, and generates tubulovesicular carriers that deliver cargoes to target membranes. We also examine how cells adapt to distinct metabolic states by coordinating retromer expression and function. We contrast similarities and differences between retromer and its related complexes: retriever and commander/CCC, as well as their interplay in receptor trafficking. We elucidate how loss of retromer regulation is central to the pathology of various neurogenerative and metabolic diseases, as well as microbial infections, and highlight both opportunities and cautions for therapeutics that target retromer. Finally, with a focus on understanding the mechanisms that govern retromer regulation, we outline new directions for the field moving forward.
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Affiliation(s)
- Julian M. Carosi
- Lysosomal Health in Ageing, Lifelong Health, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
- Centre for Cancer Biology, University of South Australia (UniSA), Adelaide, South Australia, Australia
- School of Biological Sciences, Faculty of Sciences, Engineering and Technology, The University of Adelaide, Adelaide, South Australia, Australia
| | - Donna Denton
- Centre for Cancer Biology, University of South Australia (UniSA), Adelaide, South Australia, Australia
| | - Sharad Kumar
- Centre for Cancer Biology, University of South Australia (UniSA), Adelaide, South Australia, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Timothy J. Sargeant
- Lysosomal Health in Ageing, Lifelong Health, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, South Australia, Australia
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17
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Zhao Y, Caron C, Chan YY, Lee CK, Xu X, Zhang J, Masubuchi T, Wu C, Bui JD, Hui E. cis-B7:CD28 interactions at invaginated synaptic membranes provide CD28 co-stimulation and promote CD8 + T cell function and anti-tumor immunity. Immunity 2023; 56:1187-1203.e12. [PMID: 37160118 PMCID: PMC10330546 DOI: 10.1016/j.immuni.2023.04.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 01/30/2023] [Accepted: 04/07/2023] [Indexed: 05/11/2023]
Abstract
B7 ligands (CD80 and CD86), expressed by professional antigen-presenting cells (APCs), activate the main co-stimulatory receptor CD28 on T cells in trans. However, in peripheral tissues, APCs expressing B7 ligands are relatively scarce. This raises the questions of whether and how CD28 co-stimulation occurs in peripheral tissues. Here, we report that CD8+ T cells displayed B7 ligands that interacted with CD28 in cis at membrane invaginations of the immunological synapse as a result of membrane remodeling driven by phosphoinositide-3-kinase (PI3K) and sorting-nexin-9 (SNX9). cis-B7:CD28 interactions triggered CD28 signaling through protein kinase C theta (PKCθ) and promoted CD8+ T cell survival, migration, and cytokine production. In mouse tumor models, loss of T cell-intrinsic cis-B7:CD28 interactions decreased intratumoral T cells and accelerated tumor growth. Thus, B7 ligands on CD8+ T cells can evoke cell-autonomous CD28 co-stimulation in cis in peripheral tissues, suggesting cis-signaling as a general mechanism for boosting T cell functionality.
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Affiliation(s)
- Yunlong Zhao
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.
| | - Christine Caron
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
| | - Ya-Yuan Chan
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Calvin K Lee
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
| | - Xiaozheng Xu
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jibin Zhang
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Takeya Masubuchi
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Chuan Wu
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jack D Bui
- Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA.
| | - Enfu Hui
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.
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18
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Simonetti B, Daly JL, Cullen PJ. Out of the ESCPE room: Emerging roles of endosomal SNX-BARs in receptor transport and host-pathogen interaction. Traffic 2023; 24:234-250. [PMID: 37089068 PMCID: PMC10768393 DOI: 10.1111/tra.12885] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/22/2023] [Accepted: 03/28/2023] [Indexed: 04/25/2023]
Abstract
Several functions of the human cell, such as sensing nutrients, cell movement and interaction with the surrounding environment, depend on a myriad of transmembrane proteins and their associated proteins and lipids (collectively termed "cargoes"). To successfully perform their tasks, cargo must be sorted and delivered to the right place, at the right time, and in the right amount. To achieve this, eukaryotic cells have evolved a highly organized sorting platform, the endosomal network. Here, a variety of specialized multiprotein complexes sort cargo into itineraries leading to either their degradation or their recycling to various organelles for further rounds of reuse. A key sorting complex is the Endosomal SNX-BAR Sorting Complex for Promoting Exit (ESCPE-1) that promotes the recycling of an array of cargos to the plasma membrane and/or the trans-Golgi network. ESCPE-1 recognizes a hydrophobic-based sorting motif in numerous cargoes and orchestrates their packaging into tubular carriers that pinch off from the endosome and travel to the target organelle. A wide range of pathogens mimic this sorting motif to hijack ESCPE-1 transport to promote their invasion and survival within infected cells. In other instances, ESCPE-1 exerts restrictive functions against pathogens by limiting their replication and infection. In this review, we discuss ESCPE-1 assembly and functions, with a particular focus on recent advances in the understanding of its role in membrane trafficking, cellular homeostasis and host-pathogen interaction.
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Affiliation(s)
- Boris Simonetti
- Charles River Laboratories, Discovery House, Quays Office ParkConference Avenue, PortisheadBristolUK
| | - James L. Daly
- Department of Infectious DiseasesSchool of Immunology and Microbial Sciences, Guy's Hospital, King's College LondonLondonUK
| | - Peter J. Cullen
- School of Biochemistry, Faculty of Life Sciences, Biomedical Sciences BuildingUniversity of BristolBristolUK
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19
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Xie Y, Zhang Y, Wang Y, Feng Y. Mechanism and Modulation of SidE Family Proteins in the Pathogenesis of Legionella pneumophila. Pathogens 2023; 12:pathogens12040629. [PMID: 37111515 PMCID: PMC10143409 DOI: 10.3390/pathogens12040629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 04/29/2023] Open
Abstract
Legionella pneumophila is the causative agent of Legionnaires' disease, causing fever and lung infection, with a death rate up to 15% in severe cases. In the process of infection, Legionella pneumophila secretes over 330 effectors into host cell via the Dot/Icm type IV secretion system to modulate multiple host cellular physiological processes, thereby changing the environment of the host cell and promoting the growth and propagation of the bacterium. Among these effector proteins, SidE family proteins from Legionella pneumophila catalyze a non-canonical ubiquitination reaction, which combines mono-ADP-ribosylation and phosphodiesterase activities together to attach ubiquitin onto substrates. Meanwhile, the activity of SidE family proteins is also under multiple modulations by other effectors. Herein we summarize the key insights into recent studies in this area, emphasizing the tight link between the modular structure of SidE family proteins and the pathogen virulence as well as the fundamental mechanism and modulation network for further extensive research.
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Affiliation(s)
- Yongchao Xie
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271002, China
| | - Yi Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an 271002, China
| | - Yue Feng
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing Key Laboratory of Bioprocess, State Key Laboratory of Chemical Resource Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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20
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Buser DP, Spang A. Protein sorting from endosomes to the TGN. Front Cell Dev Biol 2023; 11:1140605. [PMID: 36895788 PMCID: PMC9988951 DOI: 10.3389/fcell.2023.1140605] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 02/09/2023] [Indexed: 02/23/2023] Open
Abstract
Retrograde transport from endosomes to the trans-Golgi network is essential for recycling of protein and lipid cargoes to counterbalance anterograde membrane traffic. Protein cargo subjected to retrograde traffic include lysosomal acid-hydrolase receptors, SNARE proteins, processing enzymes, nutrient transporters, a variety of other transmembrane proteins, and some extracellular non-host proteins such as viral, plant, and bacterial toxins. Efficient delivery of these protein cargo molecules depends on sorting machineries selectively recognizing and concentrating them for their directed retrograde transport from endosomal compartments. In this review, we outline the different retrograde transport pathways governed by various sorting machineries involved in endosome-to-TGN transport. In addition, we discuss how this transport route can be analyzed experimentally.
