Doctor of Philosophy

dissertationThe integrated stress response (ISR) is a highly conserved protective mechanism that is activated in response to a wide variety of stress conditions including heme deficiency, viral infection, amino acid deprivation, and endoplasmic reticulum stress. At its core, this pathway modulates the availability of two central translation factors. It then utilizes the resulting change in translation initiation to first attenuate canonical translation and upregulate transcription of stress response genes, and then restore canonical translation for the expression of those genes. The players central to this system are the translation factors eIF2 and eIF2B, a set of four eIF2 kinases, GCN2, PKR, PERK, and HRI, and the transcription factor ATF4. The translation factor eIF2 is necessary for translation initiation, and eIF2B recycles eIF2 from its inactive state to its active state after each round of translation. During stress conditions, a stress-specific signal activates one of the four kinases and the resulting eIF2 phosphorylation diverts both eIF2 and eIF2B from the canonical translation pathway. This limits availability of active eIF2 GTP for translation initiation, and the ISR harnesses a stochastic binding mechanism to paradoxically downregulate canonical translation while simultaneously upregulating translation of ATF4. Finally, ATF4 induces transcription of stress response genes as well as a phosphatase that restores canonical translation and allows these genes to be translated. The cell's ultimate survival depends on both the strength and duration of stress conditions and the cellular context provided by interacting pathways. In this dissertation, I present a model of translation regulation by the ISR in three parts: a core translation model, an activation model, and a model of phosphatase activity. I then use these models to explore the role of eIF2B, activation mechanism, and phosphatase on the emergent behavior of the pathway. I show that the ISR is a dimmer-switch translation regulation pathway with eIF2B tuning the balance between an analog dimmer translation response and a digital switch-like translation response. I then present evidence that the stress-dependent ISR activation mechanisms may control the time spent in each response as well as the stress level necessary to "flip the switch" between analog and digital behaviors. Finally, I discuss the role of phosphatases in the initiation of the pathway and on the restoration of canonical translation and present results showing that the constitutive phosphatase CreP regulates entry into the analog phase of the response and may also influence the restoration of canonical translation by ATF4 transcription products. i