Natrialba magadii virus φCh1:: first complete nucleotide sequence and functional organization of a virus infecting a haloalkaliphilic archaeon

The double-stranded (ds)DNA virus phi Ch1 infects the haloalkaliphilic archaeon Natrialba magadii. The complete DNA sequence of 58 498 bp of the temperate virus was established, and the probable functions of 21 of 98 phi Ch1-encoded open reading frames (ORFs) have been assigned. This knowledge has been used to propose functional modules each required for specific functions during virus development. The phi Ch1 DNA is terminally redundant and circularly permuted and therefore appears to be packaged by the so-called headful mechanism. The presence of ORFs encoding homologues of proteins involved in plasmid replication as well as experimental evidence indicate a plasmid-mediated replication strategy of the virus. Results from nanosequencing of virion components suggest covalent cross-linking of monomers of at least one of the structural proteins during virus maturation. A comparison of the phi Ch1 genome with the partly sequenced genome of Halobacterium salinarum virus phi H revealed a close relationship between the two viruses, although their host organisms live in distinct environments with respect to the different pH values required for growth.