M2 student position for 2025

Posted on Jul 3, 2024

M2 internship to study mRNA degradation

A position to study the biochemistry and molecular biology of RNA degradation in the pathogenic yeast Cryptococcus neoformans is available starting January 2025. Compared to Saccharomyces cerevisiae, a fantastic model for understanding mRNA degradation, C. neoformans retained splicing-related proteins, such as those composing the core exon-exon junction complex (EJC). Moreover, unlike in budding yeast, the presence of introns is an absolute requirement for gene expression. Finally, recent technical developments allow genetic manipulations of cryptococcal strains that was not possible until now.

Outline of the project and its context

Title: Coordination of nuclear and cytoplasmic RNA quality control in Cryptococcus neoformans

Description: Nonsense-mediated mRNA decay (NMD) is a major degradation pathway that ensure a robust transcriptome and protects eukaryotic cells from viral infection. Our previous work in yeast, Saccharomyces cerevisiae, using large-scale genetics (Decourty et al., Nucl Acids Res, 2021) and interaction proteomics (Dehecq et al., EMBOJ, 2018) identified protein-protein interactions that are important for NMD and conserved from yeast to humans. This work also led to new hypotheses about fundamental mechanisms of RNA degradation (Audebert et al., bioRxiv 2023, in revision). We propose to use the distant pathogenic fungus, Cryptococcus neoformans, a Basidiomycete of major publich health importance, to investigate mechanisms of NMD that have been lost in S. cerevisiae. In particular, the exon junction complex (EJC) has been proposed to be essential to trigger NMD. Preliminary results on the role of this complex in C. neoformans indicated its importance in the use of correct RNA splicing signals, in conjuction with NMD degradation of aberrant splicing variants. We propose to investigate EJC and NMD complexes and their function in this organism and perform a comparative functional analysis with data from yeast to decipher molecular mechanisms of mRNA degradation that are either specific to branches of eukaryotic evolution or are universally conserved. These investigations will involve affinity purification of RNA-protein complexes, quantitative mass-spectrometry and RNA sequencing. Knowledge of these mechanisms can be useful in understanding the pathogeny of fungal infections, in developing new therapeutic strategies and in better understanding the molecular biology of gene expression in living cells.

Strong effect of NMD inactivation (deletion of UPF1) in C. neoformans on a specific transcript, as detected by short read RNA sequencing