skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: RNAi-suppression of barley caffeic acid O-methyltransferase modifies lignin despite redundancy in the gene family

Abstract

Caffeic acid O-methyltransferase (COMT), the lignin biosynthesis gene modified in many brown-midrib high-digestibility mutants of maize and sorghum, was targeted for downregulation in the small grain temperate cereal, barley (Hordeum vulgare), to improve straw properties. Phylogenetic and expression analyses identified the barley COMT orthologue(s) expressed in stems, defining a larger gene family than in brachypodium or rice with three COMT genes expressed in lignifying tissues. RNAi significantly reduced stem COMT protein and enzyme activity, and modestly reduced stem lignin content while dramatically changing lignin structure. Lignin syringyl-to-guaiacyl ratio was reduced by ~50%, the 5-hydroxyguaiacyl (5-OH-G) unit incorporated into lignin at 10-–15-fold higher levels than normal, and the amount of p-coumaric acid ester-linked to cell walls was reduced by ~50%. No brown-midrib phenotype was observed in any RNAi line despite significant COMT suppression and altered lignin. The novel COMT gene family structure in barley highlights the dynamic nature of grass genomes. Redundancy in barley COMTs may explain the absence of brown-midrib mutants in barley and wheat. The barley COMT RNAi lines nevertheless have the potential to be exploited for bioenergy applications and as animal feed.

Authors:
 [1];  [1];  [1];  [2];  [3];  [4];  [5];  [5];  [1];  [6];  [7];  [7];  [7];  [6]; ORCiD logo [1]
  1. Univ. of Dundee at the James Hutton Inst., Dundee (United Kingdom)
  2. Univ. of Dundee at the James Hutton Inst., Dundee (United Kingdom); Univ. of Adelaide, SA (Australia)
  3. Univ. Paris-Saclay, Versaille (France)
  4. Univ. of Dundee at the James Hutton Inst., Dundee (United Kingdom); James Hutton Inst., Dundee (United Kingdom)
  5. James Hutton Inst., Dundee (United Kingdom)
  6. Great Lakes Bioenergy Research Center, Madison, WI (United States); Univ. of Wisconsin, Madison, WI (United States)
  7. VIB Center for Plant Systems Biology, Ghent (Belgium); Ghent Univ. (Belgium)
Publication Date:
Research Org.:
Great Lakes Bioenergy Research Center, Madison, WI (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1505792
Grant/Contract Number:  
SC0018409
Resource Type:
Accepted Manuscript
Journal Name:
Plant Biotechnology Journal
Additional Journal Information:
Journal Volume: 17; Journal Issue: 3; Journal ID: ISSN 1467-7644
Publisher:
Society for Experimental Biology; Association of Applied Biology
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; caffeic acid O-methyltransferase (COMT), lignin, brown-midrib, barley (Hordeum vulgare), straw, RNAi, biofuels, biorefineries

