Degree Type


Date of Award


Degree Name

Doctor of Philosophy


Genetics, Development and Cell Biology



First Advisor

Yanhai Yin


Understanding how plants balance growth and stress responses is essential to optimize crop yield in an ever-changing environment. Brassinosteroids (BRs) regulate plant growth and stress responses, including that of drought. BRs signal to control the activities of the BES1/BZR1 family transcription factors (TFs), which in turn mediate the expression of more than 5,000 BR-responsive genes. The network through which BES1 regulates the large number of target genes and the factors that modulate BES1 during stress are only beginning to be understood. In this thesis, I investigated several mechanisms that converge on BES1 to balance BR-regulated growth and stress responses. First, BES1 is degraded by selective autophagy during stress. BES1 interacts with the ubiquitin receptor protein DSK2 and is targeted to the autophagy pathway during stress via the interaction of DSK2 with ATG8, a ubiquitin-like protein directing autophagosome formation and cargo recruitment. DSK2 is phosphorylated by the GSK3-like kinase BIN2, a negative regulator in the BR pathway. BIN2 phosphorylation of DSK2 flanking its ATG8 interacting motifs (AIMs) promotes the interaction of DSK2 with ATG8, thereby targeting BES1 for degradation under stress conditions. Accordingly, loss-of-function dsk2 plants accumulate BES1, have altered global gene expression profiles, and have compromised responses to drought and fixed-carbon starvation stresses.

In addition, BES1 interacts with other TFs to coordinate growth and drought responses. RD26 is induced by drought and inhibits the activity of BES1 on target gene promoters during drought conditions. In contrast, under growth promoting conditions BES1 cooperates with a large network of TFs including WRKY46/54/70 to inhibit drought responses, thereby enabling BR-regulated growth. To more fully characterize the BR-regulatory network, we used genome-wide chromatin immunoprecipitation (ChIP), transcriptome and TF interactome datasets to identify 657 BR-related Transcription Factors (BR-TFs). We then took an integrated approach involving computational modeling, phenomics and functional genomics to study the networks through which BRs, BES1/BZR1 and BR-TFs function. Initially, 11,760 publicly available microarray datasets were used to build comprehensive gene regulatory networks (GRNs). BR-TFs are significantly enriched for BR and drought target genes in the GRNs, suggesting that these TFs function in growth and stress responses. BR-TFs were prioritized for functional studies using NEST (Network Essentiality Scoring Tool). Next, we developed BR response assays to conduct BR phenomics experiments for over 300 BR-TFs using more than 1000 knockout or overexpression lines. These studies identified numerous BR-TF mutants that displayed altered BR responses, allowing us to characterize the function of PLATZ and HMG as A/T-rich binding TFs that oppositely regulate BR-responsive gene expression. Finally, BR and drought phenomics experiments in soil-grown plants using time-lapse imaging and a robotic phenotyping system revealed that tcp mutants have increased BR-regulated growth and improved survival during drought compared to wild-type. These studies provide a paradigm for network-based discovery and characterization of hormone response pathways through the integration of genomics, network analysis and phenomics. Taken together, BES1 is emerging as a critical hub for BR-drought crosstalk, allowing plants to efficiently balance growth and stress responses.

Copyright Owner

Trevor Nolan



File Format


File Size

343 pages