Abstract
Background Staphylococcus aureus is a versatile bacterial opportunist responsible for a wide spectrum of infections. The severity of these infections is highly variable and depends on multiple parameters including the genome content of the bacterium as well as the condition of the infected host. Clinically and epidemiologically, S. aureus shows a particular capacity to survive and adapt to drastic environmental changes including the presence of numerous antimicrobial agents. Mechanisms triggering this adaptation remain largely unknown despite important research efforts. Most studies evaluating gene content have so far neglected to analyze the so-called intergenic regions as well as potential antisense RNA molecules.Principal FindingsUsing high-throughput sequencing technology, we performed an inventory of the whole transcriptome of S. aureus strain N315. In addition to the annotated transcription units, we identified more than 195 small transcribed regions, in the chromosome and the plasmid of S. aureus strain N315. The coding strand of each transcript was identified and structural analysis enabled classification of all discovered transcripts. RNA purified at four time-points during the growth phase of the bacterium allowed us to define the temporal expression of such transcripts. A selection of 26 transcripts of interest dispersed along the intergenic regions was assessed for expression changes in the presence of various stress conditions including pH, temperature, oxidative shocks and growth in a stringent medium. Most of these transcripts showed expression patterns specific for the defined stress conditions that we tested.ConclusionsThese RNA molecules potentially represent important effectors of S. aureus adaptation and more generally could support some of the epidemiological characteristics of the bacterium.
Highlights
Staphylococcus aureus is a ubiquitous Gram-positive bacterium responsible for a wide spectrum of infections ranging from localized to life-threatening diseases
Analysis of the Illumina RNA-Seq coverage profiles In order to analyze the S. aureus N315 transcriptome obtained by Illumina-high-throughput sequencing (HTS) in depth, and to detect the nonannotated regions, we applied the following three criteria to characterize each transcript: (i) detection, (ii) orientation and (iii) expression during S. aureus N315 growth in rich medium (MHB)
Antisense RNAs appear to be widespread with estimates that they comprise up to 25% of the transcripts [72,73]. This number is generally lower in bacteria and in this S. aureus N315 strain where we identified this type of organization for only 1.3% of mRNAs, considering our cut-off
Summary
Staphylococcus aureus is a ubiquitous Gram-positive bacterium responsible for a wide spectrum of infections ranging from localized to life-threatening diseases. The high diversity of diseases caused by S. aureus and the breadth of environments colonized by this bacterium strongly relies on the expression regulation of numerous genes, such as virulence and/or metabolism genes Confronted with these epidemiological changes, there is a marked need to better understand the pathogenicity and virulence of this organism, and to more precisely define the emergence of epidemic clones, as well as their adaptation during the infection phase and their spreading in the hospital or the community. The pathogenicity, virulence or emergence of epidemic clones within MRSA populations is not clearly defined at a genetic level, despite several attempts to identify common molecular features between strains sharing similar epidemiological and/or virulence behavior These studies included pattern profiling analyses such as MLVA [16], AFLP [17], MLST [18], or microarrays [19]. Most studies evaluating gene content have so far neglected to analyze the so-called intergenic regions as well as potential antisense RNA molecules
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