Identifying potential human and medicinal plant microRNAs against SARS-CoV-2 3′UTR region: A computational genomics assessment

Abstract

The coronavirus disease of 2019 (COVID-19) began as an outbreak and has taken a toll on human lives. The current pandemic requires scientific attention; hence we designed a systematic computational workflow to identify the cellular microRNAs (miRNAs) from human host possessing the capability to target and silence 3'UTR of SARS-CoV-2 genome. Based on this viewpoint, we extended our miRNA search to medicinal plants like Ocimum tenuiflorum , Zingiber officinale and Piper nigrum , which are well-known to possess antiviral properties, and are often consumed raw or as herbal decoctions. Such an approach, that makes use of miRNA of one species to interact and silence genes of another species including viruses is broadly categorized as cross-kingdom interactions. As a part of our genomics study on host-virus-plant interaction, we identified one unique 3’UTR conserved site 'GGAAGAG' amongst 5024 globally submitted SARS-CoV-2 complete genomes, which can be targeted by the human miRNA ‘hsa-miR-1236-3p’ and by Z. officinale miRNA ‘zof-miR2673b’. Additionally, we also predicted that the members of miR477 family commonly found in these three plant genomes possess an inherent potential to silence viral genome RNA and facilitate antiviral defense against SARS-CoV-2 infection. In conclusion, this study reveals a universal site in the SARS-CoV-2 genome that may be crucial for targeted therapeutics to cure COVID-19.

miRNA expression in COVID-19

“… ( McDonald et al, 2021a ) hsa-miR-1236–3p, zof-miR2673b Bioinformatics ‘GGAAGAG’ in 5024 SARS-CoV-2 3′UTR The target of these microRNAs represents a region concentrated in the SARS CoV 2 genome that may become a promising target for the fight against COVID 19. ( Mangukia et al, 2021 ) miR-200c In vitro Neonatal rat cardiomyocytes (NRCMs) and Neonatal rat cardiac fibroblasts (NRCFs) ACE2 MiR-200c modulates ACE2 expression in both rat and human cardiomyocytes, which can be used to treat cardiovascular complications of COVID-19. ( Lu et al, 2020 ) miR-155, miR-130a Clinical Recovered COVID-19 patients and healthy 70 Blood samples miR-155 and miR-130a levels were higher in the mild/moderate group compared to the severe/critical ( Li et al, 2021 ) hsa-miR-15b-5p, hsa-miR-195-5p, hsa-miR-221-3p, hsa-miR-140-3p, and hsa-miR-422a In vitro and bioinformatics Hamster lung tissues hsa-miR-15b-5p, hsa-miR-140-3p, and hsa-miR-422a have been decreased, and hsa-miR-195-5p and hsa-miR-221-3p have been increased in affected specimens.…”

Gene Network Analysis of the Transcriptome Impact of SARS-CoV-2 Interacting MicroRNAs in COVID-19 Disease

“…Upon abstract collection, 44 research papers (23 in silico [ 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 ] and 21 experimental studies [ 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 ]) met the inclusion criteria and were used for downstream analysis. The entire workflow of the current study is depicted in Figure 1 .…”

Unveiling the nature's fruit basket to computationally identify Citrus sinensis csi-mir169–3p as a probable plant miRNA against Reference and Omicron SARS-CoV-2 genome

“…Whilst five conserved plant miRNAs: miR-166, miR-169, miR-172, miR-390, and miR-399 that were very likely to align and interact onto the six HBV gene sequences [ 19 ]. A report from our study group also revealed a cross-species interaction of plant miRNAs belonging to the family of miR477 ubiquitously found in all three medicinal plant genomes of O. tenuiflorum , P. nigrum and Z. officinale to pinpoint a plausible role of plant derived dietary miRNAs to mediate viral mRNA silencing and provide antiviral defence against SARS-CoV-2 infection [ 23 ]. These are all amongst the evidence which suggest the conjecture of the inhibitory role of exogenous miRNAs being inhibitory for SARS-CoV-2 viral replication.…”

“…A total of five plant miRNAs from three medicinal plants Ocimum tenuiflorum , Piper nigrum and Zingiber officinale were obtained having potential to align with the SARS-CoV-2 3′ UTR region. From a family of plant miRNAs, mir477 and miR2673 were identified to bind and regulate the expression of SARS-CoV-2 viral mRNA using in-silico approach [ 23 ].…”