Interdomain linkers of homologous response regulators determine their mechanism of action

Journal of Bacteriology

Volumn 185, Issue 1, 2003, Pages 317-324

  Walthers, Don ^a   Tran, Van K ^a   Kenney, Linda J ^a  

^a OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

REGULATOR PROTEIN; RNA POLYMERASE;

AMINO TERMINAL SEQUENCE; BACTERIAL GENETICS; CARBOXY TERMINAL SEQUENCE; CHIMERA; CONFERENCE PAPER; DNA BINDING; GENE CONTROL; GENE EXPRESSION REGULATION; NONHUMAN; PHOSPHORYLATION; PRIORITY JOURNAL; REGULATOR GENE;

BACTERIAL OUTER MEMBRANE PROTEINS; BACTERIAL PROTEINS; DNA; DNA-BINDING PROTEINS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; MULTIENZYME COMPLEXES; PHOSPHORYLATION; PROTEIN CONFORMATION; RECOMBINANT FUSION PROTEINS; TRANS-ACTIVATION (GENETICS); TRANS-ACTIVATORS;

BACTERIA (MICROORGANISMS);

EID: 0037216806     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.185.1.317-324.2003     Document Type: Conference Paper

References (66)

1. Aiba, H., T. Mizuno, and S. Mizushima. 1989. Transfer of phosphoryl group between two regulatory proteins involved in osmoregulatory expression of the ompF and ompC genes in Escherichia coli. J. Biol. Chem. 264:8563-8567.
2. Aiba, H., F. Nakasai, S. Mizushima, and T. Mizuno. 1989. Phosphorylation of a bacterial activator protein, OmpR, by a protein kinase, EnvZ, results in stimulation of its DNA-binding ability. J. Biochem. (Tokyo) 106:5-7.
3. Allen, M. P., K. B. Zumbrennen, and W. R. McCleary. 2001. Genetic evidence that the α5 helix of the receiver domain of PhoB is involved in interdomain interactions. J. Bacteriol. 183:2204-2211.
4. Alphen, W. V., and B. Lugtenberg. 1977. Influence of osmolarity of the growth medium on the outer membrane protein pattern of Escherichia coli. J. Bacteriol. 131:623-630.
5. Ames, S. K., N. Frankema, and L. J. Kenney. 1999. C-terminal DNA binding stimulates N-terminal phosphorylation of the outer membrane protein regulator OmpR from Escherichia coli. Proc. Natl. Acad. Sci. USA 96:11792-11797.
6. Brennan, R. G. 1993. The winged-helix DNA-binding motif: Another helix-turn-helix takeoff. Cell 74:773-776.
7. Brissette, R. E., K. Tsung, and M. Inouye. 1992. Mutations in a central highly conserved non-DNA-binding region of OmpR, an Escherichia coli transcriptional activator, influence its DNA-binding ability. J. Bacteriol. 174:4907-4912.
8. Cervin, M. A., and G. B. Spiegelman. 1999. The SpoOA sof mutations reveal regions of the regulatory domain that interact with a sensor kinase and RNA polymerase. Mol. Microbiol. 31:597-607.
9. Datsenko, K. A., and B. L. Wanner. 2000. One-step inactivation of chromosomal genes in Escherichia coli. K-12 using PCR products. Proc. Natl. Acad. Sci. USA 97:6640-6645.
10. Delgado, J., S. Forst, S. Harlocker, and M. Inouye. 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. Mol. Microbiol. 10:1037-1047.
11. Ellison, D. W., and W. R. McCleary. 2000. The unphosphorylated receiver domain of PhoB silences the activity of its output domain. J. Bacteriol. 182:6592-6597.
12. Forst, S., D. Comeau, S. Norioka, and M. Inouye. 1987. Localization and membrane topology of EnvZ, a protein involved in osmoregulation of OmpF and OmpC in Escherichia coli. J. Biol. Chem. 262:16433-16438.
13. Forst, S., J. Delgado, and M. Inouye. 1989. Phosphorylation of OmpR by the osmosensor EnvZ modulates expression of the ompF and ompC genes in Escherichia coli. Proc. Natl. Acad. Sci. USA 86:6052-6056.
