PIKFYVE explained

PIKfyve, a FYVE finger-containing phosphoinositide kinase, is an enzyme that in humans is encoded by the PIKFYVE gene.

Function

The principal enzymatic activity of PIKfyve is to phosphorylate PtdIns3P to PtdIns(3,5)P2. PIKfyve activity is responsible for the production of both PtdIns(3,5)P2 and phosphatidylinositol 5-phosphate (PtdIns5P).^{[1] [2] [3]} PIKfyve is a large protein, containing a number of functional domains and expressed in several spliced forms. The reported full-length mouse and human cDNA clones encode proteins of 2052 and 2098 amino acid residues, respectively. By directly binding membrane PtdIns(3)P, the FYVE finger domain of PIKfyve is essential in localizing the protein to the cytosolic leaflet of endosomes. Impaired PIKfyve enzymatic activity by dominant-interfering mutants, siRNA- mediated ablation or pharmacological inhibition causes lysosome enlargement and cytoplasmic vacuolation due to impaired PtdIns(3,5)P2 synthesis and impaired lysosome fission process and homeostasis.^[4] Thus, via PtdIns(3,5)P2 production, PIKfyve participates in several aspects of vesicular dynamics, thereby affecting a number of trafficking pathways that emanate from or traverse the endosomal system en route to the trans-Golgi network or later compartments along the endocytic pathway.

Medical significance

PIKfyve mutations affecting one of the two PIKFYVE alleles are found in 8 out of 10 families with Francois-Neetens corneal fleck dystrophy. Disruption of both PIKFYVE alleles in the mouse is lethal at the stage of pre-implantation embryo. PIKfyve’s role in pathogen invasion is deduced by evidence from cell studies implicating PIKfyve activity in HIV and Salmonella replication. A link of PIKfyve with type 2 diabetes is inferred by the observations that PIKfyve perturbation inhibits insulin-regulated glucose uptake. Concordantly, mice with selective Pikfyve gene disruption in skeletal muscle, the tissue mainly responsible for the decrease of postprandial blood sugar, exhibit systemic insulin resistance; glucose intolerance; hyperinsulinemia; and increased adiposity, i.e. symptoms, typical for human prediabetes.^[5]

PIKfyve inhibitors as potential therapeutics in Cancer

Several small molecule PIKfyve inhibitors have shown promise as cancer therapeutics in preclinical studies due to selective toxicity in non-Hodgkin lymphoma B cells ^[6] or in U-251 glioblastoma cells. ^[7] PIKfyve inhibitors cause cell death also in A-375 melanoma cells, which depend on autophagy for growth and proliferation, due to impaired lysosome homeostasis. ^[8] The potential therapeutic use of PIKfyve inhibitors awaits clinical trials.

Interactions

PIKfyve physically associates with its regulator ArPIKfyve, a protein encoded by the human gene VAC14, and the Sac1 domain-containing PtdIns(3,5)P2 5-phosphatase Sac3, encoded by FIG4, to form a stable ternary heterooligomeric complex that is scaffolded by ArPIKfyve homooligomeric interactions. The presence of two enzymes with opposing activities for PtdIns(3,5)P2 synthesis and turnover in a single complex indicates the requirement for a tight control of PtdIns(3,5)P2 levels. PIKfyve also interacts with the Rab9 effector RABEPK and the kinesin adaptor JLP, encoded by SPAG9. These interactions link PIKfyve to microtubule-based endosome to trans-Golgi network traffic. Under sustained activation of glutamate receptors PIKfyve binds to and facilitates the lysosomal degradation of Ca_v1.2, voltage-dependent calcium channel type 1.2, thereby protecting the neurons from excitotoxicity. PIKfyve negatively regulates Ca²⁺-dependent exocytosis in neuroendocrine cells without affecting voltage-gated calcium channels.

