The white lupin CCR1 receptor-like kinase controls systemic Autoregulation of Cluster Root and Nodule Development

Laurence Marquès, Fanchon Divol, Alexandra Boultif, Fanny Garcia, Alexandre Soriano, Cléa Maurines-     Carboneill, Virginia Fernandez, Inge Verstraeten, Hélène Pidon, Esther Izquierdo, Bárbara Hufnagel, and Benjamin Péret

PNAS May 22, 2025; 122 (21) e2418411122; https://doi.org/10.1073/pnas.2418411122

Significance

Plants adapt root and shoot development to environmental cues through systemic signaling pathways. In white lupin (Lupinus albus), we identified mutants with excessive cluster roots that also exhibited hypernodulation. The responsible gene, LalbCCR1, encodes a leucine-rich-repeat receptor-like kinase (LRR-RLK), an orthologue of the HAR1/SUNN/NARK receptors central to Autoregulation of Nodulation (AoN). This gene regulates nodule formation and cluster root development via the NIN/LBD16-NFYA module. This mechanism, termed Autoregulation of Cluster Root and Nodule Development (AoDev), highlights the pivotal role of a single LRR-RLK in orchestrating nodulation and cluster root formation, providing a unified framework linking systemic signaling to coordinated root organogenesis.

Abstract

Root development is tightly regulated in plants to optimize nutrient acquisition and interactions with soil microorganisms. In legumes, the Autoregulation of Nodulation (AoN) pathway systemically controls the proliferation of root nodules, which are energy-intensive organs. Mutations affecting the AoN pathway result in a hypernodulation phenotype accompanied by altered root development. However, it remains unclear whether this modification of root development is also systemic and coordinated with nodulation. In this study, we report the identification of the constitutive cluster root 1 (ccr1) mutant in white lupin (Lupinus albus), which exhibits constitutive production of an excessive number of cluster roots. We demonstrate that CCR1 is an ortholog of HAR1/SUNN/NARK leucin-rich repeat-receptor like kinases (LRR-RLKs), which are key regulators of the AoN pathway. Furthermore, we show that CCR1 negatively regulates both nodule and cluster root development. Interspecific grafting experiments between white and narrow-leaved lupin (Lupinus angustifolius), a species incapable of producing cluster roots, show that ccr1 shoots can induce the formation of cluster-like roots in narrow-leaved lupin rootstocks. This highlights the conservation of a CCR1-dependent signaling cascade. Transcriptome analyses reveal that CCR1 targets the conserved NIN/LBD16-NFYA regulatory module, which connects nodule and lateral root development through a shared inhibitory systemic pathway. We propose that this pathway represents a broader developmental control mechanism of root organogenesis, termed Autoregulation of Cluster Root and Nodule Development (AoDev).

See https://www.pnas.org/doi/10.1073/pnas.2418411122

Figure 1. Phenotypes of the four allelic ccr1 mutants. (A) Representative images of the upper part of the root system from 20-d-old wild-type (WT) and the four ccr1 mutant plants grown on either phosphate-rich medium (+P) or phosphate-deficient medium (−P). (Scale bar, 1 cm.) (B) Quantitative analysis of various root traits in wild-type (WT) and ccr1 mutant plants, including CR abundance within the upper 10 cm of the root systems, maximum lateral root length, and root system dry weight. Statistical analysis was performed using two-way ANOVA with Tuckey correction, P < 0.05. (C) Apotome imaging of a CR section from the ems5 mutant compared to wild-type (WT) plants. DAPI staining revealed rootlet primordia, identifiable by their small nuclei. (Scale bar, 100 µm.) (D) Density distribution of rootlets along 1 cm of cluster root in the ems5 mutant. Statistical analysis was performed using two-way ANOVA with Tuckey correction, n = 8, P < 0.05.