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Validation that human microbiome phages use alternative genetic coding with TAG stop read as Q

Samantha L. Peters, View ORCID ProfileAdair L. Borges, Richard J. Giannone, Michael J. Morowitz, Jillian F. Banfield, Robert L. Hettich
doi: https://doi.org/10.1101/2022.01.06.475225
Samantha L. Peters
1Biosciences Division, Oak Ridge National Laboratory; Oak Ridge, TN, USA
2Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville; Knoxville, TN, USA
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Adair L. Borges
3Innovative Genomics Institute, University of California, Berkeley, CA, USA
4Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
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  • ORCID record for Adair L. Borges
Richard J. Giannone
1Biosciences Division, Oak Ridge National Laboratory; Oak Ridge, TN, USA
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Michael J. Morowitz
5Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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Jillian F. Banfield
3Innovative Genomics Institute, University of California, Berkeley, CA, USA
4Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
6Earth and Planetary Science, University of California, Berkeley, CA, USA
7Lawrence Berkeley National Laboratory, Berkeley, CA, USA
8Chan Zuckerberg Biohub, San Francisco, CA, USA
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  • For correspondence: jbanfield@berkeley.edu hettichrl@ornl.gov
Robert L. Hettich
1Biosciences Division, Oak Ridge National Laboratory; Oak Ridge, TN, USA
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  • For correspondence: jbanfield@berkeley.edu hettichrl@ornl.gov
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Abstract

Metagenomic findings suggesting that bacteriophages (phages) can use genetic codes different from those of their host bacteria reveal a new dimension of phage-host interaction dynamics. Whereas reassignment of stop codons to code for amino acids has been predicted, there has been no proteomic validation of alternative coding in phages. In fact, one code where the stop codon TAG is reassigned to glutamine (code 15) has never been experimentally validated in any biological system. Here, we characterized stop codon reassignment in two crAss-like phages found in the human gut microbiome using LC-MS/MS-based metaproteomics. The proteome data from several phage structural proteins clearly demonstrates reassignment of the TAG stop codon to glutamine, establishing for the first time the expression of genetic code 15.

One-Sentence Summary Mass spectrometry confirms protein expression of predicted alternate genetic coding in phage genomes from human microbiomes.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://ggkbase.berkeley.edu/Alternatively_coded_phage_proteomics/organisms

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted January 06, 2022.
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Validation that human microbiome phages use alternative genetic coding with TAG stop read as Q
Samantha L. Peters, Adair L. Borges, Richard J. Giannone, Michael J. Morowitz, Jillian F. Banfield, Robert L. Hettich
bioRxiv 2022.01.06.475225; doi: https://doi.org/10.1101/2022.01.06.475225
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Validation that human microbiome phages use alternative genetic coding with TAG stop read as Q
Samantha L. Peters, Adair L. Borges, Richard J. Giannone, Michael J. Morowitz, Jillian F. Banfield, Robert L. Hettich
bioRxiv 2022.01.06.475225; doi: https://doi.org/10.1101/2022.01.06.475225

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