In the Medicago truncatula/Sinorhizobium meliloti symbiosis, the plant undergoes a series of developmental changes simultaneously, creating a root nodule and allowing bacterial entry and differentiation. Our studies of plant genes reveal novel transcriptional regulation during the establishment of the symbiosis and identify molecular markers that distinguish classes of plant and bacterial symbiotic mutants. We have identified three symbiotically regulated plant genes encoding a ,1-3 endoglucanase (MtBGLU1), a lectin (MtLEC4), and a cysteine-containing protein (MtN31). MtBGLU1 is down-regulated in the plant 24 h after exposure to the bacterial signal, Nod factor. The non-nodulating plant mutant dmi1 is defective in the ability to down-regulate MtBGLU1. MtLEC4 and MtN31 are induced 1 and 2 weeks after bacterial inoculation, respectively. We examined the regulation of these two genes and three previously identified genes (MtCAM1, ENOD2, and MtLB1) in plant symbiotic mutants and wild-type plants inoculated with bacterial symbiotic mutants. Plant (bit1, rit1, and Mtsym1) and bacterial (exoA and exoH) mutants with defects in the initial stages of invasion are unable to induce MtLEC4, MtN31, MtCAM1, ENOD2, and MtLB1. Bacterial mutants (fixJ and nifD) and a subset of plant mutants (dnf2, dnf3, dnf4, dnf6, and dnf7) defective for nitrogen fixation induce the above genes. The bacA bacterial mutant, which senesces upon deposition into plant cells, and two plant mutants with defects in nitrogen fixation (dnf1 and dnf5) induce MtLEC4 and ENOD2 but not MtN31, MtCAM1, or MtLB1. These data suggest the presence of at least three transcriptionally distinct developmental stages during invasion of M. truncatula by S. meliloti.The two partners in the legume-Rhizobium symbiosis navigate a complex developmental pathway, resulting in the formation of a plant-derived root nodule in which bacteria reside and reduce molecular nitrogen for use by the plant. Nodulation initiates with chemical signaling between the plant and the bacteria; the plant secretes flavonoid molecules into the rhizosphere, and the bacteria respond with lipochitooligosaccharide signaling molecules termed Nod factors (Long, 1996). The plant responds to bacterial Nod factors by initiating cortical cell divisions to build the nodule. Rhizobia enter the plant through a tubular plant-derived structure constructed in the root hair termed the infection thread (Bauer, 1981). Once the infection thread reaches the inner cortical cells of the plant, the bacteria are released into the plant cell, encapsulated in plant membranes. Within these symbiosomes, the bacteria differentiate into bacteroids that in the presence of low oxygen tension express the proteins necessary to reduce molecular nitrogen into ammonia for transport to the plant (Oke and Long, 1999b).Bacterial mutants have revealed distinct developmental signals and stages in the progression of the symbiosis. Bacterial mutants that cannot provoke the cell divisions necessary for nodule formation (Nod Ϫ ) have defects in...