Project description:The enterococci comprise a genus of 49 low-GC content Gram-positive commensal species within the Firmicutes phylum that are known to occupy diverse habitats, notably the gastrointestinal core microbiota of nearly every phylum, including human. Of particular clinical relevance are two rogue species of enterococci, Enterococcus faecalis and the distantly related Enterococcus faecium, standing among the nefarious multi-drug resistant and hospital-acquired pathogens. Despite increasing evidence for RNA-based regulation in the enterococci, including regulation of virulence factors, their transcriptome structure and arsenal of regulatory small sRNAs (sRNAs) are not thoroughly understood. Using dRNA-seq, we have mapped at single-nucleotide resolution the primary transcriptomes of E. faecalis V583 and E. faecium AUS0004. We identified 2517 and 2771 transcription start sites (TSS) in E. faecalis and E. faecium, respectively. Based on the identified TSS, we created a global map of s70 promoter motifs. We also revealed features of 5’ and 3’UTRs across the genomes. The transcriptome maps also predicted 150 and 128 sRNA candidates in E. faecalis and E. faecium, respectively, some of which have been identified in previous studies and many of which are new. Finally, we validated several of the predicted sRNAs by Northern Blot in biologically relevant conditions. Comprehensive TSS mapping of two representative strains will provide a valuable resource for the continued development of RNA biology in the Enterococci.

2020-11-25 | GSE115009 | GEO

Grad-seq Enterococcus faecalis and faecium

Project description:Grad-seq in Enterococcus faecalis V583 and Enterococcus faecium AUS004.

2022-11-28 | PXD031577 | Pride

Bacteriocin producing Enterococcus faecium

Project description:Proteomic Characterization of Bacteriocin-Producing Enterococcus faecium Strains from foodstuffs

2023-03-11 | PXD037241 | Pride

Proteomic analysis Enterococcus faecium

Project description:Proteomic analysis Enterococcus faecium samples to assess proteomic alterations (20220922_NSco_Stinear)

2024-08-15 | PXD039831 | Pride

Transcriptome analysis Enterococcus faecium during mid-exponential growth phase in presence and absence of ampicillin

Project description:Effect of 20 ug/ml ampicillin on gene expression of Enterococcus faecium E1162 during mid-exponential growth phase

2012-03-01 | E-MEXP-3564 | biostudies-arrayexpress

Enterococcus faecium strain:4995/20 | isolate:4995/20

Project description:Enterococcus faecium strain:4995/20 | isolate:4995/20 Genome sequencing

| PRJNA766534 | ENA

A dual T-box riboswitch in Enterococcus faecium binds two tRNAs

Project description:A set of small RNAs was identified in Vancomycin-resistant Enterococcus faecium, a leading cause of MDR infections. We described here the function of srn_2050, acting as a T-box riboswitch to regulate expression of downstream genes encoding the HisRS and AspRS aminoacyl-tRNA synthetases. Comparative RNAseq between Aus0004 and isogenic srn_2050 mutant identified the genes whose expression is impacted by the RNA. srn_2050 structure in its ‘off state’ was deciphered by in-line probing, containing T-box consensus sequences, a pseudoknot, a specifier loop and a terminator. Transcription binding assays between the riboswitch and either tRNAAsp or tRNAHis indicate that each deacylated tRNA interacts with the T-box. Their anticodons bind to a GACAC sequence within the specifier loop (GAC and CAC are Asp and His codons, respectively), whereas tRNATyr (UA/C-U) does not. A pioneering evaluation of E. faecium amino acid auxotrophy, with emphasis on E. faecium strain Aus0004, revealed auxotrophy for Histidine but not for Aspartic acid. Based on comparative growths and RNAseq between Aus004 and Aus004-srn2050, the riboswitch is shown essential for growth under aspartate starvation. This is the first example of a functional riboswitch in E. faecium with two overlapping codons allowing a dual tRNA-dependent regulation at transcriptional level.

2020-11-16 | GSE161499 | GEO

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