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Structural basis of ribosomal 30S subunit degradation by RNase R

ABSTRACT: Protein synthesis is a major energy-consuming process of the cell, which requires controlled production and turnover of ribosomes. While the last years have seen major advances in our understanding of ribosome biogenesis, structural insight into the degradation of ribosomes has been lacking. Here we present native structures of two distinct small ribosomal 30S subunit degradation intermediates associated with the 3’ to 5’ exonuclease, RNase R. The structures reveal that RNase R binds initially to the 30S platform to facilitate degradation of the functionally important anti-Shine-Dalgarno sequence and decoding site helix 44. RNase R then encounters a roadblock when it reaches the neck region of the 30S, which is overcome by a major structural rearrangement of the 30S head, involving loss of ribosomal proteins. RNase R parallels this movement, relocating to the decoding site, by using its N-terminal helix-turn-helix domain as an anchor. In vitro degradation assays suggest that head rearrangement poses a major kinetic barrier for RNase R, but also that the enzyme alone is sufficient for complete 30S degradation. Collectively, our results provide a mechanistic basis for RNase R-mediated 30S degradation and reveal that RNase R targets orphaned 30S subunits using a dynamic anchored binding site switching mechanism.

ORGANISM(S): Bacillus subtilis

PROVIDER: GSE251701 | GEO | 2023/12/25

REPOSITORIES: GEO

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Ribosome collisions in bacteria promote ribosome rescue by triggering mRNA cleavage by SmrB

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2022-08-01 | GSE179691 | GEO

Anatomy of footprint extension in ribosome profiling reveals translational landscape mediated by S1 protein in bacteria

Project description:Ribosome profiling — RNase footprinting of ribosome-bound mRNA — has been a unique and powerful method, applied to widespread organisms to survey ribosome traversal along mRNAs. In contrast to eukaryotes, bacterial ribosome footprints show a broad range of sizes, reflecting the differential states of ribosomes. However, the origin remains unclear. Here, we show that rotated state of ribosomes and intramolecular RNA duplexes each extend bacterial ribosome footprints at the 5′ end. Combining elongation inhibitors, cryo-electron microscopy, and ribosome profiling, we demonstrated that the rotated state of ribosomes results in long footprints. Along the subunit rotation, ribosomal protein S1 — a 30S-subunit RNA-binding protein — sterically protects mRNA at the 5′ end of the ribosome from RNase digestion and facilitates elongation of the ribosome. Moreover, we found that ribosomes stalled on ycbZ mRNA generate prolonged footprints because of their unique RNA secondary structure proximal to ribosomes. Through the studies of footprint extension, our results revealed S1-mediated stabilization of translation elongation and provide ribosome profiling approach to probe the conformational diversity of ribosomes in bacteria.

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2015-10-21 | GSE63817 | GEO

Coding sequence targeting by MicC RNA reveals bacterial mRNA silencing downstream of translational initiation

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2010-05-16 | E-GEOD-16540 | biostudies-arrayexpress

Sensing of individual stalled 80S ribosomes by Fap1 for non-functional rRNA turnover. Li et al

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2022-09-15 | GSE159329 | GEO

Transient RNA-DNA Hybrids Are Required for Efficient Double-Strand Break Repair

Project description:RNA-DNA hybrids are a major internal cause of DNA damage within cells, and their degradation by RNAse H enzymes is important for maintaining genomic stability. Here, we identified an unexpected role for RNA-DNA hybrids and RNase H enzymes in DNA repair. Using a site-specific DNA double-stranded break (DSB) system in Schizosaccharomyces pombe, we showed that RNA-DNA hybrids form as part of the homologous recombination (HR)-mediated DSB repair process and RNase H enzymes are essential for their degradation and efficient completion of DNA repair. Deleting RNase H stabilizes RNA-DNA hybrids around DSB sites and strongly impairs recruitment of the ssDNA-binding RPA complex. In contrast, overexpressing RNase H1 destabilizes these hybrids, leading to excessive strand resection and RPA recruitment, and to severe loss of repeat regions around DSBs. Our study challenges the existing model of HR-mediated DSB repair, and reveals a surprising role for RNA-DNA hybrids in maintaining genomic stability.

2016-10-28 | GSE80398 | GEO

Transient RNA-DNA Hybrids Are Required for Efficient Double-Strand Break Repair

2016-10-28 | GSE84882 | GEO

Antisense Transcripts Impede Uridylation-induced Exonucleolytic Degradation to Generate Guide RNAs

Project description:Small non-coding RNA biogenesis typically involves cleavage of structured precursors by RNase III-like endonucleases. However, guide RNAs that direct U-insertion/deletion mRNA editing in mitochondria of trypanosomes maintain 5′ triphosphate characteristic of transcription start site and possess U-tail indicative of 3′ processing and uridylation. Here, we identified a protein complex composed of RET1 TUTase and 3′-5′ DSS1 exonuclease, and three additional subunits. This complex, termed mitochondrial 3′ processome (MPsome), is responsible for primary uridylation of ~800-nt gRNA precursors, their processive degradation to a mature length of 50-60 nt, and secondary U-tail addition. Both strands of gRNA gene are transcribed giving rise to sense and antisense precursors of similar size. Head-to-head hybridization of these transcripts blocks symmetrical 3′-5′ degradation at the fixed distance from the double-stranded region. Together, our findings suggest a model in which gRNA is derived from the 5′ extremity of a primary molecule by uridylation-induced, antisense transcription-controlled exonucleolytic degradation.

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