Comparative Proteomics of Dehalococcoides spp. Reveals Strain-Specific Peptides Associated with Activity

Abstract

Anaerobic reductive dehalogenation by Dehalococcoides spp. is an ideal system for studying functional diversity of closely related strains of bacteria. In Dehalococcoides spp., reductive dehalogenases (RDases) are key respiratory enzymes involved in the anaerobic detoxification of halogenated compounds at contaminated sites globally. Although housekeeping genes sequenced from Dehalococcoides spp. are >85% identical at the amino acid level, different strains are capable of dehalogenating diverse ranges of compounds, depending largely on the suite of RDase genes that each strain harbors and expresses. We identified RDase proteins that corresponded to known functions in four characterized cultures and predicted functions in an uncharacterized Dehalococcoides-containing mixed culture. Homologues within RDase subclusters containing PceA, TceA, and VcrA were among the most frequently identified proteins. Several additional proteins, including a formate dehydrogenase-like protein (Fdh), had high coverage in all strains and under all growth conditions.Comparative genomic studies have revealed that many of the phenotypic differences observed among closely related microbial species in nature are due to genetic islands of diversity that are frequently copied, rearranged, and laterally transferred. Pathogenicity islands, which are mobile genetic elements that confer virulence, are well known in host-associated microorganisms (8). A recent comparative genomic study of the marine photoautotroph Prochlorococcus suggests that natural populations of microorganisms may also contain genetic islands that confer unique phenotypic traits on closely related strains (3). A comparative genomic study of representatives from the Dehalococcoides lineage within the Chloroflexi phylum of bacteria, a group which reductively dehalogenates chlorinated organic pollutants (25), suggests that reductive dehalogenases (RDases) are key enzymes conferring functional differences on closely related strains of Dehalococcoides (14).Sequenced Dehalococcoides genomes (strains 195, CBDB1, and BAV1 [unfinished]) share a high degree of genomic similarity and synteny in nearly all "housekeeping" genes. There are, however, differences in the total numbers and types of RDases that these strains harbor and in their corresponding substrate ranges (1, 2, 14, 17). In Dehalococcoides ethenogenes (strain 195), RDases are responsible for reductive dechlorination of chlorinated organic compounds, such as the common groundwater contaminants and suspected human carcinogens tetrachloroethene (PCE) and trichloroethene (TCE). In strains 195 and CBDB1, the majority of putative RDase genes are in clusters located near the predicted origin of replication, and while the locations of the clusters are similar, the RDase gene contents are different. The complete genome sequence of strain 195 revealed 19 potential RDase genes, 4 of which were contained within putative integrated mobile genetic elements that may have been acquired recently or are marked for dissemination (23). Thirty...

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