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Characterization of promoters in archaeal genomes based on DNA structural parameters
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  • Gustavo Martinez,
  • Sharmilee Sarkar,
  • Aditya Kumar,
  • Ernesto Perez-Rueda,
  • Scheila Silva
Gustavo Martinez
Programa de Pós-Graduação em Biotecnologia
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Sharmilee Sarkar
Tezpur University
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Aditya Kumar
Tezpur University
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Ernesto Perez-Rueda
Instituto de Investigaciones en Matemáticas Aplicadas
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Scheila Silva
Universidade de Caxias do Sul
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Abstract

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, operonic and gene organization. Furthermore, earlier studies have found that a structural analysis gains more information compared to 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 in order to identify differences among these two classes of promoters. The structural analysis reveals variations in archaeal promoters’ architecture, i.e., 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 energetic/structural features.

Peer review status:ACCEPTED

14 Jul 2021Submitted to MicrobiologyOpen
16 Jul 2021Submission Checks Completed
16 Jul 2021Assigned to Editor
16 Jul 2021Reviewer(s) Assigned
20 Jul 2021Review(s) Completed, Editorial Evaluation Pending
22 Jul 2021Editorial Decision: Revise Minor
27 Jul 20211st Revision Received
28 Jul 2021Submission Checks Completed
28 Jul 2021Assigned to Editor
29 Jul 2021Review(s) Completed, Editorial Evaluation Pending
29 Jul 2021Editorial Decision: Accept