14. Forst, S. A., J. Delgado, and M. Inouye. 1989. DNA-binding properties of the transcription activator (OmpR) for the upstream sequences of ompF in Escherichia coli are altered by envZ mutations and medium osmolarity. J. Bacteriol. 171:2949-2955.
15. Hall, M. N., and T. J. Silhavy. 1981. Genetic analysis of the ompB locus in Escherichia coli K-12. J. Mol. Biol. 151:1-15.
16. Head, C. G., A. Tardy, and L. J. Kenney. 1998. Relative binding affinities of OmpR and OmpR-phosphate at the ompF and ompC regulatory sites. J. Mol. Biol. 281:857-870.
17. Huang, K. J., and M. M. Igo. 1996. Identification of the bases in the ompF regulatory region, which interact with the transcription factor OmpR. J. Mol. Biol. 262:615-628.
18. Huang, K. J., J. L. Schieberl, and M. M. Igo. 1994. A distant upstream site involved in the negative regulation of the Escherichia coli ompF gene. J. Bacteriol. 176:1309-1315.
19. Igarashi, K., A. Hanamura, K. Makino, H. Aiba, T. Mizuno, A. Nakata, and A. Ishihama. 1991. Functional map of the α subunit of Escherichia coli RNA polymerase: two modes of transcription activation by positive factors. Proc. Natl. Acad. Sci. USA 88:8958-8962.
20. Igo, M. M., and T. J. Silhavy. 1988. EnvZ, a transmembrane environmental sensor of Escherichia coli K-12, is phosphorylated in vitro. J. Bacteriol. 170:5971-5973.
21. Igo, M. M., A. J. Ninfa, J. B. Stock, and T. J. Silhavy. 1989. Phosphorylation and dephosphorylation of a bacterial transcriptional activator by a transmembrane receptor. Genes Dev. 3:1725-1734.
22. Igo, M. M., A. J. Ninfa, and T. J. Silhavy. 1989. A bacterial environmental sensor that functions as a protein kinase and stimulates transcriptional activation. Genes Dev. 3:598-605.
23. Itou, H., and I. Tanaka. 2001. The OmpR-family of proteins: Insight into the tertiary structure and functions of two-component regulator proteins. J. Biochem. (Tokyo) 129:343-350.
24. Kanamaru, K., H. Aiba, and T. Mizuno. 1990. Transmembrane signal transduction and osmoregulation in Escherichia coli: I. Analysis by site-directed mutagenesis of the amino acid residues involved in phosphotransfer between the two regulatory components, EnvZ and OmpR. J. Biochem. (Tokyo) 108:483-487.
25. Kato, M., H. Aiba, S. Tate, Y. Nishimura, and T. Mizuno. 1989. Location of phosphorylation site and DNA-binding site of a positive regulator, OmpR, involved in activation of the osmoregulatory genes of Escherichia coli. FEBS Lett. 249:168-172.
26. Kenney, L. J. 2002. Structure/function relationships in OmpR and other winged-helix transcription factors. Curr. Opin. Microbiol. 5:135-141.
27. Kenney, L. J., M. D. Bauer, and T. J. Silhavy. 1995. Phosphorylation-dependent conformational changes in OmpR, an osmoregulatory DNA-binding protein of Escherichia coli. Proc. Natl. Acad. Sci. USA 92:8866-8870.
28. Kenney, L. J. 1997. Kinase activity of EnvZ, an osmoregulatory signal transducing protein of Escherichia coli. Arch. Biochem. Biophys. 346:303-311.
29. Kim, S. K., K. Makino, M. Amemura, A. Nakata, and H. Shinagawa. 1995. Mutational analysis of the role of the first helix of region 4.2 of the σ70 subunit of Escherichia coli RNA polymerase in transcriptional activation by activator protein PhoB. Mol. Gen. Genet. 248:1-8.
30. Kim, S. K., M. R. Wilmes-Riesenberg, and B. L. Wanner. 1996. Involvement of the sensor kinase EnvZ in the in vivo activation of the response-regulator PhoB by acetyl phosphate. Mol. Microbiol. 22:135-147.
