Transcription profile ofEscherichia coli: genomic SELEX search for regulatory targets of transcription factors

Abstract

Bacterial genomes are transcribed by DNA-dependent RNA polymerase (RNAP), which achieves gene selectivity through interaction with sigma factors that recognize promoters, and transcription factors (TFs) that control the activity and specificity of RNAP holoenzyme. To understand the molecular mechanisms of transcriptional regulation, the identification of regulatory targets is needed for all these factors. We then performed genomic SELEX screenings of targets under the control of each sigma factor and each TF. Here we describe the assembly of 156 SELEX patterns of a total of 116 TFs performed in the presence and absence of effector ligands. The results reveal several novel concepts: (i) each TF regulates more targets than hitherto recognized; (ii) each promoter is regulated by more TFs than hitherto recognized; and (iii) the binding sites of some TFs are located within operons and even inside open reading frames. The binding sites of a set of global regulators, including cAMP receptor protein, LeuO and Lrp, overlap with those of the silencer H-NS, suggesting that certain global regulators play an anti-silencing role. To facilitate sharing of these accumulated SELEX datasets with the research community, we compiled a database, ‘Transcription Profile of Escherichia coli’ (www.shigen.nig.ac.jp/ecoli/tec/).

Transcription factor DecR (YbaO) controls detoxification of L-cysteine in Escherichia coli

“…Taken together, we predicted involvement of YhaOM in importation and catabolism of cysteine in E. coli. We have so far performed genomic SELEX screening for regulatory targets for more than 200 TFs from a single E. coli strain K-12 W3110 [for details, see Ishihama et al (2016) and the TEC database (https://shigen.nig.ac.jp/ecoli/tec/)]. One surprising finding is that the single-target TF is rather rare, even though most of E. coli TFs have long been believed to regulate only one specific target gene or operon (Ishihama, 2010(Ishihama, , 2012.…”

“…As an attempt to examine the regulatory function of YbaO, we first searched in this study for its regulatory target(s). As a shortcut approach for identification of the regulation targets by as many as about 300 DNA-binding TFs in E. coli, we have developed an improved system of genomic SELEX (systematic evolution of ligands by exponential enrichment) (Shimada et al, 2005), and have successfully applied this approach for the identification of the regulation targets for a number of TFs (for instance, see Ishihama et al, 2016). The genomic SELEX screening system is particularly useful for identification of regulation targets and regulatory roles of hitherto uncharacterized TFs, such as YeaM (renamed to NimR), YbjK (renamed to RcdA), YcjZ (renamed to PgrR), YcdC (renamed to RutR), YdcN (renamed to SutR), YdhM (renamed to NemR) and YgiP (renamed to Dan) (all cited in Ishihama et al, 2016), YbiH (renamed to CecR) (Yamanaka et al, 2016) and YedW (renamed to HprR) (H. Urano and others, unpublished).…”

Transcription factor CecR (YbiH) regulates a set of genes affecting the sensitivity of Escherichia coli against cefoperazone and chloramphenicol

“…A total of seven species of sigma factor, the promoter recognition subunit of RNA polymerase (RNAP) and about 300 species of transcription factor (TF) are together involved in this gene selection process (Riley et al, 2006;Ishihama, 2009Ishihama, , 2010. At present, however, the regulatory functions are not known for about one-fifth of the E. coli TFs (Ishihama et al, 2016). In the absence of knowledge of factors and conditions affecting the expression of regulatory functions, the ordinary genetic approach is not useful for identification of regulator targets of hitherto uncharacterized TFs.…”

“…Bacterial DNA-binding TFs bind to DNA and regulate the genes nearby, and thus the prediction of regulation target promoters, genes and operons is possible based on knowledge of the location of recognition sequences by test TFs. As a short cut for identification of the regulation targets by uncharacterized TFs, we have developed an improved system of genomic SELEX (systematic evolution of ligands by exponential enrichment) (Shimada et al, 2005), and successfully applied it for identification of the regulation targets for a number of TFs (see Ishihama, 2012;Ishihama et al, 2016). The genomic SELEX screening system is particularly useful for identification of regulation targets of hitherto uncharacterized TFs.…”

Deciphering the protein‐DNA code of bacterial winged helix‐turn‐helix transcription factors

“…Larger collections of binding sites generated using genomic SELEX [18][19][20][21], ChIP-seq [22,23], and gene expression analysis [24,25] have greatly increased the quantitative resolution of specificity models. However, the DNA sequences of native genomic binding sites are not selected solely for optimal affinity, so these models may not accurately reflect energetic preferences.…”