Biology, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Guanajuato, Guanajuato, México.
Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autonoma de Mexico, Mexico City, México.
PeerJ. 2022 Jul 20;10:e13772. doi: 10.7717/peerj.13772. eCollection 2022.
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. 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.
生物需要有机制来感知环境，并根据环境变化或危险的存在做出相应的反应。转录因子（TFs）通过控制所需基因的表达，使细胞能够对环境做出反应。几十年来，一直是模式细菌，但在其基因组中仍有一些特征尚未研究。迄今为止，尽管已经通过实验确定了它们的结合位点，但仍有 58 个 TFs 特征描述较差。本研究表明，这些 TF 在第三个密码子位置的 G+C 含量上存在序列变异，但保持与注释功能转录因子相同的密码子适应指数（CAI）趋势。这些转录因子大多数位于基因组中存在大量重复和移动元件的区域。序列分歧表明存在具有独特序列特征的组，但保持相同类型的 DNA 结合结构域。最后，对 58 个 TF 的启动子序列进行分析表明，富含 A+T 的区域与水平转移基因的特征一致。这里报告的研究结果为这些 TF 的未来研究铺平了道路，这可能揭示它们在核心 TF 功能丧失突变的情况下作为备用因子的作用，并追溯它们的进化历史。
