Correction: Population distribution analyses reveal a hierarchy of molecular players underlying parallel endocytic pathways (PLoS ONE (2014) 9, 6 (e100554) DOI:10.1371/journal.pone.0100554);Population distribution analyses reveal a hierarchy of molecular players underlying parallel endocytic pathways

PLoS ONE

Volumn 9, Issue 6, 2014, Pages

  Gupta, Gagan D ^a,c   Dey, Gautam ^a,f   Swetha, M G ^a,i   Ramalingam, Balaji ^a,d   Shameer, Khader ^a,e   Thottacherry, Joseph Jose ^a   Kalappurakkal, Joseph Mathew ^a   Howes, Mark T ^b   Chandran, Ruma ^a   Das, Anupam ^a,g   Menon, Sindhu ^a,h   Parton, Robert G ^b   Sowdhamini, R ^a   Thattai, Mukund ^a   Mayor, Satyajit ^a  

^a UNIVERSITY OF AGRICULTURAL SCIENCES   (India)

^b UNIVERSITY OF QUEENSLAND   (Australia)

^c MOUNT SINAI HOSPITAL   (Canada)

^d NCBS GKVK Campus   (India)

^e MAYO CLINIC   (United States)

^f STANFORD UNIVERSITY   (United States)

^g INDIAN INSTITUTE OF CHEMICAL BIOLOGY   (India)

^h UNIVERSITY OF MÜNSTER   (Germany)

ⁱ YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE DIPHOSPHATE RIBOSYLATION FACTOR 1; CLATHRIN HEAVY CHAIN; DOUBLE STRANDED RNA; DYNAMIN; MUNC18 PROTEIN; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATASE; SMALL INTERFERING RNA; SYNTAXIN 1A; CARNATION PROTEIN, DROSOPHILA; CLATHRIN; DNA BINDING PROTEIN; DROSOPHILA PROTEIN; EYE PROTEIN; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE; SYNTAXIN; SYNTAXIN, DROSOPHILA;

ADULT; ARF1 GENE; ARTICLE; BIOGENESIS; CELL POPULATION; CELLULAR DISTRIBUTION; CONTROLLED STUDY; DROSOPHILA STRAIN; ENDOCYTOSIS; ENDOSOME; ENZYME ACTIVITY; FEMALE; GENE; GENE CONTROL; GENE FUNCTION; GENE LOCATION; GENE MAPPING; GENE ONTOLOGY; GENE SILENCING; HOUSEKEEPING GENE; HUMAN; HUMAN CELL; INTRACELLULAR SIGNALING; INTRACELLULAR TRANSPORT; MALE; MAMMAL CELL; MUTANT DROSOPHILA; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PROTEIN PROTEIN INTERACTION; RNA SEQUENCE; SEC23 GENE; SINGLE CELL ANALYSIS; ANIMAL; ANTAGONISTS AND INHIBITORS; BLOOD CELL; CELL CULTURE; CHEMISTRY; CHO CELL LINE; CRICETULUS; CYTOLOGY; DROSOPHILA; GENE EXPRESSION PROFILING; GENETICS; HAMSTER; METABOLISM; PHYSIOLOGY; RNA INTERFERENCE;

ANIMALS; CELLS, CULTURED; CHO CELLS; CLATHRIN; CRICETINAE; CRICETULUS; DNA-BINDING PROTEINS; DROSOPHILA; DROSOPHILA PROTEINS; ENDOCYTOSIS; EYE PROTEINS; GENE EXPRESSION PROFILING; HEMOCYTES; HUMANS; QA-SNARE PROTEINS; RNA INTERFERENCE; RNA, SMALL INTERFERING; VACUOLAR PROTON-TRANSLOCATING ATPASES;

EID: 84903544968     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0204770     Document Type: Erratum

References (84)

