title: The transcriptional landscape of the deep-sea bacterium Photobacterium profundum in both a toxR mutant and its parental strain.
abstract: BACKGROUND
  The deep-sea bacterium Photobacterium profundum is an established model for studying high pressure adaptation. In this paper we analyse the parental strain DB110 and the toxR mutant TW30 by massively parallel cDNA sequencing (RNA-seq). ToxR is a transmembrane DNA-binding protein first discovered in Vibrio cholerae, where it regulates a considerable number of genes involved in environmental adaptation and virulence. In P. profundum the abundance and activity of this protein is influenced by hydrostatic pressure and its role is related to the regulation of genes in a pressure-dependent manner.
  
  
  RESULTS
  To better characterize the ToxR regulon, we compared the expression profiles of wt and toxR strains in response to pressure changes. Our results revealed a complex expression pattern with a group of 22 genes having expression profiles similar to OmpH that is an outer membrane protein transcribed in response to high hydrostatic pressure. Moreover, RNA-seq allowed a deep characterization of the transcriptional landscape that led to the identification of 460 putative small RNA genes and the detection of 298 protein-coding genes previously unknown. We were also able to perform a genome-wide prediction of operon structure, transcription start and termination sites, revealing an unexpected high number of genes (992) with large 5'-UTRs, long enough to harbour cis-regulatory RNA structures, suggesting a correlation between intergenic region size and UTR length.
  
  
  CONCLUSIONS
  This work led to a better understanding of high-pressure response in P. profundum. Furthermore, the high-resolution RNA-seq analysis revealed several unexpected features about transcriptional landscape and general mechanisms of controlling bacterial gene expression.
authors.affiliation: Department of Biology and CRIBI Biotechnology Centre, University of Padua, Via Ugo Bassi 58/B, Padova 35131, Italy. stefano.campanaro@unipd.it
authors.forename: Stefano
authors.initials: S
authors.lastname: Campanaro
authors.forename: Fabio De
authors.initials: FD
authors.lastname: Pascale
authors.forename: Andrea
authors.initials: A
authors.lastname: Telatin
authors.forename: Riccardo
authors.initials: R
authors.lastname: Schiavon
authors.forename: Douglas H
authors.initials: DH
authors.lastname: Bartlett
authors.forename: Giorgio
authors.initials: G
authors.lastname: Valle
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D002875:Chromosomes / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D006874:Hydrostatic Pressure; D009154:Mutation; D009792:Oceans and Seas; D009876:Operon / Q000235:genetics; D010776:Photobacterium / Q000235:genetics*; D012313:RNA / Q000737:chemistry / Q000378:metabolism; D017423:Sequence Analysis, RNA; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D014158:Transcription, Genetic; D020506:Untranslated Regions
chemical_list: D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D014157:Transcription Factors; D020506:Untranslated Regions; C066719:toxR protein, bacteria; D012313:RNA