Phosphatidylinositol (PI) is an essential structural component of eukaryotic membranes that also serves as the common precursor for polyphosphoinositide (PPIn) lipids. Despite the recognized importance of PPIn species for signal transduction and membrane homeostasis, there is still a limited understanding of the relationship between PI availability and the turnover of subcellular PPIn pools. To address these shortcomings, we established a molecular toolbox for investigations of PI distribution within intact cells by exploiting the properties of a bacterial enzyme, PI-specific PLC (PI-PLC). Using these tools, we find a minor presence of PI in membranes of the ER, as well as a general enrichment within the cytosolic leaflets of the Golgi complex, peroxisomes, and outer mitochondrial membrane, but only detect very low steady-state levels of PI within the plasma membrane (PM) and endosomes. Kinetic studies also demonstrate the requirement for sustained PI supply from the ER for the maintenance of monophosphorylated PPIn species within the PM, Golgi complex, and endosomal compartments.

Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Prague Czech Republic

Section on Molecular Signal Transduction Eunice Kennedy Shriver National Institute of Child Health and Human Development National Institutes of Health Bethesda MD

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J Cell Biol. 2020 Mar 2;219(3):e202001185. doi: 10.1083/jcb.202001185. PubMed

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Adams P.D., Afonine P.V., Bunkóczi G., Chen V.B., Davis I.W., Echols N., Headd J.J., Hung L.W., Kapral G.J., Grosse-Kunstleve R.W., et al. . 2010. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66:213–221. 10.1107/S0907444909052925 PubMed DOI PMC

Ahyayauch H., Sot J., Collado M.I., Huarte N., Requejo-Isidro J., Alonso A., and Goñi F.M.. 2015. End-product diacylglycerol enhances the activity of PI-PLC through changes in membrane domain structure. Biophys. J. 108:1672–1682. 10.1016/j.bpj.2015.02.020 PubMed DOI PMC

Ardail D., Privat J.P., Egret-Charlier M., Levrat C., Lerme F., and Louisot P.. 1990. Mitochondrial contact sites. Lipid composition and dynamics. J. Biol. Chem. 265:18797–18802. PubMed

Asp L., Kartberg F., Fernandez-Rodriguez J., Smedh M., Elsner M., Laporte F., Bárcena M., Jansen K.A., Valentijn J.A., Koster A.J., et al. . 2009. Early stages of Golgi vesicle and tubule formation require diacylglycerol. Mol. Biol. Cell. 20:780–790. 10.1091/mbc.e08-03-0256 PubMed DOI PMC

Baba T., Toth D.J., Sengupta N., Kim Y.J., and Balla T.. 2019. Phosphatidylinositol 4,5-bisphosphate controls Rab7 and PLEKHM1 membrane cycling during autophagosome-lysosome fusion. EMBO J. 38:e100312 10.15252/embj.2019102837 PubMed DOI PMC

Bago R., Malik N., Munson M.J., Prescott A.R., Davies P., Sommer E., Shpiro N., Ward R., Cross D., Ganley I.G., and Alessi D.R.. 2014. Characterization of VPS34-IN1, a selective inhibitor of Vps34, reveals that the phosphatidylinositol 3-phosphate-binding SGK3 protein kinase is a downstream target of class III phosphoinositide 3-kinase. Biochem. J. 463:413–427. 10.1042/BJ20140889 PubMed DOI PMC

Balla T. 2013. Phosphoinositides: tiny lipids with giant impact on cell regulation. Physiol. Rev. 93:1019–1137. 10.1152/physrev.00028.2012 PubMed DOI PMC

Balla A., Tuymetova G., Tsiomenko A., Várnai P., and Balla T.. 2005. A plasma membrane pool of phosphatidylinositol 4-phosphate is generated by phosphatidylinositol 4-kinase type-III alpha: studies with the PH domains of the oxysterol binding protein and FAPP1. Mol. Biol. Cell. 16:1282–1295. 10.1091/mbc.e04-07-0578 PubMed DOI PMC

Baron C.L., and Malhotra V.. 2002. Role of diacylglycerol in PKD recruitment to the TGN and protein transport to the plasma membrane. Science. 295:325–328. 10.1126/science.1066759 PubMed DOI

Baumlova A., Chalupska D., Róźycki B., Jovic M., Wisniewski E., Klima M., Dubankova A., Kloer D.P., Nencka R., Balla T., and Boura E.. 2014. The crystal structure of the phosphatidylinositol 4-kinase IIα. EMBO Rep. 15:1085–1092. 10.15252/embr.201438841 PubMed DOI PMC

Belshaw P.J., Ho S.N., Crabtree G.R., and Schreiber S.L.. 1996. Controlling protein association and subcellular localization with a synthetic ligand that induces heterodimerization of proteins. Proc. Natl. Acad. Sci. USA. 93:4604–4607. 10.1073/pnas.93.10.4604 PubMed DOI PMC

