RRC ID 36734
著者 Ishihama A, Shimada T, Yamazaki Y.
タイトル Transcription profile of Escherichia coli: genomic SELEX search for regulatory targets of transcription factors.
ジャーナル Nucleic Acids Res
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/).
巻・号 44(5)
ページ 2058-74
公開日 2016-3-18
DOI 10.1093/nar/gkw051
PII gkw051
PMID 26843427
PMC PMC4797297
MeSH Binding Sites Cyclic AMP Receptor Protein / genetics Cyclic AMP Receptor Protein / metabolism DNA, Bacterial / genetics DNA, Bacterial / metabolism DNA-Directed RNA Polymerases / genetics* DNA-Directed RNA Polymerases / metabolism Escherichia coli / genetics* Escherichia coli / metabolism Escherichia coli Proteins / genetics Escherichia coli Proteins / metabolism Gene Expression Regulation, Bacterial* Genome, Bacterial* Leucine-Responsive Regulatory Protein / genetics Leucine-Responsive Regulatory Protein / metabolism Promoter Regions, Genetic Protein Binding SELEX Aptamer Technique Transcription Factors / genetics* Transcription Factors / metabolism Transcription, Genetic*
IF 11.502
引用数 43
WOS 分野 BIOCHEMISTRY & MOLECULAR BIOLOGY
リソース情報
原核生物(大腸菌) ME9780