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The SIX team seeks to shed light on the molecular mechanisms allowing the adaptation of phytopathogenic bacteria to their hosts with the long-term objective of proposing strategies to fight against plant diseases.

Our work is focused on the phytopathogenic bacteria Xanthomonas campestris pv. campestris (Xcc), the causative agent of black rot in Brassicaceae. This bacterium infects plants of agronomic interest such as cabbage, broccoli or cauliflower as well as the model plant Arabidopsis thaliana.

Xcc belongs to a genus comprising 27 species which together affect more than 400 species of host plants. The genomes of several hundred strains of Xanthomonas affecting plants of agronomic interest such as rice, lemon, banana, tomato and beans are sequenced and available, making this bacterial genus interesting for comparative genomic studies.

We focus our work on three major processes controlling the interaction with the plant:

The early stages of natural entry into plant tissues via hydathodes

Type 3 Effectors (ET3) which are bacterial proteins injected into plant cells by the Type 3 Secretion System (SST3). ET3s manipulate the physiology of the host plant both to suppress immunity or to modify the physiology of the plant.

The physiological and regulatory processes allowing the adaptation of Xcc to the “plant” environment.

To carry out this work, we combine several approaches ranging from molecular biology, genetics, biochemistry, transcriptomics or genomics.


(A) Symptoms in cabbage leaf 16 days after hydathode infection with Xcc. (B) Imprint on rich medium of the underside of a cabbage leaf showing the microbial community 10 days after soaking with Xcc. Xcc colonies are present at the leaf margins. (C) Confocal microscopic visualization of GFP labeled Xcc (in green) on the surface of cabbage leaves.

Contact: Laurent NOEL

Nom equipe


Xcc and plant hydathodes: studying the rules of a first encounter

Xcc epiphytes enter the leaves via hydathodes. These organs are watery pores present at the leaf margins through which xylem sap exudes under conditions of high humidity and low transpiration. We are interested in the anatomy and physiology of this very poorly understood organ which allows direct access to the xylem vessels. We wish to characterize the structure and tissue organization of the hydathodes of several Brassicaceae as well as to identify the genes of plant immunity controlling infection at the level of hydathodes. This project will provide a better understanding of the molecular dialogue between the plant and vascular pathogens during infection. This project is carried out in collaboration with the microscopy platform of the FR3450 (Toulouse, France).




Arabidopsis hydathodes are the major entry points for Xcc. (A) Visualization of Xcc labeled with the GUS gene (in blue) 10 days after infection with hydathodes. (B) Guttation drops on the underside of an Arabidopsis leaf. (C) Hydathode observed by scanning electron microscopy. (D) Early stages of infection of a hydathode by Xcc-GUS (in blue) before the stage of vascularization.

Xanthomonas campestris Type 3 Effectors

We have studied the conservation and distribution of ET3 in different strains of Xanthomonas campestris for which genomes are available. Interestingly, we have shown that TALE (Transcription-Activator-Like Effectors) effectors are present in at least one strain of Xcc.

The mechanisms of recognition of AvrAC by the immune system of the plant having been elucidated, we are now looking for the plant targets of the other 30 Xcc effectors by direct or reverse genetic screens and by biochemical approaches (for example ANR CROpTAL project).



Recognition mechanisms of AvrAC and HopZ1a by the Arabidopsis immune system

Contact: Laurent Noël

Adaptation of Xanthomonas to the “plant” environment

The way in which bacteria adapt and behave on / in plant tissues has been little studied so far and only the major determinants of pathogenicity have been identified. We want to characterize the leaf microbiome and the impact of Xcc infection on its composition.


We also want to capture plant and bacterial co-transcriptomes during the infectious process. Last but not least, we will use a screen in planta to identify the genes that contribute to bacterial fitness during the life cycle of Xcc in the different compartments of the plant (Collaboration J. Lewis, UC Berkeley, CA). For this purpose, we develop a strategy of mutagenesis by labeled transposons.


In parallel, we are also using direct genetics and synthetic biology to study the function of multigenic families such as TonB-dependent Transporters (TBDTs). TBDTs are outer membrane transporters involved in the active and selective transport of trace nutrients such as metals, vitamins or carbohydrates. At Xcc, some TBDTs belong to CUT systems (Cabohydrate Utilization systems with TBDTs) involved in the exploitation of carbohydrates such as xylan, pectin, glycans, sucrose or other macromolecules.


