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



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.