Dynamic regulation of mRNA processing in adapting fungi

Fungi detect and adapt to stressful environmental changes by reorganizing their messenger RNA (mRNA) and protein. Better understanding of how this works is essential to counter the global human health threat from fungal pathogens. I propose three interlinked aims that bring together mechanistic insight, high-throughput biology, and machine learning to investigate this: 1. Which sequences in the terminal/3’ regulatory region (3’UTR) of an mRNA encode its stress-responsive localization, translation, and decay? I will synthesize a large library of chimeric mRNAs, measure their mRNA processing in Saccharomyces cerevisiae by RNA sequencing, and use modelling to find out which combinations of sequence and stress inputs drive which outputs. 2. How does the conserved RNA-binding protein Ssd1 enable fungal stress tolerance and virulence? Ssd1 is essential for fungi to survive stress, regulating specific mRNAs through their 3’UTRs, but its exact RNA-binding sites are unknown. I will measure these sites, before and after stress, to discover Ssd1’s mechanism of action. 3. How does the fungal pathogen Cryptococcus neoformans begin infecting a human lung? I will use RNA sequencing and other high-throughput approaches to characterize the transcriptional and post-transcriptional processes enabling C. neoformans to adapt and grow in a lung-like environment.