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PXD008827-1

PXD008827 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleEvolutionary Instability of CUG-Leu in the Genetic Code of Budding Yeasts
DescriptionThe standard genetic code is almost universal, and the evolutionary factors that caused a few organisms to deviate from it are poorly understood. We report that three independent changes of the genetic code occurred during the evolution of budding yeasts, each of which was a reassignment of the codon CUG from leucine to another amino acid. We identify five major yeast clades that differ by translating CUG as either Ser (2 clades), Ala (1 clade), or Leu (2 clades). The newly discovered Ser2 clade is in the final stages of transition from one genetic code to another. It appears to use only a novel tRNASer (tSCAG) to translate CUG codons, but the gene for the ancestral tRNALeu (tLCAG) is still intact in most species in the clade, consistent with the ‘ambiguous intermediate’ theory. We propose that the three parallel changes of the genetic code in yeasts were not driven by natural selection in favor of their effects on the proteome, but by selection to eliminate the ancestral tLCAG, possibly in response to a killer toxin.
HostingRepositoryPRIDE
AnnounceDate2018-05-21
AnnouncementXMLSubmission_2018-05-21_04:08:08.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterTadeusz Krassowski
SpeciesList scientific name: Lipomyces starkeyi; NCBI TaxID: 29829; scientific name: Pichia kudriavzevii; NCBI TaxID: 4909; scientific name: Citeromyces matritensis; NCBI TaxID: 36909; scientific name: Cyberlindnera jadinii; NCBI TaxID: 4903; scientific name: Pachysolen tannophilus; NCBI TaxID: 4918; scientific name: Komagataella phaffii; NCBI TaxID: 460519; scientific name: Candida parapsilosis; NCBI TaxID: 5480; scientific name: Peterozyma xylosa; NCBI TaxID: 1337056; scientific name: Kuraishia capsulata; NCBI TaxID: 317047; scientific name: Ambrosiozyma philentoma; NCBI TaxID: 43984; scientific name: Ogataea polymorpha; NCBI TaxID: 460523; scientific name: Tortispora caseinolytica; NCBI TaxID: 51930; scientific name: Saturnispora dispora; NCBI TaxID: 29835; scientific name: Ascoidea rubescens; NCBI TaxID: 54195; scientific name: Nakazawaea wickerhamii; NCBI TaxID: 1538186; scientific name: [Candida] boidinii; NCBI TaxID: 5477; scientific name: Saccharomycopsis capsularis; NCBI TaxID: 36036; scientific name: Babjeviella inositovora; NCBI TaxID: 45609;
ModificationListNo PTMs are included in the dataset
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02018-01-31 10:56:19ID requested
12018-05-21 04:08:09announced
22024-10-22 03:59:29announced2024-10-22: Updated project metadata.
Publication List
Krassowski T, Coughlan AY, Shen XX, Zhou X, Kominek J, Opulente DA, Riley R, Grigoriev IV, Maheshwari N, Shields DC, Kurtzman CP, Hittinger CT, Rokas A, Wolfe KH, Evolutionary instability of CUG-Leu in the genetic code of budding yeasts. Nat Commun, 9(1):1887(2018) [pubmed]
Keyword List
curator keyword: Biological
submitter keyword: genetic code yeast cug
Contact List
Kenneth Wolfe
contact affiliationConway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
contact emailkenneth.wolfe@ucd.ie
lab head
Tadeusz Krassowski
contact affiliationUniversity College Dublin
contact emailtadeusz.krassowski@ucdconnect.ie
dataset submitter
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Dataset FTP location
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