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

Ma, Natalie Jing; Hemez, Colin F.; Barber, Karl W.; Rinehart, Jesse; Isaacs, Farren J.

doi:10.7554/eLife.34878

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

Journal Article · 29 October 2018 · eLife

DOI: https://doi.org/10.7554/eLife.34878 · OSTI ID:1479816

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^[3]; Rinehart, Jesse ^[3];

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Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, United States, Systems Biology Institute, Yale University, West Haven, United States
Systems Biology Institute, Yale University, West Haven, United States, Department of Biomedical Engineering, Yale University, New Haven, United States
Systems Biology Institute, Yale University, West Haven, United States, Department of Cellular & Molecular Physiology, Yale University School of Medicine, New Haven, United States

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.

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Research Organization:: Yale Univ., New Haven, CT (United States)

Sponsoring Organization:: USDOE; USDOE Office of Science (SC)

Grant/Contract Number:: SC0010687

OSTI ID:: 1479816

Journal Information:: eLife, Journal Name: eLife Vol. 7; ISSN 2050-084X

Publisher:: eLife Sciences Publications, Ltd.Copyright Statement

Country of Publication:: United States

Language:: English

References (73)

Generation of phospho-ubiquitin variants by orthogonal translation reveals codon skipping George, Susanna; Aguirre, Jacob D.; Spratt, Donald E. FEBS Letters, Vol. 590, Issue 10 https://doi.org/10.1002/1873-3468.12182	journal	May 2016
Characterization of mutant spectra generated by a forward mutational assay for geneA of ?X174 from ENU-treated transgenic mouse embryonic cell line PX-2 Valentine, Carrie R.; Montgomery, Beverly A.; Miller, Scott G. Environmental and Molecular Mutagenesis, Vol. 39, Issue 1 https://doi.org/10.1002/em.10043	journal	January 2002
Complete Nucleotide Sequence of Birmingham IncPα Plasmids Pansegrau, Werner; Lanka, Erich; Barth, Peter T. Journal of Molecular Biology, Vol. 239, Issue 5 https://doi.org/10.1006/jmbi.1994.1404	journal	June 1994
Red Queen Dynamics of Protein Translation Krakauer, David C.; Jansen, Vincent A. A. Journal of Theoretical Biology, Vol. 218, Issue 1 https://doi.org/10.1006/jtbi.2002.3054	journal	September 2002
The E Site and Its Importance for Improving Accuracy and Preventing Frameshifts Pech, Markus; Vesper, Oliver; Yamamoto, Hiroshi Nucleic Acids and Molecular Biology, Vol. 24, p. 345-362 https://doi.org/10.1007/978-0-387-89382-2_16	book	October 2009
The frequency of transcriptional and translational errors at nonsense codons in the lacZ gene of Escherichia coli Rosenberger, R. F.; Hilton, J. MGG Molecular & General Genetics, Vol. 191, Issue 2 https://doi.org/10.1007/BF00334815	journal	August 1983
Synthesis and degradation of termination and premature-termination fragments of β-galactosidase in vitro and in vivo Manley, James L. Journal of Molecular Biology, Vol. 125, Issue 4 https://doi.org/10.1016/0022-2836(78)90308-X	journal	November 1978
Ribosome Excursions during mRNA Translocation Mediate Broad Branching of Frameshift Pathways Yan, Shannon; Wen, Jin-Der; Bustamante, Carlos Cell, Vol. 160, Issue 5 https://doi.org/10.1016/j.cell.2015.02.003	journal	February 2015
Genomic Recoding Broadly Obstructs the Propagation of Horizontally Transferred Genetic Elements Ma, Natalie Jing; Isaacs, Farren J. Cell Systems, Vol. 3, Issue 2 https://doi.org/10.1016/j.cels.2016.06.009	journal	August 2016
