Evolution of the family of pRN plasmids and their integrase-mediated insertion into the chromosome of the crenarchaeon Sulfolobus solfataricus

Plasmid pHEN7 from Sulfolobus islandicus was sequenced (7.83 kb) and shown to belong to the archaeal pRN family, which includes plasmids pRN1, pRN2, p SSVx and pDL10 that share a large conserved sequence region, pHEN7 is most closely related to pRN1 in this conserved region. It also shares a large va riant region containing several homologous genes with pDL10, which is absen t from the other plasmids. The variant region is flanked by the sequence mo tif TTAGAATGGGGATTC and similar duplicated motifs occur in plasmids pRN1 an d pRN2, separated by a few bases. It is inferred that recombination at thes e sites produces the main genetic variability in the plasmid family. The co nserved region of the plasmid, and duplicated copies of the motif, are also present in the genome of Sulfolobus solfataricus P2. Moreover, they are bo rdered by a partitioned integrase gene (int) and by a 45 bp perfect direct repeat corresponding to the downstream half of a tRNA(Val) gene. The integr ase and the direct repeat are highly similar in sequence to the integrase a nd the chromosomal integration site (att), respectively, of the SSV1 virus, which integrates into the chromosome of Sulfolobus shibatae. Recombination at the att repeats in S. solfataricus would produce a novel plasmid, pXQ1, which carries both an intact integrase gene and a single integration site (aft). This strongly suggests that the same mechanism of site-specific inte gration at a tRNA gene is used for both viruses and plasmids in Sulfolobus. (C) 2000 Academic Press.