Journal
VIROLOGY JOURNAL
Volume 8, Issue -, Pages -Publisher
BIOMED CENTRAL LTD
DOI: 10.1186/1743-422X-8-194
Keywords
T4-like bacteriophage terminase; high throughput sequencing
Categories
Funding
- Hi-Tech Research and Development (863) Program of China [2009AA02Z111]
- National Natural Science Foundation of China [30872223]
- State Key Laboratory of Pathogen and Biosecurity
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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 vertical bar 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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