The study investigates how the regulatory protein NodD of rhizobia bacteria binds to flavonoids released by legumes at the molecular level and how these substances specifically activate it. The authors describe the spatial arrangement of the NodD binding site for flavonoids and the changes in protein shape upon binding of these molecules that lead to the activation of nod genes. They show which parts of NodD recognize different flavonoid structures and how these differences explain the specificity between plant and bacterial species. The study also details how activated NodD more efficiently binds DNA in the promoter regions of nod genes and triggers the production of Nod factors required for root tuber formation. The results provide a direct structural and functional connection between the chemical structure of the flavonoid, the conformational change of NodD and the subsequent gene activation. The authors thereby offer a precise molecular mechanism that explains how flavonoids control the initiation of symbiosis between legumes and rhizobia.