A 13C isotope labeling method for the measurement of lignin metabolic flux in Arabidopsis stems
Abstract
Background: Metabolic fluxes represent the functional phenotypes of biochemical pathways and are essential to reveal the distribution of precursors among metabolic networks. Although analysis of metabolic fluxes, facilitated by stable isotope labeling and mass spectrometry detection, has been applied in the studies of plant metabolism, we lack experimental measurements for carbon flux towards lignin, one of the most abundant polymers in nature. Results: We developed a feeding strategy of excised Arabidopsis stems with 13C labeled phenylalanine (Phe) for the analysis of lignin biosynthetic flux. We optimized the feeding methods and found the stems continued to grow and lignify. Consistent with lignification profiles along the stems, higher levels of phenylpropanoids and activities of lignin biosynthetic enzymes were detected in the base of the stem. In the feeding experiments, 13C labeled Phe was quickly accumulated and used for the synthesis of phenylpropanoid intermediates and lignin. The intermediates displayed two different patterns of labeling kinetics during the feeding period. Analysis of lignin showed rapid incorporation of label into all three subunits in the polymers. Conclusions: Our feeding results demonstrate the effectiveness of the stem feeding system and suggest a potential application for the investigations of other aspects in plant metabolism. Moreover, the supplymore »
- Authors:
- Publication Date:
- Research Org.:
- Purdue Univ., West Lafayette, IN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1618906
- Alternate Identifier(s):
- OSTI ID: 1499868
- Grant/Contract Number:
- SC0008628
- Resource Type:
- Published Article
- Journal Name:
- Plant Methods
- Additional Journal Information:
- Journal Name: Plant Methods Journal Volume: 14 Journal Issue: 1; Journal ID: ISSN 1746-4811
- Publisher:
- Springer Science + Business Media
- Country of Publication:
- United Kingdom
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 09 BIOMASS FUELS; Stable isotope labeling; Stem feeding; Lignin; Phenylpropanoids
Citation Formats
Wang, Peng, Guo, Longyun, Jaini, Rohit, Klempien, Antje, McCoy, Rachel M., Morgan, John A., Dudareva, Natalia, and Chapple, Clint. A 13C isotope labeling method for the measurement of lignin metabolic flux in Arabidopsis stems. United Kingdom: N. p., 2018.
Web. doi:10.1186/s13007-018-0318-3.
Wang, Peng, Guo, Longyun, Jaini, Rohit, Klempien, Antje, McCoy, Rachel M., Morgan, John A., Dudareva, Natalia, & Chapple, Clint. A 13C isotope labeling method for the measurement of lignin metabolic flux in Arabidopsis stems. United Kingdom. https://doi.org/10.1186/s13007-018-0318-3
Wang, Peng, Guo, Longyun, Jaini, Rohit, Klempien, Antje, McCoy, Rachel M., Morgan, John A., Dudareva, Natalia, and Chapple, Clint. Sat .
"A 13C isotope labeling method for the measurement of lignin metabolic flux in Arabidopsis stems". United Kingdom. https://doi.org/10.1186/s13007-018-0318-3.
