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Transfer-messenger RNA (tmRNA\/SsrA RNA) and SmpB are the main effectors of<jats:italic>trans-<\/jats:italic>translation, an RNA and protein quality control system that resolves challenges associated with stalled ribosomes on non-stop mRNAs.<jats:italic>Trans<\/jats:italic>-translation has also been associated with deficiencies in stress-response mechanisms and pathogenicity.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>In this work we study the expression of RNase R in the human pathogen<jats:italic>Streptococcus pneumoniae<\/jats:italic>and analyse the interplay of this enzyme with the main components of the<jats:italic>trans<\/jats:italic>-translation machinery (SmpB and tmRNA\/SsrA). We show that RNase R is induced after a 37\u00b0C to 15\u00b0C temperature downshift and that its levels are dependent on SmpB. On the other hand, our results revealed a strong accumulation of the<jats:italic>smpB<\/jats:italic>transcript in the absence of RNase R at 15\u00b0C. Transcriptional analysis of the<jats:italic>S. pneumoniae rnr<\/jats:italic>gene demonstrated that it is co-transcribed with the flanking genes,<jats:italic>secG<\/jats:italic>and<jats:italic>smpB<\/jats:italic>. Transcription of these genes is driven from a promoter upstream of<jats:italic>secG<\/jats:italic>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.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>This study unravels an additional contribution of RNase R to the<jats:italic>trans<\/jats:italic>-translation system by demonstrating that<jats:italic>smpB<\/jats:italic>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,<jats:italic>trans<\/jats:italic>-translation and cold-shock response in an important human pathogen.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2180-12-268","type":"journal-article","created":{"date-parts":[[2012,11,20]],"date-time":"2012-11-20T15:14:26Z","timestamp":1353424466000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":24,"title":["Synergies between RNA degradation and trans-translation in Streptococcus pneumoniae: cross regulation and co-transcription of RNase R and SmpB"],"prefix":"10.1186","volume":"12","author":[{"given":"Ricardo N","family":"Moreira","sequence":"first","affiliation":[]},{"given":"Susana","family":"Domingues","sequence":"additional","affiliation":[]},{"given":"Sandra C","family":"Viegas","sequence":"additional","affiliation":[]},{"given":"M\u00f3nica","family":"Amblar","sequence":"additional","affiliation":[]},{"given":"Cec\u00edlia M","family":"Arraiano","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,11,20]]},"reference":[{"issue":"6","key":"1803_CR1","doi-asserted-by":"publisher","first-page":"818","DOI":"10.1002\/wrna.94","volume":"2","author":"IJ Silva","year":"2011","unstructured":"Silva IJ, Saramago M, Dressaire C, Domingues S, Viegas SC, Arraiano CM: Importance and key events of prokaryotic RNA decay: the ultimate fate of an RNA molecule. 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