1. Mayor S, Pagano RE (2007) Pathways of clathrin-independent endocytosis. Nat Rev Mol Cell Biol 8: 603-612. (Pubitemid 47106613)
2. Doherty GJ, McMahon HT (2009) Mechanisms of endocytosis. Annual review of biochemistry 78: 857-902.
3. Kumari S, Mg S, Mayor S (2010) Endocytosis unplugged: multiple ways to enter the cell. Cell Res 20: 256-275.
4. Howes MT, Mayor S, Parton RG (2010) Molecules, mechanisms, and cellular roles of clathrin-independent endocytosis. Current opinion in cell biology 22: 519-527.
5. Donaldson JG, Porat-Shliom N, Cohen LA (2009) Clathrin-independent endocytosis: a unique platform for cell signaling and PM remodeling. Cell Signal 21: 1-6.
6. Eyster CA, Higginson JD, Huebner R, Porat-Shliom N, Weigert R, et al. (2009) Discovery of new cargo proteins that enter cells through clathrin-independent endocytosis. Traffic 10: 590-599.
7. Guha A, Sriram V, Krishnan KS, Mayor S (2003) Shibire mutations reveal distinct dynamin-independent and -dependent endocytic pathways in primary cultures of Drosophila hemocytes. J Cell Sci 116: 3373-3386. (Pubitemid 37038985)
8. Gupta GD, Swetha MG, Kumari S, Lakshminarayan R, Dey G, et al. (2009) Analysis of endocytic pathways in Drosophila cells reveals a conserved role for GBF1 in internalization via GEECs. PloS one 4: e6768.
9. Howes MT, Kirkham M, Riches J, Cortese K, Walser PJ, et al. (2010) Clathrin-independent carriers form a high capacity endocytic sorting system at the leading edge of migrating cells. The Journal of cell biology 190: 675-691.
10. Sabharanjak S, Sharma P, Parton RG, Mayor S (2002) GPI-anchored proteins are delivered to recycling endosomes via a distinct cdc42-regulated, clathrin-independent pinocytic pathway. Dev Cell 2: 411-423. (Pubitemid 34436571)
11. Kalia M, Kumari S, Chadda R, Hill MM, Parton RG, et al. (2006) Arf6-independent GPI-anchored protein-enriched early endosomal compartments fuse with sorting endosomes via a Rab5/phosphatidylinositol-3′-kinase- dependent machinery. Mol Biol Cell 17: 3689-3704. (Pubitemid 44156459)
12. Chadda R, Howes MT, Plowman SJ, Hancock JF, Parton RG, et al. (2007) Cholesterol-sensitive Cdc42 activation regulates actin polymerization for endocytosis via the GEEC pathway. Traffic 8: 702-717. (Pubitemid 46785152)
13. Kirkham M, Fujita A, Chadda R, Nixon SJ, Kurzchalia TV, et al. (2005) Ultrastructural identification of uncoated caveolin-independent early endocytic vehicles. The Journal of cell biology 168: 465-476. (Pubitemid 40205068)
14. Kumari S, Mayor S (2008) ARF1 is directly involved in dynamin-independent endocytosis. Nat Cell Biol 10: 30-41.
15. Lundmark R, Doherty GJ, Howes MT, Cortese K, Vallis Y, et al. (2008) The GTPase-activating protein GRAF1 regulates the CLIC/GEEC endocytic pathway. Current biology: CB 18: 1802-1808.
16. Brideau C, Gunter B, Pikounis B, Liaw A (2003) Improved statistical methods for hit selection in high-throughput screening J Biomol Screen 8: 634-647.
17. Malo N, Hanley JA, Cerquozzi S, Pelletier J, Nadon R (2006) Statistical practice in highthroughput screening data analysis. Nat Biotechnol 24: 167-175. (Pubitemid 43221699)
18. Snijder B, Sacher R, Ramo P, Damm EM, Liberali P, et al. (2009) Population context determines cell-to-cell variability in endocytosis and virus infection. Nature 461: 520-523.
19. Altschuler SJ, Wu LF (2010) Cellular heterogeneity: do differences make a difference? Cell 141: 559-563.
20. Slack M, Winkler D, Kramer J, Hesterkamp T (2009) A multiplexed approach to hit finding. Current opinion in drug discovery & development 12: 351-357.
