Ubiquinone biosynthesis over the entire O₂range: characterization of a conserved, O₂-independent pathway

SUMMARYMost bacteria can generate ATP by respiratory metabolism, in which electrons are shuttled from reduced substrates to terminal electron acceptors, via quinone molecules likeubiquinone. Dioxygen (O2) is the terminal electron acceptor of aerobic respiration and serves as a co-substrate in the biosynthesis ofubiquinone. Here, we characterize a novel, O2-independent pathway for the biosynthesis ofubiquinone. This pathway relies on three proteins UbiT (YhbT), UbiU (YhbU) and UbiV (YhbV). UbiT contains an SCP2 lipid-binding domain and is likely an accessory factor of the biosynthetic pathway, while UbiU-UbiV are involved in hydroxylation reactions and represent a novel class of O2-independent hydroxylases. We demonstrate that UbiU-UbiV form a heterodimer, wherein each protein binds a 4Fe-4S cluster via conserved cysteines that are essential for activity. The UbiT, -U, -V proteins are found in α-, β-, γ-proteobacterial clades including several human pathogens, supporting the widespread distribution of a previously-unrecognized capacity to synthesizeubiquinone in the absence of O2. Together, the O2-dependent and O2-independentubiquinone biosynthesis pathways contribute to optimize bacterial metabolism over the entire O2range.IMPORTANCEIn order to colonize environments with large O2gradients or fluctuating O2levels, bacteria have developed metabolic responses that remain incompletely understood. Such adaptations have been recently linked to antibiotic resistance, virulence and the capacity to develop in complex ecosystems like the microbiota. Here, we identify a novel pathway for the biosynthesis ofubiquinone, a molecule with a key role in cellular bioenergetics. We link three uncharacterized genes ofEscherichia colito this pathway and show that the pathway functions independently from O2. In contrast, the long-described pathway forubiquinone biosynthesis requires O2as substrate. In fact, we find that many proteobacteria are equipped with the O2-dependent and O2-independent pathways, supporting that they are able to synthesizeubiquinone over the entire O2range. Overall, we propose that the novel O2-independent pathway is part of the metabolic plasticity developed by proteobacteria to face varying environmental O2levels.