Qi Lei, Yue Lei, Feng Deqin, Qi Fengxia, Li Jie, Dong Xiuzhu
State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No.1 Beichen West Road, Chaoyang District, Beijing 100101, PR China.
University of Chinese Academy of Sciences, No. 19A Yuquan Road, Shijingshan District, Beijing 100049, PR China.
Nucleic Acids Res. 2017 Jul 7;45(12):7285-7298. doi: 10.1093/nar/gkx454.
Unlike stable RNAs that require processing for maturation, prokaryotic cellular mRNAs generally follow an 'all-or-none' pattern. Herein, we used a 5΄ monophosphate transcript sequencing (5΄P-seq) that specifically captured the 5΄-end of processed transcripts and mapped the genome-wide RNA processing sites (PSSs) in a methanogenic archaeon. Following statistical analysis and stringent filtration, we identified 1429 PSSs, among which 23.5% and 5.4% were located in 5΄ untranslated region (uPSS) and intergenic region (iPSS), respectively. A predominant uridine downstream PSSs served as a processing signature. Remarkably, 5΄P-seq detected overrepresented uPSS and iPSS in the polycistronic operons encoding ribosomal proteins, and the majority upstream and proximal ribosome binding sites, suggesting a regulatory role of processing on translation initiation. The processed transcripts showed increased stability and translation efficiency. Particularly, processing within the tricistronic transcript of rplA-rplJ-rplL enhanced the translation of rplL, which can provide a driving force for the 1:4 stoichiometry of L10 to L12 in the ribosome. Growth-associated mRNA processing intensities were also correlated with the cellular ribosomal protein levels, thereby suggesting that mRNA processing is involved in tuning growth-dependent ribosome synthesis. In conclusion, our findings suggest that mRNA processing-mediated post-transcriptional regulation is a potential mechanism of ribosomal protein synthesis and stoichiometry.
与需要加工才能成熟的稳定RNA不同，原核细胞mRNA通常遵循“全或无”模式。在此，我们使用了5΄单磷酸转录本测序（5΄P-seq），该方法专门捕获加工后转录本的5΄末端，并绘制了产甲烷古菌全基因组RNA加工位点（PSS）图谱。经过统计分析和严格筛选，我们鉴定出1429个PSS，其中分别有23.5%和5.4%位于5΄非翻译区（uPSS）和基因间区（iPSS）。一个主要的尿苷下游PSS作为加工特征。值得注意的是，5΄P-seq在编码核糖体蛋白的多顺反子操纵子中检测到过量的uPSS和iPSS，以及大多数上游和近端核糖体结合位点，这表明加工对翻译起始具有调控作用。加工后的转录本显示出稳定性和翻译效率的提高。特别是，rplA-rplJ-rplL三顺反子转录本内的加工增强了rplL的翻译，这可以为核糖体中L10与L12的1:4化学计量比提供驱动力。与生长相关的mRNA加工强度也与细胞核糖体蛋白水平相关，从而表明mRNA加工参与调节生长依赖性核糖体合成。总之，我们的研究结果表明，mRNA加工介导的转录后调控是核糖体蛋白合成和化学计量的潜在机制。
