Conserved Bacterial RNase YbeY Plays Key Roles in 70S Ribosome Quality Control and 16S rRNA Maturation

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Molecular cell (Impact Factor: 14.02). 12/2012; 49(3). DOI: 10.1016/j.molcel.2012.11.025
Source: PubMed


Quality control of ribosomes is critical for cellular function since protein mistranslation leads to severe physiological consequences. We report evidence of a previously unrecognized ribosome quality control system in bacteria that operates at the level of 70S to remove defective ribosomes. YbeY, a previously unidentified endoribonuclease, and the exonuclease RNase R act together by a process mediated specifically by the 30S ribosomal subunit, to degrade defective 70S ribosomes but not properly matured 70S ribosomes or individual subunits. Furthermore, there is essentially no fully matured 16S rRNA in a ΔybeY mutant at 45°C, making YbeY the only endoribonuclease to be implicated in the critically important processing of the 16S rRNA 3' terminus. These key roles in ribosome quality control and maturation indicate why YbeY is a member of the minimal bacterial gene set and suggest that it could be a potential target for antibacterial drugs.

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    • "The universe of sRNA regulators in S. meliloti silencing (Pandey et al. 2011). In E. coli YbeY acts as an RNase involved in 16S rRNA maturation and 70S ribosome quality control that also influences Hfq-dependent and Hfqindependent sRNA-mediated regulation (Jacob et al. 2013; Pandey et al. 2014). In S. meliloti lack of YbeY results into a phenotypic pleiotropy resembling that of hfq mutants (Pandey et al. 2011). "
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    ABSTRACT: High-throughput transcriptome profiling (RNAseq) has uncovered large and heterogeneous populations of small noncoding RNA species (sRNAs) with potential regulatory roles in bacteria. These sRNAs act mostly by protein-assisted base-pairing with target mRNAs to fine-tune post-transcriptional reprogramming of gene expression underlying bacterial responses to changing environments. Riboregulation impacts virtually any physiological process, and has been shown to largely influence virulence of pathogenic bacteria. Here, we review our current knowledge on the structure, conservation and function of the noncoding transcriptome of the α-rhizobia Sinorhizobium meliloti, the nitrogen-fixing symbiotic partner of alfalfa and related medics. Several RNAseq-based surveys in S. meliloti have shown abundant transcription from hitherto regarded as noncoding intergenic regions (IGRs), strikingly high numbers of mRNA-derived RNAs and pervasive antisense transcription of protein-coding genes. sRNAs encoded within IGRs constitute the most extensively studied group of bacterial riboregulators. They are differentially expressed and modulate translation and/or stability of trans-encoded target mRNAs by short antisense interactions that, in enteric model bacteria, are facilitated by the RNA chaperone Hfq. Among symbiotic rhizobia, regulatory sRNAs have been functionally characterized only in S. meliloti to date. The trans-sRNAs AbcR1 and AbcR2 are examples of Hfq-dependent sRNAs whereas EcpR1 does not bind Hfq. We will provide insights into the transcriptional regulation and activity mechanisms of these sRNAs for the targeting and control of multiple mRNAs involved in nutrient uptake (AbcR1/2) and cell cycle progression (EcpR1).
    Full-text · Article · Oct 2015 · Symbiosis
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    • "It was also shown to interact with the ribosomal protein S12 (Ge et al., 2010; Liang and Deutscher, 2013; Strader et al., 2013). Together with the YbeY nuclease, RNase R is able to efficiently cleave defective ribosomes in vitro (Jacob et al., 2013). The quality control of ribosomes is critical to ensure proper protein translation. "

    Full-text · Article · Jun 2014 · Frontiers in Cellular and Infection Microbiology
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    • "Substantial incorporation of immature 30S subunit into the 70S ribosome itself could be a cellular disorder due to the processing defect in the rRNA maturation. Indeed, characterization of some types of these 17S rRNA-containing ribosomes reveals a defect in translational fidelity (Davies et al., 2010; Roy-Chaudhuri et al., 2010), and more importantly, it was recently demonstrated that the immature 30S subunits in these 70S ribosomes could trigger degradation of defective 70S ribosomes by YbeY and RNase R (Jacob et al., 2013). Therefore, these results show that bacterial cells possess multiple quality control systems that make use of the rRNA maturation at different stages to ensure the integrity of the 70S ribosome. "
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    ABSTRACT: The in vivo assembly of ribosomal subunits is a highly complex process, with a tight coordination between protein assembly and rRNA maturation events, such as folding and processing of rRNA precursors, as well as modifications of selected bases. In the cell, a large number of factors are required to ensure the efficiency and fidelity of subunit production. Here we characterize the immature 30S subunits accumulated in a factor-null Escherichia coli strain (∆rsgA∆rbfA). The immature 30S subunits isolated with varying salt concentrations in the buffer system show interesting differences on both protein composition and structure. Specifically, intermediates derived under the two contrasting salt conditions (high and low) likely reflect two distinctive assembly stages, the relatively early and late stages of the 3′ domain assembly, respectively. Detailed structural analysis demonstrates a mechanistic coupling between the maturation of the 5′ end of the 17S rRNA and the assembly of the 30S head domain, and attributes a unique role of S5 in coordinating these two events. Furthermore, our structural results likely reveal the location of the unprocessed terminal sequences of the 17S rRNA, and suggest that the maturation events of the 17S rRNA could be employed as quality control mechanisms on subunit production and protein translation. Electronic supplementary material The online version of this article (doi:10.1007/s13238-014-0044-1) contains supplementary material, which is available to authorized users.
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