A Revolutionary Paradigm of Bacterial Genome Regulation

The whole set of the constitutive promoters recognized by four minor sigma subunits of Escherichia coli RNA polymerase

“…The intragenic binding site was referred to type-D site. The height of binding intensity identified by SELEX-chip system is generally in good agreement with the number of clones identified by SELEX-clos (cloning-sequencing) system, indicating that these two parameters correlate with the binding affinity of test TF to DNA [ 4 , 5 , 8 , 9 ].…”

“…RpoS-dependent constitutive promoter(s) also exists upstream of the nanCMS operon (N-acetylneuraminic acid transport and utilization) and/or the fimB gene (regulator for fimA encoding fimbrin, the major type-1 pili) ( Fig 1 and Table 1 ). Noteworthy is that most of the RpoS-dependent promoters listed in the current databases might be those under the indirect control of RpoS [ 8 , 9 , 27 ]. Otherwise a set of RpoS-dependent promoters, designated as the inducible promoters, might be activated in the presence of additional supporting factors.…”

“…For adaptation to stressful environments, the pattern of genome transcription is, however, altered by modulating the promoter selectivity of RNAP through two-step interaction with two groups of the regulatory factor, i . e ., 7 species of the sigma factor with promoter recognition activity at the first step [ 5 , 6 ] and then approximately 300 species of the transcription factor (TF) including both protein and nucleotide factors at the second step [ 4 , 5 , 7 , 8 ]. For understanding the genome regulation at molecular level, therefore, three kinds of the basic knowledge are absolutely needed for both all the sigma and TF factors [ 8 , 9 ]: (1) the whole set of regulatory target promoters, genes or operons under the control of each regulatory factor; (2) the binding affinity of the test regulatory protein to target DNA; and (3) the intracellular concentrations of the functional forms of each regulatory protein [note that the activity of TF is often controlled by effector ligands or protein modification such as phosphorylation].…”

“…coli is reassessed as the model organism. The binding sites of RNAP and TF identified in vivo using these modern techniques, however, do not represent the whole set of their binding sites because: i) their binding to regulatory sites is often interfered by other DNA-binding proteins, thereby masking their binding target sequences by antagonistic inhibitory proteins [ 8 , 9 , 24 ]; and ii) in the case of activator-dependent transcription, their binding to targets depends on the simultaneous presence of supporting factors [ 8 , 9 , 25 ]. Under the in vivo situations, therefore, it is in principle impossible to obtain the whole set of binding sites for both RNAP and TFs.…”

“…In order to avoid the problems associated with these in vivo experiments, we then decided to employ the in vitro approaches. For identification of the binding sites of RNAP and TFs, we developed the Genomic SELEX system [ 26 ] and successfully employed for search of regulatory targets for a number of TFs [ 8 , 9 ]. We also employed the Genomic SELEX for mapping of promoters.…”