Integrated Multi-omic Framework of the Plant Response to Jasmonic Acid

Abstract

27Understanding the systems-level actions of transcriptional responses to hormones provides 28 insight into how the genome is reprogrammed in response to environmental stimuli. Here, we 29 investigate the signaling pathway of the hormone jasmonic acid (JA), which controls a plethora of 30 critically important processes in plants and is orchestrated by the transcription factor MYC2 and 31 its closest relatives in Arabidopsis thaliana. We generated an integrated framework of the 32 response to JA that spans from the activity of master and secondary-regulatory transcription 33 factors, through gene expression outputs and alternative splicing to protein abundance changes, 34 protein phosphorylation and chromatin remodeling. We integrated time series transcriptome 35 analysis with (phospho)proteomic data to reconstruct gene regulatory network models. These 36 enable us to predict previously unknown points of crosstalk from JA to other signaling pathways 37 and to identify new components of the JA regulatory mechanism, which we validated through 38 targeted mutant analysis. These results provide a comprehensive understanding of how a plant 39 hormone remodels cellular functions and plant behavior, the general principles of which provide 40 a framework for analysis of cross-regulation between other hormone and stress signaling 41 pathways. 42 43 44 45 46 47 48 49 50 51 52 5 2004, Fernandez-Calvo et al. , 2011). myc3 and myc4 single mutants behave like wildtype with 104 regards to JA-induced root growth inhibition. However, in combination with the myc2 mutant, 105 myc2 myc3 double mutants exhibit an increased JA hyposensitivity, almost as pronounced as in 106 myc2 myc3 myc4 triple mutants (Fernandez-Calvo et al., 2011). We consequently selected MYC3 107 for an in-depth analysis. 108In order to better understand how the master TFs MYC2 and MYC3 control the JA-109 induced transcriptional cascade, we determined their genome-wide binding sites using chromatin 110 immunoprecipitation sequencing (ChIP-seq). Four biological replicates of JA-treated (2 hours) 111 three-day-old etiolated Arabidopsis seedlings that express a native promoter-driven and epitope 112 (YPet)-tagged version of MYC2 and three biological replicates of MYC3 (Col-0 MYC2::MYC2-113 Ypet, Col-0 MYC3::MYC3-Ypet) were used (Gimenez-Ibanez et al., 2017). The genome-wide 114distributions of MYC2 and MYC3 binding sites were highly similar (Fig. 1c, d). We identified 6,736 115 MYC2 and 3,982 MYC3 binding sites of high confidence, equating to 6,178 MYC2 and 4,092

Specialist root herbivore modulates plant transcriptome and downregulates defensive secondary metabolites in a brassicaceous plant

“…In the past decade, sequencing technology has broadened our understanding of defence signalling in plants. This led to extensive studies on how Arabidopsis thaliana (Arabidopsis hereafter) plants respond to exogenous application of JA (Hickman et al, 2017;Zander et al, 2020), SA (Hickman et al, 2019), or combinations of these hormones (Hickman et al, 2019). Coolen et al (2016) studied how the Arabidopsis leaf transcriptome changes after stress by drought, infection by the necrotrophic pathogen Botrytis cinerea, chewing insect herbivory by Pieris rapae, or combinations of these stresses.…”

Pseudomonas syringae activates ZAT18 to inhibit salicylic acid accumulation by repressing EDS1 transcription for bacterial infection

“…S7), suggesting that there are other regulators downstream of COI1-MYC2 and probably parallel to ZAT18. As indicated by the ChIP-seq data in the study by Zander et al (2020), MYC2/ MYC3 directly target many TFs, including ZAT18, NAC055, and ATAF2, although this work was not performed under P. syringae infection. NAC055 and its homologs NAC019 and NAC072 have been shown to be activated by COR and then to directly bind the promoter of ICS1 and inhibit its expression (Zheng et al, 2012).…”

“…MYC2 binds to the G-box motif (CACGTG) and its variants, such as the E-box (CANNTG), to regulate the expression of target genes (Dombrecht et al, 2007;Godoy et al, 2011;Zander et al, 2020). We found several potential MYC2-binding ciselements in the 1-kb promoter sequence of ZAT18 (Fig.…”

“…These results further indicate that ZAT18 functions downstream of the JA signaling pathway in a COI1-dependent manner. MYC2, MYC3, and MYC4 are important regulators downstream of COI1 in the JA signaling pathway, and a large-scale ChIP-seq study has shown that MYC2 and MYC3 bind to the promoter of ZAT18 (Zander et al, 2020), suggesting that ZAT18 might be regulated by MYCs. To investigate whether Pst DC3000induced ZAT18 expression is also MYC2, MYC3, and/or MYC4 dependent, we performed the infection experiment in these myc mutants.…”