Biology subjects

Felden, B.

Publications and source records attributed to Felden, B..

4 recordsLinked to original sources

bioRxiv2022

sRNA-controlled iron sparing response in Staphylococci

Staphylococcus aureus, a human opportunist pathogen, adjusts its metabolism to cope with iron deprivation within the host. We investigated the potential role of small non-coding RNAs (sRNAs) in dictating this process. A single sRNA, named here IsrR, emerged from a competition assay with tagged-mutant libraries as being required during iron starvation. IsrR is iron-repressed and predicted to target mRNAs expressing iron-containing enzymes. Among them, we demonstrated that IsrR down-regulates the translation of mRNAs of enzymes that catalyze anaerobic nitrate respiration. The IsrR sequence reveals three single-stranded C-rich regions (CRRs). Mutational and structural analysis indicated a differential contribution of these CRRs according to targets. We also report that IsrR is required for full lethality of S. aureus in a mouse septicemia model, underscoring its role as a major contributor to the iron-sparing response for bacterial survival during infection. IsrR is conserved among staphylococci, but it is not ortholog to the proteobacterial sRNA RyhB, nor to other characterized sRNAs down-regulating mRNAs of iron-containing enzymes. Remarkably, these distinct sRNAs regulate common targets, illustrating that RNA-based regulation provides optimal evolutionary solutions to improve bacterial fitness when iron is scarce.

microbiology↗

bioRxiv2022

6S RNA-dependent antibiotic susceptibility

Bacterial small RNAs (sRNAs) contribute to a variety of regulatory mechanisms that modulate wide ranging pathways, including metabolism, virulence, and antibiotic resistance. We investigated the involvement of sRNAs in rifampicin resistance in the opportunistic pathogen Staphylococcus aureus. Using a competition assay with an sRNA mutant library, we identified 6S RNA as being required for protection against low concentrations of rifampicin, an RNA polymerase (RNAP) inhibitor. This effect applied to rifabutin and fidaxomicin, two other RNAP-targeting antibiotics. 6S RNA is highly conserved in bacteria and its absence in two other major pathogens, Salmonella enterica and Clostridioides difficile, also impaired susceptibility to RNAP inhibitors. In S. aureus, 6S RNA is produced from an autonomous gene and accumulates in stationary phase. In contrast to what was reported in Escherichia coli, S. aureus 6S RNA does not appear to play a critical role in the transition from exponential to stationary phase, but affects {sigma}B-regulated expression in prolonged stationary phase. Nevertheless, its protective effect against rifampicin is independent of alternative sigma factor {sigma}B activity. Our results suggest that 6S RNA helps maintain RNAP-{sigma}A integrity in S. aureus, which could in turn help bacteria withstand low concentrations of RNAP inhibitors.

microbiology↗

bioRxiv2021

A cis-RNA-mediated expression regulation of the tet(M) resistance gene in Enterococcus faecium

A set of putative novel small RNAs was recently identified as expressed in Enterococcus faecium, a major opportunistic pathogen involved in numerous healthcare-associated infections and hospital outbreaks. The aim of this study was to characterize the first functional analysis of one of them, srn0030, by phenotypic, genomic and transcriptomic approaches. By genomic analysis and RACE mapping, we revealed the presence of this RNA (previously designated as Ptet) within the 5-untrasnlated region (UTR) of tet(M), a gene conferring tetracycline resistance through ribosomal protection. The regulatory mechanism has previously been described as transcriptional attenuation, but has actually been poorly characterized. Hence, we provide original additional data, especially the presence of three upstream transcripts of ~100, ~150 and ~230 nt within the 5-UTR of tet(M), suggesting an alternative regulatory mechanism. The total deletion of these three transcripts causes an unexpected decreasing of tetracycline resistance in E. faecium. The attenuation mechanism was investigated, and we confirmed that the transcriptional read-through and tet(M) overexpression induced by tetracycline addition but the function of putative peptide leader on attenuation mechanism was not supported by our data. We report here new phenotypic and transcriptomic observations in E. faecium demonstrating an alternative regulatory mechanism of tet(M) gene expression.

microbiology↗

bioRxiv2020

Protein homeostasis imprinting across evolution

Protein homeostasis (a.k.a. proteostasis) is associated with the primary functions of life, and therefore with evolution. However, it is unclear how the cellular proteostasis machines have evolved to adjust the protein biogenesis needs to environmental constraints. Herein, we describe a novel computational approach, based on semantic network analysis, to evaluate proteostasis differentiation during evolution. We show that the molecular components of the proteostasis network (PN) are reliable metrics to deconvolute the life forms into Archaea, Bacteria and Eukarya and to assess the evolution rates among species. Topological properties of semantic graphs were used as new criteria to evaluate PN complexity of 93 Eukarya, 250 Bacteria and 62 Archaea, thus representing a novel strategy for taxonomic classification. This functional analysis provides information about species divergence and pointed towards taxonomic clades that evolved faster than others. Kingdom-specific PN were identified, suggesting that PN complexity correlates evolution. Through the analysis of gene conservation, we found that the gains or losses that occurred throughout PN evolution revealed a dichotomy within both the PN conserved modules and within kingdom-specific modules. Since the PN is implicated in cell fitness, aging and disease onset, it could be used as a new metric to tackle mechanisms underlying gain-of-functions, and their biological ramifications.

bioinformatics↗