A dynamic model of lignin biosynthesis in Brachypodium distachyon

Mojdeh Faraji,Timothy J Tschaplinski,Zamin K Yang,Jaime Barros-Rios,Richard A Dixon,Nancy L Engle,Luis Escamilla-Treviño,Luis L Fonseca,Eberhard O Voit

doi:10.1186/s13068-018-1241-6

Abstract

BackgroundLignin is a crucial molecule for terrestrial plants, as it offers structural support and permits the transport of water over long distances. The hardness of lignin reduces plant digestibility by cattle and sheep; it also makes inedible plant materials recalcitrant toward the enzymatic fermentation of cellulose, which is a potentially valuable substrate for sustainable biofuels. Targeted attempts to change the amount or composition of lignin in relevant plant species have been hampered by the fact that the lignin biosynthetic pathway is difficult to understand, because it uses several enzymes for the same substrates, is regulated in an ill-characterized manner, may operate in different locations within cells, and contains metabolic channels, which the plant may use to funnel initial substrates into specific monolignols.ResultsWe propose a dynamic mathematical model that integrates various datasets and other information regarding the lignin pathway in Brachypodium distachyon and permits explanations for some counterintuitive observations. The model predicts the lignin composition and label distribution in a BdPTAL knockdown strain, with results that are quite similar to experimental data.ConclusionGiven the present scarcity of available data, the model resulting from our analysis is presumably not final. However, it offers proof of concept for how one may design integrative pathway models of this type, which are necessary tools for predicting the consequences of genomic or other alterations toward plants with lignin features that are more desirable than in their wild-type counterparts.

Highlights

Lignin is a crucial molecule for terrestrial plants, as it offers structural support and permits the trans‐ port of water over long distances
Review of features of the static model of lignin biosynthesis in Brachypodium We described elsewhere the procedures for designing a stoichiometric model for the pathway of lignin biosynthesis in Brachypodium [13] and it suffices here to review the main features, which are important for the following
As a positive upshot of this initially failed analysis, the systematic exploration of the model led us to the proposal of a twocompartment model, which reproduced all data faithfully, and, in particular, captured the differential channeling of 13C-labeled precursors

Summary

Introduction

Lignin is a crucial molecule for terrestrial plants, as it offers structural support and permits the trans‐ port of water over long distances. The hardness of lignin reduces plant digestibility by cattle and sheep; it makes inedible plant materials recalcitrant toward the enzymatic fermentation of cellulose, which is a potentially valuable substrate for sustainable biofuels. Lignin makes plant materials, such as stems and roots, very hard. As a consequence, it poses a substantial challenge in terms of animal feed digestibility, because its irregular aromatic structure is difficult to decompose enzymatically. It is difficult to predict how the pathway might respond to knockdowns of genes coding for enzymes that catalyze distinct reactions within the pathway Further complicating these challenges is the observation that the lignin pathway is similar, but not exactly the same in structure and regulation across different plant species. It was shown in recent years that computational modeling can greatly assist in comprehending the functionality of the lignin pathway [8,9,10,11,12]

Methods

Results

Discussion

Conclusion