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Cluster J mycobacteriophages: intron splicing in capsid and tail genes

Welkin H Pope1, Deborah Jacobs-Sera, Aaron A Best

  • 1Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America .

Plos One
|July 23, 2013
PubMed

Insights

Newly discovered mycobacteriophages in Cluster J exhibit unique, long genomes and mosaic architecture. These phages offer novel insights into phage genome evolution, gene function, and capsid structure.

Area of Science:

  • Microbiology
  • Virology
  • Genomics

Background:

  • Bacteriophages infecting Mycobacterium smegmatis mc(2)155 display diverse genomes with mosaic architecture and many genes of unknown function.
  • A novel group, Cluster J, comprises six Siphoviridae mycobacteriophages with substantial nucleotide sequence similarity and unusually long genomes (106.3–117 kbp).

Purpose of the Study:

  • To characterize the unique Cluster J mycobacteriophages.
  • To investigate phage genome architecture, gene function, capsid structure, and evolutionary mechanisms.

Main Methods:

  • Cryo-electron microscopy was used to reconstruct the capsid structure of mycobacteriophage BAKA.
  • Comparative genomic analysis was performed on the six Cluster J genomes.
  • Phage integration sites and intron splicing events were identified.

Main Results:

  • Cluster J phages are temperate, homoimmune, and integrate into a previously unidentified tRNA-Leu gene.
  • Mycobateriophage BAKA possesses an icosahedral capsid (triangulation number 13).
  • Two instances of intron splicing in virion structural genes and numerous HNH homing endonucleases were observed, contributing to genome mosaicism.

Conclusions:

  • The Cluster J genomes reveal novel aspects of phage genome organization, gene function, and capsid morphology.
  • These findings enhance understanding of phage gene mobility, intron splicing mechanisms, and evolutionary processes.

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