Dataset of phage genes in Escherichia coli K-12

Phages
engage in an evolutionary dance with bacteria and archaea, and play a role in
regulating their numbers. Given that bacteriophage could enter the lysogeny
cycle during unfavourable circumstances, it comes as not a surprise that genome
of bacterial species harbour phage genes. Although such genes may not remain
intact due to evolutionary pressure on them or the action of transposon, they
nevertheless represent a chronicle of the types of phages that have infected a
bacterial species. With this perspective in mind, this work sought to
categorize the different types of bacteriophages that have infected Escherichia
coli K-12, and integrated their genome into the bacterial genome through
lysogeny. Profiling the annotated genome of E. coli K-12 revealed the
presence of 10 prophages, each with their complement of phage genes. Many of
the phages are likely deactivated given the large number of phage genes that
have been transposed through the action of insertion element or transposon.
Hence, these defective prophages in E. coli K-12 represents a treasure
trove of information for understanding the action of transposon on genome
maintenance, and their role in guiding the evolution of the bacterial species.
Each set of genes belonging to a prophage has been categorized to different
bins depending on their function in DNA replication, transcription, and
structural function. But, persistently, a large set of genes have to be
categorized as miscellaneous, and these predominantly include phage genes whose
identities have been swapped with those of structural genes in the host genome.
Collectively, this dataset of phage genes in Escherichia coli should
serve as a useful starting point for further studies seeking to understand the
role of bacteriophages in shaping the evolution of this model organism.