Background: Drought is a natural hazard that affects crops by inducing water stress. Water stress, induced by drought, accounts for more loss in crop yield than all the other causes combined. With the increasing frequency and intensity of droughts worldwide, it is essential to develop drought-resistant crops to ensure food security. In this paper, we model multiple drought signaling pathways in Arabidopsis using Bayesian networks to identify potential regulators of drought-responsive reporter genes. Genetically intervening at these regulators can help develop drought-resistant crops.Result: We create the Bayesian network model from the biological literature and determine its parameters from publicly available data. We conduct inference on this model using a stochastic simulation technique known as likelihood weighting to determine the best regulators of drought-responsive reporter genes. Our analysis reveals that activating MYC2 or inhibiting ATAF1 are the best single node intervention strategies to regulate the drought-responsive reporter genes. Additionally, we observe simultaneously activating MYC2 and inhibiting ATAF1 is a better strategy.Conclusion: The Bayesian network model indicated that MYC2 and ATAF1 are possible regulators of the drought response. Validation experiments showed that ATAF1 negatively regulated the drought response. Thus intervening at ATAF1 has the potential to create drought-resistant crops.

Drought is a natural hazard that affects crops by inducing water stress. Water stress, induced by drought, accounts for more loss in crop yield than all the other causes combined. With the increasing frequency and intensity of droughts worldwide, it is essential to develop drought-resistant crops to ensure food security. In this paper, we model multiple drought signaling pathways in Arabidopsis using Bayesian networks to identify potential regulators of drought-responsive reporter genes. Genetically intervening at these regulators can help develop drought-resistant crops. We create the Bayesian network model from the biological literature and determine its parameters from publicly available data. We conduct inference on this model using a stochastic simulation technique known as likelihood weighting to determine the best regulators of drought-responsive reporter genes. Our analysis reveals that activating MYC2 or inhibiting ATAF1 are the best single node intervention strategies to regulate the drought-responsive reporter genes. Additionally, we observe simultaneously activating MYC2 and inhibiting ATAF1 is a better strategy. The Bayesian network model indicated that MYC2 and ATAF1 are possible regulators of the drought response. Validation experiments showed that ATAF1 negatively regulated the drought response. Thus intervening at ATAF1 has the potential to create drought-resistant crops.

Innate immune responses are initiated by recognition of pathogen-associated molecular patterns (PAMPs) via pattern recognition receptors (PRRs) in both animals and plants. In animal, perception of bacteria flagellin by TLR5 transduces signal through MyD88-IRAK1-IRAK4 to ubiquitin E3 ligase TRAF6. TRAF6 coordinates with UBC13 to produce K63-linked polyubiquitination chains serving as scaffold to mediate downstream signaling. In plant, flagellin is recognized by receptor-like kinase FLS2 and co-receptor BAK1. Upon flagellin perception, BAK1 directly phosphorylates an IRAK-like cytoplasmic kinase BIK1, leading to BIK1 dissociation from the FLS2-BAK1 complex to relay signal. How BIK1 activation is regulated and how it transduces signal to downstream remain largely elusive. We report here that flagellin perception triggers rapid monoubiquitination of BIK1 in planta. Time course and mutational analysis suggested that flagellin-induced BIK1 phosphorylation precedes its monoubiquitination. Using a yeast-two-hybrid screen we identified a RING type E3 ligase LUCKY that interacts with BIK1 and monoubiquitinates multiple residues of BIK1. Mass spectrometry analysis of in vitro-ubiquitinated BIK1 revealed nine lysine residues and the BIK19KR mutant with all nine lysine-to-arginine substitutions blocked flagellin-triggered BIK1 ubiquitination. Transgenic complementation assays indicated that BIK19KR was unable to execute normal BIK1 functions. Moreover, we found that monoubiquitination of BIK1 controls ligand-induced BIK1 dissociation from receptor FLS2. Our study revealed that the ligand-induced monoubiquitination of a key PRR complex component positively regulates innate immunity.