Promiscuously replication of betasatellites; in silico study of interaction between betasatellite iteron-like sequence and Rep of helper geminiviruses

Betasatellites, single-stranded circular DNAs, are multifunctional agents associated with monopartite begomoviruses (family Geminiviridae), that act as symptoms determinant. Begomoviruses are replicated by species-specific interactions between the viral replication-associated protein (Rep) and iteron motifs at the upstream of the origin of replication (ori). In contrast, promiscuous replication of betasatellites could be supported by different geminiviruses. In this study, the interaction of Cotton leaf curl Multan virus (CLCuMuV, genus Begomovirus) and Beet curly top virus (BCTV, genus Curtovirus) encoded Rep proteins with the iteron-like sequence of betasatellite, 5́-GAGGACC-3́, was investigated using in silico approaches. Nucleotide sequences of two Rep-encoding genes were obtained from the GenBank database, NCBI. Physicochemical characteristics of Rep proteins and their secondary and tertiary structures were predicted using the SOMPA tool and I-TASSER servers, respectively. The binding affinity of the best-predicted models of both proteins toward betasatellite iteron-like sequence was assessed using Docking simulations. The results represented reliable tertiary structures and showed structural similarity for Rep of different analyzed geminiviruses. Cluster analysis of HADDOCK revealed more total binding energy for CLCuMuV Rep toward the iteron-like sequence than BCTV complex. These in silico results confirmed the more trans-replication activity for relative geminiviruses in replication of betasatellite genomes. They emphasized the role of iteron-like sequences in interactions with the Rep of helper geminiviruses. Furthermore, targeting of identified activate sites within Rep protein structures to interact with betasatellite genomes could be considered as a control measure for begomovirus/betasatellite complexes.