Abstract
BACKGROUND: Cyclin-dependent kinases (CDKs) critically regulate plant cell cycle transitions, including mitosis-to-endoreduplication switches essential for growth and adaptation. In Medicago truncatula, nodules form through symbiotic nitrogen fixation with rhizobia. The terminal differentiation of bacteroids within nodule cells is critical for efficient nitrogen fixation. To maintain and optimize the functionality of these differentiated symbiosomes, host nodule cells undergo repeated rounds of endoreduplication. However, which CDKs are involved in regulating endoreduplication in nodule cells to support effective symbiotic nitrogen fixation remains largely unknown. RESULTS: We identified and characterized 29 CDK genes (15 CDKs and 14 CDKLs) classified into eight conserved subgroups. These genes displayed diverse exon/intron structures and protein motifs, with CDKA, CDKB, and CDKL subfamilies showing strong conservation with Arabidopsis thaliana. Expression analysis revealed specific downregulation of CDKB1;1, CDKB2;2, and CDKL13 in nodule infection to fixation zones. Protein-protein interaction (PPI) network and Gene ontology (GO) analyses demonstrated CDKB1;1 and CDKB2;2 involvement in cell cycle regulation. Overexpression of CDKB1;1 or CDKB2;2 disrupted endoreduplication and nitrogen fixation, with CDKB1;1 having the most pronounced effect, while CDKL13 appeared dispensable for symbiosis. CONCLUSION: Our study presents the comprehensive genome-wide analysis of the CDK gene family in M. truncatula, demonstrating that the essential role of CDKB1;1 and CDKB2;2 downregulation in symbiotic nitrogen fixation and endoreduplication offers new insights into cell cycle regulation in nodules. It also identifies potential targets for improving nitrogen fixation efficiency in legumes.