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Lipid kinases VPS34 and PIKfyve coordinate a phosphoinositide cascade to regulate retriever-mediated recycling on endosomes

Giridharan, Sai Srinivas Panapakkam, Luo, Guangming, Rivero-Rios, Pilar, Steinfeld, Noah, Tronchere, Helene, Singla, Amika, Burstein, Ezra, Billadeau, Daniel D, Sutton, Michael A, Weisman, Lois S·2022·eLife

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Abstract

Cell surface receptors control how cells respond to their environment. Many cell surface receptors recycle from endosomes to the plasma membrane via a recently discovered pathway, which includes sorting-nexin SNX17, Retriever, WASH, and CCC complexes. Here, using mammalian cells, we discover that PIKfyve and its upstream PI3-kinase VPS34 positively regulate this pathway. VPS34 produces phosphatidylinositol 3-phosphate (PI3P), which is the substrate for PIKfyve to generate PI3,5P 2 . We show that PIKfyve controls recycling of cargoes including integrins, receptors that control cell migration. Furthermore, endogenous PIKfyve colocalizes with SNX17, Retriever, WASH, and CCC complexes on endosomes. Importantly, PIKfyve inhibition results in displacement of Retriever and CCC from endosomes. In addition, we show that recruitment of SNX17 is an early step and requires VPS34. These discoveries suggest that VPS34 and PIKfyve coordinate an ordered pathway to regulate recycling from endosomes and suggest how PIKfyve functions in cell migration.

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  1. Bissig, 2017, PIKfyve activity regulates reformation of terminal storage lysosomes from endolysosomes, Traffic, 18, 747, 10.1111/tra.12525 · DOI
  2. Bissig, 2019, The PIKfyve complex regulates the early melanosome homeostasis required for physiological amyloid formation, Journal of Cell Science, 132, 10.1242/jcs.229500 · DOI
  3. Böttcher, 2012, Sorting nexin 17 prevents lysosomal degradation of β1 integrins by binding to the β1-integrin tail, Nature Cell Biology, 14, 584, 10.1038/ncb2501 · DOI · Paper page
  4. Chandra, 2019, Classification of the human phox homology (PX) domains based on their phosphoinositide binding specificities, Nature Communications, 10, 10.1038/s41467-019-09355-y · DOI
  5. Chen, 2017, Structure of mammalian endolysosomal TRPML1 channel in nanodiscs, Nature, 550, 415, 10.1038/nature24035 · DOI
  6. Chen, 2019, Towards a molecular understanding of endosomal trafficking by Retromer and Retriever, Traffic, 20, 465, 10.1111/tra.12649 · DOI · Paper page
  7. Chow, 2007, Mutation of FIG4 causes neurodegeneration in the pale tremor mouse and patients with CMT4J, Nature, 448, 68, 10.1038/nature05876 · DOI
  8. Choy, 2018, Lysosome enlargement during inhibition of the lipid kinase PIKfyve proceeds through lysosome coalescence, Journal of Cell Science, 131, 10.1242/jcs.213587 · DOI
  9. Christoforidis, 1999, Phosphatidylinositol-3-OH kinases are Rab5 effectors, Nature Cell Biology, 1, 249, 10.1038/12075 · DOI · Paper page
  10. Cinato, 2021, Apilimod alters TGFβ signaling pathway and prevents cardiac fibrotic remodeling, Theranostics, 11, 6491, 10.7150/thno.55821 · DOI
  11. Cullen, 2018, To degrade or not to degrade: mechanisms and significance of endocytic recycling, Nature Reviews. Molecular Cell Biology, 19, 679, 10.1038/s41580-018-0053-7 · DOI · Paper page
  12. Daly, 2020, Neuropilin-1 is a host factor for SARS-CoV-2 infection, Science, 370, 861, 10.1126/science.abd3072 · DOI · Paper page
  13. Dayam, 2017, The Lipid Kinase PIKfyve Coordinates the Neutrophil Immune Response through the Activation of the Rac GTPase, Journal of Immunology, 199, 2096, 10.4049/jimmunol.1601466 · DOI
