Formation of a Viral Replication Focus in Sulfolobus Cells Infected by the Rudivirus Sulfolobus islandicus Rod-Shaped Virus 2

Abstract

Viral factories are compartmentalized centers for viral replication and assembly in infected eukaryotic cells. Here, we report the formation of a replication focus by prototypical archaeal Sulfolobus islandicus rod-shaped virus 2 (SIRV2) in the model archaeon Sulfolobus. This rod-shaped virus belongs to the viral family Rudiviridae, carrying linear double-stranded DNA (dsDNA) genomes, which are very common in geothermal environments. We demonstrate that SIRV2 DNA synthesis is confined to a focus near the periphery of infected cells. Moreover, viral and cellular replication proteins are recruited to, and concentrated in, the viral replication focus. Furthermore, we show that of the four host DNA polymerases (DNA polymerase I [Dpo1] to Dpo4), only Dpo1 participates in viral DNA synthesis. This constitutes the first report of the formation of a viral replication focus in archaeal cells, suggesting that organization of viral replication in foci is a widespread strategy employed by viruses of the three domains of life. IMPORTANCEThe organization of viral replication in foci or viral factories has been mostly described for different eukaryotic viruses and for several bacteriophages. This work constitutes the first report of the formation of a viral replication center by a virus infecting members of the Archaea domain.KEYWORDS replication focus, archaeal virus, SIRV2, DNA polymerase T he compartmentalization of viral genome replication is a well-known feature of many eukaryotic viruses, where replication is confined to specific subcellular microenvironments termed viral factories, viroplasms, viral replication compartments, or viral replication centers. In general, viral factories function as a scaffold containing viral genomes and proteins involved in viral replication and assembly, and this is hypothesized to increase the efficiency of viral replication and confer protection from the cellular antiviral immune responses (1, 2).The formation of viral factories has been observed for DNA, double-stranded RNA (dsRNA), positive-sense single-stranded RNA (ssRNA), and negative-sense ssRNA viruses, and it has been extensively studied for nucleocytoplasmic large DNA viruses (e.g., poxviruses and asfarviruses) and positive-sense ssRNA viruses, including flaviviruses, coronaviruses, picornaviruses, and togaviruses (1). Although these viruses infect a wide range of hosts and their corresponding viral factories differ in their morphologies, components, and intracellular locations, their modes of formation share some similarities. First, formation of viral factories usually involves extensive organizational changes in the host cell membranes and/or cytoskeleton. Second, viral factories constitute a scaffold for the concentration of viral genomes and of viral and cellular proteins required for viral replication and assembly (1, 2).To date, the formation of viral factories has been studied mainly for eukaryotic viruses, although the organization of viral replication has been reported for bacteriophages 29, PRD1, SSP1, and 20...

A Unique B-Family DNA Polymerase Facilitating Error-Prone DNA Damage Tolerance in Crenarchaeota

“…Choi et al, 2011). Nevertheless, genetic analysis has revealed that only dpo1 gene is essential in S. islandicus, as shown here and in previous works (Martinez-Alvarez et al, 2017;Zhang et al, 2018). For this reason, if Dpo3 could be a component of the S. islandicus replication machinery as suggested for the S. solfataricus replisome (Yan et al, 2017), it should be a dispensable one.…”

Stable maintenance of the rudivirus SIRV3 in a carrier state in Sulfolobus islandicus despite activation of the CRISPR-Cas immune response by a second virus SMV1

“…The proportion of SIRV3-infected cells in rich medium over 84 hpi fluctuated between 2% and 17% ( Figure 3(a)). Importantly, there was no increase in the infection level with time and, given that the lytic life cycle of rudiviruses is about 12 hours [4,24,25], the results indicate that active SIRV3 was stably maintained. Consistent with this inference, the growth curves and cellular DNA contents of the SIRV3-infected cultures, showed no significant differences from those of the uninfected control culture (Figure 3(b,c)).…”

“…Then we estimated the cell fraction of strain REY15A carrying active SIRV3 over 84 hpi by expressing the core virus-encoded single-strand DNA binding protein gp12 using fluorescence microscopy [23,24]. Samples were taken at regular time intervals after infecting with SIRV3 at MOI 1.…”

Comparative genetic and genomic analysis of the novel fusellovirus Sulfolobus spindle-shaped virus 10

“…However, since it would seem that Sulfolobus viruses are forming virus factories at the cellular membrane ( Quemin and Quax 2015 ; Quemin et al. 2016 ; Martínez-Alvarez et al. 2017 ), it is likely that these ORFs are involved in the rearrangement of and anchoring to said membrane in order to facilitate the production and egress of mature virions.…”