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首页> 外文期刊>Genetica >The DNA-binding domain as a functional indicator: the case of the AraC/XylS family of transcription factors
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The DNA-binding domain as a functional indicator: the case of the AraC/XylS family of transcription factors

机译：DNA结合结构域作为功能指标：AraC / XylS家族的转录因子

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摘要

The AraC/XylS family of transcription factors, which include proteins that are involved in the regulation of diverse biological processes, has been of considerable interest recently and has been constantly expanding by means of in silico predictions and experimental analysis. In this work, using a HMM based on the DNA binding domain of 58 experimentally characterized proteins from the AraC/XylS (A/X), 1974 A/X proteins were found in 149 out of 212 bacterial genomes. This domain was used as a template to generate a phylogenetic tree and as a tool to predict the putative regulatory role of the new members of this family based on their proximity to a particular functional cluster in the tree. Based on this approach we assigned a functional regulatory role for 75% of the TFs dataset. Of these, 33.7% regulate genes involved in carbon-source catabolism, 9.6% global metabolism, 8.3% nitrogen metabolism, 2.9% adaptation responses, 8.9% stress responses, and 11.7% virulence. The abundance of TFs involved in the regulation of metabolic processes indicates that bacteria have optimized their regulatory systems to control energy uptake. In contrast, the lower percentage of TFs required for stress, adaptation and virulence regulation reflects the specialization acquired by each subset of TFs associated with those processes. This approach would be useful in assigning regulatory roles to uncharacterized members of other transcriptional factor families and it might facilitate their experimental analysis.
机译：转录因子的AraC / XylS家族，其中包括参与多种生物过程调控的蛋白质，最近引起了人们的极大兴趣，并且已通过计算机预测和实验分析不断扩展。在这项工作中，使用基于58种AraC / XylS（A / X）实验鉴定蛋白的DNA结合域的HMM，在212个细菌基因组中的149个中发现了1974种A / X蛋白。该域用作生成系统树的模板，并根据其与树中特定功能簇的接近程度来预测该家族新成员的假定调控作用。基于这种方法，我们为TFs数据集中的75％分配了职能监管角色。其中33.7％的调节基因参与碳源分解代谢，9.6％的整体代谢，8.3％的氮代谢，2.9％的适应性反应，8.9％的应激反应和11.7％的毒力。参与代谢过程调节的TF含量丰富，表明细菌已经优化了其调节系统以控制能量吸收。相反，压力，适应和毒力调节所需的TF百分比较低，反映了与这些过程相关的TF的每个子集所获得的专业化。该方法在将调节作用分配给其他转录因子家族的未表征成员方面将很有用，并且可能有助于它们的实验分析。

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