The silent assassins: Informatics of plant viral silencing suppressors

Abstract

The arms race continues - silencing suppressors have emerged as the silent weapon of counter defense against the indigenous plant RNA silencing machinery. Several reports have identified their presence and in higher plants, these proteins are involved in the inhibition of RNA silencing, which reduces the defense of plants against the pathogen, as well as play important roles for regulation of gene expression during growth and development. These viral silencing suppressors interfere with the various steps of the RNA silencing pathways either by binding to double-stranded RNA or by interfering with the effector proteins and altering their conformation. The informatics challenge lies in the elucidation and unraveling of the diverse structures of these proteins and in understanding and conceptualizing the structure paradigm of these proteins. The basic methods of informatics such as molecular modeling and dynamic simulations would be effective tools for the design and implementation of the above mandates, but advanced techniques such as SVM classification, network analyses, and a systems level approach including phylogenetic analyses should provide a robust framework for such elucidations. This chapter provides a brief overview of the viral silencing suppressors that have been identified so far and provides insights on how they have been studied in the wet lab. Apart from this it focuses on the possibilities of the bioinformatics analyses of the viral silencing suppressors with specific case studies and conceptualizes a future framework for application-oriented use of these silent assassins.