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

Sánchez, Mónica; Payen, Célia; Cheong, Frances; Hovde, Blake T.; Bissonnette, Sarah; Arkin, Adam P.; Skerker, Jeffrey M.; Brem, Rachel B.; Caudy, Amy A.; Dunham, Maitreya J.

doi:10.1101/218305

Cited by 9 publications

(20 citation statements)

References 45 publications

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“…A large fraction of regulatory variations observed between the species was lost when comparing the two hybrid alleles. This indicates prominence of trans effects, in agreement with other experimental systems (Albert et al, 2018;Liu et al, 2019;McManus et al, 2010;Sanchez et al, 2019;Yvert et al, 2003).…”

Section: Discussionsupporting

confidence: 91%

Independent evolution of transcript abundance and gene regulatory dynamics

Krieger

Lupo

Levy³

et al. 2020

Preprint

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Changes in gene expression drive novel phenotypes, raising interest in how gene expression evolves. In contrast to the static genome, cells regulate gene expression to accommodate changing conditions. Previous comparative studies focused on specific conditions, describing inter-species variation in expression levels, but providing limited information about variations in gene regulation. To close this gap, we profiled gene expression of related yeast species in hundreds of conditions, and used co-expression analysis to distinguish variations in transcription regulation from variations in expression levels or environmental perception. The majority of genes whose expression varied between the species maintained a conserved transcriptional regulation. Profiling the interspecific hybrid provided insights into the basis of variations, showed that trans-varying alleles interact dominantly, and revealed complementation of cis-variations by variations in trans.Our data suggests that gene expression diverges primarily through changes in promoter strength that do not alter gene positioning within the transcription network.

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Section: Discussionsupporting

confidence: 91%

Independent evolution of transcript abundance and gene regulatory dynamics

Krieger

Lupo

Levy³

et al. 2020

Preprint

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“…Though we deleted a small number of S. uvarum genes to compare with the orthologous S. cerevisiae allele deletions, we did not explore S. uvarum genes genome wide. We hope to remedy this in the future using our recently created S. uvarum insertional mutagenesis library (Sanchez et al 2017b). In vivo transposition is another potential approach that has recently been applied to S. paradoxus x S. cerevisiae hybrids (Weiss et al 2018).…”

Section: Discussionmentioning

confidence: 99%

“…These plates were then transferred to liquid selective media and pooled.S. uvarum deletion strains were provided by Sarah Bissonnette and Jasper Rine (UC Berkeley)(Sanchez et al 2017b). All collections were grown as pools in duplicate in three different chemostat mediaglucose limited, phosphate limited, and sulfate limited.…”

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confidence: 99%

Fitness Benefits of Loss of Heterozygosity in SaccharomycesHybrids

Lancaster

Payen

Heil

et al. 2018

Preprint

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With two genomes in the same organism, interspecific hybrids have unique opportunities and costs. In both plants and yeasts, wild, pathogenic, and domesticated hybrids may eliminate portions of one parental genome, a phenomenon known as loss of heterozygosity (LOH).Laboratory evolution of hybrid yeast recapitulates these results, with LOH occurring in just a few hundred generations of propagation. In this study, we systematically looked for alleles that are beneficial when lost in order to determine how prevalent this mode of adaptation may be, and to determine candidate loci that might underlie the benefits of larger-scale chromosome rearrangements. These aims were accomplished by mating Saccharomyces uvarum with the S. cerevisiae deletion collection to create hybrids, such that each nonessential S. cerevisiae allele is deleted. Competitive fitness assays of these pooled, barcoded, hemizygous strains, and accompanying controls, revealed a large number of loci for which LOH is beneficial. We found that the fitness effects of hemizygosity are dependent on the species context, the selective environment, and the species origin of the deleted allele. Further, we found that hybrids have a larger distribution of fitness consequences vs. matched S. cerevisiae hemizygous diploids. Our results suggest that LOH can be a successful strategy for adaptation of hybrids to new environments, and we identify candidate loci that drive the chromosomal rearrangements observed in evolution of yeast hybrids.

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“…PAN1). Calling of essential genes from transposon insertion datasets could be improved by also incorporating datasets from diploids, where very few heterozygous gene knockouts exhibit strong fitness defects (13,21).…”

Section: Identification Of Essential Genesmentioning

confidence: 99%

“…However, the collection is highly biased toward regulatory genes of interest to the community. In a pioneering approach, thousands of random Tn7 transposon insertions also were generated in vitro and integrated into the C. glabrata genome, which were then arrayed and screened individually for susceptibility to antifungals (12,13).…”

Section: Introductionmentioning

confidence: 99%

Identification of essential genes and fluconazole resistance genes inCandida glabrataby profiling ofHermestransposon insertions

Gale

Sakhawala

Levitan

et al. 2020

Preprint

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Within the budding yeasts, the opportunistic pathogen Candida glabrata and other members of the Nakaseomyces clade have developed virulence traits independently from the CTG clade that includes Candida albicans. To begin exploring the genetic basis of C. glabrata virulence and its innate resistance to antifungals, we launched the Hermes transposon from a plasmid and obtained more than 500,000 different semi-random insertions throughout the genome.Using machine learning, we identify up to 1278 protein-encoding genes (25% of total) that cannot tolerate transposon insertions and are thus essential for C. glabrata fitness in vitro.Interestingly, genes involved in mRNA splicing were less likely to be essential in C. glabrata than their orthologs in S. cerevisiae, whereas the opposite is true for genes involved in kinetochore function and chromosome segregation. Insertions in several known genes (e.g. PDR1, CDR1, PDR16, PDR17, UPC2A, DAP1) caused hypersensitivity to the first-line antifungal fluconazole, and we identify 12 additional genes that also contribute to innate fluconazole resistance (KGD1, KGD2, YHR045W, etc). Insertions in 200 other genes conferred significant resistance to fluconazole, two-thirds of which function in mitochondria and likely down-regulate Pdr1 expression or function. These findings show the utility of transposon insertion profiling in genome-wide forward-genetic investigations of fungal pathogens. IMPORTANCE Pathogenic yeasts cause mucosal and systemic infections in millions of people each year. The innate resistance of Candida glabrata to fluconazole and its ability to acquire resistance to

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

Abstract: Abstract

Cited by 9 publications

References 45 publications

Independent evolution of transcript abundance and gene regulatory dynamics

Independent evolution of transcript abundance and gene regulatory dynamics

Fitness Benefits of Loss of Heterozygosity in SaccharomycesHybrids

Identification of essential genes and fluconazole resistance genes inCandida glabrataby profiling ofHermestransposon insertions

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