31. Lukat, G. S., B. H. Lee, J. M. Mottonen, A. M. Stock, and J. B. Stock. 1991, Roles of the highly conserved aspartate and lysine residues in the response regulator of bacterial chemotaxis. J. Biol. Chem. 266:8348-8354.
32. Maeda, S., and T. Mizuno. 1990. Evidence for multiple OmpR-binding sites in the upstream activation sequence of the ompC promoter in Escherichia coli: A single OmpR-binding site is capable of activating the promoter. J. Bacteriol. 172:501-503.
33. Makino, K., H. Shinagawa, M. Amemura, S. Kimura, A. Nakata, and A. Ishihama. 1988. Regulation of the phosphate regulon of Escherichia coli. Activation of pstS transcription by PhoB protein in vitro. J. Mol. Biol. 203:85-95.
34. Makino, K., H. Shinagawa, M. Amemura, T. Kawamoto, M. Yamada, and A. Nakata. 1989. Signal transduction in the phosphate regulon of Escherichia coli involves phosphotransfer between PhoR and PhoB proteins. J. Mol. Biol. 210:551-559.
35. Makino, K., M. Amemura, S. K. Kim, A. Nakata, and H. Shinagawa. 1993. Role of the σ70 subunit of RNA polymerase in transcriptional activation by activator protein PhoB in Escherichia coli. Genes Dev. 7:149-160.
36. Makino, K., M. Amemura, T. Kawamoto, S. Kimura, H. Shinagawa, A. Nakata, and M. Suzuki. 1996. DNA binding of PhoB and its interaction with RNA polymerase. J. Mol. Biol. 259:15-26.
37. Makino, K., H. Shinagawa, and A. Nakata. 1985. Regulation of the phosphate regulon of Escherichia coli K-12: Regulation and role of the regulatory gene phoR. J. Mol. Biol. 184:231-240.
38. Martinez-Hackert, E., and A. M. Stock. 1997. Structural relationships in the OmpR family of winged-helix transcription factors. J. Mol. Biol. 269:301-312.
39. Martinez-Hackert, E., and A. M. Stock. 1997. The DNA-binding domain of OmpR: Crystal structures of a winged helix transcription factor. Structure 5:109-124.
40. Mattison, K., R. Oropeza, N. Byers, and L. J. Kenney. 2002. A phosphorylation site mutant of OmpR reveals different binding conformations at ompF and ompC. J. Mol. Biol. 315:497-511.
41. Mattison, K., R. Oropeza, and L. J. Kenney. 2002. The linker region plays an important role in the inter-domain communication of the response regulator OmpR. J. Biol. Chem. 277:32714-32721.
42. Mayer, M. P. 1995. A new set of useful cloning and expression vectors derived from pBlueScript. Gene 163:41-46.
43. Mizuno, T. 1997. Compilation of all genes encoding two-component phosphotransfer signal transducers in the genome of Escherichia coli. DNA Res. 4:161-168.
44. Nakashima, K., K. Kanamaru, H. Aiba, and T. Mizuno. 1991. Signal transduction and osmoregulation in Escherichia coli. A novel type of mutation in the phosphorylation domain of the activator protein, OmpR, results in a defect in its phosphorylation-dependent DNA binding. J. Biol. Chem. 266:10775-10780.
45. Okamura, H., S. Hanaoka, A. Nagadoi, K. Makino, and Y. Nishimura. 2000. Structural comparison of the PhoB and OmpR DNA-binding/transactivation domains and the arrangement of PhoB molecules on the phosphate box. J. Mol. Biol. 295:1225-1236.
46. Pratt, L. A., and T. J. Silhavy. 1994. OmpR mutants specifically defective for transcriptional activation. J. Mol. Biol. 243:579-594.
47. Rampersaud, A., S. L. Harlocker, and M. Inouye. 1994. The OmpR protein of Escherichia coli binds to sites in the ompF promoter region in a hierarchical manner determined by its degree of phosphorylation. J. Biol. Chem. 269:12559-12566.
