Current Version  1.5  

TEC (Transcription Profile of Escherichia coli) Database

TEC - Transcription Factor Profiling of Escherichia coli

      The bacterial genome is transcribed by a single species of DNA-dependent RNA polymerase (RNAP). The gene selectivity of RNAP is, however, modulated after interaction with two groups of the regulatory protein, the sigma factor with promoter recognition activity and the transcription factor (TF) that controls the activity and specificity of RNAP holoenzyme (1,2). In order to understand the molecular mechanisms underlying transcription regulation of the genome as a whole, the identification of regulation targets of all sigma factors and all TFs and the regulatory mode of each sigma and each TF are absolutely necessary. Towards this ultimate purpose, we have performed several lines of research using Escherichia coli K-12 as a model organism, including that: 1) Genomic SELEX screening of regulation target promoters, genes and operons under the control of each sigma factor and each TF (3); 2) PS(promoter-specific)-TF screening for identification of the whole set of TFs involved in regulation of each promoter (4); 3) determination of intracellular levels of all sigma factors and all TFs under various growth phases and various culture conditions (5).

     For enhance the research of genome-wide regulation in E. coli, we decided to share all these accumulated data sets with a variety of research communities. For this purpose, we developed a novel database “Transcription Profiling of Escherichia coli” (TEC) and to make it open to the public (6). In this first edition of TEC, we included a set of SELEX-chip screening of regulatory targets of a total of 116 TFs in the absence and presence of effector ligands, altogether a total of 156 SELEX data. The SELEX research was performed by a research group, headed by Akira ISHIHAMA (Hosei University, Tokyo, Japan), including a number of teams as listed in the list of project organization.
     The most important and unique aspect of this genome-wide research is that all experiments were performed using a single E. coli strain, the same experimental protocols with use of the same set of resources, and in the same research group. At present, this care is particularly important because the heterogeneity in genetic, metabolic and regulatory grounds even between the same E. coli strains but from different laboratories is widely accepted, raising a risk alarm of misunderstanding and incorrect prediction with use of experimental data obtained using different laboratories.
     Details of SELEX screening of individual TFs will be described in publications from each team [Note that some of the SELEX results have already been published as listed in the publication list]. TEC could be effectively used in conjunction with PEC (Profile of Escherichia coli) database.

  References:

  1. Ishihama, A.: Prokaryotic genome regulation: Multi-factor promoters, multi-target regulators and hierarchic networks. FEMS Microbial Reviews, 34, 628-645 (2010) PMID: 20491932.
  2. Ishihama, A.: Prokaryotic genome regulation: A revolutionary paradigm. Proc. Jpn. Acad., Ser. B, Phys. Biol. Sci., 88, 485-508 (2012) PMID: 23138451.
  3. Shimada, T., Fujita, N., Maeda, M. and Ishihama, A.: Systematic search for the Cra-binding promoters using genomic SELEX system. Genes Cells, 10, 907-918 (2005). PMID: 16115199.
  4. Shimada, T., Shimada, K., Matsui, M., Kitai, Y., Igarashi, J., Suga, H. and Ishihama, A.: Roles of cell division control factor SdiA: Recognition of quorum sensing signals and modulation of transcription regulation targets. Genes Cells 19, 405-418 (2014). DOI: 10.1111/gtc.12139.
  5. Ishihama, A., Kori, A., Koshio, E., Yamada, K., Maeda, H., Shimada, T., Makinoshima, H., Iwata, A. and Fujita, N.: Intracellular concentrations of transcription factors in Escherichia coli: 65 species with known regulatory functions. J. Bacteriol. 196, 2718-2727 (2014) DOI: 10.1128/JB.01579-14.
  6. Ishihama, A., Shimada, T. and Yamazaki, Y.: Transcription profile of Escherichia coli: Genomic SELEX search for regulation targets of transcription factors. Nucleic Acids Res., 44(5) 2058-2074 (2016) DOI: 10.1093/nar/gkw051.

Citation of TEC Database

      The first edition of TEC (Transcription Profiling of Escherichia coli) database provides transcription factor (TF) binding sites and intensities genomewidely determined for a total of 115 transcription factors (TFs) under a total of 156 conditions as identified by SELEX-chip screening as noted in “About TEC”. This TEC database can be used freely, but we kindly request to cite TEC in your presentations and publications as follows:

Ishihama, A., Shimada, T. and Yamazaki, Y.: Transcription profile of Escherichia coli: Genomic SELEX search for regulation targets of transcription factors. Nucleic Acids Res., 44(5) 2058-2074 (2016) DOI: 10.1093/nar/gkw051

Organization of TEC Project

  [TEC Steering Committee]

Akira ISHIHAMA (Chair person)

Hosei University, Micro-Nano Technology Research Center, Koganei, Tokyo 184-8584, Japan

Yukiko YAMAZAKI

National Institute of Genetics, Genetic Informatics Laboratory, Mishima 411-8540, Japan

Tomohiro SHIMADA

Chemical Resources Laboratory, Tokyo Institute of Technology, Nagatsuda, Yokohama 226-8503, Japan

Hiroshi OGASAWARA

Shinshu University, Research Center for Supports to Advanced Science, Division of Gene Research, Ueda, Nagano 386-8567, Japan

  [TEC Advisory Committee]

Junichi KATO

Tokyo Metropolitan University, Graduate School of Science, Department of Biological Science, Tokyo 192-0387, Japan

Hirotada MORI

Nara Institute of Science and Technology, Graduate School of Biological Sciences, Division of Systems Microbiology, Nara 630-0101, Japan

Hironori NIKI

National Institute of Genetics, Genetic Strains Research Center, Microbial Genetics Laboratory, Mishima, Shizuoka 411-8540, Japan

Taku OSHIMA

Nara Institute of Science and Technology, Graduate School of Biological Sciences, Division of System, Biology, Nara 630-0101, Japan

Kan TANAKA

Tokyo Institute of Technology, Institute of Innovative Research, Laboratory of Chemistry and Life Science, Nagatsuda, Yokohama 226-8503, Japan

Kaneyoshi YAMAMOTO

Hosei University, Faculty of Bioscience and Applied Chemistry, Department of Frontier Bioscience, Koganei, Tokyo 184-8584, Japan

  [Genomic SELEX Research Group]

Akira ISHIHAMA (Group leader)

Hosei University, Micro-Nano Technology Research Center, Koganei, Tokyo 184-8584, Japan

Ishihama Lab

Akira ISHIHAMA (Lab head)
Hosei University, Micro-Nano Technology Research Center, Koganei, Tokyo 184-8584, Japan

Shimada Lab

Tomohiro SHIMADA
Tokyo Institute of Technology, Institute of Innovative Research, Laboratory for Chemistry and Life Science, Nagatsuda, Yokohama 226-8503, Japan

Ogasawara Lab

Horoshi OGASAWARA
Shinshu University, Research Center for Supports to Advanced Science, Division of Gene Research, Ueda, Nagano 386-8567, Japan

Yamamoto Lab

Kaneyoshi YAMAMOTO
Hosei University, Faculty of Bioscience and Applied Chemistry, Department of Frontier Bioscience, Koganei, Tokyo 184-8584, Japan