Evolution of Ubiquinone Biosynthesis: Multiple Proteobacterial Enzymes with Various Regioselectivities To Catalyze Three Contiguous Aromatic Hydroxylation Reactions.
The ubiquitous ATP synthase uses an electrochemical gradient to synthesize cellular energy in the form of ATP. The production of this electrochemical gradient relies on liposoluble proton carriers like ubiquinone (UQ), which is used in the respiratory chains of eukaryotes and proteobacteria. The biosynthesis of UQ requires three hydroxylation reactions on contiguous positions of an aromatic ring. InEscherichia coli, each of three UQ flavin monooxygenases (FMOs), called UbiF, UbiH, and UbiI, modifies a single position of the aromatic ring. This pattern of three hydroxylation reactions/three proteins has been accepted as a paradigm in UQ biology. Using a phylogenetic analysis, we found that UbiF, UbiH, and UbiI are detected only in a small fraction of proteobacteria, and we identified two new types of UQ FMOs: UbiM, which is distributed in members of the alpha, beta, and gamma classes of proteobacteria, and UbiL, which is restricted to members of the alphaproteobacteria. Remarkably, theubiLandubiMgenes were found in genomes with fewer than three UQ hydroxylase-encoding genes. We demonstrated, using biochemical approaches, that UbiL fromRhodospirillum rubrumand UbiM fromNeisseria meningitidishydroxylate, respectively, two and three positions of the aromatic ring during UQ biosynthesis. We conclude that bacteria have evolved a large repertoire of hydroxylase combinations for UQ biosynthesis, including pathways with either three specialist enzymes or pathways with one or two generalist enzymes of broader regioselectivity. The emergence of the latter is potentially related to genome reduction events.IMPORTANCEUQ, a key molecule for cellular bioenergetics that is conserved from proteobacteria to humans, appeared in an ancestral proteobacterium more than 2 billion years ago. UQ biosynthesis has been studied only in a few model organisms, and thus, the diversity of UQ biosynthesis pathways is largely unknown. In the work reported here, we conducted a phylogenomic analysis of hydroxylases involved in UQ biosynthesis. Our results support the existence of at least two UQ hydroxylases in the proteobacterial ancestor, and yet, we show that their number varies from one to four in extant proteobacterial species. Our biochemical experiments demonstrated that bacteria containing only one or two UQ hydroxylases have developed generalist enzymes that are able to catalyze several steps of UQ biosynthesis. Our study documents a rare case where evolution favored the broadening of an enzyme's regioselectivity, which resulted in gene loss in several proteobacterial species with small genomes.
Laboratoire Technologies de l'Ingénierie Médicale et de la Complexité-Informatique, Mathématiques et Applications, Grenoble (TIMC-IMAG), University of Grenoble Alpes, Grenoble, France; Centre National de Recherche Scientifique (CNRS), TIMC-IMAG, UMR5525, Grenoble, France.
Ludovic
L
Pelosi
School of Fisheries and Ocean Sciences, University of Alaska-Fairbanks, Fairbanks, Alaska, USA.
Anne-Lise
AL
Ducluzeau
Aix-Marseille Université, CNRS, Laboratoire de Chimie Bactérienne, UMR 7283, Institut de Microbiologie de la Méditerranée, Marseille, France.
Laurent
L
Loiseau
Aix-Marseille Université, CNRS, Laboratoire de Chimie Bactérienne, UMR 7283, Institut de Microbiologie de la Méditerranée, Marseille, France.
Frédéric
F
Barras
Laboratoire Technologies de l'Ingénierie Médicale et de la Complexité-Informatique, Mathématiques et Applications, Grenoble (TIMC-IMAG), University of Grenoble Alpes, Grenoble, France; Centre National de Recherche Scientifique (CNRS), TIMC-IMAG, UMR5525, Grenoble, France.
Dominique
D
Schneider
Laboratoire Technologies de l'Ingénierie Médicale et de la Complexité-Informatique, Mathématiques et Applications, Grenoble (TIMC-IMAG), University of Grenoble Alpes, Grenoble, France; Centre National de Recherche Scientifique (CNRS), TIMC-IMAG, UMR5525, Grenoble, France.
Ivan
I
Junier
Laboratoire Technologies de l'Ingénierie Médicale et de la Complexité-Informatique, Mathématiques et Applications, Grenoble (TIMC-IMAG), University of Grenoble Alpes, Grenoble, France; Centre National de Recherche Scientifique (CNRS), TIMC-IMAG, UMR5525, Grenoble, France.
Fabien
0000-0003-2083-3002
F
Pierrel
biosynthesis; evolution; proteobacteria