Major 3′–5′ Exoribonucleases in the Metabolism of Coding and Non-coding RNA

Santos, Ricardo F. dos; Quendera, Ana Patrícia; Boavida, Sofia; Seixas, André F.; Arraiano, Cecília M.; Andrade, José M.

doi:10.1016/bs.pmbts.2018.07.005

Cited by 24 publications

(21 citation statements)

References 248 publications

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“…Some predicted RNases were indeed shown to carry other functions (see, for example, the L-PSP/RidA enzyme; Niehaus et al, 2014), and new RNases keep being discovered in bacteria, some of them with a chloroplast homolog awaiting characterization (see, for example, the Rae1/YacP endoribonuclease; Condon et al, 2018). Indeed, as direct evidence of its cyanobacterial origin, nearly all chloroplast RNase homologs are present in bacteria Germain et al, 2013;dos Santos et al, 2018). Based on their chlorotic or embryo-lethal phenotypes and the associated disruption in RNA patterns, there are five major RNases whose putative roles are discussed below.…”

Section: Plastidial Rnasesmentioning

confidence: 99%

Organellar and Secretory Ribonucleases: Major Players in Plant RNA Homeostasis

MacIntosh

Castandet

2020

Plant Physiol.

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Section: Plastidial Rnasesmentioning

confidence: 99%

Organellar and Secretory Ribonucleases: Major Players in Plant RNA Homeostasis

MacIntosh

Castandet

2020

Plant Physiol.

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“…Hfq and RNase R are two important posttranscriptional regulators acting on multiple pathways of RNA metabolism ( 9 , 21 ). Hence, the growth defects caused by their inactivation could arise from a disturbance in RNA metabolism.…”

Section: Resultsmentioning

confidence: 99%

“…Our previous work also demonstrated that RNase R associated with ribosomes and comigrated with the 30S ribosomal subunits ( 6 ). RNase R belongs to the RNB family of ribonucleases ( 7 – 9 ) that can globally impact gene expression ( 10 ), and RNase R mutants helped to elucidate the catalysis of structured RNA ( 11 ). In fact, RNase R is a unique exoribonuclease involved in various RNA surveillance pathways.…”

Section: Introductionmentioning

confidence: 99%

“…Furthermore, RNase R can affect the expression levels of r-proteins, as it was shown to degrade the mRNA encoding ribosomal protein S15 ( rpsO gene) under conditions that favor RNA polyadenylation-dependent decay ( 16 ). The intimate relationship between RNase R and ribosomes is further underlined by the evidence that RNase R is involved in the 3′ end processing of the 16S rRNA precursor (17S rRNA) and that ribosomes regulate RNase R stability ( 9 , 17 , 18 ).…”

Section: Introductionmentioning

confidence: 99%

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Hfq and RNase R Mediate rRNA Processing and Degradation in a Novel RNA Quality Control Process

Santos

Andrade

Pissarra

et al. 2020

mBio

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RNA quality control pathways are critical for cell survival. Here, we describe a new surveillance process involved in the degradation of highly structured and stable ribosomal RNAs. The results demonstrated that the RNA chaperone Hfq and the 3′–5′ exoribonuclease R mediate the elimination of detrimental rRNA fragments and are required for the correct processing of rRNA precursors. Escherichia coli cells lacking both Hfq and RNase R accumulate a high level of 16S- and 23S-derived rRNA fragments. Hfq and RNase R were also shown to participate in the maturation of 16S and 23S rRNA precursors. This correlates with the fact that in the absence of Hfq and RNase R, there are severe ribosome assembly defects and a sharp reduction in 70S ribosome levels. Hfq and RNase R may act independently or in a complex, as protein interaction studies revealed that these RNA-binding proteins can associate. This is the first demonstration that the well-conserved Hfq and RNase R proteins act on common regulatory pathways, unraveling previously unknown mechanisms of rRNA surveillance with important consequences for translation and cell survival. IMPORTANCE Quality control pathways that oversee the quality of stable RNA molecules are critical for the cell. In this work, we demonstrate, for the first time, a functional link between Hfq and RNase R in the processing and degradation of the highly structured rRNAs. These RNA-binding proteins are required for the maturation of 16S and 23S rRNAs and correct ribosome assembly. Furthermore, they participate in the degradation of rRNAs and clearance of toxic rRNA fragments from the cell. Our studies have also shown that Hfq and RNase R can form a complex. In summary, the cooperation between Hfq and RNase R in metabolic pathways of stable RNAs may represent a broader mechanism of RNA quality control, given the high conservation of these RNA-binding proteins throughout evolution.

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“…In contrast, the double mutant RNase II/RNase R is viable but has not yet been analyzsed. The roles of these exoribonucleases have been studied in both growth phases 10,11 however most studies are focused in specific RNA targets and mechanisms.…”

Section: Introductionmentioning

confidence: 99%

Defining the impact of exoribonucleases in the shift between exponential and stationary phases

Pobre

Barahona

Dobrzanski

et al. 2019

Sci Rep

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The transition between exponential and stationary phase is a natural phenomenon for all bacteria and requires a massive readjustment of the bacterial transcriptome. Exoribonucleases are key enzymes in the transition between the two growth phases. PNPase, RNase R and RNase II are the major degradative exoribonucleases in Escherichia coli. We analysed the whole transcriptome of exponential and stationary phases from the WT and mutants lacking these exoribonucleases (Δpnp, Δrnr, Δrnb, and ΔrnbΔrnr). When comparing the cells from exponential phase with the cells from stationary phase more than 1000 transcripts were differentially expressed, but only 491 core transcripts were common to all strains. There were some differences in the number and transcripts affected depending on the strain, suggesting that exoribonucleases influence the transition between these two growth phases differently. Interestingly, we found that the double mutant RNase II/RNase R is similar to the RNase R single mutant in exponential phase while in stationary phase it seems to be closer to the RNase II single mutant. This is the first global transcriptomic work comparing the roles of exoribonucleases in the transition between exponential and stationary phase.

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Major 3′–5′ Exoribonucleases in the Metabolism of Coding and Non-coding RNA

Cited by 24 publications

References 248 publications

Organellar and Secretory Ribonucleases: Major Players in Plant RNA Homeostasis

Organellar and Secretory Ribonucleases: Major Players in Plant RNA Homeostasis

Hfq and RNase R Mediate rRNA Processing and Degradation in a Novel RNA Quality Control Process

Defining the impact of exoribonucleases in the shift between exponential and stationary phases

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