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

Abstract

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 switchgrassmore » 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.« less

Authors:
 [1];  [1];  [2];  [2]; ORCiD logo [1]
  1. Georgia Inst. of Technology and Emory University, Atlanta, GA (United States). The Wallace H. Coulter Dept. of Biomedical Engineering; Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioEnergy Science Center (BESC)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioEnergy Science Center (BESC); Univ. of North Texas, Denton, TX (United States)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1260580
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Biotechnology for Biofuels
Additional Journal Information:
Journal Volume: 8; Journal Issue: 1; Journal ID: ISSN 1754-6834
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 09 BIOMASS FUELS; Biochemical systems theory; Lignin biosynthesis; Panicum virgatum; Pathway analysis; Recalcitrance; Switchgrass

Citation Formats

Faraji, Mojdeh, Fonseca, Luis L., Escamilla-Treviño, Luis, Dixon, Richard A., and Voit, Eberhard O. Computational inference of the structure and regulation of the lignin pathway in Panicum virgatum. United States: N. p., 2015. Web. doi:10.1186/s13068-015-0334-8.
Faraji, Mojdeh, Fonseca, Luis L., Escamilla-Treviño, Luis, Dixon, Richard A., & Voit, Eberhard O. Computational inference of the structure and regulation of the lignin pathway in Panicum virgatum. United States. doi:10.1186/s13068-015-0334-8.
Faraji, Mojdeh, Fonseca, Luis L., Escamilla-Treviño, Luis, Dixon, Richard A., and Voit, Eberhard O. Thu . "Computational inference of the structure and regulation of the lignin pathway in Panicum virgatum". United States. doi:10.1186/s13068-015-0334-8. https://www.osti.gov/servlets/purl/1260580.
@article{osti_1260580,
title = {Computational inference of the structure and regulation of the lignin pathway in Panicum virgatum},
author = {Faraji, Mojdeh and Fonseca, Luis L. and Escamilla-Treviño, Luis and Dixon, Richard A. and Voit, Eberhard O.},
abstractNote = {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.},
doi = {10.1186/s13068-015-0334-8},
journal = {Biotechnology for Biofuels},
number = 1,
volume = 8,
place = {United States},
year = {Thu Sep 17 00:00:00 EDT 2015},
month = {Thu Sep 17 00:00:00 EDT 2015}
}

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Works referenced in this record:

Functional characterization of the switchgrass (Panicum virgatum) R2R3-MYB transcription factor PvMYB4 for improvement of lignocellulosic feedstocks
journal, October 2011


Genetic manipulation of lignin reduces recalcitrance and improves ethanol production from switchgrass
journal, February 2011

  • Fu, Chunxiang; Mielenz, Jonathan R.; Xiao, Xirong
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 9, p. 3803-3808
  • DOI: 10.1073/pnas.1100310108

Distinct cinnamoyl CoA reductases involved in parallel routes to lignin in Medicago truncatula
journal, September 2010

  • Zhou, Rui; Jackson, Lisa; Shadle, Gail
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 41, p. 17803-17808
  • DOI: 10.1073/pnas.1012900107

Downregulation of Cinnamyl Alcohol Dehydrogenase (CAD) Leads to Improved Saccharification Efficiency in Switchgrass
journal, January 2011