Translation regulation by autophagy and nutrient stress

Protein translation is necessary for cell function, but it is an incredibly energy demanding process, and is therefore tightly regulated by the metabolic state of the cell. There are a plethora of translation control mechanisms that are only recently being elucidated. My thesis research has investigated how perturbing the metabolic state of the cell, both subtly via autophagy inhibition and with a sledge-hammer of acute amino acid starvation, impacts translation rates on both a global and mRNA by mRNA basis. Overall, I found that these stresses do not repress translation as expected, indicating the identification of novel mechanisms of protein translation regulation.The majority of my thesis focused on the role of autophagy in regulating protein translation. Autophagy, a cellular sorting, degradation and recycling system, is crucial for the survival of cells under stress and has been demonstrated to play a role in the progression of many human diseases, including cancer and neurodegeneration. By promoting protein degradation, autophagy is proposed to maintain amino acid pools to sustain protein synthesis during metabolic stress. I utilized ribosome profiling to delineate the effects of acute genetic ablation of autophagy on protein translational control. Instead of shaping overall global rates of cap dependent translation, autophagy supports the translation of specific mRNAs, most notably targets involved in cell cycle control and DNA damage repair, by modulating the availability of RNA binding proteins to interact with mRNAs. Specifically, by enabling the protein translation of the DNA damage repair protein BRCA2, autophagy is functionally required to attenuate DNA damage as well as promote cell survival in response to PARP inhibition. This helps to explain the reported increased DNA damage in autophagy deficient cells, and is an important consideration for autophagy inhibitors as adjuvant chemotherapies, which are being tested now. I have also uncovered a novel mechanism of protein translation regulation following acute amino acid starvation. Although mTORC1 signaling indicates repressed translation, 35S-methionine incorporation rates more than double following amino acid withdrawal. This increase in translation rates can be prevented by addition of leucine, although the molecular mechanisms controlling this novel process remain to be identified