Prevalence and Functional Significance of Regulated Alternative Splicing in Plant Pathogenic Fungi

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Understanding the molecular basis of microbial pathogenicity is vital for deciphering the biological process of disease, and for designing new and effective disease control methods. In spite of advances in treatment of microbial diseases, fungal diseases continue to pose an increasing threat to humans, animals, and plants that often endanger food security and human well-being. The last few decades, in particular, have seen an unprecedented increase in emerging infectious fungal diseases, while the continuous loss to microbial drug resistance of available chemistries for disease control, intensifies the problem and necessitates the development of novel therapeutic strategies. Key to this process is the elucidation of the molecular mechanisms employed by microbes to infect their hosts. In this respect, alternative splicing (AS), a key element in eukaryotic gene expression by which different protein variants are generated from the same gene, is an unexplored feature of microbial pathogenicity which could promote microbial virulence by regulating the optimal production of virulence factors during infection. Thus, the project will focus on a systematic analysis of AS in plant pathogenic fungi, with an emphasis on deciphering its functional significance for parasitic infections. The findings will significantly advance our understanding of fungal pathogenesis and could be used for the development of novel therapeutic treatments for plant diseases through the pharmaceutical manipulation of fungal AS during infection of the host. The project will also be used as a basis for raising public awareness on infectious fungal diseases and training of a diverse student body in molecular plant sciences. Most studies on fungal pathogenesis on plants have focused on the discovery and biochemical characterization of virulence factors that contribute to infections and disease, but much less attention has been placed on the epigenetic mechanisms that control transcriptome diversity of virulence-associated genes. AS splicing is perhaps the most crucial posttranscriptional regulatory mechanism of gene expression but, despite its importance in generating proteome diversity and functional complexity in eukaryotic cells, its prevalence, biological role, and functional consequence for fungal pathogenicity have been barely studied. The goal in this project is to systematically identify and characterize AS events in plant pathogenic fungi during a complete infection cycle of their host, in order to provide critical answers to fundamental questions regarding its pervasiveness, species conservation, and contribution to microbial virulence. This area of study is important because regulated AS of virulence-associated genes is a relatively unexplored feature of microbial pathogenicity, which potentially enables microbes to quickly modulate and fine-tune interactions with their host. To achieve its goals, the project will integrate genome-wide transcriptome profiling, with selective detection of novel splice isoforms through targeted proteomics approaches, and functional analyses of candidate AS genes by RNAi-mediated isoform-specific gene targeting. To assess the generality of the findings, the analysis will be done in two phylogenetically related plant pathogenic fungi when infecting their common host. The successful completion of this project could trigger a paradigm-shift in the field of host-microbe interactions by highlighting the importance of AS-mediated post-transcriptional regulation in parasite fitness and virulence.