Enhanced phosphoserine insertion during Escherichia coli protein synthesis via partial UAG codon reassignment and release factor 1 deletion Heinemann, Ilka U.; Rovner, Alexis J.; Aerni, Hans R. FEBS Letters, Vol. 586, Issue 20 https://doi.org/10.1016/j.febslet.2012.08.031	journal	September 2012
ArfA Recruits RF2 into Stalled Ribosomes Shimizu, Yoshihiro Journal of Molecular Biology, Vol. 423, Issue 4 https://doi.org/10.1016/j.jmb.2012.08.007	journal	November 2012
The role of alternative genetic codes in viral evolution and emergence Shackelton, Laura A.; Holmes, Edward C. Journal of Theoretical Biology, Vol. 254, Issue 1 https://doi.org/10.1016/j.jtbi.2008.05.024	journal	September 2008
Nascent polypeptide sequences that influence ribosome function Cruz-Vera, Luis Rogelio; Sachs, Matthew S.; Squires, Catherine L. Current Opinion in Microbiology, Vol. 14, Issue 2 https://doi.org/10.1016/j.mib.2011.01.011	journal	April 2011
Synthetic microbial communities Großkopf, Tobias; Soyer, Orkun S. Current Opinion in Microbiology, Vol. 18 https://doi.org/10.1016/j.mib.2014.02.002	journal	April 2014
A fully decompressed synthetic bacteriophage øX174 genome assembled and archived in yeast Jaschke, Paul R.; Lieberman, Erica K.; Rodriguez, Jon Virology, Vol. 434, Issue 2 https://doi.org/10.1016/j.virol.2012.09.020	journal	December 2012
An RNA polymerase mutant with reduced accuracy of chain elongation Blank, A.; Gallant, Jonathan A.; Burgess, Richard R. Biochemistry, Vol. 25, Issue 20 https://doi.org/10.1021/bi00368a013	journal	October 1986
Lateral gene transfer and the nature of bacterial innovation Ochman, Howard; Lawrence, Jeffrey G.; Groisman, Eduardo A. Nature, Vol. 405, Issue 6784 https://doi.org/10.1038/35012500	journal	May 2000
Rewiring the keyboard: evolvability of the genetic code Knight, Robin D.; Freeland, Stephen J.; Landweber, Laura F. Nature Reviews Genetics, Vol. 2, Issue 1 https://doi.org/10.1038/35047500	journal	January 2001
Determinants of translation efficiency and accuracy Gingold, Hila; Pilpel, Yitzhak Molecular Systems Biology, Vol. 7, Issue 1 https://doi.org/10.1038/msb.2011.14	journal	January 2011
Quality control by the ribosome following peptide bond formation Zaher, Hani S.; Green, Rachel Nature, Vol. 457, Issue 7226 https://doi.org/10.1038/nature07582	journal	December 2008
Programming cells by multiplex genome engineering and accelerated evolution Wang, Harris H.; Isaacs, Farren J.; Carr, Peter A. Nature, Vol. 460, Issue 7257, p. 894-898 https://doi.org/10.1038/nature08187	journal	July 2009
The anti-Shine–Dalgarno sequence drives translational pausing and codon choice in bacteria Li, Gene-Wei; Oh, Eugene; Weissman, Jonathan S. Nature, Vol. 484, Issue 7395 https://doi.org/10.1038/nature10965	journal	March 2012
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification Cox, Jürgen; Mann, Matthias Nature Biotechnology, Vol. 26, Issue 12 https://doi.org/10.1038/nbt.1511	journal	November 2008
ProteomeXchange provides globally coordinated proteomics data submission and dissemination Vizcaíno, Juan A.; Deutsch, Eric W.; Wang, Rui Nature Biotechnology, Vol. 32, Issue 3 https://doi.org/10.1038/nbt.2839	journal	March 2014
Evolution of translation machinery in recoded bacteria enables multi-site incorporation of nonstandard amino acids Amiram, Miriam; Haimovich, Adrian D.; Fan, Chenguang Nature Biotechnology, Vol. 33, Issue 12 https://doi.org/10.1038/nbt.3372	journal	November 2015
