Intracellular concentrations of 65 species of transcription factors with known regulatory functions in Escherichia coli.
The expression pattern of the Escherichia coli genome is controlled in part by regulating the utilization of a limited number of RNA polymerases among a total of its approximately 4,600 genes. The distribution pattern of RNA polymerase changes from modulation of two types of protein-protein interactions: the interaction of core RNA polymerase with seven species of the sigma subunit for differential promoter recognition and the interaction of RNA polymerase holoenzyme with about 300 different species of transcription factors (TFs) with regulatory functions. We have been involved in the systematic search for the target promoters recognized by each sigma factor and each TF using the newly developed Genomic SELEX system. In parallel, we developed the promoter-specific (PS)-TF screening system for identification of the whole set of TFs involved in regulation of each promoter. Understanding the regulation of genome transcription also requires knowing the intracellular concentrations of the sigma subunits and TFs under various growth conditions. This report describes the intracellular levels of 65 species of TF with known function in E. coli K-12 W3110 at various phases of cell growth and at various temperatures. The list of intracellular concentrations of the sigma factors and TFs provides a community resource for understanding the transcription regulation of E. coli under various stressful conditions in nature.
Department of Frontier Bioscience and Micro-Nano Technology Research Center, Hosei University, Koganei, Tokyo, Japan Nippon Institute for Biological Science, Ome, Tokyo, Japan Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan aishiham@hosei.ac.jp.
Akira
A
Ishihama
Department of Frontier Bioscience and Micro-Nano Technology Research Center, Hosei University, Koganei, Tokyo, Japan Nippon Institute for Biological Science, Ome, Tokyo, Japan.
Ayako
A
Kori
Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan.
Etsuko
E
Koshio
Department of Frontier Bioscience and Micro-Nano Technology Research Center, Hosei University, Koganei, Tokyo, Japan Nippon Institute for Biological Science, Ome, Tokyo, Japan.
Kayoko
K
Yamada
Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan.
Hiroto
H
Maeda
Department of Frontier Bioscience and Micro-Nano Technology Research Center, Hosei University, Koganei, Tokyo, Japan Nippon Institute for Biological Science, Ome, Tokyo, Japan.
Tomohiro
T
Shimada
Nippon Institute for Biological Science, Ome, Tokyo, Japan.
Hideki
H
Makinoshima
Nippon Institute for Biological Science, Ome, Tokyo, Japan.
Akira
A
Iwata
Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka, Japan.
Nobuyuki
N
Fujita
D000222:Adaptation, Physiological; D000818:Animals; D000907:Antibodies, Bacterial / Q000096:biosynthesis; D004926:Escherichia coli / Q000235:genetics / Q000254:growth & development / Q000276:immunology / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial / Q000235:genetics*; D042541:Intracellular Space; D011401:Promoter Regions, Genetic / Q000235:genetics; D011817:Rabbits; D017384:Sequence Deletion; D012808:Sigma Factor / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism; D013312:Stress, Physiological; D013696:Temperature; D014157:Transcription Factors / Q000235:genetics / Q000276:immunology / Q000302:isolation & purification / Q000378:metabolism*
D000907:Antibodies, Bacterial; D029968:Escherichia coli Proteins; D012808:Sigma Factor; D014157:Transcription Factors