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

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

Bioanalytical Mass Spectrometry

Research output: Contribution to journal › Article › peer-review

15 Scopus citations

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.

Original language	English
Article number	5710
Journal	Nature Communications
Volume	13
Issue number	1
DOIs	https://doi.org/10.1038/s41467-022-32979-6
State	Published - Dec 2022

Funding

We acknowledge Dr. Paul Abraham for technical review of this manuscript. This work was supported by National Institutes of Health grant R01GM103600. A.L.B is funded by a UC-Berkeley Miller Basic Research Fellowship. S.L.P. is funded by the Oak Ridge Innovation Institute’s EERE Workforce Development project fellowship.

Funders	Funder number
Oak Ridge Innovation Institute’s EERE
National Institutes of Health
National Institute of General Medical Sciences	R01GM103600

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title = "Experimental validation that human microbiome phages use alternative genetic coding",

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 {\textquoteleft}genetic code 15{\textquoteright}) 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.",

author = "Peters, {Samantha L.} and Borges, {Adair L.} and Giannone, {Richard J.} and Morowitz, {Michael J.} and Banfield, {Jillian F.} and Hettich, {Robert L.}",

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AU - Hettich, Robert L.

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AB - 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.

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Experimental validation that human microbiome phages use alternative genetic coding

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