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Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

Published on: June 11, 2015

Viral lifecycle dynamics and spatial structure explain why accessory genes are associated with temperate phages.

Sultan A Nazir¹, Bram van Dijk¹

¹Theoretical Biology, Utrecht University, The Netherlands.

Genome Biology and Evolution

|July 15, 2026

Summary

Bacterial prophages can acquire virulence genes through migration and spatial dynamics, aiding bacterial adaptation. These mechanisms, unique to phages, explain the evolutionary link between mobile genetic elements and beneficial genes.

Keywords:

dispersal induction mobile genetic elements prophages spatial structure virulence

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Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

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Area of Science:

Evolutionary biology
Microbial genetics
Mathematical modeling

Background:

Genes for virulence factors are often found on prophages.
The evolutionary drivers of this association are not well understood.
Mobile genetic elements (MGEs) face challenges in associating with beneficial genes.

Purpose of the Study:

To investigate the evolutionary forces linking accessory genes, like virulence factors, to prophages.
To identify mechanisms overcoming constraints on MGE-gene associations.
To explore the unique role of phages in bacterial adaptation.

Main Methods:

Development of a mathematical model incorporating chromosomal stability and MGE competition.
Analysis of bacterial population migration dynamics.
Examination of within-population spatial dynamics and virion dispersal.

Main Results:

Migration favors prophage-gene association when genes are beneficial in specific environments that increase prophage induction.
Spatial dynamics promote association of weakly selected genes with phages via virion dispersal.
These mechanisms appear more significant for phages than other MGEs like plasmids.

Conclusions:

Prophage lifecycle dynamics and spatial heterogeneity are key drivers of MGE-gene associations.
Phages may play a unique role in bacterial adaptation by facilitating the spread of beneficial genes.
This work offers new insights into the evolution of phage-encoded virulence.