Cited by 453

The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.

A novel probe for phosphatidylinositol 4-phosphate reveals multiple pools beyond the Golgi

Hammond, Gerald R.V., Machner, Matthias P., Balla, Tamas·2014·Journal of Cell Biology

Abstract

Polyphosphoinositides are an important class of lipid that recruit specific effector proteins to organelle membranes. One member, phosphatidylinositol 4-phosphate (PtdIns4P) has been localized to Golgi membranes based on the distribution of lipid binding modules from PtdIns4P effector proteins. However, these probes may be biased by additional interactions with other Golgi-specific determinants. In this paper, we derive a new PtdIns4P biosensor using the PtdIns4P binding of SidM (P4M) domain of the secreted effector protein SidM from the bacterial pathogen Legionella pneumophila. PtdIns4P was necessary and sufficient for localization of P4M, which revealed pools of the lipid associated not only with the Golgi but also with the plasma membrane and Rab7-positive late endosomes/lysosomes. PtdIns4P distribution was determined by the localization and activities of both its anabolic and catabolic enzymes. Therefore, P4M reports a wider cellular distribution of PtdIns4P than previous probes and therefore will be valuable for dissecting the biological functions of PtdIns4P in its assorted membrane compartments.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1083/jcb.201312072

Cites

2 of 2 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 81

  1. Baird, 2008, Assembly of the PtdIns 4-kinase Stt4 complex at the plasma membrane requires Ypp1 and Efr3, J. Cell Biol., 183, 1061, 10.1083/jcb.200804003 · DOI
  2. Balla, 2002, Characterization of type II phosphatidylinositol 4-kinase isoforms reveals association of the enzymes with endosomal vesicular compartments, J. Biol. Chem., 277, 20041, 10.1074/jbc.M111807200 · DOI
  3. Balla, 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, 10.1091/mbc.E04-07-0578 · DOI
  4. Balla, 2008, Design of drug-resistant alleles of type-III phosphatidylinositol 4-kinases using mutagenesis and molecular modeling, Biochemistry., 47, 1599, 10.1021/bi7017927 · DOI
  5. Balla, 2008, Maintenance of hormone-sensitive phosphoinositide pools in the plasma membrane requires phosphatidylinositol 4-kinase IIIalpha, Mol. Biol. Cell., 19, 711, 10.1091/mbc.E07-07-0713 · DOI
  6. Balla, 2013, Phosphoinositides: tiny lipids with giant impact on cell regulation, Physiol. Rev., 93, 1019, 10.1152/physrev.00028.2012 · DOI · Paper page
  7. Balla, 2000, How accurately can we image inositol lipids in living cells?, Trends Pharmacol. Sci., 21, 238, 10.1016/S0165-6147(00)01500-5 · DOI
  8. Berger, 2011, Hepatitis C virus stimulates the phosphatidylinositol 4-kinase III alpha-dependent phosphatidylinositol 4-phosphate production that is essential for its replication, J. Virol., 85, 8870, 10.1128/JVI.00059-11 · DOI
  9. Blagoveshchenskaya, 2008, Integration of Golgi trafficking and growth factor signaling by the lipid phosphatase SAC1, J. Cell Biol., 180, 803, 10.1083/jcb.200708109 · DOI
  10. Brombacher, 2009, Rab1 guanine nucleotide exchange factor SidM is a major phosphatidylinositol 4-phosphate-binding effector protein of Legionella pneumophila, J. Biol. Chem., 284, 4846, 10.1074/jbc.M807505200 · DOI
  11. Brown, 1994, A mammalian protein targeted by G1-arresting rapamycin-receptor complex, Nature., 369, 756, 10.1038/369756a0 · DOI · Paper page
  12. Brown, 2011, Phylogenomics of phosphoinositide lipid kinases: perspectives on the evolution of second messenger signaling and drug discovery, BMC Evol. Biol., 11, 4, 10.1186/1471-2148-11-4 · DOI
  13. Bucci, 1992, The small GTPase rab5 functions as a regulatory factor in the early endocytic pathway, Cell., 70, 715, 10.1016/0092-8674(92)90306-W · DOI
  14. Budhu, 2007, Induction of a unique gene expression profile in primary human hepatocytes by hepatitis C virus core, NS3 and NS5A proteins, Carcinogenesis., 28, 1552, 10.1093/carcin/bgm075 · DOI
