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

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Author(s): Jiang Xiaofang | Jiang Huanhuan | Li Cun | Wang Sheng | Mi Zhiqiang | An Xiaoping | Chen Jiankui | Tong Yigang

Journal: Virology Journal
ISSN 1743-422X

Volume: 8;
Issue: 1;
Start page: 194;
Date: 2011;
Original page

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

ABSTRACT
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.
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