Citation Formats

Daly, Paul, McClellan, Christopher, Maluk, Marta, Oakey, Helena, Lapierre, Catherine, Waugh, Robbie, Stephens, Jennifer, Marshall, David, Barakate, Abdellah, Tsuji, Yukiko, Goeminne, Geert, Vanholme, Ruben, Boerjan, Wout, Ralph, John, and Halpin, Claire. RNAi-suppression of barley caffeic acid O-methyltransferase modifies lignin despite redundancy in the gene family. United States: N. p., 2018. Web. doi:10.1111/pbi.13001.
Daly, Paul, McClellan, Christopher, Maluk, Marta, Oakey, Helena, Lapierre, Catherine, Waugh, Robbie, Stephens, Jennifer, Marshall, David, Barakate, Abdellah, Tsuji, Yukiko, Goeminne, Geert, Vanholme, Ruben, Boerjan, Wout, Ralph, John, & Halpin, Claire. RNAi-suppression of barley caffeic acid O-methyltransferase modifies lignin despite redundancy in the gene family. United States. doi:10.1111/pbi.13001.
Daly, Paul, McClellan, Christopher, Maluk, Marta, Oakey, Helena, Lapierre, Catherine, Waugh, Robbie, Stephens, Jennifer, Marshall, David, Barakate, Abdellah, Tsuji, Yukiko, Goeminne, Geert, Vanholme, Ruben, Boerjan, Wout, Ralph, John, and Halpin, Claire. Wed . "RNAi-suppression of barley caffeic acid O-methyltransferase modifies lignin despite redundancy in the gene family". United States. doi:10.1111/pbi.13001. https://www.osti.gov/servlets/purl/1505792.
@article{osti_1505792,
title = {RNAi-suppression of barley caffeic acid O-methyltransferase modifies lignin despite redundancy in the gene family},
author = {Daly, Paul and McClellan, Christopher and Maluk, Marta and Oakey, Helena and Lapierre, Catherine and Waugh, Robbie and Stephens, Jennifer and Marshall, David and Barakate, Abdellah and Tsuji, Yukiko and Goeminne, Geert and Vanholme, Ruben and Boerjan, Wout and Ralph, John and Halpin, Claire},
abstractNote = {Caffeic acid O-methyltransferase (COMT), the lignin biosynthesis gene modified in many brown-midrib high-digestibility mutants of maize and sorghum, was targeted for downregulation in the small grain temperate cereal, barley (Hordeum vulgare), to improve straw properties. Phylogenetic and expression analyses identified the barley COMT orthologue(s) expressed in stems, defining a larger gene family than in brachypodium or rice with three COMT genes expressed in lignifying tissues. RNAi significantly reduced stem COMT protein and enzyme activity, and modestly reduced stem lignin content while dramatically changing lignin structure. Lignin syringyl-to-guaiacyl ratio was reduced by ~50%, the 5-hydroxyguaiacyl (5-OH-G) unit incorporated into lignin at 10-–15-fold higher levels than normal, and the amount of p-coumaric acid ester-linked to cell walls was reduced by ~50%. No brown-midrib phenotype was observed in any RNAi line despite significant COMT suppression and altered lignin. The novel COMT gene family structure in barley highlights the dynamic nature of grass genomes. Redundancy in barley COMTs may explain the absence of brown-midrib mutants in barley and wheat. The barley COMT RNAi lines nevertheless have the potential to be exploited for bioenergy applications and as animal feed.},
doi = {10.1111/pbi.13001},
journal = {Plant Biotechnology Journal},
number = 3,
volume = 17,
place = {United States},
year = {2018},
month = {8}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 4 works
Citation information provided by
Web of Science

Save / Share:

Works referenced in this record:

Lignin Biosynthesis
journal, June 2003


Automated saccharification assay for determination of digestibility in plant materials
journal, January 2010

  • Gomez, Leonardo D.; Whitehead, Caragh; Barakate, Abdellah
  • Biotechnology for Biofuels, Vol. 3, Issue 1
  • DOI: 10.1186/1754-6834-3-23

Tricin, a Flavonoid Monomer in Monocot Lignification
journal, February 2015


A polymer of caffeyl alcohol in plant seeds
journal, January 2012

  • Chen, F.; Tobimatsu, Y.; Havkin-Frenkel, D.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 5
  • DOI: 10.1073/pnas.1120992109

A chromosome conformation capture ordered sequence of the barley genome
journal, April 2017

  • Mascher, Martin; Gundlach, Heidrun; Himmelbach, Axel
  • Nature, Vol. 544, Issue 7651
  • DOI: 10.1038/nature22043

Structure-Function Analyses of a Caffeic Acid O -Methyltransferase from Perennial Ryegrass Reveal the Molecular Basis for Substrate Preference
journal, December 2010


CCoAOMT suppression modifies lignin composition in Pinus radiata
journal, April 2011


Cell wall fermentation kinetics are impacted more by lignin content and ferulate cross-linking than by lignin composition
journal, January 2009

  • Grabber, John H.; Mertens, David R.; Kim, Hoon
  • Journal of the Science of Food and Agriculture, Vol. 89, Issue 1
  • DOI: 10.1002/jsfa.3418

A Set of Modular Binary Vectors for Transformation of Cereals
journal, November 2007

  • Himmelbach, Axel; Zierold, Uwe; Hensel, Götz
  • Plant Physiology, Vol. 145, Issue 4
  • DOI: 10.1104/pp.107.111575