  14. de Araujo, 2020, Lysosomal size matters, Traffic, 21, 60, 10.1111/tra.12714 · DOI
  15. De Craene, 2017, Phosphoinositides, Major Actors in Membrane Trafficking and Lipid Signaling Pathways, International Journal of Molecular Sciences, 18, 10.3390/ijms18030634 · DOI
  16. de Lartigue, 2009, PIKfyve Regulation of Endosome-Linked Pathways, Traffic, 10, 883, 10.1111/j.1600-0854.2009.00915.x · DOI
  17. Derivery, 2009, The Arp2/3 Activator WASH Controls the Fission of Endosomes through a Large Multiprotein Complex, Developmental Cell, 17, 712, 10.1016/j.devcel.2009.09.010 · DOI · Paper page
  18. Devereaux, 2013, Regulation of Mammalian Autophagy by Class II and III PI 3-Kinases through PI3P Synthesis, PLOS ONE, 8, 10.1371/journal.pone.0076405 · DOI · Paper page
  19. Dong, 2010, PI(3,5)P(2) controls membrane trafficking by direct activation of mucolipin Ca(2+) release channels in the endolysosome, Nature Communications, 1, 10.1038/ncomms1037 · DOI
  20. Dove, 2009, Phosphatidylinositol 3,5-bisphosphate and Fab1p/PIKfyve underPPIn endo-lysosome function, The Biochemical Journal, 419, 1, 10.1042/BJ20081950 · DOI
  21. Dukes, 2012, The PIKfyve inhibitor YM201636 blocks the continuous recycling of the tight junction proteins claudin-1 and claudin-2 in MDCK cells, PLOS ONE, 7, 10.1371/journal.pone.0028659 · DOI
  22. Dupuis-Coronas, 2011, The nucleophosmin-anaplastic lymphoma kinase oncogene interacts, activates, and uses the kinase PIKfyve to increase invasiveness, The Journal of Biological Chemistry, 286, 32105, 10.1074/jbc.M111.227512 · DOI
  23. Farfán, 2013, A sorting nexin 17-binding domain within the LRP1 cytoplasmic tail mediates receptor recycling through the basolateral sorting endosome, Traffic, 14, 823, 10.1111/tra.12076 · DOI · Paper page
  24. Fine, 2018, Structural basis for PtdInsP2-mediated human TRPML1 regulation, Nature Communications, 9, 10.1038/s41467-018-06493-7 · DOI
  25. Gallon, 2015, Retromer and sorting nexins in endosomal sorting, Biochemical Society Transactions, 43, 33, 10.1042/BST20140290 · DOI
  26. Gomez, 2009, A FAM21-containing WASH complex regulates retromer-dependent sorting, Developmental Cell, 17, 699, 10.1016/j.devcel.2009.09.009 · DOI · Paper page
  27. Grant, 2009, Pathways and mechanisms of endocytic recycling, Nature Reviews. Molecular Cell Biology, 10, 597, 10.1038/nrm2755 · DOI · Paper page
  28. Harbour, 2010, The cargo-selective retromer complex is a recruiting hub for protein complexes that regulate endosomal tubule dynamics, Journal of Cell Science, 123, 3703, 10.1242/jcs.071472 · DOI · Paper page
  29. Harbour, 2012, Recruitment of the endosomal WASH complex is mediated by the extended “tail” of Fam21 binding to the retromer protein Vps35, The Biochemical Journal, 442, 209, 10.1042/BJ20111761 · DOI · Paper page
  30. Hasegawa, 2017, PI5P and PI(3,5)P2: Minor, but Essential Phosphoinositides, Cell Structure and Function, 42, 49, 10.1247/csf.17003 · DOI
  31. Healy, 2018, Structural insights into the architecture and membrane interactions of the conserved COMMD proteins, eLife, 7, 10.7554/eLife.35898 · DOI · Paper page
  32. Helfer, 2013, Endosomal recruitment of the WASH complex: active sequences and mutations impairing interaction with the retromer, Biology of the Cell, 105, 191, 10.1111/boc.201200038 · DOI
  33. Ho, 2012, Phosphatidylinositol-3,5-bisphosphate: no longer the poor PIP2, Traffic, 13, 1, 10.1111/j.1600-0854.2011.01246.x · DOI
  34. Hong, 2015, PI(3,5)P2 controls endosomal branched actin dynamics by regulating cortactin-actin interactions, The Journal of Cell Biology, 210, 753, 10.1083/jcb.201412127 · DOI · Paper page
