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Open Access Research article

Combining metabolomics and transcriptomics to characterize tanshinone biosynthesis in Salvia miltiorrhiza

Wei Gao12, Hai-Xi Sun3, Hongbin Xiao4, Guanghong Cui1, Matthew L Hillwig5, Alana Jackson5, Xiao Wang1, Ye Shen1, Nan Zhao4, Liangxiao Zhang4, Xiu-Jie Wang3*, Reuben J Peters5* and Luqi Huang1*

Author Affiliations

1 National Resource Center for Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing 100700, China

2 School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China

3 State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

4 Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China

5 Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa 50011, USA

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BMC Genomics 2014, 15:73  doi:10.1186/1471-2164-15-73

Published: 28 January 2014

Abstract

Background

Plant 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.

Results

Here, 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.

Conclusions

Our 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.