CE44 - Biochimie du Vivant

O2-independent hydroxylation and the anaerobic biosynthesis of ubiquinone – O2-taboo

Submission summary

Isoprenoid quinones are central for cellular physiology since they act as electrons and protons shuttles in energy-generating respiratory chains and in various processes like haem and uracil biosynthesis or disulfide bond formation. Escherichia coli and many proteobacteria possess two types of isoprenoid quinones: ubiquinone (UQ) and (demethyl)menaquinone (D)MK. Typically, UQ is considered as an “aerobic” quinone since it participates to aerobic respiration and its biosynthesis requires dioxygen (O2) for three hydroxylation steps. In contrast (D)MK have been characterized as “anaerobic” quinones as they participate to anaerobic respiration and their synthesis doesn’t depend on O2.
During the AnaeroUbi project supported by ANR (2015-2019), our consortium has discovered that E. coli can synthesize UQ by an O2-independent pathway. We identified three genes ubiT, ubiU and ubiV that are essential for the biosynthesis of UQ in anaerobic conditions . Furthermore, we found that the O2-independent UQ pathway is widely conserved in proteobacteria. Thus, our results revisit the current dogma about UQ being an aerobic quinone and show that bacteria actually synthesize UQ over the entire range of O2 concentrations. Our multidisciplinary O2-taboo project is based on this discovery and will address important issues in four interconnected tasks:

1) We propose to evaluate the regulation of the O2-independent UQ pathway and its contribution to bacterial physiology. Experiments will be conducted in laboratory cultures at various O2 levels and also inside a natural host of E. coli, where low O2 conditions prevail. Our results are likely to be applicable, at least in part, to most facultative anaerobic bacteria that count many human pathogens.
2) Three O2-independent hydroxylation steps are required in the newly-discovered UQ pathway. We have accumulated preliminary evidence that UbiU and UbiV represent a novel class of O2-independent hydroxylases. We propose to elucidate their structure, their catalytic mechanism, the role of their Fe-S clusters and to establish the identity of the OH donor in these hydroxylation reactions.
3) In the cell, the biosynthesis of UQ demands that highly hydrophobic substrates are sequentially modified by multiple enzymes. We showed recently that the O2-dependent biosynthesis of UQ takes place inside a multiprotein complex, in which UbiJ binds the hydrophobic biosynthetic intermediates via its SCP2 domain. Our preliminary data support that the O2-independent pathway organizes in a complex around the SCP2-containing UbiT protein. We propose to characterize the O2-independent complex by identifying its components and their interactions, using a combination of biochemical and bioinformatic approaches.
4) Finally, we propose to study the evolution of the O2-independent pathway to evaluate if it appeared before or after the O2-dependent pathway. Our results could challenge the current paradigm that consists in the requirement for high O2 concentration habitats for the appearance of the UQ pathway on Earth, about 2.4 billion years ago.

By combining complementary approaches, the O2-taboo project addresses forefront questions in microbial physiology, cellular biochemistry and evolutionary biology. Overall, our results will contribute significant advances by elucidating (i) the regulation and physiological importance of a new pathway conserved in proteobacteria, (ii) the molecular function and supramolecular organization of the UbiT,U,V proteins, (iii) the unprecedented chemistry of novel O2-independent hydroxylation reactions, (iv) the distribution and evolution of the UQ pathways in proteobacteria.

Project coordination

Fabien Pierrel (TIMC-IMAG)

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.


LCPB (Collège de France) Laboratoire de Chimie des Processus Biologiques

Help of the ANR 558,081 euros
Beginning and duration of the scientific project: December 2019 - 48 Months

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