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Affiliation(s)
| | - Anne Spang
- *Correspondence: Dominik P. Buser, ; Anne Spang,
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21
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Reinhart EF, Katzenell S, Andhare D, Bauer KM, Ragusa MJ. A Comparative Analysis of the Membrane Binding and Remodeling Properties of Two Related Sorting Nexin Complexes Involved in Autophagy. Biochemistry 2023; 62:657-668. [PMID: 35421303 PMCID: PMC9561124 DOI: 10.1021/acs.biochem.2c00007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The sorting nexin (SNX) proteins, Atg20 and Atg24, are involved in nonselective autophagy, are necessary for efficient selective autophagy, and are required for the cytoplasm-to-vacuole transport pathway. However, the specific roles of these proteins in autophagy are not well understood. Atg20 and Atg24 each contain a Phox homology domain that facilitates phosphoinositide binding. They also each contain an SNX-Bin/Amphiphysin/Rvs domain that forms a cup-shaped dimer, capable of binding to curved membranes and remodeling those membranes in some cases. Atg20 and Atg24 form two distinct complexes, an Atg24/Atg24 homodimer and an Atg20/Atg24 heterodimer. Despite the presence of Atg24 in both complexes, it is currently unclear if these complexes have different membrane binding and remodeling properties. Therefore, in this study, we explored the membrane binding and shaping properties of these two dimeric complexes. We found that Atg24/Atg24 and Atg20/Atg24 have distinct membrane binding preferences. Both dimers recognized membranes containing phosphatidylinositol 3-phosphate [PI(3)P] and phosphatidylinositol 3,5-bisphosphate, but Atg20/Atg24 bound to a broader array of liposomes, including those lacking phosphorylated phosphatidylinositol. In addition, we discovered that while both complexes bound to autophagosomal-like liposomes containing at least 5% PI(3)P, Atg20/Atg24 was capable of binding to autophagosomal-like liposomes lacking PI(3)P. Lastly, we observed that the Atg20/Atg24 heterodimer tubulates PI(3)P-containing and autophagosomal-like liposomes, but the Atg24/Atg24 homodimer could not tubulate these liposomes. Our findings suggest that these two dimers contain distinct membrane binding and shaping properties.
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Affiliation(s)
- Erin F. Reinhart
- Department of Chemistry, Dartmouth College, Hanover, New
Hampshire 03755, United States
| | - Sarah Katzenell
- Department of Chemistry, Dartmouth College, Hanover, New
Hampshire 03755, United States
| | - Devika Andhare
- Department of Chemistry, Dartmouth College, Hanover, New
Hampshire 03755, United States
| | - Katherine M. Bauer
- Department of Biochemistry and Cell Biology, Geisel School
of Medicine, Dartmouth College, Hanover, New Hampshire 03755, United States
| | - Michael J. Ragusa
- Department of Chemistry, Dartmouth College, Hanover, New
Hampshire 03755, United States
- Department of Biochemistry and Cell Biology, Geisel School
of Medicine, Dartmouth College, Hanover, New Hampshire 03755, United States
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22
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Atwell B, Chen CY, Christofferson M, Montfort WR, Schroeder J. Sorting nexin-dependent therapeutic targeting of oncogenic epidermal growth factor receptor. Cancer Gene Ther 2023; 30:267-276. [PMID: 36253541 PMCID: PMC9935382 DOI: 10.1038/s41417-022-00541-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 09/15/2022] [Accepted: 09/27/2022] [Indexed: 11/09/2022]
Abstract
Overexpression and/or overactivation of the Epidermal Growth Factor Receptor (EGFR) is oncogenic in several tumor types yet targeting the kinase domain of wildtype EGFR has had limited success. EGFR has numerous kinase-independent roles, one of which is accomplished through the Sorting Nexin-dependent retrotranslocation of EGFR to the nucleus, which is observed in some metastatic cancers and therapeutically resistant disease. Here, we have utilized the BAR domain of Sorting Nexin 1 to create a peptide-based therapeutic (cSNX1.3) that promotes cell death in EGFR-expressing cancer. We evaluated the efficacy of cSNX1.3 in tumor-bearing WAP-TGFα transgenic mice (an EGFR-dependent model of breast cancer), where cSNX1.3 treatment resulted in significant tumor regression without observable toxicity. Evaluation of remaining tumor tissues found evidence of increased PARP cleavage, suggesting apoptotic tumor cell death. To evaluate the mechanism of action for cSNX1.3, we found that cSNX1.3 binds the C-terminus of the EGFR kinase domain at an interface site opposite the ATP binding domain with a Kd of ~4.0 µM. In vitro analysis found that cSNX1.3 inhibits the nuclear localization of EGFR. To determine specificity, we evaluated cancer cell lines expressing wildtype EGFR (MDA-MB-468, BT20 and A549), mutant EGFR (H1975) and non-transformed lines (CHO and MCF10A). Only transformed lines expressing wildtype EGFR responded to cSNX1.3, while mutant EGFR and normal cells responded better to an EGFR kinase inhibitor. Phenotypically, cSNX1.3 inhibits EGF-, NRG-, and HGF-dependent migration, but not HA-dependent migration. Together, these data indicate that targeting retrotranslocation of EGFR may be a potent therapeutic for RTK-active cancer.
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Affiliation(s)
- Benjamin Atwell
- Department of Molecular and Cellular Biology, 1007 E Lowell St, Tucson, AZ, 85721, USA
| | - Cheng-Yu Chen
- Department of Chemistry and Biochemistry, 1007 E Lowell St, Tucson, AZ, 85721, USA
| | | | - William R Montfort
- Department of Molecular and Cellular Biology, 1007 E Lowell St, Tucson, AZ, 85721, USA.,Department of Chemistry and Biochemistry, 1007 E Lowell St, Tucson, AZ, 85721, USA.,University of Arizona Cancer Center, 1007 E Lowell St, Tucson, AZ, 85721, USA.,BIO5 Institute, University of Arizona, 1007 E Lowell St, Tucson, AZ, 85721, USA
| | - Joyce Schroeder
- Department of Molecular and Cellular Biology, 1007 E Lowell St, Tucson, AZ, 85721, USA. .,University of Arizona Cancer Center, 1007 E Lowell St, Tucson, AZ, 85721, USA. .,BIO5 Institute, University of Arizona, 1007 E Lowell St, Tucson, AZ, 85721, USA.
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23
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Gopaldass N, De Leo MG, Courtellemont T, Mercier V, Bissig C, Roux A, Mayer A. Retromer oligomerization drives SNX-BAR coat assembly and membrane constriction. EMBO J 2023; 42:e112287. [PMID: 36644906 PMCID: PMC9841331 DOI: 10.15252/embj.2022112287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/02/2022] [Accepted: 11/02/2022] [Indexed: 01/17/2023] Open
Abstract
Proteins exit from endosomes through tubular carriers coated by retromer, a complex that impacts cellular signaling, lysosomal biogenesis and numerous diseases. The coat must overcome membrane tension to form tubules. We explored the dynamics and driving force of this process by reconstituting coat formation with yeast retromer and the BAR-domain sorting nexins Vps5 and Vps17 on oriented synthetic lipid tubules. This coat oligomerizes bidirectionally, forming a static tubular structure that does not exchange subunits. High concentrations of sorting nexins alone constrict membrane tubes to an invariant radius of 19 nm. At lower concentrations, oligomers of retromer must bind and interconnect the sorting nexins to drive constriction. Constricting less curved membranes into tubes, which requires more energy, coincides with an increased surface density of retromer on the sorting nexin layer. Retromer-mediated crosslinking of sorting nexins at variable densities may thus tune the energy that the coat can generate to deform the membrane. In line with this, genetic ablation of retromer oligomerization impairs endosomal protein exit in yeast and human cells.