Structural and expressional divergence of genes encoding O -methyltransferase in wheat
journal, October 2008

  • Jung, Je Hyeong; Hong, Min Jeong; Kim, Dae Yeon
  • Genome, Vol. 51, Issue 10
  • DOI: 10.1139/G08-069

Phosphorylation is an on/off switch for 5-hydroxyconiferaldehyde O -methyltransferase activity in poplar monolignol biosynthesis
journal, June 2015

  • Wang, Jack P.; Chuang, Ling; Loziuk, Philip L.
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 27
  • DOI: 10.1073/pnas.1510473112

Lignin modification improves fermentable sugar yields for biofuel production
journal, June 2007

  • Chen, Fang; Dixon, Richard A.
  • Nature Biotechnology, Vol. 25, Issue 7, p. 759-761
  • DOI: 10.1038/nbt1316

Clade classification of monolignol biosynthesis gene family members reveals target genes to decrease lignin in Lolium perenne
journal, March 2015

  • van Parijs, F. R. D.; Ruttink, T.; Boerjan, W.
  • Plant Biology, Vol. 17, Issue 4
  • DOI: 10.1111/plb.12316

Disrupting the cinnamyl alcohol dehydrogenase 1 gene ( BdCAD1 ) leads to altered lignification and improved saccharification in Brachypodium distachyon
journal, December 2012

  • Bouvier d'Yvoire, Madeleine; Bouchabke-Coussa, Oumaya; Voorend, Wannes
  • The Plant Journal, Vol. 73, Issue 3
  • DOI: 10.1111/tpj.12053

Coniferyl aldehyde 5-hydroxylation and methylation direct syringyl lignin biosynthesis in angiosperms
journal, August 1999

  • Osakabe, K.; Tsao, C. C.; Li, L.
  • Proceedings of the National Academy of Sciences, Vol. 96, Issue 16
  • DOI: 10.1073/pnas.96.16.8955

Identification of Specific Residues Involved in Substrate Discrimination in Two Plant O-Methyltransferases
journal, August 1999

  • Wang, Jihong; Pichersky, Eran
  • Archives of Biochemistry and Biophysics, Vol. 368, Issue 1
  • DOI: 10.1006/abbi.1999.1304

Substrate preferences of O-methyltransferases in alfalfa suggest new pathways for 3-O-methylation of monolignols
journal, January 2001


Improved Sugar Conversion and Ethanol Yield for Forage Sorghum (Sorghum bicolor L. Moench) Lines with Reduced Lignin Contents
journal, August 2009


The decimal code for the growth stages of cereals, with illustrations
journal, April 1987


A TILLING Platform for Functional Genomics in Brachypodium distachyon
journal, June 2013


Introduction of chemically labile substructures into Arabidopsis lignin through the use of LigD, the Cα-dehydrogenase from Sphingobium sp. strain SYK-6
journal, January 2015

  • Tsuji, Yukiko; Vanholme, Ruben; Tobimatsu, Yuki
  • Plant Biotechnology Journal, Vol. 13, Issue 6
  • DOI: 10.1111/pbi.12316

Sustainable liquid biofuels from biomass: the writing's on the walls
journal, May 2008


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


Small Glycosylated Lignin Oligomers Are Stored in Arabidopsis Leaf Vacuoles
journal, February 2015


Measurement of cellulase activities
journal, January 1987


Genetic and molecular basis of grass cell wall biosynthesis and degradability. II. Lessons from brown-midrib mutants
journal, September 2004


Metabolic engineering of novel lignin in biomass crops
journal, October 2012


N-Methyltransferase involved in gramine biosynthesis in barley: Cloning and characterization
journal, September 2006


cDNA cloning and differential expression of three caffeic acid O-methyltransferase homologues from perennial ryegrass (Lolium perenne)
journal, January 1998


Molecular cloning of cDNAs coding for three sugarcane enzymes involved in lignification
journal, May 1999


A new mathematical model for relative quantification in real-time RT-PCR
journal, May 2001


