Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

Subscribe

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

EH and UIM: Endocytosis and More
(Supplementary Information 3)

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 5. UIM-containing proteins and their functions. UIM-containing proteins were collected both from literature and protein databases searches using a HMM profile for the UIM domain, built starting from a collection of known UIM domains (1). We searched the SwissProt (release 41) and TrEMBL (release 24) protein databases. The identified proteins were made nonredundant using the nrdb90 program (2) and by visual inspection. The protein list was compared and integrated, where necessary, with the one generated automatically at the SMART website (3). Functional annotations, interactors, knock-out (KO) and RNA interference (RNAi) phenotypic information were collected from the WormBase (4) for Caenorhabditis elegans, FlyBase (5) for Drosophila melanogaster, and The Saccharomyces Genome Database (6) for Saccharomyces cerevesiae. Annotations for the mammalian proteins were collected from literature (7-9). Results include proteins from Homo sapiens, Mus musculus, Rattus norvegicus, Bos taurus, D. melanogaster, C. elegans, S. cerevisiae, and Schizosaccharomyces pombe. 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 number of UIM domains, the name of the encoding gene, a brief description (from the TrEMBL database), other domains present (from the SMART website), any known interactors, the ability to interact with ubiquitin or monoubiquitin, and knock-out (KO) phenotypic information.

Table 1. UIM domain-containing proteins in several species. [Access Excel File]

Table 2. UIM domain-containing proteins C. elegans. Phenotype abbreviations of KO by RNA interference (RNAi): Dpy, dumpy; Emb, embryonic lethal; Gro, slow growth; Unc, uncoordinated; WT, wild type. [Access Excel File]

Table 3. UIM domain-containing proteins in D. melanogaster. [Access Excel File]

Table 4. UIM domain-containing proteins in yeast. [Access Excel File]

Table 5. UIM domain-containing proteins in mammals. [Access Excel File]

References

  1. K. Hofmann, L. Falquet, A ubiquitin-interacting motif conserved in components of the proteasomal and lysosomal protein degradation systems. Trends Biochem. Sci. 26, 347-350 (2001).[CrossRef][Medline]
  2. L. Holm, C. Sander, Removing near-neighbour redundancy from large protein sequence collections. Bioinformatics 14, 423-429 (1998).[Abstract]
  3. I. Letunic, L. Goodstadt, N. J. Dickens, T. Doerks, J. Schultz, R. Mott, F. Ciccarelli, R. R. Copley, C. P. Ponting, P. Bork, Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res. 30, 242-244 (2002).[Abstract/Free Full Text]
  4. WormBase web site, release WS114, November 2003, (http://www.wormbase.org).
  5. The FlyBase Consortium. The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res. 31,172-175 (2003). (http://flybase.org/) [Abstract/Free Full Text]
  6. The Saccharomyces Genome Database, November 2003, (http://genome-www.stanford.edu/Saccharomyces/).
  7. K. M. Donaldson, W. Li, K. A. Ching, S. Batalov, C. C. Tsai, C. A. Joazeiro, Ubiquitin-mediated sequestration of normal cellular proteins into polyglutamine aggregates. Proc. Natl. Acad. Sci. U. S. A. 100, 8892-8897 (2003). [Abstract/Free Full Text]
  8. M. Komada, P. Soriano, Hrs, a FYVE finger protein localized to early endosomes, is implicated in vesicular traffic and required for ventral folding morphogenesis. Genes Dev. 13, 1475-1485 (1999). [Abstract/Free Full Text]
  9. M. Yamada, N. Ishii, H. Asao, K. Murata, C. Kanazawa, H. Sasaki, K. Sugamura, Signal-transducing adaptor molecules STAM1 and STAM2 are required for T-cell development and survival. Mol. Cell. Biol. 22, 8648-8658 (2002).[Abstract/Free Full Text]

Technical Details

Format: Microsoft Excel spreadsheet

Size: 21 kb (Table 2) to 44 kb (Table 1)

Requirements: Microsoft Excel

------------

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


To Advertise     Find Products


Science Signaling. ISSN 1937-9145 (online), 1945-0877 (print). Pre-2008: Science's STKE. ISSN 1525-8882