Swain, Peter

Wallace, Edward

Huo, Yu

2023-07-25T12:54:30Z

2023-07-25T12:54:30Z

2023-07-25

In response to environmental changes, cells launch new programmes of gene expression. Here I address how cells with their finite proteomes regulate ribosomal levels as the environment changes in batch cultures and, given two carbon sources, how cells prioritise which to use. In the initial chapters, I describe how I measure the dynamics of both growth and ribosome levels in S. cerevisiae using microplate readers. I show that growth only enters a prolonged exponential phase if the initial sugar concentration is sufficiently high, otherwise the specific growth rate peaks rather than plateaus. Nevertheless, Monod’s law still holds for the initial sugar concentration and the maximum specific growth rate. Using GFP-tagged ribosomes, I then measure the population’s total ribosome level and demonstrate that the population’s growth rate is proportional to this level in the early phases of growth. I go on to define the effective translation rate as the ratio between the population’s growth rate and its ribosome level, and find that in exponential phase, the effective translation rate and the ribosomal fraction are constant over time. Further, the results of challenging cells with different stresses suggest an empirical upper limit to the effective translation rate. To understand these findings, I develop a minimal self-replicator model and analyse its behaviour both at and away from steady state. I extend this model to include carbon and nitrogen and derive mechanistically a form of Monod’s law for two substrates. In the final chapters, I investigate how cells prioritise the use of non-glucose sugars, specifically galactose and palatinose, which is little studied. I show that cells exhibit diauxie in galactose-palatinose mixtures, prioritising galactose. In addition, I demonstrate that constitutively active Gal4 in a gal80∆ mutant causes a long delay in palatinose metabolism, and that this delay can be mostly alleviated by deleting the gene for the galactose transporter. To investigate the cause of this effect, I perform an RNAseq Gal4 signalling. With this discovery, I build a simple model to understand how the Gal4 signal affects the inducibility of the MAL network, which predicts that the isomaltases are excessively expressed relative to MAL11 when Gal4 is constitutively active. I therefore delete IMA1, which encodes one of the two isomaltases, from the gal80∆ mutant, and, as expected, this mutant can use palatinose with little lag. My results therefore provide a novel example of non-glucose catabolite repression in S. cerevisiae and how one network can affect another by changing its inducibility.

https://hdl.handle.net/1842/40829

http://dx.doi.org/10.7488/era/3584

en

The University of Edinburgh

Montaño-Gutierrez, Luis Fernando, Nahuel Manzanaro Moreno, Iseabail L. Farquhar, Yu Huo, Lucia Bandiera, and Peter S. Swain. 2022. “Analysing and Meta-Analysing Time-Series Data of Microbial Growth and Gene Expression from Plate Readers.” Plos Computational Biology 18 (5): e1010138. https://doi.org/10.1371/journal. pcbi.1010138

non-glucose sugars

galactose preference

palatinose

GAL

ribosome levels

yeast cells

Study of how catabolite repression and ribosome levels determine cell growth in batch cultures of Saccharomyces cerevisiae

A study of how catabolite repression and ribosome levels determine cell growth in batch cultures of Saccharomyces cerevisiae

Thesis or Dissertation

Doctoral

PhD Doctor of Philosophy