Structural changes in a marine podovirus associated with release of its genome into Prochlorococcus

Abstract

Podovirus P-SSP7 infects Prochlorococcus marinus, the most abundant oceanic photosynthetic microorganism. Single particle cryo-electron microscopy (cryo-EM) yields icosahedral and asymmetrical structures of infectious P-SSP7 with 4.6 Å and 9 Å resolution, respectively. The asymmetric reconstruction reveals how symmetry mismatches are accommodated among 5 of the gene products at the portal vertex. Reconstructions of infectious and empty particles show a conformational change of the “valve” density in the nozzle, an orientation difference in the tail fibers, a disordering of the C-terminus of the portal protein, and disappearance of the core proteins. In addition, cryo-electron tomography (cryo-ET) of P-SSP7 infecting Prochlorococcus demonstrated the same tail fiber conformation as in empty particles. Our observations suggest a mechanism whereby, upon binding to the host cell, the tail fibers induce a cascade of structural alterations of the portal vertex complex that triggers DNA release.

Structural investigations of a Podoviridae streptococcus phage C1, implications for the mechanism of viral entry

“…The other additional density, located at the C1 capsid quasi-2-fold, bridges between neighboring hexameric capsomers and between neighboring hexameric and pentameric capsomers, thus aiding capsid stability. Similar densities at the capsomer interfaces had been observed in phages BPP-1, P-SSP7, and P22 (17,18,36). In Bordetella phage BPP-1 these densities were attributed to a cement protein.…”

“…In the HK97 structure, these regions have the largest structural deviation among the seven subunits that form an asymmetric unit of the HK97 capsid (27). Also, these portions of the HK97 fold were shown to have the most differences among different phages (12,14,18,36). The number of residues in gp16 of C1 is comparable to that of the HK97 capsid protein (392 a.a. versus 385 a.a.).…”

“…The capsid protein is organized into a T ¼ 4 icosahedral lattice and has a HK97 fold. This fold of the capsid protein has been observed in all tailed phages (12)(13)(14)(15)(16)(17)(18). The short C1 tail is surrounded by a skirt of 12 long appendages, each terminating with a flexible globular domain, unlike those of tailed phages studied previously.…”

Polar freshwater cyanophage S-EIV1 represents a new widespread evolutionary lineage of phages

“…The unusual morphology associated with ejection of a tail distinguishes S-EIV1 from other described phages. Other studies have shown that the release of nucleic acids can affect phage structure (Liu et al, 2011;Hu et al, 2013). Liu et al (2011) demonstrated that the release of nucleic acids in a marine podovirus led to the tail fibers being extended horizontally rather than parallel to the capsid surface.…”

Structure of β-galactosidase at 3.2-Å resolution obtained by cryo-electron microscopy

“…single-particle EM | frame alignment | CTF determination | 3D reconstruction | structure refinement R apid advances in technology for single-particle cryo-electron microscopy (cryo-EM) over the last few years have made it possible to determine high-resolution structures of large and well-ordered macromolecular assemblies such as 2D protein crystals, helical lattices, icosahedral viruses, and protein complexes with high symmetry (1)(2)(3)(4)(5)(6)(7)(8)(9)(10). More recently, continuing developments in microscope hardware and image processing software have yielded near-atomic resolution information for two smallersized complexes with low symmetry, the 700-kDa proteasome (11) and a 300-kDa mammalian ion channel (12), and for larger assemblies with no symmetry such as ribosome complexes (13)(14)(15).…”