Genetic, epigenetic and protein-based crosstalks between nucleolus functional reorganization and response to stress – RiboStress

Nucleolus activity and structure are intimately linked to ribosome biogenesis and functionally connected to protein synthesis, cell growth and proliferation. The driving force for nucleolus assembly is the transcription of hundred copies of 45S ribosomal genes (rDNA) by RNA polymerase I, with subsequent processing and assembly of 45S transcripts into ribosome particles. Wider and far less understood roles of the nucleolus in chromatin activity and post-translational regulatory mechanisms have been uncovered in recent years in humans, animals, yeast and plants. The nucleolus appears to influence the expression of coding and non-coding RNAs transcribed by all nuclear RNA polymerases, including RNA Pol II and III in animals and the plant-specific RNA Pol IV and V involved in transcriptional silencing in Arabidopsis. More recently, the nucleolus has also emerged as a structural scaffold that can sequester large chromatin domains and recruit nuclear proteins involved in multiple processes such as chromatin organization and transcription, RNA processing and modification, assembly of nuclear ribo-nucleoprotein complexes or of specific nuclear bodies. Still, the molecular bases leading to nucleolar-based sequestering or protein nucleolar hijacking and their potential interconnection with nucleolar and rRNA functional dynamics await to be investigated.

The proposed research program is aimed at uncovering and dissecting functional connections between nucleolar activities in response to heat and light stressful conditions over generations. Heat acting in conjunction with high light causes severe threats to crops, notably by inducing plant drought and impairing disease resistance, photosynthetic efficiency and consequently plant growth. RiboStress is aimed at identifying which proteins are retained in, or excluded from, the nucleolus in response to heat and high light conditions. It will also determine the origin and the role of nucleolar long non-coding RNAs lncRNAs and their implication in nucleolar protein detention. In a complementary approach, we will further explore how nucleolar organization and activity impact transcriptional and epigenetic variations over the genome as well as the cell physiology when plants face unfavorable environmental conditions over multiple generations.

A set of preliminary data and the assortment of molecular and genetic plant resources obtained by the partners constitute a solid basis to tackle the proposed objectives in assessing the impact of nucleolar structural changes and activity during stressful conditions. The combination of genetic, epigenetic and genomic resources that will benefit the different tasks is unique to the A. thaliana model species. The proposal will also benefit from large research infrastructures to perform large-scale qualitative and quantitative proteomic analyses (IR ProFI) and transgenerational studies in a perfectly controlled environment (IR ANAEE-FR ECOTRON Ile-De-France). The research program is expected to gain novel insights into how the genome sequence, epigenetic mechanisms and lncRNAs influence the structure and activity of the nucleolus. It is more generally intended to participate significantly to the intense efforts currently devoted to decipher how nuclear organization contributes to regulatory pathways and is tuned during adaptive responses of multicellular organisms to external cues, a field to which plants have much to offer. Improving the knowledge on such fundamental mechanisms is essential to understand how natural mutations affecting nucleolar function or ribosome biogenesis trigger a broad range of diseases in human (ribosomopathies, cancer, degenerative disorders) and impair plant stress response capacity.