Characterization of promoters in archaeal genomes based on DNA structural parameters

This study poses a novel method for promoter sequence location in putative regulators of archaea. AbstractThe 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, andSulfolobus 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 am...

Source: MicrobiologyOpen - October 29, 2021 Category: Microbiology Authors: Gustavo Sganzerla Martinez, Sharmilee Sarkar, Aditya Kumar, Ernesto P érez‐Rueda, Scheila de Avila e Silva Tags: ORIGINAL ARTICLE Source Type: research