Evolutionary biology

PIKFYVE belongs to a large family of evolutionarily-conserved lipid kinases. Single copy genes, encoding similarly-structured FYVE-domain–containing phosphoinositide kinases exist in most genomes from yeast to man. The plant A. thaliana has several copies of the enzyme. Higher eukaryotes (after D. melanogaster), acquire an additional DEP domain. The S. cerevisiae enzyme Fab1p is required for PtdIns(3,5)P2 synthesis under basal conditions and in response to hyperosmotic shock. PtdIns5P, made by PIKfyve kinase activity in mammalian cells, is not detected in budding yeast. Yeast Fab1p associates with Vac14p (the ortholog of human ArPIKfyve) and Fig4p (the ortholog of Sac3). The yeast Fab1 complex also includes Vac7p and probably Atg18p, proteins that are not detected in the mammalian PIKfyve complex. S. cerevisiae could survive without Fab1. In contrast, the knockout of the FYVE domain-containing enzymes in A. thaliana, D. melanogaster, C. elegans and M. musculus leads to embryonic lethality indicating that the FYVE-domain–containing phosphoinositide kinases have become essential in embryonic development of multicellular organisms. Thus, in evolution, the FYVE-domain-containing phosphoinositide kinases retain several aspects of the structural organization, enzyme activity and protein interactions from budding yeast. In higher eukaryotes, the enzymes acquire one additional domain, a role in the production of PtdIns5P, a new set of interacting proteins and become essential in embryonic development.

Further reading

• Nagase T, Ishikawa K, Suyama M, Kikuno R, Hirosawa M, Miyajima N, Tanaka A, Kotani H, Nomura N, Ohara O . 6 . Prediction of the coding sequences of unidentified human genes. XIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro . DNA Research . 6 . 1 . 63–70 . February 1999 . 10231032 . 10.1093/dnares/6.1.63 . free .
• Jiao X, Munier FL, Schorderet DF, Zografos L, Smith J, Rubin B, Hejtmancik JF . Genetic linkage of Francois-Neetens fleck (mouchetée) corneal dystrophy to chromosome 2q35 . Human Genetics . 112 . 5–6 . 593–9 . May 2003 . 12607114 . 10.1007/s00439-002-0905-1 . 1338901 .
• Ikonomov OC, Sbrissa D, Foti M, Carpentier JL, Shisheva A . PIKfyve controls fluid phase endocytosis but not recycling/degradation of endocytosed receptors or sorting of procathepsin D by regulating multivesicular body morphogenesis . Molecular Biology of the Cell . 14 . 11 . 4581–91 . November 2003 . 14551253 . 266774 . 10.1091/mbc.E03-04-0222 .
• Brill LM, Salomon AR, Ficarro SB, Mukherji M, Stettler-Gill M, Peters EC . Robust phosphoproteomic profiling of tyrosine phosphorylation sites from human T cells using immobilized metal affinity chromatography and tandem mass spectrometry . Analytical Chemistry . 76 . 10 . 2763–72 . May 2004 . 15144186 . 10.1021/ac035352d .
• Sbrissa D, Ikonomov OC, Shisheva A . Phosphatidylinositol 3-phosphate-interacting domains in PIKfyve. Binding specificity and role in PIKfyve. Endomenbrane localization . The Journal of Biological Chemistry . 277 . 8 . 6073–9 . February 2002 . 11706043 . 10.1074/jbc.M110194200 . free .
• Sbrissa D, Ikonomov OC, Strakova J, Dondapati R, Mlak K, Deeb R, Silver R, Shisheva A . 6 . A mammalian ortholog of Saccharomyces cerevisiae Vac14 that associates with and up-regulates PIKfyve phosphoinositide 5-kinase activity . Molecular and Cellular Biology . 24 . 23 . 10437–47 . December 2004 . 15542851 . 529046 . 10.1128/MCB.24.23.10437-10447.2004 .
• Rush J, Moritz A, Lee KA, Guo A, Goss VL, Spek EJ, Zhang H, Zha XM, Polakiewicz RD, Comb MJ . 6 . Immunoaffinity profiling of tyrosine phosphorylation in cancer cells . Nature Biotechnology . 23 . 1 . 94–101 . January 2005 . 15592455 . 10.1038/nbt1046 . 7200157 .
• Olsen JV, Blagoev B, Gnad F, Macek B, Kumar C, Mortensen P, Mann M . Global, in vivo, and site-specific phosphorylation dynamics in signaling networks . Cell . 127 . 3 . 635–48 . November 2006 . 17081983 . 10.1016/j.cell.2006.09.026 . 7827573 . free .

