The role of the ribosome and translation factors in mediating stress signaling - A key feature of all living organisms is their ability to respond and adapt to an everchanging environment to ensure cellular homeostasis. In response to chemical or physical stress, organisms activate a variety of processes, including quality control mechanisms that preserve the integrity of biological molecules as well as stress response pathways enabling them to mitigate the effect of damage. How and when cells switch between these responses is highly regulated. For example, recent work from my group showed that in response to chemical damage to mRNA, eukaryotes promptly activate ribosome quality control (RQC); on the other hand, if the damage persists, they activate the integrated stress response (ISR). We have known for some time that the ribosome and the translation machinery are key effectors for these pathways. Notably, however, we recently showed that the ribosome itself is widely used as a sensor for these pathways. In particular, our work revealed that collided ribosomes are the key signal for the activation of RQC and the ISR, and that they are in apparent competition with each other, where the induction of one process suppresses that of the other. We note that much of this work was motivated by our initial studies on the consequences of mRNA damage on protein synthesis. However, it is clear that other species of RNA are also susceptible to damage, including ribosomal RNA. Interestingly, the fate of chemically damaged ribosomes has received little to no attention, even though they are known to accumulate in disease states and in response to certain chemotherapeutic treatments. As a result, we will test the hypothesis that cells evolved nonfunctional ribosome decay to recognize and rapidly degrade chemically damaged ribosomes. We are also interested in establishing the mechanism by which such defective ribosomes are identified and distinguished from undamaged ones. Remarkably, emerging from our preliminary studies is the observation that not only is RQC-mediated modification of collided ribosomes critical for the ISR, but also for activation of the DNA damage response. Therefore, we will examine the hypothesis that the response to RNA damage is a hitherto unappreciated pathway for cells to protect themselves expediently from damaging agents. We propose that damaged mRNA and its induction of ribosome collisions serve as a molecular sentinel, alerting cells to hazardous conditions that could damage either DNA or RNA. Finally, in exciting preliminary data, we show that RNA polymerase II stability is intimately coupled to that of the translation factor eIF4E, which binds the capped mRNA products of the polymerase. We propose that this mechanism evolved in eukaryotes as a safeguard ensuring the flux of transcription is fine tuned to that of translation. We will test the model that RNAP II is degraded through a quality-control step during proximal-promoter pause release, acting as a critical checkpoint before elongation by the polymerase can proceed. Collectively, our proposed experiments will reveal fundamental mechanistic insights into how organisms utilize the ribosome and the translational machinery to respond to damaging agents through signaling pathways that also impact transcription and genome integrity.
