Desulfovibrio vulgaris Hildenborough
Desulfovibrio is a rod-shaped anaerobic bacterium with a 3 Mbp genome. Desulfovibrio is known for its flexibility in the variety of electron acceptors it utilizes including sulfate, sulfur, nitrate, and nitrite among others. Species of Desulfovibrio have long been of interest as bioremediators, with the ability to reduce several toxic metals such as uranium (VI), chromium (VI) and iron (III).
NCBI taxonomy ID: 882
We have initiated a program to perform a high-quality reconstruction of the transcriptional regulatory network (TRN) of DvH and build a predictive model for transcriptional control of its physiology. Our approach to this challenging problem uses two complementary approaches: i) a data-driven systems approach that relies on the integration of diverse data including high-throughput gene expression and protein-protein interactions data (cMonkey and Inferelator); ii) a genomic-driven approach based on the simultaneous analysis of several closely related genomes to decipher evolutionary conserved regulatory signals (RegPrecise). Recently we were able to demonstrate that both approaches allow us to get deep insight into transcriptional regulation of DvH and to build a large-scale TRN and high-quality predictive model for this organism. Preliminary predictions are shown below. These algorithms incorporate transcriptome data, annotations, operon predictions, genome information and evolutionary conservation from MicrobesOnline and incorporate novel data, such as high-resolution transcriptome maps via RNA-seq, collected by the Enigma consortium.
- Preliminary DvH regulons predicted by cMonkey
- Conserved DvH regulons discovered by comparative genomics