Effect of the methyltransferase domain of Japanese encephalitis virus NS5 on the polymerase activity

Japanese encephalitis virus (JEV) NS5 consists of an N-terminal guanylyltransferase/methyltransferase (MTase) domain and a C-terminal RNA-dependent RNA polymerase (RdRp) domain. We purified JEV NS5 from bacteria and examined its RdRp activity in vitro. It showed exclusive specificity for Mn2+ and alkaline conditions (pH 8–10) for RdRp activity. It showed strong RdRp activity with dinucleotide primers, and the order of template strength was poly(U) > (I) > (A) > (C). It showed weak transcription activity without primers, but could not transcribe poly(I) without primers. It bound homopolymeric RNA templates, but weakly bound poly(C). The Km (μM) values were 22.13 ± 1.11 (ATP), 21.94 ± 3.88 (CTP), 21.27 ± 1.23 (GTP), and 9.91 ± 0.30 (UTP), indicating low substrate affinity. Vmax (/min) values were 0.216 ± 0.017 (ATP), 0.781 ± 0.020 (CTP), 0.597 ± 0.049 (GTP), and 0.347 ± 0.022 (UTP), indicating high polymerization activity. The RdRp domain alone did not show RdRp activity; a structural and functional interaction between the MTase and RdRp domains via 299-EHPYRTWTYH-308 (MTase domain) and 739-LIGRARISPG-748 (RdRp domain) was predicted, because mutations in the MTase domain affected RdRp activity.

► JEV NS5 consists of an N-terminal MTase domain and a C-terminal RdRp domain.
► JEV NS5 showed both dinucleotide primer-dependent and de novo transcription activity.
► MTase domain is important for RdRp activity.