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RNA virus replication complexes.

Tao YJ, Ye Q - PLoS Pathog. (2010)

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America. ytao@rice.edu

ABSTRACT

Different replication strategies are used by (+), (−), and dsRNA viruses to limit dsRNA exposure, to regulate (+)RNA versus (−)RNA synthesis, and to modulate transcription versus replication throughout the infection cycle. The differences in the functionalities of the replication complexes are reflected in their structural composition, their subcellular localization, and in the interaction of the complex with viral RNA templates. It is expected that studies of RNA virus replication machineries will have a large impact on antiviral drug development due to their specific activities in virus replication.

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RNA virus replication machineries.(A) RdRps of hepatitis C virus and reovirus. Hepatitis C virus is a (+)RNA virus from the Flaviviridae family, while reovirus is a dsRNA virus belonging to the Reoviridae family. In both structures, the fingers, palm, and the thumb of the polymerase are colored in blue, red, and green, respectively. Yellow and magenta highlight the N- and C-terminal domains, respectively. The three aspartic acid residues in the polymerase catalytic active site are shown in cyan. Reovirus RdRP has large N- and C-terminal domains with distinct functions: the N-terminal domain maintains the closed conformation of the active site, and the C-terminal domain serves as a processivity factor like a sliding clamp. (B) The yeast L-A virus (Totiviridae family). The two independent sets of capsid protein molecules, 60 copies each, are shown in red and yellow, respectively. The viral RdRP is likely to be tethered to the inner capsid near the 5-fold symmetry axis, and viral transcripts made inside the core are released through channels on or near the 5-fold axes. (C) An influenza A virus (Orthomyxoviridae family) RNP model. Blue spheres represent NP monomers, and the green line shows vRNA. A short duplex formed between the 5′ and the 3′ ends provides the binding site for the heterotrimeric RdRp. Overall, the RNP assumes a rod-shaped, double-helical structure that remains intact even after the vRNA is removed.
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ppat-1000943-g001: RNA virus replication machineries.(A) RdRps of hepatitis C virus and reovirus. Hepatitis C virus is a (+)RNA virus from the Flaviviridae family, while reovirus is a dsRNA virus belonging to the Reoviridae family. In both structures, the fingers, palm, and the thumb of the polymerase are colored in blue, red, and green, respectively. Yellow and magenta highlight the N- and C-terminal domains, respectively. The three aspartic acid residues in the polymerase catalytic active site are shown in cyan. Reovirus RdRP has large N- and C-terminal domains with distinct functions: the N-terminal domain maintains the closed conformation of the active site, and the C-terminal domain serves as a processivity factor like a sliding clamp. (B) The yeast L-A virus (Totiviridae family). The two independent sets of capsid protein molecules, 60 copies each, are shown in red and yellow, respectively. The viral RdRP is likely to be tethered to the inner capsid near the 5-fold symmetry axis, and viral transcripts made inside the core are released through channels on or near the 5-fold axes. (C) An influenza A virus (Orthomyxoviridae family) RNP model. Blue spheres represent NP monomers, and the green line shows vRNA. A short duplex formed between the 5′ and the 3′ ends provides the binding site for the heterotrimeric RdRp. Overall, the RNP assumes a rod-shaped, double-helical structure that remains intact even after the vRNA is removed.

Mentions: Although little is known about the structure of the membrane-associated RNA replication complexes, (+)RNA virus RdRps have been well characterized to have an overall right-handed shape with three domains, the fingers, palm, and the thumb (reviewed in [6]) (Figure 1A). The palm domain contains an invariant, central, four-stranded β-sheet, with five highly conserved motifs named A to E. Motifs A and C, which contain the sequence –DxxxxD– and –GDD–, respectively, play important roles in metal ion coordination and nucleotide substrate selection during catalysis. The fingers and thumb domains are located on opposite sides of the active site canyon. Most (+)RNA virus RdRps can initiate RNA synthesis de novo, but a number of them use viral protein primers (VPgs) and produce protein-linked genomes. In the RdRp from the foot-and-mouth disease virus, uridylated VPg occupies a site similar to the typical RNA primer in the active site canyon, with the key residue Tyr3 and its associated uridylate (UMP) projected into the active site [7].


RNA virus replication complexes.