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Affiliation(s)
- Navin Gopaldass
- Department of ImmunobiologyUniversity of LausanneEpalingesSwitzerland
| | | | | | - Vincent Mercier
- Department of BiochemistryUniversity of GenevaGenevaSwitzerland
| | - Christin Bissig
- Department of ImmunobiologyUniversity of LausanneEpalingesSwitzerland
| | - Aurélien Roux
- Department of BiochemistryUniversity of GenevaGenevaSwitzerland
- Swiss National Centre for Competence in Research Program Chemical BiologyGenevaSwitzerland
| | - Andreas Mayer
- Department of ImmunobiologyUniversity of LausanneEpalingesSwitzerland
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24
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Deb S, Sun J. Endosomal Sorting Protein SNX27 and Its Emerging Roles in Human Cancers. Cancers (Basel) 2022; 15:cancers15010070. [PMID: 36612066 PMCID: PMC9818000 DOI: 10.3390/cancers15010070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/14/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022] Open
Abstract
SNX27 belongs to the sorting nexin (SNX) family of proteins that play a critical role in protein sorting and trafficking in the endocytosis pathway. This protein family is characterized by the presence of a Phox (PX) domain; however, SNX27 is unique in containing an additional PDZ domain. Recently, SNX27 has gained popularity as an important sorting protein that is associated with the retromer complex and mediates the recycling of internalized proteins from endosomes to the plasma membrane in a PDZ domain-dependent manner. Over 100 cell surface proteins have been identified as binding partners of the SNX27-retromer complex. However, the roles and underlying mechanisms governed by SNX27 in tumorigenesis remains to be poorly understood. Many of its known binding partners include several G-protein coupled receptors, such as β2-andrenergic receptor and parathyroid hormone receptor, are associated with multiple pathways implicated in oncogenic signaling and tumorigenesis. Additionally, SNX27 mediates the recycling of GLUT1 and the activation of mTORC1, both of which can regulate intracellular energy balance and promote cell survival and proliferation under conditions of nutrient deprivation. In this review, we summarize the structure and fundamental roles of SNX proteins, with a focus on SNX27, and provide the current evidence indicating towards the role of SNX27 in human cancers. We also discuss the gap in the field and future direction of SNX27 research. Insights into the emerging roles and mechanism of SNX27 in cancers will provide better development strategies to prevent and treat tumorigenesis.
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Affiliation(s)
- Shreya Deb
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Jun Sun
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612, USA
- University of Illinois at Chicago (UIC) Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
- Correspondence: ; Tel.: +1-312-996-5020
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25
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Kumar G, Duggisetty SC, Srivastava A. A Review of Mechanics-Based Mesoscopic Membrane Remodeling Methods: Capturing Both the Physics and the Chemical Diversity. J Membr Biol 2022; 255:757-777. [PMID: 36197492 DOI: 10.1007/s00232-022-00268-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/29/2022] [Indexed: 12/24/2022]
Abstract
Specialized classes of proteins, working together in a tightly orchestrated manner, induce and maintain highly curved cellular and organelles membrane morphology. Due to the various experimental constraints, including the resolution limits of imaging techniques, it is non-trivial to accurately elucidate interactions among the various components involved in membrane deformation. The spatial and temporal scales of the systems also make it formidable to investigate them using simulations with molecular details. Interestingly, mechanics-based mesoscopic models have been used with great success in recapitulating the membrane deformations observed in experiments. In this review, we collate together and discuss the various mechanics-based mesoscopic models for protein-mediated membrane deformation studies. In particular, we provide an elaborate description of a mesoscopic model where the membrane is modeled as a triangulated sheet and proteins are represented as either nematics or filaments. This representation allows us to explore the various aspects of protein-protein and protein-membrane interactions as well as examine the underlying mechanistic pathways for emergent behavior such as curvature-mediated protein localization and membrane deformation. We also put forward current efforts in the field towards back-mapping these mesoscopic models to finer-grained particle-based models-a framework that could be used to explore how molecular interactions propagate to physical scales and vice-versa. We end the review with an integrative-modeling-based road map where experimental imaging micrograph and biochemical data are combined with mesoscopic and molecular simulations methods in a theoretically consistent manner to faithfully recapitulate the multiple length and time scales in the membrane remodeling processes.
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Affiliation(s)
- Gaurav Kumar
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, C. V. Raman Road, Bangalore, Karnataka, 560012, India
| | - Satya Chaithanya Duggisetty
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, C. V. Raman Road, Bangalore, Karnataka, 560012, India
| | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science Bangalore, C. V. Raman Road, Bangalore, Karnataka, 560012, India.
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26
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Solinger JA, Spang A. Sorting of cargo in the tubular endosomal network. Bioessays 2022; 44:e2200158. [DOI: 10.1002/bies.202200158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/28/2022] [Accepted: 09/29/2022] [Indexed: 11/09/2022]
Affiliation(s)
| | - Anne Spang
- Biozentrum University of Basel Basel Switzerland
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27
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Kumar G, Srivastava A. Membrane Remodeling Due to a Mixture of Multiple Types of Curvature Proteins. J Chem Theory Comput 2022; 18:5659-5671. [PMID: 35981766 DOI: 10.1021/acs.jctc.2c00126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present an extension of the Monte Carlo based mesoscopic membrane model, where the membrane is represented as a dynamically triangulated surface and the proteins are modeled as anisotropic inclusions formulated as in-plane nematic field variables adhering to the deformable elastic sheet. In the extended model, we have augmented the Hamiltonian to study membrane deformation due to a mixture of multiple types of curvature generating proteins. This feature opens the door for understanding how multiple kinds of curvature-generating proteins may be working in a coordinated manner to induce desired membrane morphologies. For example, among other things, we study membrane deformations and tubulation due to a mixture of positive and negative curvature proteins as mimics of various proteins from BAR domain family. We also study the effect of membrane anisotropy that manifests as differential binding affinity and organization of curvature proteins, leading to insights into the tightly regulated cargo sorting and transport processes. Our simulation results show different morphology of deformed vesicles that depend on membrane tension, the curvatures and number of the participating proteins as well as on protein-protein and membrane-protein interactions.
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Affiliation(s)
- Gaurav Kumar
- Molecular Biophysics Unit (MBU), Indian Institute of Science (IISc)-Bangalore, C. V. Raman Road, Bangalore, KA 560012, India
| | - Anand Srivastava
- Molecular Biophysics Unit (MBU), Indian Institute of Science (IISc)-Bangalore, C. V. Raman Road, Bangalore, KA 560012, India
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28
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Rodgers SJ, Jones EI, Arumugam S, Hamila SA, Danne J, Gurung R, Eramo MJ, Nanayakkara R, Ramm G, McGrath MJ, Mitchell CA. Endosome maturation links PI3Kα signaling to lysosome repopulation during basal autophagy. EMBO J 2022; 41:e110398. [PMID: 35968799 PMCID: PMC9531306 DOI: 10.15252/embj.2021110398] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 12/24/2022] Open
Abstract
Autophagy depends on the repopulation of lysosomes to degrade intracellular components and recycle nutrients. How cells co‐ordinate lysosome repopulation during basal autophagy, which occurs constitutively under nutrient‐rich conditions, is unknown. Here, we identify an endosome‐dependent phosphoinositide pathway that links PI3Kα signaling to lysosome repopulation during basal autophagy. We show that PI3Kα‐derived PI(3)P generated by INPP4B on late endosomes was required for basal but not starvation‐induced autophagic degradation. PI(3)P signals were maintained as late endosomes matured into endolysosomes, and served as the substrate for the 5‐kinase, PIKfyve, to generate PI(3,5)P2. The SNX‐BAR protein, SNX2, was recruited to endolysosomes by PI(3,5)P2 and promoted lysosome reformation. Inhibition of INPP4B/PIKfyve‐dependent lysosome reformation reduced autophagic clearance of protein aggregates during proteotoxic stress leading to increased cytotoxicity. Therefore under nutrient‐rich conditions, PI3Kα, INPP4B, and PIKfyve sequentially contribute to basal autophagic degradation and protection from proteotoxic stress via PI(3,5)P2‐dependent lysosome reformation from endolysosomes. These findings reveal that endosome maturation couples PI3Kα signaling to lysosome reformation during basal autophagy.
