Escherichia coli transcription factors of unknown function: sequence features and possible evolutionary relationships
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 bacte...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2022-07-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/13772.pdf |
| _version_ | 1797425028903469056 |
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| author | Isabel Duarte-Velázquez Javier de la Mora Jorge Humberto Ramírez-Prado Alondra Aguillón-Bárcenas Fátima Tornero-Gutiérrez Eugenia Cordero-Loreto Fernando Anaya-Velázquez Itzel Páramo-Pérez Ángeles Rangel-Serrano Sergio Rodrigo Muñoz-Carranza Oscar Eduardo Romero-González Luis Rafael Cardoso-Reyes Ricardo Alberto Rodríguez-Ojeda Héctor Manuel Mora-Montes Naurú Idalia Vargas-Maya Felipe Padilla-Vaca Bernardo Franco |
| author_facet | Isabel Duarte-Velázquez Javier de la Mora Jorge Humberto Ramírez-Prado Alondra Aguillón-Bárcenas Fátima Tornero-Gutiérrez Eugenia Cordero-Loreto Fernando Anaya-Velázquez Itzel Páramo-Pérez Ángeles Rangel-Serrano Sergio Rodrigo Muñoz-Carranza Oscar Eduardo Romero-González Luis Rafael Cardoso-Reyes Ricardo Alberto Rodríguez-Ojeda Héctor Manuel Mora-Montes Naurú Idalia Vargas-Maya Felipe Padilla-Vaca Bernardo Franco |
| author_sort | Isabel Duarte-Velázquez |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T08:10:05Z |
| format | Article |
| id | doaj.art-fa59c7c0a5ff478b80bd8108c40b03ba |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T08:10:05Z |
| publishDate | 2022-07-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-fa59c7c0a5ff478b80bd8108c40b03ba2023-12-02T23:31:23ZengPeerJ Inc.PeerJ2167-83592022-07-0110e1377210.7717/peerj.13772Escherichia coli transcription factors of unknown function: sequence features and possible evolutionary relationshipsIsabel Duarte-Velázquez0Javier de la Mora1Jorge Humberto Ramírez-Prado2Alondra Aguillón-Bárcenas3Fátima Tornero-Gutiérrez4Eugenia Cordero-Loreto5Fernando Anaya-Velázquez6Itzel Páramo-Pérez7Ángeles Rangel-Serrano8Sergio Rodrigo Muñoz-Carranza9Oscar Eduardo Romero-González10Luis Rafael Cardoso-Reyes11Ricardo Alberto Rodríguez-Ojeda12Héctor Manuel Mora-Montes13Naurú Idalia Vargas-Maya14Felipe Padilla-Vaca15Bernardo Franco16Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, MéxicoDepartamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autonoma de Mexico, Mexico City, MéxicoUnidad de Biotecnología, Centro de Investigación Científica de Yucatán, A. C., Mérida, Yucatán, MexicoBiology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, MéxicoBiology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, MéxicoBiology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, MéxicoBiology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, MéxicoBiology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, MéxicoBiology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, MéxicoBiology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, MéxicoBiology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, MéxicoBiology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, MéxicoBiology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, MéxicoBiology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, MéxicoBiology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, MéxicoBiology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, MéxicoBiology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, MéxicoOrganisms 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.https://peerj.com/articles/13772.pdfTranscription factors of unknown functionMobile elementsSequence codon biasSyntenyEscherichia coliStructural features |
| spellingShingle | Isabel Duarte-Velázquez Javier de la Mora Jorge Humberto Ramírez-Prado Alondra Aguillón-Bárcenas Fátima Tornero-Gutiérrez Eugenia Cordero-Loreto Fernando Anaya-Velázquez Itzel Páramo-Pérez Ángeles Rangel-Serrano Sergio Rodrigo Muñoz-Carranza Oscar Eduardo Romero-González Luis Rafael Cardoso-Reyes Ricardo Alberto Rodríguez-Ojeda Héctor Manuel Mora-Montes Naurú Idalia Vargas-Maya Felipe Padilla-Vaca Bernardo Franco Escherichia coli transcription factors of unknown function: sequence features and possible evolutionary relationships PeerJ Transcription factors of unknown function Mobile elements Sequence codon bias Synteny Escherichia coli Structural features |
| title | Escherichia coli transcription factors of unknown function: sequence features and possible evolutionary relationships |
| title_full | Escherichia coli transcription factors of unknown function: sequence features and possible evolutionary relationships |
| title_fullStr | Escherichia coli transcription factors of unknown function: sequence features and possible evolutionary relationships |
| title_full_unstemmed | Escherichia coli transcription factors of unknown function: sequence features and possible evolutionary relationships |
| title_short | Escherichia coli transcription factors of unknown function: sequence features and possible evolutionary relationships |
| title_sort | escherichia coli transcription factors of unknown function sequence features and possible evolutionary relationships |
| topic | Transcription factors of unknown function Mobile elements Sequence codon bias Synteny Escherichia coli Structural features |
| url | https://peerj.com/articles/13772.pdf |
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