Analysis of mRNA Decay Intermediates in Bacillus subtilis 3′ Exoribonuclease and RNA Helicase Mutant Strains

Chhabra, Shivani; Mandell, Zachary F.; Liu, Bo; Babitzke, Paul; Bechhofer, David H.

doi:10.1128/mbio.00400-22

Cited by 5 publications

(3 citation statements)

References 49 publications

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“…Next, we used TERMITe to perform a comprehensive analysis of the reported here and publicly available Term-seq datasets to investigate the variability in intrinsic termination signals across bacterial species. In our analysis we included 691 and 957 intrinsic termination sites predicted by TERMITe in E. coli based on the data described in this study and Choe et al (17), respectively; 635, 1165, 984 and 1214 sites of B. subtilis based on data from Chhabra et al (15), Mandell et al (7), Dar et al (14) and Mondal et al (8), respectively; 796 terminators from E. faecalis (14); 862 terminators from L. monocytogenes (14); 206 terminators from Z. mobilis (24); 165 terminators from Synechocystis sp . (16); 629 terminators from S. coelicolor (20), 573 terminators from S. venezuelae (20); 520 terminators from S. tsukubensiis (20); 737 terminators from S. griseus (22); 495 terminators from S. lividans (20); 435 terminators from S. clavuligerus (21); 707 terminators from S. avermitilis (20) (Supplementary Figure 3A).…”

Section: Resultsmentioning

confidence: 99%

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Characterization of bacterial intrinsic transcription terminators identified with TERMITe – a novel method for comprehensive analysis of Term-seq data

Kosiński,

Ranaweera,

Chełkowska-Pauszek

et al. 2024

Preprint

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In recent years, Term-seq became a standard experimental approach for high-throughput identification of 3′ ends of bacterial transcripts. It was widely adopted to study transcription termination events and 3′ maturation of bacterial RNAs. Despite widespread utilization, a universal bioinformatics toolkit for comprehensive analysis of Term-seq sequencing data is still lacking. Here, we describeTERMITe, a novel method for the identification of stable 3′ RNA ends based on bacterial Term-seq data.TERMITeworks with data obtained from both currently available Term-seq protocols and provides robust identification of the 3′ RNA termini. Unique features ofTERMITeinclude the calculation of the transcription termination efficiency using matched RNA-seq data and the comprehensive annotation of the identified 3′ RNA ends, allowing functional analysis of the results. We have appliedTERMITeto the comparative analysis of experimentally validated intrinsic terminators spanning different species across the bacterial domain of life, revealing substantial differences in their sequence and secondary structure. We also provide a complete atlas of experimentally validated intrinsic transcription termination sites for 13 bacterial species, includingEscherichia coli,Bacillus subtilis,Listeria monocytogenes,Enterococcus faecalis,Synechocystissp.,Streptomyces clavuligerus,Streptomyces griseus,Streptomyces coelicolor,Streptomyces avermitilis,Streptomyces lividans,Streptomyces tsukubaensis,Streptomyces venezuelae, andZymomonas mobilis.

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Section: Resultsmentioning

confidence: 99%

“…Term-seq has been successfully applied to multiple bacterial and archaeal species, including B. subtilis (6–8, 14, 15), Listeria monocytogenes (14), Enterococcus faecalis (14), Synechocystis sp . (16), E. coli (17), Streptomyces sp .…”

Section: Introductionmentioning

confidence: 99%

Characterization of bacterial intrinsic transcription terminators identified with TERMITe – a novel method for comprehensive analysis of Term-seq data

Kosiński,

Ranaweera,

Chełkowska-Pauszek

et al. 2024

Preprint

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“…Thus, before entering the catalytic pocket of RNase R, RNA duplexes are thought to be unwound by the concerted action of the CSD and S1 domains that encircle the entry to the lumen of the RNB domain 18 , 19 . Although ATP is not required to unwind its substrates, RNase R is still extremely efficient at degrading highly structured RNAs when compared with other exonucleases 20 .…”

Section: Mainmentioning

confidence: 99%

Structural basis of ribosomal 30S subunit degradation by RNase R

Dimitrova-Paternoga,

Kasvandik,

Beckert

et al. 2024

Nature

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Protein synthesis is a major energy-consuming process of the cell that requires the controlled production1–3 and turnover4,5 of ribosomes. Although the past few 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 ribonuclease R (RNase R). The structures reveal that RNase R binds at first to the 30S platform to facilitate the degradation of the functionally important anti-Shine–Dalgarno sequence and the decoding-site helix 44. RNase R then encounters a roadblock when it reaches the neck region of the 30S subunit, and this is overcome by a major structural rearrangement of the 30S head, involving the loss of ribosomal proteins. RNase R parallels this movement and relocates 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 indicate that the enzyme alone is sufficient for complete degradation of 30S subunits. Collectively, our results provide a mechanistic basis for the degradation of 30S mediated by RNase R, and reveal that RNase R targets orphaned 30S subunits using a dynamic mechanism involving an anchored switching of binding sites.

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