Berman H., Henrick K., and Nakamura H.. 2003. Announcing the worldwide Protein Data Bank. Nat. Struct. Biol. 10:980 10.1038/nsb1203-980 PubMed DOI

Bigay J., and Antonny B.. 2012. Curvature, lipid packing, and electrostatics of membrane organelles: defining cellular territories in determining specificity. Dev. Cell. 23:886–895. 10.1016/j.devcel.2012.10.009 PubMed DOI

Bojjireddy N., Botyanszki J., Hammond G., Creech D., Peterson R., Kemp D.C., Snead M., Brown R., Morrison A., Wilson S., et al. . 2014. Pharmacological and genetic targeting of the PI4KA enzyme reveals its important role in maintaining plasma membrane phosphatidylinositol 4-phosphate and phosphatidylinositol 4,5-bisphosphate levels. J. Biol. Chem. 289:6120–6132. 10.1074/jbc.M113.531426 PubMed DOI PMC

Bononi A., Bonora M., Marchi S., Missiroli S., Poletti F., Giorgi C., Pandolfi P.P., and Pinton P.. 2013. Identification of PTEN at the ER and MAMs and its regulation of Ca(2+) signaling and apoptosis in a protein phosphatase-dependent manner. Cell Death Differ. 20:1631–1643. 10.1038/cdd.2013.77 PubMed DOI PMC

Bossard C., Bresson D., Polishchuk R.S., and Malhotra V.. 2007. Dimeric PKD regulates membrane fission to form transport carriers at the TGN. J. Cell Biol. 179:1123–1131. 10.1083/jcb.200703166 PubMed DOI PMC

Bruzik K.S., and Tsai M.D.. 1994. Toward the mechanism of phosphoinositide-specific phospholipases C. Bioorg. Med. Chem. 2:49–72. 10.1016/S0968-0896(00)82002-7 PubMed DOI

Calvo S.E., Clauser K.R., and Mootha V.K.. 2016. MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins. Nucleic Acids Res. 44(D1):D1251–D1257. 10.1093/nar/gkv1003 PubMed DOI PMC

Chazotte B. 2011. Labeling mitochondria with MitoTracker dyes. Cold Spring Harb. Protoc. 2011:990–992. PubMed

Cheng J., Goldstein R., Stec B., Gershenson A., and Roberts M.F.. 2012. Competition between anion binding and dimerization modulates Staphylococcus aureus phosphatidylinositol-specific phospholipase C enzymatic activity. J. Biol. Chem. 287:40317–40327. 10.1074/jbc.M112.395277 PubMed DOI PMC

Cheng J., Goldstein R., Gershenson A., Stec B., and Roberts M.F.. 2013. The cation-π box is a specific phosphatidylcholine membrane targeting motif. J. Biol. Chem. 288:14863–14873. 10.1074/jbc.M113.466532 PubMed DOI PMC

Choi J., Chen J., Schreiber S.L., and Clardy J.. 1996. Structure of the FKBP12-rapamycin complex interacting with the binding domain of human FRAP. Science. 273:239–242. 10.1126/science.273.5272.239 PubMed DOI

Chu B.B., Liao Y.C., Qi W., Xie C., Du X., Wang J., Yang H., Miao H.H., Li B.L., and Song B.L.. 2015. Cholesterol transport through lysosome-peroxisome membrane contacts. Cell. 161:291–306. 10.1016/j.cell.2015.02.019 PubMed DOI

Csordás G., Várnai P., Golenár T., Roy S., Purkins G., Schneider T.G., Balla T., and Hajnóczky G.. 2010. Imaging interorganelle contacts and local calcium dynamics at the ER-mitochondrial interface. Mol. Cell. 39:121–132. 10.1016/j.molcel.2010.06.029 PubMed DOI PMC

Daum G., and Vance J.E.. 1997. Import of lipids into mitochondria. Prog. Lipid Res. 36:103–130. 10.1016/S0163-7827(97)00006-4 PubMed DOI

de Kroon A.I., Dolis D., Mayer A., Lill R., and de Kruijff B.. 1997. Phospholipid composition of highly purified mitochondrial outer membranes of rat liver and Neurospora crassa. Is cardiolipin present in the mitochondrial outer membrane? Biochim. Biophys. Acta. 1325:108–116. 10.1016/S0005-2736(96)00240-4 PubMed DOI

Debreczeni J.É., and Emsley P.. 2012. Handling ligands with Coot. Acta Crystallogr. D Biol. Crystallogr. 68:425–430. 10.1107/S0907444912000200 PubMed DOI PMC

Díaz Añel A.M. 2007. Phospholipase C beta3 is a key component in the Gbetagamma/PKCeta/PKD-mediated regulation of trans-Golgi network to plasma membrane transport. Biochem. J. 406:157–165. 10.1042/BJ20070359 PubMed DOI PMC

