Large-scale discovery and characterization of protein regulatory motifs in eukaryotes

PLoS ONE

Volumn 5, Issue 12, 2010, Pages

  Lieber, Daniel S ^a   Elemento, Olivier ^a,b   Tavazoie, Saeed ^a  

^a PRINCETON UNIVERSITY   (United States)

^b WEILL CORNELL MEDICAL COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CELLULAR DISTRIBUTION; EUKARYOTE; NONHUMAN; PREDICTION; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN MOTIF; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE; ALGORITHM; BIOLOGY; CHEMISTRY; GENETICS; HUMAN; METABOLISM; METHODOLOGY; MITOCHONDRION; PHOSPHORYLATION; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE; PROTEOMICS; SCHIZOSACCHAROMYCES;

EUKARYOTA;

ALGORITHMS; AMINO ACID MOTIFS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; EUKARYOTA; HUMANS; MITOCHONDRIA; PHOSPHORYLATION; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEIN STRUCTURE, TERTIARY; PROTEINS; PROTEOME; PROTEOMICS; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES;

EID: 78650821937     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0014444     Document Type: Article

References (50)

1. Diella F, Haslam N, Chica C, Budd A, Michael S, et al. (2008) Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Front Biosci 13: 6580-6603.
2. Blobel G, Walter P, Chang CN, Goldman BM, Erickson AH, et al. (1979) Translocation of proteins across membranes: the signal hypothesis and beyond. Symp Soc Exp Biol 33: 9-36.
3. Hall MN, Hereford L, Herskowitz I (1984) Targeting of E. coli betagalactosidase to the nucleus in yeast. Cell 36: 1057-1065.
4. Hurt EC, Allison DS, Muller U, Schatz G (1987) Amino-terminal deletions in the presequence of an imported mitochondrial protein block the targeting function and proteolytic cleavage of the presequence at the carboxy terminus. J Biol Chem 262: 1420-1424.
5. Semenza JC, Hardwick KG, Dean N, Pelham HR (1990) ERD2, a yeast gene required for the receptor-mediated retrieval of luminal ER proteins from the secretory pathway. Cell 61: 1349-1357.
6. Subramani S (1992) Targeting of proteins into the peroxisomal matrix. J Membr Biol 125: 99-106.
7. Benham AM, Cabibbo A, Fassio A, Bulleid N, Sitia R, et al. (2000) The CXXCXXC motif determines the folding, structure and stability of human Ero1-Lalpha. Embo J 19: 4493-4502.
8. Young P, Deveraux Q, Beal RE, Pickart CM, Rechsteiner M (1998) Characterization of two polyubiquitin binding sites in the 26 S protease subunit 5a. J Biol Chem 273: 5461-5467.
9. Neduva V, Russell RB (2006) Peptides mediating interaction networks: new leads at last. Curr Opin Biotechnol 17: 465-471.
10. Aitken A (1990) Identification of protein consensus sequences: active site motifs, phosphorylation, and other post-translational modifications. New York: Ellis Horwood.167 p.
11. Diella F, Chabanis S, Luck K, Chica C, Ramu C, et al. (2009) KEPE-a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors. Bioinformatics 25: 1-5.
12. Fuxreiter M, Tompa P, Simon I (2007) Local structural disorder imparts plasticity on linear motifs. Bioinformatics 23: 950-956.
13. Russell RB, Gibson TJ (2008) A careful disorderliness in the proteome: sites for interaction and targets for future therapies. FEBS Lett 582: 1271-1275.
14. Neduva V, Russell RB (2005) Linear motifs: evolutionary interaction switches. FEBS Lett 579: 3342-3345.
15. Davey NE, Shields DC, Edwards RJ (2006) SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent. Nucleic Acids Research 34: 3546-3554.
16. Lawrence CE, Reilly AA (1990) An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins 7: 41-51.
17. Jonassen I, Collins JF, Higgins DG (1995) Finding flexible patterns in unaligned protein sequences. Protein Sci 4: 1587-1595.
18. Bailey TL, Elkan C (1995) The value of prior knowledge in discovering motifs with MEME. Proc Int Conf Intell Syst Mol Biol 3: 21-29.
19. Rigoutsos I, Floratos A (1998) Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm. Bioinformatics 14: 55-67.
20. Neduva V, Russell RB (2006) DILIMOT: discovery of linear motifs in proteins. Nucleic Acids Res 34: W350-355.
21. Schwartz D, Gygi SP (2005) An iterative statistical approach to the identification of protein phosphorylation motifs from large-scale data sets. Nat Biotechnol 23: 1391-1398.