  15. Burgess, 2012, Type II phosphatidylinositol 4-kinase regulates trafficking of secretory granule proteins in Drosophila, Development., 139, 3040, 10.1242/dev.077644 · DOI
  16. Campbell, 2002, A monomeric red fluorescent protein, Proc. Natl. Acad. Sci. USA., 99, 7877, 10.1073/pnas.082243699 · DOI
  17. Carlton, 2005, Coincidence detection in phosphoinositide signaling, Trends Cell Biol., 15, 540, 10.1016/j.tcb.2005.08.005 · DOI
  18. D’Angelo, 2007, Glycosphingolipid synthesis requires FAPP2 transfer of glucosylceramide, Nature., 449, 62, 10.1038/nature06097 · DOI
  19. Dippold, 2009, GOLPH3 bridges phosphatidylinositol-4- phosphate and actomyosin to stretch and shape the Golgi to promote budding, Cell., 139, 337, 10.1016/j.cell.2009.07.052 · DOI
  20. Fili, 2006, Compartmental signal modulation: Endosomal phosphatidylinositol 3-phosphate controls endosome morphology and selective cargo sorting, Proc. Natl. Acad. Sci. USA., 103, 15473, 10.1073/pnas.0607040103 · DOI
  21. Filonov, 2011, Bright and stable near-infrared fluorescent protein for in vivo imaging, Nat. Biotechnol., 29, 757, 10.1038/nbt.1918 · DOI
  22. Gillooly, 2000, Localization of phosphatidylinositol 3-phosphate in yeast and mammalian cells, EMBO J., 19, 4577, 10.1093/emboj/19.17.4577 · DOI · Paper page
  23. Godi, 1999, ARF mediates recruitment of PtdIns-4-OH kinase-beta and stimulates synthesis of PtdIns(4,5)P2 on the Golgi complex, Nat. Cell Biol., 1, 280, 10.1038/12993 · DOI
  24. Godi, 2004, FAPPs control Golgi-to-cell-surface membrane traffic by binding to ARF and PtdIns(4)P, Nat. Cell Biol., 6, 393, 10.1038/ncb1119 · DOI
  25. Goedhart, 2012, Structure-guided evolution of cyan fluorescent proteins towards a quantum yield of 93%, Nat. Commun., 3, 751, 10.1038/ncomms1738 · DOI
  26. Graham, 2011, Coordination of Golgi functions by phosphatidylinositol 4-kinases, Trends Cell Biol., 21, 113, 10.1016/j.tcb.2010.10.002 · DOI
  27. Guo, 1999, SAC1-like domains of yeast SAC1, INP52, and INP53 and of human synaptojanin encode polyphosphoinositide phosphatases, J. Biol. Chem., 274, 12990, 10.1074/jbc.274.19.12990 · DOI
  28. Halaszovich, 2009, Ci-VSP is a depolarization-activated phosphatidylinositol-4,5-bisphosphate and phosphatidylinositol-3,4,5-trisphosphate 5′-phosphatase, J. Biol. Chem., 284, 2106, 10.1074/jbc.M803543200 · DOI
  29. Ham, 2011, Manipulation of host membranes by bacterial effectors, Nat. Rev. Microbiol., 9, 635, 10.1038/nrmicro2602 · DOI
  30. Hama, 1999, Direct involvement of phosphatidylinositol 4-phosphate in secretion in the yeast Saccharomyces cerevisiae, J. Biol. Chem., 274, 34294, 10.1074/jbc.274.48.34294 · DOI
  31. Hammond, 2009, Immunocytochemical techniques reveal multiple, distinct cellular pools of PtdIns4P and PtdIns(4,5)P(2), Biochem. J., 422, 23, 10.1042/BJ20090428 · DOI
  32. Hammond, 2012, PI4P and PI(4,5)P2 are essential but independent lipid determinants of membrane identity, Science., 337, 727, 10.1126/science.1222483 · DOI
  33. Heo, 2006, PI(3,4,5)P3 and PI(4,5)P2 lipids target proteins with polybasic clusters to the plasma membrane, Science., 314, 1458, 10.1126/science.1134389 · DOI
  34. Idevall-Hagren, 2012, Optogenetic control of phosphoinositide metabolism, Proc. Natl. Acad. Sci. USA., 109, E2316, 10.1073/pnas.1211305109 · DOI
  35. Jaskolski, 2005, An automated method to quantify and visualize colocalized fluorescent signals, J. Neurosci. Methods., 146, 42, 10.1016/j.jneumeth.2005.01.012 · DOI
  36. Jović, 2012, Two phosphatidylinositol 4-kinases control lysosomal delivery of the Gaucher disease enzyme, β-glucocerebrosidase, Mol. Biol. Cell., 23, 1533, 10.1091/mbc.E11-06-0553 · DOI
  37. Kim, 2013, Inositol lipid regulation of lipid transfer in specialized membrane domains, Trends Cell Biol., 23, 270, 10.1016/j.tcb.2013.01.009 · DOI
