Towards the complete small RNome of Acinetobacter baumannii

Abstract

In recent years, the Gram-negative bacterium Acinetobacter baumannii has garnered considerable attention for its unprecedented capacity to rapidly develop resistance to antibacterial therapeutics. This is coupled with the seemingly epidemic emergence of new hyper-virulent strains. Although strain-specific differences for A. baumannii isolates have been well described, these studies have primarily focused on proteinaceous factors. At present, only limited publications have investigated the presence and role of small regulatory RNA (sRNA) transcripts. Herein, we perform such an analysis, describing the RNA-seq-based identification of 78 A. baumannii sRNAs in the AB5075 background. Together with six previously identified elements, we include each of these in a new genome annotation file, which will serve as a tool to investigate regulatory events in this organism. Our work reveals that the sRNAs display high expression, accounting for >50 % of the 20 most strongly expressed genes. Through conservation analysis we identified six classes of similar sRNAs, with one found to be particularly abundant and homologous to regulatory, C4 antisense RNAs found in bacteriophages. These elements appear to be processed from larger transcripts in an analogous manner to the phage C4 molecule and are putatively controlled by two further sRNAs that are strongly antisense to them. Collectively, this study offers a detailed view of the sRNA content of A. baumannii, exposing sequence and structural conservation amongst these elements, and provides novel insight into the potential evolution, and role, of these understudied regulatory molecules.

Towards the complete proteinaceous regulome of Acinetobacter baumannii

“…Since we cannot exclude the possibility that the shorter protein is the correct version (meaning the AB5075 annotation is wrong), we analysed AB5075 RNAsequencing data recently generated by our group (Fig. 5d) [32]. In so doing, we demonstrated that, although expressed at a low level, AB5075 mRNA transcripts extended the full length of the ORF, suggesting the upstream start codon is in fact used by the cell.…”

“…Given that our study is largely reliant on accurate genome annotation files, and that we have previously reported inconsistencies in prokaryotic repositories of this type [32, 92], we took an additional approach to our analysis so as to minimize the influence of annotation inaccuracies on our investigations. As such, alongside protein/annotation-based searches, we also performed nucleotide blast analyses (Table S1).…”

“…An arrow with a solid or a dashed line, respectively, highlights the start site of the annotated and hypothetical homologues in ATCC 17978 (as shown in b). This RNA sequencing data was previously published by our group [32]. …”

“…Previously, we have documented the global identification and curation of regulatory RNAs in A. baumannii strain AB5075 [32]. In the context of proteinaceous regulators, however, their essential role in cellular physiology and pathogenesis is still largely unexplored.…”

The ω Subunit Governs RNA Polymerase Stability and Transcriptional Specificity in Staphylococcus aureus

“…RNA sequencing was performed for rpoZ and sigB mutants and their respective parental strains as previously outlined by our group (8,(68)(69)(70). Briefly, RNA was isolated and the quality determined as described for Northern blot experiments.…”