ArchaealHaloarcula californiaeIcosahedral Virus 1 Highlights Conserved Elements in Icosahedral Membrane-Containing DNA Viruses from Extreme Environments

Abstract

Despite their high genomic diversity, all known viruses are structurally constrained to a limited number of virion morphotypes. One morphotype of viruses infecting bacteria, archaea, and eukaryotes is the tailless icosahedral morphotype with an internal membrane. Although it is considered an abundant morphotype in extreme environments, only seven such archaeal viruses are known. Here, we introduce Haloarcula californiae icosahedral virus 1 (HCIV-1), a halophilic euryarchaeal virus originating from salt crystals. HCIV-1 also retains its infectivity under low-salinity conditions, showing that it is able to adapt to environmental changes. The release of progeny virions resulting from cell lysis was evidenced by reduced cellular oxygen consumption, leakage of intracellular ATP, and binding of an indicator ion to ruptured cell membranes. The virion contains at least 12 different protein species, lipids selectively acquired from the host cell membrane, and a 31,314-bp-long linear double-stranded DNA (dsDNA). The overall genome organization and sequence show high similarity to the genomes of archaeal viruses in the Sphaerolipoviridae family. Phylogenetic analysis based on the major conserved components needed for virion assembly—the major capsid proteins and the packaging ATPase—placed HCIV-1 along with the alphasphaerolipoviruses in a distinct, well-supported clade. On the basis of its virion morphology and sequence similarities, most notably, those of its core virion components, we propose that HCIV-1 is a member of the PRD1-adenovirus structure-based lineage together with other sphaerolipoviruses. This addition to the lineage reinforces the notion of the ancient evolutionary links observed between the viruses and further highlights the limits of the choices found in nature for formation of a virion.

Novel haloarchaeal viruses from Lake Retba infecting Haloferax and Halorubrum species

“…D) and protein quantities (Table ), but the purified particles had specific infectivity of ~2 × 10 9 pfu/mg of protein (Table ), which is 3–4 magnitudes lower than e.g. the specific infectivities of the purified virus samples of haloarchaeal tailed virus HSTV‐1 (~9 × 10 12 pfu/mg of protein) and icosahedral membrane‐containing virus HCIV‐1 (~1 × 10 12 pfu/mg of protein), of which have been analysed structurally (Pietilä et al ., ; Demina et al ., ; Santos‐Perez et al ., ). The negative staining and TEM of the purified HFTV1 particles revealed that some of particles had lost their genome explaining partly the loss of infectivity (Fig.…”

Halophilic viruses with varying biochemical and biophysical properties are amenable to purification with asymmetrical flow field-flow fractionation

“…Broth, agar and soft-agar media contained 23, 20 and 18% (w/v) SW, respectively. Virus-specific buffers were the following: His1: 0.5 M NaCl, 35 mM MgCl2, 10 mM KCl, 1 mM CaCl2, 50 mM Tris-HCl (pH 7.2); HVTV-1: 1.2 M NaCl, 44 mM MgCl2, 47 mM MgSO4, 1.5 mM CaCl2, 28 mM KCl, 24 mM Tris-HCl (pH 7.2); HRPV-1: 1.5 M NaCl, 100 mM MgCl2, 2 mM CaCl2, 20 mM Tris-HCl (pH 7.5); and HCIV-1: 1 M NaCl, 70 mM MgCl2, 20 mM KCl, 1 mM CaCl2, 50 mM Tris-HCl (pH 7.2) (Demina et al 2016;Pietilä et al 2013a;Pietilä et al 2013b;Pietilä et al 2009). Total molar ionic strengths of the buffers were the following: His1: 0.6 M; HVTV-1: 1.6 M; HRPV-1: 1.5 M; and HCIV-1: 1.2 M.…”

“…Three different input samples for AF4 purifications were used: (i) agar stocks or culture supernatants, (ii) PEG-precipitated viruses, and (iii) pre-purified viruses from rate-zonal ultracentrifugation in sucrose and differential ultracentrifugation (designated as 1×viruses). They were prepared as previously described using virus specific buffers (Demina et al 2016;Pietilä et al 2013a;Pietilä et al 2013b;Pietilä et al 2009) (Fig. 1, Table S1).…”

“…In AF4, elevated ionic strength results in a reduced thickens of the electrical double layer and thus a closer contact of the sample components with the membrane and therefore its effect on retention and yield depends on the nature of the sample components as repulsive or attractive interactions may take place (Benincasa and Caldwell 2001;Neubauer et al 2011;Wagner et al 2014). The structural components of the studied viruses were expected to be negatively charged at neutral pH (Demina et al 2016;Pietilä et al 2009).We first addressed AF4 performance in low (2 mM), medium (0.6 M) and high (1.6 M) ionic strength conditions using standard proteins (150-669 kDa) with acidic pIs (4.4-5.6) ( Fig. S1).…”

“…Their DNA genome is enclosed by a flexible membrane vesicle that is decorated with randomly arrayed spike complexes (Pietilä et al 2012;Pietilä et al 2016). The third morphotype comprises tailless icosahedral viruses with an internal membrane (family Sphaerolipoviridae) (Demina et al 2016;Demina et al 2017;Porter et al 2005). Their capsids are decorated with spike complexes located at the five-fold vertices (Gil-Carton et al 2015;Jäälinoja et al 2008).…”