Functional classification of cNMP-binding proteins and nucleotide cyclases with implications for novel regulatory pathways in Mycobacterium tuberculosis

Genome Research

Volumn 10, Issue 2, 2000, Pages 204-219

  McCue, Lee Ann ^a   McDonough, Kathleen A ^a   Lawrence, Charles E ^a  

^a WADSWORTH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENYLATE CYCLASE; BACTERIAL ENZYME; BACTERIAL PROTEIN; CARRIER PROTEIN; CYCLIC AMP BINDING PROTEIN; CYCLIC NUCLEOTIDE; CYCLIC NUCLEOTIDE BINDING PROTEIN; CYCLIC NUCLEOTIDE DEPENDENT PROTEIN KINASE; ESTERASE; GUANYLATE CYCLASE; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENE; BAYES THEOREM; CYANOBACTERIUM; GENOME; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS;

ADENYLATE CYCLASE; AMINO ACID SEQUENCE; CARRIER PROTEINS; COMPUTATIONAL BIOLOGY; GUANYLATE CYCLASE; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM TUBERCULOSIS; NUCLEOTIDES, CYCLIC; PHOSPHORUS-OXYGEN LYASES; PHYLOGENY; SEQUENCE ALIGNMENT;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA; MYCOBACTERIUM; MYCOBACTERIUM TUBERCULOSIS; PROKARYOTA; SYNECHOCYSTIS;

EID: 0034005701     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.10.2.204     Document Type: Article

References (44)

