Synonymous sites for accessibility around microRNA binding sites in bacterial spot and speck disease resistance genes of tomato

The major causes of mass tomato infections in both covered and open ground are agents of bacterial spot and bacterial speck diseases. MicroRNAs (miRNAs) are 16-21 nucleotides in length, non-coding RNAs that inhibit translation and trigger mRNA degradation. MiRNAs play a significant part in plant resistance to abiotic and biotic stresses by mediating gene regulation via post-transcriptional RNA silencing. In this study, we analyzed a collection of bacterial resistance genes of tomato and their binding sites for tomato miRNAs and Pseudomonas syringe pv. tomato miRNAs. Our study found that two genes, bacterial spot disease resistance gene (Bs4) and bacterial speck disease resistance gene (Prf), have a 7mer-m8 perfect seed match with miRNAs. Bs4 was targeted by one tomato miRNA (sly-miR9470-3p) and three Pseudomonas syringe pv. tomato miRNAs (PSTJ4_3p_27246, PSTJ4_3p_27246, and PSTJ4_3p_27246). Again, Prf gene was found to be targeted by two tomato miRNAs namely, sly-miR9469-5p and sly-miR9474-3p. The accessibility of the miRNA-target site and its flanking regions and the relationship between relative synonymous codon usage and tRNAs were compared. Strong access to miRNA targeting regions and decreased rate of translations suggested that miRNAs might be efficient in binding to their particular targets. We also found the existence of rare codons, which suggests that it could enhance miRNA targeting even more. The codon usage pattern analysis of the two genes revealed that both were AT-rich (Bs4 = 63.2%; Prf = 60.8%). We found a low codon usage bias in both genes, suggesting that selective restriction might regulate them. The silencing property of miRNAs would allow researchers to discover the involvement of plant miRNAs in pathogen invasion. However, the efficient validation of direct targets of miRNAs is an urgent need that might be highly beneficial in enhancing plant resistance to multiple pathogenic diseases.

A Practical Guide to miRNA Target Prediction

MicroRNAs (miRNAs) are small endogenous noncoding RNA molecules that posttranscriptionally regulate gene expression. Since their discovery, a huge number of miRNAs have been identified in a wide range of species. Through binding to the 3' UTR of mRNA, miRNA can block translation or stimulate degradation of the targeted mRNA, thus affecting nearly all biological processes. Prediction and identification of miRNA target genes is crucial toward understanding the biology of miRNAs. Currently, a number of sophisticated bioinformatics approaches are available to perform effective prediction of miRNA target sites. In this chapter, we present the major features that most algorithms take into account to efficiently predict miRNA target: seed match, free energy, conservation, target site accessibility, and contribution of multiple binding sites. We also give an overview of the frequently used bioinformatics tools for miRNA target prediction. Understanding the basis of these prediction methodologies may help users to better select the appropriate tools and analyze their output.