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Title: Mathematical models of lignin biosynthesis

Abstract

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.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 themore » grass Brachypodium distachyon. 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.« less

Authors:
 [1];  [1];  [2];  [2];  [3];  [3]; ORCiD logo [3];  [2];  [1]
  1. Georgia Inst. of Technology, Atlanta, GA (United States); 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)
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). BioEnergy Science Center (BESC)
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:
1432148
Grant/Contract Number:
AC05-00OR22725
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Biotechnology for Biofuels
Additional Journal Information:
Journal Volume: 11; Journal Issue: 1; Journal ID: ISSN 1754-6834
Publisher:
BioMed Central
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Faraji, Mojdeh, Fonseca, Luis, Escamilla-Trevino, Luis, Barros-Rios, Jaime, Engle, Nancy L., Yang, Zamin Koo, Tschaplinski, Timothy J., Dixon, Richard A., and Voit, Eberhard O. Mathematical models of lignin biosynthesis. United States: N. p., 2018. Web. doi:10.1186/s13068-018-1028-9.
Faraji, Mojdeh, Fonseca, Luis, Escamilla-Trevino, Luis, Barros-Rios, Jaime, Engle, Nancy L., Yang, Zamin Koo, Tschaplinski, Timothy J., Dixon, Richard A., & Voit, Eberhard O. Mathematical models of lignin biosynthesis. United States. doi:10.1186/s13068-018-1028-9.
Faraji, Mojdeh, Fonseca, Luis, Escamilla-Trevino, Luis, Barros-Rios, Jaime, Engle, Nancy L., Yang, Zamin Koo, Tschaplinski, Timothy J., Dixon, Richard A., and Voit, Eberhard O. Fri . "Mathematical models of lignin biosynthesis". United States. doi:10.1186/s13068-018-1028-9. https://www.osti.gov/servlets/purl/1432148.
@article{osti_1432148,
title = {Mathematical models of lignin biosynthesis},
author = {Faraji, Mojdeh and Fonseca, Luis and Escamilla-Trevino, Luis and Barros-Rios, Jaime and Engle, Nancy L. and Yang, Zamin Koo and Tschaplinski, Timothy J. and Dixon, Richard A. and Voit, Eberhard O.},
abstractNote = {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.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. 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.},
doi = {10.1186/s13068-018-1028-9},
journal = {Biotechnology for Biofuels},
number = 1,
volume = 11,
place = {United States},
year = {Fri Feb 09 00:00:00 EST 2018},
month = {Fri Feb 09 00:00:00 EST 2018}
}

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