DataSheet1_Sense and antisense RNA products of the uxuR gene can affect motility and chemotaxis acting independent of the UxuR protein.pdf

Small non-coding and antisense RNAs are widespread in all kingdoms of life, however, the diversity of their functions in bacteria is largely unknown. Here, we study RNAs synthesised from divergent promoters located in the 3′-end of the uxuR gene, encoding transcription factor regulating hexuronate metabolism in Escherichia coli. These overlapping promoters were predicted in silico with rather high scores, effectively bound RNA polymerase in vitro and in vivo and were capable of initiating transcription in sense and antisense directions. The genome-wide correlation between in silico promoter scores and RNA polymerase binding in vitro and in vivo was higher for promoters located on the antisense strands of the genes, however, sense promoters within the uxuR gene were more active. Both regulatory RNAs synthesised from the divergent promoters inhibited expression of genes associated with the E. coli motility and chemotaxis independent of a carbon source on which bacteria had been grown. Direct effects of these RNAs were confirmed for the fliA gene encoding σ28 subunit of RNA polymerase. In addition to intracellular sRNAs, promoters located within the uxuR gene could initiate synthesis of transcripts found in the fraction of RNAs secreted in the extracellular medium. Their profile was also carbon-independent suggesting that intragenic uxuR transcripts have a specific regulatory role not directly related to the function of the protein in which gene they are encoded.

小型非编码及反义RNA在生命界的各个王国内广泛存在，然而，它们在细菌中功能的多样性却鲜为人知。本研究聚焦于源自uxuR基因3'端不同启动子的RNA合成，该基因编码调控艾希氏大肠杆菌己酮糖酸盐代谢的转录因子。这些重叠的启动子通过计算机模拟预测得出，具有较高的分数，并在体外及体内有效结合RNA聚合酶，并能在正链和反链方向上启动转录。就全基因组而言，与体外和体内RNA聚合酶结合的计算机模拟启动子分数与位于基因反义链上的启动子之间的相关性更高，然而，uxuR基因内的正链启动子活性更强。来自不同启动子的调控RNA抑制了与大肠杆菌运动性和趋化性相关的基因表达，且这种抑制作用与细菌生长的碳源无关。这些RNA对fliA基因的直接效应得到了证实，该基因编码RNA聚合酶σ28亚单位。除了细胞内sRNA外，uxuR基因内的启动子还能启动存在于分泌到细胞外介质RNA组分中的转录本合成。这些转录本的轮廓也表现出碳源独立性，表明基因内uxuR转录本具有特定的调控作用，这种作用并非直接与其所编码的蛋白质的功能相关。