Identification of PhoB binding sites of the yibD and ytfK promoter regions in Escherichia coli

Journal of Microbiology

Volumn 49, Issue 2, 2011, Pages 285-289

  Yoshida, Yusuke ^a   Sugiyama, Shinichiro ^a   Oyamada, Tomoya ^a   Yokoyama, Katsushi ^a   Kim, Soo Ki ^b   Makino, Kozo ^a  

^a NATIONAL DEFENSE ACADEMY   (Japan)

^b Konkuk University   (South Korea)

Author keywords

Escherichia coli; pho regulon; two component regulatory system; yibD; ytfK

Indexed keywords

BACTERIAL PROTEIN; BETA GALACTOSIDASE; DEOXYRIBONUCLEASE I; PHOB PROTEIN, BACTERIA;

ARTICLE; BACTERIAL GENE; BINDING SITE; DNA FOOTPRINTING; ESCHERICHIA COLI O157; GENE FUSION; GENETICS; METABOLISM; PROMOTER REGION; PROTEIN BINDING; REPORTER GENE;

ARTIFICIAL GENE FUSION; BACTERIAL PROTEINS; BETA-GALACTOSIDASE; BINDING SITES; DEOXYRIBONUCLEASE I; DNA FOOTPRINTING; ESCHERICHIA COLI O157; GENES, BACTERIAL; GENES, REPORTER; PROMOTER REGIONS, GENETIC; PROTEIN BINDING;

ESCHERICHIA COLI; ESCHERICHIA COLI O157:H-;

EID: 79955716684     PISSN: 12258873     EISSN: 12258873     Source Type: Journal    
DOI: 10.1007/s12275-011-0360-6     Document Type: Article

References (36)

