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Title: Organisms with alternative genetic codes resolve unassigned codons via mistranslation and ribosomal rescue

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 for impairing horizontal gene transfer and conferring genetic isolation in diverse organisms.
Authors:
ORCiD logo [1] ; ORCiD logo [2] ; ORCiD logo [3] ;  [3] ; ORCiD logo [1]
  1. Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, United States, Systems Biology Institute, Yale University, West Haven, United States
  2. Systems Biology Institute, Yale University, West Haven, United States, Department of Biomedical Engineering, Yale University, New Haven, United States
  3. Systems Biology Institute, Yale University, West Haven, United States, Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, United States
Publication Date:
Grant/Contract Number:
152339.5055249.100
Type:
Published Article
Journal Name:
eLife
Additional Journal Information:
Journal Name: eLife Journal Volume: 7; Journal ID: ISSN 2050-084X
Publisher:
eLife Sciences Publications, Ltd.
Sponsoring Org:
USDOE
Country of Publication:
United States
Language:
English
OSTI Identifier:
1479816
Alternate Identifier(s):
OSTI ID: 1479817

Ma, Natalie Jing, Hemez, Colin F., Barber, Karl W., Rinehart, Jesse, and Isaacs, Farren J.. Organisms with alternative genetic codes resolve unassigned codons via mistranslation and ribosomal rescue. United States: N. p., Web. doi:10.7554/eLife.34878.
Ma, Natalie Jing, Hemez, Colin F., Barber, Karl W., Rinehart, Jesse, & Isaacs, Farren J.. Organisms with alternative genetic codes resolve unassigned codons via mistranslation and ribosomal rescue. United States. doi:10.7554/eLife.34878.
Ma, Natalie Jing, Hemez, Colin F., Barber, Karl W., Rinehart, Jesse, and Isaacs, Farren J.. 2018. "Organisms with alternative genetic codes resolve unassigned codons via mistranslation and ribosomal rescue". United States. doi:10.7554/eLife.34878.
@article{osti_1479816,
title = {Organisms with alternative genetic codes resolve unassigned codons via mistranslation and ribosomal rescue},
author = {Ma, Natalie Jing and Hemez, Colin F. and Barber, Karl W. and Rinehart, Jesse and Isaacs, Farren J.},
abstractNote = {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 for impairing horizontal gene transfer and conferring genetic isolation in diverse organisms.},
doi = {10.7554/eLife.34878},
journal = {eLife},
number = ,
volume = 7,
place = {United States},
year = {2018},
month = {10}
}

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