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Stop codon recoding is widespread in diverse phage lineages and has the potential to regulate translation of late stage and lytic genes

View ORCID ProfileAdair L. Borges, Yue Clare Lou, Rohan Sachdeva, Basem Al-Shayeb, Alexander L. Jaffe, Shufei Lei, Joanne M. Santini, Jillian F. Banfield
doi: https://doi.org/10.1101/2021.08.26.457843
Adair L. Borges
1Innovative Genomics Institute, University of California, Berkeley, CA, USA
2Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
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  • ORCID record for Adair L. Borges
Yue Clare Lou
1Innovative Genomics Institute, University of California, Berkeley, CA, USA
3Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
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Rohan Sachdeva
1Innovative Genomics Institute, University of California, Berkeley, CA, USA
4Earth and Planetary Science, University of California, Berkeley, CA, USA
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Basem Al-Shayeb
1Innovative Genomics Institute, University of California, Berkeley, CA, USA
3Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
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Alexander L. Jaffe
3Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
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Shufei Lei
4Earth and Planetary Science, University of California, Berkeley, CA, USA
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Joanne M. Santini
5Department of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
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Jillian F. Banfield
1Innovative Genomics Institute, University of California, Berkeley, CA, USA
2Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
4Earth and Planetary Science, University of California, Berkeley, CA, USA
6Lawrence Berkeley National Laboratory, Berkeley, CA, USA
7The University of Melbourne, Australia
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  • For correspondence: jbanfield@berkeley.edu
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Abstract

The genetic code is a highly conserved feature of life. However, some “alternative” genetic codes use reassigned stop codons to code for amino acids. Here, we survey stop codon recoding across bacteriophages (phages) in human and animal gut microbiomes. We find that stop codon recoding has evolved in diverse clades of phages predicted to infect hosts that use the standard code. We provide evidence for an evolutionary path towards recoding involving reduction in the frequency of TGA and TAG stop codons due to low GC content, followed by acquisition of suppressor tRNAs and the emergence of recoded stop codons in structural and lysis genes. In analyses of two distinct lineages of recoded virulent phages, we find that lysis-related genes are uniquely biased towards use of recoded stop codons. This convergence supports the inference that stop codon recoding is a strategy to regulate the expression of late stage genes and control lysis timing. Interestingly, we identified prophages with recoded stop codons integrated into genomes of bacteria that use standard code, and hypothesize that recoding may control the lytic-lysogenic switch. Alternative coding has evolved many times, often in closely related lineages, indicating that genetic code is plastic in bacteriophages and adaptive recoding can occur over very short evolutionary timescales.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://doi.org/10.5281/zenodo.5275335

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted August 26, 2021.
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Stop codon recoding is widespread in diverse phage lineages and has the potential to regulate translation of late stage and lytic genes
Adair L. Borges, Yue Clare Lou, Rohan Sachdeva, Basem Al-Shayeb, Alexander L. Jaffe, Shufei Lei, Joanne M. Santini, Jillian F. Banfield
bioRxiv 2021.08.26.457843; doi: https://doi.org/10.1101/2021.08.26.457843
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Stop codon recoding is widespread in diverse phage lineages and has the potential to regulate translation of late stage and lytic genes
Adair L. Borges, Yue Clare Lou, Rohan Sachdeva, Basem Al-Shayeb, Alexander L. Jaffe, Shufei Lei, Joanne M. Santini, Jillian F. Banfield
bioRxiv 2021.08.26.457843; doi: https://doi.org/10.1101/2021.08.26.457843

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