1. Genome Organization & Viral Protein Expression
DV belongs to the genus Flavivirus in the family Flaviviridae. These viruses have a single stranded RNA genome of positive polarity which is about 11,000 nucleotides long. The RNA carries a single open reading frame encoding a polyprotein that is translated in a cap-dependent manner at the rough endoplasmic reticulum (rER). The viral polyprotein is co- and post-translationally processed into three structural proteins (C, prM, and E) and seven non-structural (NS) proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5). The amino termini of prM, E, NS1 and NS4B are generated upon cleavage by the host ER signal peptidase in the lumen of the ER, whereas the processing of most of the other NS proteins and the C-terminus of the C protein is carried out by the viral two-component protease NS2B-NS3 in the cytoplasm of DV infected cells. For the cleavage of the C-terminus of NS1 an unknown ER peptidase seems to be responsible, and a Golgi localized furin protease produces the cleavage of prM at a later state of infection to generate the mature form of M.
DV RNA replication occurs in close association with cellular membranes that may serve as a scaffold for the viral replication complexes (RC). NS5 was identified as the RNA-dependent RNA polymerase (RdRp) and has also a methyltransferase activity important for the formation of the RNA cap-structure. NS3 acts as the viral serine protease, which requires the protein NS2B as cofactor for activity. In addition, NS3 also comprises an RNA triphosphatase as well as an RNA helicase with nucleoside triphosphatase activity. Also for the glycoprotein NS1 it is believed that it plays a role in viral RNA replication, most probably prior to or at initial minus-strand RNA. Apart from the hydrophobic nature, not much is known about the functions of the small non-structural proteins NS2A, NS4A and NS4B. It has been suggested that they may serve to anchor the viral RC to intracellular membranes. Moreover, it is assumed that these proteins contribute to the inhibition of the host interferon response.
Fig.1: Genome Organization of Dengue
DV genome organization, polyprotein processing scheme and membrane topology of viral proteins.
A) Schematic of the single stranded RNA genome with highly structured RNA elements in the 5' and 3' NTRs.
B) DV genomic organization and functions of viral proteins. For some proteins their function in the viral life cycle is not yet established; they are marked with a '?'
C) Putative membrane topology of DV proteins and proteinases involved in polyprotein cleavage.