  35. Hussain, 2014, Sorting Nexin 27 regulates basal and activity-dependent trafficking of AMPARs, PNAS, 111, 11840, 10.1073/pnas.1412415111 · DOI · Paper page
  36. Ikonomov, 2011, The phosphoinositide kinase PIKfyve is vital in early embryonic development: preimplantation lethality of PIKfyve-/- embryos but normality of PIKfyve+/- mice, The Journal of Biological Chemistry, 286, 13404, 10.1074/jbc.M111.222364 · DOI · Paper page
  37. Ikonomov, 2015, Class III PI 3-kinase is the main source of PtdIns3P substrate and membrane recruitment signal for PIKfyve constitutive function in podocyte endomembrane homeostasis, Biochimica et Biophysica Acta, 1853, 1240, 10.1016/j.bbamcr.2015.01.008 · DOI · Paper page
  38. Itzhak, 2016, Global, quantitative and dynamic mapping of protein subcellular localization, eLife, 5, 10.7554/eLife.16950 · DOI · Paper page
  39. Jia, 2010, WASH and WAVE actin regulators of the Wiskott-Aldrich syndrome protein (WASP) family are controlled by analogous structurally related complexes, PNAS, 107, 10442, 10.1073/pnas.0913293107 · DOI · Paper page
  40. Jia, 2012, Multiple repeat elements within the FAM21 tail link the WASH actin regulatory complex to the retromer, Molecular Biology of the Cell, 23, 2352, 10.1091/mbc.e11-12-1059 · DOI · Paper page
  41. Jia, 2014, The recognition of membrane-bound PtdIns3P by PX domains, Proteins, 82, 2332, 10.1002/prot.24593 · DOI
  42. Kang, 2020, Inhibition of PIKfyve kinase prevents infection by Zaire ebolavirus and SARS-CoV-2, PNAS, 117, 20803, 10.1073/pnas.2007837117 · DOI
  43. Kim, 2014, PIKfyve Inhibition Interferes with Phagosome and Endosome Maturation in Macrophages, Traffic, 15, 1143, 10.1111/tra.12199 · DOI
  44. Krishna, 2016, PIKfyve Regulates Vacuole Maturation and Nutrient Recovery following Engulfment, Developmental Cell, 38, 536, 10.1016/j.devcel.2016.08.001 · DOI · Paper page
  45. Kvainickas, 2016, Retromer/WASH dependent sorting of nutrient transporters requires a multivalent interaction network with ANKRD50, Journal of Cell Science, 130, 382, 10.1242/jcs.196758 · DOI
  46. Lamprecht, 2007, CellProfiler: free, versatile software for automated biological image analysis, BioTechniques, 42, 71, 10.2144/000112257 · DOI
  47. Lenk, 2016, Biallelic Mutations of VAC14 in Pediatric-Onset Neurological Disease, The American Journal of Human Genetics, 99, 188, 10.1016/j.ajhg.2016.05.008 · DOI
  48. McCartney, 2014, Phosphatidylinositol 3,5-bisphosphate: Low abundance, high significance, BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology, 36, 52, 10.1002/bies.201300012 · DOI
  49. McCartney, 2014, Activity-dependent PI(3,5)P2 synthesis controls AMPA receptor trafficking during synaptic depression, PNAS, 111, E4896, 10.1073/pnas.1411117111 · DOI · Paper page
  50. Messenger, 2015, Early to Late Endosome Trafficking Controls Secretion and Zymogen Activation in Rodent and Human Pancreatic Acinar Cells, Cellular and Molecular Gastroenterology and Hepatology, 1, 695, 10.1016/j.jcmgh.2015.08.002 · DOI
  51. Moreno-Layseca, 2019, Integrin trafficking in cells and tissues, Nature Cell Biology, 21, 122, 10.1038/s41556-018-0223-z · DOI
  52. Naslavsky, 2018, The enigmatic endosome - sorting the ins and outs of endocytic trafficking, Journal of Cell Science, 131, 10.1242/jcs.216499 · DOI · Paper page
  53. Nelson, 2017, The phosphatidylinositol-3-phosphate 5-kinase inhibitor apilimod blocks filoviral entry and infection, PLOS Neglected Tropical Diseases, 11, 10.1371/journal.pntd.0005540 · DOI
  54. Oppelt, 2013, Production of phosphatidylinositol 5-phosphate via PIKfyve and MTMR3 regulates cell migration, EMBO Reports, 14, 57, 10.1038/embor.2012.183 · DOI
