title: Computational inference of the structure and regulation of the lignin pathway in Panicum virgatum.
abstract: BACKGROUND
  Switchgrass is a prime target for biofuel production from inedible plant parts and has been the subject of numerous investigations in recent years. Yet, one of the main obstacles to effective biofuel production remains to be the major problem of recalcitrance. Recalcitrance emerges in part from the 3-D structure of lignin as a polymer in the secondary cell wall. Lignin limits accessibility of the sugars in the cellulose and hemicellulose polymers to enzymes and ultimately decreases ethanol yield. Monolignols, the building blocks of lignin polymers, are synthesized in the cytosol and translocated to the plant cell wall, where they undergo polymerization. The biosynthetic pathway leading to monolignols in switchgrass is not completely known, and difficulties associated with in vivo measurements of these intermediates pose a challenge for a true understanding of the functioning of the pathway.
  
  
  RESULTS
  In this study, a systems biological modeling approach is used to address this challenge and to elucidate the structure and regulation of the lignin pathway through a computational characterization of alternate candidate topologies. The analysis is based on experimental data characterizing stem and tiller tissue of four transgenic lines (knock-downs of genes coding for key enzymes in the pathway) as well as wild-type switchgrass plants. These data consist of the observed content and composition of monolignols. The possibility of a G-lignin specific metabolic channel associated with the production and degradation of coniferaldehyde is examined, and the results support previous findings from another plant species. The computational analysis suggests regulatory mechanisms of product inhibition and enzyme competition, which are well known in biochemistry, but so far had not been reported in switchgrass. By including these mechanisms, the pathway model is able to represent all observations.
  
  
  CONCLUSIONS
  The results show that the presence of the coniferaldehyde channel is necessary and that product inhibition and competition over cinnamoyl-CoA-reductase (CCR1) are essential for matching the model to observed increases in H-lignin levels in 4-coumarate:CoA-ligase (4CL) knockdowns. Moreover, competition for 4-coumarate:CoA-ligase (4CL) is essential for matching the model to observed increases in the pathway metabolites in caffeic acid O-methyltransferase (COMT) knockdowns. As far as possible, the model was validated with independent data.
authors.affiliation: The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313, Ferst Drive, Atlanta, GA 30332 USA ; BioEnergy Sciences Center (BESC), Oak Ridge National Lab, Oak Ridge, TN USA.
authors.forename: Mojdeh
authors.initials: M
authors.lastname: Faraji
authors.affiliation: The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313, Ferst Drive, Atlanta, GA 30332 USA ; BioEnergy Sciences Center (BESC), Oak Ridge National Lab, Oak Ridge, TN USA.
authors.forename: Luis L
authors.initials: LL
authors.lastname: Fonseca
authors.affiliation: BioEnergy Sciences Center (BESC), Oak Ridge National Lab, Oak Ridge, TN USA ; Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203-5017 USA.
authors.forename: Luis
authors.initials: L
authors.lastname: Escamilla-Treviño
authors.affiliation: BioEnergy Sciences Center (BESC), Oak Ridge National Lab, Oak Ridge, TN USA ; Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203-5017 USA.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Dixon
authors.affiliation: The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313, Ferst Drive, Atlanta, GA 30332 USA ; BioEnergy Sciences Center (BESC), Oak Ridge National Lab, Oak Ridge, TN USA.
authors.forename: Eberhard O
authors.identifier: 0000-0003-1378-3043
authors.initials: EO
authors.lastname: Voit
keywords: Biochemical systems theory; Lignin biosynthesis; Panicum virgatum; Pathway analysis; Recalcitrance; Switchgrass