A dynamic model of lignin biosynthesis in Brachypodium distachyon

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.Electronic supplementary materialThe online version of this article (10.1186/s13068-018-1241-6) contains supplementary material, which is available to authorized users.

Low Lignin Mutants and Reduction of Lignin Content in Grasses for Increased Utilisation of Lignocellulose

“…The monolignols are synthesised from phenylalanine or tyrosine (exclusively for grasses) [27,28] through the general phenylpropanoid pathway, which is the precursor for numerous specialised metabolites, including flavonoids, tannins and coumarins, and monolignol-specific pathways in the cytosol, before polymerisation in the cell wall. The steps involved in the synthesis are well documented [29,30]. Briefly, phenylalanine and tyrosine are products of the shikimate pathway synthesised in the chloroplasts and exported to the cytosol, where the monolignols are synthesised via a series of enzymatic reactions, illustrated in Figure 2.…”

“…Monolignol biosynthetic pathway for grasses based on studies on Brachypodium distachyon[30,32] which is regarded model plant for grasses. The illustration was inspired by[42].…”

Modeling cross-regulatory influences on monolignol transcripts and proteins under single and combinatorial gene knockdowns in Populus trichocarpa

“…Predicting what transgenic modifications will lead to desired lignin and wood phenotypes is of current interest in the bioenergy and biomaterial industries among others [29,30]. Computational models of the monolignol pathway have become an important tool in the past decade to understanding how changes to the monolignol enzymes result in changes to the pathway outputs [18,[31][32][33][34] and lignin and wood phenotypes [4]. We add to this body of work by developing a model that incorporates observed influences at both the transcript and protein levels to estimate how the enzymes in the monolignol biosynthetic pathway are influenced by one or more monolignol gene knockdowns.…”

Systematic Analysis and Biochemical Characterization of the Caffeoyl Shikimate Esterase Gene Family in Poplar

“…Changing the mass ux in the phenylpropanoid pathway has become a new strategy for modifying lignin content (Whetten and Sederoff 1995;Boerjan et al 2003;Vanholme et al 2010;Weng and Chapple 2010;Vanholme et al 2013;Ragauskas et al 2014). Recently, dynamic ux modeling for monolignol biosynthesis was also proposed based on systematic understanding of monolignol biosynthesis pathway (Wang et al 2018a;Guo et al 2018;Faraji et al 2018a;Faraji et al 2018b). The discovery of caffeoyl shikimate esterase (CSE) as a central enzyme in the lignin biosynthetic pathway promoted a revision of our understanding of the pathway (Vanholme et al 2013).…”