Evolution of the oligopeptide transporter family

Journal of Membrane Biology

Volumn 240, Issue 2, 2011, Pages 89-110

  Gomolplitinant, Kenny M ^a   Saier Jr , Milton H ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

Evolution; Iron siderophore; Origin; Peptide; Topology; Transport

Indexed keywords

OLIGOPEPTIDE TRANSPORTER; PEPTIDES AND PROTEINS; SIDEROPHORE; TRANSMEMBRANE SPANNING ALPHA HELICAL SEGMENT; UNCLASSIFIED DRUG;

ACTINOBACTERIA; ALPHA HELIX; AMOEBA (GENUS); ARTICLE; ASPERGILLUS; ASPERGILLUS FUMIGATUS; ASPERGILLUS NIDULANS; ASPERGILLUS NIGER; ASPERGILLUS ORYZAE; ASPERGILLUS TERREUS; BACTEROIDES FRAGILIS; BACTEROIDES UNIFORMIS; BACTEROIDES VULGATUS; CANDIDA ALBICANS; COCCIDIOIDES IMMITIS; CRYPTOCOCCUS NEOFORMANS; DEBARYOMYCES HANSENII; EPSILONPROTEOBACTERIA; EUKARYOTE; EVOLUTION; FUNGUS; GENE FUSION; GIBBERELLA; KLUYVEROMYCES LACTIS; MAGNAPORTHE GRISEA; NEOSARTORYA; NEUROSPORA CRASSA; NUCLEOTIDE SEQUENCE; PHYLOGENY; PICHIA GUILLIERMONDII; PICHIA STIPITIS; PROKARYOTE; PROTEIN ANALYSIS; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; RICE; SACCHAROMYCES CEREVISIAE; SCHIZOSACCHAROMYCES POMBE; SCLEROTINIA SCLEROTIORUM; USTILAGO MAYDIS; VIRIDIPLANTAE; YARROWIA LIPOLYTICA;

AMINO ACID SEQUENCE; ARCHAEA; ARCHAEAL PROTEINS; BACTERIA; BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; DICTYOSTELIIDA; EVOLUTION, MOLECULAR; FUNGAL PROTEINS; FUNGI; MEMBRANE TRANSPORT PROTEINS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PLANT PROTEINS; PLANTS; PROTOZOAN PROTEINS; SEQUENCE ALIGNMENT; SOFTWARE;

EUKARYOTA; FUNGI; PROKARYOTA;

EID: 79953697080     PISSN: 00222631     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00232-011-9347-9     Document Type: Article

References (51)

