The molecular basis of the binding and specific activation of rhizobial NodD by flavonoids

The specific partnership between legumes and rhizobia relies on a chemical dialogue. Plant flavonoids activate the bacterial transcription factor NodD, which triggers production of Nod factors that are recognized by the plant. Structural studies of the <i>Pisum sativum</i> (pea) symbiont <i>Rhizobium leguminosarum</i> NodD revealed two pockets that are essential for its activation by flavonoids. Comparative studies with NodD1 of <i>Sinorhizobium medicae</i>, the symbiont of <i>Medicago truncatula</i>, revealed that this specificity is determined by the shape of the pocket and by specific amino acids. A chimeric NodD containing the flavonoid recognition residues from <i>S. medicae</i> NodD1 in the <i>R. leguminosarum</i> NodD backbone was sufficient to complement nitrogen fixation in <i>M. truncatula</i> by an <i>S. medicae nodD1</i> mutant, confirming the critical role of flavonoid recognition in host range.