Messenger RNA splicing is an essential part of eukaryotic gene expression as the coding regions of most eukaryotic genes are interrupted by noncoding introns. In higher eukaryotes, the process of splicing is utilized to regulate both qualitative and quantitative aspects of gene expression (reviewed in Black, 2000
; Blencowe, 2006
). Alterations in the pattern of splice site usage in multi-intronic transcripts can produce a spectrum of protein isoforms from a single genomic locus, greatly expanding the genetic repertoire of an organism. Furthermore, when coupled to nonsense-mediated decay, alternative splicing can function as an “on/off” switch by introducing premature termination codons, thereby directing mRNA degradation (Lewis et al., 2003
; Mitrovich and Anderson, 2000
By contrast, only ~5% of genes in the budding yeast Saccharomyces cerevisiae
are intron containing, and with few exceptions these genes have only a single intron (Spingola et al., 1999
). Splice site sequences in yeast introns generally conform to a strict consensus, and documented instances of alternative splicing are rare (Davis et al., 2000
). Nonetheless, a number of examples of regulated splicing have been demonstrated in yeast, including a set of transcripts that are constitutively transcribed but are efficiently spliced only during meiosis (Davis et al., 2000
; Juneau et al., 2007
; Nandabalan et al., 1993
). These introns, as well as the autoregulated introns in Rpl30 and Yra1, all contain nonconsensus splice sites, which are required for regulation (Eng and Warner, 1991
; Preker et al., 2002
). However, because most yeast introns contain consensus splice site sequences, it has remained unknown whether splicing could function as a more general regulator of gene expression.
Interestingly, the set of intron-containing genes in yeast includes many metabolic regulators and is highly enriched for ribosomal protein genes (RPGs). Of the 139 RPGs encoded in the yeast genome, 102 are interrupted by at least one intron, making this by far the largest functional category. It has been previously established that starvation for amino acids leads to transcriptional repression of RPG synthesis, repression of rRNA synthesis, a general repression of translation, and an upregulation of enzymes involved in amino acid biosynthesis through a process controlled by the nonessential kinase Gcn2 (Chen and Powers, 2006
; Cherkasova and Hinnebusch, 2003
; Dever et al., 1992
; Hinnebusch, 2005
). Because of the overrepresentation of translational components among the intron-containing genes, we hypothesized that the splicing of these transcripts might also be regulated in response to amino acid starvation.
Here we have taken a microarray-based strategy to examine the transcript-specific splicing changes resulting from exposure to two unrelated but environmentally relevant stresses: amino acid starvation and ethanol toxicity. We find that the splicing of the majority of RPGs is inhibited within minutes of inducing amino acid starvation. By comparison, exposure to toxic levels of ethanol, which is not known to induce a global repression of translation, has little effect on the splicing of the RPG transcripts. Rather, in response to the latter stress, the splicing of a different set of transcripts is downregulated, while the splicing efficiency of a third group of transcripts is improved. The specificity of these responses and the speed of their onset argue that splicing provides an important opportunity for regulation of gene expression in response to environmental stress. Furthermore, the capacity for transcription-independent regulation may explain the evolutionary retention of introns in these genes.