FIST: A sensory domain for diverse signal transduction pathways in prokaryotes and ubiquitin signaling in eukaryotes

Bioinformatics

Volumn 23, Issue 19, 2007, Pages 2518-2521

  Borziak, Kirill ^a   Zhulin, Igor B ^a  

^a Oak Ridge National Laboratory   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

F BOX PROTEIN; UBIQUITIN;

AMINO ACID METABOLISM; ARABIDOPSIS; ARCHAEBACTERIUM; ARTICLE; BRADYRHIZOBIUM JAPONICUM; CHROMOSOME ANALYSIS; CLOSTRIDIUM; COMPUTER PROGRAM; EUKARYOTE; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC VARIABILITY; HALOARCULA MARISMORTUI; MAGNETOSPIRILLUM; MARINOMONAS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROKARYOTE; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN TRANSPORT; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SIGNAL DETECTION; SIGNAL TRANSDUCTION; SPECIES DIFFERENCE; STRUCTURE ANALYSIS; SYNECHOCOCCUS;

EUKARYOTA; PROKARYOTA;

EID: 35748955207     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm384     Document Type: Article

References (24)

1. Alexander,R.P. and Zhulin,I.B. (2007) Evolutionary genomics reveals conserved structural determinants of signaling and adaptation in microbial chemo-receptors. Proc. Natl Acad. Sci. USA, 104, 2885-2890.
2. Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
3. Anantharaman,V. and Aravind,L. (2000) Cache - a signaling domain common to animal Ca(2+)-channel subunits and a class of prokaryotic chemotaxis receptors. Trends Biochem. Sci., 25, 535-537.
4. Anantharaman,V. and Aravind,L. (2001) The CHASE domain: A predicted ligand-binding module in plant cytokinin receptors and other eukaryotic and bacterial receptors. Trends Biochem. Sci., 26, 579-582.
5. Aravind,L. and Ponting,C.P. (1997) The GAF domain: An evolutionary link between diverse phototransducing proteins. Trends Biochem. Sci., 22, 458-459.
6. Citri,A. and Yarden,Y. (2006) EGF-ERBB signalling: Towards the systems level. Nat. Rev. Mol. Cell Biol., 7, 505-516.
7. Finn,R.D. et al. (2006) Pfam: Clans, web tools and services. Nucleic Acids Res., 34, D247-D251.
8. Galperin,M.Y. et al. (2001) MHYT, a new integral membrane sensor domain. FEMS Microbiol. Lett., 205, 17-23.
9. Hershko,A. and Ciechanover,A. (1998) The ubiquitin system. Annu. Rev. Bbiochem., 67, 425-479.
10. Kall,L. et al. (2004) A combined transmembrane topology and signal peptide prediction method. J. Mol. Biol., 338, 1027-1036.
11. Letunic,I. et al. (2006) SMART 5:dOmains in the context of genomes and networks. Nucleic Acids Res., 34, D257-D260.
12. McGuffin,L.J. et al. (2000) The PSIPRED protein structure prediction server. Bioinformatics, 16, 404-405.
13. Mougel,C. and Zhulin,I.B. (2001) CHASE: An extracellular sensing domain common to transmembrane receptors from prokaryotes, lower eukaryotes and plants. Trends Biochem. Sci., 26, 582-584.
14. Overbeek,R. et al. (1999) The use of gene clusters to infer functional coupling. Proc. Natl Acad. Sci. USA, 96, 2896-2901.
15. Parry,G. and Estelle,M. (2006) Auxin receptors: A new role for F-box proteins. Curr. Opin. Cell Biol., 18, 152-156.
16. Ponting,C.P. and Aravind,L. (1997) PAS: A multifunctional domain family comes to light. Curr. Biol., 7, R674-R677.
17. Shu,C.J. et al. (2003) The NIT domain: A predicted nitrate-responsive module in bacterial sensory receptors. Trends Biochem. Sci., 28, 121-124.
18. Taylor,B.L. and Zhulin,I.B. (1999) PAS domains: Internal sensors of oxygen, redox potential, and light. Microbiol. Mol. Biol. Rev., 63, 479-506.
19. Thompson,J.D. et al. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res., 25, 4876-4882.
20. Ulrich,L.E. et al. (2005) One-component systems dominate signal transduction in prokaryotes. Trends Microbiol., 13, 52-56.
21. Ulrich,L.E. and Zhulin,I.B. (2005) Four-helix bundle: A ubiquitous sensory module in prokaryotic signal transduction. Bioinformatics, 21 (Suppl. 3), iii45-iii48.
22. Ulrich,L.E. and Zhulin,I.B. (2007) MiST: A microbial signal transduction database. Nucleic Acids Res, 35, D386-D390.
23. Zhulin,I.B. et al. (1997) PAS domain S-boxes in Archaea, Bacteria and sensors for oxygen and redox. Trends Biochem. Sci, 22, 331-333.
24. Zhulin,I.B. et al. (2003) Common extracellular sensory domains in transmembrane receptors for diverse signal transduction pathways in bacteria and archaea. J. Bacteriol, 185, 285-294.