PXD009643-3

PXD009643 is an original dataset announced via ProteomeXchange.

Title	Organisms with alternative genetic codes resolve unassigned codons via mistranslation and ribosomal rescue
Description	Organisms 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.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:45:24.634.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Karl Barber
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	phosphorylated residue; monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2018-05-02 03:27:52	ID requested
1	2018-09-18 08:35:52	announced
2	2018-11-04 13:26:49	announced	Updated publication reference for PubMed record(s): 30375330.
⏵ 3	2024-10-22 04:45:33	announced	2024-10-22: Updated project metadata.

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]

10.7554/elife.34878;

curator keyword: Biological

submitter keyword: E coli, LC-MS/MS

Jesse Rinehart
contact affiliation	Department 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 email	jesse.rinehart@yale.edu
lab head
Karl Barber
contact affiliation	Yale University
contact email	karl.barber@yale.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD009643
     1. Label: PRIDE project
     2. Name: Organisms with alternative genetic codes resolve unassigned codons via mistranslation and ribosomal rescue