Symbiotic associations between legumes and rhizobia usually commence with the perception of bacterial lipochitooligosaccharides, known as Nod factors (NF), which triggers rapid cellular and molecular responses in host plants. We report here deep untargeted tandem mass spectrometry-based measurements of rapid NF-induced changes in the phosphorylation status of 13,506 phosphosites in 7739 proteins from the model legume Medicago truncatula. To place these phosphorylation changes within a biological context, quantitative phosphoproteomic and RNA measurements in wild-type plants were compared with those observed in mutants, one defective in NF perception (nfp) and one defective in downstream signal transduction events (dmi3). Our study quantified the early phosphorylation and transcription dynamics that are specifically associated with NF-signaling, confirmed a dmi3-mediated feedback loop in the pathway, and suggested "cryptic" NF-signaling pathways, some of them being also involved in the response to symbiotic arbuscular mycorrhizal fungi. Legumes have the ability to form a very efficient symbiotic association with rhizobia to meet their nitrogen demand. This results in root nodule formation, inside which the rhizobia can fix atmospheric nitrogen efficiently and transfer it to the plants, in exchange for a carbon source. This interaction is often characterized by a high level of host specificity and generally requires an exchange of diffusible signals between legumes and rhizobia. Flavonoids and isoflavonoids present in the legume root exudates induce the expression of nod genes in rhizobia, and are responsible for the production and secretion of bacterial lipochitooligosaccharides (LCOs), known as Nod factors (NF) 1 (1, 2). NF are generally required for rhizobial infection and nodule development. Mere application of purified NF at low concentrations (10 Ϫ8 to 10 Ϫ12 M) is sufficient to trigger responses in host plants similar to those elicited by the rhizobia themselves (2, 3). Responses are elicited in root cells within a few seconds to minutes after NF application and include changes in ion fluxes across the plasma membrane, as well as accumulation of reactive oxygen species (4, 5). After 15-20 min, oscillations of the nuclear and perinuclear calcium concentration (calcium spiking) are initiated and trigger the expression of early nodulin genes (3). Within the first hour, legume root hairs undergo a cytoplasmic disorganization ,which leads to a transient swelling (6), followed by root hair deformations (7).Forward and reverse genetic approaches, in the model legumes Medicago truncatula (Medicago) and Lotus japonicus (Lotus), have identified several components controlling these events (Fig. 1). NF are perceived with high specificity by LysM receptor-like kinases residing on the plasma membrane. These kinases include nod factor perception (NFP), an essential component of a signaling receptor necessary for early responses to NF and rhizobial infection (8, 9). Mutants in NFP are affected in all known cellular respons...