Validation of a metabolite–GWAS network for Populus trichocarpa family 1 UDP-glycosyltransferases

Saint-Vincent, Patricia M. B.; Furches, Anna; Galanie, Stephanie; Teixeira Prates, Erica; Aldridge, Jessa L.; Labbe, Audrey; Zhao, Nan; Martin, Madhavi Z.; Ranjan, Priya; Jones, Piet; Kainer, David; Kalluri, Udaya C.; Chen, Jin-Gui; Muchero, Wellington; Jacobson, Daniel A.; Tschaplinski, Timothy J.

doi:10.3389/fpls.2023.1210146

Title: Validation of a metabolite–GWAS network for Populus trichocarpa family 1 UDP-glycosyltransferases

Journal Article · Fri Jul 21 00:00:00 EDT 2023 · Frontiers in Plant Science

DOI:https://doi.org/10.3389/fpls.2023.1210146· OSTI ID:1991982

Saint-Vincent, Patricia M. B.; Furches, Anna; Galanie, Stephanie; Teixeira Prates, Erica; Aldridge, Jessa L.; Labbe, Audrey; Zhao, Nan; Martin, Madhavi Z.; Ranjan, Priya; Jones, Piet; Kainer, David; Kalluri, Udaya C.; Chen, Jin-Gui; Muchero, Wellington; Jacobson, Daniel A.; Tschaplinski, Timothy J.

Metabolite genome-wide association studies (mGWASs) are increasingly used to discover the genetic basis of target phenotypes in plants such as Populus trichocarpa , a biofuel feedstock and model woody plant species. Despite their growing importance in plant genetics and metabolomics, few mGWASs are experimentally validated. Here, we present a functional genomics workflow for validating mGWAS-predicted enzyme–substrate relationships. We focus on uridine diphosphate–glycosyltransferases (UGTs), a large family of enzymes that catalyze sugar transfer to a variety of plant secondary metabolites involved in defense, signaling, and lignification. Glycosylation influences physiological roles, localization within cells and tissues, and metabolic fates of these metabolites. UGTs have substantially expanded in P. trichocarpa , presenting a challenge for large-scale characterization. Using a high-throughput assay, we produced substrate acceptance profiles for 40 previously uncharacterized candidate enzymes. Assays confirmed 10 of 13 leaf mGWAS associations, and a focused metabolite screen demonstrated varying levels of substrate specificity among UGTs. A substrate binding model case study of UGT-23 rationalized observed enzyme activities and mGWAS associations, including glycosylation of trichocarpinene to produce trichocarpin, a major higher-order salicylate in P. trichocarpa. We identified UGTs putatively involved in lignan, flavonoid, salicylate, and phytohormone metabolism, with potential implications for cell wall biosynthesis, nitrogen uptake, and biotic and abiotic stress response that determine sustainable biomass crop production. Our results provide new support for in silico analyses and evidence-based guidance for in vivo functional characterization.

View Journal Article

Cite

Export

Save

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC05-00OR22725, DE-AC02-05CH11231; AC05-00OR22725; AC02-05CH11231

OSTI ID:: 1991982

Alternate ID(s):: OSTI ID: 1992749

Journal Information:: Frontiers in Plant Science, Journal Name: Frontiers in Plant Science Vol. 14; ISSN 1664-462X

Publisher:: Frontiers Media SACopyright Statement

Country of Publication:: Switzerland

Language:: English

References (53)

