Abstract
In Saccharomyces cerevisiae, splicing is critical for expression of ribosomal protein genes (RPGs), which are among the most highly expressed genes and are tightly regulated according to growth and environmental conditions. However, knowledge of the precise mechanisms by which RPG pre-mRNA splicing is regulated on a gene-by-gene basis is lacking. Here we show that Rpl22p has an extraribosomal role in the inhibition of splicing of the RPL22B pre-mRNA transcript. A stem loop secondary structure within the intron is necessary for pre-mRNA binding by Rpl22p in vivo and splicing inhibition in vivo and in vitro and can rescue splicing inhibition in vitro when added in trans to splicing reactions. Splicing inhibition by Rpl22p may be partly attributed to the reduction of co-transcriptional U1 snRNP recruitment to the pre-mRNA at the RPL22B locus. We further demonstrate that the inhibition of RPL22B pre-mRNA splicing contributes to the down-regulation of mature transcript during specific stress conditions, and provide evidence hinting at a regulatory role for this mechanism in conditions of suppressed ribosome biogenesis. These results demonstrate an autoregulatory mechanism that fine-tunes the expression of the Rpl22 protein and by extension Rpl22p paralog composition according to the cellular demands for ribosome biogenesis.
Highlights
Ribosomal protein genes (RPGs) constitute a majority of the most frequently transcribed genes in the budding yeast Saccharomyces cerevisiae [1]
We demonstrate that the ribosomal protein Rpl22p is able to regulate its own expression by inhibiting the processing of its own RNA transcript, leading to degradation of the RNA. We show that this self-imposed regulation plays a role in limiting RPL22 transcript levels in specific stress conditions
We previously showed that the pre-mRNA of RPL22B contains an intronic alternative 5’ splice site and that splicing at this site gives rise to a transcript that is degraded by the cytoplasmic nonsense-mediated decay (NMD) pathway [14]
Summary
Ribosomal protein genes (RPGs) constitute a majority of the most frequently transcribed genes in the budding yeast Saccharomyces cerevisiae [1]. While RPGs are tightly regulated at the transcriptional level [2], the fact that nearly half of all intron-containing genes in S. cerevisiae are RPGs [3] has led to questions regarding the importance of these introns in RPG regulation. A comprehensive deletion of the yeast RPG intronome revealed numerous cases of intron-dependent intergenic and intragenic regulation of RPG expression that impacted cell growth in various stress conditions [4]. These findings led to the conclusion that introns within RPGs govern the auto- and cross-regulation of RPG expression. While some structural elements within intronic RPGs were found to be important for splicing efficiency [5,6], the precise mechanisms by which this regulation is achieved on a gene-by-gene basis remain largely unknown
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
