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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:
; ; ; ; ; ; ; ;
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:
1618715
Alternate Identifier(s):
OSTI ID: 1432148
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Published Article
Journal Name:
Biotechnology for Biofuels
Additional Journal Information:
Journal Name: Biotechnology for Biofuels Journal Volume: 11 Journal Issue: 1; Journal ID: ISSN 1754-6834
Publisher:
Springer Science + Business Media
Country of Publication:
Netherlands
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Faraji, Mojdeh, Fonseca, Luis L., Escamilla-Treviño, Luis, Barros-Rios, Jaime, Engle, Nancy, Yang, Zamin K., Tschaplinski, Timothy J., Dixon, Richard A., and Voit, Eberhard O. Mathematical models of lignin biosynthesis. Netherlands: N. p., 2018. Web. doi:10.1186/s13068-018-1028-9.
Faraji, Mojdeh, Fonseca, Luis L., Escamilla-Treviño, Luis, Barros-Rios, Jaime, Engle, Nancy, Yang, Zamin K., Tschaplinski, Timothy J., Dixon, Richard A., & Voit, Eberhard O. Mathematical models of lignin biosynthesis. Netherlands. doi:10.1186/s13068-018-1028-9.
Faraji, Mojdeh, Fonseca, Luis L., Escamilla-Treviño, Luis, Barros-Rios, Jaime, Engle, Nancy, Yang, Zamin K., Tschaplinski, Timothy J., Dixon, Richard A., and Voit, Eberhard O. Fri . "Mathematical models of lignin biosynthesis". Netherlands. doi:10.1186/s13068-018-1028-9.
@article{osti_1618715,
title = {Mathematical models of lignin biosynthesis},
author = {Faraji, Mojdeh and Fonseca, Luis L. and Escamilla-Treviño, Luis and Barros-Rios, Jaime and Engle, Nancy and Yang, Zamin K. 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 = {Netherlands},
year = {2018},
month = {2}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
DOI: 10.1186/s13068-018-1028-9

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Cited by: 7 works
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Works referenced in this record:

Lignin Biosynthesis
journal, June 2003


New types of experimental data shape the use of enzyme kinetics for dynamic network modeling
journal, November 2013

  • Tummler, Katja; Lubitz, Timo; Schelker, Max
  • FEBS Journal, Vol. 281, Issue 2
  • DOI: 10.1111/febs.12525

Improving Bioenergy Crops through Dynamic Metabolic Modeling
journal, October 2017

  • Faraji, Mojdeh; Voit, Eberhard O.
  • Processes, Vol. 5, Issue 4
  • DOI: 10.3390/pr5040061

Stepwise inference of likely dynamic flux distributions from metabolic time series data
journal, March 2017


Biochemical systems analysis
journal, December 1969


Computational inference of the structure and regulation of the lignin pathway in Panicum virgatum
journal, September 2015

  • Faraji, Mojdeh; Fonseca, Luis L.; Escamilla-Treviño, Luis
  • Biotechnology for Biofuels, Vol. 8, Issue 1
  • DOI: 10.1186/s13068-015-0334-8

AraGEM, a Genome-Scale Reconstruction of the Primary Metabolic Network in Arabidopsis
journal, December 2009

  • de Oliveira Dal'Molin, Cristiana Gomes; Quek, Lake-Ee; Palfreyman, Robin William
  • Plant Physiology, Vol. 152, Issue 2
  • DOI: 10.1104/pp.109.148817

Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform
journal, May 2017

  • Marshall-Colon, Amy; Long, Stephen P.; Allen, Douglas K.
  • Frontiers in Plant Science, Vol. 8
  • DOI: 10.3389/fpls.2017.00786

Analysis of optimality in natural and perturbed metabolic networks
journal, November 2002

  • Segre, D.; Vitkup, D.; Church, G. M.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 23
  • DOI: 10.1073/pnas.232349399

Role of bifunctional ammonia-lyase in grass cell wall biosynthesis
journal, May 2016


