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Sci. STKE, 16 December 2003
[DOI: 10.1126/stke.2132003re17]

EH and UIM: Endocytosis and More
(Supplementary Information 2)

Simona Polo1,2,†, Stefano Confalonieri1,†, Anna Elisabetta Salcini1,2, and Pier Paolo Di Fiore1,2,3*

1Istituto FIRC di Oncologia Molecolare, Via Adamello 16, 20139 Milan, Italy.
2Istituto Europeo di Oncologia, Via Ripamonti 435, 20141 Milan, Italy.
3University of Milan, Medical School, 20122 Milan, Italy.
S. P. and S. C. contributed equally.

*Corresponding author. E-mail: difiore{at}ifom-firc.it

Tables 1 through 7. NPF-containing proteins present in public databases. NPF-containing proteins were collected from protein databases using the ScanProsite tool (1). We searched the SwissProt (release 41) and TrEMBL (release 24) protein databases, limiting the search to Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, and Schizosaccharomyces pombe. Proteins found were made nonredundant using the nrdb90 program (2), such that each group sequence shared 99% similarity. Retrieved proteins were subdivided into groups based on the number on NPF motifs harbored (from one to seven). All files are available as Microsoft Excel spreadsheets and include the organism, EMBL-SwissProt Accession number, the EMBL-SwissProt ID number, the NCBI accession number, the position of the NPF in the amino acid sequence, the name of the encoding gene, and a brief description taken from TrEMBL database.

Table 1. Proteins with 1 NPF motif. [Access Excel File]

Table 2. Proteins with 2 NPF motifs. [Access Excel File]

Table 3. Proteins with 3 NPF motifs. [Access Excel File]

Table 4. Proteins with 4 NPF motifs. [Access Excel File]

Table 5. Proteins with 5 NPF motifs. [Access Excel File]

Table 6. Proteins with 6 NPF motifs. All identified proteins were found in D. melanogaster and M. musculus. [Access Excel File]

Table 7. Proteins with 7 NPF motifs. All identified proteins were found in D. melanogaster. [Access Excel File]

References

  1. A. Gattiker, E. Gasteiger, A. Barioch, ScanProsite: A reference implementation of a PROSITE scanning tool. Applied Bioinformatics 1, 107-108 (2002). (http://us.expasy.org/tools/scanprosite)
  2. L. Holm, C. Sander, Removing near-neighbour redundancy from large protein sequence collections. Bioinformatics 14, 423-429 (1998). (http://www.ebi.ac.uk/%7Eholm/nrdb90/) [Abstract]

Table 8. Proteins with two or more NPF motifs in C. elegans. Functional annotations, interactors, and knock-out (KO) and RNAi phenotypic information were collected from the WormBase database (1) and from literature (2-5). NDA, no data available; Vpep, Viable post-embryonic phenotype; Unc, Uncoordinate; Emb, Embryonic lethal; Led, Late embryo defect; Pvl, Protruding vulva; Stp, Sterile progeny; Bmd, Body morphology defect; Lvl, Larval lethal; Mlt, Molt defect; WT, wild type [Access Excel File]

References

  1. WormBase web site, release WS114, November 2003, (http://www.wormbase.org).
  2. A. G. Fraser, R. S. Kamath, P. Zipperlen, M. Martinez-Campos, M. Sohrmann, J. Ahringer, Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature 408, 325-330 (2000).[CrossRef][Medline]
  3. R. S. Kamath, A. G. Fraser, Y. Dong, G. Poulin, R. Durbin, M. Gotta, A. Kanapin, N. Le Bot, S. Moreno, M. Sohrmann, D. P. Welchman, P. Zipperlen, J. Ahringer, Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421, 231-237 (2003).[CrossRef][Medline]
  4. I. Maeda, Y. Kohara, M. Yamamoto, A. Sugimoto, Large-scale analysis of gene function in Caenorhabditis elegans by high-throughput RNAi. Curr. Biol. 11, 171-176 (2001).[CrossRef][Medline]
  5. F. Piano, A. J. Schetter, D. G. Morton, K. C. Gunsalus, V. Reinke, S. K. Kim, K. J. Kemphues, Gene clustering based on RNAi phenotypes of ovary-enriched genes in C. elegans. Curr. Biol. 12, 1959-1964 (2002).[CrossRef][Medline]

Table. 9. Proteins with 2 or more NPF motifs in S. cerevisiae. Functional annotations, interactors, and knock-out phenotypic information were collected from The Saccharomyces Genome Database (1) and from literature (2-21). RSP5 and SJL1, which possess only one NPF motif, were included because of their relevant biological functions. [Access Excel File]