21. Stuart JM, Segal E, Koller D, Kim SK (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science 302: 249-255. (Pubitemid 37248749)
22. Dey G, Gupta GD, Ramalingam B, Sathe M, Mayor S, et al. (2014) Exploiting cell-to-cell variability to detect cellular perturbations. PloS one 9: e90540.
23. Hecht, Shlaer, Pirenne (1942) Energy, quanta, and vision. J Gen Physiol 25: 819-840.
24. Luria S, Delbruck M (1943) on spontaneous mutations in bacteria GENETICS 28: 491.
25. Ozbudak EM, Thattai M, Kurtser I, Grossman AD, Oudenaarden Av (2002) Regulation of noise in the expression of a single gene. Nat Genet 31: 69-73.
26. Levsky JM, Singer RH (2003) Gene expression and the myth of the single cell. Trends Cell Biol 13: 4
27. Raser JM, O'Shea EK (2005) Noise in gene expression: origins, consequences, and control. Science 309: 2010-2013. (Pubitemid 41362308)
28. Massey F (1951) The Kolmogorov-Smirnov Test for Goodness of Fit. Journal of the American Statistical Association 46: 68-78.
29. Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, et al. (2011) The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res 39: D561-568.
30. Krag C, Malmberg EK, Salcini AE (2010) PI3KC2alpha, a class II PI3K, is required for dynamin-independent internalization pathways. J Cell Sci 123: 4240-4250.
31. Haft CR, de la Luz Sierra M, Bafford R, Lesniak MA, Barr VA, et al. (2000) Human orthologs of yeast vacuolar protein sorting proteins Vps26, 29, and 35: assembly into multimeric complexes. Mol Biol Cell 11: 4105-4116.
32. Tai G, Lu L, Wang TL, Tang BL, Goud B, et al. (2004) Participation of the syntaxin 5/Ykt6/GS28/GS15 SNARE complex in transport from the early/recycling endosome to the trans-Golgi network. Mol Biol Cell 15: 4011-4022. (Pubitemid 39122007)
33. Defilippi P, Di Stefano P, Cabodi S (2006) p130Cas: a versatile scaffold in signaling networks. Trends Cell Biol 16: 257-263. (Pubitemid 43728873)
34. Raucher D, Sheetz MP (2000) Cell spreading and lamellipodial extension rate is regulated by membrane tension. The Journal of cell biology 148: 127-136. (Pubitemid 30046787)
35. Dai J, Sheetz MP (1999) Membrane tether formation from blebbing cells. Biophys J 77: 3363-3370.
36. Rohn (2011) JCB 194 789.
37. Raiborg C, Stenmark H (2009) The ESCRT machinery in endosomal sorting of ubiquitylated membrane proteins. Nature 458: 445-452.
38. Hurley JH, Hanson PI (2010) Membrane budding and scission by the ESCRT machinery: it's all in the neck. Nat Rev Mol Cell Biol 11: 556-566.
39. Collinet C, Stoter M, Bradshaw CR, Samusik N, Rink JC, et al. (2010) Systems survey of endocytosis by multiparametric image analysis. Nature 464: 243-249.
40. Bottcher RT, Lange A, Fassler R (2009) How ILK and kindlins cooperate to orchestrate integrin signaling. Current opinion in cell biology 21: 670-675.
41. Jani K, Schock F (2007) Zasp is required for the assembly of functional integrin adhesion sites. The Journal of cell biology 179: 1583-1597.
42. Huang TY, DerMardirossian C, Bokoch GM (2006) Cofilin phosphatases and regulation of actin dynamics. Current opinion in cell biology 18: 26-31. (Pubitemid 43107604)
43. Chan KT, Creed SJ, Bear JE (2011) Unraveling the enigma: progress towards understanding the coronin family of actin regulators. Trends Cell Biol.
44. Moseley JB, Okada K, Balcer HI, Kovar DR, Pollard TD, et al. (2006) Twinfilin is an actin-filament-severing protein and promotes rapid turnover of actin structures in vivo. J Cell Sci 119: 1547-1557. (Pubitemid 43732981)
