Designing of putative siRNA against geminiviral suppressors of RNAi to develop geminivirus-resistant papaya crop

Abstract

Geminiviruses are single-stranded circular DNA viruses causing leaf curl disease in papaya crop. Post-Transcriptional Gene Silencing (PTGS), also known as RNAi, acts as a natural antiviral defence mechanism and plays a role in genome maintenance and development in plants. PTGS suppression by viruses makes the plant RNA silencing machinery inefficient. Three geminiviral genes namely AV2, AC2 and AC4 are found to play the role in suppression of RNA silencing. siRNA degrades the target mRNA in a homology-dependent manner. In-silico designing of siRNA against these three genes of geminiviruses infecting Carica papaya was done using bioinformatics tools. This strategy may provide PTGS by specifically targeting the viral genes involved in suppression of plant RNA silencing machinery.

Identification of siRNA generating hot spots in multiple viral suppressors to generate broad-spectrum antiviral resistance in plants

“…In natural conditions, mixed viral infection of plants is a common phenomenon and this synergistic interaction among viruses helps both partners to avoid host defense mechanism and successfully propagate in the host. Previous reports suggest the strategy of in silico designing of siRNA against geminivirus suppressors as a tool to develop generic and broad spectrum resistance against tomato leaf curl disease (Saxena et al 2011(Saxena et al , 2013. The above approaches seem non feasible and impractical based on two important facts firstly, how to continuously feed these siRNAs into the field without generating transgenic plants as RNA molecules are highly labile and secondly, targeting suppressors of one virus does not offer an effective strategy as in fields single plant is infected by different viruses and the suppressor of other virus will inhibit RNA silencing.…”

“…In field condition, plants are not infected by single virus alone and targeting suppressor(s) of one particular virus will render the suppressor(s) of other viruses to inhibit RNA silencing hence making the approach non feasible. Earlier reports of in silico designing of putative siRNAs against viral suppressors (Saxena et al 2011(Saxena et al , 2013 do not provide a solution to the problem caused by mixed infection. In order to address this, we have adopted an approach of designing of highly efficient and off target filtered siRNAs using consensus sequences of suppressors of CMV and tomato infecting begomoviruses.…”

Small Interfering RNAs (siRNAs) Negatively Impact Growth and Gene Expression of Environmentally Relevant Bacteria in In Vitro Conditions

“…Model siRNA Identification and Sourcing. PVY, AC2, and AC4 siRNAs used in commercially available GM crops 4,8,27,28 were selected as model siRNAs in this experiment based on their potential for nontarget alignments determined by BLAST analysis, differing GC content (40−70%), and sequence dissimilarity across model siRNAs (Table S1). BLAST analyses were conducted in the BLASTN program by using the relevant cDNA sequence for each siRNA as the input sequence to identify potential nontarget alignments.…”