Intergenic Regions of Saccharomycotina Yeasts are Enriched in Potential to Encode Transmembrane Domains

Author:

Tassios Emilios12,Nikolaou Christoforos1ORCID,Vakirlis Nikolaos3ORCID

Affiliation:

1. Computational Genomics Group, Institute for Bioinnovation, Biomedical Sciences Research Center “Alexander Fleming” , Vari , Greece

2. School of Medicine, University of Crete , Heraklion , Greece

3. Evolutionary Genomics Lab, Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming” , Vari , Greece

Abstract

AbstractIntergenic genomic regions have essential regulatory and structural roles that impose constraints on their sequences. But regions that do not currently encode proteins also carry the potential to do so in the future. De novo gene emergence, the evolution of novel genes out of previously noncoding sequences has now been established as a potent force for genomic novelty. Recently, it was shown that intergenic regions in the genome of Saccharomyces cerevisiae harbor pervasive cryptic potential to, if theoretically translated, form transmembrane domains (TM domains) more frequently than expected by chance given their nucleotide composition, a property that we refer to as TM-forming enrichment. The source and biological relevance of this property is unknown. Here, we expand the investigation into the TM-forming potential of intergenic regions to the entire Saccharomycotina budding yeast subphylum, in an effort to explain this property and understand its importance. We find pervasive but variable enrichment in TM-forming potential across the subphylum regardless of the composition and average size of intergenic regions. This cryptic property is evenly spread across the genome, cannot be explained by the hydrophobic content of the sequence, and does not appear to localize to regions containing regulatory motifs. This TM-forming enrichment specifically, and not the actual TM-forming potential, is associated, across genomes, with more TM domains in evolutionarily young genes. Our findings shed light on this newly discovered feature of yeast genomes and constitute a first step toward understanding its evolutionary importance.

Funder

State Scholarships Foundation

European Social Fund

Publisher

Oxford University Press (OUP)

Subject

Genetics,Molecular Biology,Ecology, Evolution, Behavior and Systematics

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