45. Tilghman RW, Parsons JT (2008) Focal adhesion kinase as a regulator of cell tension in the progression of cancer. Semin Cancer Biol 18: 45-52. (Pubitemid 350266368)
46. Lai Wing Sun K, Correia JP, Kennedy TE (2011) Netrins: versatile extracellular cues with diverse functions. Development 138: 2153-2169.
47. Sriram V, Krishnan KS, Mayor S (2003) deep-orange and carnation define distinct stages in late endosomal biogenesis in Drosophila melanogaster. The Journal of cell biology 161: 593-607. (Pubitemid 36578583)
48. Price A, Seals D, Wickner W, Ungermann C (2000) The docking stage of yeast vacuole fusion requires the transfer of proteins from a cis-SNARE complex to a Rab/Ypt protein. The Journal of cell biology 148: 1231-1238.
49. Sevrioukov EA, He JP, Moghrabi N, Sunio A, Kramer H (1999) A role for the deep orange and carnation eye color genes in lysosomal delivery in Drosophila. Mol Cell 4: 479-486. (Pubitemid 29531128)
50. Rizo J and Sudhof TC (2002) Snares and Munc18 in synaptic vesicle fusion. Nat Rev Neurosci 3: 641-653. (Pubitemid 135706672)
51. Akbar MA, Ray S, Kramer H (2009) The SM protein Car/Vps33A regulates SNARE-mediated trafficking to lysosomes and lysosome-related organelles. Mol Biol Cell 20: 1705-1714.
52. Arunachalam L, Han L, Tassew NG, He Y, Wang L, et al. (2008) Munc18-1 is critical for plasma membrane localization of syntaxin1 but not of SNAP-25 in PC12 cells. Mol Biol Cell 19: 722-734. (Pubitemid 351272159)
53. Mellman I, Fuchs R, Helenius A (1986) Acidification of the endocytic and exocytic pathways. Annual review of biochemistry 55: 663-700. (Pubitemid 16070784)
54. Maxfield FR, McGraw TE (2004) Endocytic recycling. Nat Rev Mol Cell Biol 5: 121-132. (Pubitemid 38160255)
55. Mollenhauer HH, Morre DJ, Rowe LD (1990) Alteration of intracellular traffic by monensin; mechanism, specificity and relationship to toxicity. Biochim Biophys Acta 1031: 225-246.
56. Bowman BJ, McCall ME, Baertsch R, Bowman EJ (2006) A model for the proteolipid ring and bafilomycin/concanamycin-binding site in the vacuolar ATPase of Neurospora crassa. J Biol Chem 281: 31885-31893. (Pubitemid 46041451)
57. Guo Y, Walther TC, Rao M, Stuurman N, Goshima G, et al. (2008) Functional genomic screen reveals genes involved in lipid-droplet formation and utilization. Nature 453: 657-661. (Pubitemid 351769298)
58. Beller M, Sztalryd C, Southall N, Bell M, Jackle H, et al. (2008) COPI complex is a regulator of lipid homeostasis. PLoS Biol 6: e292.
59. Venkatesan K, Rual JF, Vazquez A, Stelzl U, Lemmens I, et al. (2009) An empirical framework for binary interactome mapping. Nature methods 6: 83-90.
60. Fuchs F, Pau G, Kranz D, Sklyar O, Budjan C, et al. (2010) Clustering phenotype populations by genome-wide RNAi and multiparametric imaging. Mol Syst Biol 6: 370.
61. Wang X, Castro MA, Mulder KW, Markowetz F (2012) Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations. PLoS computational biology 8: e1002566.
62. Snijder B, Liberali P, Frechin M, Stoeger T, Pelkmans L (2013) Predicting functional gene interactions with the hierarchical interaction score. Nature methods 10: 1089-1092.
63. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
64. Misselwitz B, Dilling S, Vonaesch P, Sacher R, Snijder B, et al. (2011) RNAi screen of Salmonella invasion shows role of COPI in membrane targeting of cholesterol and Cdc42. Mol Syst Biol 7: 474.
