Phylogenetic classification of transporters and other membrane proteins from Saccharomyces cerevisiae

Functional and Integrative Genomics

Volumn 2, Issue 4-5, 2002, Pages 154-170

  De Hertogh, Benoît ^a   Carvajal, Elvira ^b   Talla, Emmanuel ^c   Dujon, Bernard ^c   Baret, Philippe ^a   Goffeau, André ^d  

^a UNIVERSITÉ CATHOLIQUE DE LOUVAIN   (Belgium)

^b STATE UNIVERSITY OF RIO DE JANEIRO   (Brazil)

^c INSTITUT PASTEUR   (France)

^d ECOLE NORMALE SUPÉRIEURE   (France)

Author keywords

Membrane proteins; Phylogenetic classification; Transporters; Yeast

Indexed keywords

MEMBRANE PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN;

AMINO ACID SEQUENCE; GENOME; NONHUMAN; OPEN READING FRAME; PHYLOGENY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN TRANSPORT; REVIEW; SACCHAROMYCES CEREVISIAE; YEAST; CLASSIFICATION; METABOLISM;

SACCHAROMYCES CEREVISIAE;

MEMBRANE PROTEINS; PHYLOGENY; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 0036727680     PISSN: 1438793X     EISSN: 14387948     Source Type: Journal    
DOI: 10.1007/s10142-002-0060-8     Document Type: Review

References (35)