@article{osti_1618906,
title = {A 13C isotope labeling method for the measurement of lignin metabolic flux in Arabidopsis stems},
author = {Wang, Peng and Guo, Longyun and Jaini, Rohit and Klempien, Antje and McCoy, Rachel M. and Morgan, John A. and Dudareva, Natalia and Chapple, Clint},
abstractNote = {Background: Metabolic fluxes represent the functional phenotypes of biochemical pathways and are essential to reveal the distribution of precursors among metabolic networks. Although analysis of metabolic fluxes, facilitated by stable isotope labeling and mass spectrometry detection, has been applied in the studies of plant metabolism, we lack experimental measurements for carbon flux towards lignin, one of the most abundant polymers in nature. Results: We developed a feeding strategy of excised Arabidopsis stems with 13C labeled phenylalanine (Phe) for the analysis of lignin biosynthetic flux. We optimized the feeding methods and found the stems continued to grow and lignify. Consistent with lignification profiles along the stems, higher levels of phenylpropanoids and activities of lignin biosynthetic enzymes were detected in the base of the stem. In the feeding experiments, 13C labeled Phe was quickly accumulated and used for the synthesis of phenylpropanoid intermediates and lignin. The intermediates displayed two different patterns of labeling kinetics during the feeding period. Analysis of lignin showed rapid incorporation of label into all three subunits in the polymers. Conclusions: Our feeding results demonstrate the effectiveness of the stem feeding system and suggest a potential application for the investigations of other aspects in plant metabolism. Moreover, the supply of exogenous Phe leading to a higher lignin deposition rate indicates the availability of Phe is a determining factor for lignification rates.},
doi = {10.1186/s13007-018-0318-3},
journal = {Plant Methods},
number = 1,
volume = 14,
place = {United Kingdom},
year = {Sat Jun 23 00:00:00 EDT 2018},
month = {Sat Jun 23 00:00:00 EDT 2018}
}
https://doi.org/10.1186/s13007-018-0318-3
Web of Science
Works referenced in this record:
Quantitative relationship between phenylalanine ammonia-lyase levels and phenylpropanoid accumulation in transgenic tobacco identifies a rate-determining step in natural product synthesis.
journal, August 1994
- Bate, N. J.; Orr, J.; Ni, W.
- Proceedings of the National Academy of Sciences, Vol. 91, Issue 16
Lignin Biosynthesis
journal, June 2003
- Boerjan, Wout; Ralph, John; Baucher, Marie
- Annual Review of Plant Biology, Vol. 54, Issue 1, p. 519-546
Transport, Metabolism, and Redistribution of Xylem-Borne Amino Acids in Developing Pea Shoots
journal, May 1982
- Urquhart, Aileen A.; Joy, Kenneth W.
- Plant Physiology, Vol. 69, Issue 5
Down-Regulation of Kelch Domain-Containing F-Box Protein in Arabidopsis Enhances the Production of (Poly)phenols and Tolerance to Ultraviolet Radiation
journal, December 2014
- Zhang, Xuebin; Gou, Mingyue; Guo, Chunrong
- Plant Physiology, Vol. 167, Issue 2
Metabolic Fluxes in an Illuminated Arabidopsis Rosette
journal, February 2013
- Szecowka, Marek; Heise, Robert; Tohge, Takayuki
- The Plant Cell, Vol. 25, Issue 2
Cell-wall carbohydrates and their modification as a resource for biofuels
journal, May 2008
- Pauly, Markus; Keegstra, Kenneth
- The Plant Journal, Vol. 54, Issue 4, p. 559-568
Lignin monomer composition is determined by the expression of a cytochrome P450-dependent monooxygenase in Arabidopsis
journal, June 1998
- Meyer, K.; Shirley, A. M.; Cusumano, J. C.
- Proceedings of the National Academy of Sciences, Vol. 95, Issue 12
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
Membrane protein complexes catalyze both 4- and 3-hydroxylation of cinnamic acid derivatives in monolignol biosynthesis
journal, December 2011
- Chen, H. -C.; Li, Q.; Shuford, C. M.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 52
Derivatization Followed by Reductive Cleavage (DFRC Method), a New Method for Lignin Analysis: Protocol for Analysis of DFRC Monomers
journal, July 1997
- Lu, Fachuang; Ralph, John
- Journal of Agricultural and Food Chemistry, Vol. 45, Issue 7
Caffeoyl Shikimate Esterase (CSE) Is an Enzyme in the Lignin Biosynthetic Pathway in Arabidopsis
journal, August 2013
- Vanholme, R.; Cesarino, I.; Rataj, K.
- Science, Vol. 341, Issue 6150
Selectivity in xylem to phloem transfer of amino acids in fruiting shoots of white lupin (Lupinus albus L.)
journal, January 1975
- Sharkey, P. J.; Pate, J. S.
