Prophages inserted in archaebacterial genomes

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By analyzing archaebacterial genomic DNA sequences, three new prophages have been found inserted in tRNA genes of the host genomes: proPOF1 and proPOF2 in the genome of Pyrococcus sp. OT3, and proMJF1 in that of Methanococcus jannaschii. The three prophages possess a gene coding for site-specific tyrosine integrase, and are characterized with pairs of elements of the same 46-65 base sequences, that are positioned on the borders to the host genomes (i.e. the attachments). If the two ends of proPOF1 are connected to form a circle by overlapping the two attachments, proPOF2 possesses 33 ORFs in 9 putative transcription units (i.e. 5 operons and 4 independently transcribed ORFs) in 4 clusters inside each of which the direction of transcription is kept the same. This prophage is more likely to inherit a potential to be activated to a phage than is proPOF2, which has only 3 ORFs. In proPOF1 and proPOF2 the attachments are designed, so that their nucleotide sequences are complementary to the 3-terminal halves of the host tRNA genes. These attachments are part of the integrase genes in the prophages. Upon the integration the integrase genes were divided at the attachments into two segments and are positioned at the two ends of the prophages. In proMJF1 the integrase gene is undivided, and is positioned between the two attachments whose nucleotide sequence is the same as that of the 3-terminal half of the host tRNA gene. Thus, the type of phage-integration that created proMJF1 is different from that created proPOF1 and proPOF2.
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Prophages inserted in archaebacterial genomes

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