S174: Probing microbial processes for potential arsenic and selenium bioremediation with genomics and proteomics

Three arsenate respiring bacteria, Bacillus selenitireducens, Alkaliphilus oremlandii, and Mono Lake strain MLMS-1, and a chemolithoautotrophic arsenite oxidizing bacterium, Alkalilimnicola ehrlichii, were chosen as candidates for sequencing by the Joint Genome Institute. Three were sequenced to closure with full annotation completed while draft annotation was done for strain MLMS-1. Sequence data was used to identify arsenite oxidase (Aox), respiratory arsenate reductase (Arr), and resistance genes (Ars) in these organisms as well as other published genomes. The failure to find an arsenite oxidase (Aox) homolog in Al. ehrlichii led to the discovery of a novel enzyme (Arx) that shares greater homology and structure with Arr but functions as an arsenite oxidase. Although the core subunits of Arr are conserved across the bacterial lineages, the number of genes and regulatory elements vary. Strain MLMS-1, a Deltaproteobacterium, has a two component regulatory system that shares a high degree of identity with the regulatory elements of Desulfitobacterium hafniense, a Gram positive bacterium. The paucity of genetic and biochemical data for selenium metabolism has made it more difficult to properly annotate the genomes of selenate and selenite respiring (e.g., B. selenitireducens) organisms. A common error is this misidentification of selenoproteins that contain selenocysteine. Proteomics holds great promise for elucidating the mechanisms of arsenic and selenium transformation. Using both 2-D SDS-PAGE with MALDI-TOF and LC/MS-MS (“shotgun proteomics”), the proteome profile of an organism grown under different growth conditions can be compared to identify up- and down- regulated proteins providing valuable information for pathway identification.