A Structure-Function Diversity Survey of the RNA-Dependent RNA Polymerases From the Positive-Strand RNA Viruses

Jia, Hengxia; Gong, Peng

platform components in HCV NS5B). Both of these factors could reduce the opportunity for RdRPs to recruit additional regions to their C-termini during their evolution. Among these RdRPs containing additional functional regions, some of them have long drawn attentions in the related field but without much advances in structure and related functional characterization of the additional regions. The Coronaviridae nsp12 and Arteriviridae nsp9 have a ∼200-400 residue N-terminal region with both the structure and function remaining elusive (Gorbalenya et al., 1989; Xu et al., 2003; Beerens et al., 2007; te Velthuis et al., 2010) . The Coronaviridae nsp8, which can form a supercomplex with nsp7 (each protein contributes eight copies) (Zhai et al., 2005) , may have RNA-dependent primase activities (Imbert et al., 2006) , and were shown to facilitate the nsp12 RdRP activities along with nsp7 (Subissi et al., 2014b) . However, whether and how the N-terminal region of nsp12 might participate in RdRP catalysis or interactions with nsp7/nsp8 remain unclarified. The Permutotetraviridae RdRP that contains a ∼600-residue C-terminal region only has the catalytic module structure solved (Ferrero et al., 2015) . The nearly 2000-residue Alphatetraviridae RdRP has an MTase and a helicase in its N-terminal region and a ∼500-residue C-terminal region with unknown function (Gorbalenya et al., 2002) . The Kitaviridae RdRP has a helicase in its N-terminal region (Quito-Avila et al., 2013) . The Togaviridae nsP4 protein has a ∼150-residue N-terminal region that may interact with other viral replication proteins (Lemm et al., 1990; Tomar et al., 2006) . The N-terminal ∼300-350 residues of the Tombusviridae and Carmotetraviridae RdRPs can be produced as proteins (named P33 and P40, respectively) due to a UAG stop codon within the RdRP ORF (Kidmose et al., 2010; Walter et al., 2010) . However, the function of these N-terminal regions either as individual proteins or as portions of the RdRP proteins is unknown. Solving the 3D structures of these RdRPs, in particular in their full-length form, is essential to the understanding of these RdRPs. Aside from these RdRPs with relatively large additional regions, some RdRPs with small additional regions may have evolved important functions as well. In the Flaviviridae family RdRPs, the hepacivirus and pestivirus NS5B proteins have a 21-24 residue hydrophobic membrane anchor at their C-termini, facilitating its involvement in the replication complex that is located in membranous vesicles derived from endoplasmic reticulum (ER) (Lai et al., 1999; Schmidt-Mende et al., 2001; Appel et al., 2006; Romero-Brey and Bartenschlager, 2014) . The ∼90-residue NTD of the pestivirus NS5B modulates the fidelity of RNA synthesis through its intramolecular interactions with the RdRP palm domain (Liu et al., 2018) . Therefore, it will also be quite interesting to dissect the mechanisms involving small but potentially functional regions that may not be readily predicted in our boundary analysis.