A Structural Overview of RNA-Dependent RNA Polymerases from the Flaviviridae Family

Abstract

RNA-dependent RNA polymerases (RdRPs) from the Flaviviridae family are representatives of viral polymerases that carry out RNA synthesis through a de novo initiation mechanism. They share a ≈ 600-residue polymerase core that displays a canonical viral RdRP architecture resembling an encircled right hand with palm, fingers, and thumb domains surrounding the active site. Polymerase catalytic motifs A–E in the palm and motifs F/G in the fingers are shared by all viral RdRPs with sequence and/or structural conservations regardless of the mechanism of initiation. Different from RdRPs carrying out primer-dependent initiation, Flaviviridae and other de novo RdRPs utilize a priming element often integrated in the thumb domain to facilitate primer-independent initiation. Upon the transition to the elongation phase, this priming element needs to undergo currently unresolved conformational rearrangements to accommodate the growth of the template-product RNA duplex. In the genera of Flavivirus and Pestivirus, the polymerase module in the C-terminal part of the RdRP protein may be regulated in cis by the N-terminal region of the same polypeptide. Either being a methyltransferase in Flavivirus or a functionally unclarified module in Pestivirus, this region could play auxiliary roles for the canonical folding and/or the catalysis of the polymerase, through defined intra-molecular interactions.

Structural basis of viral RNA-dependent RNA polymerase catalysis and translocation

“…5A) (14). Motif G residues T114 and S115 pack against the template strand +1/+2 backbone linkage and likely serve as a control point for template strand movement during translocation (9). At the upstream end of this interaction cluster there is an unusual and conserved backbone conformation for the ribose-phosphate linkage of the template strand −2 nucleotide (14).…”

“…On the other hand, all RdRPs share a 50to 70-kDa polymerase core that forms a unique encircled right-hand structure with palm, fingers, and thumb domains. Among the seven classic RdRP catalytic motifs, A-E are within the most conserved palm domain, and F and G are located in the fingers; they are all arranged similarly around the active site (6)(7)(8)(9). The structural conservation of the RdRP polymerase core and the seven motifs form the basis for understanding the common features in viral RdRP catalytic mechanism and for finding intervention strategies targeting these enzymes with possible broad-spectrum potential.…”

A case for a reverse-frame coding sequence in a group of positive-sense RNA viruses

“…Putative viral sequences containing an rORF all clustered within the alphanarnaviral clade, and none in the betanarnaviral clade.However, the rORF-containing sequences appear not to form a monophyletic clade, but instead cluster in several regions of the phylogeny, and are found in sequences derived from fungi, arthropods and plants(Figure 2: red bars). The core RdRp catalytic regions -motifs A to E in the palm domain and motifs F and G in the fingers(Wu et al 2015; te Velthuis 2014) -are wellconserved despite the overall high degree of sequence divergence(Supplementary Figure S2).…”

Natural polymerase fusion as an initiation regulator?

“…The polymerase core of RdRP structurally resembles an encircled human right hand with palm, fingers, and palm domains surrounding the active site, with the unique fingers-thumb interactions to make the encirclement. Seven RdRP catalytic motifs have been identified based on sequence and/or structural homology, and the spatial organization of these motifs around the active site are highly analogous and key catalytic residues within the motifs are highly conserved [1, 2], making RdRPs overall the most conserved enzymes encoded by all RNA viruses. On the other hand, RdRPs are also diverse in several aspects including the organization of the polypeptide(s) harboring the polymerase activity.…”