The first multi-tissue diel genome-scale metabolic model of a woody plant highlights suberin biosynthesis pathways in Quercus suber

Abstract

In the last decade, genome-scale metabolic models have been increasingly used to study plant metabolic behaviour at the tissue and multi-tissue level in different environmental conditions. Quercus suber (Q. suber), also known as the cork oak tree, is one of the most important forest communities of the Mediterranean/Iberian region. In this work, we present the genome-scale metabolic model of the Q. suber (iEC7871), the first of a woody plant. The metabolic model comprises 7871 genes, 6230 reactions, and 6481 metabolites across eight compartments. Transcriptomics data was integrated into the model to obtain tissue-specific models for the leaf, inner bark, and phellogen. Each tissue's biomass composition was determined to improve model accuracy and merged into a diel multi-tissue metabolic model to predict interactions among the three tissues at the light and dark phases. The metabolic models were also used to analyze the pathways associated with the synthesis of suberin monomers. Nevertheless, the models developed in this work can provide insights about other aspects of the metabolism of Q. suber, such as its secondary metabolism and cork formation.

merlin, an improved framework for the reconstruction of high-quality genome-scale metabolic models

“…The Quercus suber GSMM ( 8 ) epitomises the first genome-scale metabolic model of a ligneous tree. This model comprises 6481 metabolites, 6230 reactions, 7871 genes, and eight different compartments.…”

“…Since the last major version, multiple tools for genome functional annotation, draft assembly, model refinement, and validation have been implemented. Over the last years, merlin's user base has grown considerably, resulting in the reconstruction of GSMMs of multiple organisms from all domains of life, ranging from small-sized genome bacteria ( 7 ) to complex higher eukaryotes, such as the cork oak tree ( 8 ). Moreover, the Kluyveromyces lactis’ model ( 9 ), developed and improved with merlin , is recognised as a reference among the yeast community, as it has served as the baseline for both experimental studies on metabolism and regulation towards biotechnological applications ( 10–16 ) and to build models of other yeasts ( 17 , 18 ).…”

A diel multi-tissue genome-scale metabolic model ofVitis vinifera

“…However, as these data are not available for V. vinifera, the biomass content was estimated based on previously published plant GSMMs and insights from the literature. Specifically, the biomass formulation for leaf, stem, and green berry was based on the models of A. thaliana (Dal'Molin et al, 2010;de Oliveira Dal'Molin et al, 2015), S. lycopersicum , and Q. suber (Cunha et al, 2023b), while the biomass of the mature berry was adjusted according to the literature (Cheng et al, 2016) and the metabolomics data available for the same samples used to obtain the RNA-Seq data (Fasoli et al, 2018). Details of the biomass composition are available in Supplementary File 3.…”

“…Phenotype predictions of the tissue-specific models were performed by pFBA, using two different strategies as applied in other plant models (Dal'Molin et al, 2010;Cunha et al, 2023b) and based on A. thaliana experimental measures (Niemann et al, 1995). The first consisted of fixing the biomass growth rate to 0.11h -1 and defining the minimization of the photon/sucrose uptake as the objective function.…”

merlin v4.0: an updated platform for the reconstruction of high-quality genome-scale metabolic models

“…Since the last major version, multiple tools for genome functional annotation, draft assembly, model refinement, and validation have been implemented. Over the last years, merlin's user base has grown considerably, resulting in the reconstruction of GSMMs of multiple organisms from all domains of life, ranging from small-sized genome bacteria (7) to complex higher eukaryotes, such as the cork oak tree (8). Moreover, the Kluyveromyces lactis' model (9), developed and improved with merlin, is recognised as a reference among the yeast community, as it has served as the baseline for both experimental studies on metabolism and regulation towards biotechnological applications (10)(11)(12)(13)(14)(15)(16) and to build models of other yeasts (17,18).…”