A quantitative method for analyzing glycome profiles of plant cell walls

Pattathil, Sivakumar; Ingwers, Miles W.; Aubrey, Doug P.; Li, Zenglu; Dahlen, Joseph

doi:10.1016/j.carres.2017.06.009

A quantitative method for analyzing glycome profiles of plant cell walls

Journal Article · Mon Jun 19 00:00:00 EDT 2017 · Carbohydrate Research

DOI:https://doi.org/10.1016/j.carres.2017.06.009· OSTI ID:1533601

Pattathil, Sivakumar ^[1]; Ingwers, Miles W. ^[2]; Aubrey, Doug P. ^[3]; Li, Zenglu ^[2]; Dahlen, Joseph ^[2]

University of Georgia, Athens, GA (United States); DOE/OSTI
University of Georgia, Athens, GA (United States)
University of Georgia, Athens, GA (United States); University of Georgia, Aiken, SC (United States). Savannah River Ecology Laboratory

Glycome profiling allows for the characterization of plant cell wall ultrastructure via sequential extractions and subsequent detection of specific epitopes with a suite of glycan-specific monoclonal antibodies (mAbs). The data are often viewed as the amount of materials recovered and coinciding colored heatmaps of mAb binding are generated. Interpretation of these data can be considered qualitative in nature as it depends on detecting subtle visual differences in antibody binding strength. In this paper we report a mixed model-based quantitative approach for glycome profile analyses, which accounts for the amount of materials recovered and displays the normalized values in revised heatmaps and statistical heatmaps depicting significant differences. The utility of this methodology was demonstrated on a previously published dataset investigating the effects of moisture stress on the roots and needles of Pinus taeda. An annotated R script for the quantitative methodology is included to allow future studies to utilize the same approach.

View Accepted Manuscript (DOE)

Research Organization:: University of Georgia, Athens, GA (United States)

Sponsoring Organization:: Agriculture and Food Research Initiative; National Institute of Food and Agriculture; National Science Foundation (NSF); USDOE; USDOE Office of Environmental Management (EM)

Grant/Contract Number:: EM0004391

OSTI ID:: 1533601

Alternate ID(s):: OSTI ID: 1547088

Journal Information:: Carbohydrate Research, Journal Name: Carbohydrate Research Journal Issue: C Vol. 448; ISSN 0008-6215

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

References (20)

