Transcriptomic analysis of Siberian ginseng (Eleutherococcus senticosus) to discover genes involved in saponin biosynthesis
© Hwang et al.; licensee BioMed Central. 2015
Received: 16 October 2014
Accepted: 19 February 2015
Published: 14 March 2015
Eleutherococcus senticosus, Siberian ginseng, is a highly valued woody medicinal plant belonging to the family Araliaceae. E. senticosus produces a rich variety of saponins such as oleanane-type, noroleanane-type, 29-hydroxyoleanan-type, and lupane-type saponins. Genomic or transcriptomic approaches have not been used to investigate the saponin biosynthetic pathway in this plant.
In this study, de novo sequencing was performed to select candidate genes involved in the saponin biosynthetic pathway. A half-plate 454 pyrosequencing run produced 627,923 high-quality reads with an average sequence length of 422 bases. De novo assembly generated 72,811 unique sequences, including 15,217 contigs and 57,594 singletons. Approximately 48,300 (66.3%) unique sequences were annotated using BLAST similarity searches. All of the mevalonate pathway genes for saponin biosynthesis starting from acetyl-CoA were isolated. Moreover, 206 reads of cytochrome P450 (CYP) and 145 reads of uridine diphosphate glycosyltransferase (UGT) sequences were isolated. Based on methyl jasmonate (MeJA) treatment and real-time PCR (qPCR) analysis, 3 CYPs and 3 UGTs were finally selected as candidate genes involved in the saponin biosynthetic pathway.
The identified sequences associated with saponin biosynthesis will facilitate the study of the functional genomics of saponin biosynthesis and genetic engineering of E. senticosus.
Eleutherococcus senticosus Maxim (= Acanthopanax senticosus) is a thorny shrub belonging to Araliaceae that grows in the Russian Far East, Northeast China, Korea and Japan. There are approximately 38 species of Eleutherococcus. E. senticosus is popularly known as Siberian ginseng because of its remarkable pharmacological effects. The cortical root and stem tissues of the plant are used as a tonic and sedative and to treat rheumatism and diabetes [1,2]. Its main ingredients are triterpenoid saponins, lignans, and phenolic compounds .
E. senticosus produces various types of triterpene saponins. Huang et al.  reviewed 43 types of triterpene saponins isolated from E. senticosus. The representative saponins of E. senticosus are oleanane-type triterpene saponins (referred to as eleutherosides I, K, L, and M and ciwujianoside A1, C3, C4, and D1). Moreover, noroleanane-type (ciwujianoside A2, B, C1, C2, D2, and E), 29-hydroxyoleanan type (ciwujianoside A3, A4, and D3) and lupane-type triterpene saponins (chiisanoside) have been isolated from E. senticosus .
Saponin synthesis starts from the acetylated coenzyme A (acetyl CoA) molecule, from which all triterpene carbon atoms are derived. The first diversifying step in triterpenoid biosynthesis is the cyclisation of 2,3-oxidosqualene catalysed by oxidosqualene cyclase (OSC) . The molecular diversity of OSCs enables more than 100 skeletal variations of triterpenoids in plants . Saponins are thought to be synthesised from subsequent hydroxylation or oxidation of triterpene skeletons by CYP and glycosylation by UGT. These enzymes exist as supergene families in the plant genome. However, the key genes involved in saponin biosynthesis in E. senticosus have not been identified.
Expressed sequence tag (EST) analysis is a powerful method to discover novel genes . Next-generation sequencing (NGS) technologies have enabled a genomics and genetics revolution in which the discovery of useful genes has been greatly accelerated [8,9]. NGS sequencing has been used in saponin-rich plant species such as the Panax species [10,11], Siraitia grosvenorii , and Buplerum chinense , and Ilex asperlla  to identify triterpene biosynthetic genes.
Despite the economic and pharmacological value of E. senticosus, it has not been characterised using genomic and transcriptomic approaches. In this research, 627,923 reads were generated using the Roche GS FLX titanium platform from a leaf cDNA library from E. senticosus. The reads were assembled to 15,217 contigs and 57,594 singletons. We focused on discovering genes encoding enzymes involved in the saponin biosynthesis pathway. Genes involved in saponin skeleton biosynthesis as well as a number of candidate genes that might be involved in modification of the triterpene saponin biosynthetic pathway skeleton, including CYPs and UGTs, were screened by elicitor treatment. Candidate CYP and UGT genes were selected based on their putative involvement in saponin biosynthesis in E. senticosus.
