Predicting N-terminal myristoylation sites in plant proteins

BMC Genomics

Volumn 5, Issue , 2004, Pages

  Podell, Sheila ^a,b   Gribskov, Michael ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

VEGETABLE PROTEIN; ACYLTRANSFERASE; ARABIDOPSIS PROTEIN; GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE; MYRISTIC ACID; PEPTIDE; PROTEIN N MYRISTOYLTRANSFERASE;

AMINO TERMINAL SEQUENCE; ARTICLE; CONTROLLED STUDY; METHODOLOGY; MYRISTYLATION; NONHUMAN; PREDICTION; PROBABILITY; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTEIN FUNCTION; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; SPECIES DIFFERENCE; STATISTICAL ANALYSIS; STATISTICAL MODEL; ALGORITHM; AMINO ACID SEQUENCE; ANIMAL; ARABIDOPSIS; BINDING SITE; BIOLOGICAL MODEL; CHEMISTRY; COMPARATIVE STUDY; ENZYME SPECIFICITY; ENZYMOLOGY; GENETICS; METABOLISM; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PREDICTIVE VALUE; PROTEIN PROCESSING; PROTEIN TERTIARY STRUCTURE; VALIDATION STUDY;

ANIMALIA;

ACYLTRANSFERASES; ALGORITHMS; AMINO ACID SEQUENCE; ANIMALS; ARABIDOPSIS; ARABIDOPSIS PROTEINS; BINDING SITES; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; MODELS, BIOLOGICAL; MYRISTIC ACID; PEPTIDES; PLANT PROTEINS; PREDICTIVE VALUE OF TESTS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEIN STRUCTURE, TERTIARY; SENSITIVITY AND SPECIFICITY; SUBSTRATE SPECIFICITY;

EID: 9144256852     PISSN: 14712164     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2164-5-37     Document Type: Article

References (51)

