Intron-mediated induction of phenotypic heterogeneity

Introns are universally present in the nuclear genomes of eukaryotes. The budding yeast, an otherwise intron-poor species, preserves two sets of ribosomal protein (RP) genes differing primarily in their introns. Despite recent findings on the role of RP introns under stress and starvation, understanding the contribution of introns to ribosome regulation remains challenging. Here, combining isogrowth profiling with single-cell protein measurements, we found that introns can mediate inducible phenotypic heterogeneity conferring a clear fitness advantage. Osmotic stress leads to bimodal expression of the small ribosomal subunit protein Rps22B, mediated by an intron in the 5′ untranslated region of its transcript. The two resulting yeast subpopulations differ in their ability to cope with starvation. Low Rps22B protein levels resulted in prolonged survival under sustained starvation, while high Rps22B levels enabled cells to grow faster after transient starvation. Further, yeast growing at high sugar concentrations – similar to those in ripe grapes – exhibit bimodal Rps22B expression when approaching stationary phase. Differential intron-mediated regulation of RP genes thus provides a way to diversify the population when starvation looms in natural environments. Our findings reveal a new role for introns in inducing phenotypic heterogeneity in changing environments and suggest that duplicated RP genes in yeast contribute to resolving the evolutionary conflict between precise expression control and environmental responsiveness. RNA samples from treatments with single stressors were obtained from cultures with automated re-inoculation every 8 hours, with a total incubation time of 24 hours, to keep cultures in exponential phase and assure the drug effects have taken place. Strains were grown in YPD with a drug, either in a concentration gradient to select samples closest to 50% of growth inhibition (LiCl, Fenpropimorph, and Myriocin), or in a single concentration (0.4 M NaCl and glucose 20%). Fenpropimorph (Sigma Aldrich cat. No. 36772) was tested in a 0.5-1.5 µM gradient, sequenced samples were treated with 0.85 µM Fenpropimorph. Myriocin (Sigma Aldrich cat. No. 476300) gradient encompassed 0.25-0.75 µg/ml; 0.32 µg/ml Myriocin samples were sequenced. For each sample of extracted RNA, both ribodepleted total RNA and mRNA Seq libraries were prepared at the Cologne Center for Genomics (CCG) and sequenced using 2×100bp paired-end reads.