References

  1. The Saccharomyces Genome Database, November 2003, (http://genome-www.stanford.edu/Saccharomyces/).
  2. J. Kaminska, B. Gajewska, A. K. Hopper, T. Zoladek, Rsp5p, a new link between the actin cytoskeleton and endocytosis in the yeast Saccharomyces cerevisiae. Mol. Cell. Biol. 22, 6946-6948 (2002).[Abstract/Free Full Text]
  3. T. Zoladek, A. Tobiasz, G. Vaduva, M. Boguta, N. C. Martin, A. K. Hopper, MDP1, a Saccharomyces cerevisiae gene involved in mitochondrial/cytoplasmic protein distribution, is identical to the ubiquitin-protein ligase gene RSP5. Genetics 145, 595-603 (1997).[Abstract/Free Full Text]
  4. B. Singer-Kruger, Y. Nemoto, L. Daniell, S. Ferro-Novick, P. De Camilli, Synaptojanin family members are implicated in endocytic membrane traffic in yeast. J. Cell Sci. 111, 3347-3356. (1998).[Abstract/Free Full Text]
  5. M. Fischer, N. Schnell, J. Chattaway, P. Davies, G. Dixon, D. Sanders, The Saccharomyces cerevisiae CCH1 gene is involved in calcium influx and mating. FEBS Lett. 419, 259-262 (1997).[CrossRef][Medline]
  6. C. Y. Chen, M. F. Ingram, P. H. Rosal, T. R. Graham, Role for Drs2p, a P-type ATPase and potential aminophospholipid translocase, in yeast late Golgi function. J. Cell Biol. 147, 1223-36 (1999).[Abstract/Free Full Text]
  7. M. Funakoshi, T. Sasaki, T. Nishimoto, H. Kobayashi, Budding yeast Dsk2p is a polyubiquitin-binding protein that can interact with the proteasome. Proc. Natl. Acad. Sci. U. S. A. 99, 745-750 (2002).[Abstract/Free Full Text]
  8. H. A. Watson, M. J. Cope, A. C. Groen, D. G. Drubin, B. Wendland, In vivo role for actin-regulating kinases in endocytosis and yeast epsin phosphorylation. Mol. Biol. Cell 12, 3668-3679 (2001).[Abstract/Free Full Text]
  9. B. Wendland, K. E. Steece, S. D. Emr, Yeast epsins contain an essential N-terminal ENTH domain, bind clathrin and are required for endocytosis. EMBO J. 18, 4383-93 (1999).[Abstract/Free Full Text]
  10. V. Paciotti, M. Clerici, M. Scotti, G. Lucchini, M. P. Longhese, Characterization of mec1 kinase-deficient mutants and of new hypomorphic mec1 alleles impairing subsets of the DNA damage response pathway. Mol. Cell. Biol. 21, 3913-3925 (2001).[Abstract/Free Full Text]
  11. J. A. Tercero, J. F. Diffley, Regulation of DNA replication fork progression through damaged DNA by the Mec1/Rad53 checkpoint. Nature 412, 553-557 (2001).[CrossRef][Medline]
  12. T. Roemer, S. Delaney, H. Bussey, SKN1 and KRE6 define a pair of functional homologs encoding putative membrane proteins involved in beta-glucan synthesis. Mol. Cell. Biol. 13, 4039-48 (1993).[Abstract]
  13. D. T. Warren, P. D. Andrews, C. W. Gourlay, K. R. Ayscough, Sla1p couples the yeast endocytic machinery to proteins regulating actin dynamics. J. Cell Sci. 115, 1703-1715 (2002).[Abstract/Free Full Text]
  14. O. Roumanie, M. F. Peypouquet, D. Thoraval, F. Doignon, M. Crouzet, Functional interactions between the VRP1-LAS17 and RHO3-RHO4 genes involved in actin cytoskeleton organization in Saccharomyces cerevisiae. Curr. Genet. 40, 317-325 (2002).[CrossRef][Medline]
  15. D. M. Kraemer, C. Strambio-de-Castillia, G. Blobel, M. P. Rout, The essential yeast nucleoporin NUP159 is located on the cytoplasmic side of the nuclear pore complex and serves in karyopherin-mediated binding of transport substrate. J. Biol. Chem. 270, 19017-21 (1995).[Abstract/Free Full Text]
  16. L. C. Gorsch, T. C. Dockendorff, C. N. Cole, A conditional allele of the novel repeat-containing yeast nucleoporin RAT7/NUP159 causes both rapid cessation of mRNA export and reversible clustering of nuclear pore complexes. J. Cell Biol. 129, 939-955 (1995).[Abstract]
  17. O. Merkel, M. Fido, J. A. Mayr, H. Pruger, F. Raab, G. Zandonella, S. D. Kohlwein, F. Paltauf, Characterization and function in vivo of two novel phospholipases B/lysophospholipases from Saccharomyces cerevisiae. J. Biol. Chem. 274, 28121-28127 (1999).[Abstract/Free Full Text]
  18. P. J. Costa, K. M. Arndt, Synthetic lethal interactions suggest a role for the Saccharomyces cerevisiae Rtf1 protein in transcription elongation. Genetics 156, 535-547 (2000).[Abstract/Free Full Text]
  19. J. Mochida, T. Yamamoto, K. Fujimura-Kamada, K. Tanaka, The novel adaptor protein, Mti1p, and Vrp1p, a homolog of Wiskott-Aldrich syndrome protein-interacting protein (WIP), may antagonistically regulate type I myosins in Saccharomyces cerevisiae. Genetics 160, 923-934 (2002).[Abstract/Free Full Text]
  20. Y. Takahashi, J. Mizoi, E. A. Toh, Y. Kikuchi, Yeast Ulp1, an Smt3-specific protease, associates with nucleoporins. J. Biochem. 128, 723-5 (2000).[Abstract]
  21. K. M. Huang, K. D'Hondt, H. Riezman, S. K. Lemmon, Clathrin functions in the absence of heterotetrameric adaptors and AP180-related proteins in yeast. EMBO J. 18, 3897-908 (1999).[Abstract/Free Full Text]

Technical Details

Format: Microsoft Excel spreadsheet

Size: 9 kb (Tables 6 and 7) to 763 kb (Table 1)

Requirements: Microsoft Excel

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Citation: S. Polo, S. Confalonieri, A. E. Salcini, P. P. Di Fiore, EH and UIM: Endocytosis and more. Sci. STKE 2003, re17 (2003).

© 2003 American Association for the Advancement of Science


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