Viral replication organelles: the highly complex and programmed replication machinery

Figures

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  Figure 1. Schematic diagram of the components of viral replication organelles (ROs) in the cytoplasm. Viral factories: represented by African swine fever virus (ASFV) and poxviruses, the ROs are formed by altering the morphology and positioning of the cellular membrane systems and cytoskeletal proteins to generate larger ROs. Spherules: generated by flaviviruses, the invaginated vesicle is formed by viral proteins that remodel the ER lumen and interact with cytoskeletal proteins. Double-membrane vesicles (DMVs): induced by SARS-CoV-2, the ROs are formed by the viral nonstructural proteins nsp3/4, which create a zippered-ER that invaginates to produce a double-membrane structure. Additionally, there DMVs form complex with nsp6 and lipid droplet (LDs) and LDs provides the energy needed for DMVs development. Tubes: created by Bunyamwera virus (BUNV), this tubular membrane structure is formed by the viral NSm protein and actin in the Golgi apparatus.

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  Figure 2. Changes in the conformation of the African swine fever virus (ASFV) pC962R and the monkeypox virus (MPXV) D5 SF3. (A) Structural diagram illustrating the conformational change of the helicase pC962R from a dodecameric form (Protein Data Bank [PDB] ID: 8IQH) to a hexameric state (PDB ID: 8IQI), with five different colors representing the individual domains of pC962R. (B) Structural transitions of the helicase D5 SF3 in the Apo form (PDB ID: 8HWC), ATP-ADP-Apo-ssDNA form (PDB ID: 8HWA), and AGS-ADP-ssDNA form (PDB ID: 8HWG). Gray, red, and cyan represent different states of the D5 SF3. The colors and letters at the vertices of the diamond-shaped diagrams correspond to the schematic representations denoting distinct states of the D5 protein SF3. The solid lines indicate tight connections and the dashed lines indicate loose connections. AGS, ATP-gamma-S (a nonhydrolyzable ATP analog). The models were generated using the ChimeraX software downloaded from https://www.cgl.ucsf.edu/chimerax/.

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  Figure 3. Interactions between ligands and adjacent amino acids (aa) in the SF3 of the pC962R or D5. Atomic models of the interaction between AMPPNP in the pC962R SF3 and ATP in the D5 SF3 with adjacent aa. The models were generated using the ChimeraX software downloaded from https://www.cgl.ucsf.edu/chimerax/. Proportions of the pC962R SF3 and D5 SF3 aa are involved in the interactions with AMPPNP and ATP, respectively. AMPPNP, adenylyl-imidodiphosphate (a nonhydrolyzable ATP analog); Iaa, identical amino acids; Daa, different amino acids. The bar chart was generated using the Prismchs software.

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  Figure 4. The sliding clamp proteins of DNA viruses exhibit comparable domain architectures. Domain architectures, oligomeric states and electrostatic potential surface distributions of human proliferating cell nuclear antigen (PCNA) and sliding clamps from DNA viruses. Red indicates negative and blue represents positive in the lower panel of the sphere style of the human PCNA and sliding clamps. PDB ID: 6GIS (human PCNA), 8I6G and 8ITE (ASFV pE301R), 2Z0L (EBV BMRF1), 1CZD (T4 bacteriophage gp45), 1T6L (HCMV UL44), 3HSL (KSHV PF-8), and 1DML (HSV UL42). The models were generated using the ChimeraX software downloaded from https://www.cgl.ucsf.edu/chimerax/.

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  Figure 5. Structural patterns of nucleotide addition cycle (NAC) modulation by the RdRp active center in RNA viruses. The RdRp active center completes one NAC through four steps: entry of NTP into the active site, closure of the active site, formation of the phosphodiester bond, and reopening of the active site. Briefly, RdRp binds to the template strand with NTP at the active site, inducing closure and conformational changes that confer catalytic activity. Two Mg2+ ions enable NTP to form phosphodiester bonds with the new RNA chain. The absence of Mg2+ results in the destabilization of the active site, leading to the opening of the RdRp complex. The open active site facilitates the binding of new NTP, thereby repeating the cycle for the synthesis of progeny RNA. T, template (lime); P, product (blue); PPB, phosphodiester bond; PDB ID: 5F8I (one), 7W9S (two), 5F8M (three), and 6LSH (four). The models were generated using the ChimeraX software downloaded from https://www.cgl.ucsf.edu/chimerax/.