Loading…

Mathematical models of lignin biosynthesis

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...

Full description

Saved in:
Bibliographic Details
Published in:Biotechnology for biofuels 2018-02, Vol.11 (1)
Main Authors: 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.
Format: Article
Language:English
Subjects:
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
cited_by
cites
container_end_page
container_issue 1
container_start_page
container_title Biotechnology for biofuels
container_volume 11
creator 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.
description 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.
format article
fullrecord <record><control><sourceid>osti</sourceid><recordid>TN_cdi_osti_scitechconnect_1618715</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>1618715</sourcerecordid><originalsourceid>FETCH-osti_scitechconnect_16187153</originalsourceid><addsrcrecordid>eNpjYuA0NDc10TWzMDZhQWJzMHAVF2cZGJgZmhuYczJo-SaWZKTmJpZkJifmKOTmp6TmFCvkpynkZKbnZeYpJGXmF1fmAVUUZxbzMLCmJeYUp_JCaW4GJTfXEGcP3fziksz44uTMktTkjOT8vLzU5JJ4QzNDC3NDU2OiFAEAxOoylg</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype></control><display><type>article</type><title>Mathematical models of lignin biosynthesis</title><source>PubMed Central(OA)</source><source>Publicly Available Content Database</source><source>Free Full-Text Journals in Chemistry</source><creator>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.</creator><creatorcontrib>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. ; Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)</creatorcontrib><description>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.</description><identifier>ISSN: 1754-6834</identifier><identifier>EISSN: 1754-6834</identifier><language>eng</language><publisher>United States: BioMed Central</publisher><subject>BASIC BIOLOGICAL SCIENCES</subject><ispartof>Biotechnology for biofuels, 2018-02, Vol.11 (1)</ispartof><woscitedreferencessubscribed>false</woscitedreferencessubscribed><orcidid>0000000295406622</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,780,784,885</link.rule.ids><backlink>$$Uhttps://www.osti.gov/biblio/1618715$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Faraji, Mojdeh</creatorcontrib><creatorcontrib>Fonseca, Luis</creatorcontrib><creatorcontrib>Escamilla-Trevino, Luis</creatorcontrib><creatorcontrib>Barros-Rios, Jaime</creatorcontrib><creatorcontrib>Engle, Nancy L.</creatorcontrib><creatorcontrib>Yang, Zamin Koo</creatorcontrib><creatorcontrib>Tschaplinski, Timothy J.</creatorcontrib><creatorcontrib>Dixon, Richard A.</creatorcontrib><creatorcontrib>Voit, Eberhard O.</creatorcontrib><creatorcontrib>Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)</creatorcontrib><title>Mathematical models of lignin biosynthesis</title><title>Biotechnology for biofuels</title><description>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.</description><subject>BASIC BIOLOGICAL SCIENCES</subject><issn>1754-6834</issn><issn>1754-6834</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><recordid>eNpjYuA0NDc10TWzMDZhQWJzMHAVF2cZGJgZmhuYczJo-SaWZKTmJpZkJifmKOTmp6TmFCvkpynkZKbnZeYpJGXmF1fmAVUUZxbzMLCmJeYUp_JCaW4GJTfXEGcP3fziksz44uTMktTkjOT8vLzU5JJ4QzNDC3NDU2OiFAEAxOoylg</recordid><startdate>20180209</startdate><enddate>20180209</enddate><creator>Faraji, Mojdeh</creator><creator>Fonseca, Luis</creator><creator>Escamilla-Trevino, Luis</creator><creator>Barros-Rios, Jaime</creator><creator>Engle, Nancy L.</creator><creator>Yang, Zamin Koo</creator><creator>Tschaplinski, Timothy J.</creator><creator>Dixon, Richard A.</creator><creator>Voit, Eberhard O.</creator><general>BioMed Central</general><scope>OTOTI</scope><orcidid>https://orcid.org/0000000295406622</orcidid></search><sort><creationdate>20180209</creationdate><title>Mathematical models of lignin biosynthesis</title><author>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.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-osti_scitechconnect_16187153</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>BASIC BIOLOGICAL SCIENCES</topic><toplevel>online_resources</toplevel><creatorcontrib>Faraji, Mojdeh</creatorcontrib><creatorcontrib>Fonseca, Luis</creatorcontrib><creatorcontrib>Escamilla-Trevino, Luis</creatorcontrib><creatorcontrib>Barros-Rios, Jaime</creatorcontrib><creatorcontrib>Engle, Nancy L.</creatorcontrib><creatorcontrib>Yang, Zamin Koo</creatorcontrib><creatorcontrib>Tschaplinski, Timothy J.</creatorcontrib><creatorcontrib>Dixon, Richard A.</creatorcontrib><creatorcontrib>Voit, Eberhard O.</creatorcontrib><creatorcontrib>Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)</creatorcontrib><collection>OSTI.GOV</collection><jtitle>Biotechnology for biofuels</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Faraji, Mojdeh</au><au>Fonseca, Luis</au><au>Escamilla-Trevino, Luis</au><au>Barros-Rios, Jaime</au><au>Engle, Nancy L.</au><au>Yang, Zamin Koo</au><au>Tschaplinski, Timothy J.</au><au>Dixon, Richard A.</au><au>Voit, Eberhard O.</au><aucorp>Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Mathematical models of lignin biosynthesis</atitle><jtitle>Biotechnology for biofuels</jtitle><date>2018-02-09</date><risdate>2018</risdate><volume>11</volume><issue>1</issue><issn>1754-6834</issn><eissn>1754-6834</eissn><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 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.</abstract><cop>United States</cop><pub>BioMed Central</pub><orcidid>https://orcid.org/0000000295406622</orcidid></addata></record>
fulltext fulltext
identifier ISSN: 1754-6834
ispartof Biotechnology for biofuels, 2018-02, Vol.11 (1)
issn 1754-6834
1754-6834
language eng
recordid cdi_osti_scitechconnect_1618715
source PubMed Central(OA); Publicly Available Content Database; Free Full-Text Journals in Chemistry
subjects BASIC BIOLOGICAL SCIENCES
title Mathematical models of lignin biosynthesis
url http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-25T14%3A18%3A09IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-osti&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Mathematical%20models%20of%20lignin%20biosynthesis&rft.jtitle=Biotechnology%20for%20biofuels&rft.au=Faraji,%20Mojdeh&rft.aucorp=Oak%20Ridge%20National%20Laboratory%20(ORNL),%20Oak%20Ridge,%20TN%20(United%20States)&rft.date=2018-02-09&rft.volume=11&rft.issue=1&rft.issn=1754-6834&rft.eissn=1754-6834&rft_id=info:doi/&rft_dat=%3Costi%3E1618715%3C/osti%3E%3Cgrp_id%3Ecdi_FETCH-osti_scitechconnect_16187153%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_id=info:pmid/&rfr_iscdi=true