Characterization of the RNase R association with ribosomes

Małecki, Michał; Bárria, Cátia; Arraiano, Cecília M.

doi:10.1186/1471-2180-14-34

Cited by 24 publications

(27 citation statements)

References 25 publications

(47 reference statements)

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“…Here, we revealed that Dss1 interacts specifically with the large ribosomal subunit, whereas Suv3 is mainly a component of the nucleoid-MIOREX complex, in line with previous observations that it copurifies with mitochondrial ribosomes (Dziembowski et al, 2003) and a cluster-like organization adjacent to RNA and DNA (Borowski et al, 2013). The interaction of an RNase with the ribosome is reminiscent of the situation in bacteria, where RNase R binding to the small ribosomal subunit (Malecki et al, 2014) both stabilizes the enzyme and sequesters it from undesired spontaneous nucleolytic activity (Liang and Deutscher, 2013). Only when the ribosome contains a damaged mRNA, RNase R is active to rescue the ribosome in a process known as transtranslation.…”

Section: Discussionsupporting

confidence: 83%

Organization of Mitochondrial Gene Expression in Two Distinct Ribosome-Containing Assemblies

et al. 2015

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Mitochondria contain their own genetic system that provides subunits of the complexes driving oxidative phosphorylation. A quarter of the mitochondrial proteome participates in gene expression, but how all these factors are orchestrated and spatially organized is currently unknown. Here, we established a method to purify and analyze native and intact complexes of mitochondrial ribosomes. Quantitative mass spectrometry revealed extensive interactions of ribosomes with factors involved in all the steps of posttranscriptional gene expression. These interactions result in large expressosome-like assemblies that we termed mitochondrial organization of gene expression (MIOREX) complexes. Superresolution microscopy revealed that most MIOREX complexes are evenly distributed throughout the mitochondrial network, whereas a subset is present as nucleoid-MIOREX complexes that unite the whole spectrum of organellar gene expression. Our work therefore provides a conceptual framework for the spatial organization of mitochondrial protein synthesis that likely developed to facilitate gene expression in the organelle.

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Section: Discussionsupporting

confidence: 83%

Organization of Mitochondrial Gene Expression in Two Distinct Ribosome-Containing Assemblies

et al. 2015

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“…Not surprisingly, a ΔybeY Δrnr double mutant presents a severe growth phenotype accompanied by a pronounced 16S rRNA maturation defect (3). Although RNase R is also recruited to the ribosome via ribosomal protein S12 (33–35) and despite the strong functional relationship between YbeY and RNase R, no B2H interaction was detected. Likewise, although our previous studies revealed a strong functional interaction between YbeY and polynucleotide phosphorylase (PNPase), similarly characterized by deficiencies in rRNA maturation in a ΔybeY Δpnp double mutant (3), we were unable to observe a direct B2H interaction between these two proteins.…”

Section: Resultsmentioning

confidence: 99%

Identification of YbeY-Protein Interactions Involved in 16S rRNA Maturation and Stress Regulation in Escherichia coli

Vercruysse

Köhrer

Shen³

et al. 2016

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YbeY is part of a core set of RNases in Escherichia coli and other bacteria. This highly conserved endoribonuclease has been implicated in several important processes such as 16S rRNA 3′ end maturation, 70S ribosome quality control, and regulation of mRNAs and small noncoding RNAs, thereby affecting cellular viability, stress tolerance, and pathogenic and symbiotic behavior of bacteria. Thus, YbeY likely interacts with numerous protein or RNA partners that are involved in various aspects of cellular physiology. Using a bacterial two-hybrid system, we identified several proteins that interact with YbeY, including ribosomal protein S11, the ribosome-associated GTPases Era and Der, YbeZ, and SpoT. In particular, the interaction of YbeY with S11 and Era provides insight into YbeY’s involvement in the 16S rRNA maturation process. The three-way association between YbeY, S11, and Era suggests that YbeY is recruited to the ribosome where it could cleave the 17S rRNA precursor endonucleolytically at or near the 3′ end maturation site. Analysis of YbeY missense mutants shows that a highly conserved beta-sheet in YbeY—and not amino acids known to be important for YbeY’s RNase activity—functions as the interface between YbeY and S11. This protein-interacting interface of YbeY is needed for correct rRNA maturation and stress regulation, as missense mutants show significant phenotypic defects. Additionally, structure-based in silico prediction of putative interactions between YbeY and the Era-30S complex through protein docking agrees well with the in vivo results.

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“…Previous studies in E. coli showed that deletion of RNase R does not impact ribosome association and the ribosome profile of the mutant was not changed when compared to the wild type strain [4]. Since RNase R is the only member of the RNB family of Figure 1.…”

Section: Rnase R Association With Ribosomes and Impact In Ribosome Prmentioning

confidence: 91%

“…We have previously shown that E. coli RNase R interacts with ribosomes, mostly with the 30S subunit [4]. To date, no studies have been performed regarding this topic in Gram positive bacteria.…”

Section: Rnase R Association With Ribosomes and Impact In Ribosome Prmentioning

confidence: 99%

“…Although RNase II and RNase R coexist in many bacteria, in S. pneumoniae only RNase R is present [3]. In Escherichia coli this enzyme has been widely studied and it was reported to be associated with ribosomes [4,5]. Ribosomes are macromolecular machines that translate mRNA into functional proteins and have been used as targets for antibiotic treatment [6].…”

Section: Introductionmentioning

confidence: 99%

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Pneumococcal RNase R globally impacts protein synthesis by regulating the amount of actively translating ribosomes

2019

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Ribosomes are macromolecular machines that carry out protein synthesis. After each round of translation, ribosome recycling is essential for reinitiating protein synthesis. Ribosome recycling factor (RRF), together with elongation factor G (EF-G), catalyse the transient split of the 70S ribosome into subunits. This splitting is then stabilized by initiation factor 3 (IF3), which functions as an anti-association factor. The correct amount of these factors ensures the precise level of 70S ribosomes in the cell. RNase R is a highly conserved exoribonuclease involved in the 3ʹ to 5ʹ degradation of RNAs. In this work we show that pneumococcal RNase R directly controls the expression levels of frr, fusA and infC mRNAs, the corresponding transcripts of RRF, EF-G and IF3, respectively. We present evidences showing that accumulation of these factors leads to a decreased amount of 70S active particles, as demonstrated by the altered sucrose gradient ribosomal pattern in the RNase R mutant strain. Furthermore, the single deletion of RNase R is shown to have a global impact on protein synthesis and cell viability, leading to a~50% reduction in bacterial CFU/ml. We believe that the fine-tuned regulation of these transcripts by RNase R is essential for maintaining the precise amount of active ribosomal complexes required for proper mRNA translation and thus we propose RNase R as a new auxiliary factor in ribosome reassociation. Considering the overall impact of RNase R on protein synthesis, one of the main targets of antibiotics, this enzyme may be a promising target for antimicrobial treatment. ARTICLE HISTORY

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Characterization of the RNase R association with ribosomes

Cited by 24 publications

References 25 publications

Organization of Mitochondrial Gene Expression in Two Distinct Ribosome-Containing Assemblies

Organization of Mitochondrial Gene Expression in Two Distinct Ribosome-Containing Assemblies

Identification of YbeY-Protein Interactions Involved in 16S rRNA Maturation and Stress Regulation in Escherichia coli

Pneumococcal RNase R globally impacts protein synthesis by regulating the amount of actively translating ribosomes

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