1. Bârzu, O. and A. Danchin. 1994. Adenylyl cyclases: A heterogeneous class of ATP-utilizing enzymes. Prog. Nucleic Acid Res. Mol. Biol. 49: 241-283.
2. Beavo, J.A. 1995. Cyclic nucleotide phosphodiesterases: Functional implications of multiple isoforms. Physiol. Rev. 75: 725-748.
3. Botsford, J.L. and J.G. Harman. 1992. Cyclic AMP in prokaryotes. Microbiol. Rev. 56: 100-122.
4. Charbonneau, H., R.K. Prusti, H. LeTrong, W.K. Sonnenburg, P.J. Mullaney, K.A. Walsh, and J.A. Beavo. 1990. Identification of a noncatalytic cGMP-binding domain conserved in both the cGMP-stimulated and photoreceptor cyclic nucleotide phosphodiesterases. Proc. Natl. Acad. Sci. 87: 288-292.
5. Cole, S.T., R. Brosch, J. Parkhill, T. Garnier, C. Churcher, D. Harris, S.V. Gordon, K. Eiglmeier, S. Gas, C.E. Barry 3rd et al. 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393: 537-544.
6. Cotta, M.A., T.R. Whitehead, and M.B. Wheeler. 1998. Identification of a novel adenylate cyclase in the ruminai anaerobe, Prevotella ruminicola D31d. FEMS Microbiol. Lett. 164: 257-260.
7. Coudart-Cavalli, M.P., O. Sismeiro, and A. Danchin. 1997. Bifunctional structure of two adenylyl cyclases from the myxobacterium Stigmatella aurantiaca. Biochimie 79: 757-767.
8. Deckers, H.M. and G. Voordouw. 1996. The dcr gene family of Desulfovibrio: Implications from the sequence of dcrH and phylogenetic comparison with other mcp genes. Antonie Van Leeuwenhoek 70: 21-29.
9. Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle.
10. Finn, J.T., M.E. Grunwald, and K.W. Yau. 1996. Cyclic nucleotide-gated ion channels: An extended family with diverse functions. Annu. Rev. Physiol. 58: 395-426.
11. Firtel, R.A. 1996. Interacting signaling pathways controlling multicellular development in Dictyostelium. Curr. Opin. Genet. Dev. 6: 545-554.
12. Fischer, H.M. 1994. Genetic regulation of nitrogen fixation in rhizobia. Microbiol. Rev. 58: 352-386.
13. Francis, S.H. and J.D. Corbin. 1994. Structure and function of cyclic nucleotide-dependent protein kinases. Annu. Rev. Physiol. 56: 237-272.
14. Grant, C.E. and A. Tsang. 1990. Cloning and characterization of cDNAs encoding a novel cyclic AMP-binding protein in Dictyostelium discoideum. Gene 96: 213-218.
15. Gross, M.K., D.C. Au, A.L. Smith, and D.R. Storm. 1992. Targeted mutations that ablate either the adenylate cyclase or hemolysin function of the bifunctional cyaA toxin of Bordetella pertussis abolish virulence. Proc. Natl. Acad. Sci. 89: 4898-4902.
16. Hobbs, A.J. 1997. Soluble guanylate cyclase: The forgotten sibling. Trends Pharmacol. Sci. 18: 484-491.
17. Hughes, P., A. Landoulsi, and M. Kohiyama. 1988. A novel role for cAMP in the control of the activity of the E. coli chromosome replication initiator protein, DnaA. Cell 55: 343-350.
18. Katayama, M. and M. Ohmori. 1997. Isolation and characterization of multiple adenylate cyclase genes from the cyanobacterium Anabaena sp. strain PCC 7120. J. Bacteriol. 179: 3588-3593.
19. Kawasaki, H., G.M. Springett, N. Mochizuki, S. Toki, M. Nakaya, M. Matsuda, D.E. Housman, and A.M. Graybiel. 1998. A family of cAMP-binding proteins that directly activate Rap1. Science 282: 2275-2279.
20. Kolb, A., S. Busby, H. Buc, S. Garges, and S. Adhya. 1993. Transcriptional regulation by cAMP and its receptor protein. Annu. Rev. Biochem. 62: 749-795.
21. Liu, J.S., A.F. Neuwald, and C.E. Lawrence. 1995. Bayesian models for multiple local sequence alignment and Gibbs sampling strategies. J. Amer. Statist. Assoc. 90: 1156-1170.
22. _. 1999. Markovian structures in biological sequence alignments. J. Amer. Statist. Assoc. 94: 1-15.
23. Liu, Y., A.E. Ruoho, V.D. Rao, and J.H. Hurley. 1997. Catalytic mechanism of the adenylyl and guanylyl cyclases: Modeling and mutational analysis. Proc. Natl. Acad. Sci. 94: 13414-13419.
24. Lowrie, D.B., V.R. Aber, and P.S. Jackett. 1979. Phagosome-lysosome fusion and cyclic adenosine 3′:5′-monophosphate in macrophages infected with Mycobacterium microti, Mycobacterium bovis BCG or Mycobacterium lepraemurium. J. Gen. Microbiol. 110: 431-441.
25. Lowrie, D.B., P.S. Jackett, and N.A. Ratcliffe. 1975. Mycobacterium microti may protect itself from intracellular destruction by releasing cyclic AMP into phagosomes. Nature 254: 600-602.
26. Masure, H.R. 1993. The adenylate cyclase toxin contributes to the survival of Bordetella pertussis within human macrophages. Microb. Pathog. 14: 253-260.
27. Neuwald, A.F., J.S. Liu, and C.E. Lawrence. 1995. Gibbs motif sampling: Detection of bacterial outer membrane protein repeats. Protein Sci. 4: 1618-1632.
28. Neuwald, A.F., J.S. Liu, D.J. Lipman, and C.E. Lawrence. 1997. Extracting protein alignment models from the sequence database. Nucleic Acids Res. 25: 1665-1677.
29. Qu, K., L.A. McCue, and C.E. Lawrence. 1998. Bayesian protein family classifier. ISMB 6: 131-139.
30. Schneider, T.D. and R.M. Stephens. 1990. Sequence logos: A new way to display consensus sequences. Nucleic Acids Res. 18: 6097-6100.
31. Shabb, J.B. and J.D. Corbin. 1992. Cyclic nucleotide-binding domains in proteins having diverse functions. J. Biol. Chem. 267: 5723-5726.
32. Sismeiro, O., P. Trotot, F. Biville, C. Vivares, and A. Danchin. 1998. Aeromonas hydrophila adenylyl cyclase 2: A new class of adenylyl cyclases with thermophilic properties and sequence similarities to proteins from hyperthermophilic archaebacteria. J. Bacteriol. 180: 3339-3344.
33. Sonnhammer, E.L., G. von Heijne, and A. Krogh. 1998. A hidden Markov model for predicting transmembrane helices in protein sequences. ISMB 6: 175-182.
34. Su, Y., W.R. Dostmann, F.W. Herberg, K. Durick, N.H. Xuong, L. Ten Eyck, S.S. Taylor, and K.I. Varughese. 1995. Regulatory subunit of protein kinase A: Structure of deletion mutant with cAMP binding domains. Science 269: 807-813.
35. Tang, W.J. and J.H. Hurley. 1998. Catalytic mechanism and regulation of mammalian adenylyl cyclases. Mol. Pharmacol. 54: 231-240.
36. Tang, W.J., S. Yan, and C.L. Drum. 1998. Class III adenylyl cyclases: Regulation and underlying mechanisms. Adv. Second Messenger Phosphoprotein Res. 32: 137-151.
37. sα, · GTPγS. Science 278: 1907-1916.
38. Tucker, C.L., J.H. Hurley, T.R. Miller, and J.B. Hurley. 1998. Two amino acid substitutions convert a guanylyl cyclase, RetGC-1, into an adenylyl cyclase. Proc. Natl. Acad. Sci. 95: 5993-5997.
39. Weber, I.T. and T.A. Steitz. 1987. Structure of a complex of catabolite gene activator protein and cyclic AMP refined at 2.5 Á resolution. J. Mol. Biol. 198: 311-326.
40. Wedel, B.J. and D.L. Garbers. 1997. New insights on the functions of the guanylyl cyclase receptors. FEBS Lett. 410: 29-33.
41. Yahr, T.L., A.J. Vallis, M.K. Hancock, J.T. Barbieri and D.W. Frank. 1998. ExoY, an adenylate cyclase secreted by the Pseudomonas aeruginosa type III system. Proc. Natl. Acad. Sci. 95: 13899-13904.
42. Yu, S., L. Avery, E. Baude and D.L. Garbers. 1997. Guanylyl cyclase expression in specific sensory neurons: A new family of chemosensory receptors. Proc. Natl. Acad. Sci. 94: 3384-3387.
43. Zhang, G., Y. Liu, A.E. Ruoho, and J.H. Hurley. 1997. Structure of the adenylyl cyclase catalytic core. Nature 386: 247-253.
44. Zhu, J., J.S. Liu, and C.E. Lawrence. 1998. Bayesian adaptive sequence alignment algorithms. Bioinformatics 14: 25-39.