Assessing the molecular and phenotypic contribution of a horizontally acquired region to yeast adaptation

Romero, A.; Bastias, C.; De Chiara, M.; Saayman, X.; Cherkaoui, H.; Barre, B. P.; Cubillos, F. A.; Martinez, C.; Kessi-Perez, E. I.; Liti, G.; Salinas, F.

doi:10.1101/2025.11.11.687820

bioRxiv · 10.1101/2025.11.11.687820

Assessing the molecular and phenotypic contribution of a horizontally acquired region to yeast adaptation

Romero, A.·Bastias, C.·De Chiara, M.·Saayman, X.·Cherkaoui, H.·Barre, B. P.·Cubillos, F. A.·Martinez, C.·Kessi-Perez, E. I.·Liti, G.·Salinas, F.

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Abstract

Horizontal Gene Transfer (HGT) is the movement of genetic material across species. In Saccharomyces cerevisiae, a DNA segment known as Region B was acquired horizontally from a distant yeast species. This region ([~]17 Kb) encodes 5 genes and is present in the genomes of yeast strains from different phylogenetic clades, with its contribution to yeast niche-specific adaptation remaining unclear. In this work, the genomic structure of Region B was analyzed in yeast strains from the ScRAP (Saccharomyces cerevisiae Reference Assembly Panel) collection, identifying 10 variants that maintain a circular continuity. To assess the role of Region B in yeast adaptation, we performed a high-throughput phenotyping of the ScRAP collection under different growth conditions, identifying that Region B is potentially associated with higher tolerance to oxidative stress. Then, we selected a single yeast strain from the ScRAP collection for characterization of the transcriptional activity of each gene within Region B using a fluorescent reporter. The results revealed that gene expression depends on the hosts genetic background and transcription factors encoded within Region B. To identify the genetic determinants involved in Region B expression within different genetic backgrounds, three expression Quantitative Trait Loci (eQTLs) were mapped and validated. Finally, by performing Region B deletion, we determine the contribution of this region to different fermentative phenotypes, including fermentation rate and amino acid consumption. Altogether, our results suggest a complex regulatory interaction between the horizontally acquired genes and the host genome that contributes to yeast adaptation under fermentation conditions.

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Romero, A., Bastias, C., De Chiara, M., Saayman, X., Cherkaoui, H., Barre, B. P., Cubillos, F. A., Martinez, C., Kessi-Perez, E. I., Liti, G., Salinas, F.. 2025-11-12. Assessing the molecular and phenotypic contribution of a horizontally acquired region to yeast adaptation. https://doi.org/10.1101/2025.11.11.687820

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