Archaeal viruses have been found to be remarkably diverse in terms of their morphologies and genomes. But knowledge about their replication cycles and interactions with their hosts is still lacking.
The aim of this work was to gain insight about the molecular mechanism of the genomic replication of the crenarchaeal virus SIRV2, a model among archaeal viruses. SIRV2 was found to employ multiple replication mechanisms, with DNA synthesis starting by a strand-displacement mode that later derived in a rolling-circle replication from a circular intermediate. Interestingly, evidence for a secondary, bidirectional mode of replication from the circular intermediate was also found.
Surprisingly, analysis of the topology of the viral replication intermediates showed the formation of network-like, large and multimeric replication intermediates. These intermediates are formed since the beginning of replication and their processing into monomeric genomes starts around the middle of the replication cycle. This suggests that, once replication starts on a parental template, it continues, forming the multimeric replication intermediates observed. Furthermore, evidence suggesting the occurrence of consecutive replication reinitiation events may partially explain the branched topology of the viral replication intermediates.
We also analyzed the intracellular location of viral replication, showing the formation of viral peripheral replication centers in SIRV2-infected cells, where viral DNA synthesis and replication-related proteins are concentrated. Our data indicates that the host DNA polymerase Dpo1 is also the viral replicative polymerase. Moreover, additional data suggests that other processes, such as translation, are also reorganized after infection. Based on our results, a model for the organization of viral replication and assembly is suggested.