RVTESTS: an efficient and comprehensive tool for rare variant association analysis using sequence data: Table 1. Zhan, Xiaowei; Hu, Youna; Li, Bingshan Bioinformatics, Vol. 32, Issue 9 https://doi.org/10.1093/bioinformatics/btw079	journal	February 2016
Flexible IO and integration for scientific codes through the adaptable IO system (ADIOS) Lofstead, Jay F.; Klasky, Scott; Schwan, Karsten Proceedings of the 6th international workshop on Challenges of large applications in distributed environments - CLADE '08 https://doi.org/10.1145/1383529.1383533	conference	January 2008
A genome-wide phylogenetic reconstruction of family 1 UDP-glycosyltransferases revealed the expansion of the family during the adaptation of plants to life on land: Phylogeny reconstruction of plant family 1 UGTs Caputi, Lorenzo; Malnoy, Mickael; Goremykin, Vadim The Plant Journal, Vol. 69, Issue 6 https://doi.org/10.1111/j.1365-313X.2011.04853.x	journal	December 2011
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading Trott, Oleg; Olson, Arthur J. Journal of Computational Chemistry https://doi.org/10.1002/jcc.21334	journal	January 2009
A quantitative genomics map of rice provides genetic insights and guides breeding Wei, Xin; Qiu, Jie; Yong, Kaicheng Nature Genetics, Vol. 53, Issue 2 https://doi.org/10.1038/s41588-020-00769-9	journal	February 2021
Variance component model to account for sample structure in genome-wide association studies Kang, Hyun Min; Sul, Jae Hoon; Service, Susan K. Nature Genetics, Vol. 42, Issue 4 https://doi.org/10.1038/ng.548	journal	March 2010
CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data Huang, Jing; MacKerell, Alexander D. Journal of Computational Chemistry, Vol. 34, Issue 25 https://doi.org/10.1002/jcc.23354	journal	July 2013
Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium Hart, Katarina; Foloppe, Nicolas; Baker, Christopher M. Journal of Chemical Theory and Computation, Vol. 8, Issue 1 https://doi.org/10.1021/ct200723y	journal	December 2011
Genome-wide efficient mixed-model analysis for association studies Zhou, Xiang; Stephens, Matthew Nature Genetics, Vol. 44, Issue 7 https://doi.org/10.1038/ng.2310	journal	June 2012
Glycosylation Is a Major Regulator of Phenylpropanoid Availability and Biological Activity in Plants Le Roy, Julien; Huss, Brigitte; Creach, Anne Frontiers in Plant Science, Vol. 7 https://doi.org/10.3389/fpls.2016.00735	journal	May 2016
Phylogenetic Analysis of the UDP-glycosyltransferase Multigene Family of Arabidopsis thaliana Li, Yi; Baldauf, Sandie; Lim, Eng-Kiat Journal of Biological Chemistry, Vol. 276, Issue 6 https://doi.org/10.1074/jbc.M007447200	journal	October 2000
Keep Sugar Away to Stay Active: Glycosylation of Methyl Salicylate Shuts Down Systemic Signaling Mhamdi, Amna Plant Physiology, Vol. 180, Issue 4 https://doi.org/10.1104/pp.19.00747	journal	July 2019
Methyl Salicylate Is a Critical Mobile Signal for Plant Systemic Acquired Resistance Park, S. -W.; Kaimoyo, E.; Kumar, D. Science, Vol. 318, Issue 5847 https://doi.org/10.1126/science.1147113	journal	October 2007
Exploiting the Reversibility of Natural Product Glycosyltransferase-Catalyzed Reactions Zhang, C. Science, Vol. 313, Issue 5791 https://doi.org/10.1126/science.1130028	journal	September 2006
Comparison of simple potential functions for simulating liquid water Jorgensen, William L.; Chandrasekhar, Jayaraman; Madura, Jeffry D. The Journal of Chemical Physics, Vol. 79, Issue 2 https://doi.org/10.1063/1.445869	journal	July 1983
