Abstract
The 3-dimensional structure of the nucleocapsid (NC) of bacteriophage φ6 is described utilizing component tree analysis, a topological and geometric image descriptor. The component trees are derived from density maps of cryo-electron microscopy single particle reconstructions. Analysis determines position and occupancy of structure elements responsible for RNA packaging and transcription. Occupancy of the hexameric nucleotide triphosphorylase (P4) and RNA polymerase (P2) are found to be essentially complete in the NC. The P8 protein lattice likely fixes P4 and P2 in place during maturation. We propose that the viral procapsid (PC) is a dynamic structural intermediate where the P4 and P2 can attach and detach until held in place in mature NCs. During packaging, the PC expands to accommodate the RNA, and P2 translates from its original site near the inner 3-fold axis (20 sites) to the inner 5-fold axis (12 sites) with excess P2 positioned inside the central region of the NC.
Highlights
Bacteriophage φ6 and its relatives are model systems for virus assembly, genome packaging and dsRNA polymerization
This ring-like artifact has been observed in previous NC single particle reconstructions of cystovirus (φ6 and φ8) [5, 16]
We demonstrate that component tree analysis provides a useful tool for understanding the spatial organization of functional elements of viral reconstructions
Summary
Bacteriophage φ6 and its relatives are model systems for virus assembly, genome packaging and dsRNA polymerization. The RNA packaging, replication, transcription mechanism, and overall structure resembles that of reoviruses making the species an excellent model system to study these important pathogens. Of particular interest is the molecular, spatial relationships and overall organization of the RNA packaging and transcription elements found in the procapsid (PC) and mature nucleocapsid (NC). We compare the relative location and occupancy of viral portal proteins in the NC and make comparisons to existing models of the pre-packaged PC. A component tree analysis is employed on single particle reconstructions of the NC to identify and locate the viral elements and to estimate protein occupancy.
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