48. Russo, F. D., and T. J. Silhavy. 1991. EnvZ controls the concentration of phosphorylated OmpR to mediate osmoregulation of the porin genes. J. Mol. Biol. 222:567-580.
49. Russo, F. D., J. M. Slauch, and T. J. Silhavy. 1993. Mutations that affect separate functions of OmpR the phosphorylated regulator of porin transcription in Escherichia coli. J. Mol. Biol. 231:261-273.
50. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular Cloning: A Laboratory Manual, 2nd Ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
51. Shinagawa, H., K. Makino, and A. Nakata. 1983. Regulation of the pho regulon in Escherichia coli K-12. Genetic and physiological regulation of the positive regulatory gene phoB. J. Mol. Biol. 168:477-488.
52. Slauch, J. M., F. D. Russo, and T. J. Silhavy. 1991. Suppressor mutations in rpoA suggest that OmpR controls transcription by direct interaction with the alpha subunit of RNA polymerase. J. Bacteriol. 173:7501-7510.
53. Slauch, J. M., and T. J. Silhavy. 1989. Genetic analysis of the switch that controls porin gene expression in Escherichia coli K-12. J. Mol. Biol. 210:281-292.
54. Slauch, J. M., and T. J. Silhavy. 1991. cis-acting ompF mutations that result in OmpR-dependent constitutive expression. J. Bacteriol. 173:4039-4048.
55. Sola, M., F. X. Gomis-Ruth, L. Serrano, A. Gonzalez, and M. Coll. 1999. Three-dimensional crystal structure of the transcription factor PhoB receiver domain. J. Mol. Biol. 285:675-687.
56. Stock, A. M., V. L. Robinson, and P. N. Goudreau. 2000. Two-component signal transduction. Annu. Rev. Biochem. 69:183-215.
57. Tate, S., M. Kato, Y. Nishimura, Y. Arata, and T. Mizuno. 1988. Location of DNA-binding segment of a positive regulator, OmpR, involved in activation of the ompF and ompC genes of Escherichia coli. FEBS Lett. 242:27-30.
58. Tran, V. K., R. Oropeza, and L. J. Kenney. 2000. A single amino acid substitution in the C terminus of OmpR alters DNA recognition and phosphorylation. J. Mol. Biol. 299:1257-1270.
59. Tsuzuki, M., K. Ishige, and T. Mizuno. 1995. Phosphotransfer circuitry of the putative multi-signal transducer, ArcB, of Escherichia coli: In vitro studies with mutants. Mol. Microbiol. 18:953-962.
60. Tsuzuki, M., H. Aiba, and T. Mizuno. 1994. Gene activation by the Escherichia coli positive regulator, OmpR. Phosphorylation-independent mechanism of activation by an OmpR mutant. J. Mol. Biol. 242:607-613.
61. Utsumi, R., S. Katayama, M. Taniguchi, T. Horie, M. Ikeda, S. Igaki, H. Nakagawa, A. Miwa, H. Tanabe, and M. Noda. 1994. Newly identified genes involved in the signal transduction of Escherichia coli K-12. Gene 140:73-77.
62. Volz, K. 1993. Structural conservation in the CheY superfamily. Biochemistry 32:11741-11753.
63. Wanner, B. L., and P. Latterell. 1980. Mutants affected in alkaline phosphatase, expression: Evidence for multiple positive regulators of the phosphate regulon in Escherichia coli. Genetics 96:353-366.
64. Wanner, B. L. 1983. Overlapping and separate controls on the phosphate regulon in Escherichia coli K12. J. Mol. Biol. 166:283-308.
65. Wanner, B. L. 1993. Gene regulation by phosphate in enteric bacteria. J. Cell. Biochem. 51:47-54.
66. Yamada, M., K. Makino, H. Shinagawa, and A. Nakata. 1990. Regulation of the phosphate regulon of Escherichia coli: Properties of phoR deletion mutants and subcellular localization of PhoR protein. Mol. Gen. Genet. 220:366-372.