Initiation of Decay of Bacillus subtilis rpsO mRNA by Endoribonuclease RNase Y

Department of Pharmacology and Systems Therapeutics, Box 1603, Mount Sinai School of Medicine of New York University, New York, NY 10029, USA.
Journal of bacteriology (Impact Factor: 2.81). 04/2010; 192(13):3279-86. DOI: 10.1128/JB.00230-10
Source: PubMed


rpsO mRNA, a small monocistronic mRNA that encodes ribosomal protein S15, was used to study aspects of mRNA decay initiation in
Bacillus subtilis. Decay of rpsO mRNA in a panel of 3′-to-5′ exoribonuclease mutants was analyzed using a 5′-proximal oligonucleotide probe and a series of
oligonucleotide probes that were complementary to overlapping sequences starting at the 3′ end. The results provided strong
evidence that endonuclease cleavage in the body of the message, rather than degradation from the native 3′ end, is the rate-determining
step for mRNA decay. Subsequent to endonuclease cleavage, the upstream products were degraded by polynucleotide phosphorylase
(PNPase), and the downstream products were degraded by the 5′ exonuclease activity of RNase J1. The rpsO mRNA half-life was unchanged in a strain that had decreased RNase J1 activity and no RNase J2 activity, but it was 2.3-fold
higher in a strain with decreased activity of RNase Y, a recently discovered RNase of B. subtilis encoded by the ymdA gene. Accumulation of full-length rpsO mRNA and its decay intermediates was analyzed using a construct in which the rpsO transcription unit was under control of a bacitracin-inducible promoter. The results were consistent with RNase Y-mediated
initiation of decay. This is the first report of a specific mRNA whose stability is determined by RNase Y.

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    • "In agreement, the concerted action of RNase Y and RNase J in exonucleolytic mode has been implicated in the turnover of S-adenosyl methionine (SAM)-dependent riboswitches [12]. Other examples of RNase Y action include a regulatory processing of the gapA operon transcript [14], initiation of the rpsO mRNA decay [19] and the uncoupling of the expression of translation factor IF3 from that of the ribosomal proteins in the infC-rpmI-rplT operon [20]. In S. aureus, RNase Y is important for the processing of virulence related mRNAs [21]. "
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    ABSTRACT: RNase Y is a key endoribonuclease affecting global mRNA stability in Bacillus subtilis. Its characterization provided the first evidence that endonucleolytic cleavage plays a major role in the mRNA metabolism of this organism. RNase Y shares important functional features with the RNA decay initiating RNase E from Escherichia coli, notably a similar cleavage specificity and a preference for 5' monophosphorylated substrates. We used high-resolution tiling arrays to analyze the effect of RNase Y depletion on RNA abundance covering the entire genome. The data confirm that this endoribonuclease plays a key role in initiating the decay of a large number of mRNAs as well as non coding RNAs. The downstream cleavage products are likely to be degraded by the 5' exonucleolytic activity of RNases J1/J2 as we show for a specific case. Comparison of the data with that of two other recent studies revealed very significant differences. About two thirds of the mRNAs upregulated following RNase Y depletion were different when compared to either one of these studies and only about 10% were in common in all three studies. This highlights that experimental conditions and data analysis play an important role in identifying RNase Y substrates by global transcriptional profiling. Our data confirmed already known RNase Y substrates and due to the precision and reproducibility of the profiles allow an exceptionally detailed view of the turnover of hundreds of new RNA substrates.
    Full-text · Article · Jan 2013 · PLoS ONE
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    • "The presence of RNA-binding KH domain and a highly conserved HD region suggested RNaseY to function in nucleic acid metabolism.41 RNaseY (YmdA) has been described as an essential RNase involved in processing of glycolytic mRNA,42 degradation of rpsO mRNA.43 It acts as an endonuclease by processing prematurely terminated mRNA transcripts.44 "
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    ABSTRACT: Membrane dynamics are involved in crucial processes in eukaryotic and prokaryotic cells. Membrane fusion and fission events are often catalyzed by proteins that belong to the dynamin family of large GTPases. It has recently been shown that members of the dynamin superfamily are also present in many bacterial species. Although structural information about full length bacterial dynamin-like proteins is available, their molecular role remains unclear. We have shown previously that DynA, a dynamin-like protein found in the firmicute Bacillus subtilis is able to fuse membranes in vitro. In contrast to other members of the dynamin family this membrane remodeling activity was not dependent on guanosine nucleotides, but required magnesium. DynA assemblies localize in foci that are often enriched at sites of septation and hence a potential role during bacterial cytokinesis was discussed. In order to identify potential interaction partners we constructed a bacterial-two hybrid (B2H) library and screened for DynA interacting proteins. Three potential interaction partner have been identified, YneK, RNaseY (YmdA), and YwpG. Localization of these proteins phenocopies that of DynA, supporting the potential interaction in vivo.
    Full-text · Article · Jul 2012 · Communicative & integrative biology
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    • "The enzymatic activity of PNPase on single-stranded DNA is in part modulated by RecA, a gene located upstream of rny [35]. Decay of the highly conserved rpsO mRNA is initiated by RNase Y followed by PNPase [66]. Recently, in Streptomyces coelicolor, it has been shown that transcripts originating at the rpsO promoter read-through into pnpA and become processed by RNase III [67]. "
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    ABSTRACT: It is widely acknowledged that RNA stability plays critical roles in bacterial adaptation and survival in different environments like those encountered when bacteria infect a host. Bacterial ribonucleases acting alone or in concert with regulatory RNAs or RNA binding proteins are the mediators of the regulatory outcome on RNA stability. We will give a current update of what is known about ribonucleases in the model Gram-positive organism Bacillus subtilis and will describe their established roles in virulence in several Gram-positive pathogenic bacteria that are imposing major health concerns worldwide. Implications on bacterial evolution through stabilization/transfer of genetic material (phage or plasmid DNA) as a result of ribonucleases' functions will be covered. The role of ribonucleases in emergence of antibiotic resistance and new concepts in drug design will additionally be discussed.
    Full-text · Article · Mar 2012 · International Journal of Microbiology
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