ИСТИНА

6S RNA is a highly abundant small non-coding RNA found in diverse classes of prokaryotes, including bacteria with extremely small genome (e.g. Aquifex aeolicus), that indicates an important role of 6S RNA in the cell. 6S RNA has a unique secondary structure which mimics DNA promoter, thus 6S RNA is able to bind RNA polymerase (RNAP) holoenzyme and inhibit transcription in case of unfavorable environment. Moreover, DNA-dependent RNAP can use 6S RNA as a template for synthesis of short pRNAs, when it needs to release from 6S RNA and proceed transcription of genes. 6S RNA was discovered and mostly studied in E. coli. Under normal conditions 6S RNA knockout does not affect E. coli growth, while it becomes essential for cell adaptation to starvation and alkaline stress. Some other bacteria express 6S RNA at highest levels under standard cultivation conditions. These facts raise a number of questions, like (1) what is the mechanism of 6S RNA-dependent transcription inhibition (and its retraction) in these bacteria, (2) whether 6S RNA is involved in some stress responses, and (3) what type of genes are affected. Therefore, we found it interesting to study the behavior of various bacteria and their 6S RNA knockout strains under extreme growth conditions. In the present work we characterized properties and functions of 6S RNAs from B. subtilis and R. sphaeroides in comparison to E. coli. It was shown that in B. subtilis 6S RNA knockouts leads to widespread changes in cellular transcriptome and proteome and results into high cell viability under alkaline conditions. For the first time, R. sphaeroides 6S RNA was characterized and osmotic and slight oxidative phenotypes of cells with deletion of 6S RNA gene were found. Surprisingly, decreased viability of E. coli 6S RNA knockout strain was observed in case of oxidative stress response, and some genes affected by the lack of 6S RNA under these conditions were revealed by qRT-PCR. Thus, for the first time we experimentally proved a great variety of 6S RNA functions in different bacteria and its involvement into diverse cellular stress responses. This work was supported by the Russian Science Foundation (project No. 14-24-00061).