Experimental validation that human microbiome phages use alternative genetic coding

Samantha L Peters; Adair L Borges; Richard J Giannone; Michael J Morowitz; Jillian F Banfield; Robert L Hettich

doi:10.1038/s41467-022-32979-6

Experimental validation that human microbiome phages use alternative genetic coding

Nat Commun. 2022 Sep 29;13(1):5710. doi: 10.1038/s41467-022-32979-6.

Authors

Samantha L Peters^{1

2}, Adair L Borges^{3

4}, Richard J Giannone¹, Michael J Morowitz⁵, Jillian F Banfield^{6

7

8

9

10}, Robert L Hettich¹¹

Affiliations

¹ Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
² Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Knoxville, TN, USA.
³ Innovative Genomics Institute, University of California, Berkeley, CA, USA.
⁴ Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
⁵ Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
⁶ Innovative Genomics Institute, University of California, Berkeley, CA, USA. jbanfield@berkeley.edu.
⁷ Environmental Science, Policy and Management, University of California, Berkeley, CA, USA. jbanfield@berkeley.edu.
⁸ Earth and Planetary Science, University of California, Berkeley, CA, USA. jbanfield@berkeley.edu.
⁹ Lawrence Berkeley National Laboratory, Berkeley, CA, USA. jbanfield@berkeley.edu.
¹⁰ Chan Zuckerberg Biohub, San Francisco, CA, USA. jbanfield@berkeley.edu.
¹¹ Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA. hettichrl@ornl.gov.

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.

Publication types

Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Research Support, Non-U.S. Gov't

MeSH terms

Bacteriophages* / genetics
Chromatography, Liquid
Codon, Terminator
Glutamine
Humans
Microbiota* / genetics
Proteomics
Tandem Mass Spectrometry

Substances

Codon, Terminator
Glutamine

Grants and funding

R01 GM103600/GM/NIGMS NIH HHS/United States