Abstract
Enterococcus faecalis and faecium are two major representative clinical strains of the Enterococcus genus and are sadly notorious to be part of the top agents responsible for nosocomial infections. Despite their critical implication in worldwide public healthcare, essential and available resources such as deep transcriptome annotations remain poor, which also limits our understanding of post-transcriptional control small regulatory RNA (sRNA) functions in these bacteria. Here, using the dRNA-seq technique in combination with ANNOgesic analysis, we successfully mapped and annotated transcription start sites (TSS) of both E. faecalis V583 and E. faecium AUS0004 at single nucleotide resolution. Analyzing bacteria in late exponential phase, we capture ~40% (E. faecalis) and 43% (E. faecium) of the annotated protein-coding genes, determine 5′ and 3′ UTR (untranslated region) length, and detect instances of leaderless mRNAs. The transcriptome maps revealed sRNA candidates in both bacteria, some found in previous studies and new ones. Expression of candidate sRNAs is being confirmed under biologically relevant environmental conditions. This comprehensive global TSS mapping atlas provides a valuable resource for RNA biology and gene expression analysis in the Enterococci. It can be accessed online at www.helmholtz-hiri.de/en/datasets/enterococcus through an instance of the genomic viewer JBrowse.
Highlights
Of the ~1,000 bacterial species that live in and on the human body, the enterococci are a group of bacteria that have become leading multidrug resistant, hospital-adapted pathogens (Lebreton et al, 2017; Jernigan et al, 2020)
The main purpose of this work has been to provide a previously lacking global resource (TSS and noncoding RNA suite) for the comparative study of E. faecalis and E. faecium, which are two bacteria that have emerged from the astounding diversity of the core gut microbiota to become leading multi-drug resistant hospital pathogens (Van Tyne and Gilmore, 2014)
The successful emergence of both of these species can be explained by genomics studies which have revealed their genomes to be over 25% larger than other commensals, notably through accretion of numerous mobile elements including prophages, insertion sequence elements, plasmids, pathogenicity islands and resistance genes such as vancomycin (Paulsen et al, 2003; Lam et al, 2012)
Summary
Of the ~1,000 bacterial species that live in and on the human body, the enterococci are a group of bacteria that have become leading multidrug resistant, hospital-adapted pathogens (Lebreton et al, 2017; Jernigan et al, 2020). The enterococci comprise a genus of 49 low-GC content gram-positive commensal species within the phylum of Firmicutes that are known to occupy diverse habitats, notably in nearly every gastrointestinal core microbiota (Schloissnig et al, 2013; Lebreton et al, 2017). These bacteria are characterized by their ability to resist harsh conditions (extreme pH, ionizing radiation, osmotic, oxidative stress, dramatic temperature changes, etc.), they have. A better understanding of how these species cause disease and spread antibiotic resistance requires a knowledge of how its genes are controlled, on both the DNA and the RNA level
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