Functional insights from the distribution and role of homopeptide repeat-containing proteins

Genome Research

Volumn 15, Issue 4, 2005, Pages 537-551

  Faux, Noel G ^a,b   Bottomley, Stephen P ^a,b   Lesk, Arthur M ^a,b,c   Irving, James A ^a,b   Morrison, John R ^b   De La Banda, Maria Garcia ^b   Whisstock, James C ^a,b  

^a MONASH UNIVERSITY   (Australia)

^b MONASH UNIVERSITY   (Australia)

^c PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; AMINO ACID; ASPARAGINE DERIVATIVE; GLUTAMINE; PROTEIN; PEPTIDE;

AMINO ACID SEQUENCE; ANALYTIC METHOD; ANOPHELES GAMBIAE; ARABIDOPSIS; ARTICLE; CAENORHABDITIS ELEGANS; CHICKEN; DATA BASE; DROSOPHILA; EUKARYOTE; FISH; FROG; GENETICS; HOUSEKEEPING GENE; HUMAN; INSECT; INTERNET; MOUSE; NEMATODE; NONHUMAN; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; ONLINE SYSTEM; PLASMODIUM FALCIPARUM; PRIORITY JOURNAL; PROKARYOTE; PROTEIN ANALYSIS; PROTEIN ASSEMBLY; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN LOCALIZATION; RAT; RICE; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION; TRANSCRIPTION INITIATION; UNINDEXED SEQUENCE; VERTEBRATE; ANIMAL; CHEMISTRY; COMPARATIVE STUDY; EUKARYOTIC CELL; FACTUAL DATABASE; METABOLISM; MOLECULAR EVOLUTION; PROKARYOTIC CELL;

CELLULAR ORGANISMS; EUKARYOTA; HEXAPODA; NEMATODA; PROKARYOTA; VERTEBRATA;

AMINO ACID SEQUENCE; ANIMALS; DATABASES, FACTUAL; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; HUMANS; INTERNET; PEPTIDES; PROKARYOTIC CELLS; REPETITIVE SEQUENCES, AMINO ACID; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 17844383699     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.3096505     Document Type: Article

References (64)

