Host of environmental interactions of members of the rhizobiales order of alphaproteobacteria

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In the past decade, the determination of the complete sequences of bacterial genomes has radically altered microbiological research. Much effort is now directed towards the identification of the functions of newly discovered genes and transcriptional regulation pathways. The well-characterized bacterium Sinorhizobium meliloti is a leading model system for this type of research. It forms alfalfa root nodules in which atmospheric nitrogen is converted to ammonia for the benefit of the plant, relieving the need for nitrogen fertilizers. S. meliloti cells use a variety of carbon substrates for growth; this omnivory probably contributes to ability to survive in the soil and near the plant roots. Several candidates for contribution to the catabolic capacity are found within the 78-member family of proteins called short chain dehydrogenases / reductases (SDR). In previous work, we have made mutations in all SDR-encoding genes in the S. meliloti genome, and through subsequent phenotypic analysis determined that several of them are in fact required for utilization of specific carbon sources, and for effective symbiosis with alfalfa. We will now focus on mutational analysis of genes surrounding each of the SDR-encoding genes, in an attempt to understand the mechanisms involved. We are also studying a key transcriptional regulatory system that is required for effective symbiosis, and is conserved in related bacteria that form symbiotic or pathogenic interactions with plants, animals and humans. We have developed a novel and simple DNA binding trap assay to identify potential transcriptional factor binding sites. We will use this assay to identify the targets for this transcriptional regulatory system, and then go on to study the functions of the target genes and evaluate their involvement in symbiosis. Finally, we are developing another bacterium, Ochrobactrum anthropi, as a model system for host pathogen interaction. Although this organism is quite closely related to the human pathogen Brucella, and is itself an opportunistic human pathogen, it also appears to be capable of a more versatile lifestyle in the soil and rhizosphere. Using comparative genomic analysis, followed by experimental analysis, we will investigate shared mechanisms.