M Sarwar Baig, Shweta, Jawaid A Khan
Plant Virology Lab, Department of Biosciences, Faculty of Natural Sciences, Jamia Millia Islamia, New Delhi-110025, India.
Cotton leaf curl Multan virus (CLCuMV), genus Begomovirus, family Gemnivirdae is the most devastating virus attributed to huge losses to the cotton crop throughout the Indian subcontinent since late 1980s. CLCuMV DNA-A and its associated betasatellites (CLCuMB) are a part of the machinery of causing CLCuD (Cotton Leaf curl Disease), and infect diverse number of hosts in the families Malvaceae and Solanaceae. CLCuMV requires satellite DNA β to induce symptoms of CLCuD in cotton plants. CLCuMB and ClCuGB (Gezira betasatellite) are the only known betasatellites to induce CLCuD in cotton. miRNAs regulate virtually every aspect of biology, including developmental timing, differentiation, proliferation, antiviral defense and metabolism. The mature miRNA targets mRNAs to repress mRNA translation, promote transcript decay or both. In this computational study bioinformatics approaches were applied to identify miRNA -regulated genes that capture the sequence and location characteristics of miRNA recognition elements (MREs) to predict Gossypium hirsutum miRNA targets in CLCuMV genomes and associated satellites. Genomic sequences of CLCuMV downloaded from NCBI GenBank (http://www.ncbi.nlm.nih.gov/genome/) were screened against a set of 69 mature miRNAs of G. hirsutum downloaded from PMRD (Plant microRNA Database) with miRanda program to search for putative targets against CLCuMV leading to antiviral activity. The genomic sequences of CLCuMV were downloaded from NCBI GenBank. This study revealed that there are 58 putative targets above threshold in DNA-A encoded proteins AC1, AC2, AC3, AC4, AV1 and AV2 and 13 putative targets in DNA β of CLCuMV. Among several available miRNA families, miR168, miR390, miR395, miR398, miR414, miR479, miR2948, miR2950 and miR3476 were found to be most potential miRNA families which could target CLCuMV at multiple loci in complete genome sequence and its associated satellites. Whole DNA β of CLCuMV is targeted by 12 different families of miRNA, miR157, miR414, miR2948 and miR2950 strongly cleaved the target sites and the miR393 is probably translational inhibitor. Among 69 miRNAs about 23 miRNAs showed hits miRNAs shows hits with AC1 encoded Rep protein. Conclusively these miRNAs families and their RNAi gene constructs can be used as novel strategies to antiviral defense in cotton plants. Read More …