Natural polymerase fusion as an initiation regulator?

Viral RNA-dependent RNA polymerases (RdRPs) are a unique class of enzymes that play the central role in replicating the genome of RNA viruses. 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. A typical polymerase core ofRdRP has a size about 50-70 kD. RdRPs such as poliovirus (PV) 3Dpol and hepatitis C virus (HCV) NS5B represent those not containing additional domains beyond the core. On the other extreme, RdRPs from negative­ strand RNA viruses have quite complicated architectures, with influenza virus three-subunit PA-PB1-PB2 replicase complex possessing both polymerase and endonuclease activities and the 250 kD vesicular stomatitis virus (VSV) L protein including at least three enzyme modules. The ≈ 105 kD flavivirus NS5 proteins fall between the two extremes with a ≈ 30 kD methyltransferase (MTase) naturally fused to theN-terminus of the RdRP through a short 10-residue linker, thus being an ideal system to study how the polymerase function is cis-regulated by its fusion partners.