AUTHOR=Michaux Charlotte , Hansen Elisabeth E. , Jenniches Laura , Gerovac Milan , Barquist Lars , Vogel Jörg 

TITLE=Single-Nucleotide RNA Maps for the Two Major Nosocomial Pathogens Enterococcus faecalis and Enterococcus faecium

JOURNAL=Frontiers in Cellular and Infection Microbiology

VOLUME=10

YEAR=2020

URL=https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2020.600325

DOI=10.3389/fcimb.2020.600325

ISSN=2235-2988

ABSTRACT=<p><italic>Enterococcus faecalis</italic> and <italic>faecium</italic> 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 <italic>E. faecalis V583</italic> and <italic>E. faecium AUS0004</italic> at single nucleotide resolution. Analyzing bacteria in late exponential phase, we capture ~40% (<italic>E. faecalis</italic>) and 43% (<italic>E. faecium</italic>) 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 <uri xlink:href="http://www.helmholtz-hiri.de/en/datasets/enterococcus" xmlns:xlink="http://www.w3.org/1999/xlink">www.helmholtz-hiri.de/en/datasets/enterococcus</uri> through an instance of the genomic viewer JBrowse.</p>