2026-01-09 中国科学院(CAS)
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- https://english.cas.cn/newsroom/research_news/life/202601/t20260109_1145515.shtml
- https://www.science.org/doi/10.1126/science.aec3061
Deciphering Symbiotic Code: Researchers Unlock “Secret Handshake” Between Legumes and Rhizobia
Editor: LIU Jia | Jan 09, 2026 Article has an altmetric score of 30
In a study published in Science on January 9, the teams of Jeremy Murray and ZHANG Yu from the Center for Excellence in Molecular Plant Sciences (CEMPS) of the Chinese Academy of Sciences, along with collaborators, have resolved, for the first time, the high-resolution crystal structure of the complex formed between the NodD protein of pea rhizobia and a flavonoid compound (hesperetin). They elucidated how NodD recognizes flavonoids and revealed key structural elements in NodD that determine the specificity of signal recognition.
In nature, root nodules formed through symbiosis between legume plants (such as soybeans and alfalfa) and rhizobia serve as highly efficient natural nitrogen fertilizer factories. Within these organs, plants provide carbon sources to rhizobia, while rhizobia convert atmospheric nitrogen into a usable form of nitrogen fertilizer for the plants. Legume roots exist in complex environments, surrounded by a multitude of rhizobia and other bacteria. How do plants allow only “compatible” rhizobia to enter their roots and form nodules?
For a long time, scientists have known that legume roots secrete a chemical signal called “flavonoids,” which is recognized by a transcription factor in the rhizobia named NodD. Although NodD was known to contribute to symbiotic specificity, how it specifically recognizes flavonoid chemical signals has remained an intriguing question.
In this study, the researchers found that the ligand-binding domain of the NodD protein from pea rhizobia recognizes hesperetin through two binding pockets: one located within a monomer of the NodD protein and the other situated at the dimer interface. This binding conformation is the first of its kind to be observed among known transcriptional regulators in the NodD family.
Further analysis indicated that NodD contains three key activation domains, along with specific critical amino acids, which collectively form a “binding pocket” that accommodates flavonoid molecules like hesperetin but not other classes of flavonoids, such as isoflavones or pterocarpans. This provides a structural explanation for why rhizobial NodD is only activated by specific flavonoids.
Furthermore, the researchers compared the NodDs from alfalfa and pea rhizobia. Despite an overall similarity of 80% between the two proteins, their “preferences” for different flavonoids are very different. Pea rhizobial NodD primarily responds to flavanones/flavones, whereas alfalfa rhizobial NodD mainly responds to chalcones.
Through domain-swapping experiments and extensive point mutation studies, the researchers identified several key amino acids located in critical activation regions. They showed that these specific amino acid residues determine the ability of the rhizobia to respond to different types of flavonoids.
So why is this specificity needed in the first place? The researchers suggested that such precise recognition stems from millions of years of co-evolution in overlapping habitats. To ensure successful partnerships, each species accurately identifies its preferred rhizobia strain through a mutual “double-lock and key” system: the bacteria recognize unique flavonoid signals from the plant and the plant recognizes specific signals in return. This prevents mix-ups when multiple species grow nearby.
This study answers the question of how legume plants and rhizobia achieve signal-specific recognition through flavonoids and NodD, and provides a new way to design efficient nitrogen fixation systems. Besides, it paves the way for designing efficient, crop-specific “tailor-made” rhizobia for enhanced nitrogen fixation, and holds the potential to extend nitrogen-fixing symbiosis to non-legume crops such as rice and corn, reducing agriculture’s reliance on chemical nitrogen fertilizers.
フラボノイドによる根粒菌NodDの結合と特異的活性化の分子基盤 The molecular basis of the binding and specific activation of rhizobial NodD by flavonoids
Yiting Ruan, Shangzhi Dong, Suyu Jiang, Yisheng Wang, […] , and Jeremy D. Murray
Science Published:8 Jan 2026
DOI:https://doi.org/10.1126/science.aec3061
Editor’s summary
Legume plants such as pea and alfalfa form an ecologically and agriculturally important symbiotic relationship with nitrogen-fixing soil bacteria called rhizobia. This interaction begins when the plant releases specific flavonoids into the soil that are selectively recognized by its symbiotic partners. The bacteria perceive these signals and produce a countersignal, initiating a chemical dialogue. This communication allows the bacteria to enter the plant’s roots and provide fixed nitrogen, showcasing a highly specific form of plant-microbe communication. Ruan et al. describe the molecular basis of how the rhizobia are able to discriminate between different flavonoids to recognize the appropriate host. —Stella M. Hurtley
Abstract
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 Pisum sativum (pea) symbiont Rhizobium leguminosarum NodD revealed two pockets that are essential for its activation by flavonoids. Comparative studies with NodD1 of Sinorhizobium medicae, the symbiont of Medicago truncatula, 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 S. medicae NodD1 in the R. leguminosarum NodD backbone was sufficient to complement nitrogen fixation in M. truncatula by an S. medicae nodD1 mutant, confirming the critical role of flavonoid recognition in host range.
