Transcript and metabolite network perturbations in lignin biosynthetic mutants of Arabidopsis.
Peng WangLongyun GuoJohn A MorganNatalia DudarevaClint ChapplePublished in: Plant physiology (2022)
Lignin, one of the most abundant polymers in plants, is derived from the phenylpropanoid pathway, which also gives rise to an array of metabolites that are essential for plant fitness. Genetic engineering of lignification can cause drastic changes in transcription and metabolite accumulation with or without an accompanying development phenotype. To understand the impact of lignin perturbation, we analyzed transcriptome and metabolite data from the rapidly lignifying stem tissue in 13 selected phenylpropanoid mutants and wild-type Arabidopsis (Arabidopsis thaliana). Our dataset contains 20,974 expressed genes, of which over 26% had altered transcript levels in at least one mutant, and 18 targeted metabolites, all of which displayed altered accumulation in at least one mutant. We found that lignin biosynthesis and phenylalanine supply via the shikimate pathway are tightly co-regulated at the transcriptional level. The hierarchical clustering analysis of differentially expressed genes (DEGs) grouped the 13 mutants into 5 subgroups with similar profiles of mis-regulated genes. Functional analysis of the DEGs in these mutants and correlation between gene expression and metabolite accumulation revealed system-wide effects on transcripts involved in multiple biological processes.
Keyphrases
- wild type
- transcription factor
- genome wide
- gene expression
- genome wide identification
- rna seq
- ionic liquid
- arabidopsis thaliana
- single cell
- dna methylation
- cell wall
- ms ms
- bioinformatics analysis
- physical activity
- cancer therapy
- high throughput
- copy number
- body composition
- big data
- high resolution
- drug delivery
- heat shock