Project description:Purpose: To investigate the global impact of lignin perturbation on transcription in plants, we analyzed transcriptomes from rapidly lignifying stem tissue in wild-type Arabidopsis and 13 selected mutants. Methods: RNA-sequencing was conducted to profile the transcriptome in basal stem tissue of Arabidopsis plants. PolyA+ RNA libraries were constructed and paired-end sequencing was performed on Illumina NovaSeq 6000. The sequence reads that passed quality filters were aligned to the TAIR10 reference genome using HISAT2. Gene counts were analyzed using HTSeq-count program and differential gene expression using DESeq2. Results: The whole dataset contains 20974 expressed genes and 5581 differentially expressed genes in at least one mutant (ANOVA, FDR < 0.05, Fold change ≥ 2 fold).
Project description:Inflorescence stems of 20 Arabidopsis thaliana mutants, each mutated in a single gene of the lignin biosynthetic pathway (PAL1 , PAL2, C4H, 4CL1, 4CL2, CCoAOMT1, CCR1, F5H1, COMT and CAD6, two mutant alleles each) were analyzed by microarrays.
Project description:af09_lignin - stem developement - Transcriptome analysis of lignin mutants and UV stress effect on secondary wall synthesis - transcription frofiling of stem developement in Arabidopsis thaliana. time course with 3 points: 2cm, 10 cm and 25cm (maturation) Keywords: time course
Project description:Transcriptomic analysis was performed on the main inflorescence stems of wild-type and lignin-modified lines growing under the same conditions.
Project description:af09_lignin - dml6 - Transcriptome analysis of lignin mutants and UV stress effect on secondary wall synthesis - DML6 vs S DML6+UV vs S+UV S vs S+UV DML6 vs DML6+UV Keywords: normal vs disease comparison,treated vs untreated comparison
Project description:Mutation of the lignin biosynthetic gene REF8, which encodes p-coumaroylshikimate 3'-hydroxylase, causes widespread changes in gene expression in Arabidopsis thaliana. Disruption of the genes encoding MED5a and MED5b, subunits of the transcriptional coregulatory complex Mediator, rescue the stunted growth of ref8-1 mutants. By comparing gene expression profiles of wild type, ref8-1, med5a/5b, and med5a/5b ref8-1 mutants, we found that the majority of gene expression changes in ref8-1 mutants depend directly or indirectly on MED5a/5b
Project description:This project aims to identify the potential interacting proteins of lignin biosynthetic P450 enzymes by affinity purification and LC-MS/MS analysis. To this end, the genomic pieces of three lignin biosynthetic P450 genes C4H, C3’H and F5H were cloned into pMDCpC4H-HPB vector to generate HPB-fusion constructs driven by C4H promoter. The resulted constructs were then respectively transformed into ref3-3 (for C4H), Col-0 WT (for C3'H), and fah1-2 (for F5H) backgrounds and pMDCpC4H-HPB empty vector (as control) was transformed into Col-0 WT to generate transgenic plants. Arabidopsis T2 transgenic plants were grown for 5 weeks in soil and 15 grams of stem tissues were collected for protein extraction. Membrane protein complex was purified by affinity purification using streptavidin beads and subject to LC-MS/MS analysis. Two biological repeats were performed for each construct. For the first repeat (gel-base proteomics), each P450 construct has its control since each experiment was performed separately. For the second repeat (affinity purification,AP-MS), one control was shared for all the three P450 genes.
Project description:ra15-06_oxmyc4 - atmyc4 overexpression in arabidopsis (ws) - identification of new transcription factors for lignin biosynthesis - Compare the gene transcription in the mature stem of Arabidopsis wild type (ws) and AtMYC4 overexpressors (inws background)
Project description:UV-B radiation regulates numerous morphogenic, biochemical and physiological responses in plants, and can stimulate some responses typically associated with other abiotic and biotic stimuli, including invertebrate herbivory. Removal of UV-B from the growing environment of various plant species has been found to increase their susceptibility to consumption by invertebrate pests, however, to date, little research has been conducted to investigate the effects of UV-B on crop susceptibility to field pests. Here, we report findings from a multi-omic and genetic-based study investigating the mechanisms of UV-B-stimulated resistance of the crop, Brassica napus (oilseed rape), to herbivory from an economically important lepidopteran specialist of the Brassicaceae, Plutella xylostella (diamondback moth). The UV-B photoreceptor, UV RESISTANCE LOCUS 8 (UVR8), was not found to mediate resistance to this pest. RNA-Seq and untargeted metabolomics identified components of the sinapate/lignin biosynthetic pathway that were similarly regulated by UV-B and herbivory. Arabidopsis mutants in genes encoding two enzymes in the sinapate/lignin biosynthetic pathway, CAFFEATE O-METHYLTRANSFERASE 1 (COMT1) and ELICITOR-ACTIVATED GENE 3-2 (ELI3-2), retained UV-B-mediated resistance to P. xylostella herbivory. However, overexpression of B. napus COMT1 in Arabidopsis further reduced plant susceptibility to P. xylostella herbivory in a UV-B-dependent manner. These findings demonstrate that overexpression of a component of the sinapate/lignin biosynthetic pathway in a member of the Brassicaceae can enhance UV-B-stimulated resistance to herbivory from P. xylostella.