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Microbial Genomics 60 Gene Expression Profiles of Rhodopseudomonas palustris Nitrogenases by Whole Genome Microarray

Rhodopseudomonas palustris is a photosynthetic bacterium that can use many forms of carbon, nitrogen, and electron donors. Under anaerobic conditions it can generate energy from light and convert nitrogen gas to ammonia and hydrogen (a biofuel) by nitrogen fixation. A striking feature of the genome sequence of R. palustris CGA009 is genes encoding three different nitrogenases and the accessory proteins needed for nitrogenase assembly. AnfHDGK, nifHDK, and vnfHDGK genes encode iron (Fe)-containing, molybdenum (Mo)-containing, and vanadium (V)-containing nitrogenases. To address the question of how R. palustris differentially regulates nitrogenase gene expression, we constructed anfHnifH, anfHvnfH, and nifHvnfH double mutants and analyzed the whole genome gene expression profiles of each mutant and wild-type cells grown under nitrogen-fixing conditions. Each mutant expressed a single functional nitrogenase (Mo, V or Fe) in a minimal medium that contained molybdenum and other trace elements. Wild-type and the Mo-nitrogenase active mutant cells expressed over 150 genes at levels of 2-fold or higher when grown under nitrogen-fixing conditions as compared to when grown with ammonia. Among these were the 30 genes in the nif gene cluster, which were expressed at 5to 200-fold higher (depending on the gene) levels in cells grown under nitrogen-fixing conditions. Genes in the anf and vnf clusters were not expressed. By contrast, cells with an active Fe-nitrogenase only or an active V-nitrogenase only expressed all of the nif genes (except nifH which was deleted), all of the anf genes, and all of the vnf genes. It makes sense that nif genes would be expressed because many of them are needed for the assembly of the Feand V-nitrogenases. These results indicate that R. palustris synthesizes both its Feand V-nitrogenases in situations where it is unable to synthesize an active Mo-nitrogenase. The mechanism by which Feand V-nitrogenase gene expression is activated is not known, but does not involve relief of Mo repression.