Functional Genomics Eukaryotes Research Program

Responsable del Programa: Georgina Hernández D, Ph.D.

This research program studies PLANTS, as a representative model of eukaryotic systems, analyzing the interactions between plants and microorganisms. The program includes four research groups lead by: Georgina Hernández, Mario Serrano, Alexandre Tromas and Damien Formey.

Three research lines from the program study of the legume-rhizobia symbiosis. Plants form the legume (Fabaceae) family have developed the capacity to grown in nitrogen-deprived soils by interacting with soil bacteria known as rhizobia. The two partners have co-evolved towards a complex and positive interaction for both of them, where symbiotic nitrogen fixation takes place to capture directly the atmospheric nitrogen thus to maintain plant growth.

The research line of the Georgina Hernández’s group is the functional genomics of common bean (Phaseolus vulgaris) for the analysis of the symbiosis with Rhizobium etli and the plant response to abiotic stresses. Common bean is the most important legume for human consumption. The P. vulgaris genome sequence was published recently ( The group performs post-genomic research on common bean using, mainly, transciptomics, both of protein-coding mRNAs as well as non-coding small RNAs identified as key regulators. One of the objectives is to decipher new global regulators of the common bean – rhizobia symbiosis: transcription factors and microRNAs. Another objective is the transcriptomic analysis of common bean in the response to abiotic stresses such as nutrient deficiency, oxidative stress and drought.

The research line of the Alex Tromas’s group is the regulation of cytoskeleton during the symbiotic nitrogen fixation. It has been established that accommodation of micro-endosymbionts like rhizobia inside the plant cell is an active process that requires proper cytoskeleton rearrangement. The Rho-GTPases (named ROP in Plants), considered as “molecular switches”, are known to activate the rearrangement of actin, one of the main cytoskeleton components. The main question is now to understand which cytoskeleton rearrangement complexes involved in the accommodation of symbiotic bacteria and understand when and where they are activated and relocalized in Lotus japonicus root hair. To address that question, a set of biosensors will be developed to allow high resolution observation of each ROP activation in Lotus japonicus root hair, during accommodation of symbiotic bacteria. The objectives of this line are: Identification of the ROP proteins interactome in root hairs. (Molecular biology and Biochemistry); Development of biosensors to follow the spatio-temporal activation of ROPs in response to rhizobia. (Molecular and Cellular biology); Functional characterization of rops mutants. (Plant physiology)

The main research line of Dr. Damien Formey is: “The characterization and evolution of the small RNAs involved in the plant-microbe interactions”. Using the Phaseolus vulgaris / Rhizobium interaction model, the project focuses on the microRNAs and PhasiRNAs regulating the symbiotic nitrogen fixation, from the diffusible factors exchange to the senescence of the symbiotic organs called nodules. Many of these small RNAs are common bean-specific and provide new insights into the co-evolution between the bacteria and their host. The variety of Phaseolus vulgaris genotypes is estimated at several tens of thousands widespread around the world. This pool of common beans represents a powerful tool to investigate the small RNA variability at an intra-specie scale and the influence of these variations on the establishment of symbiotic nitrogen fixation.

The research line of Mario Serrano’s group is: the characterization of the plant innate immunity to Botrytis cinerea. The necrotrophic fungus Botrytis cinerea, commonly known as grey mold, has been classified as the second most important plant pathogen, since it can infect over 200 plant species. The first interaction between the plant and the fungal organism takes place at the epidermis, where not only the plant has the first physical barrier, that includes the plant cuticle in aerial organs, but also where the organisms are recognized and potentially the plant immune responses are triggered. However, the early events that take place during B. cinerea infection, in particular the communication between the plant and the pathogen at the cuticle are not completely elucidated. Remarkably, several reports have shown that Arabidopsis thaliana and Solanum lycopersicum mutants affected in the synthesis of the cuticle have a common “syndrome” related with the plant-microbe interaction, including increased cuticle permeability, ROS production and resistance to B. cinerea. With this in mind, the project is based on the identification and characterization of the molecular elements that link the degradation of the cuticle and the induction of the plant innate immunity. To achieve this objective, we use the plant-pathogen system Arabidopsis thaliana-Botrytis cinerea and the traditional genomic and chemical genetic methods.