Recombinant protein folding and misfolding in Escherichia coli Baneyx, François; Mujacic, Mirna Nature Biotechnology, Vol. 22, Issue 11 https://doi.org/10.1038/nbt1029	journal	November 2004
Natural expansion of the genetic code Ambrogelly, Alexandre; Palioura, Sotiria; Söll, Dieter Nature Chemical Biology, Vol. 3, Issue 1 https://doi.org/10.1038/nchembio847	journal	December 2006
A flexible codon in genomically recoded Escherichia coli permits programmable protein phosphorylation Pirman, Natasha L.; Barber, Karl W.; Aerni, Hans R. Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms9130	journal	September 2015
Replication Blainey, Paul; Krzywinski, Martin; Altman, Naomi Nature Methods, Vol. 11, Issue 9 https://doi.org/10.1038/nmeth.3091	journal	August 2014
Recombineering: a homologous recombination-based method of genetic engineering Sharan, Shyam K.; Thomason, Lynn C.; Kuznetsov, Sergey G. Nature Protocols, Vol. 4, Issue 2 https://doi.org/10.1038/nprot.2008.227	journal	January 2009
Precise manipulation of bacterial chromosomes by conjugative assembly genome engineering Ma, Natalie J.; Moonan, Daniel W.; Isaacs, Farren J. Nature Protocols, Vol. 9, Issue 10 https://doi.org/10.1038/nprot.2014.081	journal	September 2014
Rapid editing and evolution of bacterial genomes using libraries of synthetic DNA Gallagher, Ryan R.; Li, Zhe; Lewis, Aaron O. Nature Protocols, Vol. 9, Issue 10 https://doi.org/10.1038/nprot.2014.082	journal	September 2014
Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning Baranov, Pavel V.; Atkins, John F.; Yordanova, Martina M. Nature Reviews Genetics, Vol. 16, Issue 9 https://doi.org/10.1038/nrg3963	journal	August 2015
Surveillance pathways rescuing eukaryotic ribosomes lost in translation Graille, Marc; Séraphin, Bertrand Nature Reviews Molecular Cell Biology, Vol. 13, Issue 11 https://doi.org/10.1038/nrm3457	journal	October 2012
Horizontal gene transfer, genome innovation and evolution Gogarten, J. Peter; Townsend, Jeffrey P. Nature Reviews Microbiology, Vol. 3, Issue 9 https://doi.org/10.1038/nrmicro1204	journal	August 2005
Mechanisms of ribosome rescue in bacteria Keiler, Kenneth C. Nature Reviews Microbiology, Vol. 13, Issue 5 https://doi.org/10.1038/nrmicro3438	journal	April 2015
Stop codons preceded by rare arginine codons are efficient determinants of SsrA tagging in Escherichia coli Hayes, Christopher S.; Bose, Baundauna; Sauer, Robert T. Proceedings of the National Academy of Sciences, Vol. 99, Issue 6 https://doi.org/10.1073/pnas.052707199	journal	March 2002
Rapid evolution of stability and productivity at the origin of a microbial mutualism Hillesland, K. L.; Stahl, D. A. Proceedings of the National Academy of Sciences, Vol. 107, Issue 5 https://doi.org/10.1073/pnas.0908456107	journal	January 2010
Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli Napolitano, Michael G.; Landon, Matthieu; Gregg, Christopher J. Proceedings of the National Academy of Sciences, Vol. 113, Issue 38 https://doi.org/10.1073/pnas.1605856113	journal	September 2016
The 3'-Terminal Sequence of Escherichia coli 16S Ribosomal RNA: Complementarity to Nonsense Triplets and Ribosome Binding Sites Shine, J.; Dalgarno, L. Proceedings of the National Academy of Sciences, Vol. 71, Issue 4 https://doi.org/10.1073/pnas.71.4.1342	journal	April 1974
C-terminal Extension of Truncated Recombinant Proteins in Escherichia coli with a 10Sa RNA Decapeptide Tu, Guo-Fen; Reid, Gavin E.; Zhang, Jian-Guo Journal of Biological Chemistry, Vol. 270, Issue 16 https://doi.org/10.1074/jbc.270.16.9322	journal	April 1995
