Expression of the essential mRNA export factor Yra1p is autoregulated by a splicing-dependent mechanism

Abstract

Recent evidence supports the idea that pre-mRNA splicing and mRNA export are mechanistically coupled. In metazoans, this process appears to be mediated by a multicomponent complex, which associates with the spliced RNA upstream of the exon–exon junction. One of these components (Aly/REF) has a homolog in the budding yeast Saccharomyces cerevisiae known as Yra1p. The YRA1 gene is essential for growth and required for mRNA export. Notably, YRA1 is one of the only ∼5% intron-containing genes in yeast. Moreover, the YRA1 intron has several unusual features and is conserved in other budding yeast species. Previously, overexpression of intronless YRA1 was shown to be toxic. We show here that overexpression of the intron-containing gene results in increased levels of unspliced pre-mRNA but normal levels of Yra1 protein; conversely, expression of the cDNA results in increased levels of protein and accumulation of nuclear poly(A)⁺ RNA. Two additional lines of evidence suggest that expression of Yra1p is autoregulated: First, expression of excess Yra1p from a plasmid reduces the level of tagged, chromosomal Yra1p, and, second, this effect requires wild-type protein. Replacement of the YRA1 intron with that of other S. cerevisiae genes cannot rescue the dominant-negative growth defect of intronless YRA1. We conclude that the level of Yra1p is negatively autoregulated by a mechanism that involves splicing of its unusual intron. Tight control of the levels of Yra1p might be necessary to couple the rates of pre-mRNA splicing and mRNA export.