The transcriptional landscape of the deep-sea bacterium Photobacterium profundum in both a toxR mutant and its parental strain

Stefano Campanaro,Douglas H Bartlett,Fabio De Pascale,Giorgio Valle,Andrea Telatin,Riccardo Schiavon

doi:10.1186/1471-2164-13-567

Stefano Campanaro, Douglas H Bartlett + Show 4 more

Open Access

https://doi.org/10.1186/1471-2164-13-567

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Abstract

BackgroundThe 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.ResultsTo 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.ConclusionThis 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.

Highlights

The deep-sea bacterium Photobacterium profundum is an established model for studying high pressure adaptation
In this paper we describe a study based on RNA-seq, performed in order to compare the transcriptional profile of the P. profundum toxR mutant (TW30) with the parental strain DB110
The photobacterium profundum transcriptome Global expression of chromosomes 1 and 2 We have analyzed the P. profundum transcriptome structure in DB110 strain and toxR mutant (TW30) both grown at 0.1 MPa and 28 MPa

Summary

Introduction

The deep-sea bacterium Photobacterium profundum is an established model for studying high pressure adaptation. P. profundum SS9 is a piezophilic bacterium member of the Vibrionaceae family, isolated at a depth of 2500 m [6]; it has an optimal growth pressure of 28 MPa, but it is able to grow at atmospheric pressure (0.1 MPa) This organism is only moderately piezophilic, offering some advantages over obligate piezophiles, for example it can be manipulated at atmospheric pressure and its response to pressure variations can be monitored. OmpH increases its abundance 10–100 times as the hydrostatic pressure rises from 0.1 to 28 MPa, while OmpL decreases its abundance in the same pressure range [8,9,10] These genes are under the control of ToxR, a transmembrane regulatory protein present in all Vibrionaceae so far sequenced. The toxR orthologous gene in P. profundum SS9 is required for pressuredependent regulation of OmpH and OmpL in response to hydrostatic pressure changes [10,13]

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