Proteobacterial ArfA Peptides Are Synthesized from Non-stop Messenger RNAs Schaub, Ryan E.; Poole, Stephen J.; Garza-Sánchez, Fernando Journal of Biological Chemistry, Vol. 287, Issue 35 https://doi.org/10.1074/jbc.M112.374074	journal	July 2012
Distinct Roles for Release Factor 1 and Release Factor 2 in Translational Quality Control Petropoulos, Alexandros D.; McDonald, Megan E.; Green, Rachel Journal of Biological Chemistry, Vol. 289, Issue 25 https://doi.org/10.1074/jbc.M114.564989	journal	May 2014
SsrA-mediated peptide tagging caused by rare codons and tRNA scarcity Roche, E. D. The EMBO Journal, Vol. 18, Issue 16 https://doi.org/10.1093/emboj/18.16.4579	journal	August 1999
Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements Lutz, R. Nucleic Acids Research, Vol. 25, Issue 6, p. 1203-1210 https://doi.org/10.1093/nar/25.6.1203	journal	March 1997
YaeJ is a novel ribosome-associated protein in Escherichia coli that can hydrolyze peptidyl-tRNA on stalled ribosomes Handa, Y.; Inaho, N.; Nameki, N. Nucleic Acids Research, Vol. 39, Issue 5 https://doi.org/10.1093/nar/gkq1097	journal	November 2010
Codon reassignment in the Escherichia coli genetic code Mukai, T.; Hayashi, A.; Iraha, F. Nucleic Acids Research, Vol. 38, Issue 22 https://doi.org/10.1093/nar/gkq707	journal	August 2010
Revealing the amino acid composition of proteins within an expanded genetic code Aerni, Hans R.; Shifman, Mark A.; Rogulina, Svetlana Nucleic Acids Research, Vol. 43, Issue 2 https://doi.org/10.1093/nar/gku1087	journal	November 2014
Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use Atkins, John F.; Loughran, Gary; Bhatt, Pramod R. Nucleic Acids Research https://doi.org/10.1093/nar/gkw530	journal	July 2016
Large-scale recoding of a bacterial genome by iterative recombineering of synthetic DNA Lau, Yu Heng; Stirling, Finn; Kuo, James Nucleic Acids Research, Vol. 45, Issue 11 https://doi.org/10.1093/nar/gkx415	journal	May 2017
Ribosome rescue: tmRNA tagging activity and capacity in Escherichia coli : tmRNA tagging in Moore, Sean D.; Sauer, Robert T. Molecular Microbiology, Vol. 58, Issue 2 https://doi.org/10.1111/j.1365-2958.2005.04832.x	journal	September 2005
Reduced action of polypeptide release factors induces mRNA cleavage and tmRNA tagging at stop codons in Escherichia coli Li, Xia; Yokota, Teruaki; Ito, Koichi Molecular Microbiology, Vol. 63, Issue 1 https://doi.org/10.1111/j.1365-2958.2006.05498.x	journal	January 2007
Ribosome rescue by Escherichia coli ArfA (YhdL) in the absence of trans-translation system: Ribosome rescue by E. coli ArfA (YhdL) Chadani, Yuhei; Ono, Katsuhiko; Ozawa, Shin-ichiro Molecular Microbiology, Vol. 78, Issue 4 https://doi.org/10.1111/j.1365-2958.2010.07375.x	journal	September 2010
tmRNA regulates synthesis of the ArfA ribosome rescue factor: tmRNA regulates ArfA synthesis Garza-Sánchez, Fernando; Schaub, Ryan E.; Janssen, Brian D. Molecular Microbiology, Vol. 80, Issue 5 https://doi.org/10.1111/j.1365-2958.2011.07638.x	journal	March 2011
ArfA recruits release factor 2 to rescue stalled ribosomes by peptidyl-tRNA hydrolysis in Escherichia coli : ArfA-RF2 pathway of ribosome rescue Chadani, Yuhei; Ito, Koreaki; Kutsukake, Kazuhiro Molecular Microbiology, Vol. 86, Issue 1 https://doi.org/10.1111/j.1365-2958.2012.08190.x	journal	August 2012
Virus Attenuation by Genome-Scale Changes in Codon Pair Bias Coleman, J. R.; Papamichail, D.; Skiena, S. Science, Vol. 320, Issue 5884 https://doi.org/10.1126/science.1155761	journal	June 2008
Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement Isaacs, Farren J.; Carr, Peter A.; Wang, Harris H. Science, Vol. 333, Issue 6040, p. 348-353 https://doi.org/10.1126/science.1205822	journal	July 2011
Genomically Recoded Organisms Expand Biological Functions Lajoie, M. J.; Rovner, A. J.; Goodman, D. B. Science, Vol. 342, Issue 6156, p. 357-360 https://doi.org/10.1126/science.1241459	journal	October 2013
Probing the Limits of Genetic Recoding in Essential Genes Lajoie, M. J.; Kosuri, S.; Mosberg, J. A. Science, Vol. 342, Issue 6156 https://doi.org/10.1126/science.1241460	journal	October 2013
Role of a Peptide Tagging System in Degradation of Proteins Synthesized from Damaged Messenger RNA Keiler, K. C.; Waller, P. R. H.; Sauer, R. T. Science, Vol. 271, Issue 5251 https://doi.org/10.1126/science.271.5251.990	journal	February 1996
A persistent untranslated sequence within bacteriophage T4 DNA topoisomerase gene 60 Huang, W.; Ao, S.; Casjens, S. Science, Vol. 239, Issue 4843 https://doi.org/10.1126/science.2830666	journal	February 1988
Inactivation of antibiotics and the dissemination of resistance genes Davies, J. Science, Vol. 264, Issue 5157 https://doi.org/10.1126/science.8153624	journal	April 1994
Design, synthesis, and testing toward a 57-codon genome Ostrov, N.; Landon, M.; Guell, M. Science, Vol. 353, Issue 6301 https://doi.org/10.1126/science.aaf3639	journal	August 2016
Design of a synthetic yeast genome Richardson, Sarah M.; Mitchell, Leslie A.; Stracquadanio, Giovanni Science, Vol. 355, Issue 6329 https://doi.org/10.1126/science.aaf4557	journal	March 2017
The Genome Project-Write Boeke, J. D.; Church, G.; Hessel, A. Science, Vol. 353, Issue 6295 https://doi.org/10.1126/science.aaf6850	journal	June 2016
Resolving Nonstop Translation Complexes Is a Matter of Life or Death Keiler, K. C.; Feaga, H. A. Journal of Bacteriology, Vol. 196, Issue 12 https://doi.org/10.1128/JB.01490-14	journal	April 2014
Structure of an Escherichia coli tRNA operon containing linked genes for arginine, histidine, leucine, and proline tRNAs. Hsu, L. M.; Klee, H. J.; Zagorski, J. Journal of Bacteriology, Vol. 158, Issue 3 https://doi.org/10.1128/JB.158.3.934-942.1984	journal	January 1984
Translation initiation region sequence preferences in Escherichia coli Vimberg, Vladimir; Tats, Age; Remm, Maido BMC Molecular Biology, Vol. 8, Issue 1 https://doi.org/10.1186/1471-2199-8-100	journal	January 2007
SsrA-mediated trans-translation plays a role in mRNA quality control by facilitating degradation of truncated mRNAs Yamamoto, Y. RNA, Vol. 9, Issue 4 https://doi.org/10.1261/rna.2174803	journal	April 2003
Kinetic basis for global loss of fidelity arising from mismatches in the P-site codon:anticodon helix Zaher, H. S.; Green, R. RNA, Vol. 16, Issue 10 https://doi.org/10.1261/rna.2241810	journal	August 2010
trans-translation-mediated tight regulation of the expression of the alternative ribosome-rescue factor ArfA in Escherichia coli Chadani, Yuhei; Matsumoto, Emi; Aso, Hiroaki Genes & Genetic Systems, Vol. 86, Issue 3 https://doi.org/10.1266/ggs.86.151	journal	January 2011
Preparing synthetic biology for the world Moe-Behrens, Gerd H. G.; Davis, Rene; Haynes, Karmella A. Frontiers in Microbiology, Vol. 4 https://doi.org/10.3389/fmicb.2013.00005	journal	January 2013
Ends of the line for tmRNA-SmpB Hudson, Corey M.; Lau, Britney Y.; Williams, Kelly P. Frontiers in Microbiology, Vol. 5 https://doi.org/10.3389/fmicb.2014.00421	journal	August 2014

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