An Important Role for RNase R in mRNA Decay

Cheng, Zhuan Fen; Deutscher, Murray P.

doi:10.1016/j.molcel.2004.11.048

Cited by 211 publications

(276 citation statements)

References 25 publications

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“…It has been shown in E. coli that polyadenylation by poly(A) polymerase and polynucleotide phosphorylase (PNPase) activity promotes degradation of defective tRNA Trp (Li et al, 2002). However, PNPase and RNase II have been shown to be incapable of processing through stem-loop structures (reviewed by GrunbergManago, 1999), while RNase R can process through these structures (Cheng & Deutscher, 2005;Cairrao et al, 2003).…”

Section: Introductionmentioning

confidence: 99%

Characterization of tRNACys processing in a conditional Bacillus subtilis CCase mutant reveals the participation of RNase R in its quality control

et al. 2010

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We generated a conditional CCase mutant of Bacillus subtilis to explore the participation in vivo of the tRNA nucleotidyltransferase (CCA transferase or CCase) in the maturation of the singlecopy tRNA Cys , which lacks an encoded CCA 39 end. We observed that shorter tRNA Cys species, presumably lacking CCA, only accumulated when the inducible Pspac : cca was introduced into an rnr mutant strain, but not in combination with pnp. We sequenced the tRNA 39 ends produced in the various mutant tRNA Cys species to detect maturation and decay intermediates and observed that decay of the tRNA Cys occurs through the addition of poly(A) or heteropolymeric tails. A few clones corresponding to full-size tRNAs contained either CCA or other C and/or A sequences, suggesting that these are substrates for repair and/or decay. We also observed editing of tRNA Cys at position 21, which seems to occur preferentially in mature tRNAs. Altogether, our results provide in vivo evidence for the participation of the B. subtilis cca gene product in the maturation of tRNAs lacking CCA. We also suggest that RNase R exoRNase in B. subtilis participates in the quality control of tRNA.

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Section: Introductionmentioning

confidence: 99%

Characterization of tRNACys processing in a conditional Bacillus subtilis CCase mutant reveals the participation of RNase R in its quality control

et al. 2010

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“…PNPase is also responsible for the G, C and U residues that are found at low frequency in the poly(A) tails of RNAs from wild-type E. coli (Mohanty & Kushner, 2000b). The overall model for RNA degradation that has emerged from the studies in E. coli involves the generation of RNA 39-ends via endonucleolytic cleavage by the endoribonucleases RNase E and RNase III, polyadenylation of the 39-ends by PAP I (and under some conditions by PNPase) and degradation of the resulting RNAs exonucleolytically by PNPase (with the assistance of the DEAD box helicase RhlB), RNase II and RNase R (Cheng & Deutscher, 2005;Coburn & Mackie, 1999;Mohanty & Kushner, 1999b, 2000aO'Hara et al, 1995). This model applies especially to structured RNAs, with hairpins at their 39-ends (Carpousis et al, 1999;Régnier & Arraiano, 2000).…”

Section: Introductionmentioning

confidence: 99%

RNA 3′-tail synthesis in Streptomyces: in vitro and in vivo activities of RNase PH, the SCO3896 gene product and polynucleotide phosphorylase

et al. 2006

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As in other bacteria, 39-tails are added post-transcriptionally to Streptomyces coelicolor RNA. These tails are heteropolymeric, and although there are several candidates, the enzyme responsible for their synthesis has not been definitively identified. This paper reports on three candidates for this role. First, it is confirmed that the product of S. coelicolor gene SCO3896, although it bears significant sequence similarity to Escherichia coli poly(A) polymerase I, is a tRNA nucleotidyltransferase, not a poly(A) polymerase. It is further shown that SCO2904 encodes an RNase PH homologue that possesses the polymerization and phosphorolysis activities expected for enzymes of that family. S. coelicolor RNase PH can add poly(A) tails to a model RNA transcript in vitro. However, disruption of the RNase PH gene has no effect on RNA 39-tail length or composition in S. coelicolor; thus, RNase PH does not function as the RNA 39-polyribonucleotide polymerase [poly(A) polymerase] in that organism. These results strongly suggest that the enzyme responsible for RNA 39-tail synthesis in S. coelicolor and other streptomycetes is polynucleotide phosphorylase (PNPase). Moreover, this study shows that both PNPase and the product of SCO3896 are essential. It is possible that the dual functions of PNPase in the synthesis and degradation of RNA 39-tails make it indispensable in Streptomyces.

