Modeling single-cell phenotypes links yeast stress acclimation to transcriptional repression and pre-stress cellular states

Abstract

Stress defense and cell growth are inversely related in bulk culture analyses; however, these studies do not capture cellular heterogeneity, thus obscuring true phenotypic relationships. Here, we devised a microfluidics system to characterize multiple phenotypes in single yeast cells responding dynamically to stress. We simultaneously followed cell and colony growth, cell size and volume, and cell-cycle phase plus nuclear trans-localization of two transcription factors: stress-responsive activator Msn2 and repressor Dot6 that are co-regulated during stress. Coordinated activation reflects a systemic stress response, whereas decoupled behavior indicates factor-specific responses. We scored these features before, during, and after salt stress. Modeling of multi-cell phenotypes revealed surprising new information, including unexpected discordance between Msn2 and Dot6 behavior that revealed subpopulations of cells with distinct growth properties. Although past work connected Msn2 activation to growth rate, we instead found stronger correlations with Dot6 behavior. Post-stress growth rate could be partly predicted by integrating multiple cellular phenotypes, with higher accuracy than considering any single feature alone. Our results underscore that life-history experiences partially predict how cells will respond to stress.