Phylogenomic analysis of UDP‐dependent glycosyltransferases provides insights into the evolutionary landscape of glycosylation in plant metabolism Wilson, Alexander E.; Tian, Li The Plant Journal, Vol. 100, Issue 6 https://doi.org/10.1111/tpj.14514	journal	October 2019
Metabolite‐based genome‐wide association study enables dissection of the flavonoid decoration pathway of wheat kernels Chen, Jie; Hu, Xin; Shi, Taotao Plant Biotechnology Journal, Vol. 18, Issue 8 https://doi.org/10.1111/pbi.13335	journal	March 2020
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers Abraham, Mark James; Murtola, Teemu; Schulz, Roland SoftwareX, Vol. 1-2 https://doi.org/10.1016/j.softx.2015.06.001	journal	September 2015
Highly accurate protein structure prediction with AlphaFold Jumper, John; Evans, Richard; Pritzel, Alexander Nature https://doi.org/10.1038/s41586-021-03819-2	journal	July 2021
Genome-wide association studies and expression-based quantitative trait loci analyses reveal roles of HCT2 in caffeoylquinic acid biosynthesis and its regulation by defense-responsive transcription factors in Populus Zhang, Jin; Yang, Yongil; Zheng, Kaijie New Phytologist, Vol. 220, Issue 2 https://doi.org/10.1111/nph.15297	journal	July 2018
Characterization of Indole-3-acetic Acid Biosynthesis and the Effects of This Phytohormone on the Proteome of the Plant-Associated Microbe Pantoea sp. YR343 Estenson, Kasey; Hurst, Gregory B.; Standaert, Robert F. Journal of Proteome Research, Vol. 17, Issue 4 https://doi.org/10.1021/acs.jproteome.7b00708	journal	February 2018
Phytozome: a comparative platform for green plant genomics Goodstein, David M.; Shu, Shengqiang; Howson, Russell Nucleic Acids Research, Vol. 40, Issue D1 https://doi.org/10.1093/nar/gkr944	journal	November 2011
Multitrait genome‐wide association analysis of Populus trichocarpa identifies key polymorphisms controlling morphological and physiological traits Chhetri, Hari B.; Macaya‐Sanz, David; Kainer, David New Phytologist, Vol. 223, Issue 1 https://doi.org/10.1111/nph.15777	journal	April 2019
Glycosyltransferases of Lipophilic Small Molecules Bowles, Dianna; Lim, Eng-Kiat; Poppenberger, Brigitte Annual Review of Plant Biology, Vol. 57, Issue 1 https://doi.org/10.1146/annurev.arplant.57.032905.105429	journal	June 2006
Metabolic profiling reveals altered sugar and secondary metabolism in response to UGPase overexpression in Populus Payyavula, Raja S.; Tschaplinski, Timothy J.; Jawdy, Sara S. BMC Plant Biology, Vol. 14, Issue 1 https://doi.org/10.1186/s12870-014-0265-8	journal	October 2014
Engineering the glycosylation of natural products in actinomycetes Salas, José A.; Méndez, Carmen Trends in Microbiology, Vol. 15, Issue 5 https://doi.org/10.1016/j.tim.2007.03.004	journal	May 2007
Genome-wide analysis of the structural genes regulating defense phenylpropanoid metabolism in Populus Tsai, Chung-Jui; Harding, Scott A.; Tschaplinski, Timothy J. New Phytologist, Vol. 172, Issue 1 https://doi.org/10.1111/j.1469-8137.2006.01798.x	journal	October 2006
An evolutionary view of functional diversity in family 1 glycosyltransferases Yonekura-Sakakibara, Keiko; Hanada, Kousuke The Plant Journal, Vol. 66, Issue 1 https://doi.org/10.1111/j.1365-313X.2011.04493.x	journal	March 2011
Crystal Structures of Glycosyltransferase UGT78G1 Reveal the Molecular Basis for Glycosylation and Deglycosylation of (Iso)flavonoids Modolo, Luzia V.; Li, Lenong; Pan, Haiyun Journal of Molecular Biology, Vol. 392, Issue 5 https://doi.org/10.1016/j.jmb.2009.08.017	journal	October 2009