- Planta, Vol. 127, Issue 3
Quantitative Multilevel Analysis of Central Metabolism in Developing Oilseeds of Oilseed Rape during in Vitro Culture
journal, May 2015
- Schwender, Jörg; Hebbelmann, Inga; Heinzel, Nicolas
- Plant Physiology, Vol. 168, Issue 3
The Genetics of Lignin Biosynthesis: Connecting Genotype to Phenotype
journal, December 2010
- Bonawitz, Nicholas D.; Chapple, Clint
- Annual Review of Genetics, Vol. 44, Issue 1, p. 337-363
Cuticular Lipid Composition, Surface Structure, and Gene Expression in Arabidopsis Stem Epidermis
journal, November 2005
- Suh, Mi Chung; Samuels, A. Lacey; Jetter, Reinhard
- Plant Physiology, Vol. 139, Issue 4
Multi-level engineering facilitates the production of phenylpropanoid compounds in tomato
journal, October 2015
- Zhang, Yang; Butelli, Eugenio; Alseekh, Saleh
- Nature Communications, Vol. 6, Issue 1
Comparative Distribution and Metabolism of Xylem-Borne Amino Compounds and Sucrose in Shoots of Populus deltoides
journal, February 1985
- Vogelmann, Thomas C.; Dickson, Richard E.; Larson, Philip R.
- Plant Physiology, Vol. 77, Issue 2
Kinetic and inhibition studies of cinnamoyl-CoA reductase 1 from Arabidopsis thaliana
journal, August 2005
- Baltas, M.; Lapeyre, C.; Bedos-Belval, F.
- Plant Physiology and Biochemistry, Vol. 43, Issue 8
The genetic control of lignin deposition during plant growth and development: Tansley review
journal, July 2004
- Rogers, Louisa A.; Campbell, Malcolm M.
- New Phytologist, Vol. 164, Issue 1
Metabolic Flux Analysis of the Phenylpropanoid Pathway in Wound-Healing Potato Tuber Tissue using Stable Isotope-Labeled Tracer and LC-MS Spectroscopy
journal, September 2003
- Matsuda, Fumio; Morino, Keiko; Miyashita, Masahiro
- Plant and Cell Physiology, Vol. 44, Issue 9
Can genetic engineering of lignin deposition be accomplished without an unacceptable yield penalty?
journal, April 2013
- Bonawitz, Nicholas D.; Chapple, Clint
- Current Opinion in Biotechnology, Vol. 24, Issue 2
Studies of Lignin Biosynthesis Using Isotopic Carbon: xii. the Biosynthesis and Metabolism of Sinapic acid
journal, March 1963
- Higuchi, Takayoshi; Brown, Stewart A.
- Canadian Journal of Biochemistry and Physiology, Vol. 41, Issue 3
Enzymic Controls in the Biosynthesis of Lignin and Flavonoids
journal, June 1979
- Hahlbrock, K.; Grisebach, H.
- Annual Review of Plant Physiology, Vol. 30, Issue 1
Mutations in the cinnamate 4-hydroxylase gene impact metabolism, growth and development in Arabidopsis: Arabidopsis C4H mutants
journal, December 2009
- Schilmiller, Anthony L.; Stout, Jake; Weng, Jing-Ke
- The Plant Journal, Vol. 60, Issue 5
Estimation of metabolic fluxes, expression levels and metabolite dynamics of a secondary metabolic pathway in potato using label pulse-feeding experiments combined with kinetic network modelling and simulation: Method for metabolic flux and control analysis
journal, March 2007
- Heinzle, Elmar; Matsuda, Fumio; Miyagawa, Hisashi
- The Plant Journal, Vol. 50, Issue 1
Integration of a constraint-based metabolic model of Brassica napus developing seeds with 13C-metabolic flux analysis
journal, December 2014
- Hay, Jordan O.; Shi, Hai; Heinzel, Nicolas
- Frontiers in Plant Science, Vol. 5
Down-regulation of the AtCCR1 gene in Arabidopsis thaliana: effects on phenotype, lignins and cell wall degradability
journal, February 2003
- Goujon, Thomas; Ferret, Valérie; Mila, Isabelle
- Planta, Vol. 217, Issue 2
Redirection of the phenylpropanoid pathway to feruloyl malate in Arabidopsis mutants deficient for cinnamoyl-CoA reductase 1
journal, November 2007
- Mir Derikvand, Mohammad; Sierra, Jimmy Berrio; Ruel, Katia
- Planta, Vol. 227, Issue 5
An Arabidopsis mutant defective in the general phenylpropanoid pathway.
journal, November 1992
- Chapple, C. C.; Vogt, T.; Ellis, B. E.