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Affiliation(s)
- Samuel J Rodgers
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Emily I Jones
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Senthil Arumugam
- Department of Anatomy and Developmental Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,European Molecular Biological Laboratory Australia, Monash University, Clayton, VIC, Australia
| | - Sabryn A Hamila
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Jill Danne
- Monash Ramaciotti Centre for Cryo Electron Microscopy, A Node of Microscopy Australia, Monash University, Clayton, VIC, Australia
| | - Rajendra Gurung
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Matthew J Eramo
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Randini Nanayakkara
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,Monash Ramaciotti Centre for Cryo Electron Microscopy, A Node of Microscopy Australia, Monash University, Clayton, VIC, Australia
| | - Georg Ramm
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.,Monash Ramaciotti Centre for Cryo Electron Microscopy, A Node of Microscopy Australia, Monash University, Clayton, VIC, Australia
| | - Meagan J McGrath
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Christina A Mitchell
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
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29
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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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30
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Mallik B, Bhat S, Kumar V. Role of Bin‐Amphiphysin‐Rvs (BAR) domain proteins in mediating neuronal signaling and disease. Synapse 2022; 76:e22248. [DOI: 10.1002/syn.22248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/13/2022] [Accepted: 07/18/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Bhagaban Mallik
- Department of Biological Sciences Indian Institute of Science Education and Research (IISER) Bhopal Indore Bypass Road Bhopal Madhya Pradesh 462 066 India
| | - Sajad Bhat
- Department of Biological Sciences Indian Institute of Science Education and Research (IISER) Bhopal Indore Bypass Road Bhopal Madhya Pradesh 462 066 India
| | - Vimlesh Kumar
- Department of Biological Sciences Indian Institute of Science Education and Research (IISER) Bhopal Indore Bypass Road Bhopal Madhya Pradesh 462 066 India
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31
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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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32
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Courtellemont T, De Leo MG, Gopaldass N, Mayer A. CROP: a retromer-PROPPIN complex mediating membrane fission in the endo-lysosomal system. EMBO J 2022; 41:e109646. [PMID: 35466426 PMCID: PMC9108610 DOI: 10.15252/embj.2021109646] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 01/06/2023] Open
Abstract
Endo-lysosomal compartments exchange proteins by fusing, fissioning, and through endosomal transport carriers. Thereby, they sort many plasma membrane receptors and transporters and control cellular signaling and metabolism. How the membrane fission events are catalyzed is poorly understood. Here, we identify the novel CROP complex as a factor acting at this step. CROP joins members of two protein families: the peripheral subunits of retromer, a coat forming endosomal transport carriers, and membrane inserting PROPPINs. Integration into CROP potentiates the membrane fission activity of the PROPPIN Atg18 on synthetic liposomes and confers strong preference for binding PI(3,5)P2 , a phosphoinositide required for membrane fission activity. Disrupting CROP blocks fragmentation of lysosome-like yeast vacuoles in vivo. CROP-deficient mammalian endosomes accumulate micrometer-long tubules and fail to export cargo, suggesting that carriers attempt to form but cannot separate from these organelles. PROPPINs compete for retromer binding with the SNX-BAR proteins, which recruit retromer to the membrane during the formation of endosomal carriers. Transition from retromer-SNX-BAR complexes to retromer-PROPPIN complexes might hence switch retromer activities from cargo capture to membrane fission.
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Affiliation(s)
| | | | - Navin Gopaldass
- Department of BiochemistryUniversity of LausanneEpalingesSwitzerland
| | - Andreas Mayer
- Department of BiochemistryUniversity of LausanneEpalingesSwitzerland
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33
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Popelka H, Uversky VN. Theater in the Self-Cleaning Cell: Intrinsically Disordered Proteins or Protein Regions Acting with Membranes in Autophagy. MEMBRANES 2022; 12:457. [PMID: 35629783 PMCID: PMC9143426 DOI: 10.3390/membranes12050457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/19/2022] [Accepted: 04/22/2022] [Indexed: 12/30/2022]
Abstract
Intrinsically disordered proteins and protein regions (IDPs/IDPRs) are mainly involved in signaling pathways, where fast regulation, temporal interactions, promiscuous interactions, and assemblies of structurally diverse components including membranes are essential. The autophagy pathway builds, de novo, a membrane organelle, the autophagosome, using carefully orchestrated interactions between proteins and lipid bilayers. Here, we discuss molecular mechanisms related to the protein disorder-based interactions of the autophagy machinery with membranes. We describe not only membrane binding phenomenon, but also examples of membrane remodeling processes including membrane tethering, bending, curvature sensing, and/or fragmentation of membrane organelles such as the endoplasmic reticulum, which is an important membrane source as well as cargo for autophagy. Summary of the current state of knowledge presented here will hopefully inspire new studies. A profound understanding of the autophagic protein-membrane interface is essential for advancements in therapeutic interventions against major human diseases, in which autophagy is involved including neurodegeneration, cancer as well as cardiovascular, metabolic, infectious, musculoskeletal, and other disorders.
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Affiliation(s)
- Hana Popelka
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA;
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34
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Simonetti B, Guo Q, Giménez-Andrés M, Chen KE, Moody ERR, Evans AJ, Chandra M, Danson CM, Williams TA, Collins BM, Cullen PJ. SNX27-Retromer directly binds ESCPE-1 to transfer cargo proteins during endosomal recycling. PLoS Biol 2022; 20:e3001601. [PMID: 35417450 PMCID: PMC9038204 DOI: 10.1371/journal.pbio.3001601] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 04/25/2022] [Accepted: 03/11/2022] [Indexed: 12/14/2022] Open
Abstract
Coat complexes coordinate cargo recognition through cargo adaptors with biogenesis of transport carriers during integral membrane protein trafficking. Here, we combine biochemical, structural, and cellular analyses to establish the mechanistic basis through which SNX27-Retromer, a major endosomal cargo adaptor, couples to the membrane remodeling endosomal SNX-BAR sorting complex for promoting exit 1 (ESCPE-1). In showing that the SNX27 FERM (4.1/ezrin/radixin/moesin) domain directly binds acidic-Asp-Leu-Phe (aDLF) motifs in the SNX1/SNX2 subunits of ESCPE-1, we propose a handover model where SNX27-Retromer captured cargo proteins are transferred into ESCPE-1 transport carriers to promote endosome-to-plasma membrane recycling. By revealing that assembly of the SNX27:Retromer:ESCPE-1 coat evolved in a stepwise manner during early metazoan evolution, likely reflecting the increasing complexity of endosome-to-plasma membrane recycling from the ancestral opisthokont to modern animals, we provide further evidence of the functional diversification of yeast pentameric Retromer in the recycling of hundreds of integral membrane proteins in metazoans.
