Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA.
Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, USA.
Plant Physiol. 2022 Nov 28;190(4):2828-2846. doi: 10.1093/plphys/kiac344.
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.
木质素是植物中最丰富的聚合物之一，来源于苯丙烷途径，该途径还产生了一系列对植物适应性至关重要的代谢物。木质素的基因工程可以导致转录和代谢物积累的剧烈变化，无论是否伴有发育表型。为了了解木质素扰动的影响，我们分析了 13 种选定的苯丙烷突变体和野生型拟南芥（Arabidopsis thaliana）快速木质化茎组织的转录组和代谢组数据。我们的数据集包含 20974 个表达基因，其中超过 26%的基因在至少一种突变体中改变了转录水平，18 种靶向代谢物在至少一种突变体中都显示出改变的积累。我们发现木质素生物合成和通过莽草酸途径的苯丙氨酸供应在转录水平上紧密地共同调节。差异表达基因（DEGs）的层次聚类分析将 13 种突变体分为 5 个具有相似失调基因谱的亚组。对这些突变体中 DEGs 的功能分析以及基因表达和代谢物积累之间的相关性表明，对涉及多个生物过程的转录物有系统的影响。