Donnelly M.L., Hughes L.E., Luke G., Mendoza H., ten Dam E., Gani D., and Ryan M.D.. 2001. The ‘cleavage’ activities of foot-and-mouth disease virus 2A site-directed mutants and naturally occurring ‘2A-like’ sequences. J. Gen. Virol. 82:1027–1041. 10.1099/0022-1317-82-5-1027 PubMed DOI

Downing G.J., Kim S., Nakanishi S., Catt K.J., and Balla T.. 1996. Characterization of a soluble adrenal phosphatidylinositol 4-kinase reveals wortmannin sensitivity of type III phosphatidylinositol kinases. Biochemistry. 35:3587–3594. 10.1021/bi9517493 PubMed DOI

Duan L., Che D., Zhang K., Ong Q., Guo S., and Cui B.. 2015. Optogenetic control of molecular motors and organelle distributions in cells. Chem. Biol. 22:671–682. 10.1016/j.chembiol.2015.04.014 PubMed DOI PMC

Feng J., Wehbi H., and Roberts M.F.. 2002. Role of tryptophan residues in interfacial binding of phosphatidylinositol-specific phospholipase C. J. Biol. Chem. 277:19867–19875. 10.1074/jbc.M200938200 PubMed DOI

Feng J., Bradley W.D., and Roberts M.F.. 2003. Optimizing the interfacial binding and activity of a bacterial phosphatidylinositol-specific phospholipase C. J. Biol. Chem. 278:24651–24657. 10.1074/jbc.M301207200 PubMed DOI

Fernández-Ulibarri I., Vilella M., Lázaro-Diéguez F., Sarri E., Martínez S.E., Jiménez N., Claro E., Mérida I., Burger K.N., and Egea G.. 2007. Diacylglycerol is required for the formation of COPI vesicles in the Golgi-to-ER transport pathway. Mol. Biol. Cell. 18:3250–3263. 10.1091/mbc.e07-04-0334 PubMed DOI PMC

Gandhi A.J., Perussia B., and Goldfine H.. 1993. Listeria monocytogenes phosphatidylinositol (PI)-specific phospholipase C has low activity on glycosyl-PI-anchored proteins. J. Bacteriol. 175:8014–8017. 10.1128/JB.175.24.8014-8017.1993 PubMed DOI PMC

Gässler C.S., Ryan M., Liu T., Griffith O.H., and Heinz D.W.. 1997. Probing the roles of active site residues in phosphatidylinositol-specific phospholipase C from Bacillus cereus by site-directed mutagenesis. Biochemistry. 36:12802–12813. 10.1021/bi971102d PubMed DOI

Gillooly D.J., Morrow I.C., Lindsay M., Gould R., Bryant N.J., Gaullier J.M., Parton R.G., and Stenmark H.. 2000. Localization of phosphatidylinositol 3-phosphate in yeast and mammalian cells. EMBO J. 19:4577–4588. 10.1093/emboj/19.17.4577 PubMed DOI PMC

Godi A., Di Campli A., Konstantakopoulos A., Di Tullio G., Alessi D.R., Kular G.S., Daniele T., Marra P., Lucocq J.M., and De Matteis M.A.. 2004. FAPPs control Golgi-to-cell-surface membrane traffic by binding to ARF and PtdIns(4)P. Nat. Cell Biol. 6:393–404. 10.1038/ncb1119 PubMed DOI

Grabon A., Khan D., and Bankaitis V.A.. 2015. Phosphatidylinositol transfer proteins and instructive regulation of lipid kinase biology. Biochim. Biophys. Acta. 1851:724–735. 10.1016/j.bbalip.2014.12.011 PubMed DOI PMC

Guo S., Zhang X., Seaton B.A., and Roberts M.F.. 2008. Role of helix B residues in interfacial activation of a bacterial phosphatidylinositol-specific phospholipase C. Biochemistry. 47:4201–4210. 10.1021/bi702269u PubMed DOI PMC

Guther M.L., de Almeida M.L., Rosenberry T.L., and Ferguson M.A.. 1994. The detection of phospholipase-resistant and -sensitive glycosyl-phosphatidylinositol membrane anchors by western blotting. Anal. Biochem. 219:249–255. 10.1006/abio.1994.1264 PubMed DOI

Hammond G.R., Fischer M.J., Anderson K.E., Holdich J., Koteci A., Balla T., and Irvine R.F.. 2012. PI4P and PI(4,5)P2 are essential but independent lipid determinants of membrane identity. Science. 337:727–730. 10.1126/science.1222483 PubMed DOI PMC

Hammond G.R., Machner M.P., and Balla T.. 2014. A novel probe for phosphatidylinositol 4-phosphate reveals multiple pools beyond the Golgi. J. Cell Biol. 205:113–126. 10.1083/jcb.201312072 PubMed DOI PMC

Harak C., Radujkovic D., Taveneau C., Reiss S., Klein R., Bressanelli S., and Lohmann V.. 2014. Mapping of functional domains of the lipid kinase phosphatidylinositol 4-kinase type III alpha involved in enzymatic activity and hepatitis C virus replication. J. Virol. 88:9909–9926. 10.1128/JVI.01063-14 PubMed DOI PMC

