Transmembrane domain prediction and consensus sequence identification of the oligopeptide transport family

Research in Microbiology

Volumn 157, Issue 4, 2006, Pages 395-406

  Wiles, Amy M ^a   Naider, Fred ^b   Becker, Jeffrey M ^a  

^a UNIVERSITY OF TENNESSEE   (United States)

^b CITY UNIVERSITY OF NEW YORK   (United States)

Author keywords

Amino acid; Integral membrane protein; Motifs; Sequence homology determination

Indexed keywords

AMINO ACID SEQUENCE; ARABIDOPSIS; ARTICLE; CANDIDA ALBICANS; CONTROLLED STUDY; ESCHERICHIA COLI; MEMBRANE POTENTIAL; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FAMILY; SACCHAROMYCES CEREVISIAE; SCHIZOPHYLLUM COMMUNE; SCHIZOSACCHAROMYCES POMBE; STREPTOMYCES LIVIDANS;

ALGORITHMS; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CONSENSUS SEQUENCE; MEMBRANE TRANSPORT PROTEINS; MOLECULAR SEQUENCE DATA; OLIGOPEPTIDES; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; PROTEIN TRANSPORT; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE;

ARABIDOPSIS; CANDIDA ALBICANS; ESCHERICHIA COLI; SACCHAROMYCES CEREVISIAE; SCHIZOPHYLLUM COMMUNE; SCHIZOSACCHAROMYCES POMBE; STREPTOMYCES LIVIDANS;

EID: 33646047127     PISSN: 09232508     EISSN: 17697123     Source Type: Journal    
DOI: 10.1016/j.resmic.2005.10.004     Document Type: Article

References (44)

