Study of quinones and respiratory metabolism

Head Dr Fabien Pierrel

Our group combines biochemical, genetic and evolutionary approaches to advance our molecular understanding of the biosynthesis and function of respiratory chains, which are central to cellular bioenergetics. Indeed, respiratory metabolism, which results in the complete oxidation of nutrients to CO2 and the concomitant synthesis of ATP, provides most of the energy of eukaryotic cells and many bacteria. As such, dysfunction of respiratory metabolism has severe cellular consequences and leads to mitochondrial diseases in humans.
Bacterial and eukaryotic mitochondrial respiratory chains are composed of several modules, among which quinones constitute an essential link between primary dehydrogenases and terminal reductases (Figure 1). Whereas eukaryotes only have ubiquinone, also named coenzyme Q (Q), most proteobacteria contain both Q and menaquinone. Q was discovered almost 60 years ago, yet several aspects of its biosynthesis remain obscure and notably the identity of genes catalyzing several reactions.

Figure 1: Bacterial (A) and mitochondrial (B) respiratory chains. Quinones (Q and (D)MK) transfer electrons (arrows) between respiratory enzymes, which generate a proton gradient used by ATP synthase to synthesis ATP.

Over the past 8 years our group has contributed to identify new genes required for Q biosynthesis and to uncover their molecular function by studying mainly the yeast Saccharomyces cerevisiae and the gamma-proteobacterium Escherichia coli (1-5) (Figure 2).

Figure 2: Coenzyme Q biosynthetic pathways in E. coli (protein names in blue) and S. cerevisiae (black). Significant contributions of the group are in red (Coq8, UbiJ and UbiK participate to Q biosynthesis without catalyzing chemical reactions).

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Figure 2

We also discovered that synthetic analogues of 4-hydroxybenzoic acid, the precursor of Q, can enter the Q biosynthetic pathway and restore Q deficiencies linked to impairment of given hydroxylation reactions (6,7) (Figure 3).These results have opened new perspectives for the treatment of primary coenzyme Q deficiencies in humans (8).

Figure 3: The biosynthesis of Q is restored by vanillic acid (a synthetic analog of the endogenous 4-HB substrate) in cells carrying mutant coq6 alleles.

After integrating the GEM (Genomics and Evolution of Microorganisms) team, an evolutionary perspective enriched our research. We revealed two new clades of Q hydroxylases (UbiM and UbiL) (Figure 4) and discovered that proteobacteria evolved a wide variety of solutions to catalyze the three hydroxylation reactions necessary for Q biosynthesis: some bacteria have a single hydroxylase with broad regio-selectivity, while others have three “specialist” hydroxylases with narrow regio-selectivity (9).

Figure 4: Molecular phylogeny of Q hydroxylases in alpha-, beta- and gammaproteobacteria (pink, green, and blue, respectively).

Recently, a new research project has been initiated to study the possibilities of metabolic remodeling when various modules of the mitochondrial respiratory chain are mutated. Our approach is based on experimental evolution of yeast mutants to improve their bioenergetic capacities and the subsequent genetic and biochemical characterization of the evolved strains to reveal the underlying molecular mechanisms. Our results may open new perspectives for the treatment of mitochondrial diseases.

Current research topics of the group include:
• The identity, mechanism and supramolecular organization of proteins participating to Q biosynthesis
• The possibilities of metabolic remodeling to bypass respiratory chain dysfunctions

Catherine Clarke (Department of Chemistry and Biochemistry, UCLA, USA)
Leonardo Salviati (University of Padova, Italy)
Marc Fontecave (Collège de France, Paris)
Frédéric Barras (Aix-Marseille University, France)
Dave Pagliarini (University of Wisconsin, Madison, USA
Alan Robinson (MRC, Cambridge, UK)
Roland Lill (Marburg University, Germany)
Anne-Lise Ducluzeau (University of Alaska, USA)

Current group members: Fabien Pierrel (CNRS Researcher), Ludovic Pelosi (Associate Professor), Bérengère Rascalou (Research Assistant), Amélie Amblard (Technical Assistant, ½ time).