Sequencing using the 454 genome sequencer FLX system and de novo assembly
Summary of the total 454 sequencing and the assembly results for E. senticosus leaf tissues
No. of sequences
No. of bases
Total number of reads
Average read length (bp)
Reads used in assembly
Number of contigs
Average length of contigs (bp)
Range of contig length (bp)
Number of singletons (bp)
Average length of singletons (bp)
Range of singleton length (bp)
Functional annotation and classification based on gene ontology (GO)
Summary of the annotation of the 454 assembled unique sequences
Annotation percentage (%)
Most abundant transcripts in E. senticosus leaf transcriptome
Target accession no.
Chloroplast, complete genome [Aconitum barbatum]
Chloroplast, complete genome [Cercis canadensis]
Ribulose bisphosphate carboxylase [Phaseolus vulgaris]
Hypothetical protein VITISV_032350 [Vitis vinifera]
ATP synthase subunit beta [Medicago truncatula]
Hypothetical protein Ssol98_08391 [Sulfolobus solfataricus]
Putative chlorophyll a/b binding protein, partial [Aralia elata]
Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit [Panax ginseng]
Cell wall-associated hydrolase, partial [Medicago truncatula]
PREDICTED: uncharacterised protein LOC100801029 [Glycine max]
Light harvesting chlorophyll a /b binding protein [Hedera helix]
Ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit [Panax ginseng]
Cytochrome P450-like TBP [Citrullus lanatus]
Putative ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit [Aralia elata]
Senescence-associated protein [Micromonas pusilla]
Mitochondrial protein, putative [Medicago truncatula]
Cell wall-associated hydrolase, partial [Medicago truncatula]
Conserved hypothetical protein [Clostridium botulinum]
Mevalonate pathway genes as candidates for involvement in saponin backbone biosynthesis
Triterpenes are assembled from a five-carbon isoprene unit through the cytosolic mevalonate pathway. Mevalonate is a product of the sequential condensation of three acetyl-CoA units to generate 3-hydroxy-3-methylglutaryl CoA (HMG-CoA), which is converted to mevalonate by HMG-CoA reductase (HMGR). The mevalonate is sequentially phosphorylated and decarboxylated to generate isopentenyl pyrophosphate (IPP). Condensation of dimethylallyl diphosphate (DMAPP) with one IPP generates geranyl diphosphate (GPP), and the addition of a second IPP unit generates farnesyl pyrophosphate (FPP). Squalene synthase (SS) catalyses the first enzymatic step from the central isoprenoid pathway toward sterol and triterpenoid biosynthesis . Squalene epoxidase (SQE) catalyses the first oxygenation step in phytosterol and triterpenoid saponin biosynthesis. Both phytosterols and triterpenes in plants are synthesised from the product of OSC-catalysed cyclisation of 2,3-oxidosqualene.
Number of putative unique sequences involved in saponin skeleton biosynthesis
Number of unique sequences
Number of 454 reads
Farnesyl diphosphate synthase
CYP is a superfamily of monooxygenases, a large and diverse group of enzymes that catalyse the oxidation of organic substances. CYP is involved in a wide range of biosynthetic pathways, including those for lignin, terpenoids, sterol, fatty acids, and saponins [18,19]. In our sequencing results for E. senticosus, 84 contigs and 122 singletons were annotated as CYPs. These sequences were grouped into 32 CYP families with single and multiple copies (Additional file 2). The most abundant CYP transcripts (more than 500 454 sequencing reads) in the E. senticosus leaf belonged to the CYP72, CYP76, and CYP716 families. Of the 32 CYP families, we selected 22 CYP families with more than 40 copies of transcript reads as shown in Additional file 3. Among these 22 family sequences, 9 sequences had a full ORF region.
Based on the structure of the sapogenin aglycone, the non-saccharide portion of saponins, saponins from E. senticosus can be classified as several types of triterpenoid aglycones (oleanolic acid, 29-hydroxyoleanoic acid, 30-noroleanolic acid, and 3,4-seco-betulinic acid) and steroid aglycone (β-sitosterol), as shown in Figure 3. Thus, we propose that several CYP enzymes are involved in saponin biosynthesis in E. senticosus.