The expansion of genes encoding TBDTs in Xcc reflects the adaptive potential of these systems and the contribution of some of them to fitness in planta has been shown.


(A) Impression of a cabbage leaf showing cultivable microorganisms. (B) 3D model of a TBDT of Xcc.

Contacts: Emmanuelle Lauber and Alice Boulanger

Genomic analysis of bacterial strategies used to live in association with plants: Xcc and beyond

The number of sequenced Xcc genomes has grown exponentially in recent years to several hundred. As of January 2016, there were 13 published genomes of X. campestris, 8 of them from our group. To perform association genetics and comparative genomics studies, our group sequenced 30 additional strains of Xanthomonas campestris, collected from different host plants in different regions of the world.


This work was carried out in collaboration with the Bioinformatics platform of LIPM and Anne Genissel (INRA Versailles, France). The comparative analysis of families of genes involved in the pathogenesis and / or in adaptation to the plant such as TBDTs constitutes a means of highlighting the common points and specificities of bacteria associated with plants, living on plant debris. , in aquatic environments or in the digestive system of humans or animals.

The complete sequence of Xcc genomes can be obtained by PacBio sequencing

Contact: Matthieu Arlat


  • Adam Bogdanove, Cornell University, NY

  • Jian-Min Zhou, Beijing, China

  • Jennifer Lewis, UC Berkeley, CA.

  • Anne Genissel, INRA Versailles, France

  • Richard Berthomé, Laurent Deslandes and Fabrice Roux, LIPM Toulouse, France

  • Boris Szurek & Ralf Koebnik, IRD Montpellier, France

  • Matthieu Barret, Nicolas Chen and Marie-Agnès Jacques, INRA Angers, France

  • Lionel Gagnevin and Olivier Pruvost, CIRAD Reunion, France

Ongoing funding

  • Research networks INRA SPE Department: FNX = French Network on Xanthomonads. MA Jacques, R. Koebnik, O. Pruvost and L. Noël, coordinators, 5 k € / year.

  • Generic ANR PAPTiCROPs (2016-2020) ANR-16-CE21-0005, Aptamer-based peptide interference with type III effectors for broad-spectrum and durable resistance of crop plants. R. Koebnik (IRD, Montpellier) coordinator, L. Noël (INRA, Toulouse), N. Peeters (INRA, Toulouse), JC Rain (Hybrigenics) and A. Kajava (CNRS Montpellier). € 543k (€ 110k for our group).

  • ANR NEPHRON (2018-2023) ANR-18-CE20-0020, Genetic and molecular dissection of hydathode and vascular immunity in plants. L. Noël (INRA, Toulouse) coordinator, N. Leonhardt (CEA Cadarache), P. Laufs (INRA Versailles) and L. Navarro (CNRS ENS Paris). € 760k (€ 289k for our group)

  • ANR young investigator XBOX (2019-2024) ANR-19-CE20-XXX, the making of a pathogen: How Xanthomonas adapts to plant environments. A. Boulanger, € 253k.

Thèmes de recherche
Thème 4 : Génomique
Thème 3 : Adaptation
Thème 2 : Effecteurs
Thème 1 : Hydathodes



Talbi, N., Fokkens, L., Audran, C., Petit-Houdenot, Y., Pouzet, C., Blaise, F., Gay, E. J., Rouxel, T., Balesdent, M.-H., Rep, M., & Fudal, I. (2023). The neighbouring genes AvrLm10A and AvrLm10B are part of a large multigene family of cooperating effector genes conserved in Dothideomycetes and Sordariomycetes. Molecular Plant Pathology.


Zárate-Chaves, C. A., Audran, C., Medina Culma, C. A., Escalon, A., Javegny, S., Gagnevin, L., Thomas, E., Pimparé, L.-L., López, C. E., Jacobs, J. M., Noël, L. D., Koebnik, R., Bernal, A. J., & Szurek, B. (2023). CRISPRi in Xanthomonas demonstrates functional convergence of transcription activator-like effectors in two divergent pathogens. The New Phytologist, 238(4), 1593‑1604.


You, Y., Koczyk, G., Nuc, M., Morbitzer, R., Holmes, D. R., von Roepenack-Lahaye, E., Hou, S., Giudicatti, A., Gris, C., Manavella, P. A., Noël, L. D., Krajewski, P., & Lahaye, T. (2022). The eINTACT system dissects bacterial exploitation of plant osmosignalling to enhance virulence. Nature Plants, 1‑14.