Notes and References

1. Shisheva A . PIKfyve: the road to PtdIns 5-P and PtdIns 3,5-P(2) . Cell Biology International . 25 . 12 . 1201–6 . 2001 . 11748912 . 10.1006/cbir.2001.0803 . 29411107 .
2. Sbrissa D, Ikonomov OC, Filios C, Delvecchio K, Shisheva A . Functional dissociation between PIKfyve-synthesized PtdIns5P and PtdIns(3,5)P2 by means of the PIKfyve inhibitor YM201636 . American Journal of Physiology. Cell Physiology . 303 . 4 . C436-46 . August 2012 . 22621786 . 3422984 . 10.1152/ajpcell.00105.2012 .
3. Zolov SN, Bridges D, Zhang Y, Lee WW, Riehle E, Verma R, Lenk GM, Converso-Baran K, Weide T, Albin RL, Saltiel AR, Meisler MH, Russell MW, Weisman LS . 6 . In vivo, Pikfyve generates PI(3,5)P2, which serves as both a signaling lipid and the major precursor for PI5P . Proceedings of the National Academy of Sciences of the United States of America . 109 . 43 . 17472–7 . October 2012 . 23047693 . 3491506 . 10.1073/pnas.1203106109 . 2012PNAS..10917472Z . free .
4. Sharma G, Guardia CM, Roy A, Vassilev A, Saric A, Griner LN, Marugan J, Ferrer M, Bonifacino JS, DePamphilis ML . 6 . A family of PIKFYVE inhibitors with therapeutic potential against autophagy-dependent cancer cells disrupt multiple events in lysosome homeostasis . Autophagy . 15 . 10 . 1694–1718 . February 2019 . 30806145 . 6735543 . 10.1080/15548627.2019.1586257 .
5. 23673157. 3725567. 2013. Ikonomov. O. C.. Muscle-specific Pikfyve gene disruption causes glucose intolerance, insulin resistance, adiposity, and hyperinsulinemia but not muscle fiber-type switching. American Journal of Physiology. Endocrinology and Metabolism. 305. 1. E119-31. Sbrissa. D.. Delvecchio. K.. Feng. H. Z.. Cartee. G. D.. Jin. J. P.. Shisheva. A.. 10.1152/ajpendo.00030.2013.
6. Gayle. S. Landrette. S. Beeharry. N. Conrad. C. Hernandez. M. Beckett. P. Ferguson. SM. Mendelkern. T. Zheng. M. Xu. T. Rothberg. J. Lichenstein. H. Identification of apilimod as a first-in-class PIKfyve kinase inhibitor for treatment of B-cell non-Hodgkin lymphoma. Blood . 129. 13. 1768–1778. 10.1182/blood-2016-09-736892. 28104689. 5766845. 2017.
7. Li. Z. Mbah. NE. Overmeyer. JH. Sarver. JG. George. S. Trabbic. CJ. Erhardt. PW. Maltese. WA. The JNK signaling pathway plays a key role in methuosis (non-apoptotic cell death) induced by MOMIPP in glioblastoma. BMC Cancer . 19. 1. 77. 10.1186/s12885-019-5288-y. 30651087. 6335761. 2019. free.
8. Sharma G, Guardia CM, Roy A, Vassilev A, Saric A, Griner LN, Marugan J, Ferrer M, Bonifacino JS, DePamphilis ML . 6 . A family of PIKFYVE inhibitors with therapeutic potential against autophagy-dependent cancer cells disrupt multiple events in lysosome homeostasis . Autophagy . 15 . 10 . 1694–1718 . February 2019 . 30806145 . 6735543 . 10.1080/15548627.2019.1586257 .