Open Access Highly Accessed Research article

The Saccharomyces cerevisiae transcriptome as a mirror of phytochemical variation in complex extracts of Equisetum arvense from America, China, Europe and India

Rebekah Cook1, James R Hennell1, Samiuela Lee1, Cheang S Khoo1, Maria C Carles14, Vincent J Higgins2, Suresh Govindaraghavan3 and Nikolaus J Sucher15*

Author Affiliations

1 Centre for Complementary Medicine Research, University of Western Sydney, Locked Bag 1797, Penrith, NSW 2751, Australia

2 Ramaciotti Centre for Gene Function Analysis, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia

3 Network Nutrition Pty Limited, Level 1, 1 Richardson Place, North Ryde, NSW 2153, Australia

4 Present address: Natural Sciences, Northern Essex Community College, 110 Elliot Street, Building E, Room 367, Haverhill, MA 01830, USA

5 Present address: Science, Technology, Engineering & Math, Roxbury Community College, 1234 Columbus Ave, Roxbury Crossing, Boston, MA 02120, USA

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BMC Genomics 2013, 14:445  doi:10.1186/1471-2164-14-445

Published: 4 July 2013



Pattern-oriented chemical profiling is increasingly being used to characterize the phytochemical composition of herbal medicines for quality control purposes. Ideally, a fingerprint of the biological effects should complement the chemical fingerprint. For ethical and practical reasons it is not possible to test each herbal extract in laboratory animals or humans. What is needed is a test system consisting of an organism with relevant biology and complexity that can serve as a surrogate in vitro system. The purpose of this study was to test the hypothesis that the Saccharomyces cerevisiae transcriptome might be used as an indicator of phytochemical variation of closely-related yet distinctly different extracts prepared from a single species of a phytogeographically widely distributed medicinal plant. We combined phytochemical profiling using chromatographic methods (HPTLC, HPLC-PDA-MS/MS) and gene expression studies using Affymetrix Yeast 2.0 gene chip with principal component analysis and k-nearest neighbor clustering analysis to test this hypothesis using extracts prepared from the phytogeographically widely distributed medicinal plant Equisetum arvense as a test case.


We found that the Equisetum arvense extracts exhibited qualitative and quantitative differences in their phytochemical composition grouped along their phytogeographical origin. Exposure of yeast to the extracts led to changes in gene expression that reflected both the similarities and differences in the phytochemical composition of the extracts. The Equisetum arvense extracts elicited changes in the expression of genes involved in mRNA translation, drug transport, metabolism of energy reserves, phospholipid metabolism, and the cellular stress response.


Our data show that functional genomics in S. cerevisiae may be developed as a sensitive bioassay for the scientific investigation of the interplay between phytochemical composition and transcriptional effects of complex mixtures of chemical compounds. S. cerevisiae transcriptomics may also be developed for testing of mixtures of conventional drugs (“polypills”) to discover novel antagonistic or synergistic effects of those drug combinations.

Herbal medicine; Transcriptomics; Phytochemistry; Chemometrics; Microarray; Functional genomics; Gene expression; Yeast; Phospholipid metabolism