In situ structures of the genome and genome-delivery apparatus in an ssRNA virus

Genome packaging into a protein capsid and its subsequent delivery into a host cell are two fundamental processes in the life cycle of a virus. Unlike dsDNA viruses which pump their genome into a preformed capsid(1-3), ssRNA viruses, such as bacteriophage MS2, co-assemble their capsid with genome(4-7); however, the structural basis of this co-assembly is poorly understood. MS2 infects Escherichia coli via host “sex” pilus (F-pilus)(8) and is the first fully-sequenced organism(9) and a model system for studies of gene translational regulations(10,11), RNA-protein interactions(12-14), and RNA virus assembly(15-17). Its positive-sense ssRNA genome of 3569 bases is enclosed in a capsid with one maturation protein (MP) monomer and 89 coat protein (CP) dimers arranged in a T=3 icosahedral lattice(18,19). MP 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 are not known. Here we show the MS2 structure at 3.6Å resolution determined by electron-counting cryo electron microscopy (cryoEM) and asymmetric reconstruction. We traced ~80% backbone of the viral genome, built atomic models for 16 RNA stem-loops, and identified three conserved motifs of RNA-CP interactions among 15 of these stem-loops with diverse sequences. The stem-loop at 3’ end of the genome interacts extensively with the MP, which, with just a six-helix bundle and a six-stranded β-sheet, forms a genome-delivery apparatus, and joins 89 CP-dimers to form a capsid. This first atomic description of genome-capsid interactions in a spherical ssRNA virus provides insights into genome delivery via host “sex” pilus and mechanisms underlying ssRNA-capsid co-assembly, and inspires imaginations about links between nucleoprotein complexes and the origin of viruses.