Hardeman D., Zomer H.W., Schutgens R.B., Tager J.M., and van den Bosch H.. 1990. Effect of peroxisome proliferation on ether phospholipid biosynthesizing enzymes in rat liver. Int. J. Biochem. 22:1413–1418. 10.1016/0020-711X(90)90231-Q PubMed DOI

Heim R., Prasher D.C., and Tsien R.Y.. 1994. Wavelength mutations and posttranslational autoxidation of green fluorescent protein. Proc. Natl. Acad. Sci. USA. 91:12501–12504. 10.1073/pnas.91.26.12501 PubMed DOI PMC

Heinz D.W., Ryan M., Bullock T.L., and Griffith O.H.. 1995. Crystal structure of the phosphatidylinositol-specific phospholipase C from Bacillus cereus in complex with myo-inositol. EMBO J. 14:3855–3863. 10.1002/j.1460-2075.1995.tb00057.x PubMed DOI PMC

Heinz D.W., Ryan M., Smith M.P., Weaver L.H., Keana J.F., and Griffith O.H.. 1996. Crystal structure of phosphatidylinositol-specific phospholipase C from Bacillus cereus in complex with glucosaminyl(alpha 1-->6)-D-myo-inositol, an essential fragment of GPI anchors. Biochemistry. 35:9496–9504. 10.1021/bi9606105 PubMed DOI

Heinz D.W., Essen L.O., and Williams R.L.. 1998. Structural and mechanistic comparison of prokaryotic and eukaryotic phosphoinositide-specific phospholipases C. J. Mol. Biol. 275:635–650. 10.1006/jmbi.1997.1490 PubMed DOI

Hicks S.N., Jezyk M.R., Gershburg S., Seifert J.P., Harden T.K., and Sondek J.. 2008. General and versatile autoinhibition of PLC isozymes. Mol. Cell. 31:383–394. 10.1016/j.molcel.2008.06.018 PubMed DOI PMC

Holthuis J.C., and Menon A.K.. 2014. Lipid landscapes and pipelines in membrane homeostasis. Nature. 510:48–57. 10.1038/nature13474 PubMed DOI

Hondal R.J., Zhao Z., Kravchuk A.V., Liao H., Riddle S.R., Yue X., Bruzik K.S., and Tsai M.D.. 1998. Mechanism of phosphatidylinositol-specific phospholipase C: a unified view of the mechanism of catalysis. Biochemistry. 37:4568–4580. 10.1021/bi972646i PubMed DOI

Hu A., Zhao X.T., Tu H., Xiao T., Fu T., Wang Y., Liu Y., Shi X.J., Luo J., and Song B.L.. 2018. PIP4K2A regulates intracellular cholesterol transport through modulating PI(4,5)P2 homeostasis. J. Lipid Res. 59:507–514. 10.1194/jlr.M082149 PubMed DOI PMC

Huff J. 2015. The Airyscan detector from ZEISS: confocal imaging with improved signal-to-noise ratio and super-resolution. Nat. Methods. 12:i–ii. 10.1038/nmeth.f.388 DOI

Hung V., Lam S.S., Udeshi N.D., Svinkina T., Guzman G., Mootha V.K., Carr S.A., and Ting A.Y.. 2017. Proteomic mapping of cytosol-facing outer mitochondrial and ER membranes in living human cells by proximity biotinylation. eLife. 6:e24463 10.7554/eLife.24463 PubMed DOI PMC

Hunyady L., Balla T., Nagy K., and Spät A.. 1982. Control of phosphatidylinositol turnover in adrenal glomerulosa cells. Biochim. Biophys. Acta. 713:352–357. 10.1016/0005-2760(82)90253-3 PubMed DOI

Hunyady L., Baukal A.J., Gaborik Z., Olivares-Reyes J.A., Bor M., Szaszak M., Lodge R., Catt K.J., and Balla T.. 2002. Differential PI 3-kinase dependence of early and late phases of recycling of the internalized AT1 angiotensin receptor. J. Cell Biol. 157:1211–1222. 10.1083/jcb.200111013 PubMed DOI PMC

Ikezawa H., and Taguchi R.. 1981. Phosphatidylinositol-specific phospholipase C from Bacillus cereus and Bacillus thuringiensis. Methods Enzymol. 71:731–741. 10.1016/0076-6879(81)71086-3 DOI

Jeynov B., Lay D., Schmidt F., Tahirovic S., and Just W.W.. 2006. Phosphoinositide synthesis and degradation in isolated rat liver peroxisomes. FEBS Lett. 580:5917–5924. 10.1016/j.febslet.2006.09.058 PubMed DOI

Khan H.M., He T., Fuglebakk E., Grauffel C., Yang B., Roberts M.F., Gershenson A., and Reuter N.. 2016. A Role for Weak Electrostatic Interactions in Peripheral Membrane Protein Binding. Biophys. J. 110:1367–1378. 10.1016/j.bpj.2016.02.020 PubMed DOI PMC

