Induced Genome-Wide Binding of Three Arabidopsis WRKY Transcription Factors during Early MAMP-Triggered Immunity

Abstract

During microbial-associated molecular pattern-triggered immunity (MTI), molecules derived from microbes are perceived by cell surface receptors and upon signaling to the nucleus initiate a massive transcriptional reprogramming critical to mount an appropriate host defense response. WRKY transcription factors play an important role in regulating these transcriptional processes. Here, we determined on a genome-wide scale the flg22-induced in vivo DNA binding dynamics of three of the most prominent WRKY factors, WRKY18, WRKY40, and WRKY33. The three WRKY factors each bound to more than 1000 gene loci predominantly at W-box elements, the known WRKY binding motif. Binding occurred mainly in the 500-bp promoter regions of these genes. Many of the targeted genes are involved in signal perception and transduction not only during MTI but also upon damage-associated molecular pattern-triggered immunity, providing a mechanistic link between these functionally interconnected basal defense pathways. Among the additional targets were genes involved in the production of indolic secondary metabolites and in modulating distinct plant hormone pathways. Importantly, among the targeted genes were numerous transcription factors, encoding predominantly ethylene response factors, active during early MTI, and WRKY factors, supporting the previously hypothesized existence of a WRKY subregulatory network. Transcriptional analysis revealed that WRKY18 and WRKY40 function redundantly as negative regulators of flg22-induced genes often to prevent exaggerated defense responses.

Principles and characteristics of the Arabidopsis WRKY regulatory network during early MAMP‐triggered immunity

“…From recent ChIP‐seq experiments we extracted data showing which WRKY gene promoters were targeted by the strongly flg22‐induced and highly expressed genes WRKY18 , WRKY40 and WRKY33 (Birkenbihl et al ., ). In that study complementation lines expressing HA‐tagged versions of WRKY18 , WRKY40 and WRKY33 from their own promoters in the respective knockout mutant lines were used as no high‐quality WRKY‐specific antibodies appropriate for ChIP‐seq experiments existed.…”

“…During the early interaction of Arabidopsis with the fungus B. cinerea AtWRKY33 was shown to target its own gene promoter and 18 additional WRKY gene loci (Liu et al ., ). In the case of MAMP‐triggered immunity (MTI), treatment of Arabidopsis seedlings with flg22, a peptide derived from the bacterial flagellum (Felix et al ., ), revealed binding of AtWRKY18, AtWRKY33 and AtWRKY40 to 22, 20 and 27 WRKY gene loci, respectively, within the first 2 h post‐elicitation (Birkenbihl et al ., ). Although promoter binding by these TFs at the investigated time point did not always alter target gene expression, in many cases binding was associated with either activation or repression suggesting extensive positive and negative auto‐ and cross‐regulation.…”

Expression of RSOsPR10 in rice roots is antagonistically regulated by jasmonate/ethylene and salicylic acid via the activator OsERF87 and the repressor OsWRKY76, respectively

“…Based on the results of our previous work, we presumed that SA induced some OsTGA or OsWRKY proteins to repress JA/ET‐dependent RSOsPR10 expression (Takeuchi et al., ). In fact, WRKY factors are known to function not only as positive regulators but also as negative regulators by targeting a number of defense‐related genes and regulating their expression through binding to W box(es) in their promoters (Birkenbihl, Kracher, & Somssich, ; Liu, Chen, et al., ). As shown in Figures and , the 3‐kb promoter region closely mimicked the in vivo expression pattern of RSOsPR10, that is, JA/ET induction, SA suppression, and root‐specific expression.…”

Reactive oxygen species dosage in Arabidopsis chloroplasts can improve resistance towards Colletotrichum higginsianum by the induction of WRKY33

“…By contrast, the chromatin immunoprecipitation study by Birkenbihl et al . () identified a total of 1100 genes (i.e. < 4% of the Arabidopsis genome) as being WRKY33 targets.…”