The role of RNases in the regulation of small RNAs

Saramago, Margarida; Bárria, Cátia; Santos, Ricardo F. dos; Silva, Inês J.; Pobre, Vânia; Domingues, Susana; Andrade, José M.; Viegas, Sandra C.; Arraiano, Cecília M.

doi:10.1016/j.mib.2014.02.009

Cited by 99 publications

(90 citation statements)

References 90 publications

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“…In addition to the full-length transcript, we investigated also the psaL 59 UTR fragment, which was shown to accumulate differently in the microarray analysis (Supplemental Table 1). Rifampicin, which prevents the de novo initiation of new transcripts by binding to the b-subunit of RNA polymerase (Campbell et al, 2001;Saramago et al, 2014), was added and samples were taken prior to (0 min) and 2, 4, 8, 16, 32, and 64 min after rifampicin addition. The amounts of psaL and the 59 fragment were quantified by RNA gel blot analysis ( Figure 8A), and differences in the loaded RNA amounts were normalized to a 23S rRNA control hybridization.…”

Section: Posttranscriptional Destabilization Of Psal Mrna Upon Psrr1 mentioning

confidence: 99%

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The Small Regulatory RNA SyR1/PsrR1 Controls Photosynthetic Functions in Cyanobacteria

Dienst²,

et al. 2014

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Little is known so far about RNA regulators of photosynthesis in plants, algae, or cyanobacteria. The small RNA PsrR1 (formerly SyR1) has been discovered in Synechocystis sp PCC 6803 and appears to be widely conserved within the cyanobacterial phylum. Expression of PsrR1 is induced shortly after a shift from moderate to high-light conditions. Artificial overexpression of PsrR1 led to a bleaching phenotype under moderate light growth conditions. Advanced computational target prediction suggested that several photosynthesis-related mRNAs could be controlled by PsrR1, a finding supported by the results of transcriptome profiling experiments upon pulsed overexpression of this small RNA in Synechocystis sp PCC 6803. We confirmed the interaction between PsrR1 and the ribosome binding regions of the psaL, psaJ, chlN, and cpcA mRNAs by mutational analysis in a heterologous reporter system. Focusing on psaL as a specific target, we show that the psaL mRNA is processed by RNase E only in the presence of PsrR1. Furthermore, we provide evidence for a posttranscriptional regulation of psaL by PsrR1 in the wild type at various environmental conditions and analyzed the consequences of PsrR1-based regulation on photosystem I. In summary, computational and experimental data consistently establish the small RNA PsrR1 as a regulatory factor controlling photosynthetic functions.

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Section: Posttranscriptional Destabilization Of Psal Mrna Upon Psrr1 mentioning

confidence: 99%

“…In bacteria, sRNA-guided processing of mRNAs is frequently facilitated by RNase E (Saramago et al, 2014). Using an in vitro assay, we investigated whether a 130-nucleotide psaL 59 fragment ( Figure 9B; Supplemental Figure 8B) could be cleaved by RNase E alone or in a PsrR1-dependent manner.…”

Section: Psrr1-dependent Processing Of Psal By Rnase Ementioning

confidence: 99%

The Small Regulatory RNA SyR1/PsrR1 Controls Photosynthetic Functions in Cyanobacteria

Dienst²,

et al. 2014

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“…In eukaryotes, RNase III-like proteins are involved in RNA interference (RNAi) and RNA maturation (Hammond, 2005). In bacteria, RNase III regulates its own synthesis, is responsible for rRNA operon maturation, processing of cellular and phage RNAs, control of plasmid copy number and maturation of type II CRISPR RNAs (Arraiano et al, 2010; Saramago et al, 2014a, 2015). As a double-strand specific endoribonuclease, this enzyme is a major effector of mRNA processing and decay driven by antisense transcription, and participates in regulation by trans -acting sRNAs (Lasa et al, 2011; Viegas et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Sinorhizobium meliloti RNase III: Catalytic Features and Impact on Symbiosis

