Genome–Scale Metabolic Networks Shed Light on the Carotenoid Biosynthesis Pathway in the Brown Algae Saccharina japonica and Cladosiphon okamuranus

Delphine Nègre (1, 2, 3) , Méziane Aite (4) , Arnaud Belcour (4) , Clémence Frioux (5, 4) , Loraine Brillet-Guéguen (1, 2, 6, 7) , Xi Liu (2, 6, 7) , Philippe Bordron (2) , Olivier Godfroy (1) , Agnieszka P. Lipinska (1) , Catherine Leblanc (1) , Anne Siegel (4) , Simon Dittami (1) , Erwan Corre (2, 6, 7) , Gabriel V. Markov (1)

1 LBI2M - Laboratoire de Biologie Intégrative des Modèles Marins
2 ABIMS - ABiMS - Informatique et bioinformatique = Analysis and Bioinformatics for Marine Science
3 MMS - Mer, molécules et santé EA 2160
4 Dyliss - Dynamics, Logics and Inference for biological Systems and Sequences
5 Quadram Institute
6 FR2424 - Fédération de recherche de Roscoff
7 SBR - Station biologique de Roscoff = Roscoff Marine Station

Understanding growth mechanisms in brown algae is a current scientific and economic challenge that can benefit from the modeling of their metabolic networks. The sequencing of the genomes of Saccharina japonica and Cladosiphon okamuranus has provided the necessary data for the reconstruction of Genome–Scale Metabolic Networks (GSMNs). The same in silico method deployed for the GSMN reconstruction of Ectocarpus siliculosus to investigate the metabolic capabilities of these two algae, was used. Integrating metabolic profiling data from the literature, we provided functional GSMNs composed of an average of 2230 metabolites and 3370 reactions. Based on these GSMNs and previously published work, we propose a model for the biosynthetic pathways of the main carotenoids in these two algae. We highlight, on the one hand, the reactions and enzymes that have been preserved through evolution and, on the other hand, the specificities related to brown algae. Our data further indicate that, if abscisic acid is produced by Saccharina japonica, its biosynthesis pathway seems to be different in its final steps from that described in land plants. Thus, our work illustrates the potential of GSMNs reconstructions for formalizing hypotheses that can be further tested using targeted biochemical approaches.

Domaines: Bio-informatique [q-bio.QM]

Delphine Nègre, Méziane Aite, Arnaud Belcour, Clémence Frioux, Loraine Brillet-Guéguen, et al.. Genome–Scale Metabolic Networks Shed Light on the Carotenoid Biosynthesis Pathway in the Brown Algae Saccharina japonica and Cladosiphon okamuranus. Antioxidants , 2019, 8 (11), pp.564. ⟨10.3390/antiox8110564⟩. ⟨hal-02395080⟩