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Affiliation(s)
- Boris Simonetti
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Qian Guo
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Manuel Giménez-Andrés
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Kai-En Chen
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Edmund R. R. Moody
- School of Biological Sciences, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Ashley J. Evans
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Mintu Chandra
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Chris M. Danson
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Tom A. Williams
- School of Biological Sciences, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
| | - Brett M. Collins
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland, Australia
| | - Peter J. Cullen
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol, United Kingdom
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35
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Zhou C, Wu Z, Du W, Que H, Wang Y, Ouyang Q, Jian F, Yuan W, Zhao Y, Tian R, Li Y, Chen Y, Gao S, Wong CCL, Rong Y. Recycling of autophagosomal components from autolysosomes by the recycler complex. Nat Cell Biol 2022; 24:497-512. [PMID: 35332264 DOI: 10.1038/s41556-022-00861-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 02/04/2022] [Indexed: 11/09/2022]
Abstract
Autolysosomes contain components from autophagosomes and lysosomes. The contents inside the autolysosomal lumen are degraded during autophagy, while the fate of autophagosomal components on the autolysosomal membrane remains unknown. Here we report that the autophagosomal membrane components are not degraded, but recycled from autolysosomes through a process coined in this study as autophagosomal components recycling (ACR). We further identified a multiprotein complex composed of SNX4, SNX5 and SNX17 essential for ACR, which we termed 'recycler'. In this, SNX4 and SNX5 form a heterodimer that recognizes autophagosomal membrane proteins and is required for generating membrane curvature on autolysosomes, both via their BAR domains, to mediate the cargo sorting process. SNX17 interacts with both the dynein-dynactin complex and the SNX4-SNX5 dimer to facilitate the retrieval of autophagosomal membrane components. Our discovery of ACR and identification of the recycler reveal an important retrieval and recycling pathway on autolysosomes.
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Affiliation(s)
- Chuchu Zhou
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhe Wu
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wanqing Du
- The State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Huilin Que
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yufen Wang
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qinqin Ouyang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Fenglei Jian
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weigang Yuan
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Zhao
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rui Tian
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Li
- The State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yang Chen
- Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Peking University, Beijing, China.,School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing, China
| | - Shuaixin Gao
- Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Peking University, Beijing, China.,School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing, China
| | - Catherine C L Wong
- Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Peking University, Beijing, China.,School of Basic Medical Sciences, Peking University Health Science Center, Peking University, Beijing, China
| | - Yueguang Rong
- School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China. .,Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan, China.
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36
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Goyal S, Segarra VA, N, Stecher AM, Truman AW, Reitzel AM, Chi RJ. Vps501, a novel vacuolar SNX-BAR protein cooperates with the SEA complex to regulate TORC1 signaling. Traffic 2022; 23. [PMID: 35098628 PMCID: PMC9305297 DOI: 10.1111/tra.12833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 12/01/2022]
Abstract
The sorting nexins (SNX), constitute a diverse family of molecules that play varied roles in membrane trafficking, cell signaling, membrane remodeling, organelle motility and autophagy. In particular, the SNX-BAR proteins, a SNX subfamily characterized by a C-terminal dimeric Bin/Amphiphysin/Rvs (BAR) lipid curvature domain and a conserved Phox-homology domain, are of great interest. In budding yeast, many SNX-BARs proteins have well-characterized endo-vacuolar trafficking roles. Phylogenetic analyses allowed us to identify an additional SNX-BAR protein, Vps501, with a novel endo-vacuolar role. We report that Vps501 uniquely localizes to the vacuolar membrane and has physical and genetic interactions with the SEA complex to regulate TORC1 inactivation. We found cells displayed a severe deficiency in starvation-induced/nonselective autophagy only when SEA complex subunits are ablated in combination with Vps501, indicating a cooperative role with the SEA complex during TORC1 signaling during autophagy induction. Additionally, we found the SEACIT complex becomes destabilized in vps501Δsea1Δ cells, which resulted in aberrant endosomal TORC1 activity and subsequent Atg13 hyperphosphorylation. We have also discovered that the vacuolar localization of Vps501 is dependent upon a direct interaction with Sea1 and a unique lipid binding specificity that is also required for its function. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Shreya Goyal
- Department of Biological SciencesUniversity of North CarolinaCharlotteNorth CarolinaUSA
| | | | - Nitika
- Department of Biological SciencesUniversity of North CarolinaCharlotteNorth CarolinaUSA
| | - Aaron M. Stecher
- Department of Biological SciencesUniversity of North CarolinaCharlotteNorth CarolinaUSA
| | - Andrew W. Truman
- Department of Biological SciencesUniversity of North CarolinaCharlotteNorth CarolinaUSA
| | - Adam M. Reitzel
- Department of Biological SciencesUniversity of North CarolinaCharlotteNorth CarolinaUSA
| | - Richard J. Chi
- Department of Biological SciencesUniversity of North CarolinaCharlotteNorth CarolinaUSA
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37
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Ecker M, Schregle R, Kapoor-Kaushik N, Rossatti P, Betzler VM, Kempe D, Biro M, Ariotti N, Redpath GMI, Rossy J. SNX9-induced membrane tubulation regulates CD28 cluster stability and signalling. eLife 2022; 11:e67550. [PMID: 35050850 PMCID: PMC8786313 DOI: 10.7554/elife.67550] [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: 02/15/2021] [Accepted: 01/12/2022] [Indexed: 12/12/2022] Open
Abstract
T cell activation requires engagement of a cognate antigen by the T cell receptor (TCR) and the co-stimulatory signal of CD28. Both TCR and CD28 aggregate into clusters at the plasma membrane of activated T cells. While the role of TCR clustering in T cell activation has been extensively investigated, little is known about how CD28 clustering contributes to CD28 signalling. Here, we report that upon CD28 triggering, the BAR-domain protein sorting nexin 9 (SNX9) is recruited to CD28 clusters at the immunological synapse. Using three-dimensional correlative light and electron microscopy, we show that SNX9 generates membrane tubulation out of CD28 clusters. Our data further reveal that CD28 clusters are in fact dynamic structures and that SNX9 regulates their stability as well as CD28 phosphorylation and the resulting production of the cytokine IL-2. In summary, our work suggests a model in which SNX9-mediated tubulation generates a membrane environment that promotes CD28 triggering and downstream signalling events.
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Affiliation(s)
- Manuela Ecker
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South WalesSydneyAustralia
| | - Richard Schregle
- Biotechnology Institute Thurgau (BITg) at the University of KonstanzKreuzlingenSwitzerland
- Department of Biology, University of KonstanzKonstanzGermany
| | - Natasha Kapoor-Kaushik
- Electron Microscopy Unit, Mark Wainwright Analytical Centre, University of New South WalesSydneyAustralia
| | - Pascal Rossatti
- Biotechnology Institute Thurgau (BITg) at the University of KonstanzKreuzlingenSwitzerland
| | - Verena M Betzler
- Biotechnology Institute Thurgau (BITg) at the University of KonstanzKreuzlingenSwitzerland
| | - Daryan Kempe
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South WalesSydneyAustralia
| | - Maté Biro
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South WalesSydneyAustralia
| | - Nicholas Ariotti
- Electron Microscopy Unit, Mark Wainwright Analytical Centre, University of New South WalesSydneyAustralia
- Institute for Molecular Bioscience (IMB), University of QueenslandBrisbaneAustralia
| | - Gregory MI Redpath
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South WalesSydneyAustralia
| | - Jeremie Rossy
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South WalesSydneyAustralia
- Biotechnology Institute Thurgau (BITg) at the University of KonstanzKreuzlingenSwitzerland
- Department of Biology, University of KonstanzKonstanzGermany
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38
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EGF-SNX3-EGFR axis drives tumor progression and metastasis in triple-negative breast cancers. Oncogene 2022; 41:220-232. [PMID: 34718348 PMCID: PMC8883427 DOI: 10.1038/s41388-021-02086-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 10/14/2021] [Accepted: 10/18/2021] [Indexed: 01/14/2023]
Abstract
Epidermal growth factor receptor (EGFR) has critical roles in epithelial cell physiology. Over-expression and over-activation of EGFR have been implicated in diverse cancers, including triple-negative breast cancers (TNBCs), prompting anti-EGFR therapies. Therefore, developing potent therapies and addressing the inevitable drug resistance mechanisms necessitates deciphering of EGFR related networks. Here, we describe Sorting Nexin 3 (SNX3), a member of the recycling retromer complex, as a critical player in the epidermal growth factor (EGF) stimulated EGFR network in TNBCs. We show that SNX3 is an immediate and sustained target of EGF stimulation initially at the protein level and later at the transcriptional level, causing increased SNX3 abundance. Using a proximity labeling approach, we observed increased interaction of SNX3 and EGFR upon EGF stimulation. We also detected colocalization of SNX3 with early endosomes and endocytosed EGF. Moreover, we show that EGFR protein levels are sensitive to SNX3 loss. Transient RNAi models of SNX3 downregulation have a temporary reduction in EGFR levels. In contrast, long-term silencing forces cells to recover and overexpress EGFR mRNA and protein, resulting in increased proliferation, colony formation, migration, invasion in TNBC cells, and increased tumor growth and metastasis in syngeneic models. Consistent with these results, low SNX3 and high EGFR mRNA levels correlate with poor relapse-free survival in breast cancer patients. Overall, our results suggest that SNX3 is a critical player in the EGFR network in TNBCs with implications for other cancers dependent on EGFR activity.