1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402 (Pubitemid 27359211)
2. Black PN, DiRusso CC (2007) Vectorial acylation: linking fatty acid transport and activation to metabolic trafficking. Novartis Found Symp 286:127-138 (discussion 138-141, 162-163, 196-203)
3. Busch W, Saier MH Jr (2004) The IUBMB-endorsed transporter classification system. Mol Biotechnol 27:253-262 (Pubitemid 41490593)
4. Cagnac O, Bourbouloux A, Chakrabarty D, Zhang MY, Delrot S (2004) AtOPT6 transports glutathione derivatives and is induced by primisulfuron. Plant Physiol 135:1378-1387 (Pubitemid 39009385)
5. Chung YJ, Krueger C, Metzgar D, Saier MH Jr (2001) Size comparisons among integral membrane transport protein homologues in bacteria, Archaea, and Eucarya. J Bacteriol 183:1012-1021 (Pubitemid 32095311)
6. Curie C, Panaviene Z, Loulergue C, Dellaporta SL, Briat JF, Walker EL (2001) Maize yellow stripe1 encodes a membrane protein directly involved in Fe(III) uptake. Nature 409:346-349 (Pubitemid 32151239)
7. Dayhoff MO, Barker WC, Hunt LT (1983) Establishing homologies in protein sequences. Methods Enzymol 91:524-545
8. Devereux J, Haeberli P, Smithies O (1984) A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res 12:387-395
9. Dworeck T, Wolf K, Zimmermann M (2009) SpOPT1, a member of the oligopeptide family (OPT) of the fission yeast Schizosaccharomyces pombe, is involved in the transport of glutathione through the outer membrane of the cell. Yeast 26:67-73
10. Eddy SR (2008) A probabilistic model of local sequence alignment that simplifies statistical significance estimation. PLoS Comput Biol 4:e1000069
11. Eichinger L, Pachebat JA, Glockner G, Rajandream MA, Sucgang R, Berriman M, Song J, Olsen R, Szafranski K, Xu Q, Tunggal B, Kummerfeld S, Madera M, Konfortov BA, Rivero F, Bankier AT, Lehmann R, Hamlin N, Davies R, Gaudet P, Fey P, Pilcher K, Chen G, Saunders D, Sodergren E, Davis P, Kerhornou A, Nie X, Hall N, Anjard C, Hemphill L, Bason N, Farbrother P, Desany B, Just E, Morio T, Rost R, Churcher C, Cooper J, Haydock S, van Driessche N, Cronin A, Goodhead I, Muzny D, Mourier T, Pain A, Lu M, Harper D, Lindsay R, Hauser H, James K, Quiles M, Madan Babu M, Saito T, Buchrieser C, Wardroper A, Felder M, Thangavelu M, Johnson D, Knights A, Loulseged H, Mungall K, Oliver K, Price C, Quail MA, Urushihara H, Hernandez J, Rabbinowitsch E, Steffen D, Sanders M, Ma J, Kohara Y, Sharp S, Simmonds M, Spiegler S, Tivey A, Sugano S, White B, Walker D, Woodward J, Winckler T, Tanaka Y, Shaulsky G, Schleicher M, Weinstock G, Rosenthal A, Cox EC, Chisholm RL, Gibbs R, Loomis WF, Platzer M, Kay RR, Williams J, Dear PH, Noegel AA, Barrell B, Kuspa A (2005) The genome of the social amoeba Dictyostelium discoideum. Nature 435:43-57 (Pubitemid 40655903)
12. Hauser M, Narita V, Donhardt AM, Naider F, Becker JM (2001) Multiplicity and regulation of genes encoding peptide transporters in Saccharomyces cerevisiae. Mol Membr Biol 18:105-112 (Pubitemid 32521603)
13. Herbert M, Sauer E, Smethurst G, Kraiss A, Hilpert AK, Reidl J (2003) Nicotinamide ribosyl uptake mutants in Haemophilus influenzae. Infect Immun 71:5398-5401 (Pubitemid 37070792)
14. Hirsch D, Stahl A, Lodish HF (1998) A family of fatty acid transporters conserved from mycobacterium to man. Proc Natl Acad Sci USA 95:8625-8629 (Pubitemid 28350538)
15. Kall L, Krogh A, Sonnhammer EL (2007) Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server. Nucleic Acids Res 35:W429-W432
16. Kaur J, Srikanth CV, Bachhawat AK (2009) Differential roles played by the native cysteine residues of the yeast glutathione transporter, Hgt1p. FEMS Yeast Res 9:849-866
17. Koh S, Wiles AM, Sharp JS, Naider FR, Becker JM, Stacey G (2002) An oligopeptide transporter gene family in Arabidopsis. Plant Physiol 128:21-29 (Pubitemid 34119507)
18. Krogh A, Larsson B, von Heijne G, Sonnhammer EL (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305:567-580 (Pubitemid 33032862)
19. Kuan J, Saier MH Jr (1993a) The mitochondrial carrier family of transport proteins: structural, functional, and evolutionary relationships. Crit Rev Biochem Mol Biol 28:209-233 (Pubitemid 23160985)
20. Kuan J, Saier MH Jr (1993b) Expansion of the mitochondrial carrier family. Res Microbiol 144:671-672 (Pubitemid 24014243)
21. Lee JH, Harvat EM, Stevens JM, Ferguson SJ, Saier MH Jr (2007) Evolutionary origins of members of a superfamily of integral membrane cytochrome c biogenesis proteins. Biochim Biophys Acta 1768:2164-2181 (Pubitemid 47379604)
22. Lubkowitz M (2006) The OPT family functions in long-distance peptide and metal transport in plants. Genet Eng (NY) 27:35-55
