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

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 approximately 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.     

Identical G+1 to A mutations in three different introns of the type III procollagen gene (COL3A1) produce different patterns of RNA splicing in three variants of Ehlers-Danlos syndrome. IV. An explanation for exon skipping some mutations and not others

Identical G+1 mutations in three different introns of the gene for type III procollagen (COL3A1) that cause aberrant splicing of RNA were found in three probands with life-threatening variants of Ehlers-Danlos syndrome. Because the three mutations were in a gene with multiple and homologous exons, they provided an interesting test for factors that influence aberrant splicing. The G+1 to A mutation in intron 16 caused extensive exon skipping, the G+1 to A mutation in intron 20 caused both use of a cryptic splice site and retention of all the intron sequences, and the G+1 to A mutation in intron 42 caused efficient use of a single cryptic splice site. The different patterns of RNA splicing were not explained by evaluation of potential cryptic splice sites in the introns by either their homology with 5'-splice sites from other genes or by their delta G(0)37 values for binding to U1 RNA. Instead, the results suggested that the patterns of aberrant RNA splicing were primarily determined by the relative rates at which adjacent introns were normally spliced.     

CRS1 is a novel group II intron splicing factor that was derived from a domain of ancient origin

Protein-dependent group II intron splicing provides a forum for exploring the roles of proteins in facilitating RNA-catalyzed reactions. The maize nuclear gene crs1 is required for the splicing of the group II intron in the chloroplast atpF gene. Here we report the molecular cloning of the crs1 gene and an initial biochemical characterization of its gene product. Several observations support the notion that CRS1 is a bona fide group II intron splicing factor. First, CRS1 is found in a ribonucleoprotein complex in the chloroplast, and cofractionation data provide evidence that this complex includes atpF intron RNA. Second, CRS1 is highly basic and includes a repeated domain with features suggestive of a novel RNA-binding domain. This domain is related to a conserved free-standing open reading frame of unknown function found in both the eubacteria and archaea. crs1 is the founding member of a gene family in plants that was derived by duplication and divergence of this primitive gene. In addition to its previously established role in atpF intron splicing, new genetic data implicate crs1 in chloroplast translation. The chloroplast splicing and translation functions of crs1 may be mediated by the distinct protein products of two crs1 mRNA forms that result from alternative splicing of the crs1 pre-mRNA.