GEPHE SUMMARY
Gephebase Gene
Entry Status
Published
GepheID
GP00001872
Main curator
Courtier
PHENOTYPIC CHANGE
Trait Category
Trait State in Taxon A
freeze-thaw–tolerant
Trait State in Taxon B
freeze-thaw–sensitive and higher growth rate in sugar-rich medium
Ancestral State
Taxon A
Taxonomic Status
Taxon A
Common Name
baker's yeast
Synonyms
Saccharomyces capensis; Saccharomyces italicus; Saccharomyces oviformis; Saccharomyces uvarum var. melibiosus; baker's yeast; S. cerevisiae; brewer's yeast; ATCC 18824; ATCC:18824; CBS 1171; CBS:1171; NRRL Y-12632; NRRL:Y:12632; Saccaromyces cerevisiae; Saccharomyce cerevisiae; Saccharomyes cerevisiae; Sccharomyces cerevisiae
Rank
species
Lineage
cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
NCBI Taxonomy ID
is Taxon A an Infraspecies?
Yes
Taxon A Description
YPS163 - collected from Pennsylvania oak trees
Taxon B
Common Name
baker's yeast
Synonyms
Saccharomyces capensis; Saccharomyces italicus; Saccharomyces oviformis; Saccharomyces uvarum var. melibiosus; baker's yeast; S. cerevisiae; brewer's yeast; ATCC 18824; ATCC:18824; CBS 1171; CBS:1171; NRRL Y-12632; NRRL:Y:12632; Saccaromyces cerevisiae; Saccharomyce cerevisiae; Saccharomyes cerevisiae; Sccharomyces cerevisiae
Rank
species
Lineage
cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Ascomycota; saccharomyceta; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
NCBI Taxonomy ID
is Taxon B an Infraspecies?
Yes
Taxon B Description
laboratory strain S288c
GENOTYPIC CHANGE
Generic Gene Name
AQP1
Synonyms
CO; CHIP28; AQP-CHIP
Sequence Similarities
Belongs to the MIP/aquaporin (TC 1.A.8) family.
GO - Biological Process
GO:0043066 : negative regulation of apoptotic process ... show more
UniProtKB
Homo sapiens
GenebankID or UniProtKB
Mutation #1
Presumptive Null
Yes
Molecular Type
Aberration Type
SNP
SNP Coding Change
Nonsynonymous
Molecular Details of the Mutation
aquaporin yeast 1 gene on chromosome 12 - V121M and P255T - both mutations have an effect on water transport - tested in Xenopus oocytes - GenBank accession numbers for AQY1 and AQY2: GQ848552-74 and GQ870433-54
Experimental Evidence
Taxon A Taxon B Position
Codon - ATG -
Amino-acid Val Met 121
Authors
Will JL; Kim HS; Clarke J; Painter JC; Fay JC; Gasch AP
Abstract
A major goal in evolutionary biology is to understand how adaptive evolution has influenced natural variation, but identifying loci subject to positive selection has been a challenge. Here we present the adaptive loss of a pair of paralogous genes in specific Saccharomyces cerevisiae subpopulations. We mapped natural variation in freeze-thaw tolerance to two water transporters, AQY1 and AQY2, previously implicated in freeze-thaw survival. However, whereas freeze-thaw-tolerant strains harbor functional aquaporin genes, the set of sensitive strains lost aquaporin function at least 6 independent times. Several genomic signatures at AQY1 and/or AQY2 reveal low variation surrounding these loci within strains of the same haplotype, but high variation between strain groups. This is consistent with recent adaptive loss of aquaporins in subgroups of strains, leading to incipient balancing selection. We show that, although aquaporins are critical for surviving freeze-thaw stress, loss of both genes provides a major fitness advantage on high-sugar substrates common to many strains' natural niche. Strikingly, strains with non-functional alleles have also lost the ancestral requirement for aquaporins during spore formation. Thus, the antagonistic effect of aquaporin function-providing an advantage in freeze-thaw tolerance but a fitness defect for growth in high-sugar environments-contributes to the maintenance of both functional and nonfunctional alleles in S. cerevisiae. This work also shows that gene loss through multiple missense and nonsense mutations, hallmarks of pseudogenization presumed to emerge after loss of constraint, can arise through positive selection.
Mutation #2
Presumptive Null
Yes
Molecular Type
Aberration Type
SNP
SNP Coding Change
Nonsynonymous
Molecular Details of the Mutation
aquaporin yeast 1 gene on chromosome 12 - V121M and P255T - both mutations have an effect on water transport - tested in Xenopus oocytes - GenBank accession numbers for AQY1 and AQY2: GQ848552-74 and GQ870433-54
Experimental Evidence
Taxon A Taxon B Position
Codon - - -
Amino-acid Pro Thr 255
Authors
Will JL; Kim HS; Clarke J; Painter JC; Fay JC; Gasch AP
Abstract
A major goal in evolutionary biology is to understand how adaptive evolution has influenced natural variation, but identifying loci subject to positive selection has been a challenge. Here we present the adaptive loss of a pair of paralogous genes in specific Saccharomyces cerevisiae subpopulations. We mapped natural variation in freeze-thaw tolerance to two water transporters, AQY1 and AQY2, previously implicated in freeze-thaw survival. However, whereas freeze-thaw-tolerant strains harbor functional aquaporin genes, the set of sensitive strains lost aquaporin function at least 6 independent times. Several genomic signatures at AQY1 and/or AQY2 reveal low variation surrounding these loci within strains of the same haplotype, but high variation between strain groups. This is consistent with recent adaptive loss of aquaporins in subgroups of strains, leading to incipient balancing selection. We show that, although aquaporins are critical for surviving freeze-thaw stress, loss of both genes provides a major fitness advantage on high-sugar substrates common to many strains' natural niche. Strikingly, strains with non-functional alleles have also lost the ancestral requirement for aquaporins during spore formation. Thus, the antagonistic effect of aquaporin function-providing an advantage in freeze-thaw tolerance but a fitness defect for growth in high-sugar environments-contributes to the maintenance of both functional and nonfunctional alleles in S. cerevisiae. This work also shows that gene loss through multiple missense and nonsense mutations, hallmarks of pseudogenization presumed to emerge after loss of constraint, can arise through positive selection.
COMMENTS
The paralogs AQY1 and AQY2 may have arisen in the whole-genome duplication (WGD) event in the Saccharomyces lineage since all post-WGD species all have two aquaporins whereas most pre-WGD species have a single ortholog (Dana Wohlbach and A.P.G., unpublished). @SeveralMutationsWithEffect
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