Predicting inter-species cross-talk in two-component signalling systems

PLoS ONE

Volumn 7, Issue 5, 2012, Pages

  Pawelczyk, Sonja ^a   Scott, Kathryn A ^a   Hamer, Rebecca ^a,b   Blades, Gareth ^a   Deane, Charlotte M ^a,b   Wadhams, George H ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOINFORMATICS; HOST CELL; IN VITRO STUDY; IN VIVO STUDY; MOLECULAR INTERACTION; NONHUMAN; ORGANISMS; PHOSPHOSIGNALLING PATHWAY; PREDICTION; SIGNAL TRANSDUCTION; SYNTHETIC BIOLOGY;

MODELS, GENETIC; PHOSPHORYLATION; PROTEIN KINASES; SIGNAL TRANSDUCTION;

EID: 84861324027     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0037737     Document Type: Article

References (48)

1. Bashor CJ, Horwitz AA, Peisajovich SG, Lim WA, (2010) Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems. Annual Review of Biophysics 39: 515-537.
2. Lim WA, (2010) Designing customized cell signalling circuits. Nat Rev Mol Cell Biol 11: 393-403.
3. Jacob F, Monod J, (1961) Genetic regulatory mechanisms in the synthesis of proteins. Journal of Molecular Biology 3: 318-356.
4. Jacob F, Monod J, (1961) On Regulation of gene activity. Cold Spring Harbor Symposia on Quantitative Biology 26 193
5. Bashor CJ, Helman NC, Yan S, Lim WA, (2008) Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics. Science 319: 1539-1543.
6. Ninfa AJ, Selinsky S, Perry N, Atkins S, Xiu Song Q, et al. (2007) Using two-component systems and other bacterial regulatory factors for the fabrication of synthetic genetic devices. In: Melvin I. Simon BRC, Alexandrine C, editors. Methods in Enzymology: Academic Press pp. 488-512.
7. McClean MN, Mody A, Broach JR, Ramanathan S, (2007) Cross-talk and decision making in MAP kinase pathways. Nat Genet 39: 409-414.
8. Haruo S, (2010) Regulation of cross-talk in yeast MAPK signaling pathways. Current Opinion in Microbiology 13: 677-683.
9. Fisher SL, Jiang W, Wanner BL, Walsh CT, (1995) Cross-talk between the histidine protein kinase VanS and the response regulator PhoB. Journal of Biological Chemistry 270: 23143-23149.
10. Antunes MS, Morey KJ, Tewari-Singh N, Bowen TA, Smith JJ, et al. (2009) Engineering key components in a synthetic eukaryotic signal transduction pathway. Mol Syst Biol 5.
11. Wuichet K, Cantwell BJ, Zhulin IB, (2010) Evolution and phyletic distribution of two-component signal transduction systems. Current Opinion in Microbiology 13: 219-225.
12. Laub MT, Goulian M, (2007) Specificity in two-component signal transduction pathways. Annual Review of Genetics 41: 121-145.
13. Szurmant H, Hoch JA, (2010) Interaction fidelity in two-component signaling. Current Opinion in Microbiology 13: 190-197.
14. Mattison K, Oropeza R, Byers N, Kenney LJ, (2002) A phosphorylation site mutant of OmpR reveals different binding conformations at ompF and ompC. Journal of Molecular Biology 315: 497-511.
15. Verhamme DT, Arents JC, Postma PW, Crielaard W, Hellingwerf KJ, (2002) Investigation of in vivo cross-talk between key two-component systems of Escherichia coli. Microbiology 148: 69-78.
16. Skerker JMP, Melanie S, Perchuk BS, Biondi EG, Laub MT, (2005) T Two-component signal transduction ppathways regulating growth and cell cycle progression in a bacterium: A system-level analysis. PLoS Biol 3: e334.
17. Gao R, Stock AM, (2009) Biological insights from structures of two-component proteins. Annual Review of Microbiology 63: 133-154.
18. McCleary WR, Stock JB, (1994) Acetyl phosphate and the activation of two-component response regulators. Journal of Biological Chemistry 269: 31567-31572.
19. Skerker JM, Perchuk BS, Siryaporn A, Lubin EA, Ashenberg O, et al. (2008) Rewiring the specificity of two-component signal transduction systems. Cell 133: 1043-1054.
20. Stock JB NA, Stock AM, (1989) Protein phosphorylation and regulation of adaptive responses in bacteria. Microbiol Rev 53: 450-490.
21. Forst SA, Roberts DL, (1994) Signal transduction by the EnvZ-OmpR phosphotransfer system in bacteria. Research in Microbiology 145: 363-373.
22. Russo FD, Silhavy TJ, (1991) EnvZ controls the concentration of phosphorylated OmpR to mediate osmoregulation of the porin genes. Journal of Molecular Biology 222: 567-580.
23. Utsumi R, Brissette R, Rampersaud A, Forst S, Oosawa K, et al. (1989) Activation of bacterial porin gene expression by a chimeric signal transducer in response to aspartate. Science 245: 1246-1249.