Luneau, J. S., Baudin, M., Quiroz Monnens, T., Carrère, S., Bouchez, O., Jardinaud, M.-F., Gris, C., François, J., Ray, J., Torralba, B., Arlat, M., Lewis, J. D., Lauber, E., Deutschbauer, A. M., Noël, L. D., & Boulanger, A. (2022). Genome-wide identification of fitness determinants in the Xanthomonas campestris bacterial pathogen during early stages of plant infection. The New Phytologist.


Bellenot, Caroline, Jean-Marc Routaboul, Patrick Laufs, et Laurent D. Noël. « Hydathodes ». Current Biology 32, no 14 (25 juillet 2022): R763‑64.


Bellenot, C., Carrère, S., Gris, C., Noël, L. D., & Arlat, M. (2022). Genome Sequences of 17 Strains from Eight Races of Xanthomonas campestris pv. Campestris. Microbiology Resource Announcements, 11(7), e0027922.


Luneau, J. S., Noël, L. D., Lauber, E., & Boulanger, A. (2022). A β-glucuronidase (GUS) Based Bacterial Competition Assay to Assess Fine Differencesin Fitness during Plant Infection. Bio-protocol, 12(13), e3776.


Dubrow, Zoe, Sara Carpenter, Morgan E. Carter, Ayress Grinage, Carine Gris, Emmanuelle Lauber, Jules Butchacas, et al. « Cruciferous Weed Isolates of Xanthomonas Campestris Yield Insight into Pathovar Genomic Relationships and Genetic Determinants of Host- and Tissue-Specificity ». Molecular Plant-Microbe Interactions: MPMI, 10 mai 2022.


Luneau, Julien S., Aude Cerutti, Brice Roux, Sébastien Carrère, Marie-Françoise Jardinaud, Antoine Gaillac, Carine Gris, et al. « Xanthomonas Transcriptome inside Cauliflower Hydathodes Reveals Bacterial Virulence Strategies and Physiological Adaptations at Early Infection Stages ». Molecular Plant Pathology 23, no 2 (février 2022): 159‑74.



Zhu, Xiaoyang, Julie Mazard, Eugénie Robe, Sarah Pignoly, Marielle Aguilar, Hélène San Clemente, Emmanuelle Lauber, Richard Berthomé, et Jean-Philippe Galaud. « The Same against Many: AtCML8, a Ca2+ Sensor Acting as a Positive Regulator of Defense Responses against Several Plant Pathogens ». International Journal of Molecular Sciences 22, no 19 (28 septembre 2021): 10469.



Jauneau, Alain, Aude Cerutti, Marie-Christine Auriac, et Laurent D. Noël. « Anatomy of Leaf Apical Hydathodes in Four Monocotyledon Plants of Economic and Academic Relevance ». PloS One 15, no 9 (2020): e0232566.


González-Fuente, Manuel, Sébastien Carrère, Dario Monachello, Benjamin G. Marsella, Anne-Claire Cazalé, Claudine Zischek, Raka M. Mitra, et al. « EffectorK, a Comprehensive Resource to Mine for Ralstonia, Xanthomonas, and Other Published Effector Interactors in the Arabidopsis Proteome ». Molecular Plant Pathology 21, no 10 (octobre 2020): 1257‑70.


Gluck-Thaler, Emile, Aude Cerutti, Alvaro L. Perez-Quintero, Jules Butchacas, Verónica Roman-Reyna, Vishnu Narayanan Madhavan, Deepak Shantharaj, et al. « Repeated Gain and Loss of a Single Gene Modulates the Evolution of Vascular Plant Pathogen Lifestyles ». Science Advances 6, no 46 (novembre 2020): eabc4516.


Arroyo-Velez, Noe, Manuel González-Fuente, Nemo Peeters, Emmanuelle Lauber, et Laurent D. Noël. « From Effectors to Effectomes: Are Functional Studies of Individual Effectors Enough to Decipher Plant Pathogen Infectious Strategies? » PLoS Pathogens 16, no 12 (décembre 2020): e1009059.


Cerutti, Aude, Alain Jauneau, Patrick Laufs, Nathalie Leonhardt, Martin H. Schattat, Richard Berthomé, Jean-Marc Routaboul, et Laurent D. Noël. « Mangroves in the Leaves: Anatomy, Physiology, and Immunity of Epithemal Hydathodes ». Annual Review of Phytopathology 57 (25 août 2019): 91‑116.



