The amino acid-polyamine-organocation superfamily

Journal of Molecular Microbiology and Biotechnology

Volumn 22, Issue 2, 2012, Pages 105-113

  Wong, Foon H ^a   Chen, Jonathan S ^a   Reddy, Vamsee ^a   Day, Jonathan L ^a   Shlykov, Maksim A ^a   Wakabayashi, Steven T ^a   Saier Jr , Milton H ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

Amino acid polyamine organocation superfamily; Evolution; Membranes; Phylogeny; SuperfamilyTree programs; Transport proteins

Indexed keywords

AMINO ACID; AMINO ACID POLYAMINE ORGANOCATION SUPERFAMILY; CATION; POLYAMINE; UNCLASSIFIED DRUG;

ALPHA HELIX; AMINO ACID SEQUENCE; ARTICLE; DNA HAIRPIN; GENE INSERTION; STATISTICAL ANALYSIS;

AMINO ACID MOTIFS; AMINO ACIDS; CRYSTALLOGRAPHY, X-RAY; EVOLUTION, MOLECULAR; MEMBRANE PROTEINS; MEMBRANE TRANSPORT PROTEINS; PHYLOGENY; POLYAMINES; PROTEIN TRANSPORT; PROTEOMICS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE;

EID: 84861197312     PISSN: 14641801     EISSN: 16602412     Source Type: Journal    
DOI: 10.1159/000338542     Document Type: Article

References (50)