24. Jin T, Inouye M, (1993) Ligand binding to the receptor domain regulates the ratio of kinase to phosphatase activities of the signaling domain of the hybrid Escherichia coli transmembrane receptor, Taz1. Journal of Molecular Biology 232: 484-492.
25. Yoshida T, Phadtare S, Inouye M, (2007) The design and development of Tar/EnvZ chimeric receptors. In: Melvin I. Simon BRC, Alexandrine C, editors. Methods in Enzymology: Academic Press pp. 166-183.
26. Finn RD, Mistry J, Tate J, Coggill P, Heger A, et al. (2010) The Pfam protein families database. Nucleic Acids Research 38: D211-D222.
27. Enright AJ, Van Dongen S, Ouzounis CA, (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Research 30: 1575-1584.
28. Hamer R, Chen P-Y, Armitage J, Reinert G, Deane C, (2010) Deciphering chemotaxis pathways using cross species comparisons. BMC Systems Biology 4: 3.
29. Ulrich LE, Zhulin IB, (2010) The MiST2 database: a comprehensive genomics resource on microbial signal transduction. Nucl Acids Res 38: D401-407.
30. Ohta N, Newton A, (2003) The core dimerization domains of histidine kinases contain recognition specificity for the cognate response regulator. Journal of Bacteriology 185: 4424-4431.
31. Porter SL, Wilkinson DA, Byles ED, Wadhams GH, Taylor S, et al. (2011) Genome sequence of Rhodobacter sphaeroides strain WS8N. The Journal of Bacteriology pp. JB.05257-05211.
32. Tatusova TA, Madden TL, (1999) BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 174: 247-250.
33. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. Journal of Molecular Biology 215: 403-410.
34. Yoshida T, Qin L, Inouye M, (2002) Formation of the stoichiometric complex of EnvZ, a histidine kinase, with its response regulator, OmpR. Molecular Microbiology 46: 1273-1282.
35. Shah DSH, Porter SL, Harris DC, Wadhams GH, Hamblin PA, et al. (2000) Identification of a fourth cheY gene in Rhodobacter sphaeroides and interspecies interaction within the bacterial chemotaxis signal transduction pathway. Molecular Microbiology 35: 101-112.
36. Ind AC, Porter SL, Brown MT, Byles ED, de Beyer JA, et al. (2009) Inducible-expression plasmid for Rhodobacter sphaeroides and Paracoccus denitrificans. Appl Environ Microbiol 75: 6613-6615.
37. Delgado J, Forst S, Harlocker S, Inouye M, (1993) Identification of a phosphorylation site and functional analysis of conserved aspartic acid residues of OmpR, a transcriptional activator for ompF and ompC in Escherichia coli. Molecular Microbiology 10: 1037-1047.
38. Wadhams GH, Martin AC, Porter SL, Maddock JR, Mantotta JC, et al. (2002) TlpC, a novel chemotaxis protein in Rhodobacter sphaeroides, localizes to a discrete region in the cytoplasm. Molecular Microbiology 46: 1211-1221.
39. Pratt L, STJ, (1995) Two-component signal transduction. eds Hoch J, Silhavy TJ American Society for Microbiology Press, Washington, D. C pp. 105-107.
40. Eddy SR, (1998) Profile hidden Markov models. Bioinformatics 14: 755-763.
41. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25: 3389-3402.
42. Bachman B, (1972) Pedigrees of some mutant strains of Escherichia coli K-12. Bacteriol Rev 36: 252-557.
43. Schäfer A TA, Jäger W, Kalinowski J, Thierbach G, Pühler A, (1994) Small mobilizable multipurpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19- Selection of defined deletions in the chromosome of Corynebacterium glutamicum. Gene 145: 69-73.
44. Penfold RJ, Pemberton JM, (1992) An improved suicide vector for construction of chromosomal insertion mutations in bacteria. Gene 118: 145-146.
45. Martin AC, Wadhams GH, Armitage JP, (2001) The roles of the multiple CheW and CheA homologues in chemotaxis and in chemoreceptor localization in Rhodobacter sphaeroides. Molecular Microbiology 40: 1261-1272.
46. Porter SL, Wadhams GH, Armitage JP, (2008) Rhodobacter sphaeroides: complexity in chemotactic signalling. Trends in Microbiology 16: 251-260.
47. Scott KA, Porter SL, Bagg EAL, Hamer R, Hill JL, et al. (2010) Specificity of localization and phosphotransfer in the CheA proteins of Rhodobacter sphaeroides. Molecular Microbiology 76: 318-330.
48. Porter SL, Armitage JP, (2002) Phosphotransfer in Rhodobacter sphaeroides chemotaxis. Journal of Molecular Biology 324: 35-45.