Transcription factors (TFs) are instrumental in the bacterial response to new environmental conditions. They can act as direct signal sensors and subsequently induce changes in gene expression leading to physiological adaptation. Here, by combining transcriptome sequencing (RNA-seq) and cistrome determination (DAP-seq), we studied a family of eight TFs in Pseudomonas aeruginosa. This family, encompassing TFs with XRE-like DNA-binding and cupin signal-sensing domains, includes the metabolic regulators ErfA, PsdR, and PauR and five so-far-unstudied TFs. The genome-wide delineation of their regulons identified 39 regulatory interactions with genes mostly involved in metabolism. We found that the XRE-cupin TFs are inhibitors of their neighboring genes, forming local, functional units encoding proteins with functions in condition-specific metabolic pathways. Growth phenotypes of isogenic mutants highlighted new roles for PauR and PA0535 in polyamines and arginine metabolism. The phylogenetic analysis of this family of regulators across the bacterial kingdom revealed a wide diversity of such metabolic regulatory modules and identified species with potentially higher metabolic versatility. Numerous genes encoding uncharacterized XRE-cupin TFs were found near metabolism-related genes, illustrating the need of further systematic characterization of transcriptional regulatory networks in order to better understand the mechanisms of bacterial adaptation to new environments.

中文翻译：

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具有XRE DNA结合和铜氨信号传感域的转录抑制剂可驱动假单胞菌的代谢多样化。

转录因子（TFs）有助于细菌对新环境条件的反应。它们可以充当直接信号传感器，并随后诱导基因表达的变化，从而导致生理适应。在这里，我们通过结合转录组测序（RNA-seq）和犯罪确定（DAP-seq），研究了铜绿假单胞菌中的八个TF家族。。该家族包括具有XRE样DNA结合和铜氨信号感应域的TF，包括代谢调节剂ErfA，PsdR和PauR和五个迄今尚未研究的TF。他们的调节子的全基因组描述确定了39种与大多数参与代谢的基因的调节相互作用。我们发现，XRE-cupin TFs是其邻近基因的抑制剂，形成编码蛋白质的局部功能单位，这些蛋白质在条件特定的代谢途径中具有功能。等基因突变体的生长表型突显了PauR和PA0535在多胺和精氨酸代谢中的新作用。对整个细菌界的调节剂家族的系统发育分析表明，这类代谢调节模块种类繁多，并鉴定出具有更高代谢多功能性的物种。