22. Edwards RJ, Davey NE, Shields DC (2007) SLiMFinder: a probabilistic method for identifying over-represented, convergently evolved, short linear motifs in proteins. PLoS One 2: e967.
23. Balla S, Thapar V, Verma S, Luong T, Faghri T, et al. (2006) Minimotif Miner: a tool for investigating protein function. Nat Methods 3: 175-177.
24. Dinkel H, Sticht H (2007) A computational strategy for the prediction of functional linear peptide motifs in proteins. Bioinformatics 23: 3297-3303.
25. Neduva V, Linding R, Su-Angrand I, Stark A, de Masi F, et al. (2005) Systematic discovery of new recognition peptides mediating protein interaction networks. PLoS Biol 3: e405.
26. Gstaiger M, Aebersold R (2009) Applying mass spectrometry-based proteomics to genetics, genomics and network biology. Nat Rev Genet 10: 617-627.
27. Yu H, Braun P, Yildirim MA, Lemmens I, Venkatesan K, et al. (2008) Highquality binary protein interaction map of the yeast interactome network. Science 322: 104-110.
28. Cover TM, Thomas JA (2006) Elements of information theory. HobokenN.J.: Wiley-Interscience. xxiii, 748 p.
29. Elemento O, Slonim N, Tavazoie S (2007) A universal framework for regulatory element discovery across all genomes and data types. Mol Cell 28: 337-350.
30. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, et al. (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
31. Xie X, Lu J, Kulbokas EJ, Golub TR, Mootha V, et al. (2005) Systematic discovery of regulatory motifs in human promoters and 39 UTRs by comparison of several mammals. Nature 434: 338-345.
32. Goodarzi H, Elemento O, Tavazoie S (2009) Revealing global regulatory perturbations across human cancers. Mol Cell 36: 900-911.
33. Rush J, Moritz A, Lee KA, Guo A, Goss VL, et al. (2005) Immunoaffinity profiling of tyrosine phosphorylation in cancer cells. Nat Biotechnol 23: 94-101.
34. Ficarro SB, McCleland ML, Stukenberg PT, Burke DJ, Ross MM, et al. (2002) Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat Biotechnol 20: 301-305.
35. Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, et al. (2006) BioGRID: a general repository for interaction datasets. Nucleic Acids Res 34: D535-539.
36. Puntervoll P, Linding R, Gemund C, Chabanis-Davidson S, Mattingsdal M, et al. (2003) ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Research 31: 3625-3630.
37. Remenyi A, Good MC, Lim WA (2006) Docking interactions in protein kinase and phosphatase networks. Curr Opin Struct Biol 16: 676-685.
38. Denis CL, Kemp BE, Zoller MJ (1991) Substrate specificities for yeast and mammalian cAMP-dependent protein kinases are similar but not identical. J Biol Chem 266: 17932-17935.
39. Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, et al. (2005) Global analysis of protein phosphorylation in yeast. Nature 438: 679-684.
40. Edwards RJ, Davey NE, Shields DC (2008) CompariMotif: quick and easy comparisons of sequence motifs. Bioinformatics 24: 1307-1309.
41. Rao VD, Misra S, Boronenkov IV, Anderson RA, Hurley JH (1998) Structure of type IIbeta phosphatidylinositol phosphate kinase: a protein kinase fold flattened for interfacial phosphorylation. Cell 94: 829-839.
42. Martoglio B, Dobberstein B (1998) Signal sequences: more than just greasy peptides. Trends Cell Biol 8: 410-415.
43. Beer MA, Tavazoie S (2004) Predicting gene expression from sequence. Cell 117: 185-198.
44. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, et al. (2003) Global analysis of protein localization in budding yeast. Nature 425: 686-691.
45. Kalderon D, Richardson WD, Markham AF, Smith AE (1984) Sequence requirements for nuclear location of simian virus 40 large-T antigen. Nature 311: 33-38.
46. Chelsky D, Ralph R, Jonak G (1989) Sequence requirements for synthetic peptide-mediated translocation to the nucleus. Mol Cell Biol 9: 2487-2492.
47. Gavel Y, von Heijne G (1990) Cleavage-site motifs in mitochondrial targeting peptides. Protein Eng 4: 33-37.
48. Vogtle FN, Wortelkamp S, Zahedi RP, Becker D, Leidhold C, et al. (2009) Global analysis of the mitochondrial N-proteome identifies a processing peptidase critical for protein stability. Cell 139: 428-439.
49. Slonim N, Atwal GS, Tkacik G, Bialek W (2005) Information-based clustering. Proc Natl Acad Sci U S A 102: 18297-18302.
50. Belle A, Tanay A, Bitincka L, Shamir R, O'Shea EK (2006) Quantification of protein half-lives in the budding yeast proteome. Proc Natl Acad Sci U S A 103: 13004-13009.