Similar Datasets
Project description:RsaE is a regulatory RNA highly conserved amongst Firmicutes that lowers the amount of mRNAs associated with the TCA cycle and folate metabolism. A search for new RsaE targets in Staphylococcus aureus revealed that in addition to previously described substrates, RsaE down-regulates several genes associated with arginine catabolism. In particular, RsaE targets the arginase rocF mRNA via direct interactions involving G-rich motifs. Two duplicated C-rich motifs of RsaE can independently downregulate rocF expression. The faster growth rate of ?rsaE compared to its parental strain in media containing amino acids as sole carbon source points to an underlying role for RsaE in amino acid catabolism. Collectively, the data support a model in which RsaE acts as a global regulator of functions associated with metabolic adaptation.
| S-EPMC6158497 | biostudies-literature
Project description:Bacterial regulatory RNAs (sRNA) generally act by base-pairing with target mRNAs. While identification of sRNA targets is the essential step in sRNA characterization, it remains a stumbling block in most studies. To study sRNA-regulated networks in the major human pathogen Staphylococcus aureus, we used a RNA-RNA interactome screening method for identifying sRNA targets based on synthetic sRNAs that are used in vitro as bait to trap their corresponding targets. In addition, the transcriptomic effects of sRNA deletion and sRNA accumulation were analyzed by differential expression analyzes of RNA-seq data. This strategy was applied to study RsaE, a regulatory RNA highly conserved amongst Firmicutes and revealed that RsaE targets the arginase rocF mRNA via direct interactions involving G-rich motifs. Two duplicated C-rich motifs of RsaE can independently downregulate rocF expression. However, the relative activity of these motifs is substrate dependent. Metabolite quantifications in wild-type and ΔrsaE cultures indicate that the absence of RsaE affects amino acid metabolism. Collectively, the data support the model that RsaE acts as a global regulator downregulating functions associated to metabolic adaptation.
2018-06-16 | GSE106456 | GEO
Project description:Bacterial regulatory RNAs (sRNA) generally act by base-pairing with target mRNAs. While identification of sRNA targets is the essential step in sRNA characterization, it remains a stumbling block in most studies. To study sRNA-regulated networks in the major human pathogen Staphylococcus aureus, we used a RNA-RNA interactome screening method for identifying sRNA targets based on synthetic sRNAs that are used in vitro as bait to trap their corresponding targets. The key to target discovery lies in the differential analysis of RNA-seq data from captures with different sRNAs and from ΔrsaE and RsaE over-expressing strains. This strategy was applied to study RsaE, a regulatory RNA highly conserved amongst Firmicutes and revealed that RsaE targets the arginase rocF mRNA via direct interactions involving G-rich motifs. Two duplicated C-rich motifs of RsaE can independently downregulate rocF expression. However, the relative activity of these motifs is substrate dependent. Metabolite quantifications in wild-type and ΔrsaE cultures indicate that the absence of RsaE affects amino acid metabolism. Collectively, the data support the model that RsaE acts as a global regulator downregulating functions associated to metabolic adaptation.
2018-06-16 | GSE106327 | GEO
Project description:The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus
| PRJNA416918 | ENA
Project description:The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus [ssRNA-Seq]
| PRJNA416921 | ENA
Project description:The conserved regulatory RNA RsaE down-regulates the arginine degradation pathway in Staphylococcus aureus [Hybrid-Trap-seq]
| PRJNA416319 | ENA
Project description:Staphylococcus aureus is a leading cause of community-associated and nosocomial infections. Imperative to the success of S. aureus is the ability to adapt and utilize nutrients that are readily available. Genomic sequencing suggests that S. aureus has the genes required for synthesis of all twenty amino acids. However, in vitro experimentation demonstrates that staphylococci have multiple amino acid auxotrophies, including arginine. Although S. aureus possesses the highly conserved anabolic pathway that synthesizes arginine via glutamate, we demonstrate here that inactivation of ccpA facilitates the synthesis of arginine via the urea cycle utilizing proline as a substrate. Mutations within putA, rocD, arcB1, argG and argH abolished the ability of S. aureus JE2 ccpA::tetL to grow in the absence of arginine, whereas an interruption in argJBCF, arcB2, or proC had no effect. Furthermore, nuclear magnetic resonance demonstrated that JE2 ccpA::ermB produced (13)C(5) labeled arginine when grown with (13)C(5) proline. Taken together, these data support the conclusion that S. aureus synthesizes arginine from proline during growth on secondary carbon sources. Furthermore, although highly conserved in all sequenced S. aureus genomes, the arginine anabolic pathway (ArgJBCDFGH) is not functional under in vitro growth conditions. Finally, a mutation in argH attenuated virulence in a mouse kidney abscess model in comparison to wild type JE2 demonstrating the importance of arginine biosynthesis in vivo via the urea cycle. However, mutations in argB, argF, and putA did not attenuate virulence suggesting both the glutamate and proline pathways are active and they, or their pathway intermediates, can complement each other in vivo.
