Table1_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在生物圈的各个界中普遍存在，然而，它们在细菌中的功能多样性尚处于认知盲区。本研究聚焦于从位于uxuR基因3′端的不同启动子合成的RNA，该基因编码调控艾希氏菌己酮糖代谢的转录因子。这些重叠的启动子通过计算机模拟预测，具有较高的得分，能够在体外及体内有效结合RNA聚合酶，并能够从正向及反向启动转录。计算机模拟的启动子评分与体外及体内RNA聚合酶结合的基因组广域相关性，在位于基因反义链的启动子中表现更显著，然而，uxuR基因内的正向启动子活性更高。由这些不同启动子合成的调控RNA，能够抑制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亚基。除了细胞内的小RNA外，uxuR基因内的启动子还能够启动存在于分泌到细胞外介质RNA组分中的转录本合成。这些转录本的特性也表现出与碳源无关，暗示着基因内uxuR转录本具有特定的调控作用，这种作用并非直接关联于其编码的蛋白质功能。