SILAB Anglais

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TEAM SILAB / Florian Frugier

Presentation

Signaling pathways regulating Legume root system Architecture through Beneficial bacteria

SiLAB’s scientific project deals with the interactions between plant root systems and beneficial bacteria. This includes both nitrogen-fixing bacteria, collectively called rhizobia, which interact with legume plants to form a new symbiotic organ, the root nodule; and plant growth-promoting bacteria, especially those that are endophytes of legume nodules.

Our research aims to understand how the host plant regulates these beneficial interactions, particularly in relation to mineral nitrogen availability. This involves: 1) local signaling pathways in roots that enable the perception and recognition of these bacteria as beneficial and to modulate their entry depending on local mineral nitrogen availability; and 2) long distance systemic pathways acting between roots and shoots to integrate plant nutritional needs.

The regulatory pathways analyzed involve peptide and non-peptide hormones, with a focus on CLE and CEP signaling peptide families, as well as on cytokinin, gibberellin, and ethylene hormones. We also emphasize the integration of chromatin and transcriptional regulations linked to nutritional and hormonal signals related to these beneficial plant-microbe interactions.

More broadly, in the context of climate change, we aim to understand, how other mineral nutrients environmental cues, such as carbon or phosphate, integrate with these beneficial bacteria and nitrogen-related systemic regulatory pathways. We also explore how these plant-beneficial bacteria interactions modulate root system architecture (root growth and branching) and root cell-type differentiation, as well as environmental stress responses and notably the systemic priming of plant defense.

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Publications

2026
Fonouni-Farde, C., Ma, X., Sánchez-Rodríguez, F., Latrasse, D., Brik-Chaouche, R., Ferrero, L., Daviddi, N., He, X., Wang, Q., Brault, M., Tan, S., Laffont, C., Tian, Y., Clappe, C., Ma, X., Lelandais, C., Ariel, F., Crespi, M., Benhamed, M., and Frugier, F. (2026). Three-dimensional genome reorganization enables cytokinin activation of NODULE INCEPTION during symbiotic nodulation. Plant Commun., in press (doi: 10.1016/j.xplc.2026.101986)
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2026
Lopez-Raez, J.A., Banasiak, J., Becana, M., Goormachtig, S., Lanfranco, L., Larrainzar, E., Lefebvre, B., Veneault-Fourrey, C., and Frugier, F. (2026). Molecular mechanisms modulating beneficial plant root-microbe interactions: What's common? Plant Commun., 7(1):101592
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2026
Teyssendier de la Serve, J., Gautrat, P., and Frugier F. (2026). Signaling peptides at the crossroad of root endosymbioses. Trends Plant Sci., 31(6):830-840.
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2026
Velandia K., Correa-Lozano, A., Tomkinson, A., Boivin, S., François, T., Dalmais, M., Klein, A., Le Signor, C., Bendahmane, A., Frugier, F., Reid, J.B., and Foo, E. (2026). The cytokinin histidine kinase receptors regulate nodulation, shoot and root development in Pisum sativum. Front. Plant Sci. 17:1750990. Front. Plant Sci. 17:1750990.
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2025
Teyssendier de la Serve, J., Gautrat, P., Laffont, C., Lesterps, Z., Huault, E., Guerard, F., San Clemente, H., Aguilar, M., Bensmihen, S., Gakière, B., Frei-dit-Frey, N., and Frugier, F. (2025). The sTDIF signaling peptide modulates the root stele diameter and primary metabolism to accommodate symbiotic nodulation. Current Biol., 35(18):4337-4348.e4.
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2024
Argirò, L., Laffont, C., Moreau, C., Moreau, C., Su, Y., Pervent, M., Parrinello, H., Blein, T., Kohlen, W., Lepetit, M., and Frugier, F. (2024). The Compact Root Architecture 2 systemic pathway is required for the repression of cytokinins and miR399 accumulation in Medicago truncatula N-limited plants. J. Exp. Bot., 75(18):5667-5680
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2024
Gao, J.P., Su, Y., Jiang, S., Liang, W., Lou, Z., Frugier, F., Xu, P., and Murray, J.D. (2024). Applying conventional and cell-type-specific CRISPR/Cas9 genome editing in legume plants. aBIOTECH, s42994-024-00190-4.
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2024
Laffont, C., and Frugier, F. (2024). Rhizobium symbiotic efficiency meets CEP signaling peptides. New Phytol., 241(1):24-27.
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2024
Pedinotti, L., Teyssendier de la Serve, J., Roudaire, T., San Clemente, H., Aguilar, M., Kohlen, W., Frugier*, F., and Frei dit Frey*, N. (2024). The CEP peptide-CRA2 receptor module promotes arbuscular mycorrhizal symbiosis. Current Biol., 34 (22):5366-5373. (*, co-corresponding authors)
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Collaborations

Ongoing Projects

Projet ANR : Determinate « Evolution and function of symbiotic nodule determinacy in legume plants » (2026-2029). Partenaire: Jean-Malo Couzigou (LRSV-Toulouse).

Projet ANR : CLIPS « CEP, CLE, and IDA peptides at the crossroad of Parasitic and Symbiotic interactions » (2026-2029). Partenaire: Nicolas Frei-dit-Frey (LRSV-Toulouse).

