Structure of small RNA phages

Abstract: Small RNA phages belonging to the family Leviviridae are among the simplest known viruses. They have been used extensively as models for studies of various problems in molecular biology, including protein-RNA interactions, repression of translation, virus assembly and virus evolution.The small RNA phage particle contains a single-stranded RNA genome, surrounded by a T=3 protein shell, which is composed of 180 chemically identical monomers. There are very strong dimer interactions between the monomers, and the capsid can be regarded as built up from 90 dimersBesides their structural role, the dimers are acting also as translation repressors of the replicase subunit gene of the phage. The complex formed by the coat protein dimer and the viral RNA is alsothought to be the initiation of capsid assembly.The current work presents the crystal structure of two phages: Enterobacteria phage GA and Pseudomonas phage PP7. The structure of a deletion mutant of Enterobacteria phage fr capsid has also been solved. Comparison of the solved structures with earlier solved ones (including the phages MS2, fr and Qß) has revealed several aspects of virus assembly and structural evolution.When comparing the protein shells of Leviviridae phages, a high degree of similarity is found in the RNA binding sites, whereas larger structural differences are located in the loop regions of the coat protein, especially in the FG loop, connecting strands ßF and ßG. These loops are forming contacts around the 5-fold and quasi-6-fold axes. In many cases, mutations in the FG loop preventcapsid formation suggesting that this region is of major importance during the particle assembly.However, in the phage fr deletion mutant, apart of the FG loop was deleted, but particles stillformed. The crystal structure of the mutant showed that the FG loops do not make any contacts andare therefore unlikely to be important during the assembly.Based on analysis of the conserved inter-dimer interactions, we now suggest that the capsidassembly in the small RNA phages is guided by the relatively rigid interacting surfaces of thesubunits. It seems that the RNA phages lack any obvious switching mechanisms between pentamericand hexameric units, in contrast to several plant and insect viruses.