Plant microRNAs and their role in defense against viruses: a bioinformatics approach

Abstract

BackgroundmicroRNAs (miRNAs) are non-coding short RNAs that regulate gene expression in eukaryotes by translational inhibition or cleavage of complementary mRNAs. In plants, miRNAs are known to target mostly transcription factors and are implicated in diverse aspects of plant growth and development. A role has been suggested for the miRNA pathway in antiviral defense in plants. In this work, a bioinformatics approach was taken to test whether plant miRNAs from six species could have antiviral activity by targeting the genomes of plant infecting viruses.ResultsAll plants showed a repertoire of miRNAs with potential for targeting viral genomes. The viruses were targeted by abundant and conserved miRNA families in regions coding for cylindrical inclusion proteins, capsid proteins, and nuclear inclusion body proteins. The parameters for our predicted miRNA:target pairings in the viral genomes were similar to those for validated targets in the plant genomes, indicating that our predicted pairings might behave in-vivo as natural miRNa-target pairings. Our screening was compared with negative controls comprising randomly generated miRNAs, animal miRNAs, and genomes of animal-infecting viruses. We found that plant miRNAs target plant viruses more efficiently than any other sequences, but also, miRNAs can either preferentially target plant-infecting viruses or target any virus without preference.ConclusionsOur results show a strong potential for antiviral activity of plant miRNAs and suggest that the miRNA pathway may be a support mechanism to the siRNA pathway in antiviral defense.

Virus versus Host Plant MicroRNAs: Who Determines the Outcome of the Interaction?

“…The latter criterion was used for miRNA target prediction in various plants [51]–[52]. To score the complementarity between miRNA and their target transcript, the default cut-off threshold 0–2.0 for lower false positive and 4.0–5.0 for higher prediction coverage were used in psRNATarget analyses [49].…”

Endogenous rice ( Oryza Sativa ) miRNAs and their potential targets against Rice Tungro Virus using various string matching algorithms

“…Perez-Quintero et al [10] discovered that miRNAs are non-coding short RNAs around 22 nucleotides long that regulate gene expression by translational inhibition in animals or cleavage of complementary mRNAs in case of plants. Here the set of plant miRNA from six plants was targeted against plant viruses and miRanda is a web base tool, which was used for target prediction.…”

Mining of miRNAs and potential targets from gene oriented clusters of transcripts sequences of the anti-malarial plant, Artemisia annua

“…Potential targets for the mature miRNAs with identified precursors in A. annua were predicted by screening against the A. annua UniGenes using a modified version of the software miRanda (v. September 2008) with parameters described elsewhere (Enright et al 2003;Pérez-Quintero et al 2010). The criteria to consider a sequence as a putative miRNA target were: four or fewer mismatches overall, only one or none mismatches in the 5 0 region of the miRNA (positions 1-12), no more than two consecutives mismatches in positions 13-21, no mismatches in positions 10 and 11.…”