Abstract
Brassinosteroids (BRs) are plant steroid hormones that regulate cell division and stress response. Here we use a systems biology approach to integrate multi-omic datasets and unravel the molecular signaling events of BR response in Arabidopsis. We profile the levels of 26,669 transcripts, 9,533 protein groups, and 26,617 phosphorylation sites from Arabidopsis seedlings treated with brassinolide (BL) for six different lengths of time. We then construct a network inference pipeline called Spatiotemporal Clustering and Inference of Omics Networks (SC-ION) to integrate these data. We use our network predictions to identify putative phosphorylation sites on BES1 and experimentally validate their importance. Additionally, we identify BRONTOSAURUS (BRON) as a transcription factor that regulates cell division, and we show that BRON expression is modulated by BR-responsive kinases and transcription factors. This work demonstrates the power of integrative network analysis applied to multi-omic data and provides fundamental insights into the molecular signaling events occurring during BR response.
Highlights
Brassinosteroids (BRs) are plant steroid hormones that regulate cell division and stress response
BR has been implicated in stem cell division and maintenance: roots treated with BL have excessive Quiescent Center (QC) divisions and altered expression patterns of QC cell identity markers[22,23,24]
In BRZtreated seedlings, we found that BRI1-EMS-SUPPRESSOR 1 (BES1) predominantly exists in its phosphorylated form, while BL-treated seedlings showed an accumulation of dephosphorylated BES1 over time
Summary
Brassinosteroids (BRs) are plant steroid hormones that regulate cell division and stress response. In the absence of BR, the GSK3 kinase BRASSINOSTEROID INSENSITIVE 2 (BIN2) phosphorylates numerous substrates including the transcription factors (TFs) BRI1-EMS-SUPPRESSOR 1 (BES1), and BRASSINAZOLE-RESISTANT 1 (BZR1)[7,9,10,11,12]. When BRs are present, the BRI1/BAK1 complex activates a kinase-signaling cascade resulting in the inactivation of BIN2 and the dephosphorylation of BES1 and BZR1 This allows BES1 and BZR1 to regulate target gene expression in the nucleus[12,13,14,15,16,17,18]. We inferred a set of integrated, TF-centered Gene Regulatory Networks (GRNs) using our newly-developed Spatiotemporal Clustering and Inference of Omics Networks (SCION) pipeline These networks illustrated how the phosphorylation state of TFs is important for predicting their downstream target genes.
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