The miRNAome of Catharanthus roseus: identification, expression analysis, and potential roles of microRNAs in regulation of terpenoid indole alkaloid biosynthesis

Abstract

MicroRNAs (miRNAs) regulate numerous crucial biological processes in plants. However, information is limited on their involvement in the biosynthesis of specialized metabolites in plants, including Catharanthus roseus that produces a number of pharmaceutically valuable, bioactive terpenoid indole alkaloids (TIAs). Using small RNA-sequencing, we identified 181 conserved and 173 novel miRNAs (cro-miRNAs) in C. roseus seedlings. Genome-wide expression analysis revealed that a set of cro-miRNAs are differentially regulated in response to methyl jasmonate (MeJA). In silico target prediction identified 519 potential cro-miRNA targets that include several auxin response factors (ARFs). The presence of cleaved transcripts of miRNA-targeted ARFs in C. roseus cells was confirmed by Poly(A) Polymerase-Mediated Rapid Amplification of cDNA Ends (PPM-RACE). We showed that auxin (indole acetic acid, IAA) repressed the expression of key TIA pathway genes in C. roseus seedlings. Moreover, we demonstrated that a miRNA-regulated ARF, CrARF16, binds to the promoters of key TIA pathway genes and repress their expression. The C. roseus miRNAome reported here provides a comprehensive account of the cro-miRNA populations, as well as their abundance and expression profiles in response to MeJA. In addition, our findings underscore the importance of miRNAs in posttranscriptional control of the biosynthesis of specialized metabolites.

Integration of the Pokeweed miRNA and mRNA Transcriptomes Reveals Targeting of Jasmonic Acid-Responsive Genes

“…Although we identified many JA-responsive miRNAs, only two were conserved with other plants: miR172 and miR395, which decreased and increased with JA, respectively. In contrast, others have reported several conserved, JA-responsive miRNAs (Qiu et al, 2009 ; Bozorov et al, 2012 ; Zhang et al, 2012 ; Xu et al, 2016 ; Shen et al, 2017 ). One reason for this discrepancy may be our stringent requirements for differential expression, owing to the availability of biological replicates.…”

“…miRNAs have been implicated in numerous abiotic and biotic stress responses, such as those induced by temperature, salinity, drought, light, nutrient deficiencies, oxidative stress, and pathogens (reviewed in Khraiwesh et al, 2012 ; Li et al, 2017 ; Islam et al, 2018 ). Previous reports have characterized the effect of JA or its methyl ester (JA-Me) on miRNAs in Arabidopsis, Nicotiana attenuata, Taxus chinensis, Lycoris aurea , and Catharanthus roseus (Qiu et al, 2009 ; Bozorov et al, 2012 ; Zhang et al, 2012 ; Xu et al, 2016 ; Shen et al, 2017 ). Control of JA biosynthesis through miR319-targeted TCP transcription factors has also been established (Schommer et al, 2008 ; Zhao et al, 2015 ).…”

Comparative Analysis and Expression Patterns of the PLP_deC Genes in Dendrobium officinale

“…Many studies have suggested that the expression levels of PLP_deC genes are also influenced by abiotic and biotic stresses [28][29][30]. Furthermore, plant hormones such as ABA, SA, and ethylene also modulate the expression of these genes [17,29,30].…”

Identification, expression analysis, and potential roles of microRNAs in the regulation of polysaccharide biosynthesis in Polygonatum cyrtonema Hua

“…Generally, miRNAs exhibit tissue or stage-specific expression patterns, and participate in the regulation of the accumulation of secondary metabolites such as steroids and ketones by negatively regulating the expression of target genes [8][9][10]. For instance, miRNAs are involved in the biosynthesis of terpenoid indole alkaloids in Catharanthus roseus [ 11]. Additionally, miR156, miR828, miR858, and miR5072 regulate anthocyanin accumulation in apple peel [ 12].…”