title: In situ structures of the genome and genome-delivery apparatus in a single-stranded RNA virus.
abstract: 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.
authors.affiliation: Department of Molecular and Medical Pharmacology, University of California, Los Angeles (UCLA), Los Angeles, California 90095, USA.|The California NanoSystems Institute (CNSI), UCLA, Los Angeles, California 90095, USA.
authors.forename: Xinghong
authors.initials: X
authors.lastname: Dai
authors.affiliation: The California NanoSystems Institute (CNSI), UCLA, Los Angeles, California 90095, USA.|Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California 90095, USA.|State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Xiamen University, Xiamen, Fujian 361102, China.
authors.forename: Zhihai
authors.initials: Z
authors.lastname: Li
authors.affiliation: Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California 90095, USA.
authors.forename: Mason
authors.initials: M
authors.lastname: Lai
authors.affiliation: Department of Molecular and Medical Pharmacology, University of California, Los Angeles (UCLA), Los Angeles, California 90095, USA.
authors.forename: Sara
authors.initials: S
authors.lastname: Shu
authors.affiliation: Department of Molecular and Medical Pharmacology, University of California, Los Angeles (UCLA), Los Angeles, California 90095, USA.
authors.forename: Yushen
authors.initials: Y
authors.lastname: Du
authors.affiliation: The California NanoSystems Institute (CNSI), UCLA, Los Angeles, California 90095, USA.|Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California 90095, USA.
authors.forename: Z Hong
authors.initials: ZH
authors.lastname: Zhou
authors.affiliation: Department of Molecular and Medical Pharmacology, University of California, Los Angeles (UCLA), Los Angeles, California 90095, USA.|The California NanoSystems Institute (CNSI), UCLA, Los Angeles, California 90095, USA.
authors.forename: Ren
authors.initials: R
authors.lastname: Sun
mesh_terms: D002213:Capsid / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure*; D036022:Capsid Proteins / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure; D020285:Cryoelectron Microscopy; D010861:Fimbriae, Bacterial / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure; D016679:Genome, Viral / Q000502:physiology*; D017909:Levivirus / Q000737:chemistry / Q000235:genetics / Q000378:metabolism* / Q000648:ultrastructure*; D008958:Models, Molecular; D008968:Molecular Conformation; D055503:Protein Multimerization; D012367:RNA, Viral / Q000737:chemistry / Q000378:metabolism / Q000648:ultrastructure*; D019065:Virus Assembly
chemical_list: D036022:Capsid Proteins; D012367:RNA, Viral