Domain-based identification and analysis of glutamate receptor ion channels and their relatives in prokaryotes

PLoS ONE

Volumn 5, Issue 10, 2010, Pages

  Ger, Mao Feng ^a   Rendon, Gloria ^b   Tilson, Jeffrey L ^c   Jakobsson, Eric ^a,b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^c Renaissance Computing Institute   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLUTAMATE RECEPTOR; GLUTAMIC ACID; ION CHANNEL;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; MOLECULAR PHYLOGENY; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PROKARYOTE; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN MOTIF; CHEMISTRY; GENETICS; METABOLISM; MOLECULAR GENETICS; PHYLOGENY; PROKARYOTIC CELL;

EUKARYOTA; PROKARYOTA;

AMINO ACID SEQUENCE; ION CHANNELS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROKARYOTIC CELLS; RECEPTORS, GLUTAMATE;

EID: 78049319867     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0012827     Document Type: Article

References (25)

1. Stevens TJ, Arkin IT (2000) Do more complex organisms have a greater proportion of membrane proteins in their genomes? Proteins 39: 417-420.
2. Gouaux E, Mackinnon R (2005) Principles of selective ion transport in channels and pumps. Science 310: 1461-1465.
3. Pohorille A, Schweighofer K, Wilson MA (2005) The origin and early evolution of membrane channels. Astrobiology 5: 1-17.
4. Ashcroft FM (2006) From molecule to malady. Nature 440: 440-447.
5. Chen GQ, Cui C, Mayer ML, Gouaux E (1999) Functional characterization of a potassium-selective prokaryotic glutamate receptor. Nature 402: 817-821.
6. Mayer ML (2006) Glutamate receptors at atomic resolution. Nature 440: 456-462.
7. Booth IR, Edwards MD, Miller S (2003) Bacterial ion channels. Biochemistry 42: 10045-10053.
8. Kuner T, Seeburg PH, Guy HR (2003) A common architecture for K+ channels and ionotropic glutamate receptors? Trends Neurosci 26: 27-32.
9. Kung C, Blount P (2004) Channels in microbes: so many holes to fill. Mol Microbiol 53: 373-380.
10. Doyle DA, Morais Cabral J, Pfuetzner RA, Kuo A, Gulbis JM, et al. (1998) The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science 280: 69-77.
11. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
12. Tasneem A, Iyer LM, Jakobsson E, Aravind L (2005) Identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal Cys-loop ion channels. Genome Biol 6: R4.
13. Bocquet N, Prado de Carvalho L, Cartaud J, Neyton J, Le Poupon C, et al. (2007) A prokaryotic proton-gated ion channel from the nicotinic acetylcholine receptor family. Nature 445: 116-119.
14. Hilf RJ, Dutzler R (2008) X-ray structure of a prokaryotic pentameric ligandgatedion channel. Nature 452: 375-379.
15. Saier MH, Jr. (2000) A functional-phylogenetic classification system for transmembrane solute transporters. Microbiol Mol Biol Rev 64: 354-411.
16. Mayer ML, Olson R, Gouaux E (2001) Mechanisms for ligand binding to GluR0 ion channels: crystal structures of the glutamate and serine complexes and a closed apo state. J Mol Biol 311: 815-836.
17. Moller S, Croning MD, Apweiler R (2001) Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics 17: 646-653.
18. 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.
19. Felsenstein J (1993) PHYLIP (Phylogeny Inference Package). 3.5c ed.
20. Hu Z, Frith M, Niu T, Weng Z (2003) SeqVISTA: a graphical tool for sequence feature visualization and comparison. BMC Bioinformatics 4: 1.
21. Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340: 783-795.
22. Zdobnov EM, Apweiler R (2001) InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics 17: 847-848.
23. Tilson JL, Rendon G, Ger M-F, Jakobsson E (2007) MotifNetwork: A Gridenabled Workflow for High-throughput Domain Analysis of Biological Sequences. Bioinformatics and Bioengineering, 2007 BIBE 2007 Proceedings of the 7th IEEE International Conference. pp 620-627.
24. Mackey SR, Golden SS (2007) Winding up the cyanobacterial circadian clock. Trends Microbiol 15: 381-388.
25. Kalsbeek A, Kreier F, Fliers E, Sauerwein HP, Romijn JA, et al. (2007) Minireview: Circadian control of metabolism by the suprachiasmatic nuclei. Endocrinology 148: 5635-5639.