- The Plant Cell, Vol. 4, Issue 11
Altered Xylem-Phloem Transfer of Amino Acids Affects Metabolism and Leads to Increased Seed Yield and Oil Content in Arabidopsis
journal, November 2010
- Zhang, Lizhi; Tan, Qiumin; Lee, Raymond
- The Plant Cell, Vol. 22, Issue 11
Arogenate Dehydratase Isoenzymes Profoundly and Differentially Modulate Carbon Flux into Lignins
journal, February 2012
- Corea, Oliver R. A.; Ki, Chanyoung; Cardenas, Claudia L.
- Journal of Biological Chemistry, Vol. 287, Issue 14
Rapid, Microscale, Acetyl Bromide-Based Method for High-Throughput Determination of Lignin Content in Arabidopsis thaliana
journal, August 2008
- Chang, Xue Feng; Chandra, Richard; Berleth, Thomas
- Journal of Agricultural and Food Chemistry, Vol. 56, Issue 16
Nitrogen Redistribution during Grain Growth in Wheat ( Triticum aestivum L.) : IV. Development of a Quantitative Model of the Translocation of Nitrogen to the Grain
journal, January 1983
- Simpson, Richard J.; Lambers, Hans; Dalling, Michael J.
- Plant Physiology, Vol. 71, Issue 1
Analysis of Metabolic Flux Phenotypes for Two Arabidopsis Mutants with Severe Impairment in Seed Storage Lipid Synthesis
journal, September 2009
- Lonien, Joachim; Schwender, Jörg
- Plant Physiology, Vol. 151, Issue 3
Targeted Metabolomics of the Phenylpropanoid Pathway in Arabidopsis thaliana using Reversed Phase Liquid Chromatography Coupled with Tandem Mass Spectrometry : Measuring Lignin Precursors by LC-MS
journal, February 2017
- Jaini, Rohit; Wang, Peng; Dudareva, Natalia
- Phytochemical Analysis, Vol. 28, Issue 4
Contribution of CoA Ligases to Benzenoid Biosynthesis in Petunia Flowers
journal, May 2012
- Klempien, Antje; Kaminaga, Yasuhisa; Qualley, Anthony
- The Plant Cell, Vol. 24, Issue 5
Protein–Protein and Protein–Membrane Associations in the Lignin Pathway
journal, November 2012
- Bassard, Jean-Etienne; Richert, Ludovic; Geerinck, Jan
- The Plant Cell, Vol. 24, Issue 11
Functional characterization of two p-coumaroyl ester 3′-hydroxylase genes from coffee tree: evidence of a candidate for chlorogenic acid biosynthesis
journal, February 2007
- Mahesh, Venkataramaiah; Million-Rousseau, Rachel; Ullmann, Pascaline
- Plant Molecular Biology, Vol. 64, Issue 1-2
Transgene-Mediated and Elicitor-Induced Perturbation of Metabolic Channeling at the Entry Point into the Phenylpropanoid Pathway
journal, August 1999
- Rasmussen, Susanne; Dixon, Richard A.
- The Plant Cell, Vol. 11, Issue 8
New routes for lignin biosynthesis defined by biochemical characterization of recombinant ferulate 5-hydroxylase, a multifunctional cytochrome P450-dependent monooxygenase
journal, August 1999
- Humphreys, J. M.; Hemm, M. R.; Chapple, C.
- Proceedings of the National Academy of Sciences, Vol. 96, Issue 18
14 C Tracer Evidence for Synthesis of Choline and Betaine via Phosphoryl Base Intermediates in Salinized Sugarbeet Leaves
journal, March 1983
- Hanson, Andrew D.; Rhodes, David
- Plant Physiology, Vol. 71, Issue 3
Metabolic networks in motion: 13 C‐based flux analysis
journal, January 2006
- Sauer, Uwe
- Molecular Systems Biology, Vol. 2, Issue 1
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
Improvement of biomass through lignin modification
journal, May 2008
- Li, Xu; Weng, Jing-Ke; Chapple, Clint
- The Plant Journal, Vol. 54, Issue 4
Rewriting the lignin roadmap
journal, June 2002
- Humphreys, John M.; Chapple, Clint
- Current Opinion in Plant Biology, Vol. 5, Issue 3
Metabolism of Phenylpropanoid Compounds in Salvia: ii. Biosynthesis of Phenolic Cinnamic Acids
journal, April 1959
- McCalla, D. R.; Neish, A. C.
