Replication of Viral Genomes

The genome replication of crenarchaeal viruses has not been studied experimentally. Consequently, the knowledge about the replication mechanisms employed and participating enzymes is very scarce. Nevertheless, some clues about possible replication strategies of crenarchaeal viruses could be obtained from the sequences of the genomes and the genome arrangements.

Linear genomes of some lipothrixviruses exhibit an internal, repeat-rich, non-protein-coding region. The AFV2 carries a 1008 bp element bordered by an ITR that is rich in repeat sequences. Such regions could constitute internal origins of replication.

Even more remarkable are the genomic features of the STSV1. Its circular genome is highly asymmetric and divides into equal halves with respect to gene orientation. Between the two halves of the genome was located the 1.4 kbp long intergenic region with an unusually high AT content, including two sets of tandem repeats and two sets of inverted repeats. This region constitutes the putative origin of replication. Most likely, genome replication proceeds bidirectionally in the theta-mode from the proposed origin.

The genomic termini of lipotrixvirus AFV1 do not resemble any other virus. The two very short (11 bp) ITRs are preceded by about a 300 bp region consisting of many direct repeats of the pentanucleotide TTGTT, or close variants thereof. Such structures resemble telo-meric ends of eukaryotic chromosomes and raise the possibility of a primitive telomeric mechanism operating in AFV1 genome replication.

Rudivirus S1RV1 replicates its genome via head-to-head and tail-to-tail linked intermediates. This suggested a self-priming mechanism of replication, similar to that proposed for large eukaryotic dsDNA viruses including poxviruses. Consistent with this proposal are the similarities in the structures of linear genomes of these archaeal and eukaryal viruses, including long 1TRs and covalently closed termini. Moreover, each of these viruses encodes a Holliday junction resolvase which is likely to resolve the replicative intermediates into single-progeny genomes. The large 1TRs of the rudiviruses carry highly conserved sequence located 100—150 bp from the genomic termini that could serve as signal for the initiation of replication.

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