Escherichia coli transcription factors of unknown function: sequence features and possible evolutionary relationships
Por:
Duarte-Velazquez, Isabel, de la Mora, Javier, Ramírez-Prado J.H., Aguillon-Barcenas, Alondra, Tornero-Gutierrez, Fatima, Cordero-Loreto, Eugenia, Anaya-Velazquez, Fernando, Paramo-Perez, Itzel, Rangel-Serrano, Angeles, Muñoz-Carranza S.R., Romero-González O.E., Cardoso-Reyes L.R., Rodríguez-Ojeda R.A., Mora-Montes H.M., Vargas-Maya N.I., Padilla-Vaca, Felipe, Franco, Bernardo
Publicada:
1 ene 2022
Resumen:
Organisms need mechanisms to perceive the environment and respond accordingly to environmental changes or the presence of hazards. Transcription factors (TFs) are required for cells to respond to the environment by controlling the expression of genes needed. Escherichia coli has been the model bacterium for many decades, and still, there are features embedded in its genome that remain unstudied. To date, 58 TFs remain poorly characterized, although their binding sites have been experimentally determined. This study showed that these TFs have sequence variation at the third codon position G+C content but maintain the same Codon Adaptation Index (CAI) trend as annotated functional transcription factors. Most of these transcription factors are in areas of the genome where abundant repetitive and mobile elements are present. Sequence divergence points to groups with distinctive sequence signatures but maintaining the same type of DNA binding domain. Finally, the analysis of the promoter sequences of the 58 TFs showed A+T rich regions that agree with the features of horizontally transferred genes. The findings reported here pave the way for future research of these TFs that may uncover their role as spare factors in case of lose-of-function mutations in core TFs and trace back their evolutionary history. © Copyright 2022 Duarte-Velázquez et al.
Filiaciones:
Duarte-Velazquez, Isabel:
Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, Mexico
de la Mora, Javier:
Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
Ramírez-Prado J.H.:
Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A. C., Yucatán, Mérida, Mexico
Aguillon-Barcenas, Alondra:
Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, Mexico
Tornero-Gutierrez, Fatima:
Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, Mexico
Cordero-Loreto, Eugenia:
Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, Mexico
Anaya-Velazquez, Fernando:
Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, Mexico
Paramo-Perez, Itzel:
Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, Mexico
Rangel-Serrano, Angeles:
Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, Mexico
Muñoz-Carranza S.R.:
Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, Mexico
Romero-González O.E.:
Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, Mexico
Cardoso-Reyes L.R.:
Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, Mexico
Rodríguez-Ojeda R.A.:
Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, Mexico
Mora-Montes H.M.:
Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, Mexico
Vargas-Maya N.I.:
Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, Mexico
Padilla-Vaca, Felipe:
Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, Mexico
Franco, Bernardo:
Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, Mexico
gold, Green Published, All Open Access, Gold, Green
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