New Insights Into Lignification via Network and Multi-Omics Analyses of Arogenate Dehydratase Knock-Out Mutants in Arabidopsis thaliana

Hixson, Kim K.; Marques, Joaquim V.; Wendler, Jason P.; McDermott, Jason E.; Weitz, Karl K.; Clauss, Therese R.; Monroe, Matthew E.; Moore, Ronald J.; Brown, Joseph M.; Lipton, Mary S.; Bell, Callum; Pasa-Tolic, Ljiljana; Davin, Laurence B.; Lewis, Norman G.

doi:10.3389/fpls.2021.664250

New Insights Into Lignification via Network and Multi-Omics Analyses of Arogenate Dehydratase Knock-Out Mutants in Arabidopsis thaliana

Journal Article · Tue May 25 04:00:00 EDT 2021 · Frontiers in Plant Science

DOI:https://doi.org/10.3389/fpls.2021.664250· OSTI ID:1807537

Hixson, Kim K. ^[1]; Marques, Joaquim V. ^[2]; Wendler, Jason P. ^[1]; ^[1]; Weitz, Karl K. ^[1]; Clauss, Therese R. ^[3]; ^[1]; Moore, Ronald J. ^[1]; Brown, Joseph M. ^[4]; ^[1]; Bell, Callum ^[5]; Pasa-Tolic, Ljiljana ^[1]; Davin, Laurence B. ^[2]; Lewis, Norman G. ^[2]

BATTELLE (PACIFIC NW LAB)
Washington State University
HANFORD LABORATORY MGMT & INTEGRATION
University of Utah
National Center for Genome Resources

Multiple Arabidopsis arogenate dehydratase (ADT) knock-out (KO) mutants, with phenotypes having variable lignin levels (up to circa 70% reduction), were studied to investigate how differential reductions in ADTs perturb its overall plant systems biology. Integrated "omics" analyses (metabolome, transcriptome, and proteome) of wild type (WT), single and multiple ADT KO lines were conducted. Transcriptome and proteome data were collapsed into gene ortholog (GO) data, with this allowing for enzymatic reaction and metabolome cross-comparisons to uncover dominant or likely metabolic biosynthesis reactions affected. Network analysis of enzymes-highly correlated to stem lignin levels-deduced the involvement of novel putative lignin related proteins or processes. These included those associated with ribosomes, the spliceosome, mRNA transport, aminoacyl tRNA biosynthesis, and phosphorylation. While prior work helped explain lignin biosynthesis regulation at the transcriptional level, our data here provide support for a new hypothesis that there are additional post-transcriptional and translational level processes that need to be considered. These findings are anticipated to lead to development of more accurate depictions of lignin/phenylpropanoid biosynthesis models in situ, with new protein targets identified for further biochemical analysis and/or plant bioengineering. Additionally, using KEGG defined functional categorization of proteomics and transcriptomics analyses, we detected significant changes to glucosinolate, a-linolenic acid, nitrogen, carotenoid, aromatic amino acid, phenylpropanoid, and photosynthesis-related metabolic pathways in ADT KO mutants. Metabolomics results also revealed that putative carotenoid and galactolipid levels were generally increased in amount, whereas many glucosinolates and phenylpropanoids (including flavonoids and lignans) were decreased in the KO mutants.

Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: AC05-76RL01830

OSTI ID:: 1807537

Report Number(s):: PNNL-SA-163837

Journal Information:: Frontiers in Plant Science, Journal Name: Frontiers in Plant Science Vol. 12

Country of Publication:: United States

Language:: English

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New Insights Into Lignification via Network and Multi-Omics Analyses of Arogenate Dehydratase Knock-Out Mutants in Arabidopsis thaliana

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