| Summary: | <p>Abstract</p> <p>Background</p> <p>The deep-sea bacterium <it>Photobacterium profundum</it> is an established model for studying high pressure adaptation. In this paper we analyse the parental strain DB110 and the <it>toxR</it> mutant TW30 by massively parallel cDNA sequencing (RNA-seq). ToxR is a transmembrane DNA-binding protein first discovered in <it>Vibrio cholerae</it>, where it regulates a considerable number of genes involved in environmental adaptation and virulence. In <it>P. profundum</it> 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.</p> <p>Results</p> <p>To better characterize the ToxR regulon, we compared the expression profiles of <it>wt</it> and <it>toxR</it> 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<sup>′</sup>-UTRs, long enough to harbour cis-regulatory RNA structures, suggesting a correlation between intergenic region size and UTR length.</p> <p>Conclusion</p> <p>This work led to a better understanding of high-pressure response in <it>P. profundum</it>. Furthermore, the high-resolution RNA-seq analysis revealed several unexpected features about transcriptional landscape and general mechanisms of controlling bacterial gene expression.</p>
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