Table 3.
Salient features identified by bioinformatic analysis.
| Protein | Bioinformatic analysis of genomic segments of PPSMVs |
|---|---|
| RNA-dependent RNA polymerase (RNA-1) | Conserved sequences known to play role in “cap snatching” mechanism was identified at N’-terminal leader sequences in the SRD-1 region of the RdRp. Typical conserved 3D structure of endonuclease has been described A signature divalent cation binding residues occur in core fold of endonucleases in PPSMVs in a pattern H…PD…ExK similar to members of Orthobunyavirus and Tospovirus genera |
| 3D pol structure has been studied in the SRD-2 central region of RdRp with characteristic Fingers, Palm and Thumb subdomains and functional conserved motifs A-F in both PPSMVs were identified | |
| Moderately conserved (between PPSMVs) stretch of thirteen amino acid sequence residing at the same positions in the SRD-3 domain at the C’-termini of RdRp that are similar to cap binding described for other Bunyaviruses were identified. Other emaraviruses; FMV, RRV and EMARaV also showed these sequences | |
| Glycoprotein (RNA-2) | An in depth study of the 3D structure for glycoprotein precursor of both the viruses has been conducted. We showed the croissant shaped precursor protein with a panhandle containing several attributes including the putative cleavage sites and “Phlebovirus” motif |
| Nucleocapsid protein (RNA-3) | Conserved residues in RNA-3 of the PPSMVs and probable RNA binding region were identified |
| Movement protein (RNA-4) | The RNA-4 of both the PPSMVs encodes respective P4 proteins assumed involved in cell-to-cell movement. Highest sequence similarity of PPSMV-II with FMV homolog was noticed. The P4s contain different elements in sequential order; the N’-terminal signal peptide, the TMV 30 kDa movement protein domain which showed typical structural pattern of α-helices and β-sheets in its secondary structure. Presence of likely DnaK domain in the C-terminal half have been identified. The conservation (I/V and D) at the N-terminal end showing beta-1 and beta-2 sheets seems almost universal in members of 30 K family of MPs, is critical for the movement function |