Different mechanisms for human rhinovirus survival in the presence of deleterious amino acid substitutions at virion protein-protein or RNA-protein interfaces

Figures

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  Fig 1. RV-B14 virion structure and amino acid residues at capsid pentamer-pentamer or capsid-duplex RNA interfaces that were subjected to deleterious replacements. (A) Atomic structure of the RV-B14 virion, as determined at a high resolution by cryo-EM (PDB ID: 8PNF) (67). (B) Schematic diagram of the icosahedral RV capsid. In panel A, two neighbor capsid pentamers are, respectively, colored light yellow and cyan. In both panels A and B, these two pentamers are delimited by green lines; one capsid protomer is colored blue (VP1), green (VP2), and red (VP3); and some icosahedral capsid 5-fold, 3-fold, and 2-fold symmetry axes are, respectively, indicated by cyan pentagonal, triangular, and rhomboidal symbols. (C) Cutaway view of the RV-B14 virion structure, rotated 180° around the vertical axis relative to the orientation represented in panel A. The same color code and symbols used in panel A to highlight two capsid pentamers, one capsid protomer, and some capsid icosahedral symmetry axes are used in panel C. The internal VP4 polypeptide belonging to the highlighted capsid protomer is colored deep yellow. The structured duplex RNA elements bound to the inner capsid wall (67) are colored…

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  Fig 2. Effects on virion assembly efficiency and thermostability of deleterious primary amino acid substitutions, and infectivity-restoring amino acid substitutions at pentamer-pentamer interfaces in the virion. (A) Relative assembly efficiency and (B) relative thermostability of RV-B14 wt (black bar) and mutant virions carrying deleterious primary substitutions at pentamer-pentamer interfaces, either alone (light gray bars) or accompanied by infectivity-restoring second-site substitutions (dark gray bars). Error bars are indicated.

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  Fig 3. Localization of deleterious primary amino acid substitutions at pentamer-pentamer interfaces in the RV virion and of infectivity-restoring amino acid substitutions. Each panel represents the same close-up view of a pentamer-pentamer interface in the RV-B14 virion structure (67), as viewed from inside the virion. Parts of the structures of the two interacting pentamers are, respectively, represented using light yellow and cyan ribbon models. A capsid-bound RNA duplex element is represented using a magenta ribbon model. The capsid residues at the pentamer-pentamer interfaces whose primary replacement by alanine impaired viral infectivity are represented as red space filling models. The residues involved in infectivity-compensating substitutions that occurred during serial infections by infectivity-impaired virus mutants are represented as green space filling models. In each panel, the corresponding amino acid substitution in the original infectivity-impaired mutant is labeled in red color, and the second-site amino acid substitution that restored infectivity during the serial infections is labeled in green color.

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  Fig 4. Effects on virion assembly efficiency and thermostability of deleterious primary amino acid substitutions, and infectivity-restoring amino acid substitutions at capsid-duplex RNA interfaces in the virion. (A) Relative assembly efficiency and (B) relative thermostability of RV-B14 wt (black bar) and mutant virions carrying deleterious primary substitutions at capsid-duplex RNA interfaces, either alone (light gray bars) or accompanied by infectivity-restoring second-site substitutions (dark gray bars). Error bars are indicated.

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  Fig 5. Localization of deleterious primary amino acid substitutions at capsid-duplex RNA interfaces in the RV virion, and of infectivity-restoring amino acid substitutions. Each panel represents the same close-up view of a pentamer-pentamer interface in the RV-B14 virion structure (67), as viewed from inside the virion. Parts of the structures of the two interacting pentamers are, respectively, represented using light yellow and cyan ribbon models. A capsid-bound RNA duplex element is represented using a magenta ribbon model. The capsid residues interacting with the RNA whose primary replacement by alanine impaired viral infectivity are represented as red space filling models. The capsid residues where infectivity-compensating substitutions occurred during serial infections with the infectivity-impaired virus mutants are represented as green space filling models. In the larger panel, the green residue farthest from the interface is T4039. In each panel, the corresponding amino acid substitution in the original infectivity-impaired mutant is labeled in red color, and the second-site amino acid substitution that restored viral infectivity is labeled in green color. In cases where a…