1. Akey, C.W. and Luger, K. 2003. Histone chaperones and nucleosome assembly. Curr. Opin. Struct. Biol. 13: 6-14.
2. Alba, M.M. and Guigo, R. 2004. Comparative analysis of amino acid repeats in rodents and humans. Genome Res. 14: 549-554.
3. Alba, M.M., Laskowski, R.A., and Hancock, J.M. 2002. Detecting cryptically simple protein sequences using the SIMPLE algorithm. Bioinformatics 18: 672-678.
4. Barton, G.J. 1993. ALSCRIPT: A tool to format multiple sequence alignments. Protein Eng. 6: 37-40.
5. Bateman, A., Coin, L., Durbin, R., Finn, R.D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E.L., et al. 2004. The Pfam protein families database. Nucleic Acids Res. 32: D138-D141.
6. Becher, M.W., Kotzuk, J.A., Sharp, A.H., Davies, S.W., Bates, G.P., Price, D.L., and Ross, C.A. 1998. Intranuclear neuronal inclusions in Huntington's disease and dentatorubral and pallidoluysian atrophy: Correlation between the density of inclusions and IT15 CAG triplet repeat length. Neurobiol. Dis. 4: 387-397.
7. Brown, L.Y. and Brown, S.A. 2004. Alanine tracts: The expanding story of human illness and trinucleotide repeats. Trends Genet. 20: 51-58.
8. Burack, W.R. and Shaw, A.S. 2000. Signal transduction: Hanging on a scaffold. Curr. Opin. Cell. Biol. 12: 211-216.
9. Calnan, B.J., Tidor, B., Biancalana, S., Hudson, D., and Frankel, A.D. 1991. Arginine-mediated RNA recognition: The arginine fork. Science 252: 1167-1171.
10. Chow, M.K., Ellisdon, A.M., Cabrita, L.D., and Bottomley, S.P. 2004a. Polyglutamine expansion in Ataxin-3 does not affect protein stability: Implications for misfolding and disease. J. Biol. Chem. 279: 47643-47651.
11. Chow, M.K., Lomas, D.A., and Bottomley, S.P. 2004b. Promiscuous β-strand interactions and the conformational diseases. Curr. Med. Chem. 11: 491-499.
12. Chow, M.K., Paulson, H.L., and Bottomley, S.P. 2004c. Destabilization of a non-pathological variant of ataxin-3 results in fibrillogenesis via a partially folded intermediate: A model for misfolding in polyglutamine disease. J. Mol. Biol. 335: 333-341.
13. Craig, E.A., Weissman, J.S., and Horwich, A.L. 1994. Heat shock proteins and molecular chaperones: Mediators of protein conformation and turnover in the cell. Cell 78: 365-372.
14. Cummings, C.J. and Zoghbi, H.Y. 2000. Fourteen and counting: Unraveling trinucleotide repeat diseases. Hum. Mol. Genet. 9: 909-916.
15. Dorsman, J.C., Pepers, B., Langenberg, D., Kerkdijk, H., Ijszenga, M., den Dunnen, J.T., Roos, R.A., and van Ommen, G.J. 2002. Strong aggregation and increased toxicity of polyleucine over polyglutamine stretches in mammalian cells. Hum. Mol. Genet. 11: 1487-1496.
16. Enright, A.J. and Ouzounis, C.A. 2000. GeneRAGE: A robust algorithm for sequence clustering and domain detection. Bioinformatics 16: 451-457.
17. Fan, X., Dion, P., Laganiere, J., Brais, B., and Rouleau, G.A. 2001. Oligomerization of polyalanine expanded PABPN1 facilitates nuclear protein aggregation that is associated with cell death. Hum. Mol. Genet. 10: 2341-2351.
18. Fandrich, M. and Dobson, C.M. 2002. The behaviour of polyamino acids reveals an inverse side chain effect in amyloid structure formation. EMBO J. 21: 5682-5690.
19. FlyBase Consortium. 2003. The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res. 31: 172-175.
20. Friedl, J.E.F. 2002. Mastering regular expressions. O'Reilly, Sebastopol, CA.
21. Gerber, H.P., Seipel, K., Georgiev, O., Hofferer, M., Hug, M., Rusconi, S., and Schaffner, W. 1994. Transcriptional activation modulated by homopolymeric glutamine and proline stretches. Science 263: 808-811.
22. Giri, K., Ghosh, U., Bhattacharyya, N.P., and Basak, S. 2003. Caspase 8 mediated apoptotic cell death induced by β-sheet forming polyalanine peptides. FEBS Lett. 555: 380-384.
23. Gonzalo, P. and Reboud, J.P. 2003. The puzzling lateral flexible stalk of the ribosome. Biol. Cell 95: 179-193.
