Beet curly top Iran virus (BCTIV) and Beet curly top virus (BCTV) are responsible for the curly top disease in sugar beet Beta vulgaris L. and many other plants. Mixed infection by BCTIV and BCTV in sugar beet plants results in a synergistic interaction, with more severe symptoms than plants infected by either virus, accompanied by an increase in BCTIV and a decrease in BCTV titers. Interaction of the Replication associated protein (Rep) with the nonanucleotide motif within the origin of replication is crucial for the replication of the geminivirus genome. Using an in silico approach, we investigated the possible contribution of the interaction between Rep and the nonanucleotide motifs in the interference between BCTIV and BCTV in mixed infections. The physicochemical characterization of both Reps was performed, and their secondary and tertiary structures were predicted by SOMPA tool and I-TASSER server, respectively. Then, the binding affinity of each Rep towards cognate and non-cognate viral nonanucleotide motifs was assessed using Docking simulations. Cluster analysis of HADDOCK revealed that the total binding energy of BCTV Rep toward its cognate nonanucleotide motif was lower than for the BCTIV complex, confirming a higher affinity of BCTV encoded Rep for its nonanucleotide motif. Interestingly, the BCTIV Rep showed the highest affinity for the nonanucleotide motif of the non-cognate BCTV nonanucleotide motif. Since the replication of geminiviruses relies on species-specific Rep interactions and activities, this result could be considered responsible for the competitive interference of BCTIV towards BCTV.
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