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Mobile regulatory cassettes mediate modular shuffling in T4-type phage genomes

Christine Arbiol1, André M Comeau, Mzia Kutateladze

  • 1Institut d'Exploration Fonctionnelle des Génomes, CNRS-IFR109, Toulouse, France.

Genome Biology and Evolution
|March 25, 2010
PubMed

Insights

Coliphage phi1 and RB49 share high amino acid identity but differ in gene content, particularly within hyperplastic regions. Recombination between promoter elements drives divergence and may facilitate horizontal gene transfer via mini-circles.

Area of Science:

  • Microbiology
  • Virology
  • Genomics

Background:

  • Coliphage phi1, used in phage therapy, is closely related to the T-like myovirus RB49.
  • Both phages encode approximately 275 open reading frames with 95.8% average amino acid identity.

Purpose of the Study:

  • To investigate the genomic differences and evolutionary mechanisms between coliphage phi1 and RB49.
  • To understand the role of hyperplastic regions and promoter elements in phage genome evolution.

Main Methods:

  • Comparative genomic analysis of coliphage phi1 and RB49.
  • Identification and characterization of hyperplastic regions (HPRs) and promoter(early) stem-loops (PeSLs).

Main Results:

  • RB49 lacks 7 phi1 genes, while 10 phi1 genes are missing from RB49, many with unknown functions.
  • Genomic divergence is concentrated in HPRs, which contain nonessential genes and PeSLs.
  • Recombination between PeSLs drives modular shuffling and sequence divergence.
  • PeSL exchanges can generate small circular DNAs (mini-circles) encapsidated by the virus.

Conclusions:

  • Modular shuffling within HPRs, mediated by PeSLs, is a key driver of sequence divergence between phi1 and RB49.
  • PeSL mini-circles represent a potential mechanism for horizontal gene transfer in these phages.
Keywords:
T4-like phagegenome evolutionmodular shufflingregulatory cassette

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