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: 14.46). 12/2012; 49. DOI: 10.1016/j.molcel.2012.11.025
Source: PubMed

ABSTRACT 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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    • "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. "
    Frontiers in Cellular and Infection Microbiology 06/2014; 4:68. DOI:10.3389/fcimb.2014.00068 · 2.62 Impact Factor
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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.
    Protein & Cell 03/2014; 5(5). DOI:10.1007/s13238-014-0044-1 · 2.85 Impact Factor
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    • "RNase R is a versatile 3 –5 exoribonuclease with the distinctive ability to unwind and degrade structured RNA substrates without ATP consumption (Cheng and Deutscher, 2002; Vincent and Deutscher, 2009). RNase R does not exhibit sequence specificity and is thus involved in the processing and turnover of a diverse array of cellular RNAs, including mRNA, rRNA, and tRNAs (Cheng and Deutscher, 2003; Jacob et al., 2013). Given the broad range of RNase R functions, it is of high interest to understand its overall architecture and the spatial arrangement of its distinct N-and C-terminal domains. "
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    ABSTRACT: Decoding of aberrant mRNAs leads to unproductive ribosome stalling and sequestration of components of the translation machinery. Bacteria have evolved three seemingly independent pathways to resolve stalled translation complexes. The trans-translation process, orchestrated by the hybrid transfer-messenger RNA (tmRNA) and its essential protein co-factor, small protein B (SmpB), is the principal translation quality control system for rescuing unproductively stalled ribosomes. Two specialized alternative rescue pathways, coordinated by ArfA and ArfB, have been recently discovered. The SmpB-tmRNA mediated trans-translation pathway, in addition to re-mobilizing stalled translation complexes, co-translationally appends a degradation tag to the associated nascent polypeptides, marking them for proteolysis by various cellular proteases. Another unique feature of trans-translation, not shared by the alternative rescue pathways, is the facility to recruit ribonuclease R (RNase R) for targeted degradation of non-stop mRNAs, thus preventing further futile cycles of translation. The distinct C-terminal lysine-rich (K-rich) domain of RNase R is essential for its recruitment to stalled ribosomes. To gain new insights into the structure and function of RNase R, we investigated its global architecture, the spatial arrangement of its distinct domains, and the identities of key functional residues in its unique K-rich domain. Small-angle X-ray scattering models of RNase R reveal a tri-lobed structure with flexible N- and C-terminal domains, and suggest intimate contacts between the K-rich domain and the catalytic core of the enzyme. Alanine-scanning mutagenesis of the K-rich domain, in the region spanning residues 735 and 750, has uncovered the precise amino acid determinants required for the productive engagement of RNase R on tmRNA-rescued ribosomes. Theses analyses demonstrate that alanine substitution of conserved residues E740 and K741result in profound defects, not only in the recruitment of RNase R to rescued ribosomes but also in the targeted decay of non-stop mRNAs. Additionally, an RNase R variant with alanine substitution at residues K749 and K750 exhibits extensive defects in ribosome enrichment and non-stop mRNA decay. In contrast, alanine substitution of additional conserved residues in this region has no effect on the known functions of RNase R. In vitro RNA degradation assays demonstrate that the consequential substitutions (RNase R(E740A/K741A) and RNase R(K749A/K750A)) do not affect the ability of the enzyme to degrade structured RNAs, indicating that the observed defect is specific to the trans-translation related activities of RNase R. Taken together, these findings shed new light on the global architecture of RNase R and provide new details of how this versatile RNase effectuates non-stop mRNA decay on tmRNA-rescued ribosomes.
    Frontiers in Microbiology 03/2014; 5:93. DOI:10.3389/fmicb.2014.00093 · 3.94 Impact Factor
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