1. André B (1995) An overview of membrane transport proteins in Saccharomyces cerevisiae. Yeast 11:1575-1611
2. Belenkiy R, Haefele A, Eisen MB, Wohlrab H (2000) The yeast mitochondrial transport proteins: new sequences and consensus residues, lack of direct relation between consensus residues and transmembrane helices, expression patterns of the transport protein genes, and protein-protein interactions with other proteins. Biochim Biophys Acta 1467:207-218
3. Blandin G, Durrens P, Tekaia F, Aigle M, Bolotin-Fukuhara M, Bon E, Casaregola S, Montigny J de, Gaillardin C, Lepingle A, Llorente A, Malpertuy A, Neuveglise C, Ozier-Kalogeropoulos O, Perrin A, Potier S, Souciet J, Talla E, Toffano-Nioche C, Wesolowski-Louvel M, Marck C, Dujon B (2000) Genomic exploration of the hemiascomycetous yeasts: 4. The genome Saccharomyces cerevisiae revisited. FEBS Lett 487:31-36
4. Catty P, Exaerde AD d', Goffeau A (1997) The complete inventory of the yeast Saccharomyces cerevisiae P-type Transport ATPases. FEBS Lett 409:325-332
5. Decottignies A, Goffeau A (1997) Complete inventory of the yeast ABC proteins. Nat Genet 15:137-145
6. Gaillardin C, Duchateau-Nguyen G, Tekaia F, Llorente B, Casaregola S, Toffano-Nioche C, Aigle M, Artiguenave F, Blandin G, Bolotin-Fukuhara M, Bon E, Brottier P, Montigny J de, Dujon B, Durrens P, Lepingle A, Malpertuy A, Neuveglise C, Ozier-Kalogeropoulos O, Potier S, Saurin W, Termier M, Wesolowski-Louvel M, Wincker P, Souciet JL, Weissenbach J (2000) Comparative functional classification of genes. FEBS Lett 487:134-149
7. Goffeau A, Slonimski P, Nakai K, Risler JL (1993a) How many yeast genes code for membrane spanning proteins? Yeast 9:691-702
8. Goffeau A, Nakai K, Slonimski P, Risler JL (1993b) The membrane proteins encoded by chromosome III genes. FEBS Lett 325:112-117
9. Gofffeau A, Barrell BG, Bussey RW, Davis RW, Dujon B, Feldmann H, Galibert F, Hoheisel JD, Jacq C, Johnston M, Louis EJ, Mewes HW, Murakami Y, Philippsen P, Tettelin H, Oliver SG (1996) Life with 6000 genes. Science 274:546-567
10. Goffeau A, Park J, Paulsen IT, Jonniaux JL, Dinh T, Mordant P, Saier MH (1997) Multidrug-resistant transport proteins in yeast: complete inventory and phylogenetic characterization of yeast open reading frames within the major facilitator superfamily. Yeast 13:43-54
11. Jack DL, Paulsen IT, Saier MH (2000) The amino acid/polyamine/ organocation (APC) superfamily of transporters specific for amino acids, polyamines and organocations. Microbiology 146:1797-1814
12. Jack DL, Yang NM, Saier MH (2001) The drug/metabolite transporter superfamily. Eur J Biochem 268:3620-3639
13. Kruckeberg AL (1996) The hexose transporter family of Saccharomyces cerevisiae. Arch Microbiol 166:283-292
14. Lesuisse E, Simon-Casteras M, Labbe P (1998) Siderophore-mediated iron uptake in Saccharomyces cerevisiae: the SIT1 gene encodes a ferrioxamine B permease that belongs to the major facilitator superfamily. Microbiology 144:3455-3462
15. Llorente B, Dujon B (2000) Transcriptional regulation of the Saccharomyces cerevisiae DAL5 gene family and identification of the high affinity nicotinic acid permease TNA1 (YGR260w). FEBS Lett 475:237-241
16. Marger MD, Saier MH (1993) A major superfamily of transmembrane facilitators that catalyze uniport, symport and antiport. Trends Biochem Sci 18:13-20
17. Marini AM, Soussi Boudekou S, Vissers S, André B (1997) A family of ammonium transporters in Saccharomyces cerevisiae. Mol Cell Biol 17:4282-4293
18. Möller S, Croning MDR, Apweiler R (2001) Evaluation of methods for the prediction of membrane spanning region. Bioinformatics 17:646-653
19. Moualij B el, Duyckaerts C, Lamotte Brasseur J, Sluse FE (1997) Phylogenetic classification of the mitochondrial carrier family of Saccharomyces cerevisiae. Yeast 13:573-581
20. Nelissen B, Mordant P, Jonniaux JL, De Wachter R, Goffeau A (1995) Phylogenetic classification of the major superfamily of membrane transport facilitators, as deduced from yeast genome sequencing. FEBS Lett 377:232-236
21. Nelissen B, De Wachter R, Goffeau A (1997) Classification of all putative permeases and other membrane plurispanners of the major facilitator superfamily encoded by the complete genome of Saccharomyces cerevisiae. FEMS Microbiol Rev 21:113-134
