PXD003898

PXD003898 is an original dataset announced via ProteomeXchange.

Title	Pachysolen tannophilus LC-MSMS
Description	The genetic code is the cellular translation table for the conversion of nucleotide sequences into amino acid sequences. Changes to the meaning of sense codons would introduce errors into almost every translated message and are expected to be highly detrimental. However, reassignment of single or multiple codons in mitochondria and nuclear genomes, although extremely rare, demonstrates that the code can evolve. Several models for the mechanism of alteration of nuclear genetic codes have been proposed (including ‘codon capture’, ‘genome streamlining’ and ‘ambiguous intermediate’ theories), but with little resolution. Here, we report a novel sense codon reassignment in Pachysolen tannophilus, a yeast related to the Pichiaceae. By generating proteomics data and using tRNA sequence comparisons we show that Pachysolen translates CUG codons as alanine and not as the more usual leucine. The Pachysolen tRNA(CAG) is an anticodon-mutated Ala-tRNA containing all major alanine tRNA recognition sites. The polyphyly of the CUG-decoding tRNAs in yeasts is best explained by a tRNA loss driven codon reassignment mechanism. Loss of the CUG-tRNA in the ancient yeast is followed by gradual decrease of respective codons and subsequent codon capture by tRNAs whose anticodon is not part of the aminoacyl-tRNA synthetase recognition region.
HostingRepository	PRIDE
AnnounceDate	2016-05-06
AnnouncementXML	Submission_2016-05-06_06:57:43.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Martin Kollmar
SpeciesList	scientific name: Pachysolen tannophilus NRRL Y-2460; NCBI TaxID: 669874;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2016-04-04 03:17:29	ID requested
⏵ 1	2016-05-06 06:57:44	announced

Dataset with its publication pending

curator keyword: Biological

submitter keyword: yeast CUG codon usage

Martin Kollmar
contact affiliation	Group Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany
contact email	mako@nmr.mpibpc.mpg.de
lab head
Martin Kollmar
contact affiliation	MPI for Biophysical Chemistry
contact email	mako@nmr.mpibpc.mpg.de
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/2016/05/PXD003898

PRIDE project URI

• PRIDE
  1. PXD003898
     1. Label: PRIDE project
     2. Name: Pachysolen tannophilus LC-MSMS