1. Abramson J, Wright EM: Structure and function of Na(+)-symporters with inverted repeats. Curr Opin Struct Biol 2009; 19: 425-432.
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990; 215: 403-410.
3. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25:3389-3402. (Pubitemid 27359211)
4. Bailey TL, Elkan C: The value of prior knowledge in discovering motifs with MEME. Proc Int Conf Intell Syst Mol Biol 1995; 3:21-29.
5. Cai W, Pei J, Grishin NV: Reconstruction of ancestral protein sequences and its applications. BMC Evol Biol 2004; 4:33.
6. Chan H, Babayan V, Blyumin E, Gandhi C, Hak K, Harake D, Kumar K, Lee P, Li TT, Liu HY, Lo TC, Meyer CJ, Stanford S, Zamora KS, Saier MH Jr: The p-type ATPase superfami-ly. J Mol Microbiol Biotechnol 2010; 19: 5-104.
7. Chang AB, Lin R, Keith Studley W, Tran CV, Sai-er MH Jr: Phylogeny as a guide to structure and function of membrane transport proteins. Mol Membr Biol 2004; 21: 171-181. (Pubitemid 38745646)
8. Chen JS, Reddy V, Chen JH, Shlykov MA, Zheng WH, Cho J, Yen MR, Saier MH Jr: Phyloge-netic characterization of transport protein superfamilies: superiority of Superfamily-Tree programs over those based on multiple alignments. J Mol Microbiol Biotechnol 2011; 21:83-96.
9. Chen LQ, Hou BH, Lalonde S, Takanaga H, Har-tung ML, Qu XQ, Guo WJ, Kim JG, Underwood W, Chaudhuri B, Chermak D, Antony G, White FF, Somerville SC, Mudgett MB, Frommer WB: Sugar transporters for intercellular exchange and nutrition of pathogens. Nature 2010; 468: 527-532.
10. Cooper GR, Moir A: Amino acid residues in the GerAB protein important in the function and assembly of the alanine spore germination receptor of Bacillus subtilis 168. J Bacte-riol 2011; 193: 2261-2267.
11. Dayhoff MO, Barker WC, Hunt LT: Establishing homologies in protein sequences. Methods Enzymol 1983; 91:524-545.
12. Devereux J, Haeberli P, Smithies O: A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res 1984; 12:387-395.
13. Fang Y, Jayaram H, Shane T, Kolmakova-Partensky L, Wu F, Williams C, Xiong Y, Miller C: Structure of a prokaryotic virtual proton pump at 3.2 A resolution. Nature 2009; 460:1040-1043.
14. Fitch WM, Margoliash E: Construction of phy-logenetic trees. Science 1967; 155: 279-284.
15. Gao X, Zhou L, Jiao X, Lu F, Yan C, Z eng X, Wa ng J, Shi Y: Mechanism of substrate recognition and transport by an amino acid antiporter. Nature 2010; 463:828-832.
16. Gascuel O, Steel M: Neighbor-joining revealed. Mol Biol Evol 2006; 23: 1997-2000. (Pubitemid 44536808)
17. Gilbert RJ: Cholesterol-dependent cytolysins. Adv Exp Med Biol 2010; 677: 56-66.
18. Hotze EM, Tweten RK: Membrane assembly of the cholesterol-dependent cytolysin pore complex. Biochim Biophys Acta 2012; 1818: 1028-1038.
19. Jack DL, Paulsen IT, Saier MH: The amino acid/polyamine/organocation (APC) superfamily of transporters specific for amino acids, polyamines and organocations. Microbiology 2000; 146:1797-1814. (Pubitemid 30639257)
20. Jalilian C, Gallant EM, Board PG, Dulhunty AF: Redox potential and the response of cardiac ryanodine receptors to CLIC-2, a member of the glutathione S-transferase structural family. Antioxid Redox Signal 2008; 10: 1675-1686.
21. Jeckelmann JM, Palacin M, Fotiadis D: A tool for the qualitative comparison of membrane-embedded and detergent-solubilized membrane protein structures in projection. J Str uct Biol 2011; 173: 375-381.
22. Kondos SC, Hatfaludi T, Voskoboinik I, Trapani JA, Law RH, Whisstock JC, Dunstone MA: The structure and function of mammalian membrane-attack complex/perforin-like proteins. Tissue Antigens 2010; 76: 341-351.
23. Kowalczyk L, Ratera M, Paladino A, Bartoccioni P, Errasti-Murugarren E, Valencia E, Portella G, Bial S, Zorzano A, Fita I, Orozco M, Carpena X, Vazquez-Ibar JL, Palacin M: Molecular basis of substrate-induced permeation by an amino acid antiporter. Proc Natl Acad Sci USA 2011; 108:3935-3940.
24. Lam VH, Lee JH, Silverio A, Chan H, Gomolpli-tinant KM, Povolotsky TL, Orlova E, Sun EI, Welliver CH, Saier MH Jr: Pathways of transport protein evolution: recent advances. Biol Chem 2011; 392: 5-12.
25. Li W, Godzik A: Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006; 22:1658-1659. (Pubitemid 43985301)
26. Li W, Jaroszewski L, Godzik A: Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformat-ics 2001; 17:282-283. (Pubitemid 32288218)
27. Li W, Jaroszewski L, Godzik A: Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformat-ics 2002; 18: 77-82. (Pubitemid 34145034)
28. Linhartova I, Bumba L, Masin J, Basler M, Osic-ka R, Kamanova J, Prochazkova K, Adkins I, Hejnova-Holubova J, Sadilkova L, Morova J, Sebo P: RTX proteins: a highly diverse family secreted by a common mechanism. FEMS Microbiol Rev 2010; 34: 1076-1112.
29. Littler DR, Harrop SJ, Goodchild SC, Phang JM, Mynott AV, Jiang L, Valenzuela SM, Maz-zanti M, Brown LJ, Breit SN, Curmi PM: The enigma of the CLIC proteins: ion channels, redox proteins, enzymes, scaffolding proteins? FEBS Lett 2010; 584: 2093-2101.
30. 2+ (CR AC) cha nnels appear to be homolo-gous to and derived from the ubiquitous cation diffusion facilitators. BMC Res Notes 2010; 3:158.
31. McNeil AK, Rescher U, Gerke V, McNeil PL: Requirement for annexin A1 in plasma membrane repair. J Biol Chem 2006; 281: 35202-35207. (Pubitemid 46036558)
32. Ostroumova OS, Schagina LV, Mosevitsky MI, Zakharov VV: Ion channel activity of brain abundant protein BASP1 in planar lipid bi-layers. FEBS J 2011; 278: 461-469.
33. Perocchi F, Gohil VM, Girgis HS, Bao XR, Mc-Combs JE, Palmer AE, Mootha VK: MICU1 encodes a mitochondrial EF hand protein required for Ca(2+) uptake. Nature 2010; 467: 291-296.
34. Popoff MR: Epsilon toxin: a fascinating pore-forming tox in. FEBS J 2011; 278: 4602-4615.
35. Reddy V, Saier MH Jr: BioV Suite-a collection of programs for the study of transport protein evolution. FEBS J 2012, Mar 30. DOI: 10.1111/j.1742-4658. 2012.08590.x.(E-pub ahead of print).
36. Sael L, Chitale M, Kihara D: Structure-and sequence-based function prediction for non-homologous proteins. J Struct Funct Ge-nomics 2012, E-pub ahead of print.
37. Saier MH: Genome archeology leading to the characterization and classification of transport proteins. Curr Opin Microbiol 1999; 2: 555-561.
38. Saier MH Jr: Phylogenetic approaches to the identification and characterization of protein families and superfamilies. Microb Comp Genomics 1996; 1:129-150.
39. Saier MH Jr: A functional-phylogenetic classification system for transmembrane solute transporters. Microbiol Mol Biol Rev 2000; 64:354-411. (Pubitemid 30412678)
40. Saier MH Jr: Tracing pathways of transport protein evolution. Mol Microbiol 2003; 48:1145-1156. (Pubitemid 36718212)
41. Saier MH Jr, Tran CV, Barabote RD: TCDB: the Transporter Classification Database for membrane transport protein analyses and information. Nucleic Acids Res 2006; 34:D181-D186.
42. Saier MH Jr, Yen MR, Noto K, Tamang DG, El-kan C: The Transporter Classification Database: recent advances. Nucleic Acids Res 2009; 37:D274-D278.
43. Saitou N, Nei M: The neighbor-joining method: a new method for reconstructing phyloge-netic trees. Mol Biol Evol 1987; 4: 406-425.
44. Shenoy SR, Jayaram B: Proteins: sequence to structure and function-current status. Curr Protein Pept Sci 2010; 11:498-514.
45. Thompson JD, Gibson TJ, Plewniak F, Jeanmou-gin F, Higgins DG: The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25: 4876-4882.
46. Wang B, Dukarevich M, Sun EI, Yen MR, Saier MH Jr: Membrane porters of ATP-binding cassette transport systems are polyphyletic. J Membr Biol 2009; 231: 1-10.
47. Yen MR, Chen JS, Marquez JL, Sun EI, Saier MH: Multidrug resistance: phylogenetic characterization of superfamilies of secondary carriers that include drug exporters. Methods Mol Biol 2010; 637:47-64.
48. Yen MR, Choi J, Saier MH Jr: Bioinformatic analyses of transmembrane transport: novel software for deducing protein phylogeny, topology, and evolution. J Mol Microbiol Bio-technol 2009; 17: 163-176.
49. Young GB, Jack DL, Smith DW, Saier MH Jr: The amino acid/auxin:proton symport permease family. Biochim Biophys Acta 1999; 1415: 306-322. (Pubitemid 29065296)
50. Zhai Y, Tchieu J, Saier MH Jr: A Web-based Tree View (TV) program for the visualization of phylogenetic trees. J Mol Microbiol Biotech-nol 2002; 4:69-70. (Pubitemid 33121214)