Thesis defenses at IPS2 in spring 2025
Sébastien SKIADA
Ribonucleases and Chloroplast Transcriptome Quality Control: Function of RNase J and Prevalence of Double-Stranded RNAs
Keywords: Chloroplast, Ribonucleases, RNA isoforms, Double-Stranded RNA,
Chloroplasts contain a genome whose expression is regulated by post-transcriptional quality control mechanisms involving ribonucleases. Among these mechanisms, the role of antisense RNAs, and more globally of double-stranded RNAs, remain poorly understood. During my PhD, I developed a methodology to identify, characterize, and quantify RNA–RNA duplexes. My results reveal their high abundance in a PNPase mutant (ribonuclease with a 3’-to-5’ activity), where they accumulate as granules at the vicinity of the chloroplast nucleoid. I then focused on RNase J, the only ribonuclease with a 5'-to-3' activity. Using KO lines complemented with modified versions of the enzyme, I showed that its GT-1 domain binds double-stranded RNAs in vivo and prevents their accumulation by guiding the enzyme’s activity. Altogether, my findings suggest that chloroplast RNA quality control may involve the sequestration of both RNA and protein factors within functional sub-compartments of the chloroplast.
PhD defense: June 25, 2025
PhD director: B. Castandet
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Francisco SÁNCHEZ-RODRÍGUEZ
Role of RNase III enzymes and 3D chromatin structure in the Medicago truncatula nitrogen-fixing symbiosis
Key-words: Rhizobium-legume symbiosis, RNAse III, Small RNAs, RNA-directed DNA methylation, Chromatin topology
The rhizobium–legume symbiosis enables nitrogen fixation in root nodules and is regulated by epigenetic mechanisms, including RNA-directed DNA methylation via 24-nt small interfering RNAs (siRNAs) and chromatin accessibility changes. During my PhD, I focused on RNase III enzymes, which modulate sRNAs biogenesis by processing double-stranded RNA. I first studied MtDCL3, a canonical RNase III involved in 24-nt siRNA biogenesis, and then characterized MtRTL1b, a Medicago homolog of Arabidopsis AtRTL1. Unlike its counterpart, MtRTL1b regulates target genes, including NODULE-SPECIFIC CYSTEINE-RICH PEPTIDES, independently of the siRNA pathway. Finally, using high-throughput -omics technologies, we uncovered extensive chromatin reorganizations during nodule differentiation. Altogether, this work highlights how RNase III enzymes and chromatin dynamics shape gene expression during symbiotic nitrogen fixation.
PhD defense: May 6, 2025
PhD supervisors: M. Crespi; C. Lelandais-Brière
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Tiffanie SCANDOLERA
Plant–virus interactions: impact of elevated atmospheric CO₂ and high temperatures on plant resistance/susceptibility to viruses in the context of climate change
Keywords: common bean, virus, elevated CO₂, heatwave, plant defense responses, plant immunity
Climate change, characterized by increased atmospheric CO₂ levels and rising temperatures, may alter interactions between plants and pathogens. Climate projections predict an increase in atmospheric CO₂ concentration from 400 µL·L⁻¹ in 2014 to 1000 µL·L⁻¹ by 2100, along with a global temperature rise of 4.6 °C. This PhD project investigated the effects of these environmental factors on the resistance of common bean (Phaseolus vulgaris) to the Bean pod mottle virus (BPMV). Two genotypes were studied: BAT93 (resistant) and Black Valentine (susceptible). The study included: (1) a targeted analysis of defense-related genes to assess the separate impact of elevated CO₂ and heatwaves, and (2) a transcriptomic analysis to evaluate their combined effect in BAT93. This work contributed to a better understanding of how climate change may influence plant antiviral resistance mechanisms in the future.
PhD defense date: March 18, 2025
PhD director: S. Pflieger
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Juliette TEYSSENDIER DE LA SERVE
Signaling peptides regulating root endosymbioses in the legume model plant Medicago truncatula
Keywords: peptides, mycorrhization, nodulation, roots, legumes
Due to their sessile lifestyle, plants adjust their development to nutrient availability by integrating environmental signals at the whole-plant level, notably through small signaling peptides (SSPs) such as CLE, CEP, and IDA. These mobile peptides act between tissues and organs to regulate plant development, and notably root symbioses. My PhD focused on exploring the function of these peptides in the Medicago truncatula model legume. At first, I showed that a subgroup of CEP peptides promotes mycorrhization under phosphate deficit through the CRA2 receptor, by stimulating the production of strigolactones. Then, I identified a type-B CLE peptide, sTDIF (symbiotic TDIF), which increases the diameter of the root stele and promotes nodulation. Finally, I showed that the IDA20 peptide likely inhibits nodulation, and that the HAESA receptor likely promotes mycorrhization.
PhD defense date: March 8, 2025
PhD supervisors: F. Frugier, N. Frei-Dit-Frey (LRSV Toulouse)
