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Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans-acting effects influencing species dependent essential genes

By Monica R. Sanchez, Celia Payen, Frances Cheong, Blake T Hovde, Sarah Bissonnette, Adam P. Arkin, Jeffrey M Skerker, Rachel B Brem, Amy A. Caudy, Maitreya J. Dunham

Posted 12 Nov 2017
bioRxiv DOI: 10.1101/218305 (published DOI: 10.1101/gr.232330.117)

To understand how complex genetic networks perform and regulate diverse cellular processes, the function of each individual component must be defined. Comprehensive phenotypic studies of mutant alleles have been successful in model organisms in determining what processes depend on the normal function of a gene. These results are often translated to the increasing number of newly sequenced genomes by using sequence homology. However, sequence similarity does not always mean identical function or phenotype, suggesting that new methods are required to functionally annotate newly sequenced species. We have implemented comparative functional analysis by high-throughput experimental testing of gene dispensability in Saccharomyces uvarum, a sister species of S. cerevisiae. We created haploid and heterozygous diploid Tn7 insertional mutagenesis libraries in S. uvarum to identify species dependent essential genes, with the goal of detecting genes with divergent function. Comprehensive gene dispensability comparisons with S. cerevisiae revealed that approximately 12% of conserved orthologs are predicted to display diverged dispensability, including 22 confirmed differentially essential genes. Surprisingly, despite their differences in essentiality, these genes are capable of cross-species complementation, demonstrating that other trans-acting factors that are background dependent contribute to differential gene essentiality. Furthermore, we identified an instance of swapped essentiality between two paralogs, CDC25 and SDC25 between these two species. This data set provides direct experimental evidence of gene function across species, which can inform comparative genomic analyses, improve gene annotation and be applied across a diverse set of microorganisms to further our understanding of gene function evolution.

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