PXD008827

PXD008827 is an original dataset announced via ProteomeXchange.

Title	Evolutionary Instability of CUG-Leu in the Genetic Code of Budding Yeasts
Description	The 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.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_03:59:21.520.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Tadeusz 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;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-01-31 10:56:19	ID requested
1	2018-05-21 04:08:09	announced
⏵ 2	2024-10-22 03:59:29	announced	2024-10-22: Updated project metadata.

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]

10.1038/s41467-018-04374-7;

curator keyword: Biological

submitter keyword: genetic code yeast cug

Kenneth Wolfe
contact affiliation	Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
contact email	kenneth.wolfe@ucd.ie
lab head
Tadeusz Krassowski
contact affiliation	University College Dublin
contact email	tadeusz.krassowski@ucdconnect.ie
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2018/05/PXD008827

PRIDE project URI

• PRIDE
  1. PXD008827
     1. Label: PRIDE project
     2. Name: Evolutionary Instability of CUG-Leu in the Genetic Code of Budding Yeasts