Genomic Characteristics And Function Prediction Of The Encoded Proteins Of Southern Rice Black Streaked Dwarf Virus In Yunan

In recent years, the outbreak of rice disease induced by Southern rice black streakeddwarf virus has caused great economic losses on rice in China. At present researchers, theworld have been carried out on the studies of ocurrence, epidemiology, taxonomic status,detection methods, disease forecasting and prevention, genome structure and proteinfunction analysis, and host-virus interaction about SRBSDV. However, the mechanismsabout the viruses infect host and how the replicate an spread remain poor; the taxonomicstatus and origin of SRBSDV is not fully determined, even more, nothing is known aboutthe functions of most of the proteins encoded by SRBSDV. Therefore, analysis the viralprotein function that are involved in viral infection and spread is very important to thedevelopment of disease prevention measures.The total RNA was extracted from the rice plant infected by SRBSDV in Mangshi,Yunnan province (SRBSDV-YNMShi). The primers were designed on the terminalconservative sequence and the conservative sequence, and the complete genome ofSRBSDV-YNMShi is amplified by RT-PCR. The complete nucleotide sequences of eachgenomic segment from S1to S10were assembled and deposited in the GenBank databases,respectively. The complete nucleotide sequences have29123nt. The sequence analysisresults showed that, the nucleotide and amino acid sequences of SRBSDV-YNMShi shared96.1%-99.7%,96.7%-100%homology with that of SRBSDV-GD and SRBSDV-HN,respectively. From multiple nucleotide sequence alignment, it was found the most sitemutations were base transitions (A/G or C/T) and most of them occurred on the third baseof condones in the ORF, it probably doesn’t change the function of the protein becausemost mutations were substitution between the similar amino acid. Only onedeletion of Asnoccurred at position aa800in the S3ORF of SRBSDV-HB. The genomic size and featuresof SRBSDV-YNMShi were very similar to the corresponding segments of SRBSDV-GD,SRBSDV-HN and SRBSDV-HB. SRBSDV has the similar conserved terminal sequenceswith the members in Fijivirus group2.At the same time, the homology analysis results ofand phylogenetic relationships of SRBSDV with other species of fijiviruses showed thatSRBSDV should be to the group2of Fijivirus. From the phylogenetic relationships ofSRBSDV-YNMShi P7-1and P10(out-ercoat protein) with others corresponding protein ofSRBSDV isolates from different place, the homology among of them are above99%, theydidn’t separates because of place, it respects they originate from the identical ancestor. At last, computer-assisted search analysis have detected conserved domains in thisvirus family consisted of several fijiviruses S1, S2, S3, S8and S10. The P4might be theout coat protein, have an effect possibly in nucleic acid RNA forms GpppAmpGp structureas a RNA glucoside acid radical transferase. P5have the transmembrane area, the Z-fingerdomain, and carbohydrate-binding domain, includesthe same inhibitor129domain with P2and P8. P5share24%and28%with Ribose ABC superfamily ATP binding cassettetransporter had monosaccharidetransporting ATPase activity and Putative serine-threonineprotein kinase had ATP-binding, protein serine/threonine kinase activity and transferase. Atthe same time, it can predict P5may be the core coat protein based on the similar structureand functionof corresponding protein in Reovirus, interacting with P2and P8form viralcore. P7-1has ATP/GTP binding and Ig-Like motif, possibly as viral transcriptionalregulator. P5, P7-1, P9-2all contain transmembrane helix area，maybe playing importantrole of viral core form, infection and replication. The overall comparison betweenSRBSDV and NLRV genomes showed that the SRBSDV protein that lacks NLRVcounterpartis P7-2. This was also noticed when comparing complete FDV, RBSDV andMRCV genomes to NLRV. Considering that NLRV multiplies only in insects, P7-2couldbe involved in the ability of the virus to replicate within the plant.