Tao YJ, Ye Q - PLoS Pathog. (2010)

RNA virus replication machineries.(A) RdRps of hepatitis C virus and reovirus. Hepatitis C virus is a (+)RNA virus from the Flaviviridae family, while reovirus is a dsRNA virus belonging to the Reoviridae family. In both structures, the fingers, palm, and the thumb of the polymerase are colored in blue, red, and green, respectively. Yellow and magenta highlight the N- and C-terminal domains, respectively. The three aspartic acid residues in the polymerase catalytic active site are shown in cyan. Reovirus RdRP has large N- and C-terminal domains with distinct functions: the N-terminal domain maintains the closed conformation of the active site, and the C-terminal domain serves as a processivity factor like a sliding clamp. (B) The yeast L-A virus (Totiviridae family). The two independent sets of capsid protein molecules, 60 copies each, are shown in red and yellow, respectively. The viral RdRP is likely to be tethered to the inner capsid near the 5-fold symmetry axis, and viral transcripts made inside the core are released through channels on or near the 5-fold axes. (C) An influenza A virus (Orthomyxoviridae family) RNP model. Blue spheres represent NP monomers, and the green line shows vRNA. A short duplex formed between the 5′ and the 3′ ends provides the binding site for the heterotrimeric RdRp. Overall, the RNP assumes a rod-shaped, double-helical structure that remains intact even after the vRNA is removed.
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Related In: Results  -  Collection

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ppat-1000943-g001: RNA virus replication machineries.(A) RdRps of hepatitis C virus and reovirus. Hepatitis C virus is a (+)RNA virus from the Flaviviridae family, while reovirus is a dsRNA virus belonging to the Reoviridae family. In both structures, the fingers, palm, and the thumb of the polymerase are colored in blue, red, and green, respectively. Yellow and magenta highlight the N- and C-terminal domains, respectively. The three aspartic acid residues in the polymerase catalytic active site are shown in cyan. Reovirus RdRP has large N- and C-terminal domains with distinct functions: the N-terminal domain maintains the closed conformation of the active site, and the C-terminal domain serves as a processivity factor like a sliding clamp. (B) The yeast L-A virus (Totiviridae family). The two independent sets of capsid protein molecules, 60 copies each, are shown in red and yellow, respectively. The viral RdRP is likely to be tethered to the inner capsid near the 5-fold symmetry axis, and viral transcripts made inside the core are released through channels on or near the 5-fold axes. (C) An influenza A virus (Orthomyxoviridae family) RNP model. Blue spheres represent NP monomers, and the green line shows vRNA. A short duplex formed between the 5′ and the 3′ ends provides the binding site for the heterotrimeric RdRp. Overall, the RNP assumes a rod-shaped, double-helical structure that remains intact even after the vRNA is removed.
Mentions: Although little is known about the structure of the membrane-associated RNA replication complexes, (+)RNA virus RdRps have been well characterized to have an overall right-handed shape with three domains, the fingers, palm, and the thumb (reviewed in [6]) (Figure 1A). The palm domain contains an invariant, central, four-stranded β-sheet, with five highly conserved motifs named A to E. Motifs A and C, which contain the sequence –DxxxxD– and –GDD–, respectively, play important roles in metal ion coordination and nucleotide substrate selection during catalysis. The fingers and thumb domains are located on opposite sides of the active site canyon. Most (+)RNA virus RdRps can initiate RNA synthesis de novo, but a number of them use viral protein primers (VPgs) and produce protein-linked genomes. In the RdRp from the foot-and-mouth disease virus, uridylated VPg occupies a site similar to the typical RNA primer in the active site canyon, with the key residue Tyr3 and its associated uridylate (UMP) projected into the active site [7].

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, United States of America. ytao@rice.edu

ABSTRACT

Different replication strategies are used by (+), (−), and dsRNA viruses to limit dsRNA exposure, to regulate (+)RNA versus (−)RNA synthesis, and to modulate transcription versus replication throughout the infection cycle. The differences in the functionalities of the replication complexes are reflected in their structural composition, their subcellular localization, and in the interaction of the complex with viral RNA templates. It is expected that studies of RNA virus replication machineries will have a large impact on antiviral drug development due to their specific activities in virus replication.

Show MeSH
Related in: MedlinePlus