Protein phosphorylation is one of the most prevalent post-translational modifications found in eukaryotic systems and serves as a key molecular mechanism by which protein function is regulated in response to environmental stimuli. The Mut9-Like Kinases (MLKs) are a plant-specific family of Ser/Thr kinases that have been linked to light, circadian, and abiotic stress signaling. Here we use quantitative phosphoproteomics in conjunction with global proteomic analysis to explore the role of the MLKs in daily protein dynamics. In the absence of MLK family kinases, proteins involved in light, circadian, and hormone signaling as well as several chromatin modifying enzymes were found to have altered phosphorylation profiles. Additionally, mlk mutant seedlings were found to have elevated glucosinolate accumulation and increased sensitivity to DNA damage. Our analysis in combination with previously reported data supports the involvement of MLKs in a diverse set of stress responses and developmental processes, suggesting that the MLKs may serve as key regulators linking environmental inputs to developmental outputs.

Quantitative Proteomics and Phosphoproteomics Supports a Role for Mut9-Like Kinases in Multiple Metabolic and Signaling Pathways in Arabidopsis