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

T he 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 calciumand 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 wildtype 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 is nearly twice the size of the human genome and 10 times the size of the M. truncatula genome, suggesting that transcript-based cloning may be a powerful tool for functional genomics in a range of biological systems. A Long-Standing Question One of the classic conundrums in plant biology has been the molecular basis of host specificity in the Rhizobium–legume symbiosis. This subterranean rendezvous between otherwise saprophytic bacteria and the roots of legume plants results in the dramatic transformation of each partner. The end product is a unique plant organ that provides the context for a fine-tuned metabolic collaboration, wherein atmospheric dinitrogen is converted into biologically useful organic nitrogen. Beyond its importance as a major source of reduced nitrogen in both agricultural and natural ecosystems, the Rhizobium–legume symbiosis involves a cross-kingdom molecular dialogue that has fascinated plant biologists