Bacillus subtilis RNase J1 endonuclease and 5′ exonuclease activities in the turnover of ΔermC mRNA

Department of Pharmacology and Systems Therapeutics, Mount Sinai School of Medicine of New York University, New York, New York 10029, USA.
RNA (Impact Factor: 4.94). 10/2009; 15(12):2331-9. DOI: 10.1261/rna.1749109
Source: PubMed


RNase J1, a ribonuclease with 5' exonuclease and endonuclease activities, is an important factor in Bacillus subtilis mRNA decay. A model for RNase J1 endonuclease activity in mRNA turnover has RNase J1 binding to the 5' end and tracking to a target site downstream, where it makes a decay-initiating cleavage. The upstream fragment from this cleavage is degraded by 3' exonucleases; the downstream fragment is degraded by RNase J1 5' exonuclease activity. Previously, DeltaermC mRNA was used to show 5'-end dependence of mRNA turnover. Here we used DeltaermC mRNA to probe RNase J1-dependent degradation, and the results were consistent with aspects of the model. DeltaermC mRNA showed increased stability in a mutant strain that contained a reduced level of RNase J1. In agreement with the tracking concept, insertion of a strong stem-loop structure at +65 resulted in increased stability. Weakening this stem-loop structure resulted in reversion to wild-type stability. RNA fragments containing the 3' end were detected in a strain with reduced RNase J1 expression, but were undetectable in the wild type. The 5' ends of these fragments mapped to the upstream side of predicted stem-loop structures, consistent with an impediment to RNase J1 5' exonuclease processivity. A DeltaermC mRNA deletion analysis suggested that decay-initiating endonuclease cleavage could occur at several sites near the 3' end. However, even in the absence of these sites, stability was further increased in a strain with reduced RNase J1, suggesting alternate pathways for decay that could include exonucleolytic decay from the 5' end.

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Available from: Josh Sharp, Jun 25, 2014
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    • "Similar to the daa operon, pausing during ermC translation results in mRNA cleavage upstream of the paused ribosome and stabilization of the downstream sequence (Bechhofer and Zen, 1989; Drider et al., 2002). David Bechhofer and colleagues have discovered that this mRNA processing is mediated by RNase J1 (Yao et al., 2009), an essential enzyme with both endonuclease and 5′-to-3′ exonuclease activities (Mathy et al., 2007). Although tmRNA activity has not been examined during ErmC-mediated ribosome pausing, like the DaaP-arrested ribosome, the intact downstream message should preclude ribosome rescue. "
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    • "Consistent with the conclusion that RNase J1 is principally responsible for degrading monophosphorylated yhxA-glpP mRNA, the concentration of that decay intermediate increased threefold relative to its triphosphorylated precursor when RNase J1 was depleted (Figure 5B). Prior evidence that RNase J1 depletion prolongs the lifetime of ΔermC mRNA (Yao et al., 2009) suggests that the monophosphorylated form of that message is degraded by a similar mechanism. "
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    • "RNase J has been shown to play an extensive role in mRNA turnover, with B. subtilis being the best-characterized organism in this regard (Deikus et al., 2008; Mä der et al., 2008; Yao et al., 2009). RNase J is also involved in the maturation of 16S and 23S ribosomal RNA in both B. subtilis and S. meliloti, although in B. subtilis its function in 23S rRNA maturation is as a backup to the primary pathway catalyzed by Mini-RNase III (Madhugiri and Evguenieva-Hackenberg, 2009; Redko and Condon, 2010). "
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