Structure and Function Analysis of Nucleocapsid Protein of Tomato Spotted Wilt Virus Interacting with RNA Using Homology Modeling

Abstract

Background:The crystal structure of viral proteins is not available for many plant viruses including tomato spotted wilt virus (TSWV). Results: By homology modeling, we mapped the RNA binding sites and discovered a protective feature of TSWV nucleocapsid (N). Conclusion: Homology modeling provided a basis for functional analysis of TSWV N interacting with RNA. Significance: This approach might be applicable for other plant viruses.

The RNA-binding properties and domain of Rice stripe virus nucleocapsid protein

“…This finding was consistent with recent data from TWSV and Bunyamwera virus (BUNV) studies [11,16]. Study on TWSV N protein showed that it could bind nonspecifically to E. coli cellular RNA [11].…”

“…This finding was consistent with recent data from TWSV and Bunyamwera virus (BUNV) studies [11,16]. Study on TWSV N protein showed that it could bind nonspecifically to E. coli cellular RNA [11]. Study on BUNV suggested that N protein did not obligatorily require a sequence or structure for RNA encapsidation because neither common linear sequence nor structure was present in the extracted RNAs bound to RNPs [16].…”

“…However, like other identified nucleic acid binding domains, a vast amount of charged and polar amino acids were found in the RNA-binding domain of RSV NP. The charged or polar amino acids on NPs of some bunyaviruses were previously reported to be responsible for NP-RNA interaction [11,17,18]. For example, the residues of BUNV NP that interact with the RNA were primarily charged residues, including S14, S15, D18, R47, K50, T75, R94, Y176, R182, Q183, R184, and N217 [17].…”

“…For the segmented, negative-sense RNA viruses, encapsidation of viral genomic RNA by NP plays multiple important roles in the viral replication cycles including transcription, replication and the assembly of viral particles. Viruses in the family Bunyaviridae only use the ribonucleoprotein complexes (RNPs), but not the naked RNAs as the template for viral genome replication and gene transcription [11]. The genomic and antigenomic RNAs of these viruses contain highly conserved, complementary terminus sequence which might serve as the signal for encapsidation.…”

“…The trimeric Hantavirus N protein specifically recognized the panhandle structure formed by the base pairing of the 5 0 and 3 0 complementary ends [13]. However, Tomato spotted wilt virus (TSWV) N protein has been shown to bind ssRNA irrespective of sequence [11]. RSV NP is the major component of the viral particle.…”