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39
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Abubakar YS, Qiu H, Fang W, Zheng H, Lu G, Zhou J, Wang Z, Zheng W. FgRab5 and FgRab7 are essential for endosomes biogenesis and non-redundantly recruit the retromer complex to the endosomes in Fusarium graminearum. STRESS BIOLOGY 2021; 1:17. [PMID: 37676350 PMCID: PMC10441910 DOI: 10.1007/s44154-021-00020-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/22/2021] [Indexed: 09/08/2023]
Abstract
The retromer complex, composed of the cargo-selective complex (CSC) Vps35-Vps29-Vps26 in complex with the sorting nexin dimer Vps5-Vps17, mediates the sorting and retrograde transport of cargo proteins from the endosomes to the trans-Golgi network in eukaryotic cells. Rab proteins belong to the Ras superfamily of small GTPases and regulate many trafficking events including vesicle formation, budding, transport, tethering, docking and fusion with target membranes. Herein, we investigated the potential functional relationship between the retromer complex and the 11 Rab proteins that exist in Fusarium graminearum using genetic and high-resolution laser confocal microscopic approaches. We found that only FgRab5 (FgRab5A and FgRab5B) and FgRab7 associate with the retromer complex. Both FgVps35-GFP and FgVps17-GFP are mis-localized and appear diffused in the cytoplasm of ΔFgrab5A, ΔFgrab5B and ΔFgrab7 mutants as compared to their punctate localization within the endosomes of the wild-type. FgRab7 and FgRab5B were found to co-localize with the retromer on endosomal membranes. Most strikingly, we found that these three Rab GTPases are indispensable for endosome biogenesis as both early and late endosomes could not be detected in the cells of the mutants after FM4-64 staining of the cells, while they were very clearly seen in the wild-type PH-1. Furthermore, FgRab7 was found to recruit FgVps35 but not FgVps17 to the endosomal membranes, whereas FgRab5B recruits both FgVps35 and FgVps17 to the membranes. Thus, we conclude that the Rab proteins FgRab5A, FgRab5B and FgRab7 play critical roles in the biogenesis of endosomes and in regulating retromer-mediated trafficking in F. graminearum.
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Affiliation(s)
- Yakubu Saddeeq Abubakar
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Han Qiu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenqin Fang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huawei Zheng
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jie Zhou
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China.
- Institute of Oceanography, Minjiang University, Fuzhou, China.
| | - Wenhui Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China.
- Key Laboratory of Integrated Pest Management for Fujian-Taiwan Crops, Ministry of Agriculture, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China.
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40
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Placidi G, Campa CC. Deliver on Time or Pay the Fine: Scheduling in Membrane Trafficking. Int J Mol Sci 2021; 22:11773. [PMID: 34769203 PMCID: PMC8583995 DOI: 10.3390/ijms222111773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/23/2021] [Accepted: 10/27/2021] [Indexed: 12/12/2022] Open
Abstract
Membrane trafficking is all about time. Automation in such a biological process is crucial to ensure management and delivery of cellular cargoes with spatiotemporal precision. Shared molecular regulators and differential engagement of trafficking components improve robustness of molecular sorting. Sequential recruitment of low affinity protein complexes ensures directionality of the process and, concomitantly, serves as a kinetic proofreading mechanism to discriminate cargoes from the whole endocytosed material. This strategy helps cells to minimize losses and operating errors in membrane trafficking, thereby matching the appealed deadline. Here, we summarize the molecular pathways of molecular sorting, focusing on their timing and efficacy. We also highlight experimental procedures and genetic approaches to robustly probe these pathways, in order to guide mechanistic studies at the interface between biochemistry and quantitative biology.
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Affiliation(s)
- Giampaolo Placidi
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, 10060 Candiolo, Italy;
- Candiolo Cancer Institute, FPO-IRCCS, Str. Prov.le 142, km 3.95, 10060 Candiolo, Italy
| | - Carlo C. Campa
- Italian Institute for Genomic Medicine, c/o IRCCS, Str. Prov.le 142, km 3.95, 10060 Candiolo, Italy;
- Candiolo Cancer Institute, FPO-IRCCS, Str. Prov.le 142, km 3.95, 10060 Candiolo, Italy
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41
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Markworth R, Dambeck V, Steinbeck LM, Koufali A, Bues B, Dankovich TM, Wichmann C, Burk K. Tubular microdomains of Rab7-positive endosomes retrieve TrkA, a mechanism disrupted in Charcot-Marie-Tooth disease 2B. J Cell Sci 2021; 134:272650. [PMID: 34486665 DOI: 10.1242/jcs.258559] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 08/23/2021] [Indexed: 01/04/2023] Open
Abstract
Axonal survival and growth requires signalling from tropomyosin receptor kinases (Trks). To transmit their signals, receptor-ligand complexes are endocytosed and undergo retrograde trafficking to the soma, where downstream signalling occurs. Vesicles transporting neurotrophic receptors to the soma are reported to be Rab7-positive late endosomes and/or multivesicular bodies (MVBs), where receptors localize within so-called intraluminal vesicles (herein Rab7 corresponds to Rab7A unless specified otherwise). Therefore, one challenging question is how downstream signalling is possible given the insulating properties of intraluminal vesicles. In this study, we report that Rab7-positive endosomes and MVBs retrieve TrkA (also known as NTRK1) through tubular microdomains. Interestingly, this phenotype is absent for the EGF receptor. Furthermore, we found that endophilinA1, endophilinA2 and endophilinA3, together with WASH1 (also known as WASHC1), are involved in the tubulation process. In Charcot-Marie-Tooth disease 2B (CMT2B), a neuropathy of the peripheral nervous system, this tubulating mechanism is disrupted. In addition, the ability to tubulate correlates with the phosphorylation levels of TrkA as well as with neurite length in neuronal cultures from dorsal root ganglia. In all, we report a new retrieval mechanism of late Rab7-positive endosomes, which enables TrkA signalling and sheds new light onto how neurotrophic signalling is disrupted in CMT2B. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Ronja Markworth
- Department of Neurology, University Medical Center Göttingen, Robert Koch Straße 40, 37075 Göttingen, Germany.,European Neuroscience Institute, Grisebachstraße 5, 37077 Göttingen, Germany.,Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Von-Siebold Straße 3A, 37075 Göttingen, Germany
| | - Vivian Dambeck
- Department of Neurology, University Medical Center Göttingen, Robert Koch Straße 40, 37075 Göttingen, Germany.,Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Von-Siebold Straße 3A, 37075 Göttingen, Germany
| | - Lars Malte Steinbeck
- Department of Neurology, University Medical Center Göttingen, Robert Koch Straße 40, 37075 Göttingen, Germany.,Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Von-Siebold Straße 3A, 37075 Göttingen, Germany
| | - Angeliki Koufali
- Department of Neurology, University Medical Center Göttingen, Robert Koch Straße 40, 37075 Göttingen, Germany.,Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Von-Siebold Straße 3A, 37075 Göttingen, Germany
