Project description:Here we report the massively parallel cDNA sequencing (RNA-seq) analysis performed using high throughput sequencing of wild type (DB110) and toxR (TW30) mutant strains of the deep-sea bacterium Photobacterium profundum. ToxR is a transmembrane DNA-binding protein first discovered in Vibrio cholerae and able to regulate numerous genes involved in virulence. In P. profundum the abundance and activity of the same protein is influenced by hydrostatic pressure and is able to regulate genes in a pressure-dependent manner. To better characterize the ToxR regulon, we have compared the genes differentially expressed in response to pressure changes with those whose expression is altered between wild type and toxR mutant strains.
Project description:Here we report the massively parallel cDNA sequencing (RNA-seq) analysis performed using high throughput sequencing of wild type (DB110) and toxR (TW30) mutant strains of the deep-sea bacterium Photobacterium profundum. ToxR is a transmembrane DNA-binding protein first discovered in Vibrio cholerae and able to regulate numerous genes involved in virulence. In P. profundum the abundance and activity of the same protein is influenced by hydrostatic pressure and is able to regulate genes in a pressure-dependent manner. To better characterize the ToxR regulon, we have compared the genes differentially expressed in response to pressure changes with those whose expression is altered between wild type and toxR mutant strains. Four samples were analyzed: DB110 strain grown at 0.1 MPa, DB110 strain grown at 28 MPa, TW30 strain grown at 0.1 MPa, TW30 strain grown at 28 MPa. Two independent coltures (replicates) were grown for each sample, RNA was extracted from each replicate and RNAs from the two replicates were pooled together to reduce biological variability. No replicates were included in experimental design.
Project description:<p>Deep-sea hydrothermal vents are unique ecosystems that may release chemically distinct dissolved organic matter to the deep ocean. Here, we describe the composition and concentrations of polar dissolved organic compounds observed in low and high temperature hydrothermal vent fluids at 9°50′N on the East Pacific Rise. The concentration of dissolved organic carbon was 46 µM in the low temperature hydrothermal fluids and 14 µM in the high temperature hydrothermal fluids. In the low temperature vent fluids, quantifiable dissolved organic compounds were dominated by water-soluble vitamins and amino acids. Derivatives of benzoic acid and the organic sulfur compound 2,3-dihydroxypropane-1-sulfonate (DHPS) were also present in low and high temperature hydrothermal fluids. The low temperature vent fluids contain organic compounds that are central to biological processes, suggesting that they are a by-product of biological activity in the subseafloor. These compounds may fuel heterotrophic and other metabolic processes at deep-sea hydrothermal vents and beyond.</p>
