What is the role of RNase J in mRNA turnover?

Condon, Ciarán

doi:10.4161/rna.7.3.11913

Cited by 70 publications

(71 citation statements)

References 31 publications

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“…It is yet to be determined whether the endonuclease or exonuclease activity of RNase J1 is more important for RNA turnover in B. subtilis (11). Our work suggests that, although the exonucleolytic decay pathway is obviously 5Ј enddependent, a decay pathway that begins with an endonucleolytic cleavage may be 5Ј end-independent.…”

mentioning

confidence: 62%

“…However, this secondary exonucleolytic pathway is unaffected by lowering RNase J1 levels (cf. half-life of NotI RNA in wild-type and RNase J1 mutant strains) because the K m for the RNase J1 exonucleolytic reaction is much lower than for the endonucleolytic reaction (11) and is therefore insensitive to the 5-fold decrease in cellular RNase J1 concentration. Addition of the 5Ј-SSS to trp leader RNA does not affect the dominant pathway for decay initiation that involves RNase J1 cleavage at nt 101 because the target site can be accessed independently of the 5Ј end (see below).…”

Section: Resultsmentioning

confidence: 99%

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5′ End-independent RNase J1 Endonuclease Cleavage of Bacillus subtilis Model RNA

Deikus

Bechhofer

2011

Journal of Biological Chemistry

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Background: Endonuclease cleavage initiates messenger RNA decay in bacteria. Result: Cleavage of a model RNA by the endonuclease RNase J1 is unaffected by strong secondary structure at the 5Ј end. Conclusion: RNase J1-initiated RNA decay occurs by endonuclease cleavage independent of the 5Ј end. Significance: Although mRNA stability is generally 5Ј end-dependent, mRNAs may contain sites that circumvent this dependence.

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mentioning

confidence: 62%

Section: Resultsmentioning

confidence: 99%

5′ End-independent RNase J1 Endonuclease Cleavage of Bacillus subtilis Model RNA

Deikus

Bechhofer

2011

Journal of Biological Chemistry

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“…Within higher plants, two chloroplast endonucleases have been identified, RNase E (Mudd et al 2008) and RNase J (Olinares et al 2010). RNase J also harbors 59-to-39 exonuclease nuclease activity, based on studies of the Bacillus subtilis orthologs (for review, see Condon 2010). We wished to ascertain if plants deficient for these enzymes would exhibit abnormalities in 5S rRNA biogenesis, and compare them to previously studied exoribonuclease mutants rnr1 and pnp, which lacks polynucleotide phosphorylase (Marchive et al 2009).…”

Section: Rnase E and Rnase J May Mediate Endonuclease Cleavage Withinmentioning

confidence: 99%

Overaccumulation of the chloroplast antisense RNA AS5 is correlated with decreased abundance of 5S rRNA in vivo and inefficient 5S rRNA maturation in vitro

Sharwood¹,

Hotto²,

Bollenbach³

et al. 2010

RNA

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Post-transcriptional regulation in the chloroplast is exerted by nucleus-encoded ribonucleases and RNA-binding proteins. One of these ribonucleases is RNR1, a 39-to-59 exoribonuclease of the RNase II family. We have previously shown that Arabidopsis rnr1-null mutants exhibit specific abnormalities in the expression of the rRNA operon, including the accumulation of precursor 23S, 16S, and 4.5S species and a concomitant decrease in the mature species. 5S rRNA transcripts, however, accumulate to a very low level in both precursor and mature forms, suggesting that they are unstable in the rnr1 background. Here we demonstrate that rnr1 plants overaccumulate an antisense RNA, AS5, that is complementary to the 5S rRNA, its intergenic spacer, and the downstream trnR gene, which encodes tRNA Arg , raising the possibility that AS5 destabilizes 5S rRNA or its precursor and/or blocks rRNA maturation. To investigate this, we used an in vitro system that supports 5S rRNA and trnR processing. We show that AS5 inhibits 5S rRNA maturation from a 5S-trnR precursor, and shorter versions of AS5 demonstrate that inhibition requires intergenic sequences. To test whether the sense and antisense RNAs form double-stranded regions in vitro, treatment with the single-strand-specific mung bean nuclease was used. These results suggest that 5S-AS5 duplexes interfere with a sense-strand secondary structure near the endonucleolytic cleavage site downstream from the 5S rRNA coding region. We hypothesize that these duplexes are degraded by a dsRNA-specific ribonuclease in vivo, contributing to the 5S rRNA deficiency observed in rnr1.

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“…1B; Shahbabian et al 2009;Yao and Bechhofer 2010). The 59-terminal part of the mRNA can then be degraded by 39-to-59 exonucleases (Oussenko et al 2005;Condon 2010). Similar to E. coli RNase E, both B. subtilis RNase Y and RNase J1 prefer a 59-monophosphate for their endo-or exonucleolytic activities, respectively (de la Sierra-Gallay et al 2008;Shahbabian et al 2009).…”

Section: Introductionmentioning

confidence: 99%

Identification of an RNase J ortholog in Sulfolobus solfataricus: Implications for 5′-to-3′ directional decay and 5′-end protection of mRNA in Crenarchaeota

Hasenöhrl¹,

Konrat²,

Bläsi³

2010

RNA

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In both Bacteria and Eukaryotes, degradation is known to start at the 59 and at the 39 extremities of mRNAs. Until the recent discovery of 59-to-39 exoribonucleases in hyperthermophilic Euryarchaeota, the exosome was assumed to be the key enzyme in mRNA degradation in Archaea. By means of zymogram assays and bioinformatics, we have identified a 59-to-39 exoribonuclease activity in the crenarchaeum Sulfolobus solfataricus (Sso), which is affected by the phosphorylation state of the 59-end of the mRNA. The protein comprises typical signature motifs of the b-CASP family of metallo-b-lactamases and was termed Sso-RNAse J. Thus, our study provides the first evidence for a 59-to-39 directional mRNA decay pathway in the crenarchaeal clade of Archaea. In Bacteria the 59-end of mRNAs is often protected by a tri-phosphorylated 59-terminus and/or by stem-loop structures, while in Eukaryotes the cap-binding complex is responsible for this task. Here, we show that binding of translation initiation factor a/eIF2(g) to the 59-end of mRNA counteracts the 59-to-39 exoribonucleolytic activity of Sso-RNase J in vitro. Hence, 59-to-39 directional decay and 59-end protection appear to be conserved features of mRNA turnover in all kingdoms of life.

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What is the role of RNase J in mRNA turnover?

Cited by 70 publications

References 31 publications

5′ End-independent RNase J1 Endonuclease Cleavage of Bacillus subtilis Model RNA

5′ End-independent RNase J1 Endonuclease Cleavage of Bacillus subtilis Model RNA

Overaccumulation of the chloroplast antisense RNA AS5 is correlated with decreased abundance of 5S rRNA in vivo and inefficient 5S rRNA maturation in vitro

Identification of an RNase J ortholog in Sulfolobus solfataricus: Implications for 5′-to-3′ directional decay and 5′-end protection of mRNA in Crenarchaeota

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