Small double-stranded RNA with anti-HIV activity abundantly produced by Bacillus subtilis MTCC5480 isolated from fermented soybean

Abstract

Anti-viral RNA therapy is on high demand nowadays due to the emergence of several new viral infections. The small non-coding regulatory RNAs (dsRNA) from the microbial sources are not yet explored for anti-viral activity. In this study, we assessed the anti-HIV activity of the small dsRNA produced by 12 different microbial species isolated from naturally fermented foods of North-East India. For this, we selectively extracted the dsRNA from the microbial culture, confirmed its double-stranded nature by immunoblotting, and deep sequenced the cDNA library using Illumina platform. Further, we used conventional algorithms to predict the potential targets of the dsRNA sequences within the 3'-UTR region of HIV-1. A small dsRNA fragment with 34 bases in size with a sequence of 3'-UUGGUACACGAGAUGGUUCGACUCGAUGAAGGGC-5' produced abundantly (9.17% of the total dsRNA fraction) by Bacillus subtilis MTCC5480 showed a much higher base complementarity values than previously reported miRNAs analysed against HIV-1. We separated the dsRNA fraction and validated the anti-HIV activity against human peripheral blood mononuclear cells (PBMC) infected with JRCSF strain of HIV-1 virus and the EC₅₀ value ranges from 0.2-0.3 μM. This small dsRNA abundantly produced by B. subtilis could be studied further for its application as an anti-viral therapeutic agent.

Keywords: Anti-HIV activity; Bacillus subtilis; Fermented soybean; In-silico target prediction; Small RNA-seq; dsRNA fraction.