Department of Genetics, University of Georgia, Athens, Georgia, USA.
Department of Microbiology, University of Georgia, Athens, Georgia, USA.
Mol Microbiol. 2022 Jan;117(1):121-142. doi: 10.1111/mmi.14808. Epub 2021 Sep 25.
Ribonuclease P (RNase P), which is required for the 5'-end maturation of tRNAs in every organism, has been shown to play a limited role in other aspects of RNA metabolism in Escherichia coli. Using RNA-sequencing (RNA-seq), we demonstrate that RNase P inactivation affects the abundances of ~46% of the expressed transcripts in E. coli and provide evidence that its essential function is its ability to generate pre-tRNAs from polycistronic tRNA transcripts. The RNA-seq results agreed with the published data and northern blot analyses of 75/83 transcripts (mRNAs, sRNAs, and tRNAs). Changes in transcript abundances in the RNase P mutant also correlated with changes in their half-lives. Inactivating the stringent response did not alter the rnpA49 phenotype. Most notably, increases in the transcript abundances were observed for all genes in the cysteine regulons, multiple toxin-antitoxin modules, and sigma S-controlled genes. Surprisingly, poly(A) polymerase (PAP I) modulated the abundances of ~10% of the transcripts affected by RNase P. A comparison of the transcriptomes of RNase P, RNase E, and RNase III mutants suggests that they affect distinct substrates. Together, our work strongly indicates that RNase P is a major player in all aspects of post-transcriptional RNA metabolism in E. coli.
核糖核酸酶 P（RNase P）是所有生物中 tRNA 5'端成熟所必需的，它在大肠杆菌中 RNA 代谢的其他方面的作用有限。通过 RNA 测序（RNA-seq），我们证明 RNase P 的失活会影响大肠杆菌中约 46%表达转录物的丰度，并提供证据表明其必需的功能是从多顺反子 tRNA 转录本生成前 tRNA。RNA-seq 结果与已发表的数据和 75/83 个转录物（mRNA、sRNA 和 tRNA）的 northern blot 分析一致。RNase P 突变体中转录物丰度的变化也与它们半衰期的变化相关。严格反应的失活不会改变 rnpA49 表型。最值得注意的是，所有半胱氨酸调控基因、多个毒素-抗毒素模块和 sigma S 调控基因的转录物丰度都增加了。令人惊讶的是，多聚（A）聚合酶（PAP I）调节了受 RNase P 影响的约 10%转录物的丰度。RNase P、RNase E 和 RNase III 突变体的转录组比较表明，它们影响不同的底物。总的来说，我们的工作强烈表明，RNase P 是大肠杆菌中所有转录后 RNA 代谢方面的主要参与者。
