Release of the Medicinal Plant Consortium Metabolomic Resources
The Medicinal Plant Consortium (MPC) is an NIH supported project (GM092521) consisting of 13 collaborating research units from 7 institutions focused on providing transcriptomic (http://medicinalplantgenomics.msu.edu/) and metabolomics (http://medicinalplantmetabolomicsresource.org/) resources to the worldwide research community for 14 key medicinal plants for the advancement of drug production and development.
The Principal Investigators of the MPC are Cornelius Barry1, C. Robin Buell1, Joe Chappell2, Dean DellaPenna1, Natalia Dudareva3, Mahmoud A. ElSohly4, A. Daniel Jones1, Ikhlas A. Khan4, Thomas D. McKnight5, Basil J. Nikolau6, Sarah E. O'Connor7, Troy Smillie4, and Eve Syrkin Wurtele6
1Michigan State University, East Lansing, MI; 2University of Kentucky, Lexington, KY; 3Purdue University, West Lafayette, IN; 4University of Mississippi, Oxford, MS; 5Texas A&M University, College Station, TX; 6Iowa State University, Ames, IA; 7 The John Innes Centre, Norwich NR4 7UH, UK
This announcement from the MPC pertains to the release of first metabolomic dataset for Atropa belladonna and Digitalis purpurea on Nov. 1, 2011 at the anonymous web portal http://medicinalplantmetabolomicsresource.org/.
The server window will ultimately provide searching capability for the metabolomes for all 14 plant species:
- Atropa belladonna
- Camptotheca acuminata
- Cannabis sativa
- Catharanthus roseus
- Digitalis purpurea
- Dioscorea villosa
- Echinacea purpurea
- Ginkgo biloba
- Hoodia gordonii
- Hypericum perforatum
- Panax quinquefolius
- Rauvolfia serpentina
- Rosmarinus officinalis
- Valeriana officinalis
Release of the metabolomic resources for Camptotheca acuminata, and Echinacea purpurea are anticipated for Nov. 4th, 2011, to be followed by the metabolomes of the remaining plant species as these are qualified and verified by the MPC by no later than Dec. 16th, 2011.
The Medicinal Plant Metabolomics Resources home page provides background information on the goals of the MPC project and a primer on what metabolomics attempts to measure. The green tabs on the left hand side of the homepage provide additional information about the personnel involved in the MPC, the project objectives, links to other associated and useful web portals, contact information for persons responsible for the Metabolomics Resources, and a sign-up site to receive future release notices. All the plants whose metabolomes have been determined are listed under the species tab and those highlighted in green are those currently available. Selecting a highlighted species tab pulls up the main page for that plant, which also provides a link to a general overview about the species.
This announcement pertains to the release of the metabolomes for Atropa belladonna and Digitalis purpurea. The metabolomes are derived by extracting the small organic compounds (1,000 to 2,000 different metabolites per plant) from up to 20 different tissue types/treatments for each plant species, then analyzing each extract independently by Liquid Chromatography-Time-Of-Flight Mass Spectrometry (LC-TOF MS). Individual metabolites are identified and their relative abundances measured on the basis of their molecular mass as reflected by their parent ion generated upon ionization, plus adducts with various salts (e.g. NH4+ and Na+) and, in special cases, possible oligomeric forms (e.g. twice the actual parent ion mass).
For example, the known cardiac muscle stimulant digitoxin is found in extracts of Digitalis purpurea. Though this molecule has a molecular mass of 764 Daltons, the mass spectrometer detects it as a positive ion formed by attachment of ammonium (NH4+) yielding an ion with a mass-to-charge ratio of 782.477 instead of the mass of the neutral digitoxin molecule. Some metabolites are ionized by attaching different positive ions (e.g. H+ or Na+) instead. By selecting digitoxin in the box of chemically defined compounds, an information box with links to PubChem and a histogram representing the relative distribution of digitoxin in the various tissue types are shown. The histogram bars show the relative abundance of digitoxin averaged across multiple independent determinations (shown as green dots on the graph and normalized to tissue dry weight).
One can search for additional metabolites using the search window option found at the main page for each plant species by inputting search terms, molecular mass, selecting for a particular mass range or other pull-down, selectable criteria. Metabolites identified by a search can then be selected to view their distribution across tissue/treatment samples. For example, a search for metabolites of the plant Digitalis purpurea detected as an ion with a molecular mass of 304 Da turns up a metabolite labeled FS-Dig-HPLC-E-POS-F1-304.31-12.43. This nomenclature refers to a metabolite from the Digitalis purpurea metabolome (Dig), determined by TOF-MS operating in the positive mode after HPLC separation and electrospray ionization (HPLC-E-POS) yielding a metabolite having a molecular mass of 304.31 Da that eluted from the HPLC system with a retention time of 12.43 minutes. The large number of detected metabolites precluded confirmation of many metabolite structures, but it is anticipated that the molecular mass information can help guide further metabolite identification. This metabolite was found exclusively in petiole and leaf tissues.
The homepage also contains an advanced search window that allows users to perform a text search for metabolites by name, elemental formula, mass, and several other properties across all the plant species.
The ratio plot window allows one to compare the relative metabolite levels between any two tissue/treatment types. All measured metabolites are shown with their relative amount in a tissue listed along the x-axis with a log2 scale. The y-axis scale in the ratio plots are indicators of the metabolite's position in the list of all metabolites, while the volcano plots represent a p-value level of statistical significance for each metabolite. The smaller the y-axis value (higher position on the plot), the greater the probability that a metabolite's accumulation level is significant.
One can view or download the entire data spreadsheet for a plant species using the View Data or Processed Data tabs. Downloads are performed anonymously.
Additional information/metadata about the HPLC and MS conditions are also provided by the selectable tabs found on the main page for each plant species.
To assure receipt of future MPC notices of data release and announcements, please register at the mailing list sign-up form on the project website (http://medicinalplantgenomics.msu.edu).
Further inquiries may be directed to Joe Chappell at email@example.com.