Using systems biology to determine how budding yeast coordinates carbon and nitrogen sensing for efficient growth

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

A key ability of cells is to coordinate sensing of extracellular carbon and nitrogen to enable efficient growth. Although we know that this ability comes from conserved intracellular molecules, how these molecules interact to generate decision-making is unclear. Research is hindered by the difficulty of measuring the activities of signalling molecules over time as cells respond. Using budding yeast, we will combine time-lapse microscopy with mathematical modelling to uncover the strategy they use for carbon and nitrogen sensing. To overcome the lack of real-time reporters, we will exploit that for yeast changes in extracellular nutrients cause tens of transcription factors to move into or out of the nucleus, with each transcription factor therefore a potential reporter once tagged with a fluorescent protein. With novel microfluidics, we will identify new translocating reporters for carbon and nitrogen sensing through a systematic single-cell study of almost all yeast's transcription factors. We will further develop a novel scalable technique that uses these reporters and transient perturbations to measure kinase and phosphatase activities over time in changing environments. Growth rate correlates with fitness in yeast, and we will use growth rate as a global output of signalling. Concurrently measuring growth rate and the activities of key molecules such as TOR and AMP kinase via the transcription factors, we will systematically characterise signalling in dynamic levels of extracellular carbon and nitrogen. To uncover how the molecules interact to enable growth, we will use mathematics to infer from our data the strategy cells use. This task, of deciding how fast to grow in changing availabilities of carbon and nitrogen, is fundamental and ancient, and the principles and the logic of signalling we discover should therefore impact widely.