Auxin has a profound impact on plant physiology and participates in almost all aspects of plant development processes. Auxin exerts profound pleiotropic effects on plant growth and differentiation by regulating the auxin response genes’ expressions. The classical auxin reaction is usually mediated by auxin response factors (ARFs), which bind to the auxin response element (AuxRE) in the promoter region of the target gene. Experiments have generated only a limited number of plant genes with well-characterized functions. It is still unknown how many genes respond to exogenous auxin treatment. An economical and effective method was proposed for the genome-wide discovery of genes responsive to auxin in a model plant, Arabidopsis thaliana (A. thaliana). Our method relies on cis-regulatory-element-based targeted gene finding across different promoters in a genome. We first exploit and analyze auxin-specific cis-regulatory elements for the transcription of the target genes, and then identify putative auxin responsive genes whose promoters contain the elements in the collection of over 25,800 promoters in the A. thaliana genome. Evaluating our result by comparing with a published database and the literature, we found that this method has an accuracy rate of 65.2% (309/474) for predicting candidate genes responsive to auxin. Chromosome distribution and annotation of the putative auxin-responsive genes predicted here were also mined. The results can markedly decrease the number of identified but merely potential auxin target genes and also provide useful clues for improving the annotation of gene that lack functional information.

The mitogen-activated protein kinase (MAPK) cascade constitutes a core component of signal transduction pathways in eukaryotic organisms. With its precise, efficient, and specific mechanism of action, this cascade pathway integrates, amplifies, and rapidly transmits signals. Among them, the specificity and functional diversity of the MPK3 cascade depend on the phosphorylation interaction between MKK and MPK3, as well as the specific interaction between MPK3 and its substrates. MPK3 targets an extremely diverse array of substrates, including transcription factors, RNA-binding proteins, enzymes, and transporters. The summary of the regulatory role of the MPK3 signal mainly focuses on three functional mechanisms: The most well-known regulatory mechanism is to recognize and phosphorylate substrate proteins or transcription factors, thereby affecting the stability and transcriptional activity of downstream substrates, and thus regulating the transcriptional regulatory activity and expression of downstream genes. MPK3 can also participate in downstream functional regulation by triggering the MAPKKK-MKK4/5-MPK3/6 signaling pathways or feedback mechanisms. MPK3 can exert regulatory effects independently or together with MPK6. The redundancy of the MPK3/6 function is related to the synergistic effect of the component cascade reaction, as well as the dose-dependent activation effect. This article presents a comprehensive synthesis of the latest research progress on the regulatory role of MPK3, in plant growth, development, and stress adaptation and defence. Moreover, it provides critical evaluations and forward-looking perspectives on the future investigation of the underlying molecular mechanisms governing MPK3-mediated regulation.