Alternative Splicing and Subfunctionalization Generates Functional Diversity in Fungal Proteomes

Abstract

Alternative splicing is commonly used by the Metazoa to generate more than one protein from a gene. However, such diversification of the proteome by alternative splicing is much rarer in fungi. We describe here an ancient fungal alternative splicing event in which these two proteins are generated from a single alternatively spliced ancestral SKI7/HBS1 gene retained in many species in both the Ascomycota and Basidiomycota. While the ability to express two proteins from a single SKI7/HBS1 gene is conserved in many fungi, the exact mechanism by which they achieve this varies. The alternative splicing was lost in Saccharomyces cerevisiae following the whole-genome duplication event as these two genes subfunctionalized into the present functionally distinct HBS1 and SKI7 genes. When expressed in yeast, the single gene from Lachancea kluyveri generates two functionally distinct proteins. Expression of one of these proteins complements hbs1, but not ski7 mutations, while the other protein complements ski7, but not hbs1. This is the first known case of subfunctionalization by loss of alternative splicing in yeast. By coincidence, the ancestral alternatively spliced gene was also duplicated in Schizosaccharomyces pombe with subsequent subfunctionalization and loss of splicing. Similar subfunctionalization by loss of alternative splicing in fungi also explains the presence of two PTC7 genes in the budding yeast Tetrapisispora blattae, suggesting that this is a common mechanism to preserve duplicate alternatively spliced genes.

Alternative splicing and the evolution of phenotypic novelty

“…Other examples of duplicate genes retained and evolving to resemble ancestral alternative splicing isoforms preceding gene duplication are characterized in the MITF [55], FoxP [56] and Syn-Timp families [57]. Moreover, two genome-wide studies have shown that alternatively spliced genes are more likely to be found as duplicate copies in vertebrates [58] and fungi [59].…”

Plant Actin-Depolymerizing Factors Possess Opposing Biochemical Properties Arising from Key Amino Acid Changes throughout Evolution

“…In general, functional divergence has been proposed to occur via changes in gene expression patterns at the transcriptional level (Force et al, 1999;Hittinger and Carroll, 2007;Gagnon-Arsenault et al, 2013) as well as changes in biochemical function. The primary mechanisms responsible for divergence in biochemical function among paralogs include site-specific regulatory modification of proteins (Marques et al, 2008;Freschi et al, 2011), variation of splicing sites among isoforms (Marshall et al, 2013;Nguyen Ba et al, 2014), and changes in enzymatic activity and protein specificity (Force et al, 1999;Voordeckers et al, 2012). Thus, analyzing key amino acids or functional motifs related to functional divergence could help reconstruct the evolutionary process of paralogs to a certain extent.…”

Nucleotide sequence composition adjacent to intronic splice sites improves splicing efficiency via its effect on pre-mRNA local folding in fungi

“…Nevertheless, in S. cerevisiae the intronic genes are highly expressed and account for >70% of its proteome; in addition, several intron sequences are known to be duplicated within ribosomal protein paralogs Juneau et al 2006). Conversely, in Schizosaccharomyces pombe (an organism with ∼5000 genes) there are ∼5000 introns spreading over one-third of its genome, with up to 20 introns mediating a single gene (Wood et al 2002) and with few known genes displaying AS (Habara et al 1998;Okazaki and Niwa 2000;Marshall et al 2013). Other fungi such as Aspergillus nidulans and Candida albicans show variations in intronic characteristics as well (Kupfer et al 2004;Mitrovich et al 2007).…”