Proteome profile and proteogenomics of the organohalide-respiring bacterium Dehalococcoides mccartyi strain CBDB1 grown on hexachlorobenzene as electron acceptor

Abstract

Dehalococcoides mccartyi strain CBDB1 is an obligate organohalide-respiring anaerobic bacterium that is able to transform a wide range of highly relevant halogenated organic contaminants and has been detected in natural and engineered environments. In order to understand the molecular principles, we generated a protein profile of CBDB1 cultivated in a synthetic anaerobic medium with hexachlorobenzene as the sole electron acceptor. The proteome characterization through two different proteomic techniques resulted in 8491 distinct peptides corresponding to 1023 proteins that covered 70% of the annotated 1458 protein-coding sequences. From the 32 annotated reductive dehalogenases homologous genes (rdhA) we were able to detect 16 RdhA proteins. High-quality MS spectra were further used to build a spectra library to provide a platform for precise and fast proteomic searches. In addition, the derived proteome data set was used to apply a proteogenomic approach that led to a refinement of genome annotation of CBDB1. This was mostly due to protein prolongation (13 cases) and detection of translated sequences without an obvious link to existing annotations (5 cases). These data go beyond the current knowledge of the bacterial proteome and provide an expanded platform for a better understanding of the functional cellular.

Biological significance: Anaerobic reductive dehalogenation of chlorinated organic molecules is a key process for the recycling of halogenated organic substances in natural habitats and highly relevant for groundwater bioremediation. The ability to couple reductive dehalogenation of halogenated compounds to ATP-generation via a respiratory chain is one remarkable capability prevalent in the model organism D. mccartyi strain CBDB1. Therefore, a reference proteome map was generated by comprehensive LC-MS analysis and converted into a SpectraST library to provide a platform for precise and fast shotgun proteomic searches. A proteogenomics approach led to a refinement of gene annotation of CBDB1 and will extend the current knowledge of the bacterial proteome. The approach provides an expanded platform for a better understanding of the functional cellular metabolism and thereby constitutes a tool for comparative studies of protein expression as well as further research on organohalide respiration.

Keywords: Dehalococcoides mccartyi strain CBDB1; Proteogenomics; Proteomic reference profile; Shotgun proteomics.