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“…B oth polynucleotide phosphorylase (PNPase) and RNase R are responsible for degrading a variety of transcripts in bacteria, such as mRNAs, defective rRNAs, and antisense regulatory RNAs (1)(2)(3)(4). Although strains of Escherichia coli remain viable with a loss of either enzyme, the elimination of both results in an accumulation of rRNA fragments and cell death (3).…”

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confidence: 99%

“…In contrast, RNase R is unique among bacterial exoribonucleases, in that it can digest highly structured RNA without additional factors (4), suggesting that the enzyme may have significant helicase activity. In particular, RNase R has been observed to unwind and degrade completely dsRNA substrates of nearly 20 bp (4,7,21).…”

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confidence: 99%

Direct observation of processive exoribonuclease motion using optical tweezers

Fazal

Koslover

Luisi

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Bacterial RNases catalyze the turnover of RNA and are essential for gene expression and quality surveillance of transcripts. In Escherichia coli, the exoribonucleases RNase R and polynucleotide phosphorylase (PNPase) play critical roles in degrading RNA. Here, we developed an optical-trapping assay to monitor the translocation of individual enzymes along RNA-based substrates. Single-molecule records of motion reveal RNase R to be highly processive: one molecule can unwind over 500 bp of a structured substrate. However, enzyme progress is interrupted by pausing and stalling events that can slow degradation in a sequence-dependent fashion. We found that the distance traveled by PNPase through structured RNA is dependent on the A+U content of the substrate and that removal of its KH and S1 RNA-binding domains can reduce enzyme processivity without affecting the velocity. By a periodogram analysis of single-molecule records, we establish that PNPase takes discrete steps of six or seven nucleotides. These findings, in combination with previous structural and biochemical data, support an asymmetric inchworm mechanism for PNPase motion. The assay developed here for RNase R and PNPase is well suited to studies of other exonucleases and helicases.single-molecule biophysics | optical trap | exoribonuclease | processivity | step size B oth polynucleotide phosphorylase (PNPase) and RNase R are responsible for degrading a variety of transcripts in bacteria, such as mRNAs, defective rRNAs, and antisense regulatory RNAs (1-4). Although strains of Escherichia coli remain viable with a loss of either enzyme, the elimination of both results in an accumulation of rRNA fragments and cell death (3). To degrade RNA, both ribonucleases require an unstructured binding site of at least 7-10 nt at the 3′ end of the substrate (5-7), a sequence that often is supplied by posttranscriptional polyadenylation (8-10). After binding RNA, PNPase and RNase R processively digest the substrate in the 3′-to-5′ direction (11-13).PNPase consists of a trimer that degrades RNA at catalytic sites within a central channel (9,14). The enzyme is homologous to eukaryotic and archaeal exosomes and, like these hexameric proteins, possesses a core of six RNase PH domains arranged in a ringlike configuration (two per protomer) (6, 15). Each protomer also carries a KH and an S1 RNA-binding domain at its C terminus, both of which are connected to the body of the enzyme by flexible linkers (6, 16). These domains are thought to bind RNA upstream of the catalytic sites, and recent structural evidence suggests that they may guide the substrate into the central channel through a "hands gripping a rope" mechanism (16,17). By itself, PNPase may stall on structured RNA, particularly on G:C hairpins comprising more than six base pairs (18). PNPase often associates with the DEAD-box helicase RhlB to move through structured regions and generally does so in the context of the multienzyme degradosome (2, 19). However, there is some evidence that PNPase can digest structured tra...

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An Important Role for RNase R in mRNA Decay

Cited by 211 publications

References 25 publications

Characterization of tRNACys processing in a conditional Bacillus subtilis CCase mutant reveals the participation of RNase R in its quality control

Characterization of tRNACys processing in a conditional Bacillus subtilis CCase mutant reveals the participation of RNase R in its quality control

RNA 3′-tail synthesis in Streptomyces: in vitro and in vivo activities of RNase PH, the SCO3896 gene product and polynucleotide phosphorylase

Direct observation of processive exoribonuclease motion using optical tweezers

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