Analysis of Two New Arabinosyltransferases Belonging to the Carbohydrate-Active Enzyme (CAZY) Glycosyl Transferase Family1 Provides Insights into Disease Resistance and Sugar Donor Specificity Louveau, Thomas; Orme, Anastasia; Pfalzgraf, Hans The Plant Cell, Vol. 30, Issue 12 https://doi.org/10.1105/tpc.18.00641	journal	November 2018
MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis Schwacke, Rainer; Ponce-Soto, Gabriel Y.; Krause, Kirsten Molecular Plant, Vol. 12, Issue 6 https://doi.org/10.1016/j.molp.2019.01.003	journal	June 2019
The impact of enzyme engineering upon natural product glycodiversification Williams, Gavin J.; Gantt, Richard W.; Thorson, Jon S. Current Opinion in Chemical Biology, Vol. 12, Issue 5 https://doi.org/10.1016/j.cbpa.2008.07.013	journal	October 2008
Canonical sampling through velocity rescaling Bussi, Giovanni; Donadio, Davide; Parrinello, Michele The Journal of Chemical Physics, Vol. 126, Issue 1 https://doi.org/10.1063/1.2408420	journal	January 2007
Genome Wide Analysis of Family-1 UDP Glycosyltransferases in Populus trichocarpa Specifies Abiotic Stress Responsive Glycosylation Mechanisms Rehman, Hafiz Mamoon; Khan, Uzair Muhammad; Nawaz, Sehar Genes, Vol. 13, Issue 9 https://doi.org/10.3390/genes13091640	journal	September 2022
Pleiotropic and Epistatic Network-Based Discovery: Integrated Networks for Target Gene Discovery Weighill, Deborah; Jones, Piet; Shah, Manesh Frontiers in Energy Research, Vol. 6 https://doi.org/10.3389/fenrg.2018.00030	journal	May 2018
LINCS: A linear constraint solver for molecular simulations Hess, Berk; Bekker, Henk; Berendsen, Herman J. C. Journal of Computational Chemistry, Vol. 18, Issue 12 https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H	journal	September 1997
Enzymatic Glucosylation of Salidroside from Starch by α-Amylase Wang, Ke; Qi, Tingting; Guo, Longcheng Journal of Agricultural and Food Chemistry, Vol. 67, Issue 7 https://doi.org/10.1021/acs.jafc.8b06618	journal	January 2019
Getting back to the grass roots: harnessing specialized metabolites for improved crop stress resilience Ding, Yezhang; Northen, Trent R.; Khalil, Ahmed Current Opinion in Biotechnology, Vol. 70 https://doi.org/10.1016/j.copbio.2021.05.010	journal	August 2021
Glycosyltransferases: key players involved in the modification of plant secondary metabolites Wang, Jun; Hou, Bingkai Frontiers of Biology in China, Vol. 4, Issue 1 https://doi.org/10.1007/s11515-008-0111-1	journal	December 2008
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks Shannon, P. Genome Research, Vol. 13, Issue 11 https://doi.org/10.1101/gr.1239303	journal	November 2003
Discovery of salicyl benzoate UDP‐glycosyltransferase, a central enzyme in poplar salicinoid phenolic glycoside biosynthesis Fellenberg, Christin; Corea, Oliver; Yan, Lok‐Hang The Plant Journal, Vol. 102, Issue 1 https://doi.org/10.1111/tpj.14615	journal	February 2020
Finding New Cell Wall Regulatory Genes in Populus trichocarpa Using Multiple Lines of Evidence Furches, Anna; Kainer, David; Weighill, Deborah Frontiers in Plant Science, Vol. 10 https://doi.org/10.3389/fpls.2019.01249	journal	October 2019
Poplar Carbohydrate-Active Enzymes. Gene Identification and Expression Analyses Geisler-Lee, Jane; Geisler, Matt; Coutinho, Pedro M. Plant Physiology, Vol. 140, Issue 3 https://doi.org/10.1104/pp.105.072652	journal	January 2006
lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests Mariani, Valerio; Biasini, Marco; Barbato, Alessandro Bioinformatics, Vol. 29, Issue 21 https://doi.org/10.1093/bioinformatics/btt473	journal	August 2013
Unusual sugar biosynthesis and natural product glycodiversification Thibodeaux, Christopher J.; Melançon, Charles E.; Liu, Hung-wen Nature, Vol. 446, Issue 7139 https://doi.org/10.1038/nature05814	journal	April 2007
Genome-Wide Association Study of Wood Anatomical and Morphological Traits in Populus trichocarpa Chhetri, Hari B.; Furches, Anna; Macaya-Sanz, David Frontiers in Plant Science, Vol. 11 https://doi.org/10.3389/fpls.2020.545748	journal	September 2020
Crystal Structures of a Multifunctional Triterpene/Flavonoid Glycosyltransferase from Medicago truncatula Shao, Hui; He, Xianzhi; Achnine, Lahoucine The Plant Cell, Vol. 17, Issue 11 https://doi.org/10.1105/tpc.105.035055	journal	October 2005
Structure–function relationship of terpenoid glycosyltransferases from plants Kurze, Elisabeth; Wüst, Matthias; Liao, Jieren Natural Product Reports, Vol. 39, Issue 2 https://doi.org/10.1039/d1np00038a	journal	January 2022
Biosynthesis of Phenolic Glycosides from Phenylpropanoid and Benzenoid Precursors in Populus Babst, Benjamin A.; Harding, Scott A.; Tsai, Chung-Jui Journal of Chemical Ecology, Vol. 36, Issue 3 https://doi.org/10.1007/s10886-010-9757-7	journal	February 2010
The Ancient Salicoid Genome Duplication Event: A Platform for Reconstruction of De Novo Gene Evolution in Populus trichocarpa Yates, Timothy B.; Feng, Kai; Zhang, Jin Genome Biology and Evolution, Vol. 13, Issue 9 https://doi.org/10.1093/gbe/evab198	journal	September 2021
Functional Characterization of UDP-Glycosyltransferases Involved in Anti-viral Lignan Glycosides Biosynthesis in Isatis indigotica Tan, Yuping; Yang, Jian; Jiang, Yinyin Frontiers in Plant Science, Vol. 13 https://doi.org/10.3389/fpls.2022.921815	journal	June 2022
The nature of the progression of drought stress drives differential metabolomic responses in Populus deltoides Tschaplinski, Timothy James; Abraham, Paul E.; Jawdy, Sara S. Annals of Botany, Vol. 124, Issue 4 https://doi.org/10.1093/aob/mcz002	journal	January 2019
Down-regulation of the caffeic acid O-methyltransferase gene in switchgrass reveals a novel monolignol analog Tschaplinski, Timothy J.; Standaert, Robert F.; Engle, Nancy L. Biotechnology for Biofuels, Vol. 5, Issue 1 https://doi.org/10.1186/1754-6834-5-71	journal	January 2012

Similar Records

Rhizosphere microbiomes diverge among Populus trichocarpa plant-host genotypes and chemotypes, but it depends on soil origin

Journal Article · Sat May 18 00:00:00 EDT 2019 · Microbiome · OSTI ID:1991982

Veach, Allison M.; Morris, Reese; Yip, Daniel Z.; +5 more

Structure-based enzyme engineering improves donor-substrate recognition of Arabidopsis thaliana glycosyltransferases

Journal Article · Fri Aug 07 00:00:00 EDT 2020 · Biochemical Journal · OSTI ID:1991982

Akere, Aishat; Chen, Serena; Liu, Xiaohan; +5 more

Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa

Journal Article · Wed Nov 20 00:00:00 EST 2019 · BMC Genomics · OSTI ID:1991982

Guerra, Fernando P.; Suren, Haktan; Holliday, Jason; +8 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
glycosyltransferase
Populus
functional genomics
high throughput
GWAS
metabolite-gene validation
metabolomics

Title: Validation of a metabolite–GWAS network for Populus trichocarpa family 1 UDP-glycosyltransferases

Citation Formats

References (53)

Similar Records

Related Subjects