Infection by viruses is a major cause for reduced crop yields. A detailed study of the architecture, genome organization and expression of these viruses is necessary to unravel the molecular mechanisms involved in the infection process. Such a study will also enable design of suitable strategies for controlling the diseases.
In particular, viruses such as Physalis mottle virus (PhMV), Sesbania mosaic virus (SeMV), Pepper vein banding virus (PVBV), Tomato leaf curl Bangalore virus (ToLCBV), Cotton leaf curl virus (CLCuV) and Peanut bud necrosis virus (PBNV) are being investigated. The complete genomic sequences of PhMV, SeMV, PVBV, CLCuV and ToLCV have been determined. PhMV, SeMV and PVBV are shown to be new members of their respective genera. Potential recombination sites in ToLCV and CLCuV have been identified. A conserved zinc-finger motif present in the coat protein of ToLCV and CLCuV is shown to be responsible for binding to genomic DNA. The CP, AV2 and AC4 proteins together are responsible for cell to cell movement of the virus. In collaboration with Prof Laksmi Sita, transgenic cotton plants expressing antisense AV2gene of CLCuV have been generated.
Virus like particles (VLPs) serves as excellent model systems to identify pathways of virus assembly. In PhMV, structure based mutation of residues involved in intersubunit interactions is shown to disrupt both subunit folding and particle assembly. In SeMV, the N-terminal arginine-rich motif (NARM) is essential for RNA encapsidation and its length controls the size of assembled particles. Metal ion mediated inter subunit interactions are not crucial for assembly but they increase the stability of VLPs. In PVBV, the surface exposed amino and carboxy terminal residues are crucial for initiation of assembly. The VLPs are biodegradable nano carriers. The research on their possible use in biomedical applications is in progress.
Polyprotein processing is a common strategy used by many viruses to generate different functional products from a single protein. Viral proteases play a crucial role in this maturation process. Natively unfolded VPg modulates the function of the protease in the processing of the poly protein in both SeMV and PVBV. In fact, the interaction of VPg with the protease results in the gain of a novel ATPase activity by the PVBV VPg. The full length infectious cDNA of SeMV has been obtained and the mutational analysis of the cleavage sites resulted in the failure of replication and SeMV infection. The recombinant non structural protein NSs from PBNV was shown to possess an ATP dependent helicase activity. Further studies on the in vivo functions of the SeMV, PVBV and PBNV encoded proteins and their intermediates are in progress.
Pyridoxal phosphate (PLP) dependent enzymes exhibit unique features of substrate and reaction specificity and they are invariably multimeric. Structure-function relationship of two of the PLP dependent enzymes -Serine hydroxymethyltransferase (SHMT) and Di amino propionate ammonia lyase(DAP lyase) are being investigated to establish the role of specific amino acid residues in substrate and reaction specificities, cofactor binding ,catalysis and in the maintenance of oligomeric structure. In the coming years, the following aspects of research will be carried out.
1. Determination of genomic sequences of new gemini and poty viruses and their strains from India to establish the genetic variability and diversity in the viral genomic sequences.
2. Structure-function relationship of structural and non-structural proteins of viruses through protein engineering.
3. Identification of host factors interacting with viral proteins/genomes and their functional characterization.
4. Protein engineering to establish the origin of substrate and reaction specificities in PLP- dependent enzymes.
Sesbania Mosaic Virus (SeMV) Infectious Clone: Possible Mechanism of 3' and 5' End Repair and Role of Polyprotein Processing in Viral Replication. Govind K, Mäkinen K, Savithri HS. PLoS One. 2012;7(2):e31190. Epub 2012 Feb 15.
Functional regulation of PVBV Nuclear Inclusion protein-a protease activity upon interaction with Viral Protein genome-linked and phosphorylation. C. Mathur, V.K. Jimsheena, S. Banerjee, K. Makinen, L.R. Gowda, H.S. Savithri. Virology 422, 254-264 Virology (2012)
Interaction of Sesbania mosaic virus movement protein with the coat protein - implications for viral spread. Chowdhury SR, Savithri HS. FEBS J. (2011) 278(2):257-72. (2011)
Functional characterization of coat protein and V2 involved in cell to cell movement of Cotton leaf curl Kokhran virus-Dabawali. C.G. Poornima Priyadarshini, M.V. Ambika and Handanahal S. Savithri. PLoS One. ;6(11):e26929 (2011)
5. Primer-independent initiation of RNA synthesis by SeMV recombinant RNA-dependent RNA polymerase. Govind K, Savithri HS. Virology. 2010 Mar 22. [Epub ahead of print]
6. Structural and functional studies of Bacillus stearothermophilus serine hydroxymethyltransferase: the role of Asn(341), Tyr(60) and Phe(351) in tetrahydrofolate binding. Pai VR, Rajaram V, Bisht S, Bhavani BS, Rao NA, Murthy MR, Savithri HS. Biochem J. 2009 Mar 15;418(3):635-42
Copyright © 2014 - All Rights Reserved - Department of Biochemistry, IISc