The sapogenin structure of eleutherosides I, K, L, and M and ciwujianosides A1, C3, C4, and D1 in E. senticosus is oleanolic acid which is derived from β-amyrin (Figure 3). β-amyrin is converted to oleanolic acid after hydroxylation by CYP716A subfamily enzymes [23,25,26]. CYP716A12 from Medicago truncatula and CYP716A52v2 from P. ginseng are β-amyrin 28-oxidases (oleanolic acid synthases) belonging to the CYP85 clan [23,26]. The full sequences of the CYP-18 gene are 92% and 95% similar to CYP716A52v2 from P. ginseng and CYP716A12 from M. truncatula, respectively. Thus, we propose that the CYP-18 sequence is the best candidate CYP gene determining sapogenin formation in the biosynthesis of eleutherosides I, K, L, and M and ciwujianosides A1, C3, C4, and D1. The enzymes responsible for 29-hydroxyoleanolic acid formation from oleanolic acid, 30-noroleanolic acid formation from 30-nor β-amyrin, and 3,4-seco-betulinic acid formation from 3,4-seco-lupeol have not been identified. Thus, E. senticosus CYP enzymes and their effect on sapogenin aglycone formation merit further study.
Saponins are high molecular weight glycosides consisting of a sugar moiety linked to a triterpenoid or steroid aglycone. All saponins feature one or more sugar chains attached to the aglycone. Glycosylation contributes to the highly diverse nature of plant secondary metabolites. UGT is a superfamily of enzymes that catalyses the addition of the glycosyl group from a UTP-sugar to a sapogenin molecule. Thus, UGTs are important for the regulation of saponin biosynthesis. Normally, UGTs act at the last stage of natural plant secondary metabolites and have a significant role in the stability of products and modification of biological activity . In this study, 144 unique UGT sequences were identified in the E. senticosus transcriptome. They were classified into 18 UGT families as shown in Additional file 4. The UGT85 family gene had the most reads, with 39 unique sequences and 309 reads. The UGT73 family had the second highest number of reads, including 4 subfamilies and 14 unique sequences.
In the present study, transcriptomic analysis of E. senticosus leaves was performed using the GS FLX Titanium platform. A total of 15,217 contigs and 57,594 singletons were generated by assembling 627,923 reads. The most abundant cDNA sequences of the leaf transcriptome of E. senticosus were chloroplast-specific genes. However, we identified all sequences involved in the upstream region of the mevalonate pathway for saponin biosynthesis, from acetyl-CoA to SS, in E. senticosus by searching these transcripts against sequence databases using the blastX algorithm. E. senticosus leaves are rich in saponins. Of a total of 43 triterpenoid saponins in E. senticosus, 26 were isolated from leaves .
SQE enzymes catalyse the conversion of squalene to 2,3-oxidosqualene. In the transcriptomic analysis of E. senticosus, sequences encoding SQE represented the highest number (17) of unique sequences among transcripts associated with the mevalonate metabolic pathway, with 213 sequence reads. SQE is likely an important regulatory enzyme in this pathway . Single copies of the SQE gene are found in yeast and mouse, and thus disruption of SQE in these organisms is lethal . By contrast, plants examined thus far have two or more copies of SQE genes. In Arabidopsis thaliana, 6 SQE isoforms have been identified , of which SQE1, SQE2, and SQE3 encode functional SQEs, while SQE4, SQE5, and SQE6 fail to complement the yeast erg1 mutation. Rasbery et al.  suggested that SQE genes have different isoform-dependent functions in Arabidopsis. In Medicago truncatula cell cultures, the SQE gene MtSQE2 was up-regulated by treatment with MeJA, while MtSQE1 was not . Han et al.  reported that the expression of PgSQE1 and PgSQE2 regulated in different manners and that PgSQE1 regulates the biosynthesis of ginsenoside but not phytosterols in P. ginseng. The SQE gene responsible for saponin biosynthesis among the 17 unique SQE sequences in E. senticosus remains to be identified.
The cyclisation of 2, 3-oxidosqualene is a branch point of phytosterol and saponin synthesis, which play an important role in carbon flux regulation in other metabolic branches. In the transcriptomic analysis of E. senticosus, sequences encoding lupeol and cycloartenol synthase were represented in 31 and 35 reads, respectively. β-Amyrin synthase represented four unique sequences with 323 reads and thus had the most reads among the upstream genes of saponin biosynthesis (Table 4). This result suggests that transcriptional activity for oleanane-type saponin biosynthesis starting from β-amyrin may be very high in leaves of E. senticosus. Among the Arabidopsis OSC enzymes, ATBAS (AT1G78950) encodes a multifunctional OSC yielding more than nine products, including β-amyrin, α-amyrin and lupeol . Tomato SlTTS1 (SlBAS) forms β-amyrin as its sole product, while SlTTS2 catalyses the formation of seven different triterpenoids, with δ-amyrin as the major product . E. senticosus may produce 30-nor β-amyrin and 3,4-seco-lupeol, and the characterisation of the OSC genes involved in the biosynthesis of these triterpenes will be of interest in future work.