24. Gotoh, T., Terada, K., Oyadomari, S., and Mori, M. 2004. hsp70-DnaJ chaperone pair prevents nitric oxide- and CHOP-induced apoptosis by inhibiting translocation of Bax to mitochondria. Cell Death Differ. 11: 390-402.
25. Gragerov, A., Nudler, E., Komissarova, N., Gaitanaris, G.A., Gottesman, M.E., and Nikiforov, V. 1992. Cooperation of GroEL/GroES and DnaK/DnaJ heat shock proteins in preventing protein misfolding in Escherichia coli. Proc. Natl. Acad. Sci. 89: 10341-10344.
26. Grigoryev, S.A. 2004. Keeping fingers crossed: Heterochromatin spreading through interdigitation of nucleosome arrays. FEBS Lett. 564: 4-8.
27. Hendrick, J.P., Langer, T., Davis, T.A., Hartl, F.U., and Wiedmann, M. 1993. Control of folding and membrane translocation by binding of the chaperone DnaJ to nascent polypeptides. Proc. Natl. Acad. Sci. 90: 10216-10220.
28. Holm, L. and Sander, C. 1998. Removing near-neighbour redundancy from large protein sequence collections. Bioinformatics 14: 423-429.
29. Holmberg, M., Duyckaerts, C., Durr, A., Cancel, G., Gourfinkel-An, I., Damier, P., Faucheux, B., Trottier, Y., Hirsch, E.C., Agid, Y., et al. 1998. Spinocerebellar ataxia type 7 (SCA7): A neurodegenerative disorder with neuronal intranuclear inclusions. Hum. Mol. Genet. 7: 913-918.
30. Huntley, M. and Golding, G.B. 2000. Evolution of simple sequence in proteins. J. Mol. Evol. 51: 131-140.
31. _. 2002. Simple sequences are rare in the Protein Data Bank. Proteins 48: 134-140.
32. Inoue, K. and Keegstra, K. 2003. A polyglycine stretch is necessary for proper targeting of the protein translocation channel precursor to the outer envelope membrane of chloroplasts. Plant J. 34: 661-669.
33. Karlin, S. and Burge, C. 1996. Trinucleotide repeats and long homopeptides in genes and proteins associated with nervous system disease and development. Proc. Natl. Acad. Sci. 93: 1560-1565.
34. Korschen, H.G., Beyermann, M., Muller, F., Heck, M., Vantler, M., Koch, K.W., Kellner, R., Wolfrum, U., Bode, C., Hofmann, K.P., et al. 1999. Interaction of glutamic-acid-rich proteins with the cGMP signalling pathway in rod photoreceptors. Nature 400: 761-766.
35. Kreil, D.P. and Kreil, G. 2000. Asparagine repeats are rare in mammalian proteins. Trends Biochem. Sci. 25: 270-271.
36. Letunic, I., Copley, R.R., Schmidt, S., Ciccarelli, F.D., Doerks, T., Schultz, J., Ponting, C.P., and Bork, P. 2004. SMART 4.0: Towards genomic data integration. Nucleic Acids Res. 32: D142-D144.
37. Li, M., Miwa, S., Kobayashi, Y., Merry, D.E., Yamamoto, M., Tanaka, F., Doyu, M., Hashizume, Y., Fischbeck, K.H., and Sobue, G. 1998. Nuclear inclusions of the androgen receptor protein in spinal and bulbar muscular atrophy. Ann. Neurol. 44: 249-254.
38. Mar Alba, M., Santibanez-Koref, M.F., and Hancock, J.M. 1999. Amino acid reiterations in yeast are overrepresented in particular classes of proteins and show evidence of a slippage-like mutational process. J. Mol. Evol. 49: 789-797.
39. Marcotte, E.M., Pellegrini, M., Yeates, T.O., and Eisenberg, D. 1999. A census of protein repeats. J. Mol. Biol. 293: 151-160.
40. Nam, Y.S., Petrovic, A., Jeong, K.S., and Venkatesan, S. 2001. Exchange of the basic domain of human immunodeficiency virus type 1 Rev for a polyarginine stretch expands the RNA binding specificity, and a minimal arginine cluster is required for optimal RRE RNA binding affinity, nuclear accumulation, and trans-activation. J. Virol. 75: 2957-2971.
41. Notredame, C., Higgins, D.G., and Heringa, J. 2000. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302: 205-217.
42. Oma, Y., Kino, Y., Sasagawa, N., and Ishiura, S. 2004. Intracellular localization of homopolymeric amino acid-containing proteins expressed in mammalian cells. J. Biol. Chem. 279: 21217-21222.
