Abstract
Several gene products, including three two-component systems, make up a signal transduction network that controls the phosphate starvation response in Bacillus subtilis. Epistasis experiments indicate that PhoP, a response regulator, is furthest downstream of the known regulators in the signaling pathway that regulates Pho regulon genes. We report the overexpression, purification, and use of PhoP in investigating its role in Pho regulon gene activation. PhoP was a substrate for both the kinase and phosphatase activities of its cognate sensor kinase, PhoR. It was not phosphorylated by acetyl phosphate. Purified phosphorylated PhoP (PhoPP) had a half-life of approximately 2.5 h, which was reduced to about 15 min by addition of the same molar amount of *PhoR (the cytoplasmic region of PhoR). ATP significantly increased phosphatase activity of *PhoR on PhoPP. In gel filtration and cross-linking studies, both PhoP and PhoPP were shown to be dimers. The dimerization domain was located within the 135 amino acids at the N terminus of PhoP. Phosphorylated or unphosphorylated PhoP bound to one of the alkaline phosphatase gene promoters, the phoB promoter. Furthermore, PhoP bound exclusively to the -18 to -73 region (relative to the transcriptional start site +1) of the phosphate starvation-inducible promoter (Pv) but not to the adjacent developmentally regulated promoter (Ps). These data corroborate the genetic data for phoB regulation and suggest that activation of phoB is via direct interaction between PhoP and the phoB promoter. Studies of the phosphorylation, oligomerization, and DNA binding activity of the PhoP protein demonstrate that its N-terminal phosphorylation and dimerization domain and its C-terminal DNA binding domain function independently of one another, distinguishing PhoP from other response regulators, such as PhoB (Escherichia coli) and NtrC.
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- Asayama M., Yamamoto A., Kobayashi Y. Dimer form of phosphorylated Spo0A, a transcriptional regulator, stimulates the spo0F transcription at the initiation of sporulation in Bacillus subtilis. J Mol Biol. 1995 Jun 30;250(1):11–23. doi: 10.1006/jmbi.1995.0354. [DOI] [PubMed] [Google Scholar]
- Baikalov I., Schröder I., Kaczor-Grzeskowiak M., Grzeskowiak K., Gunsalus R. P., Dickerson R. E. Structure of the Escherichia coli response regulator NarL. Biochemistry. 1996 Aug 27;35(34):11053–11061. doi: 10.1021/bi960919o. [DOI] [PubMed] [Google Scholar]
- Birkey S. M., Sun G., Piggot P. J., Hulett F. M. A pho regulon promoter induced under sporulation conditions. Gene. 1994 Sep 15;147(1):95–100. doi: 10.1016/0378-1119(94)90045-0. [DOI] [PubMed] [Google Scholar]
- Bookstein C., Edwards C. W., Kapp N. V., Hulett F. M. The Bacillus subtilis 168 alkaline phosphatase III gene: impact of a phoAIII mutation on total alkaline phosphatase synthesis. J Bacteriol. 1990 Jul;172(7):3730–3737. doi: 10.1128/jb.172.7.3730-3737.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Boucher P. E., Murakami K., Ishihama A., Stibitz S. Nature of DNA binding and RNA polymerase interaction of the Bordetella pertussis BvgA transcriptional activator at the fha promoter. J Bacteriol. 1997 Mar;179(5):1755–1763. doi: 10.1128/jb.179.5.1755-1763.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bourret R. B., Borkovich K. A., Simon M. I. Signal transduction pathways involving protein phosphorylation in prokaryotes. Annu Rev Biochem. 1991;60:401–441. doi: 10.1146/annurev.bi.60.070191.002153. [DOI] [PubMed] [Google Scholar]
- Bradford M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976 May 7;72:248–254. doi: 10.1016/0003-2697(76)90527-3. [DOI] [PubMed] [Google Scholar]
- Chesnut R. S., Bookstein C., Hulett F. M. Separate promoters direct expression of phoAIII, a member of the Bacillus subtilis alkaline phosphatase multigene family, during phosphate starvation and sporulation. Mol Microbiol. 1991 Sep;5(9):2181–2190. doi: 10.1111/j.1365-2958.1991.tb02148.x. [DOI] [PubMed] [Google Scholar]
