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Selected breakthroughs

Plant pathogenic oomycetes produce DNA-binding effectors that trigger host DNA damage

By working on CRN13 effector for the legume pathogen Aphanomyces euteiches and its homolog from Batrachochytrium dendrobatidis (amphibian pathogen) in collaboration with colleagues from the Centre de Biologie du Développement and the Cell Imaging Platform in Toulouse, we have shown that AeCRN13 and BdCRN13 are nuclear-localized proteins when overexpressed in plant cells or Xenopus embryos. Both CRN13s trigger aberrant cells and embryo development leading to cell death [1]. Using Förster Resonance Energy Transfer (FRET) experiments in plant cells, we showed that both CRN13s interact with nuclear DNA and trigger plant DNA damage response (DDR) thanks to a nuclease motif. Finally, we showed that AeCRN13 contributes to oomycete virulence during host infection. This work reveals that CRN13 effectors from unrelated filamentous pathogens, target host DNA through DNA-binding effector in order to trigger DNA damage probably to facilitate host colonization. This new mode of action suggested a putative links between DDR and plant immune responses

[1] Ramirez-Garcés, Camborde et al. (2016) New Phytologist 210 : 602–617

Genomic signature of selective sweeps illuminates adaptation of Medicago truncatula to root-associated microorganisms

M. truncatula is a model legume species used to investigate plant–microorganism interactions, notably root symbioses and root pathogen attacks. Massive population genomic and transcriptomic data now available for this species open the way for a comprehensive investigation of genomic variations associated with the adaptation of M. truncatula to its environment. Here we performed a fine-scale genome scan of selective sweep signatures in M. truncatula using more than 15 millions of Single Nucleotide Polymorphisms (SNPs) identified in 283 accessions, and identified 58 genomic regions showing signature of selective sweep. Functional annotation of underlying genes, together with the analysis of their transcriptional profiles in various conditions (published transcriptomics data) allowed inference of four clusters of co-regulated genes, showing that natural selection targeted gene networks. These clusters are putatively involved in the adaptive control of symbiotic carbon flow and nodule senescence, as well as in other root adaptations upon infection with soil microorganisms. We demonstrate that molecular adaptations in M. truncatula were primarily triggered by selective pressures from root-associated microorganisms [1].

[1] Bonhomme et al. Mol Biol Evol. 2015 32 : 2097-2110.

Discovery of miPEPs encoded by microRNAs and of their biological function

MicroRNAs are small RNAs (approximately 21 nucleotides) that control most biological processes, negatively regulating the expression of many target genes. They are present in plants and animals, including humans, in which they are involved in many diseases when their expression is deregulated. MicroRNAs are derived from primary transcripts, which are larger RNA molecules produced by transcription of the DNA. Primary transcripts of microRNAs have long been regarded as non-coding RNAs.

We have shown that the primary transcripts encode small regulatory peptides (miPEPs) [1]. These miPEPs are naturally produced by plants and are specific to each microRNA. The miPEPs activate transcription of their associated microRNAs. Thus, the treatment of plants by miPEPs increases the amount of microRNAs produced by these plants. By carefully choosing the target microRNAs, we can improve plant development, which allows to consider many agricultural applications.

[1] Lauressergues et al. (2015) Nature 520 : 90-93

Calmodulins and Calmodulins-like protein emergence in the green lineage ?

Calcium ions play a central role in numerous signal transduction cascades in plants. It is well established that external stimuli induce complex spatio-temporal patterns of calcium changes within plant cells thought to encode information and drive specific adaptive responses. However, these calcium fingerprints must be relayed and decoded by calcium-binding proteins, termed calcium sensors such as Calmodulins (CaMs), Calmodulins-like (CMLs), Calcium-dependent Protein Kinases (CPKs) and Calcineurins-B-like (CBLs), to carry out the appropriate responses.

During the last decade, the genomes of many organisms, from green algae to land plants were sequenced allowing comparative phylogenomics studies on different proteins families. We explore the genomes of 15 organisms from Chlorophyceae to land plants to search for CaMs and CMLs homologues and to analyze gene duplication and evolution [1]. A striking diversity of CaMs and CMLs evolved in Angiosperms during terrestrial colonization and reveals the emergence of new CML classes throughout the green lineage that correlates with the acquisition of novel biological traits. We speculate that the expansion of the CML family was driven by selective pressures to process environmental signals efficiently as plants adapted to land environments. A comparative analysis of the four calcium sensor families and their evolution was performed among the green lineage to have a better picture of the contribution of calcium signaling and calcium sensors involvement in the adaptation of plants to the multiple constraints they encounter in the terrestrial environment.

[1] Zhu et al.(2015) Trends Plant Sci 20 : 483-489.