  55. Oppelt, 2014, PIKfyve, MTMR3 and their product PtdIns5P regulate cancer cell migration and invasion through activation of Rac1, The Biochemical Journal, 461, 383, 10.1042/BJ20140132 · DOI
  56. Ou, 2020, Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV, Nature Communications, 11, 10.1038/s41467-020-15562-9 · DOI · Paper page
  57. Phillips-Krawczak, 2015, COMMD1 is linked to the WASH complex and regulates endosomal trafficking of the copper transporter ATP7A, Molecular Biology of the Cell, 26, 91, 10.1091/mbc.E14-06-1073 · DOI · Paper page
  58. Qiu, 2018, Ebola virus requires phosphatidylinositol (3,5) bisphosphate production for efficient viral entry, Virology, 513, 17, 10.1016/j.virol.2017.09.028 · DOI
  59. Rink, 2005, Rab conversion as a mechanism of progression from early to late endosomes, Cell, 122, 735, 10.1016/j.cell.2005.06.043 · DOI
  60. Riva, 2020, Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing, Nature, 586, 113, 10.1038/s41586-020-2577-1 · DOI
  61. Rutherford, 2006, The mammalian phosphatidylinositol 3-phosphate 5-kinase (PIKfyve) regulates endosome-to-TGN retrograde transport, Journal of Cell Science, 119, 3944, 10.1242/jcs.03153 · DOI
  62. Sbrissa, 1999, PIKfyve, a mammalian ortholog of yeast Fab1p lipid kinase, synthesizes 5-phosphoinositides. Effect of insulin, The Journal of Biological Chemistry, 274, 21589, 10.1074/jbc.274.31.21589 · DOI
  63. Schindelin, 2012, Fiji: an open-source platform for biological-image analysis, Nature Methods, 9, 676, 10.1038/nmeth.2019 · DOI · Paper page
  64. Seaman, 2009, Membrane recruitment of the cargo-selective retromer subcomplex is catalysed by the small GTPase Rab7 and inhibited by the Rab-GAP TBC1D5, Journal of Cell Science, 122, 2371, 10.1242/jcs.048686 · DOI · Paper page
  65. Seebohm, 2007, Regulation of endocytic recycling of KCNQ1/KCNE1 potassium channels, Circulation Research, 100, 686, 10.1161/01.RES.0000260250.83824.8f · DOI
  66. Seebohm, 2012, Identification of a novel signaling pathway and its relevance for GluA1 recycling, PLOS ONE, 7, 10.1371/journal.pone.0033889 · DOI
  67. She, 2018, Structural insights into the voltage and phospholipid activation of the mammalian TPC1 channel, Nature, 556, 130, 10.1038/nature26139 · DOI
  68. She, 2019, Structural mechanisms of phospholipid activation of the human TPC2 channel, eLife, 8, 10.7554/eLife.45222 · DOI
  69. Shi, 2018, Caught in the “Akt”: Cross-talk between EphA2 and EGFR through the Akt-PIKfyve axis maintains cellular sensitivity to EGF, Science Signaling, 11, 10.1126/scisignal.aau1207 · DOI
  70. Shisheva, 2012, PIKfyve and its Lipid products in health and in sickness, Current Topics in Microbiology and Immunology, 362, 127, 10.1007/978-94-007-5025-8_7 · DOI
  71. Simonetti, 2019, Actin-dependent endosomal receptor recycling, Current Opinion in Cell Biology, 56, 22, 10.1016/j.ceb.2018.08.006 · DOI · Paper page
  72. Steinberg, 2012, SNX17 protects integrins from degradation by sorting between lysosomal and recycling pathways, The Journal of Cell Biology, 197, 219, 10.1083/jcb.201111121 · DOI · Paper page
  73. Steinberg, 2013, A global analysis of SNX27-retromer assembly and cargo specificity reveals a function in glucose and metal ion transport, Nature Cell Biology, 15, 461, 10.1038/ncb2721 · DOI · Paper page
  74. Stenmark, 2002, The phosphatidylinositol 3-phosphate-binding FYVE finger, FEBS Letters, 513, 77, 10.1016/s0014-5793(01)03308-7 · DOI · Paper page
  75. Strunk, 2020, Roles for a lipid phosphatase in the activation of its opposing lipid kinase, Molecular Biology of the Cell, 31, 1835, 10.1091/mbc.E18-09-0556 · DOI
  76. Takasuga, 2013, Critical roles of type III phosphatidylinositol phosphate kinase in murine embryonic visceral endoderm and adult intestine, PNAS, 110, 1726, 10.1073/pnas.1213212110 · DOI