et al. 2018

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Members of the ribonuclease (RNase) III family of enzymes are metal-dependent double-strand specific endoribonucleases. They are ubiquitously found and eukaryotic RNase III-like enzymes include Dicer and Drosha, involved in RNA processing and RNA interference. In this work, we have addressed the primary characterization of RNase III from the symbiotic nitrogen-fixing α-proteobacterium Sinorhizobium meliloti. The S. meliloti rnc gene does encode an RNase III-like protein (SmRNase III), with recognizable catalytic and double-stranded RNA (dsRNA)-binding domains that clusters in a branch with its α–proteobacterial counterparts. Purified SmRNase III dimerizes, is active at neutral to alkaline pH and behaves as a strict metal cofactor-dependent double-strand endoribonuclease, with catalytic features distinguishable from those of the prototypical member of the family, the Escherichia coli ortholog (EcRNase III). SmRNase III prefers Mn2+ rather than Mg2+ as metal cofactor, cleaves the generic structured R1.1 substrate at a site atypical for RNase III cleavage, and requires higher cofactor concentrations and longer dsRNA substrates than EcRNase III for optimal activity. Furthermore, the ultraconserved E125 amino acid was shown to play a major role in the metal-dependent catalysis of SmRNase III. SmRNase III degrades endogenous RNA substrates of diverse biogenesis with different efficiency, and is involved in the maturation of the 23S rRNA. SmRNase III loss-of-function neither compromises viability nor alters morphology of S. meliloti cells, but influences growth, nodulation kinetics, the onset of nitrogen fixation and the overall symbiotic efficiency of this bacterium on the roots of its legume host, alfalfa, which ultimately affects plant growth. Our results support an impact of SmRNase III on nodulation and symbiotic nitrogen fixation in plants.

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“…10 Most of the characterized transencoded ncRNAs interact with multiple target mRNAs with the assistence of the RNA chaperone Hfq 11 and act in concert with RNases that cleave the target mRNA and control its halflife. 12,13 Other types of riboregulators are RNA thermometers, 14,15 and riboswitches. 16 These sensory RNA elements are found in the 5 0 -untranslated regions (5 0 -UTRs) or within intergenic regions, and control expression of the downstream gene through structural remodeling of the RNA segment.…”

Section: Molecular Mechanisms Underlying Rna-based Control Of Virulencementioning

confidence: 99%

RNA-based mechanisms of virulence control in Enterobacteriaceae

2016

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Enteric pathogens of the family Enterobacteriaceae colonize various niches within animals and humans in which they compete with intestinal commensals and are attacked by the host immune system. To survive these hostile environments they possess complex, multilayer regulatory networks that coordinate the control of virulence factors, host-adapted metabolic functions and stress resistance. An important part of these intricate control networks are RNA-based control systems that enable the pathogen to fine-tune its responses. Recent next-generation sequencing approaches revealed a large repertoire of conserved and species-specific riboregulators, including numerous cis-and trans-acting non-coding RNAs, sensory RNA elements (RNA thermometers, riboswitches), regulatory RNA-binding proteins and RNA degrading enzymes which regulate colonization factors, toxins, host defense processes and virulence-relevant physiological and metabolic processes. All of which are important cues for pathogens to sense and respond to fluctuating conditions during the infection. This review covers infection-relevant riboregulators of E. coli, Salmonella, Shigella and Yersinia, highlights their versatile regulatory mechanisms, complex target regulons and functions, and discusses emerging topics and future challenges to fully understand and exploit RNA-based control to combat bacterial infections.

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The role of RNases in the regulation of small RNAs

Cited by 99 publications

References 90 publications

The Small Regulatory RNA SyR1/PsrR1 Controls Photosynthetic Functions in Cyanobacteria

The Small Regulatory RNA SyR1/PsrR1 Controls Photosynthetic Functions in Cyanobacteria

Sinorhizobium meliloti RNase III: Catalytic Features and Impact on Symbiosis

RNA-based mechanisms of virulence control in Enterobacteriaceae

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