In 2019, the seventh member of the Coronaviridae named severe acute respiratory coronavirus II (or COVID-19) emerged in Wuhan, China. It could rapidly turn into a global pandemic. Therefore, searching for a natural/ novel therapy is urgently essential to prevent disease distribution. Based on the principle of cross-kingdom interaction, plants are a candidate as a potential source of exogenous miRNAs that can efficiently affect the host cell gene expression by promote target mRNA degradation or repress protein translation, and, or virus RNA translation/replication. The possibility of taking up the diet-derived plant-originated/artificially miRNA(s) in addition to their biological role in the host provides a pivotal clue for the study of synthesized/artificially expressed active therapeutic plant-originated miRNA(s) to promote antiviral activity. In this study, plant miRNAs, which can potentially interact with the COVID-19 genome within the 3’-UTR region and prompt antiviral function, were searched using bioinformatics approaches. RNAHybrid, RNA22, and STarMir miRNA/target detection tools were served for the possible plant miRNA/target recognition on the 3’-UTR flanking region of the COVID-19 genome by different algorithms. The RNAHybrid algorithm resulted in 63 plant miRNAs having hybridization energy with less or equal to -25 kcal/mol. They interact with diverse classes of miRNA/target binding patterns. However, each RNA22 and STarMir tools identified eight probable miRNA/target interaction candidates, in which pvu-miR159a.2 and sbi-miR5387b detected by both the RNA22 and STarMir tools at the same position. For us, they are suitable plant-derived miRNA candidates, which have the great chance of targeting the COVID-19 genome in the 3’-UTR region in vitro to induce the virus degradation and translational repression and for antiviral miRNA-based therapies without any side effects in vivo.
Background:
In 2019, severe acute respiratory coronavirus II (or SARS-COV-2) emerged in Wuhan, China, rapidly turned global pandemic. Coronavirus genus (Coronaviridae) has the largest single-stranded positive-sense RNA genome (~30 kb) among the human infected single-stranded RNA viruses.
Objectives:
The possibility of up taking the plant-originated miRNAs and their biological role in the host cell provides a pivotal clue for the study of active therapeutic plant-derived miRNA(s). In this study, we bioinformatically searched plant miRNAs that can potentially interact with the Sars-CoV-2 genome within the 3’-UTR region and have prompt antiviral activity.
Materials and Methods:
We searched the plant miRNAs that target the 3’-UTR flanking region of the Sars-CoV-2 genome by employing the RNAHybrid, RNA22, and STarMir miRNA/target prediction tools.
Results:
The RNAHybrid algorithm found 63 plant miRNAs having hybridization energy with less or equal to -25 kcal.mol-1. Besides, RNA22 and STarMir tools identified eight interactions between the plant miRNAs and the targeted RNA sequence. pvu-miR159a.2 and sbi-miR5387b were predicted as the most effectively interacting miRNAs in targeting the 3’-UTR sequence, not only by the RNA22 tool but also by the STarMir tool at the same position. However, the GC content of the pvu-miR159a.2 is 55% instead of sbi-miR5387b, which is a GC enriched sequence (71.43%) that may be activating the TLR receptors.
Conclusions:
In our opinion, they are potent plant-derived miRNA candidates that have a great chance of targeting the Sars-CoV-2 genome in the 3’-UTR region in vitro. Therefore, we propose pvu-miR159a.2 for studying antiviral miRNA-based therapies without any essential side effects in vivo.
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