Functional characterization of cinnamyl alcohol dehydrogenase and caffeic acid O-methyltransferase in Brachypodium distachyon
journal, January 2013

  • Trabucco, Gina M.; Matos, Dominick A.; Lee, Scott J.
  • BMC Biotechnology, Vol. 13, Issue 1
  • DOI: 10.1186/1472-6750-13-61

Functional Analyses of Caffeic Acid O-Methyltransferase and Cinnamoyl-CoA-Reductase Genes from Perennial Ryegrass ( Lolium perenne )
journal, October 2010


Global potential bioethanol production from wasted crops and crop residues
journal, April 2004


Tricin-lignins: occurrence and quantitation of tricin in relation to phylogeny
journal, November 2016

  • Lan, Wu; Rencoret, Jorge; Lu, Fachuang
  • The Plant Journal, Vol. 88, Issue 6
  • DOI: 10.1111/tpj.13315

Lignins: Natural polymers from oxidative coupling of 4-hydroxyphenyl- propanoids
journal, January 2004


Functional Expression of an Arabidopsis cDNA Clone Encoding a Flavonol 3′-O-Methyltransferase and Characterization of the Gene Product
journal, March 2000

  • Muzac, Ingrid; Wang, Jing; Anzellotti, Dominique
  • Archives of Biochemistry and Biophysics, Vol. 375, Issue 2
  • DOI: 10.1006/abbi.1999.1681

Methyl Jasmonate Induces an O-Methyltransferase in Barley1
journal, January 1997


A Root-specific O -Methyltransferase Gene Expressed in Salt-tolerant Barley
journal, January 2003

  • Sugimoto, Manabu; Okada, Yoshihiro; Sato, Kazuhiro
  • Bioscience, Biotechnology, and Biochemistry, Vol. 67, Issue 5
  • DOI: 10.1271/bbb.67.966

Lignin content in natural Populus variants affects sugar release
journal, March 2011

  • Studer, M. H.; DeMartini, J. D.; Davis, M. F.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 15, p. 6300-6305
  • DOI: 10.1073/pnas.1009252108

Genome-Wide Characterization of the Lignification Toolbox in Arabidopsis
journal, November 2003

  • Raes, Jeroen; Rohde, Antje; Christensen, Jørgen Holst
  • Plant Physiology, Vol. 133, Issue 3
  • DOI: 10.1104/pp.103.026484

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

Whole plant cell wall characterization using solution-state 2D NMR
journal, August 2012


Deciphering key features in protein structures with the new ENDscript server
journal, April 2014

  • Robert, Xavier; Gouet, Patrice
  • Nucleic Acids Research, Vol. 42, Issue W1
  • DOI: 10.1093/nar/gku316

Let them eat (GM) straw
journal, December 2003


Comprehensive Quantification of Monolignol-Pathway Enzymes in Populus trichocarpa by Protein Cleavage Isotope Dilution Mass Spectrometry
journal, May 2012

  • Shuford, Christopher M.; Li, Quanzi; Sun, Ying-Hsuan
  • Journal of Proteome Research, Vol. 11, Issue 6
  • DOI: 10.1021/pr300205a

Degradation of lignin β-aryl ether units in Arabidopsis thaliana expressing LigD , LigF and LigG from Sphingomonas paucimobilis SYK-6
journal, November 2016

  • Mnich, Ewelina; Vanholme, Ruben; Oyarce, Paula
  • Plant Biotechnology Journal, Vol. 15, Issue 5
  • DOI: 10.1111/pbi.12655

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

Down-Regulation of Caffeic Acid O -Methyltransferase in Maize Revisited Using a Transgenic Approach
journal, November 2002

  • Piquemal, Joel; Chamayou, Simon; Nadaud, Isabelle
  • Plant Physiology, Vol. 130, Issue 4
  • DOI: 10.1104/pp.012237

Solution-state 2D NMR of ball-milled plant cell wall gels in DMSO-d6/pyridine-d5
journal, January 2010

  • Kim, Hoon; Ralph, John
  • Org. Biomol. Chem., Vol. 8, Issue 3
  • DOI: 10.1039/B916070A

