Project description:For identification of plant gene networks which interact to initiate and support both rhizobial nodulation and AM fungal colonization, the transcription profiles of soybean genes induced during rhizobial, AM and their dual symbioses.
Project description:we compared changes in the transcriptome and the translatome of M. truncatula roots upon rhizobial infection using direct RNA-seq and Translating Ribosome Affinity Purification (TRAP) combined with RNA-seq (TRAP-seq), respectively. TRAP is a ribosome immunopurification approach that has been extensively used in plants and mammals to assess translational changes
Project description:Fine-tuning of the immune response plays a key role in legume-rhizobial symbiosis. Rhizobial Nod factors can suppress the defense responses during symbiosis, but the possible mechanisms of such regulation remain poorly understood. Here, we observe that Nod factors effectively suppress the expression of genes encoding defense markers (WRKYs, PRs, PALs), the reactive oxygen species (ROS) formation, and reduce the content of pattern recognition receptor (PRR) LYK9 induced by treatment with deacetylated chitooligosaccharide CO8-DA in pea roots. Since PRR LYK9 may recognize both chitin/COs and peptidoglycan, it likely plays an important role in the activation of defense responses during rhizobial inoculation. To identify potential regulators through which Nod factors suppress the immune response in plants during symbiosis with rhizobia, proteome and transcriptome analyses were performed. This allowed identifying several potential candidates activated by Nod factors, such as superoxide dismutase and catalase enzymes, which prevent excessive ROS accumulation and the development of oxidative stress. We also found ubiquitin ligases and ubiquitin-conjugating enzymes that may target PRRs activated in response to rhizobial inoculation. LYK9 degradation via ubiquitinylation was shown to prevent a hypersensitive response in plants. Nod factors activate enzymes involved in jasmonic acid biosynthesis, which in turn activates the transcription factor ABR1, suppressing the abscisic acid-induced responses and decreasing the immune response. Finally, we showed that LysM-receptor-like kinases PsLYK11/MtLYK11, probable homologs of Arabidopsis AtLYK3 in pea and Medicago, are involved in regulation of the immune response.
Project description:The extend of chromatin accessibility changes and its consequent impact on the transcriptional control of rhizobial infection, colonization, and nodule development, remain unknown. This understanding requires that the dynamic behavior of gene expression and chromatin accessibility be quantified. Thus, we uncovered the gene regulatory network in response to LCOs in M. truncatula roots by quantifying temporal changes in the transcriptome (RNA-seq) and genome-wide chromatin accessibility (ATAC-seq) after Sinorhizobium meliloti LCO treatment.
Project description:We have undertaken a detailed study to identify mechanisms regulating expression of NCRs. We used a custom Affymetrix oligonucleotide microarray to examine the expression changes of 566 NCRs in different stages of nodule development. Additionally, rhizobial mutants were used to understand the importance of the rhizobial components in induction of NCRs. Early NCRs were detected during the initial infection of rhizobia in nodules and continue to be expressed into the late stages of nodule development. Late NCRs were induced concomittant with bacteroid development in the nodules. The induction of these groups of genes was correlated with the number and morphology of rhizobia in the nodule.
Project description:We treated Populus tremula x alba roots with rhizobial LCOs. We analyzed gene expression by RNA sequencing at seven time-points: 0 hr (control treatment), 15, 30 min, 1, 2, 4, 8, 24 hours over the following 24 hours.