Kim P.K., Mullen R.T., Schumann U., and Lippincott-Schwartz J.. 2006. The origin and maintenance of mammalian peroxisomes involves a de novo PEX16-dependent pathway from the ER. J. Cell Biol. 173:521–532. 10.1083/jcb.200601036 PubMed DOI PMC

Kim Y.J., Guzman-Hernandez M.L., and Balla T.. 2011. A highly dynamic ER-derived phosphatidylinositol-synthesizing organelle supplies phosphoinositides to cellular membranes. Dev. Cell. 21:813–824. 10.1016/j.devcel.2011.09.005 PubMed DOI PMC

Kim Y.J., Guzman-Hernandez M.L., Wisniewski E., and Balla T.. 2015. Phosphatidylinositol-Phosphatidic Acid Exchange by Nir2 at ER-PM Contact Sites Maintains Phosphoinositide Signaling Competence. Dev. Cell. 33:549–561. 10.1016/j.devcel.2015.04.028 PubMed DOI PMC

King C.E., Stephens L.R., Hawkins P.T., Guy G.R., and Michell R.H.. 1987. Multiple metabolic pools of phosphoinositides and phosphatidate in human erythrocytes incubated in a medium that permits rapid transmembrane exchange of phosphate. Biochem. J. 244:209–217. 10.1042/bj2440209 PubMed DOI PMC

Komatsu T., Kukelyansky I., McCaffery J.M., Ueno T., Varela L.C., and Inoue T.. 2010. Organelle-specific, rapid induction of molecular activities and membrane tethering. Nat. Methods. 7:206–208. 10.1038/nmeth.1428 PubMed DOI PMC

Krug M., Weiss M.S., Heinemann U., and Meuller U.. 2012. XDSAPP: a graphical user interface for the convenient processing of diffraction data using XDS. J. Appl. Cryst. 45:568–572. 10.1107/S0021889812011715 DOI

Kuppe A., Evans L.M., McMillen D.A., and Griffith O.H.. 1989. Phosphatidylinositol-specific phospholipase C of Bacillus cereus: cloning, sequencing, and relationship to other phospholipases. J. Bacteriol. 171:6077–6083. 10.1128/JB.171.11.6077-6083.1989 PubMed DOI PMC

Lehto M.T., and Sharom F.J.. 2002. PI-specific phospholipase C cleavage of a reconstituted GPI-anchored protein: modulation by the lipid bilayer. Biochemistry. 41:1398–1408. 10.1021/bi011579w PubMed DOI

Lewis K.A., Garigapati V.R., Zhou C., and Roberts M.F.. 1993. Substrate requirements of bacterial phosphatidylinositol-specific phospholipase C. Biochemistry. 32:8836–8841. 10.1021/bi00085a014 PubMed DOI

Liang J., Choi J., and Clardy J.. 1999. Refined structure of the FKBP12-rapamycin-FRB ternary complex at 2.2 A resolution. Acta Crystallogr. D Biol. Crystallogr. 55:736–744. 10.1107/S0907444998014747 PubMed DOI

Liang H., He S., Yang J., Jia X., Wang P., Chen X., Zhang Z., Zou X., McNutt M.A., Shen W.H., and Yin Y.. 2014. PTENα, a PTEN isoform translated through alternative initiation, regulates mitochondrial function and energy metabolism. Cell Metab. 19:836–848. 10.1016/j.cmet.2014.03.023 PubMed DOI PMC

Litvak V., Dahan N., Ramachandran S., Sabanay H., and Lev S.. 2005. Maintenance of the diacylglycerol level in the Golgi apparatus by the Nir2 protein is critical for Golgi secretory function. Nat. Cell Biol. 7:225–234. 10.1038/ncb1221 PubMed DOI

Liu Z., Chen O., Wall J.B.J., Zheng M., Zhou Y., Wang L., Ruth Vaseghi H., Qian L., and Liu J.. 2017. Systematic comparison of 2A peptides for cloning multi-genes in a polycistronic vector. Sci. Rep. 7:2193 10.1038/s41598-017-02460-2 PubMed DOI PMC

McCoy A.J., Grosse-Kunstleve R.W., Adams P.D., Winn M.D., Storoni L.C., and Read R.J.. 2007. Phaser crystallographic software. J. Appl. Cryst. 40:658–674. 10.1107/S0021889807021206 PubMed DOI PMC

Moser J., Gerstel B., Meyer J.E., Chakraborty T., Wehland J., and Heinz D.W.. 1997. Crystal structure of the phosphatidylinositol-specific phospholipase C from the human pathogen Listeria monocytogenes. J. Mol. Biol. 273:269–282. 10.1006/jmbi.1997.1290 PubMed DOI

Mueller U., Darowski N., Fuchs M.R., Förster R., Hellmig M., Paithankar K.S., Pühringer S., Steffien M., Zocher G., and Weiss M.S.. 2012. Facilities for macromolecular crystallography at the Helmholtz-Zentrum Berlin. J. Synchrotron Radiat. 19:442–449. 10.1107/S0909049512006395 PubMed DOI PMC

