Adaptations in electron transport chain complexes of clinical Rhodococcus equi revealed through comparative genomics

Rhodococcus equi is an important veterinary and zoonotic pathogen that survives inside macrophage phagolysosomes. Nitrate reductase NarGHI is a known virulence factor for this pathogen. This enzyme complex serves as the terminal electron acceptor in anaerobic respiration in other pathogens, such as the phylogenetically related Mycobacterium tuberculosis. A recent study demonstrated that R. equi survives under anaerobic conditions. In this work, we endeavored to uncover the electron transport chain complexes of R. equi. By in silico comparison to known complexes in the Transporter Classification Database, 67 putative respiratory chain proteins were identified in R. equi 103S. Their distribution was evaluated in the genomes of 37 clinical (animal and human infections) and 297 non-clinical (environmental) Rhodococcus isolates from the NCBI RefSeq database. NarGHI subunits were found in 100% of clinical and 35% of non-clinical genomes. Loci encoding four potential electron donor complexes (a membrane-bound formate dehydrogenase, a succinate dehydrogenase, and two Ni-Fe hydrogenases) were present in > 80% of clinical and < 50% of non-clinical isolates. Loci encoding a nitric oxide reductase, a potential terminal electron acceptor, were identified in 40.5% of clinical and 2% of non-clinical isolates. The results show that the respiratory chain in R. equi is highly complex, and point to potential metabolic adaptations of this species to hypoxic conditions.