Intron-mediated induction of phenotypic heterogeneity

Abstract

Intragenic regions that are removed during maturation of the RNA transcript—introns—are universally present in the nuclear genomes of eukaryotes1. The budding yeast, an otherwise intron-poor species, preserves two sets of ribosomal protein genes that differ primarily in their introns2,3. Although studies have shed light on the role of ribosomal protein introns under stress and starvation4–6, understanding the contribution of introns to ribosome regulation remains challenging. Here, by combining isogrowth profiling7 with single-cell protein measurements8, we show that introns can mediate inducible phenotypic heterogeneity that confers a clear fitness advantage. Osmotic stress leads to bimodal expression of the small ribosomal subunit protein Rps22B, which is 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 levels of Rps22B protein result in prolonged survival under sustained starvation, whereas high levels of Rps22B enable cells to grow faster after transient starvation. Furthermore, yeasts growing at high concentrations of sugar, similar to those in ripe grapes, exhibit bimodal expression of Rps22B when approaching the stationary phase. Differential intron-mediated regulation of ribosomal protein genes thus provides a way to diversify the population when starvation threatens in natural environments. Our findings reveal a role for introns in inducing phenotypic heterogeneity in changing environments, and suggest that duplicated ribosomal protein genes in yeast contribute to resolving the evolutionary conflict between precise expression control and environmental responsiveness9.

Single‐cell isogrowth profiling: Uniform inhibition uncovers non‐uniform drug responses

“…We recently developed single‐cell isogrowth profiling, an approach to identify and measure non‐genetic heterogeneity induced by drug treatment. 4 A major source of inaccuracy in the study of responses to chemical interventions is that, in addition to the drug‐specific response, there is a non‐specific effect of stress and slowed growth. In isogrowth profiling, a combination of two drugs is precisely titrated in different ratios to always achieve the same overall growth inhibition in the target population 5 (Figure 1 ).…”

“…Adapted from Refs. 4 and 5 under CC‐BY 4.0 licence; parts of this figure were created with BioRender.com…”

“…We recently developed single‐cell isogrowth profiling, an approach to identify and measure non‐genetic heterogeneity induced by drug treatment 4 . A major source of inaccuracy in the study of responses to chemical interventions is that, in addition to the drug‐specific response, there is a non‐specific effect of stress and slowed growth.…”

“…Adapted from Refs. 4 and 5 under CC-BY 4.0 licence; parts of this figure were created with BioRender.com for the presence of introns, which were known to modulate gene expression levels of ribosomal proteins, but their role in cell-to-cell expression heterogeneity had not been observed. This drug-induced effect was dose-and growth rate-dependent, which possibly explains why it had been overlooked in previous approaches.…”

RNA structure landscape ofS. cerevisiaeintrons

“…Though progress has been made identifying splice sites, predicting steady-state splicing levels, and understanding the spliceosome's structure, [1][2][3] many of the mechanisms that regulate splicing remain unclear. In addition, functional roles for introns beyond splicing have been proposed [4][5][6][7][8] but are not well understood.…”