| S-EPMC3510247 | biostudies-literature
Project description:Arginine phosphorylation was only recently discovered to play a significant and relevant role in the Gram-positive bacterium Bacillus subtilis. In addition, arginine phosphorylation was also detected in Staphylococcus aureus, suggesting a widespread role in bacteria. However, the large-scale analysis of protein phosphorylation, and especially those that involve a phosphoramidate bond, comes along with several challenges. The substoichiometric nature of protein phosphorylation requires proper enrichment strategies prior to LC-MS/MS analysis, and the acid instability of phosphoramidates was long thought to impede those enrichments. Furthermore, good spectral quality is required, which can be impeded by the presence of neutral losses of phosphoric acid upon higher energy collision-induced dissociation. Here we show that pArg is stable enough for commonly used Fe3+-IMAC enrichment followed by LC-MS/MS and that HCD is still the gold standard for the analysis of phosphopeptides. By profiling a serine/threonine kinase (Stk1) and phosphatase (Stp1) mutant from a methicillin-resistant S. aureus mutant library, we identified 1062 pArg sites and thus the most comprehensive arginine phosphoproteome to date. Using synthetic arginine phosphorylated peptides, we validated the presence and localization of arginine phosphorylation in S. aureus. Finally, we could show that the knockdown of Stp1 significantly increases the overall amount of arginine phosphorylation in S. aureus. However, our analysis also shows that Stp1 is not a direct protein-arginine phosphatase but only indirectly influences the arginine phosphoproteome.
| S-EPMC9112008 | biostudies-literature
Project description:BACKGROUND:Staphylococcus aureus (S. aureus) infection accounts for more than 50% of the osteomyelitis cases. Currently, methicillin-resistant S. aureus (MRSA) strains present an urgent medical problem. The YycFG two-component regulatory system (TCS) can allow bacteria to rapidly adapt to physical, chemical, and biological stresses. To define the role of YycFG in modulation virulence of S. aureus in osteomyelitis, we isolated clinical MRSA strains and compared these with ATCC29213 methicillin-sensitive S. aureus (MSSA). METHODS:In the present study, 13 MRSA strains from chronic osteomyelitis tissues were isolated. The in-depth sequencing of 16S rRNA amplicons of the samples was conducted. Bacterial growth was monitored, and biofilm biomass was determined by crystal violet microtiter assay. Furthermore, quantitative RT-PCR analysis was adopted to identify the expression of yycF/G/H and icaA/D in MRSA and MSSA strains. Analysis of variance with one-way ANOVA was used for statistical analysis. RESULTS:The in-depth sequencing of 16S rRNA amplicons of the clinical samples indicated a polymicrobial infection, with the phylum Firmicutes made up 13% of the microbial population. The MRSA strains showed an accelerated growth rate compared to the MSSA strains. Of note, MRSA biofilms showed an accumulation of an intercellular polysaccharides matrix and enhanced biomass upon microscopic examination. Furthermore, MRSA strains had a higher expression of the yycF/G/H and icaA/D genes and adhesion force. CONCLUSIONS:These data suggested the roles of intercellular polysaccharide in S. aureus pathogenesis, indicating a possible association between YycFG pathways and MRSA strain virulence.
| S-EPMC6325680 | biostudies-other
Project description:Staphylococcus aureus is a major human bacterial pathogen responsible for deep tissue skin infections. Recent observations have suggested that rapid, localized digestion of hyaluronic acid in the extracellular matrix (ECM) of the dermis may influence bacterial invasion and tissue inflammation. In this study we find that cell migration-inducing protein (Cemip) is the major inducible gene responsible for hyaluronan catabolism in mice. Cemip-/- mice failed to digest hyaluronan and had significantly less evidence of infection after intradermal bacterial challenge by S. aureus. Stabilization of large-molecular-weight hyaluronan enabled increased expression of cathelicidin antimicrobial peptide (Camp) that was due in part to enhanced differentiation of preadipocytes to adipocytes, as seen histologically and by increased expression of Pref1, PPARg, and Adipoq. Cemip-/- mice challenged with S. aureus also had greater IL-6 expression and neutrophil infiltration. These observations describe a mechanism for hyaluronan in the dermal ECM to regulate tissue inflammation and host antimicrobial defense.
| S-EPMC7029423 | biostudies-literature