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Title: A dynamic model of lignin biosynthesis in Brachypodium distachyon

Lignin 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. Here, we 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. Given 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 maymore » 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.« less
Authors:
 [1] ;  [1] ;  [2] ;  [2] ;  [3] ;  [3] ; ORCiD logo [3] ;  [2] ; ORCiD logo [1]
  1. Georgia Inst. of Technology and Emory Univ., Atlanta, GA (United States). 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). BioDiscovery Inst. and Dept. of Biological Sciences
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioEnergy Science Center (BESC)
Publication Date:
Grant/Contract Number:
AC05-00OR22725; MCB-1517588
Type:
Accepted Manuscript
Journal Name:
Biotechnology for Biofuels
Additional Journal Information:
Journal Volume: 11; Journal Issue: 1; Journal ID: ISSN 1754-6834
Publisher:
BioMed Central
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); USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); National Science Foundation (NSF)
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; 97 MATHEMATICS AND COMPUTING; Brachypodium distachyon; Medicago truncatula; Panicum virgatum; Pathway analysis; Populus trichocarpa; Recalcitrance
OSTI Identifier:
1471826

Faraji, Mojdeh, Fonseca, Luis L., Escamilla-Treviño, Luis, Barros-Rios, Jaime, Engle, Nancy L., Yang, Zamin K., Tschaplinski, Timothy J., Dixon, Richard A., and Voit, Eberhard O.. A dynamic model of lignin biosynthesis in Brachypodium distachyon. United States: N. p., Web. doi:10.1186/s13068-018-1241-6.
Faraji, Mojdeh, Fonseca, Luis L., Escamilla-Treviño, Luis, Barros-Rios, Jaime, Engle, Nancy L., Yang, Zamin K., Tschaplinski, Timothy J., Dixon, Richard A., & Voit, Eberhard O.. A dynamic model of lignin biosynthesis in Brachypodium distachyon. United States. doi:10.1186/s13068-018-1241-6.
Faraji, Mojdeh, Fonseca, Luis L., Escamilla-Treviño, Luis, Barros-Rios, Jaime, Engle, Nancy L., Yang, Zamin K., Tschaplinski, Timothy J., Dixon, Richard A., and Voit, Eberhard O.. 2018. "A dynamic model of lignin biosynthesis in Brachypodium distachyon". United States. doi:10.1186/s13068-018-1241-6. https://www.osti.gov/servlets/purl/1471826.
@article{osti_1471826,
title = {A dynamic model of lignin biosynthesis in Brachypodium distachyon},
author = {Faraji, Mojdeh and Fonseca, Luis L. and Escamilla-Treviño, Luis and Barros-Rios, Jaime and Engle, Nancy L. and Yang, Zamin K. and Tschaplinski, Timothy J. and Dixon, Richard A. and Voit, Eberhard O.},
abstractNote = {Lignin 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. Here, we 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. Given 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.},
doi = {10.1186/s13068-018-1241-6},
journal = {Biotechnology for Biofuels},
number = 1,
volume = 11,
place = {United States},
year = {2018},
month = {9}
}

Works referenced in this record:

Lignin Biosynthesis
journal, June 2003

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