RNA antitoxin SprF1 binds ribosomes to attenuate translation and promote persister cell formation in Staphylococcus aureus

Pinel-Marie, Marie-Laure; Brielle, Régine; Riffaud, Camille; Germain-Amiot, Noëlla; Polacek, Norbert; Felden, Brice

doi:10.1038/s41564-020-00819-2

Cited by 25 publications

(31 citation statements)

References 49 publications

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“…This suggests that these molecules were protected from degradation by binding the ribosome [32] and may thus act as rancRNAs. While rancRNAs are poorly characterized in bacteria, very recently, an antitoxin RNA has been identified as rancRNA in Staphylococcus aureus that downregulates global protein synthesis by affecting tRNA binding, which, in turn, promotes persister cell formation [43]. As such, our enriched ribosome-associated sRNAs could play similar roles in dimming translation, a critical process for establishing and maintaining bacterial stationary phase.…”

Section: Srnas In Stationary Phase Biologymentioning

confidence: 96%

Transcriptome-Wide Analysis of Stationary Phase Small ncRNAs in E. coli

Raad

Luidalepp

Fasnacht

et al. 2021

IJMS

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Almost two-thirds of the microbiome’s biomass has been predicted to be in a non-proliferating, and thus dormant, growth state. It is assumed that dormancy goes hand in hand with global downregulation of gene expression. However, it remains largely unknown how bacteria manage to establish this resting phenotype at the molecular level. Recently small non-protein-coding RNAs (sRNAs or ncRNAs) have been suggested to be involved in establishing the non-proliferating state in bacteria. Here, we have deep sequenced the small transcriptome of Escherichia coli in the exponential and stationary phases and analyzed the resulting reads by a novel biocomputational pipeline STARPA (Stable RNA Processing Product Analyzer). Our analysis reveals over 12,000 small transcripts enriched during both growth stages. Differential expression analysis reveals distinct sRNAs enriched in the stationary phase that originate from various genomic regions, including transfer RNA (tRNA) fragments. Furthermore, expression profiling by Northern blot and RT-qPCR analyses confirms the growth phase-dependent expression of several enriched sRNAs. Our study adds to the existing repertoire of bacterial sRNAs and suggests a role for some of these small molecules in establishing and maintaining stationary phase as well as the bacterial stress response. Functional characterization of these detected sRNAs has the potential of unraveling novel regulatory networks central for stationary phase biology.

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Section: Srnas In Stationary Phase Biologymentioning

confidence: 96%

Transcriptome-Wide Analysis of Stationary Phase Small ncRNAs in E. coli

Raad

Luidalepp

Fasnacht

et al. 2021

IJMS

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“…However, at the stationary growth phase, the comparison of intracellular proteomes between the strains allows us to carefully suggest the SprF1 antitoxin as downregulating protein expression. We recently demonstrated that SprF1 is a dual function type I RNA antitoxin [ 16 ]. At its 3′-end, SprF1 acts as an antitoxin to prevent SprG1 toxicity towards competing bacteria and host cells [ 12 ].…”

Section: Discussionmentioning

confidence: 99%

“…At its 3′-end, SprF1 acts as an antitoxin to prevent SprG1 toxicity towards competing bacteria and host cells [ 12 ]. Thanks to a purine-rich sequence located at its 5′-end, SprF1 also interacts with a subset of polysomes and ribosomes that could promote translation attenuation and antibiotic persister cell formation [ 16 ]. Among the proteins downregulated in the wild-type and the SprF1 antitoxin overexpressing strain or upregulated in the sprG1/sprF1 deleted strain ( Table 2 ), six are glycolysis-related enzymes: pyruvate dehydrogenase E1 component subunit β (PdhB), succinate-CoA ligase (ADP-forming) subunit α (SucD), ATP-dependent 6-phosphofructokinase (PfkA), 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (GpmI), fructose-bisphosphate aldolase class 1 (Fda), and glyceraldehyde-3-phosphate dehydrogenase 1 (GapA1) ( Supplementary Figure S4 ).…”

Section: Discussionmentioning

confidence: 99%

“…Although such a role in staphylococci was not confirmed experimentally, PdhB was reported as the only cellular protein belonging to the core exoproteome of the bovine S. aureus mastitis isolates [ 38 ]. Moreover, the intracellular proteins identified as downregulated by SprF1, especially PfkA and GapA1, were suggested in the S. aureus persister cell formation [ 16 ]. In general, the results suggest that the SprF1 RNA antitoxin influences the expression of some intracellular proteins.…”

Section: Discussionmentioning

confidence: 99%

“…Recently, we demonstrated that the SprF1 is a dual-function RNA antitoxin that, beyond protection from SprG1 toxicity, binds ribosomes to attenuate translation initiation by interfering with initiator transfer RNA binding. This translation attenuation mechanism mediated by SprF1 promotes antibiotic persister cell formation [ 16 ]. This may suggest a global regulatory role for the SprG1/SprF1 TA system, similar to already known staphylococcal gene expression regulators (such as agr , sarA , and saeRS ) [ 17 ], albeit through completely different molecular mechanisms.…”

Section: Introductionmentioning

confidence: 99%

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Impacts of the Type I Toxin–Antitoxin System, SprG1/SprF1, on Staphylococcus aureus Gene Expression

Chlebicka

Bonar

Suder

et al. 2021

Genes

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Type I toxin–antitoxin (TA) systems are widespread genetic modules in bacterial genomes. They express toxic peptides whose overexpression leads to growth arrest or cell death, whereas antitoxins regulate the expression of toxins, acting as labile antisense RNAs. The Staphylococcus aureus (S. aureus) genome contains and expresses several functional type I TA systems, but their biological functions remain unclear. Here, we addressed and challenged experimentally, by proteomics, if the type I TA system, the SprG1/SprF1 pair, influences the overall gene expression in S. aureus. Deleted and complemented S. aureus strains were analyzed for their proteomes, both intracellular and extracellular, during growth. Comparison of intracellular proteomes among the strains points to the SprF1 antitoxin as moderately downregulating protein expression. In the strain naturally expressing the SprG1 toxin, cytoplasmic proteins are excreted into the medium, but this is not due to unspecific cell leakages. Such a toxin-driven release of the cytoplasmic proteins may modulate the host inflammatory response that, in turn, could amplify the S. aureus infection spread.

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