1. Abramson J., Smirnova I., Kasho V., Verner G., Kaback H.R., and Iwata S. Structure and mechanism of the lactose permease of Escherichia coli. Science 301 (2003) 610-615
2. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
3. Arai M., Mitsuke H., Ikeda M., Xia J.X., Kikuchi T., Satake M., and Shimizu T. ConPred II: A consensus prediction method for obtaining transmembrane topology models with high reliability. Nucleic Acids Res. 32 (2004) W390-W393
4. Bendtsen J.D., Nielsen H., von Heijne G., and Brunak S. Improved prediction of signal peptides: SignalP 3.0. J. Mol. Biol. 340 (2004) 783-795
5. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., and Bourne P.E. The Protein Data Bank. Nucleic Acids Res. 28 (2000) 235-242
6. Bertaccini E., and Trudell J.R. Predicting the transmembrane secondary structure of ligand-gated ion channels. Protein Eng. 15 (2002) 443-454
7. Bill R.M. Yeast-a panacea for the structure-function analysis of membrane proteins?. Curr. Genet. 40 (2001) 157-171
8. Braun B.R., van Het Hoog M., d'Enfert C., Martchenko M., Dungan J., Kuo A., Inglis D.O., Uhl M.A., Hogues H., Berriman M., Lorenz M., Levitin A., Oberholzer U., Bachewich C., Harcus D., Marcil A., Dignard D., Iouk T., Zito R., Frangeul L., Tekaia F., Rutherford K., Wang E., Munro C.A., Bates S., Gow N.A., Hoyer L.L., Kohler G., Morschhauser J., Newport G., Znaidi S., Raymond M., Turcotte B., Sherlock G., Costanzo M., Ihmels J., Berman J., Sanglard D., Agabian N., Mitchell A.P., Johnson A.D., Whiteway M., and Nantel A. A human-curated annotation of the Candida albicans genome. PLoS Genet. 1 (2005) e1
9. Cartwright C.P., and Tipper D.J. In vivo topological analysis of Ste2, a yeast plasma membrane protein, by using β-lactamase gene fusions. Mol. Cell Biol. 11 (1991) 2620-2628
10. + conduction and selectivity. Science 280 (1998) 69-77
11. Felsenstein J. PHYLIP (Phylogeny Inference Package) version 3.6, distributed by the author (2004), Department of Genome Sciences, Univ. of Washington, Seattle
12. Garnier C., Blondel M.-O., and Haguenauer-Tsapis R. Membrane topology of the yeast uracil permease. Mol. Microbiol. 21 (1996) 1061-1073
13. Gilstring C.F., and Ljungdahl P.O. A method for determining the in vivo topology of yeast polytopic membrane proteins demonstrates that Gap1p fully integrates into the membrane independently of Shr3p. J. Biol. Chem. 275 (2000) 31488-31495
14. Green G.N., Hansen W., and Walter P. The use of gene-fusions to determine membrane protein topology in Saccharomyces cerevisiae. J. Cell Sci. Suppl. 11 (1989) 109-113
15. Hamm H.E. The many faces of G protein signaling. J. Biol. Chem. 273 (1998) 669-672
16. Hofmann K., and Stoffel W. TMbase-a database of membrane spanning proteins segments. Biol. Chem. 374 (1993) 166
17. Jayasinghe S., Hristova K., and White S.H. MPtopo: A database of membrane protein topology. Protein Sci. 10 (2001) 455-458
18. Koh S., Wiles A.M., Sharp J.S., Naider F.R., Becker J.M., and Stacey G. An oligopeptide transporter gene family in Arabidopsis. Plant Physiol. 128 (2002) 21-29
19. Kolbe M., Besir H., Essen L.-O., and Oesterhelt D. Structure of the light-driven chloride pump halorhodopsin at 1.8 Å resolution. Science 288 (2000) 1390-1396
20. Krogh A., Larsson B., von Heijne G., and Sonnhammer E.L. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol. 305 (2001) 567-580
21. Kyte J., and Doolittle R.F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157 (1982) 105-132
22. Lengeler K.B., and Kothe E. Mated: A putative peptide transporter of Schizophyllum commune expressed in dikaryons. Curr. Genet. 36 (1999) 159-164
23. Lorenz M.C., Bender J.A., and Fink G.R. Transcriptional response of Candida albicans upon internalization by macrophages. Eukaryot. Cell 3 (2004) 1076-1087
24. Lubkowitz M.A., Hauser L., Breslav M., Naider F., and Becker J.M. An oligopeptide transport gene from Candida albicans. Microbiology 143 Pt 2 (1997) 387-396
25. Luecke H., Schobert B., Richter H.-T., Cartailler J.-P., and Lanyi J.K. Structure of bacteriorhodopsin at 1.55 Å resolution. J. Mol. Biol. 291 (1999) 899-911
26. Mayer B.J. SH3 domains: Complexity in moderation. J. Cell Sci. 114 (2001) 1253-1263
27. Moller S., Croning M.D., and Apweiler R. Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics 17 (2001) 646-653
28. Nilsson J., Persson B., and Von Heijne G. Prediction of partial membrane protein topologies using a consensus approach. Protein Sci. 11 (2002) 2974-2980
29. Ott C.M., and Lingappa V.R. Integral membrane protein biosynthesis: Why topology is hard to predict. J. Cell Sci. 115 (2002) 2003-2009
30. Payne J.W., and Smith M.W. Peptide transport by micro-organisms. Adv. Microb. Physiol. 36 (1994) 1-80
31. Rost B., Fariselli P., and Casadio R. Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Sci. 5 (1996) 1704-1718
32. Rubin-Bejerano I., Fraser I., Grisafi P., and Fink G.R. Phagocytosis by neutrophils induces an amino acid deprivation response in Saccharomyces cerevisiae and Candida albicans. Proc. Natl. Acad. Sci. USA 100 (2003) 11007-11012
33. Sato S., Suzuki H., Widyastuti U., Hotta Y., and Tabata S. Identification and characterization of genes induced during sexual differentiation in Schizosaccharomyces pombe. Curr. Genet. 26 (1994) 31-37
34. Schaffer A.A., Aravind L., Madden T.L., Shavirin S., Spouge J.L., Wolf Y.I., Koonin E.V., and Altschul S.F. Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res. 29 (2001) 2994-3005
35. Sipos L., and von Heijne G. Predicting the topology of eukaryotic membrane proteins. Eur. J. Biochem. 213 (1993) 1333-1340
36. Soll D.R., Lockhart S.R., and Zhao R. Relationship between switching and mating in Candida albicans. Eukaryot. Cell 2 (2003) 390-397
37. Sonnhammer E.L., von Heijne G., and Krogh A. A hidden Markov model for predicting transmembrane helices in protein sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol. 6 (1998) 175-182
38. Tsong A.E., Miller M.G., Raisner R.M., and Johnson A.D. Evolution of a combinatorial transcriptional circuit: A case study in yeasts. Cell 115 (2003) 389-399
39. von Heijne G. A day in the life of Dr. K. or how I learned to stop worrying and love lysozyme: A tragedy in six acts. J. Mol. Biol. 293 (1999) 367-379
40. von Heijne G. The distribution of positively charged residues in bacterial inner membrane proteins correlates with the trans-membrane topology. Embo J. 5 (1986) 3021-3027
41. von Heijne G. Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J. Mol. Biol. 225 (1992) 487-494
42. Yen M.R., Tseng Y.H., and Saier Jr. M.H. Maize Yellow Stripe1, an iron-phytosiderophore uptake transporter, is a member of the oligopeptide transporter (OPT) family. Microbiology 147 (2001) 2881-2883
43. Yuan Z., Mattick J.S., and Teasdale R.D. SVMtm: Support vector machines to predict transmembrane segments. J. Comput. Chem. 25 (2004) 632-636
44. Zhang M.Y., Bourbouloux A., Cagnac O., Srikanth C.V., Rentsch D., Bachhawat A.K., and Delrot S. A novel family of transporters mediating the transport of glutathione derivatives in plants. Plant Physiol. 134 (2004) 482-491