Ribosome biogenesis: The yin and yang of protein homeostasis – RASTR

Protein homeostasis or proteostasis is the concept that integrated biological pathways within cells maintain proteins in the correct concentration, folding, and subcellular location. A key feature of protein homeostasis in all organisms is involvement of proteasome components and the expression of ubiquitous chaperone proteins often referred to as protein quality control (PQC) systems. The transcription factor Hsf1 drives the expression of PQC components in eukaryotes and is considered as the guardian of protein homeostasis from yeast to human. Ribosome biogenesis in rapidly growing cells produces thousands of ribosomes per minute in eukaryotes and is critical for sustaining high rates of growth (mass accumulation) and proliferation. At the same time, though, ribosome assembly poses a constant threat to cellular protein homeostasis, since it requires the coordinated and large-scale assembly of tens of thousands of Ribosomal Proteins (RPs), which are highly prone to aggregation. Indeed, due to their particular features, such as a highly basic amino acid composition and enrichment in disorder promoting residues, the vast majority of RPs are mostly unstructured in their unbound state, which may promote non-specific interactions resulting in insolubility. This implies that perturbations of ribosome assembly could lead to a rapid and dramatic increase in unassembled RPs, i.e. “orphan” RPs, which could seriously disrupt protein homeostasis.

My recent discovery of a novel regulatory system in yeast, the Ribosome Assembly STress Response (RASTR), that rapidly adjusts chaperone and RP production in response to ribosome biogenesis disruption, sheds new light on regulation of protein homeostasis in eukaryotes. Our published and unpublished data indicate that any perturbation of ribosome assembly causes a rapid increase in unassembled RPs forming nuclear aggregates, leading to a conserved homeostatic response impacting transcription, translation and cell cycle regulation through an unknown dynamic aggregation mechanism. Furthermore, our findings suggest that RASTR represents the earliest transcriptional response to several different types of stress (temperature, starvation) to which cells must adapt in order to survive.

The aim of this project is to identify the components and the mechanisms that make up this system operating at the intersection between proteostasis and ribosome biogenesis, driven by dynamic protein condensation. This project will address numerous questions as fundamental as the physiological consequences on proteostasis of the frenetic pace of ribosome assembly in rapidly growing cells. This project is a fundamental research project that is relevant to virtually all organisms. The RASTR studies promise to revolutionize our understanding of a fundamental interplay between ribosome biogenesis and proteostasis networks by the characterization of a new branch of stress response in eukaryotes dedicated to balance the proteotoxic burden of ribosome biogenesis with proteostasis network capacity. Importantly, we expect to characterize a new nuclear membrane-less compartment whose formation is driven by opposite electrostatic charge densities, namely the positive charges of “orphan” RPs and negative charges of glutamic acid motifs enriched in proteins found in insoluble fraction during RASTR. Given the high evolutionary conservation of RP features (small, highly charged, intrinsically disordered domains enriched) in virtually all kingdoms of life, such a discovery will represent ground-breaking advances in the stress regulation field. Lastly, RASTR project should generate results interesting for a broad audience, beyond the limits of our research community, and will directly contribute to medical research as highlighted by citation of our first study (Albert et al, 2019, Elife) describing RASTR in very recent publications related to cancer development, neurodegenerative disorders and recently ribosomopathies.