- Canadian Journal of Biochemistry and Physiology, Vol. 37, Issue 4
Genetic manipulation of lignocellulosic biomass for bioenergy
journal, December 2015
- Wang, Peng; Dudareva, Natalia; Morgan, John A.
- Current Opinion in Chemical Biology, Vol. 29
Understanding in Vivo Benzenoid Metabolism in Petunia Petal Tissue
journal, July 2004
- Boatright, Jennifer; Negre, Florence; Chen, Xinlu
- Plant Physiology, Vol. 135, Issue 4
Molecular Phenotyping of the pal1 and pal2 Mutants of Arabidopsis thaliana Reveals Far-Reaching Consequences on Phenylpropanoid, Amino Acid, and Carbohydrate Metabolism
journal, September 2004
- Rohde, Antje; Morreel, Kris; Ralph, John
- The Plant Cell, Vol. 16, Issue 10
Mediator Complex Subunits MED2, MED5, MED16, and MED23 Genetically Interact in the Regulation of Phenylpropanoid Biosynthesis
journal, December 2017
- Dolan, Whitney L.; Dilkes, Brian P.; Stout, Jake M.
- The Plant Cell, Vol. 29, Issue 12
The Diurnal Project: Diurnal and Circadian Expression Profiling, Model-based Pattern Matching, and Promoter Analysis
journal, January 2007
- Mockler, T. C.; Michael, T. P.; Priest, H. D.
- Cold Spring Harbor Symposia on Quantitative Biology, Vol. 72, Issue 1
Disruption of Mediator rescues the stunted growth of a lignin-deficient Arabidopsis mutant
journal, March 2014
- Bonawitz, Nicholas D.; Kim, Jeong Im; Tobimatsu, Yuki
- Nature, Vol. 509, Issue 7500, p. 376-380
Metabolic Flux Analysis in Plants: From Intelligent Design to Rational Engineering
journal, June 2008
- Libourel, Igor G. L.; Shachar-Hill, Yair
- Annual Review of Plant Biology, Vol. 59, Issue 1
Metabolic Flux Analysis of the Phenylpropanoid Pathway in Elicitor-treated Potato Tuber Tissue
journal, March 2005
- Matsuda, Fumio; Morino, Keiko; Ano, Rieko
- Plant and Cell Physiology, Vol. 46, Issue 3
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
Studies of Lignin Biosynthesis Using Isotopic Carbon: xii. the Biosynthesis and Metabolism of Sinapic acid
journal, January 1963
- Higuchi, Takayoshi; Brown, Stewart A.
- Canadian Journal of Biochemistry and Physiology, Vol. 41, Issue 1
Works referencing / citing this record:
Methyl Jasmonate Changes the Composition and Distribution Rather than the Concentration of Defence Compounds: a Study on Pyrrolizidine Alkaloids
journal, October 2018
- Wei, Xianqin; Vrieling, Klaas; Mulder, Patrick P. J.
- Journal of Chemical Ecology, Vol. 45, Issue 2
4-Coumarate 3-hydroxylase in the lignin biosynthesis pathway is a cytosolic ascorbate peroxidase
journal, April 2019
- Barros, Jaime; Escamilla-Trevino, Luis; Song, Luhua
- Nature Communications, Vol. 10, Issue 1
Lignin biosynthesis: old roads revisited and new roads explored
journal, December 2019
- Dixon, Richard A.; Barros, Jaime
- Open Biology, Vol. 9, Issue 12
Production and Application of Stable Isotope-Labeled Internal Standards for RNA Modification Analysis
journal, January 2019
- Borland, Kayla; Diesend, Jan; Ito-Kureha, Taku
- Genes, Vol. 10, Issue 1