The solute carrier families have a remarkably long evolutionary history with the majority of the human families present before divergence of Bilaterian species

Molecular Biology and Evolution

Volumn 28, Issue 4, 2011, Pages 1531-1541

  Höglund, Pär J ^a   Nordström, Karl J V ^a   Schiöth, Helgi B ^a   Fredriksson, Robert ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

Pfam; SLC; solute carrier; transporter

Indexed keywords

MEMBRANE PROTEIN; SLC1 PROTEIN; SLC10 PROTEIN; SLC12 PROTEIN; SLC15 PROTEIN; SLC16 PROTEIN; SLC17 PROTEIN; SLC18 PROTEIN; SLC19 PROTEIN; SLC2 PROTEIN; SLC21 PROTEIN; SLC22 PROTEIN; SLC23 PROTEIN; SLC24 PROTEIN; SLC26 PROTEIN; SLC29 PROTEIN; SLC32 PROTEIN; SLC36 PROTEIN; SLC37 PROTEIN; SLC38 PROTEIN; SLC4 PROTEIN; SLC43 PROTEIN; SLC45 PROTEIN; SLC46 PROTEIN; SLC5 PROTEIN; SLC7 PROTEIN; SLC8 PROTEIN; SLC9 PROTEIN; SOLUTE CARRIER PROTEIN; UNCLASSIFIED DRUG;

ANOPHELES GAMBIAE; ARTICLE; BILATERIA; CAENORHABDITIS ELEGANS; CENTRAL NERVOUS SYSTEM FUNCTION; DICTYOSTELIUM DISCOIDEUM; DROSOPHILA MELANOGASTER; EUKARYOTE; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC ANALYSIS; HUMAN; MOLECULAR EVOLUTION; MONOSIGA BREVICOLLIS; MOUSE; NEMATOSTELLA VECTENSIS; NONHUMAN; OSTREOCOCCUS TAURI; PARAMECIUM TETRAURELIA; SCHIZOSACCHAROMYCES POMBE; SPECIES DIFFERENCE; TRICHOPLAX ADHAERENS; TRYPANOSOMA CRUZI;

ANIMALS; BIOLOGICAL EVOLUTION; CLUSTER ANALYSIS; DATABASES, GENETIC; EVOLUTION, MOLECULAR; HUMANS; MEMBRANE TRANSPORT PROTEINS; MULTIGENE FAMILY; PHYLOGENY;

BILATERIA; CAENORHABDITIS ELEGANS; EUKARYOTA; HEXAPODA; HOMO SAPIENS; MAMMALIA;

EID: 79952845375     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msq350     Document Type: Article

References (46)

