Differential paralog divergence modulates genome evolution across yeast species
| Autor: | Mei Huang, Ivan Liachko, Monica R. Sanchez, Maitreya J. Dunham, Erica Alcantara, Aaron W. Miller, Margaret L. Hoang, Dave A. Pai, Cheryl M. Tucker, Anna B. Sunshine, Bryony Lynch, Christopher G. DeSevo |
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| Rok vydání: | 2017 |
| Předmět: |
Evolutionary Genetics
0301 basic medicine Cancer Research Genetic Fitness Yeast and Fungal Models Paradoxus Fungal Evolution Genome Evolution Genetics (clinical) 2. Zero hunger Genetics Experimental evolution Sulfates Genomics Adaptation Physiological Chemistry Experimental Organism Systems Sulfate Transporters Physical Sciences Genome Fungal Research Article Genome evolution Saccharomyces cerevisiae Proteins Genotype lcsh:QH426-470 Anion Transport Proteins Saccharomyces cerevisiae Locus (genetics) Mycology Biology Research and Analysis Methods Molecular Evolution Evolution Molecular Saccharomyces 03 medical and health sciences Model Organisms Selection Genetic Molecular Biology Ecology Evolution Behavior and Systematics Comparative genomics Evolutionary Biology Human evolutionary genetics Organisms Fungi Gene Amplification Chemical Compounds Biology and Life Sciences Computational Biology Genetic Variation Comparative Genomics biology.organism_classification Yeast lcsh:Genetics 030104 developmental biology Genetic Loci Evolutionary biology Mutation Salts |
| Zdroj: | PLoS Genetics, Vol 13, Iss 2, p e1006585 (2017) PLoS Genetics |
| ISSN: | 1553-7404 |
| Popis: | Evolutionary outcomes depend not only on the selective forces acting upon a species, but also on the genetic background. However, large timescales and uncertain historical selection pressures can make it difficult to discern such important background differences between species. Experimental evolution is one tool to compare evolutionary potential of known genotypes in a controlled environment. Here we utilized a highly reproducible evolutionary adaptation in Saccharomyces cerevisiae to investigate whether experimental evolution of other yeast species would select for similar adaptive mutations. We evolved populations of S. cerevisiae, S. paradoxus, S. mikatae, S. uvarum, and interspecific hybrids between S. uvarum and S. cerevisiae for ~200–500 generations in sulfate-limited continuous culture. Wild-type S. cerevisiae cultures invariably amplify the high affinity sulfate transporter gene, SUL1. However, while amplification of the SUL1 locus was detected in S. paradoxus and S. mikatae populations, S. uvarum cultures instead selected for amplification of the paralog, SUL2. We measured the relative fitness of strains bearing deletions and amplifications of both SUL genes from different species, confirming that, converse to S. cerevisiae, S. uvarum SUL2 contributes more to fitness in sulfate limitation than S. uvarum SUL1. By measuring the fitness and gene expression of chimeric promoter-ORF constructs, we were able to delineate the cause of this differential fitness effect primarily to the promoter of S. uvarum SUL1. Our data show evidence of differential sub-functionalization among the sulfate transporters across Saccharomyces species through recent changes in noncoding sequence. Furthermore, these results show a clear example of how such background differences due to paralog divergence can drive changes in genome evolution. Author summary Both comparative genomics and experimental evolution are powerful tools that can be used to make inferences about evolutionary processes. Together, these approaches provide the opportunity to observe evolutionary adaptation over millions of years where selective history is largely unknown, and over short timescales under controlled selective pressures in the laboratory. We have used comparative experimental evolution to observe the evolutionary fate of an adaptive mutation, and determined to what degree the outcome is conditional on the genetic background. We evolved several populations of different yeast species for over 200 generations in sulfate-limited conditions to determine how the differences in genomic context can alter evolutionary routes when challenged with a nutrient limitation selection pressure. We find that the gene encoding a high affinity sulfur transporter becomes amplified in most species of Saccharomyces, except in S. uvarum, in which the amplification of the paralogous sulfate transporter gene SUL2 is recovered. We attribute this change in amplification preference to mutations in the non-coding region of SUL1, likely due to reduced expression of this gene in S. uvarum. We conclude that the adaptive mutations selected for in each organism depend on the genomic context, even when faced with the same environmental condition. |
| Databáze: | OpenAIRE |
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