Structure of the archaeal head-tailed virus HSTV-1 completes the HK97 fold story

Abstract

It has been proposed that viruses can be divided into a small number of structure-based viral lineages. One of these lineages is exemplified by bacterial virus Hong Kong 97 (HK97), which represents the head-tailed dsDNA bacteriophages. Seemingly similar viruses also infect archaea. Here we demonstrate using genomic analysis, electron cryomicroscopy, and image reconstruction that the major coat protein fold of newly isolated archaeal Haloarcula sinaiiensis tailed virus 1 has the canonical coat protein fold of HK97. Although it has been anticipated previously, this is physical evidence that bacterial and archaeal head-tailed viruses share a common architectural principle. The HK97-like fold has previously been recognized also in herpesviruses, and this study expands the HK97-like lineage to viruses from all three domains of life. This is only the second established lineage to include archaeal, bacterial, and eukaryotic viruses. Thus, our findings support the hypothesis that the last common universal ancestor of cellular organisms was infected by a number of different viruses.

Keywords: archaeal virus; major capsid protein fold; virus evolution.

Fig. 1.

Podovirus HSTV-1 tolerates salinity changes. (A) Cryo-EMs of HSTV-1 at 4-μm underfocus. (I) Virions incubated in 9% (wt/vol) SW containing 1.2 M NaCl, (II) virions in 20 mM Tris·HCl (pH 7.2) buffer, and (III) virions first incubated in 20 mM Tris·HCl (pH 7.2) and then restored in 9% (wt/vol) SW. (Inset) (6-μm underfocus) A particle viewed along the tail and showing possible tail fibers. (Scale bars, 50 nm.) (B) Specific infectivity of HSTV-1 virions at a logarithmic scale. (I, II, and III) High and low salinity conditions as in A.

Fig. 2.

Genome and proteins of HSTV-1. (A) Genome of HSTV-1 is presented with markers spaced at 1-kbp and 100-bp intervals. The predicted genes are shown as boxes either above or below the genome, depending on whether they are rightward or leftward transcribed, respectively. The gene numbers are shown for annotated genes, and putative functions are shown above the genes. Abbreviated functions are histidine-asparagine-histidine homing endonuclease (HNH), proliferating cell nuclear antigen family of sliding clamps (PCNA), and a minichromosome maintenance helicase (MCM). (B) Protein profile of the purified virions in a tricine-SDS-polyacrylamide gel stained with Coomassie blue. Numbers on the left indicate molecular mass markers. The identified proteins are indicated by the corresponding gp (gene product) number. (C) N-terminal sequences determined from the protein bands gp12, gp29, and gp14. The first two amino acids of the N-terminal sequence of gp12 and gp29 could not be identified. The theoretical molecular masses of the mature proteins are in parentheses.

Fig. 3.

HSTV-1 capsid structures. (A) A 2.26-Å-thick central section of the HSTV-1 icosahedral reconstruction viewed along an icosahedral twofold axis. Twofold (ellipse), threefold (triangle), and fivefold (pentagon) symmetry axes are indicated. (Scale bar, 10 nm.) (B–D) Capsid isosurface representations along an icosahedral twofold axis. The HSTV-1 capsid is displayed at σ = 0.9 (B) and σ = 3.0 (C and D) threshold. The empty HSTV-1 (D) capsid is shown sectioned with the front half of the capsid removed. The empty capsid was generated by manually removing most of the genome density in UCSF Chimera. The symmetry axes are indicated as in A. The models were colored using radial-depth cueing (bars, 210- to 360-Å radius) in UCSF Chimera (56).

Fig. 4.

HSTV-1 gp14 has the HK97 fold. (Left) Viewed from the capsid interior; (Right) viewed from the capsid exterior. (A) Cryo-EM density of an HSTV-1 asymmetric unit drawn at σ = 3.0 threshold (gray transparent). The atomic model of HK97 asymmetric unit (PDB ID 1OHG) (32) is shown in red ribbon after rigid body fitting into the density in UCSF Chimera (56). (B) Averaged density of the six segmented subunits from one hexamer shown at σ = 3.5 threshold (gray transparent). HK97 chain E in red ribbon (PDB ID 1OHG) (32) and homology model of gp14 in blue ribbon (33, 34) after rigid body fitting into the density in UCSF Chimera (56). (C) Red surface represents a hexamer built from six copies of the averaged subunit. Green wireframe shows the position of the pentameric subunit that has a significantly different conformation than the hexameric units and thus was not included in the averaging.