  38. Komatsu, 2010, Organelle-specific, rapid induction of molecular activities and membrane tethering, Nat. Methods., 7, 206, 10.1038/nmeth.1428 · DOI
  39. Kono, 2013, Impaired α-TTP-PIPs interaction underlies familial vitamin E deficiency, Science., 340, 1106, 10.1126/science.1233508 · DOI
  40. Levine, 2002, Targeting of Golgi-specific pleckstrin homology domains involves both PtdIns 4-kinase-dependent and -independent components, Curr. Biol., 12, 695, 10.1016/S0960-9822(02)00779-0 · DOI
  41. Li, 2013, Genetically encoded fluorescent probe to visualize intracellular phosphatidylinositol 3,5-bisphosphate localization and dynamics, Proc. Natl. Acad. Sci. USA., 110, 21165, 10.1073/pnas.1311864110 · DOI
  42. Lippincott-Schwartz, 1989, Rapid redistribution of Golgi proteins into the ER in cells treated with brefeldin A: evidence for membrane cycling from Golgi to ER, Cell., 56, 801, 10.1016/0092-8674(89)90685-5 · DOI
  43. Machner, 2007, A bifunctional bacterial protein links GDI displacement to Rab1 activation, Science., 318, 974, 10.1126/science.1149121 · DOI
  44. Méresse, 1995, The rab7 GTPase resides on a vesicular compartment connected to lysosomes, J. Cell Sci., 108, 3349, 10.1242/jcs.108.11.3349 · DOI
  45. Mesmin, 2013, A four-step cycle driven by PI(4)P hydrolysis directs sterol/PI(4)P exchange by the ER-Golgi tether OSBP, Cell., 155, 830, 10.1016/j.cell.2013.09.056 · DOI
  46. Minogue, 2006, Phosphatidylinositol 4-kinase is required for endosomal trafficking and degradation of the EGF receptor, J. Cell Sci., 119, 571, 10.1242/jcs.02752 · DOI
  47. Minogue, 2010, Relationship between phosphatidylinositol 4-phosphate synthesis, membrane organization, and lateral diffusion of PI4KIIalpha at the trans-Golgi network, J. Lipid Res., 51, 2314, 10.1194/jlr.M005751 · DOI
  48. Müller, 2010, The Legionella effector protein DrrA AMPylates the membrane traffic regulator Rab1b, Science., 329, 946, 10.1126/science.1192276 · DOI
  49. Nakatsu, 2012, PtdIns4P synthesis by PI4KIIIα at the plasma membrane and its impact on plasma membrane identity, J. Cell Biol., 199, 1003, 10.1083/jcb.201206095 · DOI · Paper page
  50. Nemoto, 2000, Functional characterization of a mammalian Sac1 and mutants exhibiting substrate-specific defects in phosphoinositide phosphatase activity, J. Biol. Chem., 275, 34293, 10.1074/jbc.M003923200 · DOI
  51. Olivo-Marin, 2002, Extraction of spots in biological images using multiscale products, Pattern Recognit., 35, 1989, 10.1016/S0031-3203(01)00127-3 · DOI
  52. Polevoy, 2009, Dual roles for the Drosophila PI 4-kinase four wheel drive in localizing Rab11 during cytokinesis, J. Cell Biol., 187, 847, 10.1083/jcb.200908107 · DOI
  53. Reaves, 1992, Perturbation of the morphology of the trans-Golgi network following Brefeldin A treatment: redistribution of a TGN-specific integral membrane protein, TGN38, J. Cell Biol., 116, 85, 10.1083/jcb.116.1.85 · DOI
  54. Reiss, 2011, Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment, Cell Host Microbe., 9, 32, 10.1016/j.chom.2010.12.002 · DOI
  55. Reiss, 2013, The lipid kinase phosphatidylinositol-4 kinase III alpha regulates the phosphorylation status of hepatitis C virus NS5A, PLoS Pathog., 9, e1003359, 10.1371/journal.ppat.1003359 · DOI
  56. Rocha, 2009, Cholesterol sensor ORP1L contacts the ER protein VAP to control Rab7–RILP–p150Glued and late endosome positioning, J. Cell Biol., 185, 1209, 10.1083/jcb.200811005 · DOI
  57. Rohde, 2003, The human phosphatidylinositol phosphatase SAC1 interacts with the coatomer I complex, J. Biol. Chem., 278, 52689, 10.1074/jbc.M307983200 · DOI
  58. Rojas, 2008, Regulation of retromer recruitment to endosomes by sequential action of Rab5 and Rab7, J. Cell Biol., 183, 513, 10.1083/jcb.200804048 · DOI · Paper page
  59. Rong, 2012, Clathrin and phosphatidylinositol-4,5-bisphosphate regulate autophagic lysosome reformation, Nat. Cell Biol., 14, 924, 10.1038/ncb2557 · DOI · Paper page
  60. Roth, 2004, Phosphoinositides in constitutive membrane traffic, Physiol. Rev., 84, 699, 10.1152/physrev.00033.2003 · DOI
