Abstract
Key message
Metabolic module, gene expression pattern and PLS modeling were integrated to precisely identify the terpene synthase responsible for sesquiterpene formation. Functional characterization confirmed the feasibility and sensitivity of this strategy.
Abstract
Plant secondary metabolite biosynthetic pathway elucidation is crucial for the production of these compounds with metabolic engineering. In this study, an integrated strategy was employed to predict the gene function of sesquiterpene synthase (STS) genes using turmeric as a model. Parallel analysis of gene expression patterns and metabolite modules narrowed the candidates into an STS group in which the STSs showed a similar expression pattern. The projections to latent structures by means of partial least squares model was further employed to establish a clear relationship between the candidate STS genes and metabolites and to predict three STSs (ClTPS16, ClTPS15 and ClTPS14) involved in the biosynthesis of several sesquiterpene skeletons. Functional characterization revealed that zingiberene and β-sesquiphellandrene were the major products of ClTPS16, and β-eudesmol was produced by ClTPS15, both of which indicated the accuracy of the prediction. Functional characterization of a control STS, ClTPS1, produced a small amount of β-sesquiphellandrene, as predicted, which confirmed the sensitivity of metabolite module analysis. This integrated strategy provides a methodology for gene function predictions, which represents a substantial improvement in the elucidation of biosynthetic pathways in nonmodel plants.
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Abbreviations
- DGE:
-
Digital gene expression profiling
- FPP:
-
Farnesyl pyrophosphate
- HCA:
-
Hierarchical cluster analysis
- NIST:
-
National Institute of Standards and Technology
- MET-IDEA:
-
Metabolomics ion-based data extraction algorithm
- PLS:
-
Projections to latent structures by means of partial least squares
- qRT-PCR:
-
Quantitative real-time polymerase chain reaction analysis
- STS:
-
Sesquiterpene synthase
- SD-Trp:
-
Synthetic defined medium lacking tryptophan
- TPS:
-
Terpene synthase
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Acknowledgements
This work was supported by Grants from the National Natural Science Foundation of China (81603244, 81822046, and 81573532), China Postdoctoral Science Foundation (2015M571252), key project at central government level: The ability establishment of sustainable use for valuable Chinese medicine resources (2060302) and National Mega-Project for Innovative Drugs (2018ZX09711001-006-004). We thank Doctor Qingmiao Li and Doctor Xianjian Zhou from the Institute of Traditional Chinese Medicine Resources and Planting, Sichuan Academy of Traditional Chinese Medicine for help in collecting samples. We thank Professor Xueli Zhang and Doctor Zhubo Dai from Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences for providing the FPP production yeast strain BY-T15.
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LQH and JG were leading the project and designed the work. JRS, XHM, ZLZ and YM sampled the plant and did the chemical experiment. TZQ, CJSL, and WZ helped to analyze the chemical data. GHC, WG, YJZ, JFT, HZL, and YS performed gene functional characterization and bacterial engineering. YNW and TC performed transcriptome analysis. JRS, GHC, and JG wrote the paper.
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Sun, J., Cui, G., Ma, X. et al. An integrated strategy to identify genes responsible for sesquiterpene biosynthesis in turmeric. Plant Mol Biol 101, 221–234 (2019). https://doi.org/10.1007/s11103-019-00892-0
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DOI: https://doi.org/10.1007/s11103-019-00892-0