Flaviviral Replication Complex: Coordination between RNA Synthesis and 5’-RNA Capping

Abstract

Genome replication in flavivirus requires (−) strand RNA synthesis, (+) strand RNA synthesis, and 5′-RNA capping and methylation. To carry out viral genome replication, flavivirus assembles a replication complex, consisting of both viral and host proteins, on the cytoplasmic side of the endoplasmic reticulum (ER) membrane. Two major components of the replication complex are the viral non-structural (NS) proteins NS3 and NS5. Together they possess all the enzymatic activities required for genome replication, yet how these activities are coordinated during genome replication is not clear. We provide an overview of the flaviviral genome replication process, the membrane-bound replication complex, and recent crystal structures of full-length NS5. We propose a model of how NS3 and NS5 coordinate their activities in the individual steps of (−) RNA synthesis, (+) RNA synthesis, and 5′-RNA capping and methylation.

Interactions between the Dengue Virus Polymerase NS5 and Stem-Loop A

“…The 11-kb DENV genome encodes 10 proteins, including three structural proteins (capsid, premembrane, and envelope proteins) and seven nonstructural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5) (9,10). NS5 is a viral replicative RNA-dependent RNA polymerase (RdRp) consisting of 900 amino acids distributed across two functional domains (11)(12)(13)(14).…”

Japanese Encephalitis, Recent Perspectives on Virus Genome, Transmission, Epidemiology, Diagnosis and Prophylactic Interventions

“…JEV is listed under family Flaviviridae which shares similarities with other arthropod-borne flaviviruses namely, St. Louis encephalitis virus, Dengue virus, West Nile virus (WNV), TickBorne Encephalitis virus (TBEV) and Yellow fever virus (YFV) (Klema et al, 2015). Initially, JEV was categorized in group B of arbovirus under the family Togaviridae and afterward in the year 1985, listed in genus Flavivirus under the Flaviviridae family (Westaway et al, 1985).…”

“…NS2B and NS3 proteins work together as a virus-specific protease which cleaves the polyprotein in the ORF to generate 7 non-structural and 3 structural proteins (Yusof et al, 2000) while NS4A and NS4B involved in viral replication. Furthermore, NS3 also has helicase activity and 5'-RNA triphosphatase activity which needs to unwind the double-stranded RNA at some point in genome replication and 5'-RNA cap formation respectively (Klema et al, 2015). NS5 protein is largest JEV proteins which have viral RNA dependent RNA polymerase activity, responsible for the high mutation rate of JEV (Mukhopadhya et al, 2005).…”

Regulatory effects of cotranscriptional RNA structure formation and transitions

“…The 5′ capping is the first step for the maturation of a pre‐mRNA, and it involves attachment of a 7‐methylguanosine cap by a 5′–5′ linkage. This step is crucial for mRNA stability and efficient translation initiation . An example is viral RNA‐specific cap methylation, in which the 5′ end of the flavivirus plus‐sense RNA genome consists of a type 1 cap (m7GpppAmG) and a conserved stem‐loop structure.…”

“…The nonstructural protein 5 (NS5) derived from four serocomplexes of flaviviruses can specifically methylate the N‐7 cap via recognition of the flavivirus RNA 5′ terminus . Comprehensive experiments revealed that different RNA elements are essential to the methylations at guanine N‐7 of the cap and ribose 2′‐OH of the first transcribed nucleotide . The RNA‐capping process occurs as the sense strand RNA is being synthesized during the initiation of RNA synthesis, and it requires three enzymatic activities (Figure (a)).…”