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Using Optogenetics to Study Dynamic Signal Encoding and Decoding in S. cerevisiae

  • Author(s): Chen, Susan Yushan
  • Advisor(s): El-Samad, Hana
  • et al.
Abstract

Transcription factors are key mediators of environmental signals. In \textit{S. cerevisiae}, cells may change the concentration, phosphorylation state, binding partner, or temporal dynamics of transcription factors to mediate a response to upstream signals. Dynamic localization of transcription factors to and from the nucleus have been observed for a number of stress-responsive transcription factors in yeast. Two key questions arise from this observation. First, what are the upstream determinants of these nuclear localization events? And second, what are the downstream target gene interpretations?

To probe the upstream determinants of nuclear localization, the activity of PKA, an upstream regulator of the transcription factor Msn2, was perturbed using a combination of genetic mutations and optogenetics. Optogenetic activation with bacterial Photoactivatible Adenylyl Cyclase (bPAC) established a causal connection of PKA activity on Msn2 dynamic nuclear localization. Genetic deletions of PKA network components illustrated that changes to the upstream signaling network can alter Msn2 localization dynamics. The computational analyses revealed that a negative feedback on PKA could explain the observed transient dynamics of Msn2 nuclear localization, and that different PKA network components could tune those Msn2 localization dynamics.

To probe the second question of the downstream target gene interpretations of nuclear localization, another optogenetic tool was optimized and used to directly control transcription factor nuclear localization. CLASP (Controllable Light Activated Shuttling and Plasma membrane sequestration), was engineered to enable precise, modular, and reversible control of TF localization using a combination of two optimized LOV2 optogenetic constructs that sequestered the TF to the plasma membrane in the dark and delivered the TF to the nucleus in the light. CLASP achieved minute-level resolution, reversible localization of many TF cargos, large dynamic range, and tunable target gene expression. Dynamic control of the nuclear localization of Crz1, a naturally pulsatile TF, using CLASP revealed that some Crz1 target genes respond more efficiently to pulsatile TF inputs than to continuous inputs, while others exhibited the opposite behavior. Computational modeling showed that efficient gene expression in response to short pulsing required fast promoter activation and slow inactivation, and that the opposite phenotype can ensued from a multi-stage promoter activation, where a transition in the first stage was thresholded. These data directly demonstrate differential interpretation of TF pulsing dynamics by different genes, and provide plausible models that could achieve these phenotypes.

In summary, this work explored dynamic signal encoding and decoding of transcription factor nuclear localization using optogenetics in \textit{S. cerevisiae}. Control of PKA activity and deletion of PKA network components showed encoding of dynamic transcription factor nuclear localization by the PKA network. Arbitrary control of transcription factor nuclear localization identified differential decoding of transcription factor dynamics by target genes.

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