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Characterization of promoters in archaeal genomes based on DNA structural parameters.
Martinez, Gustavo Sganzerla; Sarkar, Sharmilee; Kumar, Aditya; Pérez-Rueda, Ernesto; de Avila E Silva, Scheila.
Afiliación
  • Martinez GS; Programa de Pós-Graduação em Biotecnologia, Universidade de Caxias do Sul, Caxias do Sul-RS, Brasil.
  • Sarkar S; Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India.
  • Kumar A; Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India.
  • Pérez-Rueda E; Unidad Académica de Yucatán, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México, Mérida, Yucatán, México.
  • de Avila E Silva S; Programa de Pós-Graduação em Biotecnologia, Universidade de Caxias do Sul, Caxias do Sul-RS, Brasil.
Microbiologyopen ; 10(5): e1230, 2021 10.
Article en En | MEDLINE | ID: mdl-34713600
The transcription machinery of archaea can be roughly classified as a simplified version of eukaryotic organisms. The basal transcription factor machinery binds to the TATA box found around 28 nucleotides upstream of the transcription start site; however, some transcription units lack a clear TATA box and still have TBP/TFB binding over them. This apparent absence of conserved sequences could be a consequence of sequence divergence associated with the upstream region, operon, and gene organization. Furthermore, earlier studies have found that a structural analysis gains more information compared with a simple sequence inspection. In this work, we evaluated and coded 3630 archaeal promoter sequences of three organisms, Haloferax volcanii, Thermococcus kodakarensis, and Sulfolobus solfataricus into DNA duplex stability, enthalpy, curvature, and bendability parameters. We also split our dataset into conserved TATA and degenerated TATA promoters to identify differences among these two classes of promoters. The structural analysis reveals variations in archaeal promoter architecture, that is, a distinctive signal is observed in the TFB, TBP, and TFE binding sites independently of these being TATA-conserved or TATA-degenerated. In addition, the promoter encountering method was validated with upstream regions of 13 other archaea, suggesting that there might be promoter sequences among them. Therefore, we suggest a novel method for locating promoters within the genome of archaea based on DNA energetic/structural features.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: TATA Box / Regiones Promotoras Genéticas / Archaea / ADN de Archaea / Genoma Arqueal / Conformación de Ácido Nucleico Tipo de estudio: Prognostic_studies Idioma: En Revista: Microbiologyopen Año: 2021 Tipo del documento: Article País de afiliación: Brasil Pais de publicación: Reino Unido
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: TATA Box / Regiones Promotoras Genéticas / Archaea / ADN de Archaea / Genoma Arqueal / Conformación de Ácido Nucleico Tipo de estudio: Prognostic_studies Idioma: En Revista: Microbiologyopen Año: 2021 Tipo del documento: Article País de afiliación: Brasil Pais de publicación: Reino Unido