Computational prediction of maize-encoded microRNAs targeting sugarcane mosaic virus: an approach for the development of antiviral resistance in maize (Zea mays L.)
Subject Areas : VirologyAminallah Tahmasebi 1 * , امیر غفار شهریاری 2
1 - University of Hormozgan
2 - استادیار دانشگاه اقلید
Keywords: In silico analysis, miRNA, Sugarcane mosaic virus, Zea mays.,
Abstract :
Background & Objectives: Sugarcane mosaic virus (SCMV) causes significant economic damage and severe yield losses in maize. To combat viral infections, plants have evolved diverse defense mechanisms, including miRNAs, which play a crucial role in pathogen resistance.
Materials and methods: This study aimed to explore the potential interactions between maize miRNAs and the SCMV-ZRA isolate, identify miRNA target genes, and characterize host responses.
Results: Bioinformatics analysis identified 21 common maize miRNAs targeting the SCMV genome, with inhibitory mechanisms involving 33.33% translation repression and 66.66% RNA degradation. These miRNAs were predicted to regulate 3,638 maize target genes, predominantly through RNA degradation (87.14%), while a smaller subset (12.86%) mediated translation repression. GO enrichment analysis revealed that the affected biological processes were primarily associated with energy coupled proton transmembrane transport, against electrochemical gradient, electron transport coupled proton transport, mitochondrial translation, mitochondrial gene expression, ATP synthesis coupled electron transport, oxidative phosphorylation, and respiratory electron transport chain processes. In addition, key cellular components included mitochondrial large and small ribosomal subunit, mitochondrial ribosome, organellar ribosome, respiratory chain complex I, NADH dehydrogenase complex, mitochondrial protein complex, mitochondrial matrix, and ribosome. Furthermore, the predominant molecular functions involved ubiquinone and quinone binding, NADH dehydrogenase and oxidoreductase activity. KEGG pathway analysis highlighted eight enriched pathways; plant hormone signal transduction, glycolysis/gluconeogenesis, beta-alanine metabolism, fatty acid degradation, arginine and proline metabolism, alanine, aspartate and glutamate metabolism, butanoate metabolism, and lysine degradation.
Conclusion: These findings elucidate the key miRNAs binding the SCMV genome, their host target genes, and associated signaling pathways, providing valuable insights into the molecular interplay between maize miRNAs and SCMV.