Hoffmann Ute A, Lichtenberg Elisabeth, Rogh Said N, Bilger Raphael, Reimann Viktoria, Heyl Florian, Backofen Rolf, Steglich Claudia, Hess Wolfgang R, Wilde Annegret
Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, Freiburg, Germany.
School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden.
RNA Biol. 2024 Jan;21(1):1-18. doi: 10.1080/15476286.2024.2328438. Epub 2024 Mar 12.
RNA degradation is critical for synchronising gene expression with changing conditions in prokaryotic and eukaryotic organisms. In bacteria, the preference of the central ribonucleases RNase E, RNase J and RNase Y for 5'-monophosphorylated RNAs is considered important for RNA degradation. For RNase E, the underlying mechanism is termed 5' sensing, contrasting to the alternative 'direct entry' mode, which is independent of monophosphorylated 5' ends. Cyanobacteria, such as sp. PCC 6803 (), encode RNase E and RNase J homologues. Here, we constructed a strain lacking the 5' sensing function of RNase E and mapped on a transcriptome-wide level 283 5'-sensing-dependent cleavage sites. These included so far unknown targets such as mRNAs encoding proteins related to energy metabolism and carbon fixation. The 5' sensing function of cyanobacterial RNase E is important for the maturation of rRNA and several tRNAs, including tRNA. This tRNA activates glutamate for tetrapyrrole biosynthesis in plant chloroplasts and in most prokaryotes. Furthermore, we found that increased RNase activities lead to a higher copy number of the major plasmids pSYSA and pSYSM. These results provide a first step towards understanding the importance of the different target mechanisms of RNase E outside .
RNA降解对于原核生物和真核生物中基因表达与变化的环境同步至关重要。在细菌中，中心核糖核酸酶RNase E、RNase J和RNase Y对5'-单磷酸化RNA的偏好被认为对RNA降解很重要。对于RNase E，其潜在机制被称为5'感知，这与独立于单磷酸化5'末端的另一种“直接进入”模式形成对比。蓝细菌，如集胞藻属PCC 6803（），编码RNase E和RNase J的同源物。在这里，我们构建了一个缺乏RNase E的5'感知功能的菌株，并在全转录组水平上定位了283个5'感知依赖性切割位点。这些位点包括迄今为止未知的靶点，如编码与能量代谢和碳固定相关蛋白质的mRNA。蓝细菌RNase E的5'感知功能对于rRNA和几种tRNA（包括tRNA）的成熟很重要。这种tRNA在植物叶绿体和大多数原核生物中激活谷氨酸用于四吡咯生物合成。此外，我们发现增加的RNase活性导致主要质粒pSYSA和pSYSM的拷贝数增加。这些结果为理解RNase E在体外不同靶向机制的重要性迈出了第一步。
