In situ structures of the genome and genome-delivery apparatus in a single-stranded RNA virus

A high-resolution structure of the bacteriophage MS2 sheds light on the structure of the genome and how the genome is delivered into a bacterium. Atomic structure of an ssRNA genome Hong Zhou and colleagues provide the first description of genome–capsid interactions in a spherical single-stranded RNA (ssRNA) virus, using the bacteriophage MS2 as a model. Unlike double-stranded DNA viruses that pump their genome into a preformed capsid, ssRNA viruses co-assemble their capsid with their genome. Here the authors determine the MS2 structure at 3.6 Å resolution and are able to trace around 80% of the backbone of the viral genome, identifying regions that react with the maturation protein and providing insights into the ssRNA capsid co-assembly process. Packaging of the genome into a protein capsid and its subsequent delivery into a host cell are two fundamental processes in the life cycle of a virus. Unlike double-stranded DNA viruses, which pump their genome into a preformed capsid 1 , 2 , 3 , single-stranded RNA (ssRNA) viruses, such as bacteriophage MS2, co-assemble their capsid with the genome 4 , 5 , 6 , 7 ; however, the structural basis of this co-assembly is poorly understood. MS2 infects Escherichia coli via the host ‘sex pilus’ (F-pilus) 8 ; it was the first fully sequenced organism 9 and is a model system for studies of translational gene regulation 10 , 11 , RNA–protein interactions 12 , 13 , 14 , and RNA virus assembly 15 , 16 , 17 . Its positive-sense ssRNA genome of 3,569 bases is enclosed in a capsid with one maturation protein monomer and 89 coat protein dimers arranged in a T = 3 icosahedral lattice 18 , 19 . The maturation protein is responsible for attaching the virus to an F-pilus and delivering the viral genome into the host during infection 8 , but how the genome is organized and delivered is not known. Here we describe the MS2 structure at 3.6 Å resolution, determined by electron-counting cryo-electron microscopy (cryoEM) and asymmetric reconstruction. We traced approximately 80% of the backbone of the viral genome, built atomic models for 16 RNA stem–loops, and identified three conserved motifs of RNA–coat protein interactions among 15 of these stem–loops with diverse sequences. The stem–loop at the 3′ end of the genome interacts extensively with the maturation protein, which, with just a six-helix bundle and a six-stranded β-sheet, forms a genome-delivery apparatus and joins 89 coat protein dimers to form a capsid. This atomic descript