Denancé, Nicolas, Boris Szurek, Erin L. Doyle, Emmanuelle Lauber, Lisa Fontaine-Bodin, Sébastien Carrère, Endrick Guy, et al. « Two Ancestral Genes Shaped the Xanthomonas Campestris TAL Effector Gene Repertoire ». The New Phytologist 219, no 1 (juillet 2018): 391‑407.



Cerutti, Aude, Marie-Christine Auriac, Laurent D. Noël, et Alain Jauneau. « Histochemical Preparations to Depict the Structure of Cauliflower Leaf Hydathodes ». Bio-Protocol 7, no 20 (20 octobre 2017): e2452.


Cerutti, Aude, et Alain Jauneau. « Capturing Z-Stacked Confocal Images of Living Bacteria Entering Hydathode Pores of Cauliflower ». Bio-Protocol 7, no 20 (20 octobre 2017): e2451.


Cerutti, Aude, Alain Jauneau, Marie-Christine Auriac, Emmanuelle Lauber, Yves Martinez, Serge Chiarenza, Nathalie Leonhardt, Richard Berthomé, et Laurent D. Noël. « Immunity at Cauliflower Hydathodes Controls Systemic Infection by Xanthomonas Campestris Pv Campestris ». Plant Physiology 174, no 2 (juin 2017): 700‑716.



Boulanger, Alice, et Laurent D. Noël. « Xanthomonas Whole Genome Sequencing: Phylogenetics, Host Specificity and Beyond ». Frontiers in Microbiology 7 (2016): 1100.


Denancé, Nicolas, Thomas Lahaye, et Laurent D. Noël. « Editorial: Genomics and Effectomics of the Crop Killer Xanthomonas ». Frontiers in Plant Science 7 (2016): 71.


Jacques, Marie-Agnès, Matthieu Arlat, Alice Boulanger, Tristan Boureau, Sébastien Carrère, Sophie Cesbron, Nicolas W. G. Chen, et al. « Using Ecology, Physiology, and Genomics to Understand Host Specificity in Xanthomonas ». Annual Review of Phytopathology 54 (4 août 2016): 163‑87.


Robène, I., S. Bolot, O. Pruvost, M. Arlat, L. D. Noël, S. Carrère, M.-A. Jacques, R. Koebnik, et L. Gagnevin. « High-Quality Draft Genome Sequences of Two Xanthomonas Pathotype Strains Infecting Aroid Plants ». Genome Announcements 4, no 5 (1 septembre 2016): e00902-16.



Bolot, Stéphanie, Aude Cerutti, Sébastien Carrère, Matthieu Arlat, Marion Fischer-Le Saux, Perrine Portier, Stéphane Poussier, Marie-Agnes Jacques, et Laurent D. Noël. « Genome Sequences of the Race 1 and Race 4 Xanthomonas Campestris Pv. Campestris Strains CFBP 1869 and CFBP 5817 ». Genome Announcements 3, no 5 (17 septembre 2015): e01023-15.


Pesce, Céline, Stéphanie Bolot, Edwige Berthelot, Claude Bragard, Sébastien Cunnac, Marion Fischer-Le Saux, Perrine Portier, et al. « Draft Genome Sequence of Xanthomonas Translucens Pv. Graminis Pathotype Strain CFBP 2053 ». Genome Announcements 3, no 5 (8 octobre 2015): e01174-15.


Pesce, Céline, Stéphanie Bolot, Sébastien Cunnac, Perrine Portier, Marion Fischer-Le Saux, Marie-Agnès Jacques, Lionel Gagnevin, et al. « High-Quality Draft Genome Sequence of the Xanthomonas Translucens Pv. Cerealis Pathotype Strain CFBP 2541 ». Genome Announcements 3, no 1 (12 février 2015): e01574-14.


Roux, Brice, Stéphanie Bolot, Endrick Guy, Nicolas Denancé, Martine Lautier, Marie-Françoise Jardinaud, Marion Fischer-Le Saux, et al. « Genomics and Transcriptomics of Xanthomonas Campestris Species Challenge the Concept of Core Type III Effectome ». BMC Genomics 16 (18 novembre 2015): 975.


Wang, Guoxun, Brice Roux, Feng Feng, Endrick Guy, Lin Li, Nannan Li, Xiaojuan Zhang, et al. « The Decoy Substrate of a Pathogen Effector and a Pseudokinase Specify Pathogen-Induced Modified-Self Recognition and Immunity in Plants ». Cell Host & Microbe 18, no 3 (9 septembre 2015): 285‑95.

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