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

• Published in: Nature (London) Vol. 541; no. 7635; pp. 112 - 116
• Main Authors: Dai, Xinghong, Li, Zhihai, Lai, Mason, Shu, Sara, Du, Yushen, Zhou, Z Hong, Sun, Ren
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 05.01.2017
• Subjects: Capsid - chemistry; Capsid - metabolism; Capsid - ultrastructure; Capsid Proteins - chemistry; Capsid Proteins - metabolism; Capsid Proteins - ultrastructure; Cryoelectron Microscopy; Fimbriae, Bacterial - chemistry; Fimbriae, Bacterial - metabolism; Fimbriae, Bacterial - ultrastructure; Genome, Viral - physiology; Health aspects; Levivirus - chemistry; Levivirus - genetics; Levivirus - metabolism; Levivirus - ultrastructure; Methods; Models, Molecular; Molecular Conformation; Protein Multimerization; RNA sequencing; RNA viruses; RNA, Viral - chemistry; RNA, Viral - metabolism; RNA, Viral - ultrastructure; Virus Assembly
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/nature20589

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, single-stranded RNA (ssRNA) viruses, such as bacteriophage MS2, co-assemble their capsid with the genome; however, the structural basis of this co-assembly is poorly understood. MS2 infects Escherichia coli via the host 'sex pilus' (F-pilus); it was the first fully sequenced organism and is a model system for studies of translational gene regulation, RNA-protein interactions, and RNA virus assembly. 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. The maturation protein is responsible for attaching the virus to an F-pilus and delivering the viral genome into the host during infection, 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 description of genome-capsid interactions in a spherical ssRNA virus provides insight into genome delivery via the host sex pilus and mechanisms underlying ssRNA-capsid co-assembly, and inspires speculation about the links between nucleoprotein complexes and the origins of viruses.