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

Journal Article · · Biotechnology for Biofuels
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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. 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. In conclusion, 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.

Research Organization:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC05-00OR22725
OSTI ID:
1618618
Alternate ID(s):
OSTI ID: 1260580
Journal Information:
Biotechnology for Biofuels, Journal Name: Biotechnology for Biofuels Vol. 8 Journal Issue: 1; ISSN 1754-6834
Publisher:
Springer Science + Business MediaCopyright Statement
Country of Publication:
Netherlands
Language:
English
Citation Metrics:
Cited by: 17 works
Citation information provided by
Web of Science

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Cited By (5)

A dynamic model of lignin biosynthesis in Brachypodium distachyon journal September 2018
Stepwise inference of likely dynamic flux distributions from metabolic time series data journal March 2017
The best models of metabolism: The best models of metabolism journal May 2017
Mathematical models of lignin biosynthesis journal February 2018
Improving Bioenergy Crops through Dynamic Metabolic Modeling journal October 2017

Linked Research (6)

Figures / Tables (14)

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
09 BIOMASS FUELS
Biochemical systems theory
Lignin biosynthesis
Panicum virgatum
Pathway analysis
Recalcitrance
Switchgrass