Evolutie van genregulatie en groei in veranderende omgevingen

Organisms usually respond to environmental changes by adapting the expression of genes necessary for survival. However, such transcriptional reprogramming requires time and energy, and may also leave the organism ill-adapted when the original environment returns. During my PhD, I st­­udied the dynamics of transcriptional reprogramming and fitness in the model eukaryote Saccharomyces cerevisiae in response to changing carbon environments. In one study, using population and single-cell analyses I found that some wild yeast strains rapidly and uniformly adapt gene expression and growth to changing carbon sources, whereas other strains respond more slowly, resulting in long periods of slow growth (the so-called “lag phase”) and large differences between individual cells within the population.I exploited this clonal heterogeneity to evolve a set of mutants that demonstrate how the frequency and duration of changes in carbon source can favor the growth of mutants displaying a spectrum of different carbon catabolite repression strategies. At one end of this spectrum are several “specialist” isolates that display high rates of growth in stable environments, with more stringent catabolite repression and slower transcriptional reprogramming. The other mutants are of a generalist character, displaying slower growth in stable environments, however noisier catabolite repression that allows faster transcriptional reprogramming and shorter lag phases. Whole-genome sequencing of these mutants reveals that mutations in key regulatory genes such as HXK2 and STD1 adjust the regulation and transcriptional noise of metabolic genes, with some mutations leading to alternative gene regulatory strategies that allow “stochastic sensing” of the environment. Mathematical modeling and experimentation reveals patterns of environmental change that will favor the generalist or specialist phenotypes, as well as regimes of change that will favor a stable co-existence between the two phenotypes.Together, the work presented in this thesis reveals a surprising degree of diversity in the lag phase, within clonal populations and across different yeast isolates. These results further reveal how variable and stable environments favor distinct strategies of transcriptional reprogramming and growth. Future studies will continue to examine the molecular and genetic mechanisms of growth and gene regulation in variable environments.Table of contents. 1) Why the lag phase? The costs and benefits of gene regulation, cell fate determination and adaptability in microbes. I) Introduction II) What is diauxie and the lag phase? i) Properties of exponential growth ii) How the lag phase and diauxie are measured and the effect this has on exponential growth. III) Key concepts and measures in ecological theory. i) Niche speciailization and generalization lead to phenotypic diversity. ii) Diversified growth strategies allow a mixture of specialized and generalized phenotypes. IV) Insights into the lag phase from experimental evolution. V) Molecular mechanisms of the lag phase: the repression process. VI) Molecular mechanisms of diauxie: the reprogramming process of adapting to new carbon sources. VII) Selective pressures shaping diauxie: the costs of gene expression. VIII) Conclusions. 2) Different levels of catabolite repression optimize growth in stable and variable environments 3) Expression of the MAL genes explains little of single-­‐cell variability during the lag phase in transition from glucose to maltose. 4) Conclusions. 5) Appendix. I) How environmental frequencies affect average growth rate in diauxie. II) On genes in general and what we can tell about how glucose-­‐related gene regulation plays in fitness. 6) Publications authored by Aaron Newnrpages: 131status: publishe