The e14 cryptic prophage belongs to a temperate phage lineage distributed across Escherichia and retains genes with potential anti-phage defence functions

The e14 cryptic prophage belongs to a temperate phage lineage distributed across Escherichia and retains genes with potential anti-phage defence functions

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Authors

Danna R Gifford 

Abstract

The e14 region of Escherichia coli str. K-12 is a cryptic prophage that retains functional excision and integration machinery despite extensive loss of phage reproductive functions. However, its evolutionary relationship to other bacteriophages remains poorly resolved. Here, we identify related prophages across four Escherichia species, alongside related, independently isolated bacteriophages. The putative prophages were 34.7–43.5 kb, more than twice the size of e14 (15.2 kb), and retained much of the genomic architecture required for phage reproduction. Comparative genomic and phylogenetic analyses support e14 as a highly reduced member of a broader lineage of temperate bacteriophages. The retention of genes with established or putative anti-phage functions further raises the possibility that e14 represents a form of ‘defence flotsam’, potentially protecting its host against subsequent phage infections. More broadly, cryptic prophages may provide reservoirs of anti-phage defence functions long after losing their capacity for phage reproduction.

DOI

https://doi.org/10.32942/X2W996

Subjects

Bacteriology, Bioinformatics, Biology, Evolution, Life Sciences, Other Microbiology

Keywords

Escherichia coli, cryptic prophage, comparative genomics, bacteriophage evolution, genome reduction, anti-phage defence

Dates

Published: 2026-10-22 12:05

Last Updated: 2026-10-22 12:05

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License

CC-BY Attribution-NonCommercial 4.0 International

Additional Metadata

Conflict of interest statement:
The author declares no conflict of interest.

Data and Code Availability Statement:
All genome sequences analysed in this study are publicly available from NCBI under the accessions given in the Methods. Scripts used to perform the analyses are provided on GitHub (https://github.com/dannagifford/e14-like-prophages-escherichia).

Language:
English

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