The cyclised triterpenes undergo two additional transformations (hydroxylation and glycosidation). In oleanan-type saponin biosynthesis, the oleanolic acid sapogenin is synthesised from β-amyrin after oxidation by CYP [23,26], and this sapogenin is further glycosylated by UGT to produce various type of saponins.
The major saponins of E. senticosus are the eleutherosides I, K, L, and M and the ciwujianosides A1, C3, C4, and D1, which are oleanane-type triterpenoids derived from β-amyrin triterpene. Among CYP ESTs, the sequence encoding the β-amyrin gene has the most abundant reads in E. senticosus. This result suggests that some CYPs and UGT genes involved in oleanane-type saponin biosynthetic pathway may be abundant in EST sequences of E. senticosus. CYP716A12 in M. truncatula , CYP716A16 and CYP716A17 in Vitis , and CYP716A52v2 in P. ginseng  have been identified as genes encoding β-amyrin 28-oxidase (oleanolic acid synthase). In the 454 dataset, we observed that CYP-18 of E. senticosus is highly homologous (90%) with CYP716A52v2. We suggest that this gene may convert β-amyrin to oleanolic acid in E. senticosus. Two other genes (CYP-3, CYP-17) that were increased by MeJA treatment compared to the control are also likely involved in saponin biosynthesis in E. senticosus. CYP-17 has high similarity (86%) with CYP716A47 from P. ginseng, which catalyses protopanaxadiol sapogenin formation from dammarenediol-II . Fukushima et al.  reported that CYP716A subfamily members are multifunctional oxidases in triterpenoid biosynthesis. Thus, the CYP-17 gene may be involved in saponin biosynthesis in E. senticosus. The CYP-3 gene is 67% identical to CYP72A63 from M. truncatula and 69% identical to CYP72A154 from Glycyrrhiza uralensis. All three genes encode enzymes that catalyse β-amyrin oxidation to produce different types of aglycones in saponin biosynthesis .
UGTs involved in saponin biosynthesis belonging to the UGT 71, 73, 74, and 91 clans have been identified previously . UGT73C10 to UGT73C13 in Barbarea vulgaris have been reported to be involved in C-3 glycosylation of hederagenin and oleanolic acid . UGT73F2 and UGT73P2 from Glycine max catalyse the addition of Xyl and Glc, respectively, to the Ara residue at the C-22 position of soyasapogenol A . Thus, the UGT 73 clan is the best candidate group for oleanane-type saponin biosynthesis. In this study, we identified a gene (UGT-3) belonging to the UGT 73 clan whose transcription was enhanced approximately 2-fold by MeJA treatment compared to the control. However, the UGT85 family of sequences (UGT-10 and UGT-11) exhibited the highest enhancement of transcription after MeJA treatment. Based on the most abundant transcripts in the E. senticosus transcriptome analysis, the UGT-10 and UGT-11 sequences belonging to the UGT85A subfamily are the best candidate genes for saponin biosynthesis in E. senticosus. As shown in Figure 3, the huge biodiversity of saponins in E. senticosus suggests that various UGT genes are involved in each specific step of saponin biosynthesis. Further characterisation of UGT family enzymes is needed to validate the pathway of saponin biosynthesis in E. senticosus.
In this research, a large-scale EST sequencing was performed in leaf tissues from E. senticosus. The obtained EST dataset provides a useful information for gene discovery and genetic analysis in this plants. The genes involved in saponin biosynthesis pathway as well as candidate genes that might be involved in the triterpene formation, hydroxylation or oxidation of triterpene skeletons by CYP and glycosylation by UGT will help the further research for conducting the functional genomics and transcriptomics of E. senticosus.
Fresh leaves of E. senticosus were collected from Mt. Odae, Pyeongchang, Kangwon-do, Korea. To determine the effect of elicitor treatment on the transcriptional activities of specific genes, leaves were exposed to 200 μM MeJA for 8 h, and control leaves were treated with 0.25% ethanol. All tissues were immediately frozen in liquid nitrogen and stored at −80°C until use.