Projet ANR : Insider « Understanding how symbiotic signals from rhizobium reprogram inner root tissues related to nutrition » (2025-2028). Partenaire : Sandra Bensmihen (LIPME, Toulouse).

Projet ANR : SymBase « Deciphering how symbiotic infection is triggered in lateral root base nodulated legumes » (2025-2028). Partenaires : Jean-François Arrighi (PHIM, Montpellier), Fernanda de Carvalho-Niebel (LIPME, Toulouse).

Projet ANR : OPTILEG « Optimization of microbial interactions for sustainable production of legume proteins, beneficial for the environment and health » (2024-2029). En collaboration avec 9 partenaires.

Projet ANR : CytoSYM « Understanding how a cytokinin signaling transcription factor can control both positively and negatively symbiotic nodulation » (2023-2027). Partenaire : M. Benhamed (IPS2, Gif-sur-Yvette).

Past Projects

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Projet ANR : SymbiSIL «Legume–rhizobia siRNA-mediated communication in symbiosis » (2022-2026). Partenaires : C. Lelandais (IPS2, Gif-sur-Yvette, France), L. Navarro (IBENS, Paris).

Projet ANR : SYMPA-PEP «Symbiotic & pathogenic peptides at the interface between plants and microorganisms » (2021-2025). Partenaires : N. Frei dit Frey (LRSV, Toulouse), B. Favery (ISA, Sophia-Antipolis).

Projet ANR : PIOSYM « Understanding the mode of action of a pioneer transcription factor during symbiotic nodule development » (2020-2023). Partenaires : A. Niebel (LIPM, Toulouse), M. Crespi et M. Benhamed (IPS2, Gif-sur-Yvette).

Projet ANR : PSYCHE « Plant systemic responses to changing root environments » (2017-2021). Partenaires : M. Lepetit (LSTM, Montpellier), C. Jacquet (LRSV, Toulouse).

Projet collaboratif UE (H2020-SFS-2016-2017) : EUCLEG « Breeding forage and grain legumes to increase EU’s and China’s protein self-sufficiency » (2017-2021). Partenaires : 11 Instituts/Universités françaises et 5 chinoises.

Projet ANR : STAYPINK « Mechanisms controlling the transition between nitrogen fixation and senescence in legume symbiotic nodules » (2016-2020). Partenaires : C. Bruand (LIPM-Toulouse), P. Frendo (ISA, Sophia-Antipolis).

Projet ANR : NodCCAAT « Understanding the mode of action of the symbiosis-specific NF-YA1 transcription factor in Medicago truncatula » (2016-2019). Partenaires : A. Niebel (LIPM, Toulouse), M. Crespi et M. Benhamed (IPS2, Gif-sur-Yvette).

Projet collaboratif UE (FP7-KBBE-2011-5. KBBE.2011.1.1-02) : ABSTRESS « Improving the resistance of legume crops to combined abiotic and biotic stress » (2012-2017). Partenaires : FERA (The Food and Environment Research Agency, UK), ESSEX (The University of Essex, Royaume-Uni), ABER (The University of Aberystwyth, Royaume-Uni), INRA-Dijon (France), ABC (Agricultural Biotechnology Centre, Hongrie), CSIC-Cordoba (Espagne), GenXPro (Allemagne), Arterra Bioscience (Italie), PGRO (Processors and Growers Research Organization, Royaume-Uni), AGRO (Agrovegetal, Espagne), AGRITEC (République Tchèque).

Projet ANR-Blanc International (Hongrie/France) : LEGUMICS « Expanding the genomic tools for legumes and demonstrating their power in roots and symbiotic nodule development studies » (2011-2014). Partenaires : P. Kalo (ABC, Gödöllö, Hongrie), G. Endre (BRC, Szeged, Hongrie), A. Kereszt, (BAYGEN, Szeged, Hongrie), P. Ratet (ISV-CNRS, Gif-sur-Yvette).

Projet ANR-“Plant KBBE” (Allemagne/Espagne/France) : ROOT « Root enhancement for crop improvement » (2010-2013). Partenaires : T. Schmülling (FUB, Berlin, Allemagne), A. Leyva (CNB-CSIC, Madrid, Espagne), P. Nacry (BPMP-INRA, Montpellier), M. Crespi (ISV-CNRS, Gif-sur-Yvette), A. Walter (ICG, Berlin, Allemagne), J. Weyen (SURL, Leopoldshöhe, Allemagne).

Projet bilatéral CNR-CNRS Italie-France : « Role of KNAT transcription factors in root and nodule development » (2010-2014). Partenaires : G. Frugis (CNR, Rome, Italie).

Projet ANR-Jeune Chercheur : LEGUROOT « Cytokinin signaling and legume root architecture under symbiotic and non-symbiotic conditions » (2009-2012).

Projet ANR-OGM : DIAGNOGENE « Control of epigenetic inactivation of transgenes and diagnostic instability of gene expression » (2006-2010). Partenaires : H. Vaucheret (INRA, Versailles).

Projet ECOS-Sud : « Involvement of transcription factors in the regulation of salt stress responses in M. truncatula » (2007-2010). Partenaires : R. Chan (University of Santa Fe, Argentine).

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