Year: 2025
Type: article
Abstract: Copy number variants (CNVs) are an important class of genetic variation that can mediate rapid adaptive evolution. Whereas, CNVs can increase the relative fitness of the organism, they can also incur a cost due to the associated increased gene expression and repetitive DNA. We previously evolved populations of Saccharomyces cerevisiae over hundreds of generations in glutamine-limited (Gln-) chemostats and observed the recurrent evolution of CNVs at the GAP1 locus. To understand the role that gene expression plays in adaptation, both in relation to the adaptation of the organism to the selective condition and as a consequence of the CNV, we measured the transcriptome, translatome, and proteome of 4 strains of evolved yeast, each with a unique CNV, and their ancestor in Gln- chemostats. We find CNV-amplified genes correlate with higher mRNA abundance; however, this effect is reduced at the level of the proteome, consistent with post-transcriptional dosage compensation. By normalizing each level of gene expression by the abundance of the preceding step we were able to identify widespread differences in the efficiency of each level of gene expression. Genes with significantly different translational efficiency were enriched for potential regulatory mechanisms including either upstream open reading frames, RNA-binding sites for Ssd1, or both. Genes with lower protein expression efficiency were enriched for genes encoding proteins in protein complexes. Taken together, our study reveals widespread changes in gene expression at multiple regulatory levels in lineages containing adaptive CNVs highlighting the diverse ways in which genome evolution shapes gene expression.
Source: Molecular Biology and Evolution
Authors: Pieter Spealman, Carolina de Santana, Titir De, David Gresham
Language: English
Subfield: Genetics
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,418
Awards: G1677971379, G2757478976, G4434403881, Integrating Project- and Place-based Research Experiences into General Education Courses to Increase Persistence of First-generation and Rural Undergraduates in STEM, G5185630835, Dynamics and determinants of copy number variation in evolving populations, G7791023878, Regulated and evolutionary responses to nutritional stress, The adaptive potential of translational regulation
OpenAlex ID: W4406739185