<<< Full experiment listing


PXD009643 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleOrganisms with alternative genetic codes resolve unassigned codons via mistranslation and ribosomal rescue
DescriptionOrganisms possessing genetic codes with unassigned codons raise the question of how cellular machinery resolves such codons and how this could impact horizontal gene transfer. Here, we use a genomically recoded Escherichia coli to examine how organisms address translation at unassigned UAG codons, which obstruct propagation of UAG-containing viruses and plasmids. Using mass spectrometry, we show that recoded organisms resolve translation at unassigned UAG codons via near-cognate suppression, dramatic frameshifting from at least -3 to +19 nucleotides, and rescue by ssrA-encoded tmRNA, ArfA, and ArfB. We then demonstrate that deleting tmRNA restores expression of UAG-ending proteins and propagation of UAG-containing viruses and plasmids in the recoded strain, indicating that tmRNA rescue and nascent peptide degradation is the cause of impaired virus and plasmid propagation. The ubiquity of tmRNA homologs suggests that genomic recoding is a promising path to impair horizontal gene transfer and confer genetic isolation in diverse organisms.
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterKarl Barber
SpeciesList scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationListphosphorylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue; deamidated residue
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02018-05-02 03:27:52ID requested
12018-09-18 08:35:52announced
22018-11-04 13:26:49announcedUpdated publication reference for PubMed record(s): 30375330.
Publication List
Ma NJ, Hemez CF, Barber KW, Rinehart J, Isaacs FJ, Organisms with alternative genetic codes resolve unassigned codons via mistranslation and ribosomal rescue. Elife, 7():(2018) [pubmed]
Keyword List
curator keyword: Biological
submitter keyword: E coli, LC-MS/MS
Contact List
Jesse Rinehart
contact affiliationDepartment of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, CT 06520, USA Systems Biology Institute, Yale University, West Haven, CT 06516, USA
contact emailjesse.rinehart@yale.edu
lab head
Karl Barber
contact affiliationYale University
contact emailkarl.barber@yale.edu
dataset submitter
Full Dataset Link List
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/2018/09/PXD009643
PRIDE project URI
Repository Record List
[ + ]