The innate immune effector RNase L: a window into translational control through regulation of human mRNAs

Abstract

Translational control is critical for all kingdoms of life. It ensures appropriate use of resources in the production of necessary proteins and adjusts according to need during periods of stress. Perhaps the strongest change in protein production in mammalian cells is triggered by the innate immune response to dsRNA originating from viruses or aberrant endogenous transcription. Key innate immune sensors of dsRNA initiate a fast a deep block of protein synthesis through activation of the effector endonuclease RNase L. Through systematic investigation of the molecular mechanism, we discover cell-wide mRNA destruction by RNase L halts translation during the innate immune response to dsRNA. We further find that innate immune defense transcripts are able to evade this sweeping mRNA destruction with a dynamic positive transcriptional feedback mechanism. By rapidly clearing basal transcripts, RNase L primes the cell for later translation of critical defense factors, thereby facilitating an accurate switch between housekeeping and defense functions. Interestingly, we also observed preferential targeting of active transcripts, suggesting ribosomes may influence RNase L activity. In investigating this possibility, I discover RNase L does associate with ribosomes, and that ribosomes can influence the activity of RNase L. We further proposed that abundant mRNA fragments generated by RNase L would cause ribosome stalling that requires rescue factors to enable defense gene translation. Surprisingly, we found RNase L- cleaved mRNAs do not lead to widespread ribosome stalling or engage the canonical ribosome rescue pathway. Ribosome resolution from abundant RNase L-cleaved transcripts therefore cannot be explained by currently known mechanisms. Lastly, the mRNA substrate preferences of RNase L revealed a differential abundance of coding sequence relative to untranslated regions present basally in the transcriptome, which likely results from mRNA decay pathways. The results of my investigation into the innate immune effector RNase L thus reveal novel observations of bulk mRNA composition, as well as an unprecedented paradigm in ribosome recycling.