Barley: Emergence as a New Research Material of Crop Science
journal, May 2011

  • Saisho, D.; Takeda, K.
  • Plant and Cell Physiology, Vol. 52, Issue 5
  • DOI: 10.1093/pcp/pcr049

Lignin biosynthesis perturbations affect secondary cell wall composition and saccharification yield in Arabidopsis thaliana
journal, January 2013

  • Van Acker, Rebecca; Vanholme, Ruben; Storme, Véronique
  • Biotechnology for Biofuels, Vol. 6, Article No. 46
  • DOI: 10.1186/1754-6834-6-46

Mutation in Brachypodium caffeic acid O -methyltransferase 6 alters stem and grain lignins and improves straw saccharification without deteriorating grain quality
journal, October 2015

  • Ho-Yue-Kuang, Séverine; Alvarado, Camille; Antelme, Sébastien
  • Journal of Experimental Botany, Vol. 67, Issue 1
  • DOI: 10.1093/jxb/erv446

In Search of a Maize Ideotype for Cell Wall Enzymatic Degradability Using Histological and Biochemical Lignin Characterization
journal, July 2005

  • Méchin, Valérie; Argillier, Odile; Rocher, Françoise
  • Journal of Agricultural and Food Chemistry, Vol. 53, Issue 15
  • DOI: 10.1021/jf050722f

Allelic Association, Chemical Characterization and Saccharification Properties of brown midrib Mutants of Sorghum (Sorghum bicolor (L.) Moench)
journal, October 2008


Structural Basis for the Modulation of Lignin Monomer Methylation by Caffeic Acid/5-Hydroxyferulic Acid 3/5- O -Methyltransferase
journal, June 2002

  • Zubieta, Chloe; Kota, Parvathi; Ferrer, Jean-Luc
  • The Plant Cell, Vol. 14, Issue 6
  • DOI: 10.1105/tpc.001412

SbCOMT (Bmr12) is involved in the biosynthesis of tricin-lignin in sorghum
journal, June 2017


Pathway of p-Coumaric Acid Incorporation into Maize Lignin As Revealed by NMR
journal, October 1994

  • Ralph, John; Hatfield, Ronald D.; Quideau, Stephane
  • Journal of the American Chemical Society, Vol. 116, Issue 21, p. 9448-9456
  • DOI: 10.1021/ja00100a006

The brown midrib3 (bm3) mutation in maize occurs in the gene encoding caffeic acid O-methyltransferase.
journal, April 1995

  • Vignols, F.; Rigau, J.; Torres, M. A.
  • The Plant Cell, Vol. 7, Issue 4
  • DOI: 10.1105/tpc.7.4.407

Phenolic Profiling of Caffeic Acid O -Methyltransferase-Deficient Poplar Reveals Novel Benzodioxane Oligolignols
journal, November 2004

  • Morreel, Kris; Ralph, John; Lu, Fachuang
  • Plant Physiology, Vol. 136, Issue 4
  • DOI: 10.1104/pp.104.049312

RNAi suppression of lignin biosynthesis in sugarcane reduces recalcitrance for biofuel production from lignocellulosic biomass: RNAi suppression of
journal, August 2012


Characterization of Two O .-Methyltransferase-like Genes in Barley and Maize
journal, January 2008

  • Zhou, Jian-Min; Fukushi, Yukiharu; Wollenweber, Eckhard
  • Pharmaceutical Biology, Vol. 46, Issue 1-2
  • DOI: 10.1080/13880200701729745

Grass Genomic Synteny Illuminates Plant Genome Function and Evolution
journal, November 2008


Structure and expression of the lignin O-methyltransferase gene from Zea mays L.
journal, December 1992

  • Collazo, Pablo; Montoliu, Llu�s; Puigdom�nech, Pere
  • Plant Molecular Biology, Vol. 20, Issue 5
  • DOI: 10.1007/BF00027157

A Systems Biology View of Responses to Lignin Biosynthesis Perturbations in Arabidopsis
journal, September 2012

  • Vanholme, Ruben; Storme, Véronique; Vanholme, Bartel
  • The Plant Cell, Vol. 24, Issue 9
  • DOI: 10.1105/tpc.112.102574