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Publication Abstract from PubMed

Ubiquitous and abundant in ecosystems and microbiomes, gokushoviruses constitute a Microviridae subfamily, distantly related to bacteriophages PhiX174, alpha3, and G4. A high-resolution cryo-EM structure of gokushovirus PhiEC6098 was determined, and the atomic model was built de novo. Although gokushoviruses lack external scaffolding and spike proteins, which extensively interact with the PhiX174 capsid protein, the core of the PhiEC6098 coat protein (VP1) displayed a similar structure. There are, however, key differences. At each PhiEC6098 icosahedral 3-fold axis, a long insertion loop formed mushroom-like protrusions, which have been noted in lower-resolution gokushovirus structures. Hydrophobic interfaces at the bottom of these protrusions may confer stability to the capsid shell. In PhiX174, the N-terminus of the capsid protein resides directly atop the 3-fold axes of symmetry; however, the PhiEC6098 N-terminus stretched across the inner surface of the capsid shell, reaching nearly to the 5-fold axis of the neighboring pentamer. Thus, this extended N-terminus interconnected pentamers on the inside of the capsid shell, presumably promoting capsid assembly, a function performed by the PhiX174 external scaffolding protein. There were also key differences between the PhiX174-like DNA-binding J proteins and its PhiEC6098 homologue VP8. As seen with the J proteins, C-terminal VP8 residues were bound into a pocket within the major capsid protein; however, its N-terminal residues were disordered, likely due to flexibility. We show that the combined location and interaction of VP8's C-terminus and a portion of VP1's N-terminus are reminiscent of those seen with the PhiX174 and alpha3 J proteins. IMPORTANCE There is a dramatic structural and morphogenetic divide within the Microviridae. The well-studied PhiX174-like viruses have prominent spikes at their icosahedral vertices, which are absent in gokushoviruses. Instead, gokushovirus major coat proteins form extensive mushroom-like protrusions at the 3-fold axes of symmetry. In addition, gokushoviruses lack an external scaffolding protein, the more critical of the two PhiX174 assembly proteins, but retain an internal scaffolding protein. The PhiEC6098 virion suggests that key external scaffolding functions are likely performed by coat protein domains unique to gokushoviruses. Thus, within one family, different assembly paths have been taken, demonstrating how a two-scaffolding protein system can evolve into a one-scaffolding protein system, or vice versa.

Cryo-EM Structure of Gokushovirus PhiEC6098 Reveals a Novel Capsid Architecture for a Single-Scaffolding Protein, Microvirus Assembly System.,Lee H, Baxter AJ, Bator CM, Fane BA, Hafenstein SL J Virol. 2022 Nov 9;96(21):e0099022. doi: 10.1128/jvi.00990-22. Epub 2022 Oct 18. PMID:36255280^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.