Seminars

The classic model of transcription regulation of individual genes was established using a single and homogenous model prokaryote such as Escherichia coli. This classic model is being challenged after the shift or research frontier towards understanding the genome regulation under various stressful conditions in nature. Using the newly developed strategies and tactics, a systematic study is being carried out in our laboratory for identification of the regulation target promoters, genes and operons under the control of each of 300 transcription factors in E. coli, and of the transcription factors involved in regulation of each of 2,000 promoters within the E. coli genome. Results indicate that: a number of E. coli promoters are regulated by as many as more than 10 transcription factors as in the case of eukaryotes; the number of regulation targets by a single transcription factor is more than those hitherto recognized, ranging up to hundred targets for several global regulators; and the multi-factor promoters and the multi-target transcription factors are being assembled into the multi-factor network of transcription regulation. In this workshop, I will overview the current state of our Genomic SELEX screening of regulation targets by E. coli transcription factors with known and unknown regulatory functions.


Selected recent publications related to the topics:

1. Shimada, T., Fujita, N., Yamamoto, K. and Ishihama, A.: Novel roles of cAMP receptor protein (CRP) in regulation of transport and metabolism of carbon sources. PLoSONE  6: e20081 (2011) 
2. Shimada, T., Yamamoto, K. and Ishihama, A.: Novel members of the Cra reguloninvolved in carbon metabolism in Escherichia coli. J. Bacteriol. 193, 649-659 (2011) 
3. Ogasawara, H., Yamamoto, K. and Ishihama, A.:    Cross-regulation between biofilmformationand flagella synthesis: Role of biofilm master regulator CsgD. J. Bacteriol. 193, 2587-2597 (2011) 
4. Yamamoto, K., Ishihama, A., Busby, S.J.W. and Brainger, D.C.: The Escherichia coli K-12 MntR mini-regulon includes dps that encodes the major stationary phase DNA-binding protein. J. Bacteriol. 193, 1477-1480 (2011) 
5. Ishihama, A.: Prokaryotic genome regulation: Multi-factor promoters, multi-target regulators and hierarchic networks. FEMS Microbial Reviews, 34, 628-645 (2010) 
6. Ogasawara, H., Yamada, K., Kori, A., Yamamoto, K. and Ishihama, A.:    The E. coli csgD promoter: Interplay between eight transcription factors. Microbiology 156, 2470-2483 (2010) 
7. Ogasawara, H., Yamamoto, K. and Ishihama, A.: Regulatory role of MlrA in transcription activation of csgD, the master regulator of biofilm formation in Escherichia coli. FEMS Microbiol. Lett. 312, 160-168 (2010) 
8. Teramoto, J., Yamanishi, Y., Magdy, E-S.H., Hasegawa, A., Kori, A., Nakajima,M., Arai, F., Fukuda, T. and Ishihama, A.: Single live-bacterial cell assay of promoter activity and regulation. Genes Cells 15, 1111-1112 (2010) 
9. Teramoto, J., Yoshimura, S.H., Takeyasu, K. and Ishihama, A.:    A novel nucleoid protein of Escherichia coli induced under anaerobic growth conditions.    Nucleic Acids Res. 38, 3605-3618 (2010)