65. Witke W, Podtelejnikov AV, Di Nardo A, Sutherland JD, Gurniak CB, et al. (1998) In mouse brain profilin I and profilin II associate with regulators of the endocytic pathway and actin assembly. EMBO J 17: 967-976. (Pubitemid 28077651)
66. Gasman S, Kalaidzidis Y, Zerial M (2003) RhoD regulates endosome dynamics through Diaphanous-related Formin and Src tyrosine kinase. Nat Cell Biol 5: 195-204. (Pubitemid 36322245)
67. Pelkmans L, Zerial M (2005) Kinase-regulated quantal assemblies and kiss-and-run recycling of caveolae. Nature 436: 128-133. (Pubitemid 40966198)
68. Toonen RF, de Vries KJ, Zalm R, Sudhof TC, Verhage M (2005) Munc18-1 stabilizes syntaxin 1, but is not essential for syntaxin 1 targeting and SNARE complex formation. J Neurochem 93: 1393-1400. (Pubitemid 40853262)
69. Nevins AK, Thurmond DC (2005) A direct interaction between Cdc42 and vesicle-associated membrane protein 2 regulates SNARE-dependent insulin exocytosis. J Biol Chem 280: 1944-1952.
70. Lloyd V, Ramaswami M, Kramer H (1998) Not just pretty eyes: Drosophila eye-colour mutations and lysosomal delivery. Trends Cell Biol 8: 257-259. (Pubitemid 28310222)
71. Sardiello M, Palmieri M, di Ronza A, Medina DL, Valenza M, et al. (2009) A gene network regulating lysosomal biogenesis and function. Science 325: 473-477.
72. Foley E, O'Farrell PH (2004) Functional dissection of an innate immune response by a genome-wide RNAi screen. PLoS Biol 2: E203.
73. Horn T, Sandmann T, Boutros M (2010) Design and evaluation of genome-wide libraries for RNA interference screens. Genome Biol 11: R61.
74. Felsenstein J (1997) An alternating least squares approach to inferring phylogenies from pairwise distances. Syst Biol 46: 101-111.
75. Mostafavi S, Ray D, Warde-Farley D, Grouios C, Morris Q (2008) GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function. Genome Biol 9 Suppl 1: S4.
76. Casey JR, Grinstein S, Orlowski J (2010) Sensors and regulators of intracellular pH. Nat Rev Mol Cell Biol 11: 50-61.
77. Kulkarni MM, Booker M, Silver SJ, Friedman A, Hong P, et al. (2006) Evidence of off-target effects associated with long dsRNAs in Drosophila melanogaster cell-based assays. Nat Methods 3: 833-838. (Pubitemid 44445831)
78. Sims D, Bursteinas B, Gao Q, Zvelebil M, Baum B (2006) FLIGHT: database and tools for the integration and cross-correlation of large-scale RNAi phenotypic datasets. Nucleic Acids Res 34: D479-483.
79. Gwack Y, Sharma S, Nardone J, Tanasa B, Iuga A, et al. (2006) A genome-wide Drosophila RNAi screen identifies DYRK-family kinases as regulators of NFAT. Nature 441: 646-650. (Pubitemid 43927297)
80. DasGupta R, Kaykas A, Moon RT, Perrimon N (2005) Functional Genomic Analysis of the Wnt-Wingless Signaling Pathway. Science 308: 826-833. (Pubitemid 40629258)
81. Vig M, Peinelt C, Beck A, Koomoa DL, Rabah D, et al. (2006) CRACM1 Is a Plasma Membrane Protein Essential for Store-Operated Ca2+ Entry. Science 312: 1220-1223. (Pubitemid 43801149)
82. Sathyanarayanan S, Zheng X, Kumar S, Chen CH, Chen D, et al. (2008) Identification of novel genes involved in light-dependent CRY degradation through a genome-wide RNAi screen. Genes Dev 22: 1522-1533. (Pubitemid 351793086)
83. Xu L, Yao X, Chen X, Lu P, Zhang B, et al. (2007) Msk is required for nuclear import of TGF-β/BMP-activated Smads. The Journal of cell biology 178: 981-994. (Pubitemid 47443321)
84. Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, et al. (2010) The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res 38: W214-220.