Selection for Reduced Translation Costs at the Intronic 5`end in Fungi

RNA splicing is the central process of intron removal in eukaryotes known to regulate various cellular functions. It is generally believed that introns are not translated; therefore, the potential intronic features that may be related to the translation step (occurring after splicing) have yet to be thoroughly studied. Accordingly, the roles of various sequence features affecting intronic retention and translation regulation have yet to be thoroughly studied. Here, focusing on four fungi as model organisms (Saccharomyces cerevisiae, Schizosaccharomyces pombe, Aspergillus nidulans, and Candida albicans), we performed a comprehensive large scale systems biology study to characterize for the first time how interactions between gene splicing and translation are encoded in transcripts and affects their evolution. By analyzing their intronome we provide evidence of selection for STOP codons close to the intronic 5’ end, and that the beginning of introns are selected for significantly high translation, presumably to reduce translation and metabolic costs in cases of non-spliced introns. Ribosomal profiling data analysis in S. cerevisiae supports the conjecture that in this organism intron retention frequently occurs; thus, introns are partially translated and their translation efficiency affects organismal fitness. These new discoveries are supported by population-genetics considerations. In addition, they are contributory steps towards a broader understanding of intron evolution and the effect of silent mutations on gene expression and organismal fitness; furthermore, they can be used for engineering gene expression in various biotechnological and synthetic biology applications.