1. Amemura, M., K. Makino, H. Shinagawa, N. Otsuji, and A. Nakata. 1982. Cloning of and complementation tests with alkaline phosphatase regulatory genes (phoS and phoT) of Escherichia coli. J. Bacteriol. 152, 692-701.
2. Amemura, M., K. Makino, H. Shinagawa, A. Kobayashi, and A. Nakata. 1985. Nucleotide sequence of the genes involved in phosphate transport and regulation of the phosphate regulon in Escherichia coli. J. Mol. Biol. 184, 241-250.
3. Baek, J. H. and S. Y. Lee. 2006. Novel gene members in the Pho regulon of Escherichia coli. FEMS Microbiol. Lett. 264, 104-109.
4. Hayashi, T., K. Makino, M. Ohnishi, K. Kurokawa, K. Ishii, K. Yokoyama, C. G. Han, and et al. 2001. Complete genome sequence of enterohemorrhagic Escherichia coli O157: H7 and genomic comparison with a laboratory strain K-12. DNA Res. 8, 11-22. Erratum in: DNA Res. 2001. 8, 96.
5. Hsieh, Y. J. and B. L. Wanner. 2010. Global regulation by the seven-component Pi signaling system. Curr. Opin. Microbiol. 13, 198-203.
6. Kasahara, M., K. Makino, M. Amemura, A. Nakata, and H. Shinagawa. 1991. Dual regulation of the ugp operon by phosphate and carbon starvation at two interspaced promoters. J. Bacteriol. 173, 549-558.
7. Kikuchi, Y., K. Yoda, M. Yamasaki, and G. Tamura. 1981. The nucleotide sequence of the promoter and the amino-terminal region of alkaline phosphatase structural gene (phoA) of Escherichia coli. Nucleic Acids Res. 9, 5671-5678.
8. Kim, S. K., S. Kimura, H. Shinagawa, A. Nakata, K. S. Lee, B. L. Wanner, and K. Makino. 2000. Dual transcriptional regulation of the Escherichia coli phosphate-starvation-inducible psiE gene of the phosphate regulon by PhoB and the cyclic AMP (cAMP)-cAMP receptor protein complex. J. Bacteriol. 182, 5596-5599.
9. 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 sigma 70 subunit of Escherichia coli RNA polymerase in transcriptional activation by activator protein PhoB. Mol. Gen. Genet. 248, 1-8.
10. Kim, S. K., K. Makino, M. Amemura, H. Shinagawa, and A. Nakata. 1993. Molecular analysis of the phoH gene, belonging to the phosphate regulon in Escherichia coli. J. Bacteriol. 175, 1316-1324.
11. Kimura, S., K. Makino, H. Shinagawa, M. Amemura, and A. Nakata. 1989. Regulation of the phosphate regulon of Escherichia coli: characterization of the promoter of the pstS gene. Mol. Gen. Genet. 215, 374-380.
12. 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.
13. Makino, K., M. Amemura, S. K. Kim, A. Nakata, and H. Shinagawa. 1993. Role of the 70 subunit of RNA polymerase in transcriptional activation by activator protein PhoB in Escherichia coli. Genes Dev. 7, 149-160.
14. Makino, K., M. Amemura, S. K. Kim, H. Shinagawa, and A. Nakata. 1992. Signal transduction of the phosphate regulon in Escherichia coli mediated by phosphorylation, pp. 191-200. In S. Papa, A. Azzi, and J. M. Tager (eds.), Adenine nucleotides in cellular energy transfer and signal transduction, Birkhauser Verlag, Basel, Switzerland.
15. Makino, K., M. Amemura, S. K. Kim, K. Yokoyama, and S. Kimura. 1998. Mechanism of transcriptional activation of the phosphate regulon in Escherichia coli. J. Microbiol. 36, 231-238.
16. Makino, K., S. K. Kim, H. Shinagawa, M. Amemura, and A. Nakata. 1991. Molecular analysis of the cryptic and functional phn operons for phosphonate use in Escherichia coli K-12. J. Bacteriol. 173, 2665-2672.
17. Makino, K., H. Shinagawa, M. Amemura, and A. Nakata. 1986a. Nucleotide sequence of the phoB gene, the positive regulatory gene for the phosphate regulon of Escherichia coli K-12. J. Mol. Biol. 190, 37-44.
18. Makino, K., H. Shinagawa, M. Amemura, and A. Nakata. 1986b. Nucleotide sequence of the phoR gene, a regulatory gene for the phosphate regulon of Escherichia coli. J. Mol. Biol. 192, 549-556.
19. 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.
20. 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.
21. Miller, J. H. 1992. A short course in bacterial genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA.
22. Okamura, H., K. Makino, and Y. Nishimura. 2007. NMR dynamics distinguish between hard and soft hydrophobic cores in the DNA-binding domain of PhoB and demonstrate different roles of the cores in binding to DNA. J. Mol. Biol. 367, 1093-1117.
23. Overbeeke, N., H. Bergmans, F. van Mansfeld, and B. Lugtenberg. 1983. Complete nucleotide sequence of phoE, the structural gene for the phosphate limitation inducible outer membrane pore protein of Escherichia coli K12. J. Mol. Biol. 163, 513-532.
24. Overduin, P., W. Boos, and J. Tommassen. 1988. Nucleotide sequence of the ugp genes of Escherichia coli K12: homology to the maltose system. Mol. Microbiol. 2, 767-775.
25. Oyamada, T., K. Yokoyama, M. Morinaga, M. Suzuki, and K. Makino. 2007. Expression of Escherichia coli DcuS-R two-component regulatory system is regulated by the secondary internal promoter which is activated by CRP-cAMP. J. Microbiol. 45, 234-240.
26. Reed, J. L., T. D. Vo, C. H. Schilling, and B. O. Palsson. 2003. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol. 4, R54.
27. Serres, M. H., S. Gopal, L. A. Nahum, P. Liang, T. Gaasterland, and M. Riley. 2001. A functional update of the Escherichia coli K-12 genome. Genome Biol. 2, research0035. 1-0035. 7.
28. Silhavy, T. J., M. L. Berman, and L. Enquist. 1984. Experiments with gene fusion. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA.
29. Studier, F. W. and B. A. Moffatt. 1986. Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J. Mol. Biol. 189, 113-130.
30. Sugiyama, S., Y. Yoshida, K. Yokoyama, and K. Makino. 2010. Identification of PhoP-PhoQ dependent promoters in enterohemorrhagic E. coli O157: H7 genome. Natl. Def. Med. J. 57, 83-88.
31. Wanner, B. L. 1996. Phosphorus assimilation and control of the phosphate regulon, pp. 1357-1381. In F. C. Neidhardt, R. Curtiss, 3rd, J. L. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (eds.), Escherichia coli and Salmonella typhimurium cellular and molecular biology. American Society for Microbiology Press, Washington, DC, USA.
32. Wanner, B. L. and R. McSharry. 1982. Phosphate-controlled gene expression in Escherichia coli K12 using Mudl-directed lacZ fusions. J. Mol. Biol. 158, 347-363.
33. Wanner, B. L., S. Wieder, and R. McSharry. 1981. Use of bacteriophage transposon Mudl to determine the orientation for three proC-linked phosphate-starvation-inducible (psi) genes in Escherichia coli K-12. J. Bacteriol. 146, 93-101.
34. Yokoyama, K., T. Oyamada, M. Suzuki, and K. Makino. 2005. Construction of cloning system for CRP-cAMP dependent promoters in Escherichia coli. Mem. Natl. Def. Acad. Jpn. 45, 1-9.
35. Yoshida, Y., T. Oyamada, K. Yokoyama, M. Suzuki, and K. Makino. 2008. Screening and identification of Lrp dependent promoters in Enterohemorrhagic E. coli O157: H7 genome. Natl. Def. Med. J. 55, 49-57.
36. Yoshida, Y., S. Sugiyama, T. Oyamada, K. Yokoyama, and K. Makino. 2010. Identification and characterization of novel phosphate regulon genes, ecs0540-ecs0544, in Escherichia coli O157: H7. Mol. Genet. Genomics 284, 197-205.