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.
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This work is supported partially by the Harold R. Burton Endowed Professorship to L.Y. and by the National Science Foundation under Cooperative Agreement No. 1355438 to L.Y.
Supplementary information accompanies this paper at http://www.nature.com/srep
Shen, Ethan M.; Singh, Sanjay Kumar; Ghosh, Jayadri S.; Patra, Barunava; Paul, Priyanka; Yuan, Ling; and Pattanaik, Sitakanta, "The miRNAome of Catharanthus roseus: Identification, Expression Analysis, and Potential Roles of MicroRNAs in Regulation of Terpenoid Indole Alkaloid Biosynthesis" (2017). Plant and Soil Sciences Faculty Publications. 92.