Introduction Wickham, Hadley ggplot2 https://doi.org/10.1007/978-0-387-98141-3_1	book	January 2009
Breaking the “Glycomic Code” of Cell Wall Polysaccharides May Improve Second-Generation Bioenergy Production from Biomass Buckeridge, Marcos S.; de Souza, Amanda P. BioEnergy Research, Vol. 7, Issue 4 https://doi.org/10.1007/s12155-014-9460-6	journal	April 2014
Xylan hydrolysis in Populus trichocarpa×P. deltoides and model substrates during hydrothermal pretreatment Trajano, Heather L.; Pattathil, Sivakumar; Tomkins, Bruce A. Bioresource Technology, Vol. 179 https://doi.org/10.1016/j.biortech.2014.11.090	journal	March 2015
The structure, function, and biosynthesis of plant cell wall pectic polysaccharides Caffall, Kerry Hosmer; Mohnen, Debra Carbohydrate Research, Vol. 344, Issue 14 https://doi.org/10.1016/j.carres.2009.05.021	journal	September 2009
Do plant cell walls have a code? Tavares, Eveline Q. P.; Buckeridge, Marcos S. Plant Science, Vol. 241 https://doi.org/10.1016/j.plantsci.2015.10.016	journal	December 2015
Growth of the plant cell wall Cosgrove, Daniel J. Nature Reviews Molecular Cell Biology, Vol. 6, Issue 11, p. 850-861 https://doi.org/10.1038/nrm1746	journal	November 2005
Application of monoclonal antibodies to investigate plant cell wall deconstruction for biofuels production DeMartini, Jaclyn D.; Pattathil, Sivakumar; Avci, Utku Energy & Environmental Science, Vol. 4, Issue 10 https://doi.org/10.1039/c1ee02112e	journal	January 2011
Investigating plant cell wall components that affect biomass recalcitrance in poplar and switchgrass DeMartini, Jaclyn D.; Pattathil, Sivakumar; Miller, Jeffrey S. Energy & Environmental Science, Vol. 6, Issue 3 https://doi.org/10.1039/c3ee23801f	journal	January 2013
Carbohydrate and lignin are simultaneously solubilized from unpretreated switchgrass by microbial action at high temperature Kataeva, Irina; Foston, Marcus B.; Yang, Sung-Jae Energy & Environmental Science, Vol. 6, Issue 7 https://doi.org/10.1039/c3ee40932e	journal	January 2013
Loss of function of cinnamyl alcohol dehydrogenase 1 leads to unconventional lignin and a temperature-sensitive growth defect in Medicago truncatula Zhao, Q.; Tobimatsu, Y.; Zhou, R. Proceedings of the National Academy of Sciences, Vol. 110, Issue 33 https://doi.org/10.1073/pnas.1312234110	journal	July 2013
Efficient biomass pretreatment using ionic liquids derived from lignin and hemicellulose Socha, A. M.; Parthasarathi, R.; Shi, J. Proceedings of the National Academy of Sciences, Vol. 111, Issue 35 https://doi.org/10.1073/pnas.1405685111	journal	August 2014
Comparison of Arabinoxylan Structure in Bioenergy and Model Grasses Kulkarni, Ameya R.; Pattathil, Sivakumar; Hahn, Michael G. Industrial Biotechnology, Vol. 8, Issue 4 https://doi.org/10.1089/ind.2012.0014	journal	August 2012
Insights into plant cell wall structure, architecture, and integrity using glycome profiling of native and AFEX ^TM -pre-treated biomass Pattathil, Sivakumar; Hahn, Michael G.; Dale, Bruce E. Journal of Experimental Botany, Vol. 66, Issue 14 https://doi.org/10.1093/jxb/erv107	journal	April 2015
Distribution of Fucose-Containing Xyloglucans in Cell Walls of the mur1 Mutant of Arabidopsis Freshour, Glenn; Bonin, Christopher P.; Reiter, Wolf-Dieter Plant Physiology, Vol. 131, Issue 4 https://doi.org/10.1104/pp.102.016444	journal	March 2003
A Comprehensive Toolkit of Plant Cell Wall Glycan-Directed Monoclonal Antibodies Pattathil, S.; Avci, U.; Baldwin, D. Plant Physiology, Vol. 153, Issue 2, p. 514-525 https://doi.org/10.1104/pp.109.151985	journal	April 2010
Assembly and Enlargement of the Primary cell wall in Plants Cosgrove, Daniel J. Annual Review of Cell and Developmental Biology, Vol. 13, Issue 1 https://doi.org/10.1146/annurev.cellbio.13.1.171	journal	November 1997
Determination of glycoside hydrolase specificities during hydrolysis of plant cell walls using glycome profiling Walker, Johnnie A.; Pattathil, Sivakumar; Bergeman, Lai F. Biotechnology for Biofuels, Vol. 10, Issue 1 https://doi.org/10.1186/s13068-017-0703-6	journal	February 2017
Immunological Approaches to Biomass Characterization and Utilization Pattathil, Sivakumar; Avci, Utku; Zhang, Tiantian Frontiers in Bioengineering and Biotechnology, Vol. 3 https://doi.org/10.3389/fbioe.2015.00173	journal	October 2015
Cell wall evolution and diversity Fangel, Jonatan U.; Ulvskov, Peter; Knox, J. P. Frontiers in Plant Science, Vol. 3 https://doi.org/10.3389/fpls.2012.00152	journal	January 2012
Cell Wall Ultrastructure of Stem Wood, Roots, and Needles of a Conifer Varies in Response to Moisture Availability Pattathil, Sivakumar; Ingwers, Miles W.; Victoriano, Olivia L. Frontiers in Plant Science, Vol. 7 https://doi.org/10.3389/fpls.2016.00882	journal	June 2016

Similar Records

Improving neutralization potency and breadth by combining broadly reactive HIV-1 antibodies targeting major neutralization epitopes

Journal Article · Wed Feb 04 23:00:00 EST 2015 · Journal of Virology · OSTI ID:1352359

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
cell walls
moisture stress
monoclonal antibodies
pectin
pinus taeda
xylan
xyloglucans

A quantitative method for analyzing glycome profiles of plant cell walls

Citation Formats

References (20)

Similar Records

Related Subjects