The primary transcriptome, small RNAs and regulation of antimicrobial resistance in Acinetobacter baumannii ATCC 17978

Abstract

We present the first high-resolution determination of transcriptome architecture in the priority pathogen Acinetobacter baumannii. Pooled RNA from 16 laboratory conditions was used for differential RNA-seq (dRNA-seq) to identify 3731 transcriptional start sites (TSS) and 110 small RNAs, including the first identification in A. baumannii of sRNAs encoded at the 3′ end of coding genes. Most sRNAs were conserved among sequenced A. baumannii genomes, but were only weakly conserved or absent in other Acinetobacter species. Single nucleotide mapping of TSS enabled prediction of −10 and −35 RNA polymerase binding sites and revealed an unprecedented base preference at position +2 that hints at an unrecognized transcriptional regulatory mechanism. To apply functional genomics to the problem of antimicrobial resistance, we dissected the transcriptional regulation of the drug efflux pump responsible for chloramphenicol resistance, craA. The two craA promoters were both down-regulated >1000-fold when cells were shifted to nutrient limited medium. This conditional down-regulation of craA expression renders cells sensitive to chloramphenicol, a highly effective antibiotic for the treatment of multidrug resistant infections. An online interface that facilitates open data access and visualization is provided as ‘AcinetoCom’ (http://bioinf.gen.tcd.ie/acinetocom/).

An RNA-centric global view ofClostridioides difficilereveals broad activity of Hfq in a clinically important Gram-positive bacterium

“…In addition, we have used this information to correct previous ORF annotations, to add previously overlooked small genes and to annotate sRNA loci. Inspired by other online gene expression databases such as SalCom (Kroger et al, 2013), AcinetoCom (Kröger et al, 2018) and Theta-Base (Ryan et al, 2020), we have launched an open-access interactive web browser, called 'Clost-Base' (https://www.helmholtzhiri.de/en/datasets/clostridium), for our transcriptome data. This online resource for C. difficile allows easy visualization of the transcriptomic data in the context of annotated coding and noncoding genes as well as transcript features (e.g.…”

COLRAcinetobacter baumannii sRNA Signatures: Computational Comparative Identification and Biological Targets

“…Functionally, sRNAs are involved in the regulation of a wide range of physiological responses, reacting to environmental signals, such as pH or temperature shifts (Wassarman, 2002). They can help the modulation of changes in cellular metabolism to optimize use of available nutrients and improve the probability for survival, as well as contributing to virulence (Chabelskaya et al, 2010;Gottesman and Storz, 2011;Sayed et al, 2012;Álvarez-Fraga et al, 2017;Kröger et al, 2018). sRNAs act in trans or cis depending on the transcription start position where the sRNA is transcribed with respect to their regulated gene.…”

An RNA-centric view on gut Bacteroidetes

“…In our recent work, we addressed some of these questions: application of differential RNA-seq (Sharma and Vogel 2014) to refine the transcriptome annotation of B. thetaiotaomicron type strain VPI-5482, led to the discovery of 269 noncoding RNA elements, including 151 putative sRNAs (Ryan et al 2020). This number is comparable with the sRNA complement in proteobacterial species (Dugar et al 2013;Kröger et al 2013Kröger et al , 2018Sharma et al 2010;Vogel et al 2003). Of 14 selected sRNA candidates, nine were validated by Northern blot, including a 3′ UTR-derived sRNA.…”