title: Coordinated Evolution of Transcriptional and Post-Transcriptional Regulation for Mitochondrial Functions in Yeast Strains.
abstract: Evolution of gene regulation has been proposed to play an important role in environmental adaptation. Exploring mechanisms underlying coordinated evolutionary changes at various levels of gene regulation could shed new light on how organism adapt in nature. In this study, we focused on regulatory differences between a laboratory Saccharomyces cerevisiae strain BY4742 and a pathogenic S. cerevisiae strain, YJM789. The two strains diverge in many features, including growth rate, morphology, high temperature tolerance, and pathogenicity. Our RNA-Seq and ribosomal footprint profiling data showed that gene expression differences are pervasive, and genes functioning in mitochondria are mostly divergent between the two strains at both transcriptional and translational levels. Combining functional genomics data from other yeast strains, we further demonstrated that significant divergence of expression for genes functioning in the electron transport chain (ETC) was likely caused by differential expression of a transcriptional factor, HAP4, and that post-transcriptional regulation mediated by an RNA-binding protein, PUF3, likely led to expression divergence for genes involved in mitochondrial translation. We also explored mito-nuclear interactions via mitochondrial DNA replacement between strains. Although the two mitochondrial genomes harbor substantial sequence divergence, neither growth nor gene expression were affected by mitochondrial DNA replacement in both fermentative and respiratory growth media, indicating compatible mitochondrial and nuclear genomes between these two strains in the tested conditions. Collectively, we used mitochondrial functions as an example to demonstrate for the first time that evolution at both transcriptional and post-transcriptional levels could lead to coordinated regulatory changes underlying strain specific functional variations.
authors.affiliation: Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, United States of America.|College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, P.R. China.
authors.forename: Xuepeng
authors.initials: X
authors.lastname: Sun
authors.affiliation: Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, United States of America.
authors.forename: Zhe
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, United States of America.
authors.forename: Xiaoxian
authors.initials: X
authors.lastname: Guo
authors.affiliation: College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, P.R. China.
authors.forename: Hongye
authors.initials: H
authors.lastname: Li
authors.affiliation: Division of Nutritional Sciences, Cornell University, Ithaca, New York 14853, United States of America.
authors.forename: Zhenglong
authors.initials: Z
authors.lastname: Gu
mesh_terms: D002467:Cell Nucleus / Q000235:genetics; D045222:Electron Transport Chain Complex Proteins / Q000378:metabolism; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D054629:Genome, Mitochondrial / Q000235:genetics; D006418:Heme / Q000378:metabolism; D008928:Mitochondria / Q000235:genetics* / Q000378:metabolism*; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000378:metabolism; D012270:Ribosomes / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000166:cytology* / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D013045:Species Specificity; D014158:Transcription, Genetic
chemical_list: D045222:Electron Transport Chain Complex Proteins; C510155:PUF3 protein, S cerevisiae; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D029701:Saccharomyces cerevisiae Proteins; D006418:Heme