Research Groups
Plant Biology: Plant Molecular Biology
Research Interests and Description
Research Interests
Abiotic and Biotic stress, gene expression, signalling, crop improvement, transgenics, viral replication and RNAi, microRNA.
Description of Research
Geminiviruses pose serious threat to crop and vegetable productivity. These are single stranded circular DNA viruses of about 2.7kb that replicate within the nuclei of infected plant cells. To interfere with viral growth, we are studying the mechanism of viral DNA replication using the model begomoviral systems having either a bipartite genome, i.e. Mungbean Yellow Mosaic India Virus (MYMIV) or a monopartite genome, namely, Tomato Leaf Curl virus (ToLCV). The replication origin of each virus has been mapped and the interaction of virus encoded replication initiator protein Rep with the origin sites leading to rolling circle replication (RCR) has also been characterized.
As these viruses have limited coding capacities, they are mostly dependent on the host factors for their own genome replication. As the viral Rep protein is most important for replication, we postulated that the Rep-interacting host factors might play a major role in determining viral DNA replication. Adopting various approaches like phage-display, yeast two hybrid, in-vitro pull down and co-immunoprecipitation, we have identified a plethora of host factors. Few of these, such as PCNA and RF-A, have been validated in the yeast- and in-planta model developed in the lab. We have also developed an in-vitro system for viral DNA replication using the yeast extracts and validated the role of RAD54 protein in enhancing RCR using the same system.
Besides DNA replication, we are looking into another aspect of viral growth processes in the host cell that also indirectly affects viral DNA replication. The hosts defend against the viruses using the RNAi machinery. The viruses, in turn, encode RNAi suppressor proteins as a counter defensive measure. We have developed six different assays to screen for the viral RNAi suppressor proteins. Using these, we have screened two dozens of suppressor proteins from plant viruses, and also from animal and insect viruses. From this pool of suppressors, we have chosen two potent suppressors, namely MYMIV-AC2 and FHV-B2, to decipher mechanisms of RNAi suppression. MYMIV-AC2 interacts with the host RNAi factors, namely RdRP and AGO1 and abrogates their biochemical activities, whereas FHV-B2 binds siRNA and also inhibits DICER activity. The suppressors could also be used for biotechnological gain. The MYMIV-AC2 has been used to enhance the expression of transgenes like GFP, Topo1, and PDS, in tobacco and tomato plants. This protein also aids in enhancing the activities of hammerhead ribozyme in plants. As the RNAi suppressors protect the viruses, silencing these proteins could serve as a good antiviral strategy. We have raised tomato transgenics, which overproduce artificial microRNAs designed to silence the transcripts of AC2 and AC4 suppressors of ToLCV. A few transgenic lines show immunity level resistance when challenged with ToLCNDV, a New Delhi species of ToLCV. Thus the RNAi suppressors have turned out to be extremely interesting objects of investigation.
Recent Publications
Naqvi, A.R., Choudhury, R.N., Mukherjee, S.K., Haq, Q.M. 2011. In silico analysis reveals that several microRNA/microRNA* sequences exhibit propensity to bind to ToLCV associated genomes and most of their encoded ORFs. Plant Physiol Biochem 49,13-17 PubMed link
Naqvi, A.R., Sarwat, M., Pradhan, B., Choudhury, N.R., Haq, Q.M., Mukherjee, S.K. 2011. Differential expression analyses of host genes involved in systemic infection of Tomato leaf curl New Delhi virus (ToLCNDV). Virus Research 160, 395-399 PubMed link
Pandey, P., Mukhopadhya, S., Naqvi, A.R., Mukherjee, S.K., Shekhawat, G.S., Choudhury, N.R. 2011. Molecular characterization of two distinct monopartite begomoviruses infecting tomato in India. Virol J 7, 337 PubMed link
Pasumarthy, K., Mukherjee, S.K., Choudhury, N.R., 2011. The presence of ToLCKV-AC3 enhances viral DNA replication and modulates VIGS mechanism in tomato plants. Virol J 8, 178 PubMed link
Pratap, D., Kasikar, A.R, Mukherjee, S.K. 2011. Molecular characterisation and infectivity of a ToLCNDV variant associated with newly emerging yellow mosaic disease of eggplant in India. Virol J 8, 305-317 PubMed link
Karjee, S., Minhas, A., Sood, V., Ponia, S.S., Banerjea, A.C., Chow, V., Mukherjee, S.K., Lal, S. 2010. The 7a accessory protein of SARS coronavirus acts as an RNA silencing suppressor. J Virol 84, 10396-10401 PubMed link