| | - Bastian Bues
- Department of Neurology, University Medical Center Göttingen, Robert Koch Straße 40, 37075 Göttingen, Germany.,Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Von-Siebold Straße 3A, 37075 Göttingen, Germany
| | - Tal M Dankovich
- Institute for Neuro- and Sensory Physiology, Humboldtallee 23, 37073 Göttingen, Germany
| | - Carolin Wichmann
- Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Von-Siebold Straße 3A, 37075 Göttingen, Germany.,Molecular Architecture of Synapses Group, Institute for Auditory Neuroscience and InnerEarLab, University Medical Center Göttingen, Göttingen, Germany.,Collaborative Research Centers 889 'Cellular Mechanisms of Sensory Processing' and 1286 'Quantitative Synaptology', 37099 Göttingen, Germany
| | - Katja Burk
- Department of Neurology, University Medical Center Göttingen, Robert Koch Straße 40, 37075 Göttingen, Germany.,European Neuroscience Institute, Grisebachstraße 5, 37077 Göttingen, Germany.,Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Von-Siebold Straße 3A, 37075 Göttingen, Germany
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42
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Yuan Y, Jiang X, Tang L, Wang J, Liu Q, Zou X, Duan L. SNX20AR/MiRNA-301a-3p/SNX20 Axis Associated With Cell Proliferation and Immune Infiltration in Lung Adenocarcinoma. Front Mol Biosci 2021; 8:744363. [PMID: 34604311 PMCID: PMC8484765 DOI: 10.3389/fmolb.2021.744363] [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: 07/20/2021] [Accepted: 09/08/2021] [Indexed: 12/23/2022] Open
Abstract
Lung cancer is the most common tumor with severe morbidity and high mortality. Increasing evidence has demonstrated that SNX20 plays crucial roles in the progression of human cancer. However, the functions and mechanism of SNX20 in LUAD are still barely known. Here, we employ the TCGA, GEO and CCLE databases to examine the expression of SNX20 in human varies cancer, the results shown that SNX20 is down-regulated in lung Adenocarcinoma, SNX20 level was significantly positive correlated with poor prognosis and lung cancer immune cell infiltration. We found that over-expression of SNX20 significantly restrain NSCLC cell proliferation and migration. Subsequently, we discover a network regulating SNX20 in LUAD, further study found that the decreased of the SNX20 likely caused by DNA hypermethylation. Furthermore, we identified that SNX20AR/miRNA-301a-3p mediated decreased of SNX20 correlated with lung cancer progression and cancer immune infiltration in LUAD. Our findings suggested that ncRNAs play a crucial role in the regulatory network of SNX20. Collectively, our findings demonstrate the suppressor roles of the SNX20AR/miRNA-301a-3p/SNX20 axis in Lung Adenocarcinoma, represent that SNX20 have the potential of as an effective therapeutic target in future.
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Affiliation(s)
- Yixiao Yuan
- Department of Graduate School of Kunming Medical University, Kunming, China.,Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xiulin Jiang
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Lin Tang
- Department of Graduate School of Kunming Medical University, Kunming, China.,Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Juan Wang
- Department of Graduate School of Kunming Medical University, Kunming, China.,Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Qianqian Liu
- Department of Graduate School of Kunming Medical University, Kunming, China.,Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xiaolan Zou
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Lincan Duan
- Department of Graduate School of Kunming Medical University, Kunming, China.,Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
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43
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Siva Sankar D, Dengjel J. Protein complexes and neighborhoods driving autophagy. Autophagy 2021; 17:2689-2705. [PMID: 33183148 PMCID: PMC8526019 DOI: 10.1080/15548627.2020.1847461] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 10/16/2020] [Accepted: 11/02/2020] [Indexed: 01/02/2023] Open
Abstract
Autophagy summarizes evolutionarily conserved, intracellular degradation processes targeting cytoplasmic material for lysosomal degradation. These encompass constitutive processes as well as stress responses, which are often found dysregulated in diseases. Autophagy pathways help in the clearance of damaged organelles, protein aggregates and macromolecules, mediating their recycling and maintaining cellular homeostasis. Protein-protein interaction networks contribute to autophagosome biogenesis, substrate loading, vesicular trafficking and fusion, protein translocations across membranes and degradation in lysosomes. Hypothesis-free proteomic approaches tremendously helped in the functional characterization of protein-protein interactions to uncover molecular mechanisms regulating autophagy. In this review, we elaborate on the importance of understanding protein-protein-interactions of varying affinities and on the strengths of mass spectrometry-based proteomic approaches to study these, generating new mechanistic insights into autophagy regulation. We discuss in detail affinity purification approaches and recent developments in proximity labeling coupled to mass spectrometry, which uncovered molecular principles of autophagy mechanisms.Abbreviations: AMPK: AMP-activated protein kinase; AP-MS: affinity purification-mass spectrometry; APEX2: ascorbate peroxidase-2; ATG: autophagy related; BioID: proximity-dependent biotin identification; ER: endoplasmic reticulum; GFP: green fluorescent protein; iTRAQ: isobaric tag for relative and absolute quantification; MS: mass spectrometry; PCA: protein-fragment complementation assay; PL-MS: proximity labeling-mass spectrometry; PtdIns3P: phosphatidylinositol-3-phosphate; PTM: posttranslational modification; PUP-IT: pupylation-based interaction tagging; RFP: red fluorescent protein; SILAC: stable isotope labeling by amino acids in cell culture; TAP: tandem affinity purification; TMT: tandem mass tag.
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Affiliation(s)
| | - Jörn Dengjel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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Suzuki SW, Oishi A, Nikulin N, Jorgensen JR, Baile MG, Emr SD. A PX-BAR protein Mvp1/SNX8 and a dynamin-like GTPase Vps1 drive endosomal recycling. eLife 2021; 10:69883. [PMID: 34524084 PMCID: PMC8504969 DOI: 10.7554/elife.69883] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 09/14/2021] [Indexed: 12/13/2022] Open
Abstract
Membrane protein recycling systems are essential for maintenance of the endosome-lysosome system. In yeast, retromer and Snx4 coat complexes are recruited to the endosomal surface, where they recognize cargos. They sort cargo and deform the membrane into recycling tubules that bud from the endosome and target to the Golgi. Here, we reveal that the SNX-BAR protein, Mvp1, mediates an endosomal recycling pathway that is mechanistically distinct from the retromer and Snx4 pathways. Mvp1 deforms the endosomal membrane and sorts cargos containing a specific sorting motif into a membrane tubule. Subsequently, Mvp1 recruits the dynamin-like GTPase Vps1 to catalyze membrane scission and release of the recycling tubule. Similarly, SNX8, the human homolog of Mvp1, which has been also implicated in Alzheimer’s disease, mediates formation of an endosomal recycling tubule. Thus, we present evidence for a novel endosomal retrieval pathway that is conserved from yeast to humans.
