Structure and Degradation Mechanisms of 3′ to 5′ Exoribonucleases

Matos, Rute G.; Pobre, Vânia; Reis, Filipa P.; Małecki, Michał; Andrade, José M.; Arraiano, Cecília M.

doi:10.1007/978-3-642-21078-5_8

Cited by 8 publications

(11 citation statements)

References 159 publications

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“…This implicates RNR1 in maintaining a balance between RNA processing and degradation. In E. coli , RNase II protects mRNAs by removing the 3′ overhang necessary for PNPase to bind, or for PAP1 to bind and add the oligo(A) tail that triggers degradation by either PNPase or RNase II (reviewed by Matos et al. , 2011).…”

Section: Discussionmentioning

confidence: 99%

“…The main difference between E. coli RNase II and RNase R is their sensitivity to secondary structures. Ribonuclease R is capable of processing through double‐stranded RNAs with at least seven nucleotide overhangs, while RNase II creates blunt 3′ ends by rapidly degrading extensions, impeding the binding of other exonucleases, including PNPase, thereby stabilizing RNAs (reviewed by Matos et al. , 2011).…”

Section: Discussionmentioning

confidence: 99%

“…, 2011). Ambiguity over the name of this protein derives from the fact that it is apparently the sole organellar representative of the superfamily of exoribonucleases that includes both RNase R and RNase II, which have distinct sensitivities to RNA secondary structure and consequently different biological roles (Matos et al. , 2011).…”

Section: Introductionmentioning

confidence: 99%

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Ribonuclease II preserves chloroplast RNA homeostasis by increasing mRNA decay rates, and cooperates with polynucleotide phosphorylase in 3′ end maturation

Germain

Kim²,

Gutierrez³

et al. 2012

The Plant Journal

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SUMMARYRibonuclease R (RNR1) and polynucleotide phosphorylase (cpPNPase) are the two known 3¢ fi 5¢ exoribonucleases in Arabidopsis chloroplasts, and are involved in several aspects of rRNA and mRNA metabolism. In this work, we show that mutants lacking both RNR1 and cpPNPase exhibit embryo lethality, akin to the non-viability of the analogous double mutant in Escherichia coli. We were successful, however, in combining an rnr1 null mutation with weak pnp mutant alleles, and show that the resulting chlorotic plants display a global reduction in RNA abundance. Such a counterintuitive outcome following the loss of RNA degradation activity suggests a major importance of RNA maturation as a determinant of RNA stability. Detailed analysis of the double mutant demonstrates that the enzymes catalyze a two-step maturation of mRNA 3¢ ends, with RNR1 polishing 3¢ termini created by cpPNPase. The bulky quaternary structure of cpPNPase compared with RNR1 could explain this activity split between the two enzymes. In contrast to the double mutants, the rnr1 single mutant overaccumulates most mRNA species when compared with the wild type. The excess mRNAs in rnr1 are often present in non-polysomal fractions, and half-life measurements demonstrate a substantial increase in the stability of most mRNA species tested. Together, our data reveal the cooperative activity of two 3¢ fi 5¢ exoribonucleases in chloroplast mRNA 3¢ end maturation, and support the hypothesis that RNR1 plays a significant role in the destabilization of mRNAs unprotected by ribosomes.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Ribonuclease II preserves chloroplast RNA homeostasis by increasing mRNA decay rates, and cooperates with polynucleotide phosphorylase in 3′ end maturation

Germain

Kim²,

Gutierrez³

et al. 2012

The Plant Journal

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“…Ribonuclease R (RNase R) is a processive 3’-5’ exoribonuclease that belongs to the RNase II family of enzymes [4-7]. Orthologues have been found in most sequenced genomes [8] and have been implicated in the processing and degradation of different types of RNA, such as tRNA, rRNA, mRNA and the small RNA tmRNA [9-15].…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2012

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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.

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“…Members of this family are present in all domains of life. They hydrolyze RNA in the 3'–5' direction in a processive way (reviewed in Matos et al, 2011 ). RNase II from Escherichia coli is the prototype of this family, which also includes bacterial RNase R and eukaryotic Rrp44/Dis3 proteins.…”

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confidence: 99%