Briefly, halophilic archaea dominate hypersaline environments, such as the Great Salt Lake, the Dead Sea and South San Francisco Bay, using robust physiologies that are appropriately tuned to the environment through signal transduction and gene regulatory networks. With streamlined genomes, up to 87% of which encode protein coding genes, these organisms offer an incredible opportunity to understand at a systems level mechanisms underlying environmental response systems.
To facilitate these studies we have determined the complete genome sequences for both of these organisms and have developed an array of genome scale strategies tailored to analyzing their biology.
Using these powerful tools we are applying systems approaches to dissect the complete sets of metabolic and gene regulatory networks that together modulate cell behavior in changing and often stressful environmental conditions.
There are several reasons that influenced our choice of halophilic archaea as our model system(s) –First, little is known about these organisms, which forces us to take a data-driven approach to their inquiry. Consequently, our approaches will not rely on decades of carefully conducted gene-by-gene research and as such these approaches will also be applicable for characterizing most organisms on this planet.
Second, a lot of fascinating biology exists in these environments and we se this as a wealth of biotechnology potential that remains untapped.
Third, these prokaryotic organisms have a small genome and, therefore, relatively simple and tractable in many ways to splice engineered genes in and out of the chromosome or on extra-chromosomal elements.
Finally, from an evolutionary standpoint these organisms are similar to bacteria in their genome organization and gene regulatory mechanisms but closer to eukaryotes with respect to their core genetic information processing mechanisms. This provides yet another opportunity to investigate the fascinating amalgamation of gene regulation strategies in Archaea, components of which have thus far been studied separately in Bacteria and in Eukaryotes.