  77. Vicente-Manzanares, 2009, Integrins in cell migration--the actin connection, Journal of Cell Science, 122, 199, 10.1242/jcs.018564 · DOI
  78. Vitali, 2019, Arf GAPs: A family of proteins with disparate functions that converge on a common structure, the integrin adhesion complex, Small GTPases, 10, 280, 10.1080/21541248.2017.1299271 · DOI
  79. Wang, 2017, A voltage-dependent K+ channel in the lysosome is required for refilling lysosomal Ca2+ stores, Journal of Cell Biology, 216, 1715, 10.1083/jcb.201612123 · DOI
  80. Wang, 2018, Endosomal receptor trafficking: Retromer and beyond, Traffic, 19, 578, 10.1111/tra.12574 · DOI
  81. Wozniak, 2004, Focal adhesion regulation of cell behavior, Biochimica et Biophysica Acta, 1692, 103, 10.1016/j.bbamcr.2004.04.007 · DOI
  82. Wrapp, 2020, Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation, Science, 367, 1260, 10.1126/science.abb2507 · DOI · Paper page
  83. Xu, 2020, Molecular Basis for PI(3,5)P2 Recognition by SNX11, a Protein Involved in Lysosomal Degradation and Endosome Homeostasis Regulation, Journal of Molecular Biology, 432, 4750, 10.1016/j.jmb.2020.06.010 · DOI
  84. Yordanov, 2019, Biogenesis of lysosome-related organelles complex-1 (BORC) regulates late endosomal/lysosomal size through PIKfyve-dependent phosphatidylinositol-3,5-bisphosphate, Traffic (Copenhagen, Denmark), 20, 674, 10.1111/tra.12679 · DOI
  85. Zavodszky, 2014, Mutation in VPS35 associated with Parkinson’s disease impairs WASH complex association and inhibits autophagy, Nature Communications, 5, 10.1038/ncomms4828 · DOI · Paper page
  86. Zhang, 2007, Loss of Vac14, a regulator of the signaling lipid phosphatidylinositol 3,5-bisphosphate, results in neurodegeneration in mice, PNAS, 104, 17518, 10.1073/pnas.0702275104 · DOI
  87. Zhang, 2012, Modulation of synaptic function by VAC14, a protein that regulates the phosphoinositides PI(3,5)P2 and PI(5)P, The EMBO Journal, 31, 3442, 10.1038/emboj.2012.200 · DOI
  88. Zhu, 2021, A genome-wide CRISPR screen identifies host factors that regulate SARS-CoV-2 entry, Nature Communications, 12, 10.1038/s41467-021-21213-4 · DOI
  89. Zolov, 2012, In vivo, Pikfyve generates PI(3,5)P2, which serves as both a signaling lipid and the major precursor for PI5P, PNAS, 109, 17472, 10.1073/pnas.1203106109 · DOI · Paper page

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Authors
Giridharan, S. S. P., Luo, G., Rivero-Rios, P., Steinfeld, N., Tronchere, H., Singla, A., Burstein, E., Billadeau, D. D., Sutton, M. A., & Weisman, L. S.
Affiliations
  • Life Sciences Institute and Department of Cellular and Developmental Biology, University of Michigan
  • INSERM U1048 I2MC, France and Université Paul Sabatier
  • Department of Internal Medicine, and Department of Molecular Biology, University of Texas Southwestern Medical Center
  • Division of Oncology Research and Schulze Center for Novel Therapeutics, Mayo Clinic
  • Neuroscience Graduate Program, Molecular and Behavioral Neuroscience Institute, Molecular and Integrative Physiology, University of Michigan
Venue
eLife
Published
2022-01-18
Volume
11
ISSN
2050-084X
Cited by
61
References
6
Language
en
Funders
  • National Institute of Neurological Disorders and Stroke (Research Project Grant R01 NS064015, Research Project Grant R01-NS099340)
  • National Institute of Diabetes and Digestive and Kidney Diseases (Research Project Grant R01-DK107733)
  • American Heart Association (Postdoctoral Fellowship 14POST20480137, Postdoctoral Fellowship 19POST34450253)
  • University of Michigan Protein Folding Diseases Fast Forward Initiative (Pilot grant)

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