Introduction:: To survive changing conditions, cells transmit environmental information through signaling pathways to transcription factors (TFs), which bind DNA and regulate gene expression. Cells control the activity of transcription factors (TFs) by, among other things, regulating their nuclear localization and their ability to bind DNA. For example, short nuclear bursts of the tumor suppressor p53 are sufficient to induce DNA repair genes, but activation of apoptotic genes involves both sustained nuclear p53 and post-translational modifications (PTMs) that improve its ability to bind DNA. We used the Saccharomyces cerevisiae general stress response TF Msn2 as a model system to investigate how these mechanisms interact.
Materials and Methods:: We used CLASP to control the nuclear localization of high and low affinity Msn2 mutants with light (Figure 1). We then used a programmable LED array to drive defined patterns of Msn2 localization and measured the response of downstream genes by microscopy. We fit the measurements to a computational model of gene expression and identified promoter properties that drive the signal decoding behavior of genes.
Results, Conclusions, and Discussions:: The effects of changing TF affinity were highly promoter dependent. Increasing TF affinity allowed gene activation for a wider range of localization patterns, though the relative ability to respond to pulsed versus continuous TF dynamics was set primarily by promoter. Our modeling indicated that reducing the number and affinity of TF binding sites, slow activation kinetics, or fast deactivation kinetics can cause differences in how genes decode the dynamics of high/low affinity TFs. Our results show how cells and engineers could exploit concerted control of TF localization and affinity to tune the activation of specific sets of genes. For example, pulses of a TF with a low affinity PTM can tune activation of highly sensitive targets only, whereas with a high affinity PTM it can tune all targets.
