Are seven amino acid substitutions sufficient to explain the evolution of high l‐DOPA 4,5‐dioxygenase activity leading to betalain pigmentation? Revisiting the gain‐of‐function mutants of Bean et al. (2018)

• Published in: The New phytologist 2023-09, Vol.239 (6), p.2265-2276
• Main Authors: Guerrero‐Rubio, M. Alejandra, Walker‐Hale, Nathanael, Guo, Rui, Sheehan, Hester, Timoneda, Alfonso, Gandia‐Herrero, Fernando, Brockington, Samuel F.
• Format: Article
• Language: English
• Subjects: Amino acids; Beans; betalains; caryophyllales; Catalytic activity; Colour; Comparative analysis; Dihydroxyphenylalanine; Dioxygenase; DODA; Evolution; horizontal swapping; Levodopa; l‐DOPA 4,5‐dioxygenase; Pigmentation; Residues; specialised metabolism; Vegetables
• ISSN: 0028-646X; 1469-8137
• DOI: 10.1111/nph.18981

Summary This work revisits a publication by Bean et al. (2018) that reports seven amino acid substitutions are essential for the evolution of l‐DOPA 4,5‐dioxygenase (DODA) activity in Caryophyllales. In this study, we explore several concerns which led us to replicate the analyses of Bean et al. (2018). Our comparative analyses, with structural modelling, implicate numerous residues additional to those identified by Bean et al. (2018), with many of these additional residues occurring around the active site of BvDODAα1. We therefore replicated the analyses of Bean et al. (2018) to re‐observe the effect of their original seven residue substitutions in a BvDODAα2 background, that is the BvDODAα2‐mut3 variant. Multiple in vivo assays, in both Saccharomyces cerevisiae and Nicotiana benthamiana, did not result in visible DODA activity in BvDODAα2‐mut3, with betalain production always 10‐fold below BvDODAα1. In vitro assays also revealed substantial differences in both catalytic activity and pH optima between BvDODAα1, BvDODAα2 and BvDODAα2‐mut3 proteins, explaining their differing performance in vivo. In summary, we were unable to replicate the in vivo analyses of Bean et al. (2018), and our quantitative in vivo and in vitro analyses suggest a minimal effect of these seven residues in altering catalytic activity of BvDODAα2. We conclude that the evolutionary pathway to high DODA activity is substantially more complex than implied by Bean et al. (2018).