43. Park, J., Karplus, K., Barrett, C., Hughey, R., Haussler, D., Hubbard, T., and Chothia, C. 1998. Sequence comparisons using multiple sequences detect three times as many remote homologues as pairwise methods. J. Mol. Biol. 284: 1201-1210.
44. Poetsch, A., Molday, L.L., and Molday, R.S. 2001. The cGMP-gated channel and related glutamic acid-rich proteins interact with peripherin-2 at the rim region of rod photoreceptor disc membranes. J. Biol. Chem. 276: 48009-48016.
45. Pollard, T.D. 2000. Reflections on a quarter century of research on contractile systems. Trends Biochem. Sci. 25: 607-611.
46. Ramirez, C., Shimmin, L.C., Newton, C.H., Matheson, A.T., and Dennis, P.P. 1989. Structure and evolution of the L11, L1, L10, and L12 equivalent ribosomal proteins in eubacteria, archaebacteria, and eucaryotes. Can. J. Microbiol. 35: 234-244.
47. Remacha, M., Jimenez-Diaz, A., Bermejo, B., Rodriguez-Gabriel, M.A., Guarinos, E., and Ballesta, J.P. 1995. Ribosomal acidic phosphoproteins P1 and P2 are not required for cell viability but regulate the pattern of protein expression in Saccharomyces cerevisiae. Mol. Cell. Biol. 15: 4754-4762.
48. Scherzinger, E., Lurz, R., Turmaine, M., Mangiarini, L., Hollenbach, B., Hasenbank, R., Bates, G.P., Davies, S.W., Lehrach, H., and Wanker, E.E. 1997. Huntingtin-encoded polyglutamine expansions form amyloid-like protein aggregates in vitro and in vivo. Cell 90: 549-558.
49. Skinner, P.J., Koshy, B.T., Cummings, C.J., Klement, I.A., Helin, K., Servadio, A., Zoghbi, H.Y., and Orr, H.T. 1997. Ataxin-1 with an expanded glutamine tract alters nuclear matrix-associated structures. Nature 389: 971-974.
50. Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
51. Tolhuis, B., Palstra, R.J., Splinter, E., Grosveld, F., and de Laat, W. 2002. Looping and interaction between hypersensitive sites in the active β-globin locus. Mol. Cell 10: 1453-1465.
52. Uchiumi, T., Honma, S., Endo, Y., and Hachimori, A. 2002a. Ribosomal proteins at the stalk region modulate functional rRNA structures in the GTPase center. J. Biol. Chem. 277: 41401-41409.
53. Uchiumi, T., Honma, S., Nomura, T., Dabbs, E.R., and Hachimori, A. 2002b. Translation elongation by a hybrid ribosome in which proteins at the GTPase center of the Escherichia coli ribosome are replaced with rat counterparts. J. Biol. Chem. 277: 3857-3862.
54. Venter, J.C., Remington, K., Heidelberg, J.F., Halpern, A.L., Rusch, D., Eisen, J.A., Wu, D., Paulsen, I., Nelson, K.E., Nelson, W., et al. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
55. Wall, D., Zylicz, M., and Georgopoulos, C. 1995. The conserved G/F motif of the DnaJ chaperone is necessary for the activation of the substrate binding properties of the DnaK chaperone. J. Biol. Chem. 270: 2139-2144.
56. Warrick, J.M., Paulson, H.L., Gray-Board, G.L., Bui, Q.T., Fischbeck, K.H., Pittman, R.N., and Bonini, N.M. 1998. Expanded polyglutamine protein forms nuclear inclusions and causes neural degeneration in Drosophila. Cell 93: 939-949.
57. Wetzel, R. 2002. Ideas of order for amyloid fibril structure. Structure 10: 1031-1036.
58. Whisstock, J.C. and Lesk, A.M. 2003. Prediction of protein function from protein sequence and structure. Q Rev. Biophys. 36: 307-340.
59. Whisstock, J., Skinner, R., and Lesk, A.M. 1998. An atlas of serpin conformations. Trends Biochem. Sci. 23: 63-67.
60. Web site references http://repeats.med.monash.edu.au; A database of homopeptide repeats.
61. http://www.hprd.org/; Human Protein Reference Database.
62. ftp://ftp.ncbi.nih.gov/blast/db/; NCBI ftp site of available databases.
63. http://www.ncbi.nlm.nih.gov/omim/; Online Mendelian Inheritance in Man, OMIM. McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, MD), 2000.
64. http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE/current/ wormpep.shtml; Wormpep.