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Open Access Research

Sequence characteristics of T4-like bacteriophage IME08 genome termini revealed by high throughput sequencing

Xiaofang Jiang1, Huanhuan Jiang1, Cun Li1, Sheng Wang1, Zhiqiang Mi1, Xiaoping An1, Jiankui Chen2* and Yigang Tong1*

Author Affiliations

1 State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China

2 Clinical Laboratory, No.307 Hospital, Beijing 100071, China

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Virology Journal 2011, 8:194  doi:10.1186/1743-422X-8-194

Published: 27 April 2011

Abstract

Background

T4 phage is a model species that has contributed broadly to our understanding of molecular biology. T4 DNA replication and packaging share various mechanisms with human double-stranded DNA viruses such as herpes virus. The literature indicates that T4-like phage genomes have permuted terminal sequences, and are generated by a DNA terminase in a sequence-independent manner;

Methods

genomic DNA of T4-like bacteriophage IME08 was subjected to high throughput sequencing, and the read sequences with extraordinarily high occurrences were analyzed;

Results

we demonstrate that both the 5' and 3' termini of the IME08 genome starts with base G or A. The presence of a consensus sequence TTGGA|G around the breakpoint of the high frequency read sequences suggests that the terminase cuts the branched pre-genome in a sequence-preferred manner. Our analysis also shows that terminal cleavage is asymmetric, with one end cut at a consensus sequence, and the other end generated randomly. The sequence-preferred cleavage may produce sticky-ends, but with each end being packaged with different efficiencies;

Conclusions

this study illustrates how high throughput sequencing can be used to probe replication and packaging mechanisms in bacteriophages and/or viruses.

Keywords:
T4-like bacteriophage; terminase; high throughput sequencing