Combining metabolomics and transcriptomics to characterize tanshinone biosynthesis in Salvia miltiorrhiza

Abstract

BackgroundPlant natural products have been co-opted for millennia by humans for various uses such as flavor, fragrances, and medicines. These compounds often are only produced in relatively low amounts and are difficult to chemically synthesize, limiting access. While elucidation of the underlying biosynthetic processes might help alleviate these issues (e.g., via metabolic engineering), investigation of this is hindered by the low levels of relevant gene expression and expansion of the corresponding enzymatic gene families. However, the often-inducible nature of such metabolic processes enables selection of those genes whose expression pattern indicates a role in production of the targeted natural product.ResultsHere, we combine metabolomics and transcriptomics to investigate the inducible biosynthesis of the bioactive diterpenoid tanshinones from the Chinese medicinal herb, Salvia miltiorrhiza (Danshen). Untargeted metabolomics investigation of elicited hairy root cultures indicated that tanshinone production was a dominant component of the metabolic response, increasing at later time points. A transcriptomic approach was applied to not only define a comprehensive transcriptome (comprised of 20,972 non-redundant genes), but also its response to induction, revealing 6,358 genes that exhibited differential expression, with significant enrichment for up-regulation of genes involved in stress, stimulus and immune response processes. Consistent with our metabolomics analysis, there appears to be a slower but more sustained increased in transcript levels of known genes from diterpenoid and, more specifically, tanshinone biosynthesis. Among the co-regulated genes were 70 transcription factors and 8 cytochromes P450, providing targets for future investigation.ConclusionsOur results indicate a biphasic response of Danshen terpenoid metabolism to elicitation, with early induction of sesqui- and tri- terpenoid biosynthesis, followed by later and more sustained production of the diterpenoid tanshinones. Our data provides a firm foundation for further elucidation of tanshinone and other inducible natural product metabolism in Danshen.

Identification and characterization of mRNA-like noncoding RNAs in Salvia miltiorrhiza

“…treatment RNA-seq data obtained from S. miltiorrhiza hairy roots treated with yeast extract (100 lg/ml) and Ag ? (30 lM) were downloaded from GenBank under the accession number SRR924662 (Gao et al 2014). RNA-seq reads from non-treated (0 hpi) and treated for 12 h (12 hpi), 24 h (24 hpi) and 36 h (36 hpi) were mapped to mlncRNAs using the SOAP2 software (Li et al 2009a) with the parameter v cutoff of 3 and parameter r cutoff of 2.…”

“…It is also an effective elicitor for the production of tanshinones and phenolic acids in S. miltiorrhiza (Gao et al 2014;Luo et al 2014). To further analyze the role of mlncRNAs in defense response in S. miltiorrhiza, expression patterns of 17 mlncRNAs with length over 900 bp were analyzed in leaves of plantlets treated with MeJA for 12, 24, 36 and 48 h using the quantitative real-time PCR method.…”

“…RNA-seq data of S. miltiorrhiza hairy roots treated with or without yeast extract (100 lg/ml) and Ag ? (30 lM) were obtained from GenBank (accession number SRR924662) (Gao et al 2014) and then mapped to the identified mlncRNAs using SOAP2 (Li et al 2009a). About 2.68-3.16 % of RNA-seq reads from non-treated (0 hpi) and treated for 12 h (12 hpi), 24 h (24 hpi) and 36 h (36 hpi) were perfectly mapped to mlncRNAs (Table 5).…”

“…Moreover, the biosynthesis of tanshinones in S. miltiorrhiza hairy root cultures could also be enhanced by biotic (yeast extract) and abiotic (Ag ? ) treatments (Gao et al 2014).…”

Improved Representation of Biological Information by Using Correlation as Distance Function for Heatmap Cluster Analysis

“…The numerical data matrices should to be analyzed with optimized data mining algorithms and visualization tools in order to better explain the complex link between genotype and phenotype in a worldwide crop plant such as maize. Our optimized script for heatmap correlation bicluster is not only is useful for agricultural phenomics, but also to improve the interpretation of other omic sciences, such as metabolomic fingerprints [29] [30] and transcriptomic data sets [2].…”