The analysis of transcription factors in Escherichia coli and its applications

Abstract

Cells change their states with regulating gene expression levels mediated by various transcription factors. Transcriptional regulation can be investigated systematically by transcriptome analysis, and this study provides useful information about physiological differences between strains, additional roles of a transcription factor and for biotechnological applications as follows. One of the most useful strains in biotechnology fields, Escherichia coli B strain has not been analyzed systematically, since the limitations of genome information and experimental techniques. In this study, the physiological differences in response to various environmental stresses including cold, heat, osmotic, acid and base shocks between E. coli K and B strains were examined at transcriptome levels using DNA microarray techniques. As a result, the strain specific differences could be understood related with transcriptional regulations. For example, membrane proteins such as transporters and sensor kinases in two-component regulatory systems showed large differences between the strains. In specific, PhoR-PhoB two-component regulatory system was analyzed in detail. PhoB is a global regulator related with phosphate starvation response and other metabolisms variously, but it has not been investigated in E. coli at transcriptome level yet. In this study, growth-associated and PhoB- and/or PhoR-dependent expressions were characterized in response to phosphate starvation, and additional roles of PhoB, novel gene members in the Pho regulon, could be found. The protein-protein interactions among the related proteins in this regulatory system were also characterized in vivo by using fluorescence resonance energy transfer (FRET) analysis. This combined transcriptome and protein level analyses help to understand the cellular physiology and get more complete picture of the gene regulatory system in response to phosphate starvation of E. coli. Lastly, the information about strain specific dif...