title: Towards the complete small RNome ofAcinetobacter baumannii.
abstract: In recent years, the Gram-negative bacteriumAcinetobacter baumanniihas 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 forA. baumanniiisolates 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 78A. baumanniisRNAs 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 ofA. baumannii, exposing sequence and structural conservation amongst these elements, and provides novel insight into the potential evolution, and role, of these understudied regulatory molecules.
authors.affiliation: Cell Biology, Microbiology & Molecular Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA.
authors.forename: Andy
authors.initials: A
authors.lastname: Weiss
authors.affiliation: Cell Biology, Microbiology & Molecular Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA.
authors.forename: William H
authors.initials: WH
authors.lastname: Broach
authors.affiliation: Cell Biology, Microbiology & Molecular Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA.
authors.forename: Mackenzie C
authors.initials: MC
authors.lastname: Lee
authors.affiliation: Cell Biology, Microbiology & Molecular Biology, University of South Florida, 4202 East Fowler Avenue, Tampa, FL 33620, USA.
authors.forename: Lindsey N
authors.initials: LN
authors.lastname: Shaw
mesh_terms: D040981:Acinetobacter baumannii / Q000235:genetics*; D001435:Bacteriophages / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D019143:Evolution, Molecular; D015964:Gene Expression Regulation, Bacterial; D016372:RNA, Antisense / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics*; D058727:RNA, Small Untranslated / Q000235:genetics*; D017423:Sequence Analysis, RNA
chemical_list: D016372:RNA, Antisense; D012329:RNA, Bacterial; D058727:RNA, Small Untranslated
keywords: Acinetobacter baumannii; C4 antisense RNA; RNA-seq; sRNA; sRNA annotation; sRNA modularity; small regulatory RNA