Total RNA was extracted from leaves using Trizol reagent (MRC, USA) and RNeasy® Plant Mini Kit (QIAGEN, Germany) according to the manufacturer’s instructions. Genomic DNA was removed from the total RNA using DNase following the manufacturer’s protocol (TAKARA, Japan). mRNA was isolated from 100 μg of total DNase-treated RNA using an mRNA purification kit (Stratagene, USA) according to the manufacturer’s instructions. Agarose gel electrophoresis and the OD260/280 ratio were used to assess the quality of RNA before cDNA synthesis.
cDNA preparation and sequencing
mRNA was purified using poly-T oligo-attached magnetic beads and then fragmented with the RNA fragmentation solution supplied with the GS Titanium Library Preparation kit (454 Life Sciences, Branford, CT) following the manufacturer’s recommendations. The first- and second-strand cDNAs were synthesised and end-repaired. Adaptors were ligated at the 5′ and 3′ ends. cDNA libraries were validated using a High Sensitivity Chip on the Agilent2100 Bioanalyzer™ (Agilent Technologies, CA). emPCR reactions were performed on enriched cDNA templates.
The emulsions were broken, and the DNA capture beads were collected. The enriched bead samples were counted according to the manufacturer’s instructions (Roche). Tagged libraries were combined in a picotitre plate for sequencing. A one-plate reaction of 454 pyrosequencing was conducted using the Roche 454 Genome Sequencer FLX System (Branford, CT, USA).
De novo assembly
The 454 Genome Sequencer FLX system collects the data and generates a standard flow gram file (.sff) that contains raw data for all the reads. The raw data were quality-filtered using a quality cut-off value of 40. The primer and adapter sequences that were incorporated during cDNA synthesis and normalisation were removed. Sequences of less than 50 bp were removed before contig assembly. De novo contig assembly of the reads was performed using GS De Novo Assembler software provided by 454 Life Sciences Corp, CT, USA. The assembly parameters were a minimum overlap length of 40 bp and a minimum overlap identity of 95%.
A total of 627,923 reads were assembled as 15,217 contigs and 57,594 singletons, which were functionally annotated using the BLASTN program. Putative protein-encoding sequences were compared with the databases KEGG (http://www.genome.jp/kegg/) and UniProt (http://www.uniprot.org/) and searched against the Nr (www.ncbi.nlm.nih.gov) database using the BLASTX algorithm with a cut-off E value of 10−5. The functional categories of these sequences were matched to the gene ontology (GO) algorithm.
RNA was isolated from control and MeJA-treated leaves and reverse transcribed using the ImProm-II Reverse Transcription System (Promega, Madison, WI, USA). qPCR was performed using a Qiagen Rotor Gene Q Real-time PCR detector system with SYBR Green PCR Kit (Qiagen, Germany). Two-step amplification conditions for all real-time PCRs were 95°C for 5 min, followed by 40 cycles of 95°C for 5 sec and 60°C for 10 sec. The qPCR data are presented as the average relative quantities ± SE from at least three replicates. For the MeJA inducibility experiment, the expression of each gene was used as the calibrator. The relative expression value of each gene was calculated using the -ΔΔCT method . The E. senticosus β-actin gene was used for normalisation. All primers used in the present study are listed in Additional files 4 and 7.
The deduced amino acid sequences of the EsBAS, CYP and UGT genes of E. senticosus and those of other plants were obtained from DDBJ/GenBank/EMBL for phylogenetic analysis. Multiple sequence alignments were generated using the CLUSTAL W program . Phylogenetic analysis was performed using the neighbour-joining method with the MEGA 5.0 software program . A bootstrap of 1,000 replications was used to estimate the strength of nodes in the tree .
Availability of supporting data
The transcriptome sequence data have been deposited into the NCBI Short Read Archive (SRA, http://www.ncbi.nlm.nih.gov/sra/) under the accession numbers SRR1611617. The phylogenic alignments have been deposited in TreeBase; submission ID 17087, (http://treebase.org/treebase-web/search/study/summary.html?id=17087&x-access-code=aef0b055f66288e54b73754f03fe0316).
This work was supported by a grant from the Next-Generation BioGreen 21 Program (PJ011285) of the Rural Development Administration, and by Post-Genome Multi-Ministry Genome Project, and Basic Science Research Program through the NRF of Korea funded by the Ministry of Education (NRF-2013R1A1A4A01009460).
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