23. Lubkowitz MA, Barnes D, Breslav M, Burchfield A, Naider F, Becker JM (1998) Schizosaccharomyces pombe isp4 encodes a transporter representing a novel family of oligopeptide transporters. Mol Microbiol 28:729-741 (Pubitemid 28234383)
24. 2+ (CRAC) channels are homologous to and derived from the ubiquitous cation diffusion facilitators. BCM Res Notes 3(1):158
25. + biosynthesis and nicotinamide ribosyl transport: characterization of NadR ribonucleotide kinase mutants of Haemophilus influenzae. J Bacteriol 187:4410-4420
26. Mitchell P, Moyle J (1958) Group-translocation: a consequence of enzyme-catalysed group-transfer. Nature 182:372-373
27. Nelson RD, Kuan G, Saier MH Jr, Montal M (1999) Modular assembly of voltage-gated channel proteins: a sequence analysis and phylogenetic study. J Mol Microbiol Biotechnol 1:281-287 (Pubitemid 129491948)
28. Osawa H, Stacey G, Gassmann W (2006) ScOPT1 and AtOPT4 function as proton-coupled oligopeptide transporters with broad but distinct substrate specificities. Biochem J 393:267-275 (Pubitemid 43049323)
29. Pao SS, Paulsen IT, Saier MH Jr (1998) Major facilitator superfamily. Microbiol Mol Biol Rev 62:1-34 (Pubitemid 28130794)
30. Paulsen IT, Skurray RA (1994) The POT family of transport proteins. Trends Biochem Sci 19:404 (Pubitemid 24320128)
31. Povolotsky TL, Orlova E, Tamang DG, Saier MH Jr (2010) Defense against cannibalsim: the SpdI family of bacterial immunity/signal transduction proteins. J Membr Biol 235:145-162
32. Reuss O, Morschhauser J (2006) A family of oligopeptide transporters is required for growth of Candida albicans on proteins. Mol Microbiol 60:795-812
33. Saier MH Jr (1994) Computer-aided analyses of transport protein sequences: gleaning evidence concerning function, structure, biogenesis, and evolution. Microbiol Rev 58:71-93
34. Saier MH Jr (2000a) A functional-phylogenetic classification system for transmembrane solute transporters. Microbiol Mol Biol Rev 64:354-411
35. Saier MH Jr (2000b) Families of proteins forming transmembrane channels. J Membr Biol 175:165-180
36. Saier MH Jr (2000c) Vectorial metabolism and the evolution of transport systems. J Bacteriol 182:5029-5035
37. Saier MH Jr (2003) Tracing pathways of transport protein evolution. Mol Microbiol 48:1145-1156
38. Saier MH Jr, Hvorup RN, Barabote RD (2005) Evolution of the bacterial phosphotransferase system: from carriers and enzymes to group translocators. Biochem Soc Trans 33:220-224 (Pubitemid 40313807)
39. Saier MH Jr, Tran CV, Barabote RD (2006) TCDB: the Transporter Classification Database for membrane transport protein analyses and informaiton. Nuceic Acids Res 34:181-186
40. Saier MH Jr, Yen MR, Noto K, Tamang DG, Elkan C (2009) The Transporter Classification Database: recent advances. Nucleic Acids Res 37:D274-D278
41. Stacey MG, Patel A, McClain WE, Mathieu M, Remley M, Rogers EE, Gassmann W, Blevins DG, Stacey G (2008) The Arabidopsis AtOPT3 protein functions in metal homeostasis and movement of iron to developing seeds. Plant Physiol 146:589-601 (Pubitemid 351230787)
42. Thakur A, Kaur J, Bachhawat AK (2008) Pgt1, a glutathione transporter from the fission yeast Schizosaccharomyces pombe. FEMS Yeast Res 8:916-929
43. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882 (Pubitemid 28022245)
44. Tusnady GE, Simon I (2001) The HMMTOP transmembrane topology prediction server. Bioinformatics 17:849-850 (Pubitemid 32970487)
45. Wang B, Dukarevich M, Sun EI, Yen MR, Saier MH Jr (2009) Membrane porters of ATP-binding cassette transport systems are polyphyletic. J Membr Biol 231:1-10
46. Wiles AM, Cai H, Naider F, Becker JM (2006) Nutrient regulation of oligopeptide transport in Saccharomyces cerevisiae. Microbiology 152:3133-3145 (Pubitemid 44542391)
47. Yen MR, Tseng YH, SaierMHJr (2001) Maize Yellow Stripe1, an ironphytosiderophore uptake transporter, is a member of the oligopeptide transporter (OPT) family. Microbiology 147:2881-2883
48. Yen MR, Choi J, Saier MH Jr (2009) Bioinformatic analyses of transmembrane transport: novel software for deducing protein phylogeny, topology, and evolution. J Mol Microbiol Biotechnol 17:163-176
49. Zhai Y, Saier MH Jr (2001a) A Web-based program (WHAT) for the simultaneous prediction of hydropathy, amphipathicity, secondary structure and transmembrane topology for a single protein sequence. J Mol Microbiol Biotechnol 3:501-502 (Pubitemid 32791409)
50. Zhai Y, Saier MH Jr (2001b) A Web-based program for the prediction of average hydropathy, average amphipathicity and average similarity of multiply aligned homologous proteins. J Mol Microbiol Biotechnol 3:285-286 (Pubitemid 32257914)
51. Zhai Y, Tchieu J, Saier MH Jr (2002) A Web-based Tree View (TV) program for the visualization of phylogenetic trees. J Mol Microbiol Biotechnol 4:69-70 (Pubitemid 33121214)