Microbial Genomics B11 Strategies to Harness the Metabolic Diversity of Rhodopseudomonas palustris

Rhodopseudomonas palustris is an extremely successful bacterium that can be found in virtually any temperate soil or water sample on earth. It can grow by adopting one of the four major metabolic modes: photoautotrophic growth (energy from light and carbon from C1 compounds), photoheterotrophic growth (energy from light and carbon from organic compounds), chemoheterotrophic growth (carbon and energy from organic compounds) and chemoautotrophic growth (energy from inorganic compounds and carbon from C1 compounds). Rhodopseudomonas enjoys exceptional versatility within each of these growth modes. It can grow with or without oxygen and can use many alternative forms of carbon, nitrogen and inorganic electron donors. It degrades plant biomass and chlorinated pollutants and shows promise as a catalyst for biofuel production. Rhodopseudomonas has thus become a model to probe how the web of metabolic reactions that operates in the confines of a single cell adjusts in response to subtle changes in environmental conditions. Genes for key metabolic enzymes and regulatory proteins are easily identified in the 5.49 Mb Rhodopseudomonas genome. It has a large cluster of photosynthesis genes and a collection of additional genes that encode light-responsive proteins. It has genes for the metabolism of diverse kinds of carbon sources, including lignin monomers, complex fatty acids and dicarboxylic acids. It encodes two different carbon dioxide fixation enzymes and three different nitrogen fixation enzymes, each with a different transition metal at its active site. Each of the three nitrogenases is active in Rhodopseudomonas and each catalyzes the conversion of nitrogen gas to ammonia and hydrogen, a biofuel. Rhodopseudomonas can convert sunlight to ATP and derive electrons by biodegrading plant material. ATP and electrons so generated can, in turn, be used to fix nitrogen, with accompanying hydrogen production. Because multiple systems are involved, hydrogen production is a good starting point for studies or integrative metabolism by Rhodopseudomonas. To achieve efficient hydrogen production it is important to understand how expression levels of genes involved in photosynthesis, carbon dioxide fixation, lignin monomer degradation and nitrogen fixation fluctuate in response to variations in conditions. It is also important to identify regulatory bottlenecks that restrict the flow of energy and electrons from plant biomass to hydrogen production. Towards this end we have constructed a whole genome DNA microarray of Rhodopseudomonas and we are now using the array to analyze global patterns of gene expression.