1. Zha J, Weiler S, Oh KJ, Wei MC, Korsmeyer SJ: Posttranslational N-myristoylation of BID as a molecular switch for targeting mitochondria and apoptosis. Science 2000, 290: 761-1765.
2. Zheng J, Knighton DR, Xuong NH, Taylor SS, Sowadski JM, Ten Eyck LF: Crystal structures of the myristoylated catalytic subunit of cAMP-dependent protein kinase reveal open and closed conformations. Protein Sci 1993, 2:1559-1573.
3. Resh MD: Fatty acylation of proteins: new insights into membrane targeting of myristoylated and palmitoylated proteins. Biochim Biophys Acta 1999, 1451:1-16.
4. Olsen HB, Kaarsholm NC: Structural effects of protein lipidation as revealed by LysB29-myristoyl, des(B30) insulin. Biochemistry 2000, 39:11893-11900.
5. Goldberg J: Structural basis for activation of ARF GTPase: mechanisms of guanine nucleotide exchange and GTP-myristoyl switching. Cell 1998, 95:237-248.
6. Hanakam F, Gerisch G, Lotz S, Alt T, Seelig A: Binding of hisactophilin I and II to lipid membranes is controlled by a pH-dependent myristoyl-histidine switch. Biochemistry 1996, 35: 1036-11044.
7. McLaughlin S, Aderem A: The myristoyl-electrostatic switch: a modulator of reversible protein-membrane interactions. Trends Biochem Sci 1995, 20:272-276.
8. Hermida-Matsumoto L, Resh MD: Human immunodeficiency virus type 1 protease triggers a myristoyl switch that modulates membrane binding of Pr55(gag) and p17MA. J Virol 1999, 73: 902-1908.
9. Grebe M, Xu J, Mobius W, Ueda T, Nakano A, Geuze HJ, Rook MB, Scheres B: Arabidopsis sterol endocytosis involves actin-mediated trafficking via ARA6-positive early endosomes. Curr Biol 2003, 13:1378-1387.
10. Ueda T, Yamaguchi M, Uchimiya H, Nakano A: Ara6, a plantunique novel type Rab GTPase, functions in the endocytic pathway of Arabidopsis thaliana. Embo J 2001, 20:4730-4741.
11. Ishitani M, Liu J, Halfter U, Kim CS, Shi W, Zhu JK: SOS3 function in plant salt tolerance requires N-myristoylation and calcium binding. Plant Cell 2000, 12:1667-1678.
12. Lu SX, Hrabak EM: An Arabidopsis calcium-dependent protein kinase is associated with the endoplasmic reticulum. Plant Physiol 2002, 128:1008-1021.
13. Martin ML, Busconi L: Membrane localization of a rice calcium-dependent protein kinase (CDPK) is mediated by myristoylation and palmitoylation. Plant J 2000, 24:429-435.
14. Rutschmann F, Stalder U, Piotrowski M, Oecking C, Schaller A: LeCPK1, a calcium-dependent protein kinase from tomato. Plasma membrane targeting and biochemical characterization. Plant Physiol 2002, 129:156-168.
15. Ellard-Ivey M, Hopkins RB, White TJ, Lomax TL: Cloning, expression and N-terminal myristoylation of CpCPK1, a calcium-dependent protein kinase from zucchini (Cucurbita pepo L.). Plant Mol Biol 1999, 39:199-208.
16. Raices M, Chico JM, Tellez-Inon MT, Ulloa RM: Molecular characterization of StCDPK1, a calcium-dependent protein kinase from Solanum tuberosum that is induced at the onset of tuber development. Plant Mol Biol 2001, 46:591-601.
17. Boisson B, Giglione C, Meinnel T: Unexpected protein families including cell defense components feature in the N-myristoylome of a higher eukaryote. J Biol Chem 2003, 278:43418-43429.
18. Qi Q, Rajala RV, Anderson W, Jiang C, Rozwadowski K, Selvaraj G, Sharma R, Datla R: Molecular cloning, genomic organization, and biochemical characterization of myristoyl-CoA:protein N-myristoyltransferase from Arabidopsis thaliana. J Biol Chem 2000, 275:9673-9683.
19. Falquet L, Pagni M, Bucher P, Hulo N, Sigrist CJ, Hofmann K, Bairoch A: The PROSITE database, its status in 2002. Nucleic Acids Res 2002, 30:235-238.
20. Maurer-Stroh S, Eisenhaber B, Eisenhaber F: N-terminal N-myristoylation of proteins: prediction of substrate proteins from amino acid sequence. J Mol Biol 2002, 317:541-557.
21. Maurer-Stroh S, Eisenhaber B, Eisenhaber F: N-terminal N-myristoylation of proteins: refinement of the sequence motif and its taxon-specific differences. J Mol Biol 2002, 317:523-540.
22. Eisenhaber F, Eisenhaber B, Kubina W, Maurer-Stroh S, Neuberger G, Schneider G, Wildpaner M: Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-Pi, NMT and PTS1. Nucleic Acids Res 2003, 31: 631-3634.
23. Maurer-Stroh S, Gouda M, Novatchkova M, Schleiffer A, Schneider G, Sirota FL, Wildpaner M, Hayashi N, Eisenhaber F: MYRbase: analysis of genome-wide glycine myristoylation enlarges the functional spectrum of eukaryotic myristoylated proteins. Genome Biol 2004, 5:R21.
