Masters of perception: phosphorylation-dependent signaling in plants

Plants are masters of perception, reacting to a myriad of biochemical and physical cues in a constantly changing environment. Plants rely on local cell-based signal processing to perceive and react sufficiently fast to a multitude of stimuli. The ability to respond quickly is crucial for sustaining growth, defense, and metabolism and thereby the ability to survive challenges associated with pathogens, resource limitations, environmental fluctuations, and mechanical perturbations. Protein phosphorylation networks are prominent in mediating these fast responses, shaping the cellular response. In the past decade, plant sciences have moved our understanding of these networks further; however, current understanding is largely limited to minutes- and hour-long timescales, and hardly illuminates the (sub-)second timescales at which the initial signaling processes take place. In this Tansley insight, we discuss how quantitative mass spectrometry-based phosphoproteomics can be utilized to study the rapid and dynamic initial steps of protein phosphorylation networks in plants. We highlight rapid responses and show how bioinformatic approaches and the integration of other proteomics approaches can be utilized to deconvolve phosphorylation-based signaling in a data-driven approach. We offer an outlook on how to experimentally address rapid signaling and hope to inspire new approaches in the study of phosphorylation-dependent plant signaling networks.