Unraveling the mystery of Nod factor signaling by a genomic approach in Medicago trunactula

The availability of reduced nitrogen and phosphate are limiting factors in the productivity of many terrestrial ecosystems. The majority of land plants increase phosphate nutrition by developing intimate associations with beneficial mycorrhizal fungi. Legumes are unusual among plants because they also establish a symbiosis with nitrogen-fixing bacteria, known generally as rhizobia. A high level of host specificity characterizes symbiotic nitrogen fixation, but such specificity is not observed in mycorrhizal associations. Nevertheless, genetic analyses suggest that a common signaling pathway underlies rhizobial and mycorrhizal associations (1, 2). Until recently, the molecular nature of the plant symbiosis signaling pathway was unknown, but a spate of articles, including the report by Mitra et al. (3) in this issue of PNAS, have begun to unravel this mystery. The dmi3 gene of Medicago truncatula described by Mitra et al. is necessary for both rhizobial and mycorrhizal interactions and is predicted to encode a calcium- and calmodulin-dependent protein kinase. The homology of DMI3 to calcium-regulated proteins is particularly intriguing, because oscillations in intracellular calcium are a well characterized and specific response to the Nod factor ligand produced by symbiotic rhizobia (4). By analogy to mammalian CaM kinase II (5), DMI3 may function to interpret and transduce intracellular calcium oscillations to pathways for symbiotic development. But the article by Mitra et al. is equally important for another reason, namely, the means by which dmi3 was identified. dmi3 was uncovered in a transcriptional profiling experiment wherein the candidate gene was revealed as an expression-level polymorphism between mutant and wild-type plants. Mitra et al. demonstrate the application of transcript-based cloning to large and complex plant genomes by characterizing expression-level polymorphisms associated with the rar1-2 mutant of barley. The barley genome …