Differential microRNA Analysis of Glandular Trichomes and Young Leaves in Xanthium strumarium L. Reveals Their Putative Roles in Regulating Terpenoid Biosynthesis

Abstract

The medicinal plant Xanthium strumarium L. (X. strumarium) is covered with glandular trichomes, which are the sites for synthesizing pharmacologically active terpenoids such as xanthatin. MicroRNAs (miRNAs) are a class of 21–24 nucleotide (nt) non-coding RNAs, most of which are identified as regulators of plant growth development. Identification of miRNAs involved in the biosynthesis of plant secondary metabolites remains limited. In this study, high-throughput Illumina sequencing, combined with target gene prediction, was performed to discover novel and conserved miRNAs with potential roles in regulating terpenoid biosynthesis in X. strumarium glandular trichomes. Two small RNA libraries from leaves and glandular trichomes of X. strumarium were established. In total, 1,185 conserved miRNAs and 37 novel miRNAs were identified, with 494 conserved miRNAs and 18 novel miRNAs being differentially expressed between the two tissue sources. Based on the X. strumarium transcriptome data that we recently constructed, 3,307 annotated mRNA transcripts were identified as putative targets of the differentially expressed miRNAs. KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis suggested that some of the differentially expressed miRNAs, including miR6435, miR5021 and miR1134, might be involved in terpenoid biosynthesis in the X. strumarium glandular trichomes. This study provides the first comprehensive analysis of miRNAs in X. strumarium, which forms the basis for further understanding of miRNA-based regulation on terpenoid biosynthesis.

Plastoquinone and Ubiquinone in Plants: Biosynthesis, Physiological Function and Metabolic Engineering

“…Various microRNAs have been identified to be associated with secondary metabolism (Wu et al, 2012; Lu S. et al, 2013; Fan et al, 2015; Wei et al, 2015). However, the regulatory roles of non-coding RNAs in PQ and UQ biosynthesis have not been revealed.…”

Contemporary Understanding of miRNA-Based Regulation of Secondary Metabolites Biosynthesis in Plants

“…Using NGS technology, several miRNAs involved in the sesquiterpene biosynthesis pathway have been mapped and validated in X. strumarium . For example, mRNAs of the upstream enzymes in the pathways of terpenoid biosynthesis, including 1-deoxy-D-xylulose 5-phosphate synthase (DXS), 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR), isopentenyl diphosphate (IPP)/dimethylallyl diphosphate (DMAPP) synthase (IDS), and isopenteyl diphosphate isomerase (IDI) were predicted to be targeted by miR7539, miR5021, and miR1134 (Fan et al, 2015). The complete list of miRNAs and their target genes have been provided in Table 1.…”

Identification of miRNAs and their targets involved in the secondary metabolic pathways of Mentha spp.

“…In earlier reports, the regulation of miR5021 was frequently observed for the terpenoid biosynthesis. In the case of mevalonate pathway, the regulation of HMGR was reported by miR5021 in Xanthium strumarium (Fan et al, 2015). Isopentenyl diphosphate (IPP) works as a precursor molecule for terpenoid derivatives.…”

“…Isopentenyl diphosphate (IPP) works as a precursor molecule for terpenoid derivatives. Isopentenyl diphosphate synthase (IDS) and isopenteyl diphosphate isomerase (IDI) are key enzymes reported for involvement in the formation of IPP, and being regulated by miR5021 (Fan et al, 2015). Our study revealed that the miR5021 may control the essential oil biosynthesis by controlling gene expression of enzymes involved in 2-C-methyl-D-erythritol 4-phosphate (MEP)/1-deoxy-D-xylulose 5-phosphate pathway (DOXP) including geranyl di-phosphate synthase (EC: 2.5.1.29) ( Table 2 and Supplementary 3).…”