Comparative Genomics and Phylogenomics Core (Microbes Online) Graph Database System

The Computational Core is charged with transforming the information generated by the other two Core-groups into meaningful models of the cellular regulatory networks underlying the stress response of the key organisms. This involves a set of interdependent tasks. The Computational Core is charged with stewardship of the data developed by the other two core. To serve both the experimentalists and the models, specialized pathway databases designed for efficient access and storage of "network"information will be implemented. Both experimental design and data quality will be explored in collaboration with the Functional Genomics Core. The experimental design will be optimized both for obtaining reproducible data and for producing and testing network hypotheses.

The core will also develop the tools to reverse engineer the pathway data from the perturbation response datasets generated from the Functional Genomics Core.

Ordering and clustering among these molecular responses can be used to construct hypothetical causal relations among molecular species. Molecular interaction data and regulatory element prediction are further aids to developing and validating these proposed networks.

One of the hypotheses of this work is that the three bacteria, Desulfovibrio vulgaris, Geobacter metallireducens, and Shewanella oneidensis, will respond differently to perturbation in their environment and in their pathway structure (by mutation). This is almost certainly true but these differences may be unimportant artifacts of the evolutionary divergence of these organisms, or else may serve a functional role. Discriminating between these two possibilities requires dissecting first what pieces of the pathway are absolutely necessary for function. This should be conserved across the species. Second, nonconservative regulation in the three target organisms needs to be analyzed separately to determine what added control or dynamic features of the pathway are introduced by each regulatory strategy. At this point, it may prove possible to forward a hypothesis for the different functions of the different regulatory strategies (e.g., in dealing with a microaerophilic vs. anaerobic lifestyle). However, to make a robust estimation of which regulatory strategies are niche specific (or more particularly conserved among bacteria facing the same stressors), a large set of cross-comparative analyses must be done. Ideally, one would like detailed, accurate molecular models of the homologous stress response pathways in all the microorganisms in the immediate environments of our targets. However, this is too costly and time-consuming. Instead, we will clone the homologous pathways from the uncultured organisms in the same soil sample and use the resultant sequences as a basis for a comparative analysis of regulation. These large insert clones will be used both in the operon and cis-regulatory site prediction and to understand which protein and regulatory elements co-occur in species within a niche but not across.

The ultimate goal of this research is to create a set of detailed molecular kinetic models of stress response pathways in the key organisms, develop a practical understanding of the interplay among these pathways during different environmental conditions, and understand the comparative pathway regulation that evolved with different environmental constraints. These will constitute an unprecedented level of understanding of these generally important pathways. From these, we will develop conceptual models of the expected behavior of these populations of microbes under different stress and metal/radionuclide conditions to aid in testing hypotheses of the efficacy of natural attenuation and bioremediation strategies.