Nakatsu F., Baskin J.M., Chung J., Tanner L.B., Shui G., Lee S.Y., Pirruccello M., Hao M., Ingolia N.T., Wenk M.R., and De Camilli P.. 2012. PtdIns4P synthesis by PI4KIIIα at the plasma membrane and its impact on plasma membrane identity. J. Cell Biol. 199:1003–1016. 10.1083/jcb.201206095 PubMed DOI PMC

Nemoto Y., and De Camilli P.. 1999. Recruitment of an alternatively spliced form of synaptojanin 2 to mitochondria by the interaction with the PDZ domain of a mitochondrial outer membrane protein. EMBO J. 18:2991–3006. 10.1093/emboj/18.11.2991 PubMed DOI PMC

Ohashi Y., Tremel S., and Williams R.L.. 2019. VPS34 complexes from a structural perspective. J. Lipid Res. 60:229–241. 10.1194/jlr.R089490 PubMed DOI PMC

Panaretou C., Domin J., Cockcroft S., and Waterfield M.D.. 1997. Characterization of p150, an adaptor protein for the human phosphatidylinositol (PtdIns) 3-kinase. Substrate presentation by phosphatidylinositol transfer protein to the p150.Ptdins 3-kinase complex. J. Biol. Chem. 272:2477–2485. 10.1074/jbc.272.4.2477 PubMed DOI

Petiot A., Ogier-Denis E., Blommaart E.F., Meijer A.J., and Codogno P.. 2000. Distinct classes of phosphatidylinositol 3¢-kinases are involved in signaling pathways that control macroautophagy in HT-29 cells. J. Biol. Chem. 275:992–998. 10.1074/jbc.275.2.992 PubMed DOI

Pu M., Fang X., Redfield A.G., Gershenson A., and Roberts M.F.. 2009. Correlation of vesicle binding and phospholipid dynamics with phospholipase C activity: insights into phosphatidylcholine activation and surface dilution inhibition. J. Biol. Chem. 284:16099–16107. 10.1074/jbc.M809600200 PubMed DOI PMC

Pu M., Orr A., Redfield A.G., and Roberts M.F.. 2010. Defining specific lipid binding sites for a peripheral membrane protein in situ using subtesla field-cycling NMR. J. Biol. Chem. 285:26916–26922. 10.1074/jbc.M110.123083 PubMed DOI PMC

Qian X., Zhou C., and Roberts M.F.. 1998. Phosphatidylcholine activation of bacterial phosphatidylinositol-specific phospholipase C toward PI vesicles. Biochemistry. 37:6513–6522. 10.1021/bi972650u PubMed DOI

Roberts M.F., Khan H.M., Goldstein R., Reuter N., and Gershenson A.. 2018. Search and Subvert: Minimalist Bacterial Phosphatidylinositol-Specific Phospholipase C Enzymes. Chem. Rev. 118:8435–8473. 10.1021/acs.chemrev.8b00208 PubMed DOI

Rosivatz E., and Woscholski R.. 2011. Removal or masking of phosphatidylinositol(4,5)bisphosphate from the outer mitochondrial membrane causes mitochondrial fragmentation. Cell. Signal. 23:478–486. 10.1016/j.cellsig.2010.10.025 PubMed DOI PMC

Saheki Y., Bian X., Schauder C.M., Sawaki Y., Surma M.A., Klose C., Pincet F., Reinisch K.M., and De Camilli P.. 2016. Control of plasma membrane lipid homeostasis by the extended synaptotagmins. Nat. Cell Biol. 18:504–515. 10.1038/ncb3339 PubMed DOI PMC

Sarkes D., and Rameh L.E.. 2010. A novel HPLC-based approach makes possible the spatial characterization of cellular PtdIns5P and other phosphoinositides. Biochem. J. 428:375–384. 10.1042/BJ20100129 PubMed DOI PMC

Schaaf G., Ortlund E.A., Tyeryar K.R., Mousley C.J., Ile K.E., Garrett T.A., Ren J., Woolls M.J., Raetz C.R., Redinbo M.R., and Bankaitis V.A.. 2008. Functional anatomy of phospholipid binding and regulation of phosphoinositide homeostasis by proteins of the sec14 superfamily. Mol. Cell. 29:191–206. 10.1016/j.molcel.2007.11.026 PubMed DOI PMC

Schindelin J., Arganda-Carreras I., Frise E., Kaynig V., Longair M., Pietzsch T., Preibisch S., Rueden C., Saalfeld S., Schmid B., et al. . 2012. Fiji: an open-source platform for biological-image analysis. Nat. Methods. 9:676–682. 10.1038/nmeth.2019 PubMed DOI PMC

Schon E.A. 2007. Appendix 5. Gene products present in mitochondria of yeast and animal cells. Methods Cell Biol. 80:835–876. 10.1016/S0091-679X(06)80044-0 PubMed DOI