22. Nelson DR, Felix CM, Swanson JM (1998) Highly conserved charge-pair networks in the mitochondrial carrier family. J Mol Biol 277:285-308
23. Ozcan S, Johnston M (1999) Function and regulation of yeast hexose transporters. Microbiol Mol Biol Rev 63:554-569
24. Pao SS, Paulsen IT, Saier Jr MH (1998) The major facilitator superfamily. Microbiol Mol Biol Rev 62:1-32
25. Paulsen IT, Sliwinski MK, Nelissen B, Goffeau A, Saier MH (1998a) Unified inventory of established and putative transporters encoded within the complete genome of Saccharomyces cerevisiae. FEBS Lett 430:116-125
26. Paulsen IT, Sliwinski MK, Saier MH (1998b) Microbial genome analyses: global comparisons of transport capabilities based on phylogenies, bioenergetics and substrate specificities. J Mol Biol 277:573-592
27. Regenberg B, During-Olsen L, Kielland-Brandt MC, Holmberg S (1999) Substrate specificity and gene expression of the amino-acid permeases in Saccharomyces cerevisiae. Curr Genet 36: 317-328
28. Sa Correa I, Tenreiro S (2002) The multidrug-resistance transporters of the major facilitator superfamily, five years after disclosure of Saccharomyces cerevisiae genome sequence. J Biotech (in press)
29. Saier MH (1999) Genome archeology leading to the characterization and classification of transport proteins. Curr Opin Microbiol 2:555-561
30. Saier MH (2000) A functional-phylogenetic classification system for transmembrane solute transporters. Microbiol Mol Biol Rev 64:354-411
31. Souciet JL, Aigle M, Artiguenave F, Blandin G, Bolotin-Fukuhara M, Bon E, Brottier P, Casagerola S, Montigny J de, Dujon B, Durrens P, Gaillardin C, Lepingle A, Llorente B, Malpertuy A, Neuveglise C, Ozier-Kalogeropoulos O, Potier S, Saurin W, Tekaia F, Toffano-Nioche C, Wesolowski-Louvel M, Wincker P, Weissenbach J (2000) Genomic exploration of the hemiascomycetous, yeasts. 1. A set of yeast species for molecular evolution studies. FEBS Lett 487:3-12
32. Tekaia F, Blandin G, Malpertuy A, Llorente B, Durrens P, Toffano-Nioche C, Ozier-Kalogeropoulos O, Bon E, Gaillardin C, Aigle M, Bolotin-Fukuhara M, Casagerola S, de Montigny J, Lepingle A, Neuveglise C, Potier S, Souciet JL, Wesolowski-Louvel M, Dujon B (2000) Genomic exploration of the hemiascomycetous yeasts. 3. Methods and strategies used for sequence analysis and annotation. FEBS Lett 487:17-30
33. Van Belle D, André B (2001) A genomic view of yeast membrane transporters. Curr Opin Cell Biol 13:389-398
34. Wood V, Gwilliam R, Rajandream M-A, Lyne M, Lyne R, Stewart A, Sgouros J, Peat N, Hayles J, Baker S, Basham D, Bowman S, Brooks K, Brown D, Brown S, Chillingworth T, Churcher C, Collins M, Connor R, Cronin A, Davis P, Feltwell T, Fraser A, Gentles S, Goble A, Hamlin N, Harris D, Hidalgo J, Hodgson G, Holroyd S, Hornsby T, Howarth S, Huckle EJ, Hunt S, Jagels K, James K, Jones L, Jones M, Leather S, McDonald S, McLean J, Mooney P, Moule S, Mungall K, Murphy L, Niblett D, Odell C, Oliver K, O'Neil S, Pearson D, Quail MA, Rabbinowitsch E, Rutherford K, Rutter S, Saunders D, Seeger K, Sharp S, Skelton J, Simmonds M, Squares R, Squares S, Stevens K, Taylor K, Taylor RG, Tivey A, Walsh S, Warren T, Whitehead S, Woodward J, Volckaert G, Aert R, Robben J, Grymonprez B, Weltjens I, Vanstreels E, Rieger M, Schäfer M, Müller-Auer S, Gabel C, Fuchs M, Fritzc C, Holzer E, Moestl D, Hubert H, Borzym K, Langer I, Beck A, Lehrach H, Reinhardt R, Pohl TM, Eger P, Zimmermann W, Wedler H, Wambutt R, Purnelle B, Goffeau A, Cadieu E, Dréano S, Gloux S, Lelaure V, Mottier S, Galibert F, Aves SJ, Xiang Z, Hunt C, Moore K, Hurst SM, Lucas M, Rochet M, Gaillardin C, Tallada VA, Garzon A, Thode G, Daga RR, Cruzado L, Jimenez J, Sánchez M, Rey F del, Benito J, Domínguez A, Revuelta JL, Moreno S, Armstrong J, Forsburg SL, Cerrutti L, Lowe T, McCombie WR, Paulsen I, Potashkin J, Shpakovski GV, Ussery D, Barrell BG, Nurse P (2002) The genome sequence of Schizosaccharomyces pombe. Nature 415:871-880
35. Young GB, Jack DL, Smith DW, Saier MH (1999) The amino acid/auxin: proton symport permease family. Biochim Biophys Acta Biomembr 1415:306-322