Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in Staphylococcus aureus

In Staphylococcus aureus, hundreds of
small regulatory or small RNAs (sRNAs) have been identified, yet this class of
molecule remains poorly understood and severely understudied. sRNA genes are
typically absent from genome annotation files, and as a consequence, their
existence is often overlooked, particularly in global transcriptomic studies.
To facilitate improved detection and analysis of sRNAs in S. aureus, we
generated updated GenBank files for three commonly used S. aureus strains
(MRSA252, NCTC 8325, and USA300), in which we added annotations for >260
previously identified sRNAs. These files, the first to include genome-wide
annotation of sRNAs in S. aureus, were then used as a foundation to
identify novel sRNAs in the community-associated methicillin-resistant strain
USA300. This analysis led to the discovery of 39 previously unidentified sRNAs.
Investigating the genomic loci of the newly identified sRNAs revealed a
surprising degree of inconsistency in genome anno- tation in S. aureus,
which may be hindering the analysis and functional exploration of these
elements. Finally, using our newly created annotation files as a reference, we
perform a global analysis of sRNA gene expression in S. aureus and
demonstrate that the newly identified tsr25 is the most highly
upregulated sRNA in human serum. This study provides an invaluable resource to
the S. aureus research community in the form of our newly generated
annotation files, while at the same time presenting the first examination of
differential sRNA expression in pathophysiologically relevant conditions.