1. Arabidopsis Genome Initiative, Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815.
2. Adams MDSE, Celniker RA, Holt CA, et al. (193 co-authors). 2000. The genome sequence of Drosophila melanogaster. Science 287:2185-2195.
3. Almen MS, Nordstrom KJ, Fredriksson R, Schioth HB. 2009. Mapping the human membrane proteome: a majority of the human membrane proteins can be classified according to function and evolutionary origin. BMC Biol. 7:50.
4. Arnaiz O, Cain S, Cohen J, Sperling L. 2007. ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. Nucleic Acids Res. 35:D439-D444. (Pubitemid 46056247)
5. Caenorhabditis elegans Sequencing Consortium, Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282:2012-2018.
6. Collins JE, Goward ME, Cole CG, Smink LJ, Huckle EJ, Knowles S, Bye JM, Beare DM, Dunham I. 2003. Reevaluating human gene annotation: a second-generation analysis of chromosome 22. Genome Res. 13:27-36.
7. Eddy SR. 1998. Profile hidden Markov models. Bioinformatics 14:755-763. (Pubitemid 28552108)
8. Eichinger L, Pachebat JA, Glockner G, et al. (97 co-authors). 2005. The genome of the social amoeba Dictyostelium discoideum. Nature 435:43-57. (Pubitemid 40655903)
9. El-Sayed NM, Myler PJ, Bartholomeu DC, et al. (82 co-authors). 2005. The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease. Science 309:409-415.
10. Finn RD, Mistry J, Schuster-Bockler B, et al. 2006. Pfam: clans, web tools and services. Nucl Acids Res. 34:D247-D251.
11. Finn RD, Tate J, Mistry J, et al. 2008. The Pfam protein families database. Nucl Acids Res. 36:D281-D248.
12. Flicek P, Aken BL, Beal K, et al. (59 co-authors). 2008. Ensembl 2008. Nucl Acids Res. 36:D707-D714. (Pubitemid 351149811)
13. Fredriksson R, Hagglund M, Olszewski PK, Stephansson O, Jacobsson JA, Olszewska AM, Levine AS, Lindblom J, Schioth HB. 2008. The obesity gene, FTO, is of ancient origin, up-regulated during food deprivation and expressed in neurons of feedingrelated nuclei of the brain. Endocrinology 149:2062-2071. (Pubitemid 351574484)
14. Fredriksson R, Lagerstrom MC, Lundin LG, Schioth HB. 2003. The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints. Mol Pharmacol. 63:1256-1272. (Pubitemid 36627220)
15. Fredriksson R, Nordstrom KJ, Stephansson O, Hagglund MG, Schioth HB. 2008. The solute carrier (SLC) complement of the human genome: phylogenetic classification reveals four major families. FEBS Lett. 582:3811-3816.
16. Goffeau A, Barrell BG, Bussey H, et al. (16 co-authors). 1996. Life with 6000 genes. Science 274:546-563-547.
17. Gupta BP, Sternberg PW. 2003. The draft genome sequence of the nematode Caenorhabditis briggsae, a companion to C. elegans. Genome Biol. 4:238.
18. Hampl V, Hug L, Leigh JW, Dacks JB, Lang BF, Simpson AG, Roger AJ. 2009. Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups". Proc Natl Acad Sci USA. 106:3859-3864.
19. Haydon MJ, Cobbett CS. 2007. A novel major facilitator superfamily protein at the tonoplast influences zinc tolerance and accumulation in Arabidopsis. Plant Physiol. 143: 1705-1719. (Pubitemid 46849481)
20. Hediger MA, Romero MF, Peng JB, Rolfs A, Takanaga H, Bruford EA. 2004. The ABCs of solute carriers: physiological, pathological and therapeutic implications of human membrane transport proteinsIntroduction. Pflugers Arch. 447:465-468. (Pubitemid 38241432)
21. Hoglund PJ, Adzic D, Scicluna SJ, Lindblom J, Fredriksson R. 2005. The repertoire of solute carriers of family 6: identification of new human and rodent genes. Biochem Biophys Res Commun. 336:175-189. (Pubitemid 41253419)
22. Holt RAGM, Subramanian A, Halpern GG, et al. (123 co-authors). 2002. The genome sequence of the malaria mosquito Anopheles gambiae. Science 298:129-149.
23. Horemans N, Szarka A, De Bock M, Raeymaekers T, Potters G, Levine M, Banhegyi G, Guisez Y. 2008. Dehydroascorbate and glucose are taken up into Arabidopsis thaliana cell cultures by two distinct mechanisms. FEBS Lett. 582: 2714-2718.
24. 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(Pt 8):1797-1814. (Pubitemid 30639257)
25. Jacobsson JA, Haitina T, Lindblom J, Fredriksson R. 2007. Identification of six putative human transporters with structural similarity to the drug transporter SLC22 family. Genomics. 90:595-609. (Pubitemid 350016717)
26. Kent WJ. 2002. BLAT-the BLAST-like alignment tool. Genome Res. 12:656-664.
27. King N, Westbrook MJ, Young SL, et al. (36 co-authors). 2008. The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature 451:783-788. (Pubitemid 351253174)
28. Lander ESLM, Linton B, Birren C, et al. (254 co-authors). 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
29. Law CJ, Maloney PC, Wang DN. 2008. Ins and outs of major facilitator superfamily antiporters. Annu Rev Microbiol. 62:289-305.
30. Lemieux MJ. 2007. Eukaryotic major facilitator superfamily transporter modeling based on the prokaryotic GlpT crystal structure. Mol Membr Biol. 24:333-341. (Pubitemid 47290679)
31. Madera M, Gough J. 2002. A comparison of profile hidden Markov model procedures for remote homology detection. Nucleic Acids Res. 30:4321-4328. (Pubitemid 35175200)
32. Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S. 2002. The protein kinase complement of the human genome. Science 298:1912-1934. (Pubitemid 35425239)
33. Martin F, Aerts A, Ahren D, et al. (68 co-authors). 2008. The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis. Nature 452:88-92. (Pubitemid 351355085)
34. Nozaki H, Takano H, Misumi O, et al. (18 co-authors). 2007. A 100%-complete sequence reveals unusually simple genomic features in the hot-spring red alga Cyanidioschyzon merolae. BMC Biol. 5:28.
35. Palenik B, Grimwood J, Aerts A, et al. (38 co-authors). 2007. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl Acad Sci USA. 104:7705-7710. (Pubitemid 47185970)
36. Pao SS, Paulsen IT, Saier MH Jr. 1998. Major facilitator superfamily. Microbiol Mol Biol Rev. 62:1-34. (Pubitemid 28130794)
37. Putnam NH, Srivastava M, Hellsten U, et al. (19 co-authors). 2007. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317:86-94. (Pubitemid 47056460)
38. Saier MH Jr, Beatty JT, Goffeau A, et al. (14 co-authors). 1999. The major facilitator superfamily. J Mol Microbiol Biotechnol. 1:257-279. (Pubitemid 129491947)
39. Srivastava M, Begovic E, Chapman J, et al. (21 co-authors). 2008. The Trichoplax genome and the nature of placozoans. Nature 454:955-960.
40. Sundberg BE, Waag E, Jacobsson JA, et al. (11 co-authors). 2008. The evolutionary history and tissue mapping of amino acid transporters belonging to solute carrier families SLC32, SLC36, and SLC38. J Mol Neurosci. 35:179-193.
41. Terada T, Inui K. 2008. Physiological and pharmacokinetic roles of H\+/organic cation antiporters (MATE/SLC47A). Biochem Pharmacol. 75:1689-1696.
42. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680. (Pubitemid 24354800)
43. Venter JCMD, Adams EW, Myers PW, et al. (275 co-authors). 2001. The sequence of the human genome. Science 291:1304-1351.
44. Waterston RHK, Lindblad-Toh E, Birney J, et al. (220 co-authors). 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-562.
45. Wood VR, Gwilliam MA, Rajandream M, et al. (134 co-authors). 2002. The genome sequence of Schizosaccharomyces pombe. Nature 415:871-880. (Pubitemid 34174743)
46. Yu FH, Catterall WA. 2004. The VGL-chanome: a protein super-family specialized for electrical signaling and ionic homeostasis. Sci STKE. re15:1-17.