Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks

Sandrien Desmet; Marlies Brouckaert; Wout Boerjan; Kris Morreel

doi:10.1016/j.csbj.2020.11.050

Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks

Comput Struct Biotechnol J. 2020 Dec 3:19:72-85. doi: 10.1016/j.csbj.2020.11.050. eCollection 2021.

Authors

Sandrien Desmet^{1

2}, Marlies Brouckaert^{1

2}, Wout Boerjan^{1

2}, Kris Morreel^{1

2}

Affiliations

¹ Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium.
² VIB Center for Plant Systems Biology, Ghent, Belgium.

Abstract

Over the last decade, a giant leap forward has been made in resolving the main bottleneck in metabolomics, i.e., the structural characterization of the many unknowns. This has led to the next challenge in this research field: retrieving biochemical pathway information from the various types of networks that can be constructed from metabolome data. Searching putative biochemical pathways, referred to as biotransformation paths, is complicated because several flaws occur during the construction of metabolome networks. Multiple network analysis tools have been developed to deal with these flaws, while in silico retrosynthesis is appearing as an alternative approach. In this review, the different types of metabolome networks, their flaws, and the various tools to trace these biotransformation paths are discussed.

Publication types

Review