Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis

Karine Bastard (1) , Alain Perret (2) , Aline Mariage (2) , Thomas Bessonnet (2) , Agnès Pinet-Turpault (2) , Jeanlouis Petit (2) , Ekaterina Darii (2) , Pascal Bazire (2) , Carine Vergne-Vaxelaire (3) , Clémence Brewee (2) , Adrien Debard (2) , Virginie Pellouin (2) , Marielle Besnard-Gonnet (2) , François Artiguenave (4) , Claudine Médigue (1) , David Vallenet (1) , Antoine Danchin (5) , Anne Zaparucha (3) , Jean Weissenbach (4) , Marcel Salanoubat (2) , Véronique de Berardinis (2)

1 LABGeM - Analyse Bio-Informatique pour la Génomique et le Métabolisme
2 LGBM - Laboratoire de Génomique et Biochimie du Métabolisme
3 L2BMS - Laboratoire de Biocatalyse, Biorémédiation et Métabolisme Synthétique
4 UMR 8030 - Génomique métabolique
5 ICAN - Unité de Recherche sur les Maladies Cardiovasculaires, du Métabolisme et de la Nutrition = Research Unit on Cardiovascular and Metabolic Diseases

Experimental validation of enzyme function is crucial for genome interpretation, but it remains challenging because it cannot be scaled up to accommodate the constant accumulation of genome sequences. We tackled this issue for the MetA and MetX enzyme families, phylogenetically unrelated families of acyl-L-homoserine transferases involved in L-methionine biosynthesis. Members of these families are prone to incorrect annotation because MetX and MetA enzymes are assumed to always use acetyl-CoA and succinyl-CoA, respectively. We determined the enzymatic activities of 100 enzymes from diverse species, and interpreted the results by structural classification of active sites based on protein structure modeling. We predict that >60% of the 10,000 sequences from these families currently present in databases are incorrectly annotated, and suggest that acetyl-CoA was originally the sole substrate of these isofunctional enzymes, which evolved to use exclusively succinyl-CoA in the most recent bacteria. We also uncovered a divergent subgroup of MetX enzymes in fungi that participate only in L-cysteine biosynthesis as O-succinyl-L-serine transferases.

Domains: Biochemistry, Molecular Biology

Karine Bastard, Alain Perret, Aline Mariage, Thomas Bessonnet, Agnès Pinet-Turpault, et al.. Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis. Nature Chemical Biology, 2017, 13, pp.858-866. ⟨10.1038/nchembio.2397⟩. ⟨cea-02132779⟩