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iScience. 2020 Feb 21;23(2):100849. doi: 10.1016/j.isci.2020.100849. Epub 2020 Jan 17.

Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift.

Author information

1
Univ Rennes, Inria, CNRS, IRISA, Equipe Dyliss, Rennes, France.
2
Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), 29680 Roscoff, France.
3
LBCM, IUEM, University of Bretagne-Sud, Lorient, France.
4
Sorbonne Université, CNRS, Plateforme METABOMER-Corsaire (FR2424), Station Biologique de Roscoff, Roscoff, France.
5
Sorbonne Université, CNRS, Plateforme ABiMS (FR2424), Station Biologique de Roscoff, Roscoff, France.
6
Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), 29680 Roscoff, France. Electronic address: gabriel.markov@sb-roscoff.fr.

Abstract

Inferring genome-scale metabolic networks in emerging model organisms is challenged by incomplete biochemical knowledge and partial conservation of biochemical pathways during evolution. Therefore, specific bioinformatic tools are necessary to infer biochemical reactions and metabolic structures that can be checked experimentally. Using an integrative approach combining genomic and metabolomic data in the red algal model Chondrus crispus, we show that, even metabolic pathways considered as conserved, like sterols or mycosporine-like amino acid synthesis pathways, undergo substantial turnover. This phenomenon, here formally defined as "metabolic pathway drift," is consistent with findings from other areas of evolutionary biology, indicating that a given phenotype can be conserved even if the underlying molecular mechanisms are changing. We present a proof of concept with a methodological approach to formalize the logical reasoning necessary to infer reactions and molecular structures, abstracting molecular transformations based on previous biochemical knowledge.

KEYWORDS:

Bioinformatics; Genomics; Metabolomics

Conflict of interest statement

Declaration of Interests The authors declare no competing interests.

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