Structure of Hibiscus Latent Singapore Virus Determined by X-Ray Fiber Diffraction

Abstract

Hibiscus latent Singapore virus (HLSV) is a new member of the Tobamovirus family. The HLSV genome contains a unique poly(A) tract in its 3'-UTR which is absent in other Tobamoviruses. The virion is composed of a monomeric coat protein (CP) of 18 kDa. We have determined the HLSV structure at 3.5 ? by X-ray fiber diffraction with R factor of 0.096. The structure of HLSV CP resembles that of other Tobamoviruses, with a few unique differences. In other Tobamoviruse structure, CP sequence at position 122 contains a conserved Arg residue, while the HLSV and SHMV contain His residue. Also, His122 is followed by another positively charged amino acid residue Lys which is uncharged residue in other Tobamoviruses. There is a kink observed for the first time in the LR helix of HLSV due to the presence of the unique His122, which produces a bend in the helix in the non-Pro non-Gly bends. Also, the adjacent Lys123 may destabilize the helix by positive charge repulsion, making the kink more pronounced. In the HLSV structure, we are able to see Lys123 stabilizing the phosphate 1, hence balancing the protein-nucleic acid interactions. Another residue Arg92 from the Subunit -17 is believed to be involved in stabilizing the remaining phosphate 2 and phosphate 3. Arg122 is believed to regulate the guanine 1 recognition during assembly for all other existing structures of the Tobamovirus. Uniquely, His122 at this position showed a very strong salt bridge with the neighboring Asp88 from subunit -1, hence significantly stabilizing the loop adjacent to RR helix. The carboxyl-carboxylate interactions that drive viral disassembly are also seem to be different in HLSV. The nucleotide recognition mechanism for virus assembly is similar between HLSV and RMV but different from that of TMV and CGMMV. By solving the structure of HLSV by X-ray fiber diffraction, we will be able to have a better understanding of the structural differences between HLSV and other Tobamoviruses. This research may also enhance our knowledge of virus structure at atomic details. By knowing the atomic details of this novel virus, we may be able to use it in future as a vector to express pathogenic epitopes (to develop vaccine) and to express economically important proteins.