Synergies between RNA degradation and trans-translation in Streptococcus pneumoniae: cross regulation and co-transcription of RNase R and SmpB

Ricardo N Moreira,Sandra C Viegas,Cecília M Arraiano,Mónica Amblar,Susana Domingues

doi:10.1186/1471-2180-12-268

Abstract

BackgroundRibonuclease R (RNase R) is an exoribonuclease that recognizes and degrades a wide range of RNA molecules. It is a stress-induced protein shown to be important for the establishment of virulence in several pathogenic bacteria. RNase R has also been implicated in the trans-translation process. Transfer-messenger RNA (tmRNA/SsrA RNA) and SmpB are the main effectors of trans-translation, an RNA and protein quality control system that resolves challenges associated with stalled ribosomes on non-stop mRNAs. Trans-translation has also been associated with deficiencies in stress-response mechanisms and pathogenicity.ResultsIn this work we study the expression of RNase R in the human pathogen Streptococcus pneumoniae and analyse the interplay of this enzyme with the main components of the trans-translation machinery (SmpB and tmRNA/SsrA). We show that RNase R is induced after a 37°C to 15°C temperature downshift and that its levels are dependent on SmpB. On the other hand, our results revealed a strong accumulation of the smpB transcript in the absence of RNase R at 15°C. Transcriptional analysis of the S. pneumoniae rnr gene demonstrated that it is co-transcribed with the flanking genes, secG and smpB. Transcription of these genes is driven from a promoter upstream of secG and the transcript is processed to yield mature independent mRNAs. This genetic organization seems to be a common feature of Gram positive bacteria, and the biological significance of this gene cluster is further discussed.ConclusionsThis study unravels an additional contribution of RNase R to the trans-translation system by demonstrating that smpB is regulated by this exoribonuclease. RNase R in turn, is shown to be under the control of SmpB. These proteins are therefore mutually dependent and cross-regulated. The data presented here shed light on the interactions between RNase R, trans-translation and cold-shock response in an important human pathogen.

Highlights

Ribonuclease R (RNase R) is an exoribonuclease that recognizes and degrades a wide range of RNA molecules
RNase R levels are regulated by temperature and modulated by SmpB In a previous work, we have biochemically characterized RNase R, the only hydrolytic exoribonuclease described in S. pneumoniae [30], but nothing is known about its expression and regulation
To study the expression of RNase R, total protein extracts obtained under physiological temperature and cold-shock were analysed by Western blot using specific polyclonal antibodies that we raised against the purified pneumococcal RNase R

Summary

Introduction

Ribonuclease R (RNase R) is an exoribonuclease that recognizes and degrades a wide range of RNA molecules It is a stress-induced protein shown to be important for the establishment of virulence in several pathogenic bacteria. RNase R has been implicated in the establishment of virulence in a growing number of pathogens These include Aeromonas hydrophila, Shigella flexneri, enteroinvasive E. coli, and Helicobacter pylori [18,19,20,21]. TmRNA together with SmpB are the main components of the trans-translation system, an elegant surveillance pathway that directs deficient proteins and mRNAs for degradation while rescuing stalled ribosomes (for a review see references [25,26]). In E. coli the stability of RNase R was shown to be regulated by interaction with tmRNA/SmpB, which in turn seems to depend on previous RNase R acetylation [28,29]

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