Spatiotemporal regulation of arbuscular mycorrhizal symbiosis at cellular resolution [RNA-seq]

ABSTRACT: Arbuscular mycorrhizal (AM) symbiosis develops through successive colonization of root epidermal and cortical cells, culminating in the formation of arbuscules, tree-like intracellular structures that are transient yet essential sites of nutrient exchange. To dissect the cellular and structural complexity of AM establishment in rice roots colonized by Rhizophagus irregularis, we applied dual-species spatial transcriptomics to simultaneously monitor plant and fungal gene expression at single-cell resolution. This approach revealed surprising differences in transcriptional activity between fungal structures and showed that morphologically similar arbuscules can be transcriptionally distinct. These findings suggest hidden functional diversity among arbuscules, indicating that nutrient exchange is not uniform but finely modulated across individual structures. Because arbuscules form and degenerate within only a few days, we further sought to capture translational regulation across their life span. We pioneered AM-inducible TRAP-seq (Translating Ribosome Affinity Purification followed by RNA-seq) using stage-specific promoters, enabling cell-type- and stage-resolved profiling for the first time in AM symbiosis. This revealed extensive spatiotemporal reprogramming of nutrient transport and signaling, with distinct sets of phosphate, nitrogen, and carbon transporters and regulators upregulated or repressed at different stages of arbuscule development, suggesting that nutrient exchange is dynamically regulated across the arbuscule life cycle. More broadly, cell wall biosynthesis genes and key defence markers were suppressed during arbuscule formation, whereas upon collapse, defence markers were strongly upregulated, suggesting a host-driven shift towards symbiosis termination. Together, these findings highlight the nuanced and dynamic regulation of AM symbiosis at cellular resolution, refining our understanding of how nutrient exchange and fungal development are coordinated in space and time, and providing a framework for further functional exploration.

ORGANISM(S): Oryza sativa

PROVIDER: GSE308140 | GEO | 2026/04/27

REPOSITORIES: GEO