- Dahl J. L., Wei B. Y., Kadner R. J. Protein phosphorylation affects binding of the Escherichia coli transcription activator UhpA to the uhpT promoter. J Biol Chem. 1997 Jan 17;272(3):1910–1919. doi: 10.1074/jbc.272.3.1910. [DOI] [PubMed] [Google Scholar]
- Dutta R., Inouye M. Reverse phosphotransfer from OmpR to EnvZ in a kinase-/phosphatase+ mutant of EnvZ (EnvZ.N347D), a bifunctional signal transducer of Escherichia coli. J Biol Chem. 1996 Jan 19;271(3):1424–1429. doi: 10.1074/jbc.271.3.1424. [DOI] [PubMed] [Google Scholar]
- ENGSTROM L. Incorporation of inorganic phosphate into alkaline phosphatase from Escherichia coli. Biochim Biophys Acta. 1962 Jan 29;56:606–609. doi: 10.1016/0006-3002(62)90616-9. [DOI] [PubMed] [Google Scholar]
- Eder S., Shi L., Jensen K., Yamane K., Hulett F. M. A Bacillus subtilis secreted phosphodiesterase/alkaline phosphatase is the product of a Pho regulon gene, phoD. Microbiology. 1996 Aug;142(Pt 8):2041–2047. doi: 10.1099/13500872-142-8-2041. [DOI] [PubMed] [Google Scholar]
- Feng J., Atkinson M. R., McCleary W., Stock J. B., Wanner B. L., Ninfa A. J. Role of phosphorylated metabolic intermediates in the regulation of glutamine synthetase synthesis in Escherichia coli. J Bacteriol. 1992 Oct;174(19):6061–6070. doi: 10.1128/jb.174.19.6061-6070.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Fiedler U., Weiss V. A common switch in activation of the response regulators NtrC and PhoB: phosphorylation induces dimerization of the receiver modules. EMBO J. 1995 Aug 1;14(15):3696–3705. doi: 10.1002/j.1460-2075.1995.tb00039.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Fisher S. L., Jiang W., Wanner B. L., Walsh C. T. Cross-talk between the histidine protein kinase VanS and the response regulator PhoB. Characterization and identification of a VanS domain that inhibits activation of PhoB. J Biol Chem. 1995 Sep 29;270(39):23143–23149. doi: 10.1074/jbc.270.39.23143. [DOI] [PubMed] [Google Scholar]
- Hess J. F., Bourret R. B., Simon M. I. Histidine phosphorylation and phosphoryl group transfer in bacterial chemotaxis. Nature. 1988 Nov 10;336(6195):139–143. doi: 10.1038/336139a0. [DOI] [PubMed] [Google Scholar]
- Hiratsu K., Nakata A., Shinagawa H., Makino K. Autophosphorylation and activation of transcriptional activator PhoB of Escherichia coli by acetyl phosphate in vitro. Gene. 1995 Aug 8;161(1):7–10. doi: 10.1016/0378-1119(95)00259-9. [DOI] [PubMed] [Google Scholar]
- Hulett F. M., Bookstein C., Jensen K. Evidence for two structural genes for alkaline phosphatase in Bacillus subtilis. J Bacteriol. 1990 Feb;172(2):735–740. doi: 10.1128/jb.172.2.735-740.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hulett F. M., Jensen K. Critical roles of spo0A and spo0H in vegetative alkaline phosphatase production in Bacillus subtilis. J Bacteriol. 1988 Aug;170(8):3765–3768. doi: 10.1128/jb.170.8.3765-3768.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hulett F. M., Kim E. E., Bookstein C., Kapp N. V., Edwards C. W., Wyckoff H. W. Bacillus subtilis alkaline phosphatases III and IV. Cloning, sequencing, and comparisons of deduced amino acid sequence with Escherichia coli alkaline phosphatase three-dimensional structure. J Biol Chem. 1991 Jan 15;266(2):1077–1084. [PubMed] [Google Scholar]
- Hulett F. M., Lee J., Shi L., Sun G., Chesnut R., Sharkova E., Duggan M. F., Kapp N. Sequential action of two-component genetic switches regulates the PHO regulon in Bacillus subtilis. J Bacteriol. 1994 Mar;176(5):1348–1358. doi: 10.1128/jb.176.5.1348-1358.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hulett F. M. The signal-transduction network for Pho regulation in Bacillus subtilis. Mol Microbiol. 1996 Mar;19(5):933–939. doi: 10.1046/j.1365-2958.1996.421953.x. [DOI] [PubMed] [Google Scholar]
- Igo M. M., Ninfa A. J., Silhavy T. J. A bacterial environmental sensor that functions as a protein kinase and stimulates transcriptional activation. Genes Dev. 1989 May;3(5):598–605. doi: 10.1101/gad.3.5.598. [DOI] [PubMed] [Google Scholar]
