Computational inference of the structure and regulation of the lignin pathway in Panicum virgatum

This article uses a systems biological modeling approach to address the challenge of in vivo measurements to elucidate the structure and regulation of the lignin pathway through a computational characterization of alternate candidate topologies

A dynamic model of lignin biosynthesis in Brachypodium distachyon

Article proposes 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

Mathematical models of lignin biosynthesis

Abstract Background Lignin is a natural polymer that is interwoven with cellulose and hemicellulose within plant cell walls. Due to this molecular arrangement, lignin is a major contributor to the recalcitrance of plant materials with respect to the extraction of sugars and their fermentation into ethanol, butanol, and other potential bioenergy crops. The lignin biosynthetic pathway is similar, but not identical in different plant species. It is in each case comprised of a moderate number of enzymatic steps, but its responses to manipulations, such as gene knock-downs, are complicated by the fact that several of the key enzymes are involved in several reaction steps. This feature poses a challenge to bioenergy production, as it renders it difficult to select the most promising combinations of genetic manipulations for the optimization of lignin composition and amount. Results Here, we present several computational models than can aid in the analysis of data characterizing lignin biosynthesis. While minimizing technical details, we focus on the questions of what types of data are particularly useful for modeling and what genuine benefits the biofuel researcher may gain from the resulting models. We demonstrate our analysis with mathematical models for black cottonwood (Populus trichocarpa), alfalfa (Medicago truncatula), switchgrass (Panicum virgatum) and the grass Brachypodium distachyon. Conclusions Despite commonality in pathway structure, different plant species show different regulatory features and distinct spatial and topological characteristics. The putative lignin biosynthes pathway is not able to explain the plant specific laboratory data, and the necessity of plant specific modeling should be heeded

Switchgrass (Panicum virgatum) possesses a divergent family of cinnamoyl CoA reductases with distinct biochemical properties

Article on switchgrass (Panicum virgatum) possessing a divergent family of cinnamoyl CoA reductases with distinct biochemical properties

Development and use of a switchgrass (Panicum virgatum L.) transformation pipeline by the BioEnergy Science Center to evaluate plants for reduced cell wall recalcitrance

This article provides information on the organization and outcomes of the BioEnergy Science Center Transformation Pipeline, and supplies useful information when developing coordinated, large-scale, multi-institutional reverse genetic pipelines to improve crop traits

Le Courrier

16 décembre 18221822/12/16 (A0,N350)