  61. Roy, 2004, Multiple pools of phosphatidylinositol 4-phosphate detected using the pleckstrin homology domain of Osh2p, J. Biol. Chem., 279, 44683, 10.1074/jbc.M401583200 · DOI
  62. Salazar, 2005, Phosphatidylinositol-4-kinase type II alpha is a component of adaptor protein-3-derived vesicles, Mol. Biol. Cell., 16, 3692, 10.1091/mbc.E05-01-0020 · DOI
  63. Sarkes, 2010, A novel HPLC-based approach makes possible the spatial characterization of cellular PtdIns5P and other phosphoinositides, Biochem. J., 428, 375, 10.1042/BJ20100129 · DOI
  64. Schaletzky, 2003, Phosphatidylinositol-5-phosphate activation and conserved substrate specificity of the myotubularin phosphatidylinositol 3-phosphatases, Curr. Biol., 13, 504, 10.1016/S0960-9822(03)00132-5 · DOI
  65. Schmiedeberg, 2009, A temporal threshold for formaldehyde crosslinking and fixation, PLoS ONE., 4, e4636, 10.1371/journal.pone.0004636 · DOI
  66. Schoebel, 2010, High-affinity binding of phosphatidylinositol 4-phosphate by Legionella pneumophila DrrA, EMBO Rep., 11, 598, 10.1038/embor.2010.97 · DOI
  67. Sridhar, 2013, The lipid kinase PI4KIIIβ preserves lysosomal identity, EMBO J., 32, 324, 10.1038/emboj.2012.341 · DOI · Paper page
  68. Stefan, 2011, Osh proteins regulate phosphoinositide metabolism at ER-plasma membrane contact sites, Cell., 144, 389, 10.1016/j.cell.2010.12.034 · DOI
  69. Suh, 2006, Rapid chemically induced changes of PtdIns(4,5)P2 gate KCNQ ion channels, Science., 314, 1454, 10.1126/science.1131163 · DOI · Paper page
  70. Szentpetery, 2010, Acute manipulation of Golgi phosphoinositides to assess their importance in cellular trafficking and signaling, Proc. Natl. Acad. Sci. USA., 107, 8225, 10.1073/pnas.1000157107 · DOI
  71. Tan, 2014, PI4KIIIα is required for cortical integrity and cell polarity during Drosophila oogenesis, J. Cell Sci., 127, 954, 10.1242/jcs.129031 · DOI
  72. Tóth, 2006, Phosphatidylinositol 4-kinase IIIbeta regulates the transport of ceramide between the endoplasmic reticulum and Golgi, J. Biol. Chem., 281, 36369, 10.1074/jbc.M604935200 · DOI
  73. Várnai, 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, 10.1083/jcb.143.2.501 · DOI · Paper page
  74. Várnai, 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, 10.1083/jcb.200607116 · DOI · Paper page
  75. Wakana, 2012, A new class of carriers that transport selective cargo from the trans Golgi network to the cell surface, EMBO J., 31, 3976, 10.1038/emboj.2012.235 · DOI
  76. Walch-Solimena, 1999, The yeast phosphatidylinositol-4-OH kinase pik1 regulates secretion at the Golgi, Nat. Cell Biol., 1, 523, 10.1038/70319 · DOI
  77. Wang, 2003, Phosphatidylinositol 4 phosphate regulates targeting of clathrin adaptor AP-1 complexes to the Golgi, Cell., 114, 299, 10.1016/S0092-8674(03)00603-2 · DOI
  78. Watt, 2002, Subcellular localization of phosphatidylinositol 4,5-bisphosphate using the pleckstrin homology domain of phospholipase C delta1, Biochem. J., 363, 657, 10.1042/0264-6021:3630657 · DOI
  79. Weixel, 2005, Distinct Golgi populations of phosphatidylinositol 4-phosphate regulated by phosphatidylinositol 4-kinases, J. Biol. Chem., 280, 10501, 10.1074/jbc.M414304200 · DOI
  80. Yeung, 2008, Membrane phosphatidylserine regulates surface charge and protein localization, Science., 319, 210, 10.1126/science.1152066 · DOI
  81. Zhu, 2010, Structural mechanism of host Rab1 activation by the bifunctional Legionella type IV effector SidM/DrrA, Proc. Natl. Acad. Sci. USA., 107, 4699, 10.1073/pnas.0914231107 · DOI

Cited by

Sorted by citations

Metadata

Authors
Hammond, G. R. V., Machner, M. P., & Balla, T.
Affiliations
Program in Developmental Neuroscience 1 and 2
Venue
Journal of Cell Biology
Published
2014-04-07
Volume
205
Issue
1
Pages
113-126
ISSN
  • 1540-8140
  • 0021-9525
Cited by
453
References
2
Language
en

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review