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Experimental validation that human microbiome phages use alternative genetic coding

Author

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  • Samantha L. Peters

    (Oak Ridge National Laboratory
    The University of Tennessee, Knoxville)

  • Adair L. Borges

    (University of California
    University of California)

  • Richard J. Giannone

    (Oak Ridge National Laboratory)

  • Michael J. Morowitz

    (University of Pittsburgh School of Medicine)

  • Jillian F. Banfield

    (University of California
    University of California
    University of California
    Lawrence Berkeley National Laboratory)

  • Robert L. Hettich

    (Oak Ridge National Laboratory)

Abstract

Previous bioinformatic analyses of metagenomic data have indicated that bacteriophages can use genetic codes different from those of their host bacteria. In particular, reassignment of stop codon TAG to glutamine (a variation known as ‘genetic code 15’) has been predicted. Here, we use LC-MS/MS-based metaproteomics of human fecal samples to provide experimental evidence of the use of genetic code 15 in two crAss-like phages. Furthermore, the proteomic data from several phage structural proteins supports the reassignment of the TAG stop codon to glutamine late in the phage infection cycle. Thus, our work experimentally validates the expression of genetic code 15 in human microbiome phages.

Suggested Citation

  • Samantha L. Peters & Adair L. Borges & Richard J. Giannone & Michael J. Morowitz & Jillian F. Banfield & Robert L. Hettich, 2022. "Experimental validation that human microbiome phages use alternative genetic coding," Nature Communications, Nature, vol. 13(1), pages 1-7, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-32979-6
    DOI: 10.1038/s41467-022-32979-6
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    References listed on IDEAS

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    1. Natalya Yutin & Sean Benler & Sergei A. Shmakov & Yuri I. Wolf & Igor Tolstoy & Mike Rayko & Dmitry Antipov & Pavel A. Pevzner & Eugene V. Koonin, 2021. "Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    2. Basem Al-Shayeb & Rohan Sachdeva & Lin-Xing Chen & Fred Ward & Patrick Munk & Audra Devoto & Cindy J. Castelle & Matthew R. Olm & Keith Bouma-Gregson & Yuki Amano & Christine He & Raphaël Méheust & Br, 2020. "Clades of huge phages from across Earth’s ecosystems," Nature, Nature, vol. 578(7795), pages 425-431, February.
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    Cited by:

    1. Kasimir Kienbeck & Lukas Malfertheiner & Susann Zelger-Paulus & Silke Johannsen & Christian Mering & Roland K. O. Sigel, 2024. "Identification of HDV-like theta ribozymes involved in tRNA-based recoding of gut bacteriophages," Nature Communications, Nature, vol. 15(1), pages 1-10, December.

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