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Laboratory of Plant-Microbe Interactions - LIPM

Laboratory of Plant-Microbe Interactions

Research themes - Infectious strategies of Xanthomonas

Xcc and plant hydathodes, studying the rules of a first date

Epiphytic Xcc enters the plant via leaf hydathodes. Hydathodes are water pores present at the leaf margin by which xylem sap exudes under high humidity and low transpiration. We are interested in the anatomy and physiology this poorly studied organ which provides direct access to xylem vessels. We wish to characterize the hydathodes structure and tissue organisation in several Brassicaceae plants and to identify plant immunity genes controlling infection at the hydathode. This project will give new insights into the molecular dialog between plants 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-GUS (Blue) 10 days after hydathode infection. (B) Guttation droplets on the lower leaf surface. (C) Electron scanning micrograph of an hydathode. (D) Early stages of hydathode infection by Xcc-GUS (Blue) prior to vascularization.

Contact: Laurent Noël

Type 3 effectors of Xanthomonas campestris

We have intensively studied the conservation and distribution of T3Es among Xanthomonas campestris strains for which genomes sequences are now available. Surprisingly, we showed that Transcription-Activator-Like Effectors (TALE) are present in at least one Xcc strain. Now that the mechanisms of recognition of AvrAC by the plant immunity have been elucidated, we are searching for the plant targets of the remaining 40 effectors of Xcc using unbiased forward or reverse genetic screens and biochemical approaches (e.g. ANR project CROpTAL).

Graphical abstract LNL +Pst

Mechanisms of AvrAC and HopZ1a recognition by Arabidopsis immunity

Contact: Laurent Noël

Xanthomonas adaptation to the plant environments

The way bacteria adapt and behave in/on plant tissues is poorly investigated so far and only major pathogenicity determinants have been identified to date. We first wish to characterize the leaf microbiome and the impact of infection by Xcc on this composition. We also want to capture plant and bacterial co-transcriptomes throughout the infection process. Last but not least, we wish to use in planta screens to capture genes that contribute to bacterial fitness throughout Xcc life cycle (Collaboration J. Lewis, UC Berkeley, CA). To this end, we are developing a transposon barcoding strategy to measure bacterial fitness in the different plant compartments. In parallel, we also use forward genetics and synthetic biology to investigate the function of large multigene families such as TonB-dependent transporters (TBDTs). TBDTs are outer membrane transporters involved in the high affinity active uptake of scarce nutrients such as metals, vitamins and carbohydrates. In Xcc,  some TBDTs belong to so called, Cabohydrate Utilization systems with TBDTs (CUT systems) involved in the scavenging of complex plant molecules such as xylan, pectin, glycan, sucrose and other macromolecules. The large expansion of TBDT-encoding gene family in Xcc reflects the adaptative potential of these clusters and their contribution to fitness in planta has been shown in several instances.


(A) Leaf print of culturable micro-organisms of a cabbage leaf. (B) Modelling of a Xcc TBDT 3D structure

Contacts: Emmanuelle Lauber and Alice Boulanger

Genomics of Xanthomonas campestris to identify bacterial strategies for life in association with plants: Xcc and beyond

The number of Xanthomonas genome sequences has grown exponentially of the last years to reach several hundreds. As for january 2016, 13 X. campestris genome sequences have been published, eight of which issued from our team. To launch comparative and genetic association studies, our group has sequenced the genomes of 30 additional strains of Xanthomonas campestris, collected from various host plants in different regions of the world. This analysis is carried out in collaboration with the Bioinformatics facility platform of LIPM and Anne Genissel (INRA Versailles, France). Comparative analysis of gene families involved in pathogenicity and/or adaptation to the plant environments such as TBDTs is a way to highlight the commonalities and specificities of bacterial symbionts associated to plants matrices on living plants, in aquatic environments or digestive tract of humans and animals.


Complete genome sequences of Xcc can 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 La Réunion, France

Current fundings

  • Research networks INRA SPE Department (20161-20174). French Network on Xanthomonas. M-A Jacques, R. Koebnik, O. Pruvost and L. Noël, coordinators, 5 k€/year.
  • ANR generique CROpTAL (2015-2018) ANR-14-CE19-0002-01, L. Noël (CNRS, Toulouse) coordinator, B. Szurek (IRD, Montpellier), N. Chen (INRA Angers) et L. Gagnevin (CIRAD La Réunion).  TALome-based engineering of durable pathogen resistance in crops. 499k€ (214k€ for our group).
  • ANR generique PAPTiCROPs (2016-2020) ANR-16-XXXX, 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).