Job opportunities : We are always interested in recruiting motivated students, postdoctoral or PhD candidates interested in metabolism and evolution. Applicants should contact Fabien for any project by e-mail.


Selected publications:
1. Payet, L. A., Leroux, M., Willison, J. C., Kihara, A., Pelosi, L., and Pierrel, F. (2016) Mechanistic Details of Early Steps in Coenzyme Q Biosynthesis Pathway in Yeast. Cell Chem Biol 23, 1241-1250
2. Ozeir, M., Pelosi, L., Ismail, A., Mellot-Draznieks, C., Fontecave, M., and Pierrel, F. (2015) Coq6 Is Responsible for the C4-deamination Reaction in Coenzyme Q Biosynthesis in Saccharomyces cerevisiae. J. Biol. Chem. 290, 24140-24151
3. Aussel, L., Loiseau, L., Hajj Chehade, M., Pocachard, B., Fontecave, M., Pierrel, F., and Barras, F. (2014) ubiJ, a New Gene Required for Aerobic Growth and Proliferation in Macrophage, Is Involved in Coenzyme Q Biosynthesis in Escherichia coli and Salmonella enterica Serovar Typhimurium. J. Bacteriol. 196, 70-79
4. Hajj Chehade, M., Loiseau, L., Lombard, M., Pecqueur, L., Ismail, A., Smadja, M., Golinelli-Pimpaneau, B., Mellot-Draznieks, C., Hamelin, O., Aussel, L., Kieffer-Jaquinod, S., Labessan, N., Barras, F., Fontecave, M., and Pierrel, F. (2013) ubiI, a New Gene in Escherichia coli Coenzyme Q Biosynthesis, Is Involved in Aerobic C5-hydroxylation. J. Biol. Chem. 288, 20085-20092
5. Pierrel, F., Hamelin, O., Douki, T., Kieffer-Jaquinod, S., Muhlenhoff, U., Ozeir, M., Lill, R., and Fontecave, M. (2010) Involvement of mitochondrial ferredoxin and para-aminobenzoic acid in yeast coenzyme Q biosynthesis. Chem. Biol. 17, 449-459
6. Xie, L. X., Ozeir, M., Tang, J. Y., Chen, J. Y., Kieffer-Jaquinod, S., Fontecave, M., Clarke, C. F., and Pierrel, F. (2012) Over-expression of the Coq8 kinase in Saccharomyces cerevisiae coq null mutants allows for accumulation of diagnostic intermediates of the Coenzyme Q6 biosynthetic pathway. J. Biol. Chem. 287, 23571-23581
7. Ozeir, M., Muhlenhoff, U., Webert, H., Lill, R., Fontecave, M., and Pierrel, F. (2011) Coenzyme Q biosynthesis: Coq6 Is required for the C5-hydroxylation reaction and substrate analogs rescue Coq6 deficiency. Chem. Biol. 18, 1134-1142
8. Doimo, M., Trevisson, E., Airik, R., Bergdoll, M., Santos-Ocana, C., Hildebrandt, F., Navas, P., Pierrel, F., and Salviati, L. (2014) Effect of vanillic acid on COQ6 mutants identified in patients with coenzyme Q deficiency. Biochim. Biophys. Acta 1842, 1-6
9. Pelosi, L., Ducluzeau, A. L., Loiseau, L., Barras, F., Schneider, D., Junier, I., and Pierrel, F. (2016) Evolution of Ubiquinone Biosynthesis: Multiple Proteobacterial Enzymes with Various Regioselectivities To Catalyze Three Contiguous Aromatic Hydroxylation Reactions. mSystems 1, e00091-00016

Laboratoire TIMC-IMAG, Domaine de la Merci, 38706 La Tronche Cedex

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