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Affiliation(s)
- Sho W Suzuki
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | - Akihiko Oishi
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | - Nadia Nikulin
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | - Jeff R Jorgensen
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | - Matthew G Baile
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
| | - Scott D Emr
- Weill Institute for Cell and Molecular Biology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, United States
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45
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Unveiling the cryo-EM structure of retromer. Biochem Soc Trans 2021; 48:2261-2272. [PMID: 33125482 DOI: 10.1042/bst20200552] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/10/2020] [Accepted: 09/14/2020] [Indexed: 12/29/2022]
Abstract
Retromer (VPS26/VPS35/VPS29) is a highly conserved eukaryotic protein complex that localizes to endosomes to sort transmembrane protein cargoes into vesicles and elongated tubules. Retromer mediates retrieval pathways from endosomes to the trans-Golgi network in all eukaryotes and further facilitates recycling pathways to the plasma membrane in metazoans. In cells, retromer engages multiple partners to orchestrate the formation of tubulovesicular structures, including sorting nexin (SNX) proteins, cargo adaptors, GTPases, regulators, and actin remodeling proteins. Retromer-mediated pathways are especially important for sorting cargoes required for neuronal maintenance, which links retromer loss or mutations to multiple human brain diseases and disorders. Structural and biochemical studies have long contributed to the understanding of retromer biology, but recent advances in cryo-electron microscopy and cryo-electron tomography have further uncovered exciting new snapshots of reconstituted retromer structures. These new structures reveal retromer assembles into an arch-shaped scaffold and suggest the scaffold may be flexible and adaptable in cells. Interactions with cargo adaptors, particularly SNXs, likely orient the scaffold with respect to phosphatidylinositol-3-phosphate (PtdIns3P)-enriched membranes. Pharmacological small molecule chaperones have further been shown to stabilize retromer in cultured cell and mouse models, but mechanisms by which these molecules bind remain unknown. This review will emphasize recent structural and biophysical advances in understanding retromer structure as the field moves towards a molecular view of retromer assembly and regulation on membranes.
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Wunderley L, Zhang L, Yarwood R, Qin W, Lowe M, Woodman P. Endosomal recycling tubule scission and integrin recycling involve the membrane curvature-supporting protein LITAF. J Cell Sci 2021; 134:jcs258549. [PMID: 34342350 PMCID: PMC8353527 DOI: 10.1242/jcs.258549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 06/16/2021] [Indexed: 11/20/2022] Open
Abstract
Recycling to the cell surface requires the scission of tubular membrane intermediates emanating from endosomes. Here, we identify the monotopic membrane protein LPS-induced TNF-activating factor (LITAF) and the related protein cell death involved p53 target 1 (CDIP1) as novel membrane curvature proteins that contribute to recycling tubule scission. Recombinant LITAF supports high membrane curvature, shown by its ability to reduce proteoliposome size. The membrane domains of LITAF and CDIP1 partition strongly into ∼50 nm diameter tubules labelled with the recycling markers Pacsin2, ARF6 and SNX1, and the recycling cargoes MHC class I and CD59. Partitioning of LITAF into tubules is impaired by mutations linked to Charcot Marie Tooth disease type 1C. Meanwhile, co-depletion of LITAF and CDIP1 results in the expansion of tubular recycling compartments and stabilised Rab11 tubules, pointing to a function for LITAF and CDIP1 in membrane scission. Consistent with this, co-depletion of LITAF and CDIP1 impairs integrin recycling and cell migration.
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Affiliation(s)
| | | | | | | | | | - Philip Woodman
- Faculty of Biology Medicine and Health, Manchester Academic and Health Science Centre, University of Manchester, Manchester M13 9PT, UK
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Abe T, Kuwahara T. Targeting of Lysosomal Pathway Genes for Parkinson's Disease Modification: Insights From Cellular and Animal Models. Front Neurol 2021; 12:681369. [PMID: 34194386 PMCID: PMC8236816 DOI: 10.3389/fneur.2021.681369] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/20/2021] [Indexed: 01/01/2023] Open
Abstract
Previous genetic studies on hereditary Parkinson's disease (PD) have identified a set of pathogenic gene mutations that have strong impacts on the pathogenicity of PD. In addition, genome-wide association studies (GWAS) targeted to sporadic PD have nominated an increasing number of genetic variants that influence PD susceptibility. Although the clinical and pathological characteristics in hereditary PD are not identical to those in sporadic PD, α-synuclein, and LRRK2 are definitely associated with both types of PD, with LRRK2 mutations being the most frequent cause of autosomal-dominant PD. On the other hand, a significant portion of risk genes identified from GWAS have been associated with lysosomal functions, pointing to a critical role of lysosomes in PD pathogenesis. Experimental studies have suggested that the maintenance or upregulation of lysosomal activity may protect against neuronal dysfunction or degeneration. Here we focus on the roles of representative PD gene products that are implicated in lysosomal pathway, namely LRRK2, VPS35, ATP13A2, and glucocerebrosidase, and provide an overview of their disease-associated functions as well as their cooperative actions in the pathogenesis of PD, based on the evidence from cellular and animal models. We also discuss future perspectives of targeting lysosomal activation as a possible strategy to treat neurodegeneration.
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Affiliation(s)
- Tetsuro Abe
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomoki Kuwahara
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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48
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The state of F-BAR domains as membrane-bound oligomeric platforms. Trends Cell Biol 2021; 31:644-655. [PMID: 33888395 DOI: 10.1016/j.tcb.2021.03.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/16/2022]
Abstract
Fes/Cip4 homology Bin/amphiphysin/Rvs (F-BAR) domains, like all BAR domains, are dimeric units that oligomerize and bind membranes. F-BAR domains are generally coupled to additional domains that function in protein binding or have enzymatic activity. Because of their crescent shape and ability to oligomerize, F-BAR domains have been traditionally viewed as membrane-deformation modules. However, multiple independent studies have provided no evidence that certain F-BAR domains are able to tubulate membrane. Instead, a growing body of literature featuring structural, biochemical, biophysical, and microscopy-based studies supports the idea that the F-BAR domain family can be unified only by their ability to form oligomeric assemblies on membranes to provide platforms for molecular assembly.
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Chandra M, Kendall AK, Jackson LP. Toward Understanding the Molecular Role of SNX27/Retromer in Human Health and Disease. Front Cell Dev Biol 2021; 9:642378. [PMID: 33937239 PMCID: PMC8083963 DOI: 10.3389/fcell.2021.642378] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/22/2021] [Indexed: 11/30/2022] Open
Abstract
Aberrations in membrane trafficking pathways have profound effects in cellular dynamics of cellular sorting processes and can drive severe physiological outcomes. Sorting nexin 27 (SNX27) is a metazoan-specific sorting nexin protein from the PX-FERM domain family and is required for endosomal recycling of many important transmembrane receptors. Multiple studies have shown SNX27-mediated recycling requires association with retromer, one of the best-known regulators of endosomal trafficking. SNX27/retromer downregulation is strongly linked to Down's Syndrome (DS) via glutamate receptor dysfunction and to Alzheimer's Disease (AD) through increased intracellular production of amyloid peptides from amyloid precursor protein (APP) breakdown. SNX27 is further linked to addiction via its role in potassium channel trafficking, and its over-expression is linked to tumorigenesis, cancer progression, and metastasis. Thus, the correct sorting of multiple receptors by SNX27/retromer is vital for normal cellular function to prevent human diseases. The role of SNX27 in regulating cargo recycling from endosomes to the cell surface is firmly established, but how SNX27 assembles with retromer to generate tubulovesicular carriers remains elusive. Whether SNX27/retromer may be a putative therapeutic target to prevent neurodegenerative disease is now an emerging area of study. This review will provide an update on our molecular understanding of endosomal trafficking events mediated by the SNX27/retromer complex on endosomes.
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Affiliation(s)
- Mintu Chandra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - Amy K. Kendall
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
| | - Lauren P. Jackson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
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Abstract
The sorting nexin (SNX) family of proteins deform the membrane to generate transport carriers in endosomal pathways. Here, we elucidate how a prototypic member, SNX1, acts in this process. Performing cryoelectron microscopy, we find that SNX1 assembles into a protein lattice that consists of helical rows of SNX1 dimers wrapped around tubular membranes in a crosslinked fashion. We also visualize the details of this structure, which provides a molecular understanding of how various parts of SNX1 contribute to its ability to deform the membrane. Moreover, we have compared the SNX1 structure with a previously elucidated structure of an endosomal coat complex formed by retromer coupled to a SNX, which reveals how the molecular organization of the SNX in this coat complex is affected by retromer. The comparison also suggests insight into intermediary stages of assembly that results in the formation of the retromer-SNX coat complex on the membrane.
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