- Kapp N. V., Edwards C. W., Chesnut R. S., Hulett F. M. The Bacillus subtilis phoAIV gene: effects of in vitro inactivation on total alkaline phosphatase production. Gene. 1990 Nov 30;96(1):95–100. doi: 10.1016/0378-1119(90)90346-s. [DOI] [PubMed] [Google Scholar]
- Keener J., Kustu S. Protein kinase and phosphoprotein phosphatase activities of nitrogen regulatory proteins NTRB and NTRC of enteric bacteria: roles of the conserved amino-terminal domain of NTRC. Proc Natl Acad Sci U S A. 1988 Jul;85(14):4976–4980. doi: 10.1073/pnas.85.14.4976. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
- Lee J. W., Hulett F. M. Nucleotide sequence of the phoP gene encoding PhoP, the response regulator of the phosphate regulon of Bacillus subtilis. Nucleic Acids Res. 1992 Nov 11;20(21):5848–5848. doi: 10.1093/nar/20.21.5848. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lois A. F., Weinstein M., Ditta G. S., Helinski D. R. Autophosphorylation and phosphatase activities of the oxygen-sensing protein FixL of Rhizobium meliloti are coordinately regulated by oxygen. J Biol Chem. 1993 Feb 25;268(6):4370–4375. [PubMed] [Google Scholar]
- Lukat G. S., McCleary W. R., Stock A. M., Stock J. B. Phosphorylation of bacterial response regulator proteins by low molecular weight phospho-donors. Proc Natl Acad Sci U S A. 1992 Jan 15;89(2):718–722. doi: 10.1073/pnas.89.2.718. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Makino K., Amemura M., Kawamoto T., Kimura S., Shinagawa H., Nakata A., Suzuki M. DNA binding of PhoB and its interaction with RNA polymerase. J Mol Biol. 1996 May 31;259(1):15–26. doi: 10.1006/jmbi.1996.0298. [DOI] [PubMed] [Google Scholar]
- Makino K., Shinagawa H., Amemura M., Kawamoto T., Yamada M., Nakata A. Signal transduction in the phosphate regulon of Escherichia coli involves phosphotransfer between PhoR and PhoB proteins. J Mol Biol. 1989 Dec 5;210(3):551–559. doi: 10.1016/0022-2836(89)90131-9. [DOI] [PubMed] [Google Scholar]
- Makino K., Shinagawa H., Amemura M., Kimura S., Nakata A., Ishihama A. Regulation of the phosphate regulon of Escherichia coli. Activation of pstS transcription by PhoB protein in vitro. J Mol Biol. 1988 Sep 5;203(1):85–95. doi: 10.1016/0022-2836(88)90093-9. [DOI] [PubMed] [Google Scholar]
- Manzara T., Carrasco P., Gruissem W. Developmental and organ-specific changes in promoter DNA-protein interactions in the tomato rbcS gene family. Plant Cell. 1991 Dec;3(12):1305–1316. doi: 10.1105/tpc.3.12.1305. [DOI] [PMC free article] [PubMed] [Google Scholar]
- McCleary W. R., Stock J. B., Ninfa A. J. Is acetyl phosphate a global signal in Escherichia coli? J Bacteriol. 1993 May;175(10):2793–2798. doi: 10.1128/jb.175.10.2793-2798.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
- McCleary W. R. The activation of PhoB by acetylphosphate. Mol Microbiol. 1996 Jun;20(6):1155–1163. doi: 10.1111/j.1365-2958.1996.tb02636.x. [DOI] [PubMed] [Google Scholar]
- Mizuno T., Mizushima S. Isolation and characterization of deletion mutants of ompR and envZ, regulatory genes for expression of the outer membrane proteins OmpC and OmpF in Escherichia coli. J Biochem. 1987 Feb;101(2):387–396. doi: 10.1093/oxfordjournals.jbchem.a121923. [DOI] [PubMed] [Google Scholar]
- Nakashima K., Kanamaru K., Aiba H., Mizuno T. 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. 1991 Jun 15;266(17):10775–10780. [PubMed] [Google Scholar]
- Ninfa A. J., Magasanik B. Covalent modification of the glnG product, NRI, by the glnL product, NRII, regulates the transcription of the glnALG operon in Escherichia coli. Proc Natl Acad Sci U S A. 1986 Aug;83(16):5909–5913. doi: 10.1073/pnas.83.16.5909. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ohlsen K. L., Grimsley J. K., Hoch J. A. Deactivation of the sporulation transcription factor Spo0A by the Spo0E protein phosphatase. Proc Natl Acad Sci U S A. 1994 Mar 1;91(5):1756–1760. doi: 10.1073/pnas.91.5.1756. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Perego M., Hanstein C., Welsh K. M., Djavakhishvili T., Glaser P., Hoch J. A. Multiple protein-aspartate phosphatases provide a mechanism for the integration of diverse signals in the control of development in B. subtilis. Cell. 1994 Dec 16;79(6):1047–1055. doi: 10.1016/0092-8674(94)90035-3. [DOI] [PubMed] [Google Scholar]
