Modulation of Protein Activity by Small RNA Base Pairing Internal to Coding Sequences

Most characterized interactions between bacterial small RNAs (sRNAs) and their target mRNAs occur near ribosome binding sites resulting in changes in translation initiation or target mRNA decay. To understand the consequences of sRNA pairing internal to coding sequences detected by global RNA-RNA interactome approaches, we examined the impact of sRNA overexpression on seven target proteins. Overexpression of the sRNA led to decreased target protein levels for two pairs but no differences for the others. By further examining ArcZ-ligA and ArcZ-hemK, we discovered that that ArcZ pairing with the mRNAs leads to translation pausing and increased protein activity. A ligA point mutation that eliminates sRNA pairing resulted in increased sensitivity to DNA damage revealing physiological consequences of the regulation. Thus, regulatory RNA pairing in coding sequences can locally slow translation elongation, likely impacting co-translational protein folding and allowing improved incorporation of co-factors or more optimal folding under specific conditions.已被广泛表征的细菌小RNA（small RNAs，sRNAs）与其靶mRNA之间的相互作用，大多发生在核糖体结合位点附近，进而引发翻译起始改变或靶mRNA降解。为明确通过全局RNA-RNA互作组技术检测到的、发生于编码区内部的sRNA配对所产生的调控效应，我们研究了sRNA过表达对7种靶蛋白的影响。该sRNA的过表达使2组互配对的靶蛋白水平出现下调，其余5组则未观察到显著差异。通过进一步研究ArcZ-ligA与ArcZ-hemK这两组互作对，我们发现ArcZ与mRNA的配对会引发翻译暂停，并提升靶蛋白的活性。消除sRNA配对的ligA点突变会使菌体对DNA损伤的敏感性升高，这也揭示了该调控机制的生理意义。综上，编码区内部的调控性RNA配对可在局部减缓翻译延伸过程，这大概率会影响共翻译蛋白折叠，并能在特定条件下促进辅因子的更好整合，或是实现更优化的蛋白折叠。