Scipioni L., Lanzanó L., Diaspro A., and Gratton E.. 2018. Comprehensive correlation analysis for super-resolution dynamic fingerprinting of cellular compartments using the Zeiss Airyscan detector. Nat. Commun. 9:5120 10.1038/s41467-018-07513-2 PubMed DOI PMC

Sezgin E., and Schwille P.. 2011. Fluorescence techniques to study lipid dynamics. Cold Spring Harb. Perspect. Biol. 3:a009803 10.1101/cshperspect.a009803 PubMed DOI PMC

Shevchenko A., and Simons K.. 2010. Lipidomics: coming to grips with lipid diversity. Nat. Rev. Mol. Cell Biol. 11:593–598. 10.1038/nrm2934 PubMed DOI

Shi X., Shao C., Zhang X., Zambonelli C., Redfield A.G., Head J.F., Seaton B.A., and Roberts M.F.. 2009. Modulation of Bacillus thuringiensis phosphatidylinositol-specific phospholipase C activity by mutations in the putative dimerization interface. J. Biol. Chem. 284:15607–15618. 10.1074/jbc.M901601200 PubMed DOI PMC

Sicart A., Katan M., Egea G., and Sarri E.. 2015. PLCγ1 participates in protein transport and diacylglycerol production triggered by cargo arrival at the Golgi. Traffic. 16:250–266. 10.1111/tra.12246 PubMed DOI

Sohn M., Korzeniowski M., Zewe J.P., Wills R.C., Hammond G.R.V., Humpolickova J., Vrzal L., Chalupska D., Veverka V., Fairn G.D., et al. . 2018. PI(4,5)P2 controls plasma membrane PI4P and PS levels via ORP5/8 recruitment to ER-PM contact sites. J. Cell Biol. 217:1797–1813. 10.1083/jcb.201710095 PubMed DOI PMC

Subach O.M., Cranfill P.J., Davidson M.W., and Verkhusha V.V.. 2011. An enhanced monomeric blue fluorescent protein with the high chemical stability of the chromophore. PLoS One. 6:e28674 10.1371/journal.pone.0028674 PubMed DOI PMC

Szentpetery Z., Várnai P., and Balla T.. 2010. Acute manipulation of Golgi phosphoinositides to assess their importance in cellular trafficking and signaling. Proc. Natl. Acad. Sci. USA. 107:8225–8230. 10.1073/pnas.1000157107 PubMed DOI PMC

Szymczak A.L., Workman C.J., Wang Y., Vignali K.M., Dilioglou S., Vanin E.F., and Vignali D.A.. 2004. Correction of multi-gene deficiency in vivo using a single ‘self-cleaving’ 2A peptide-based retroviral vector. Nat. Biotechnol. 22:589–594. 10.1038/nbt957 PubMed DOI

Ting A.E., and Pagano R.E.. 1990. Detection of a phosphatidylinositol-specific phospholipase C at the surface of Swiss 3T3 cells and its potential role in the regulation of cell growth. J. Biol. Chem. 265:5337–5340. PubMed

Tóth J.T., Gulyás G., Tóth D.J., Balla A., Hammond G.R., Hunyady L., Balla T., and Várnai P.. 2016. BRET-monitoring of the dynamic changes of inositol lipid pools in living cells reveals a PKC-dependent PtdIns4P increase upon EGF and M3 receptor activation. Biochim. Biophys. Acta. 1861:177–187. 10.1016/j.bbalip.2015.12.005 PubMed DOI PMC

Uster P.S., and Pagano R.E.. 1986. Synthesis and properties of fluorescent analogs of cytidine diphosphate-diacylglycerol and phosphatidylinositol. In Enzymes of Lipid Metabolism II. Freysz, L., Gatt, S., Massarelli, R., and Dreyfus, H., editors. Plenum Press, New York: 493–500. 10.1007/978-1-4684-5212-9_64 DOI

van Meer G., Voelker D.R., and Feigenson G.W.. 2008. Membrane lipids: where they are and how they behave. Nat. Rev. Mol. Cell Biol. 9:112–124. 10.1038/nrm2330 PubMed DOI PMC

Vance J.E. 2015. Phospholipid synthesis and transport in mammalian cells. Traffic. 16:1–18. 10.1111/tra.12230 PubMed DOI

Várnai P., and Balla T.. 1998. Visualization of phosphoinositides that bind pleckstrin homology domains: calcium- and agonist-induced dynamic changes and relationship to myo-[3H]inositol-labeled phosphoinositide pools. J. Cell Biol. 143:501–510. 10.1083/jcb.143.2.501 PubMed DOI PMC

Varnai P., Thyagarajan B., Rohacs T., and Balla T.. 2006. Rapidly inducible changes in phosphatidylinositol 4,5-bisphosphate levels influence multiple regulatory functions of the lipid in intact living cells. J. Cell Biol. 175:377–382. 10.1083/jcb.200607116 PubMed DOI PMC