24. Bologna G, Yvon C, Duvaud S, Veuthey AL: N-Terminal myristoylation predictions by ensembles of neural networks. Proteomics 2004, 4:1626-1632.
25. Expasy Myristoylator [http://www.expasy.org/tools/myristoylator/]
26. Holte R: Very simple classification rules perform well on most commonly used datasets. Machine Learning 1993, 11: 3-91.
27. Zweig MH, Campbell G: Receiver-operating characteristic (ROC) plots: a fundamental evaluation tool in clinical medicine. Clin Chem 1993, 39:561-577.
28. Gribskov M., Robinson NL: Use of Receiver Operating Characteristic (ROC) analysis to evaluate sequence matching. Computers Chem 1996, 20:25-33.
29. Li W, Jaroszewski L, Godzik A: Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics 2001, 17:282-283.
30. Pedley KF, Martin GB: Molecular basis of Pto-mediated resistance to bacterial speck disease in tomato. Annu Rev Phytopathol 2003, 41:215-243.
31. Gupta R, Ting JT, Sokolov LN, Johnson SA, Luan S: A tumor suppressor homolog, AtPTEN1, is essential for pollen development in Arabidopsis. Plant Cell 2002, 14:2495-2507.
32. Lakatos L, Klein M, Hofgen R, Banfalvi Z: Potato StubSNF1 interacts with StubGAL83: a plant protein kinase complex with yeast and mammalian counterparts. Plant J 1999, 17:569-574.
33. Lin SS, Manchester JK, Gordon JI: Sip2, an N-myristoylated beta subunit of Snf1 kinase, regulates aging in Saccharomyces cerevisiae by affecting cellular histone kinase activity, recombination at rDNA loci, and silencing. J Biol Chem 2003, 278:13390-13397.
34. Guyon VN, Astwood JD, Garner EC, Dunker AK, Taylor LP: Isolation and characterization of cDNAs expressed in the early stages of flavonol-induced pollen germination in petunia. Plant Physiol 2000, 123:699-710.
35. Jambunathan N, McNellis TW: Regulation of Arabidopsis COPINE 1 gene expression in response to pathogens and abiotic stimuli. Plant Physiol 2003, 132:1370-1381.
36. Bolwell GP, Blee KA, Butt VS, Davies DR, Gardner SL, Gerrish C, Minibayeva F, Rowntree EG, Wojtaszek P: Recent advances in understanding the origin of the apoplastic oxidative burst in plant cells. Free Radic Res 1999, 31 Suppl:S137-45.
37. Noordermeer MA, Veldink GA, Vliegenthart JF: Fatty acid hydroperoxide lyase: a plant cytochrome p450 enzyme involved in wound healing and pest resistance. Chembiochem 2001, 2:494-504.
38. Jakoby M, Weisshaar B, Droge-Laser W, Vicente-Carbajosa J, Tiedemann J, Kroj T, Parcy F: bZIP transcription factors in Arabidopsis. Trends Plant Sci 2002, 7:106-111.
39. Kimura Y, Saeki Y, Yokosawa H, Polevoda B, Sherman F, Hirano H: N-Terminal modifications of the 19S regulatory particle subunits of the yeast proteasome. Arch Biochem Biophys 2003, 409: 41-348.
40. The TIGR Arabidopsis thaliana Genome Annotation Database [http://www.tigr.org/tdb/e2k1/ath1/ath1.shtml]
41. Tomita A, Towatari M, Tsuzuki S, Hayakawa F, Kosugi H, Tamai K, Miyazaki T, Kinoshita T, Saito H: c-Myb acetylation at the carboxyl-terminal conserved domain by transcriptional co-activator p300. Oncogene 2000, 19:444-451.
42. CD-HI/CD-HIT. Cluster Database at High Identity / Cluster Database at High Identity with Tolerance [http://bioinformatics.ljcrf.edu/cd-hi/]
43. Eddy SR: Profile hidden Markov models. Bioinformatics 1998, 14:755-763.
44. HMMER. Sequence analysis using profile hidden Markov models [http://hmmer.wustl.edu/]
45. Gerstein M, Sonnhammer EL, Chothia C: Volume changes in protein evolution. J Mol Biol 1994, 236:1067-1078.
46. Henikoff S, Henikoff JG: Position-based sequence weights. J Mol Biol 1994, 243:574-578.
47. Sibbald PR, Argos P: Weighting aligned protein or nucleic acid sequences to correct for unequal representation. J Mol Biol 1990, 216:813-818.
48. Collins JF, Coulson AF, Lyall A: The significance of protein sequence similarities. Comput Appl Biosci 1988, 4: 7-71.
49. NMT - The MYR Predictor. MyristoylCoA:Protein N-Myristoyltransferase. [http://mendel.imp.univie.ac.at/myristate/SUPLpredictor.htm]
50. Witten IH, Eibe, F: Data Mining: Practical machine learning tools with Java implementations. San Francisco, Morgan Kaufmann; 2000.
51. Cover TM, Thomas JA: Elements of Information Theory. John Wiley & Sons Inc.; 1991.