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Thesis offers

How endophytes impact symbiotic nodulation in legume plants

Legumes are essential crops and major sources of proteins thanks to their symbiotic ability with soil bacteria called rhizobia, resulting in the establishment of root nodules that can fix atmospheric nitrogen (N), allowing them to grow without nitrogen fertilizers and thus promoting sustainable agricultural systems. Other non-N-fixing microbes are often found in nodules but their role frequently remains unclear. The proposed PhD project aims to explore the role of the endophytic bacterial strain Enterobacter sp. SA187, that was isolated from symbiotic nodules. In fields, SA187 promotes alfalfa development, and this beneficial impact was shown to be enhanced under low N conditions or in response to abiotic stresses, making this strain an interesting candidate to evaluate how nodule endophytes can influence symbiosis establishment and functioning.  Using integrative approaches (phenotyping, mutant analysis, cell biology, and transcriptomics), the thesis will be structured around four tasks: 1) characterizing SA187 beneficial effects on legume grown in symbiotic conditions; 2) determining how this interaction is regulated by already known rhizobium infection and/or N availability signaling pathways; 3) assessing whether environmental stresses, such as heat or salt, potentiate SA187 beneficial effects in different legume crops; and 4) identifying new beneficial nodule endophytes beyond SA187.Altogether, this project will increase our knowledge on how nodule endophytes influence legume growth and nodulation, as well as to identify new beneficial agents that can be used in agronomic conditions, particularly in the context of climate change.

Start of thesis:  01-10-2024

Closing date for applications: 07-05-2024

Thesis director : FRUGIER Florian (florian.frugier @ ips2.universite-paris-saclay.fr)

Co-supervisor: DE ZELICOURT Axel (axel.de-julien-de-zelicourt @ universite-paris-saclay.fr)

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Chromatin factors controlling nitrogen-fixing symbiosis in response to low-nitrogen in the model legume Medicago truncatula

Under low nitrogen (N) conditions, legume plants associate with soil bacteria referred to as rhizobia, to form symbiotic root nodules in which atmospheric N2 is fixed and assimilated by the plant. To achieve maximum gains, nodule number and N2-fixation activity are precisely controlled by the host plant through a combination of local and systemic regulatory pathways that integrate shoot and root signals. Among them, C-terminally encoded (CEP) signaling peptides systemically promote nodulation competence under low N through the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) COMPACT ROOT ARCHITECTURE 2 (CRA2) receptor, acting in shoots. The molecular effectors and targets of the CEP/CRA2 pathway remain however poorly documented despite its tremendous impact on the adaptation of root system architecture to low N. Among CRA2 systemic targets identified in roots using transcriptomic analyses, two histone-modifying enzymes were retrieved: (1) the histone deacetylase MtHDT2 (HISTONE DEACETYLASE 2) previously characterized specifically at late nodulation stages; and (2) the Trithorax group protein with a methyltransferase activity MtATX3.1 (ARABIDOPSIS TRITHORAX 3.1), not yet studied in any legume or in the context of N responses or symbiosis. Considering that the chromatin modifications underlying the N-deficit driven root competence for nodulation are largely unexplored in legume plants, the objective of this thesis project is to understand how MtHDT2 and MtATX3.1, by modifying chromatin organization and dynamics, reprogram the root transcriptome under low N in the Medicago truncatula symbiotic legume plant.

Start of thesis : 01-10-2024

Closing date for applications: 07-05-2024

Thesis director : FONOUNI-FARDE Camille (camille.fonouni-farde @ universite-paris-saclay.fr)

Co-supervisor : FRUGIER Florian (florian.frugier @ ips2.universite-paris-saclay.fr)

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Arabidopsis thaliana MAPK functions through chromatin remodelling during combined immune response and heat stress

Raising temperatures triggered by climate change pose a major risk for crop production. Heat stress also modulates plant immune responses, however, underlying mechanisms mediating the crosstalk between biotic and abiotic stresses are not known. We and others have defined mitogen-activated protein kinases (MAPKs) MPK3, MPK4 and MPK6, as early phospho-regulatory components involved in reprogramming gene expression during plant immunity. Phosphoproteomic approaches identified several putative substrates for these MAPKs, including a chromatin remodelling factor (CHR). Based on these results and literature data, we hypothesize that MPK3(/4/6) can activate CHR through phosphorylation and by this controls the expression of a key nucleotide-binding domain leucine-rich-repeat receptor (NLR) gene. The MPK3-CA line, expressing a constitutively active (CA) MPK3 protein version in the mpk3-1 knock-out mutant, exhibits autoimmune symptoms, such as dwarfism and increased salicylic acid (SA) signalling. Our preliminary results show that chr knock-out mutations partially suppress the dwarf phenotype of MPK3-CA line, supporting our hypothesis. The proposed PhD project will 1) characterize the biochemical link between MPK3/4/6 and CHR, 2) decipher the role of MPK3/4/6-CHR-NLR module in immunity, heat stress and combined stresses, and 3) unveil the function of CHR phosphorylation by MPK3/4/6. This project will clarify MAPK functions on chromatin remodelling during combined occurrence of biotic and abiotic stresses.

Start of thesis: 01-10-2024

Closing date for applications: 06-05-2024

Directeur de thèse : BIGEARD Jean (jean.bigeard @ universite-paris-saclay.fr)

Co-supervisor:: LE DEUNFF Erwan (erwan.ledeunff @ universite-paris-saclay.fr)

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lncRNA regulation of biosynthetic gene clusters

Secondary metabolic compounds are mainly synthetized through pathways where the enzymes involved need to be co-expressed at the same time and in the same cells. Multiple examples of genes encoding such pathways have been found to be grouped together in biosynthetic gene clusters (BGCs) within plant genomes and carry a peculiar chromatin signature. Long non-coding RNAs (lncRNAs) are now recognized regulators of gene expression, from chromatin conformation to protein translation. Therefore, they are good candidate to regulate BGCs. However, since the functions of lncRNAs are lower sequence constraints than for coding genes, the specific mechanisms through which most lncRNAs act remain poorly understood. We already identify MARneral Silencing (MARS) lncRNA, localized inside the BGC marneral. MARS controls the local epigenetic activation of its surrounding region in response to ABA. In this project, we propose to investigate further the mechanism of action of MARS and related lncRNAs. Using uncharacterised deregulated lines, we propose to investigate whether MARS will able to act independently to its site of transcription and how it may regulate distal targets. Interacting partners will be identified to better understand MARS mechanism. We will also investigate this type of regulation in the different BCGs of Arabidopsis and Brassicaceae to be able to identify common features of required for such regulation.

Start of thesis: 01-10-2024

Closing date for applications: 07-05-2024

Thesis director : BLEIN Thomas (thomas.blein @ cnrs.fr)

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