Nitrogen is essential for plant growth and development, and many land plants have evolved symbioses with nitrogen-fixing bacteria. One such symbiosis, the root nodule symbiosis (RNS), is characterized by the intracellular accommodation of bacteria in lateral organs called nodules. The occurrence of RNS is restricted to a specific clade of angiosperms, and it was previously hypothesized that a genetic change, or 'predisposition', in the last common ancestor of this clade enabled the evolution of RNS. However, the precise nature of this key event remained a mystery.
In this study, we discovered a novel cis-regulatory element, Predisposition Associated cis-regulatory Element (PACE), which is present in the promoters of the Nodule Inception (NIN) gene in all nodulating species within the FaFaCuRo clade. PACE is necessary and sufficient for the activation of the NIN promoter by the transcription factor Cyclops, and it drives the expression of NIN during infection thread development in the root cortex. The acquisition of PACE by the last common ancestor of the FaFaCuRo clade enabled cortical infection threads and thus laid the foundation for the evolution of RNS. Furthermore, the loss of PACE is associated with the loss of RNS, highlighting its essential role in the gain and loss of this symbiosis.
Our findings provide new insights into the evolutionary origins of RNS and the role of cis-regulatory elements in driving the development of novel traits. The discovery of PACE highlights the importance of gene regulation in shaping the evolution of complex traits and the potential for further exploration of cis-regulatory elements in other biological systems.
