Investigating how cell size and mRNA dilution impacts the nascent proteome.

Cell size is a fundamental, but poorly understood, cellular parameter. Cell size sets the scales for organelle structures, surface transport and, most crucially, biosynthetic rates. Protein and mRNA amounts must scale with cell size to maintain constant concentrations, so coordination between cell size and cellular biosynthesis is essential for optimal cellular fitness.

Using a combination of mathematical modelling, quantitative functional genomics and in vivo single-molecule tracking we have previously identified how mRNA amounts scale with cell size: RNA polymerase II recruitment to the genome is govern by a simple mass action equilibrium that shifts in a cell size-dependent manner to increase transcription in larger cells (Swaffer et al., Cell 2023). However, this mRNA scaling is only achieved within a limited cell size range. When cells get excessively large, mRNA scaling breaks down, resulting in dilution of the entire transcriptome by cell growth.

This project aims to understand the consequences of this global mRNA dilution in oversized cells. To do this, cutting-edge sequencing and proteomics-based approaches will be used to quantify how mRNA dilution impacts protein synthesis. This will dissect how global changes in protein synthesis occur, as well as how different sectors of the proteome are differentially synthesised as mRNA is diluted. These data will be used to build an integrated mathematical model of size-dependent mRNA translation, including how the temporal kinetics of mRNA metabolism (synthesis, export, deadenylation, decapping and degradation) change with size to impact translation. Together this will provide a holistic mechanistic and quantitative understanding of how excessive cell size alters proteome homeostasis.

Training opportunities

The student’s role will be to design / perform wet lab experiments in the Swaffer lab as well as develop modelling approaches with the Grima lab to introduce cellular size a as key parameter in models of RNA metabolism and protein synthesis. Experimental work will principally use budding yeast as a model system to test key hypotheses addressing the aims outlined above. The project will involve utilising a range of approaches in cell, molecular and systems biology. This includes several functional genomics sequencing-based and quantitative proteomics technologies (e.g., RNA-seq, Ribo-seq and SILAC pulse-labelling). The project will also involve extensive bioinformatics to analyse data from the above approaches.

We are looking for highly motivated applicants with some prior lab experience, but no specific expertise in the above techniques is required, as all necessary training will be provided. This project will also allow students to combine wet lab work with the opportunity to develop key skills in computational data analysis and bioinformatics.

Swaffer lab website: https://swafferlab.co.uk

Grima lab website: https://grimagroup.bio.ed.ac.uk/home