- Qi Y., Kobayashi Y., Hulett F. M. The pst operon of Bacillus subtilis has a phosphate-regulated promoter and is involved in phosphate transport but not in regulation of the pho regulon. J Bacteriol. 1997 Apr;179(8):2534–2539. doi: 10.1128/jb.179.8.2534-2539.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Roggiani M., Dubnau D. ComA, a phosphorylated response regulator protein of Bacillus subtilis, binds to the promoter region of srfA. J Bacteriol. 1993 May;175(10):3182–3187. doi: 10.1128/jb.175.10.3182-3187.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Russo F. D., Silhavy T. J. EnvZ controls the concentration of phosphorylated OmpR to mediate osmoregulation of the porin genes. J Mol Biol. 1991 Dec 5;222(3):567–580. doi: 10.1016/0022-2836(91)90497-t. [DOI] [PubMed] [Google Scholar]
- SCHWARTZ J. H., LIPMANN F. Phosphate incorporation into alkaline phosphatase of E. coli. Proc Natl Acad Sci U S A. 1961 Dec 15;47:1996–2005. doi: 10.1073/pnas.47.12.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Seki T., Yoshikawa H., Takahashi H., Saito H. Cloning and nucleotide sequence of phoP, the regulatory gene for alkaline phosphatase and phosphodiesterase in Bacillus subtilis. J Bacteriol. 1987 Jul;169(7):2913–2916. doi: 10.1128/jb.169.7.2913-2916.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Seki T., Yoshikawa H., Takahashi H., Saito H. Nucleotide sequence of the Bacillus subtilis phoR gene. J Bacteriol. 1988 Dec;170(12):5935–5938. doi: 10.1128/jb.170.12.5935-5938.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Sun G., Birkey S. M., Hulett F. M. Three two-component signal-transduction systems interact for Pho regulation in Bacillus subtilis. Mol Microbiol. 1996 Mar;19(5):941–948. doi: 10.1046/j.1365-2958.1996.422952.x. [DOI] [PubMed] [Google Scholar]
- Sun G., Sharkova E., Chesnut R., Birkey S., Duggan M. F., Sorokin A., Pujic P., Ehrlich S. D., Hulett F. M. Regulators of aerobic and anaerobic respiration in Bacillus subtilis. J Bacteriol. 1996 Mar;178(5):1374–1385. doi: 10.1128/jb.178.5.1374-1385.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Suzuki M., Brenner S. E. Classification of multi-helical DNA-binding domains and application to predict the DBD structures of sigma factor, LysR, OmpR/PhoB, CENP-B, Rapl, and Xy1S/Ada/AraC. FEBS Lett. 1995 Sep 25;372(2-3):215–221. doi: 10.1016/0014-5793(95)00988-l. [DOI] [PubMed] [Google Scholar]
- Wanner B. L., Wilmes-Riesenberg M. R. Involvement of phosphotransacetylase, acetate kinase, and acetyl phosphate synthesis in control of the phosphate regulon in Escherichia coli. J Bacteriol. 1992 Apr;174(7):2124–2130. doi: 10.1128/jb.174.7.2124-2130.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wyman C., Rombel I., North A. K., Bustamante C., Kustu S. Unusual oligomerization required for activity of NtrC, a bacterial enhancer-binding protein. Science. 1997 Mar 14;275(5306):1658–1661. doi: 10.1126/science.275.5306.1658. [DOI] [PubMed] [Google Scholar]
- Yamada M., Makino K., Shinagawa H., Nakata A. Regulation of the phosphate regulon of Escherichia coli: properties of phoR deletion mutants and subcellular localization of PhoR protein. Mol Gen Genet. 1990 Feb;220(3):366–372. doi: 10.1007/BF00391740. [DOI] [PubMed] [Google Scholar]
- Yang X., Kang C. M., Brody M. S., Price C. W. Opposing pairs of serine protein kinases and phosphatases transmit signals of environmental stress to activate a bacterial transcription factor. Genes Dev. 1996 Sep 15;10(18):2265–2275. doi: 10.1101/gad.10.18.2265. [DOI] [PubMed] [Google Scholar]