Models-of-data and models-of-processes in the post-genomic era
journal, November 2002


Lignin isolated from primary walls of hybrid aspen cell cultures indicates significant differences in lignin structure between primary and secondary cell wall
journal, August 2005

  • Christiernin, Maria; Ohlsson, Anna B.; Berglund, Torkel
  • Plant Physiology and Biochemistry, Vol. 43, Issue 8
  • DOI: 10.1016/j.plaphy.2005.07.007

Towards multiscale plant models: integrating cellular networks
journal, December 2012


Plant genome-scale metabolic reconstruction and modelling
journal, April 2013

  • de Oliveira Dal’Molin, Cristiana Gomes; Nielsen, Lars Keld
  • Current Opinion in Biotechnology, Vol. 24, Issue 2
  • DOI: 10.1016/j.copbio.2012.08.007

Caffeoyl Shikimate Esterase (CSE) Is an Enzyme in the Lignin Biosynthetic Pathway in Arabidopsis
journal, August 2013


Multiscale Metabolic Modeling: Dynamic Flux Balance Analysis on a Whole-Plant Scale
journal, August 2013

  • Grafahrend-Belau, E.; Junker, A.; Eschenroder, A.
  • PLANT PHYSIOLOGY, Vol. 163, Issue 2
  • DOI: 10.1104/pp.113.224006

Testing Biochemistry Revisited: How In Vivo Metabolism Can Be Understood from In Vitro Enzyme Kinetics
journal, April 2012


Biochemical Systems Theory: A Review
journal, January 2013


Metabolic network reconstruction of Chlamydomonas offers insight into light‐driven algal metabolism
journal, January 2011

  • Chang, Roger L.; Ghamsari, Lila; Manichaikul, Ani
  • Molecular Systems Biology, Vol. 7, Issue 1
  • DOI: 10.1038/msb.2011.52

Mathematical modeling of monolignol biosynthesis in Populus xylem
journal, November 2010


Integrative Analysis of Transgenic Alfalfa (Medicago sativa L.) Suggests New Metabolic Control Mechanisms for Monolignol Biosynthesis
journal, May 2011


Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry: Do we understand yeast glycolysis?
journal, September 2000


Monolignol biosynthesis in microsomal preparations from lignifying stems of alfalfa (Medicago sativa L.)
journal, November 2002


Comprehensive classification and perspective for modelling photorespiratory metabolism
journal, April 2013


Identification of Metabolic Pathway Systems
journal, February 2016


The best models of metabolism: The best models of metabolism
journal, May 2017

  • Voit, Eberhard O.
  • Wiley Interdisciplinary Reviews: Systems Biology and Medicine, Vol. 9, Issue 6
  • DOI: 10.1002/wsbm.1391

A model of whole plant gas exchange for herbaceous species from mountain grassland sites differing in land use
journal, January 2000


Cellular concentrations of enzymes and their substrates
journal, March 1990


Regulation of Secondary Cell Wall Development by Cortical Microtubules during Tracheary Element Differentiation in Arabidopsis Cell Suspensions
journal, February 2005

  • Oda, Yoshihisa; Mimura, Tetsuro; Hasezawa, Seiichiro
  • Plant Physiology, Vol. 137, Issue 3
  • DOI: 10.1104/pp.104.052613

What is flux balance analysis?
journal, March 2010

  • Orth, Jeffrey D.; Thiele, Ines; Palsson, Bernhard Ø
  • Nature Biotechnology, Vol. 28, Issue 3
  • DOI: 10.1038/nbt.1614

The importance and challenges of in vivo-like enzyme kinetics
journal, May 2014


A Genomics Approach to Deciphering Lignin Biosynthesis in Switchgrass
journal, November 2013


Functional Analysis of Metabolic Channeling and Regulation in Lignin Biosynthesis: A Computational Approach
journal, November 2012


Molecular-Genetic Analysis of Plant Cytochrome P450-Dependent Monooxygenases
journal, June 1998