Maturation of UTR-Derived sRNAs Is Modulated during Adaptation to Different Growth Conditions

Abstract

Small regulatory RNAs play a major role in bacterial gene regulation by binding their target mRNAs, which mostly influences the stability or translation of the target. Expression levels of sRNAs are often regulated by their own promoters, but recent reports have highlighted the presence and importance of sRNAs that are derived from mRNA 3′ untranslated regions (UTRs). In this study, we investigated the maturation of 5′ and 3′ UTR-derived sRNAs on a global scale in the facultative phototrophic alphaproteobacterium Rhodobacter sphaeroides. Including some already known UTR-derived sRNAs like UpsM or CcsR1-4, 14 sRNAs are predicted to be located in 5 UTRs and 16 in 3′ UTRs. The involvement of different ribonucleases during maturation was predicted by a differential RNA 5′/3′ end analysis based on RNA next generation sequencing (NGS) data from the respective deletion strains. The results were validated in vivo and underline the importance of polynucleotide phosphorylase (PNPase) and ribonuclease E (RNase E) during processing and maturation. The abundances of some UTR-derived sRNAs changed when cultures were exposed to external stress conditions, such as oxidative stress and also during different growth phases. Promoter fusions revealed that this effect cannot be solely attributed to an altered transcription rate. Moreover, the RNase E dependent cleavage of several UTR-derived sRNAs varied significantly during the early stationary phase and under iron depletion conditions. We conclude that an alteration of ribonucleolytic processing influences the levels of UTR-derived sRNAs, and may thus indirectly affect their mRNA targets.

A Small RNA, UdsC, Interacts with the RpoHII mRNA and Affects the Motility and Stress Resistance of Rhodobacter sphaeroides

“…It is not known whether this was due to the different effects of TorF on motility genes or to the TorF-independent effects of UdsC. The promoter of RSP_7527 -udsC is RpoHII-dependent [ 23 ], and increased levels of UdsC repress RpoHII expression (as shown in this study), suggesting a negative feedback loop.…”

“…A previous study demonstrated that the levels of UdsC are strongly increased by hydrogen peroxide treatment [ 23 ]. Therefore, we also tested the effect of UdsC on resistance to hydrogen peroxide.…”

“…For the majority of sRNAs, their function is still unknown. For the 3′ UTR-derived sRNA, UdsC, from R. sphaeroides, an influence of certain stress factors on its abundance was demonstrated [ 23 ], suggesting that it may have a function in stress responses. To better understand the function of UdsC, we constructed strains lacking or overexpressing this sRNA and performed physiological tests and a comparative RNAseq analysis.…”

“…Many sRNAs are derived from the 5′or 3′ UTRs of mRNAs either by partial termination, ribonucleolytic cleavage or the internal processing of the mRNA, or they can be transcribed by an own promoter (in the case of 3′ UTRs) (reviewed in, e.g., [ 20 , 21 ]). We recently identified eight so-far-unknown UTR-derived sRNAs in R. sphaeroides (UdsA-UdsH) and demonstrated that the maturation of sRNAs is modulated during adaptation to different growth conditions [ 23 ]. Consequently, sRNA maturation contributes to the regulation of gene expression.…”

“…The ribonucleases RNase III, RNase E, PNPase and the RNA chaperone Hfq are involved in the maturation of UdsC. UdsC levels increase in the presence of hydrogen peroxide or singlet oxygen, decrease under heat stress or iron depletion and depend on RpoHII [ 23 ]. In order to learn more about the physiological role of UdsC, we compared the transcriptomes of a strain lacking UdsC and a strain overexpressing UdsC to that of the isogenic wild type.…”