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Comput Biol Chem. 2015 Oct;58:93-103. doi: 10.1016/j.compbiolchem.2015.06.002. Epub 2015 Jun 6.

The functional landscape bound to the transcription factors of Escherichia coli K-12.

Author information

1
Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62100, Mexico; Unidad Multidisciplinaria de Docencia e Investigación, Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, Sisal, Yucatán, Mexico. Electronic address: erueda@ibt.unam.mx.
2
Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62100, Mexico.
3
Departamento de Bionanotecnología Centro de Nanociencias y Nanotecnología, Universidad Nacional Autonóma de México, Ensenada, Baja California, Mexico.
4
Programa de Genómica Computacional, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico.
5
Department of Biology, Wilfrid Laurier University, 75 University Ave. W., Waterloo, ON N2L 3C5, Canada. Electronic address: gmoreno@wlu.ca.

Abstract

Motivated by the experimental evidences accumulated in the last ten years and based on information deposited in RegulonDB, literature look up, and sequence analysis, we analyze the repertoire of 304 DNA-binding Transcription factors (TFs) in Escherichia coli K-12. These regulators were grouped in 78 evolutionary families and are regulating almost half of the total genes in this bacterium. In structural terms, 60% of TFs are composed by two-domains, 30% are monodomain, and 10% three- and four-structural domains. As previously noticed, the most abundant DNA-binding domain corresponds to the winged helix-turn-helix, with few alternative DNA-binding structures, resembling the hypothesis of successful protein structures with the emergence of new ones at low scales. In summary, we identified and described the characteristics associated to the DNA-binding TF in E. coli K-12. We also identified twelve functional modules based on a co-regulated gene matrix. Finally, diverse regulons were predicted based on direct associations between the TFs and potential regulated genes. This analysis should increase our knowledge about the gene regulation in the bacterium E. coli K-12, and provide more additional clues for comprehensive modelling of transcriptional regulatory networks in other bacteria.

KEYWORDS:

Bacteria; Evolution; Genomics; K-12; Transcription factors

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