The evolution of a counter-defense mechanism in a virus constrains its host range

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Abstract

Bacteria use diverse immunity mechanisms to defend themselves against their viral predators, bacteriophages. In turn, phages can acquire counter-defense systems, but it remains unclear how such mechanisms arise and what factors constrain viral evolution. Here, we experimentally evolved T4 phage to overcome a phage-defensive toxin-antitoxin system, toxIN, in E. coli. Through recombination, T4 rapidly acquires segmental amplifications of a previously uncharacterized gene, now named tifA, encoding an inhibitor of the toxin, ToxN. These amplifications subsequently drive large deletions elsewhere in T4's genome to maintain a genome size compatible with capsid packaging. The deleted regions include accessory genes that help T4 overcome defense systems in alternative hosts. Thus, our results reveal a trade-off in viral evolution; the emergence of one counter-defense mechanism can lead to loss of other such mechanisms, thereby constraining host range. We propose that the accessory genomes of viruses reflect the integrated evolutionary history of the hosts they infected.

Data availability

DNA sequencing data is available at SRA (BioProject ID: PRJNA824875).

The following data sets were generated

(2022) Experimental evolution of T4 to overcome E.coli toxIN
SRA, PRJNA824875.

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA824875/

Article and author information

Author details

Sriram Srikant

Department of Biology, Massachusetts Institute of Technology, Cambridge, United States

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0003-3904-0336
Chantal K Guegler

Department of Biology, Massachusetts Institute of Technology, Cambridge, United States

Competing interests
No competing interests declared.
Michael T Laub

Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States

For correspondence
laub@mit.edu

Competing interests
Michael T Laub, Reviewing editor, eLife.

"This ORCID iD identifies the author of this article:" 0000-0002-8288-7607

Funding

Howard Hughes Medical Institute

Michael T Laub

National Science Foundation (Graduate Research Fellowship)

Chantal K Guegler

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.