Várnai P., Tóth B., Tóth D.J., Hunyady L., and Balla T.. 2007. Visualization and manipulation of plasma membrane-endoplasmic reticulum contact sites indicates the presence of additional molecular components within the STIM1-Orai1 Complex. J. Biol. Chem. 282:29678–29690. 10.1074/jbc.M704339200 PubMed DOI

Várnai P., Gulyás G., Tóth D.J., Sohn M., Sengupta N., and Balla T.. 2017. Quantifying lipid changes in various membrane compartments using lipid binding protein domains. Cell Calcium. 64:72–82. 10.1016/j.ceca.2016.12.008 PubMed DOI PMC

Volinia S., Dhand R., Vanhaesebroeck B., MacDougall L.K., Stein R., Zvelebil M.J., Domin J., Panaretou C., and Waterfield M.D.. 1995. A human phosphatidylinositol 3-kinase complex related to the yeast Vps34p-Vps15p protein sorting system. EMBO J. 14:3339–3348. 10.1002/j.1460-2075.1995.tb07340.x PubMed DOI PMC

Volwerk J.J., Wetherwax P.B., Evans L.M., Kuppe A., and Griffith O.H.. 1989. Phosphatidylinositol-specific phospholipase C from Bacillus cereus: improved purification, amino acid composition, and amino-terminal sequence. J. Cell. Biochem. 39:315–325. 10.1002/jcb.240390311 PubMed DOI

Volwerk J.J., Filthuth E., Griffith O.H., and Jain M.K.. 1994. Phosphatidylinositol-specific phospholipase C from Bacillus cereus at the lipid-water interface: interfacial binding, catalysis, and activation. Biochemistry. 33(12):3464–3474. 10.1021/bi00178a002 PubMed DOI

Wahl M., Gregor I., Patting M., and Enderlein J.. 2003. Fast calculation of fluorescence correlation data with asynchronous time-correlated single-photon counting. Opt. Express. 11:3583–3591. 10.1364/OE.11.003583 PubMed DOI

Wenk M.R. 2010. Lipidomics: new tools and applications. Cell. 143:888–895. 10.1016/j.cell.2010.11.033 PubMed DOI

Wills R.C., Goulden B.D., and Hammond G.R.V.. 2018. Genetically encoded lipid biosensors. Mol. Biol. Cell. 29:1526–1532. 10.1091/mbc.E17-12-0738 PubMed DOI PMC

Xu C., Watras J., and Loew L.M.. 2003. Kinetic analysis of receptor-activated phosphoinositide turnover. J. Cell Biol. 161:779–791. 10.1083/jcb.200301070 PubMed DOI PMC

Yang B., Pu M., Khan H.M., Friedman L., Reuter N., Roberts M.F., and Gershenson A.. 2015. Quantifying transient interactions between Bacillus phosphatidylinositol-specific phospholipase-C and phosphatidylcholine-rich vesicles. J. Am. Chem. Soc. 137:14–17. 10.1021/ja508631n PubMed DOI PMC

Zewe J.P., Wills R.C., Sangappa S., Goulden B.D., and Hammond G.R.. 2018. SAC1 degrades its lipid substrate PtdIns4P in the endoplasmic reticulum to maintain a steep chemical gradient with donor membranes. eLife. 7:e35588 10.7554/eLife.35588 PubMed DOI PMC

Zhang X., Wehbi H., and Roberts M.F.. 2004. Cross-linking phosphatidylinositol-specific phospholipase C traps two activating phosphatidylcholine molecules on the enzyme. J. Biol. Chem. 279:20490–20500. 10.1074/jbc.M401016200 PubMed DOI

Zhang L., Malik S., Pang J., Wang H., Park K.M., Yule D.I., Blaxall B.C., and Smrcka A.V.. 2013. Phospholipase Cε hydrolyzes perinuclear phosphatidylinositol 4-phosphate to regulate cardiac hypertrophy. Cell. 153:216–227. 10.1016/j.cell.2013.02.047 PubMed DOI PMC

Zhao X.H., Bondeva T., and Balla T.. 2000. Characterization of recombinant phosphatidylinositol 4-kinase beta reveals auto- and heterophosphorylation of the enzyme. J. Biol. Chem. 275:14642–14648. 10.1074/jbc.275.19.14642 PubMed DOI

Zhou C., Qian X., and Roberts M.F.. 1997a Allosteric activation of phosphatidylinositol-specific phospholipase C: specific phospholipid binding anchors the enzyme to the interface. Biochemistry. 36:10089–10097. 10.1021/bi970846o PubMed DOI

Zhou C., Wu Y., and Roberts M.F.. 1997b Activation of phosphatidylinositol-specific phospholipase C toward inositol 1,2-(cyclic)-phosphate. Biochemistry. 36:347–355. 10.1021/bi960601w PubMed DOI

Exploring lipid-protein interactions in plant membranes

Non-vesicular phosphatidylinositol transfer plays critical roles in defining organelle lipid composition