Journal Articles

Comprehensive transcriptome analyses correlated with untargeted metabolome reveal differentially expressed pathways in response to cell wall alterations

March 15, 2018

Nathan T. Reem, Han-Yi Chen, Manhoi Hur, Xuefeng Zhao, Eve Syrkin Wurtele, Xu LiLing Li, Olga Zabotina (2018). Comprehensive transcriptome analyses correlated with untargeted metabolome reveal differentially expressed pathways in response to cell wall alterations. Plant Molecular Biology 1-21.

Author Affiliations

1.Department of Biochemistry, Biophysics and Molecular Biology Iowa State University Ames USA
2.Department of Genetics, Developmental and Cell Biology Iowa State University Ames USA
3.Laurence H. Baker Center for Bioinformatics and Biological Statistics Iowa State University Ames USA
4.Information Technology, College of Liberal Arts and Sciences Iowa State University Ames USA
5.Plants for Human Health Institute North Carolina State University Kannapolis USA
6.Department of Plant and Microbial Biology North Carolina State University Raleigh USA
7.Department of Biological Sciences Mississippi State University Starkville USA

Abstract

Plants respond to changes in their cell walls in order to protect themselves from pathogens and other stresses. Cell wall modifications in Arabidopsis thaliana have profound effects on gene expression and defense response, but the cell signaling mechanisms underlying these responses are not well understood. Three transgenic Arabidopsis lines, two with reduced cell wall acetylation (AnAXE and AnRAE) and one with reduced feruloylation (AnFAE), were used in this study to investigate the plant responses to cell wall modifications. RNA-Seq in combination with untargeted metabolome was employed to assess differential gene expression and metabolite abundance. RNA-Seq results were correlated with metabolite abundances to determine the pathways involved in response to cell wall modifications introduced in each line. The resulting pathway enrichments revealed the deacetylation events in AnAXE and AnRAE plants induced similar responses, notably, upregulation of aromatic amino acid biosynthesis and changes in regulation of primary metabolic pathways that supply substrates to specialized metabolism, particularly those related to defense responses. In contrast, genes and metabolites of lipid biosynthetic pathways and peroxidases involved in lignin polymerization were downregulated in AnFAE plants. These results elucidate how primary metabolism responds to extracellular stimuli. Combining the transcriptomics and metabolomics datasets increased the power of pathway prediction, and demonstrated the complexity of pathways involved in cell wall-mediated signaling.

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