Phytochelatin database: a resource for phytochelatin complexes of nutritional and environmental metals

• Type of Material: Article
• Authors: Kristine K Dennis, Emory University; Karan Uppal, Emory University; Ken H Liu, Emory University; Chunyu Ma, Emory University; Bill Liang, Emory University; Young-Mi Go, Emory University; Dean P Jones, Emory University
• Language: English
• Date: 2019-07-02
• Publisher: Oxford University Press (OUP): Policy C - Option A
• Publication Version: Final Published Version
• Copyright Statement: © The Author(s) 2019. Published by Oxford University Press.
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1093/database/baz083
• Title of Journal or Parent Work: Database
• ISSN: 1758-0463
• Volume: 2019
• Grant/Funding Information: National Institute of Diabetes and Digestive and Kidney Diseases (T32 DK007734); National Institute of Environmental Health Sciences (R01 ES023485, U2C ES030163); and National Institutes of Health, Office of the Director (S10 OD018006).
• Keywords: Life Sciences & Biomedicine; Science & Technology; HG; CADMIUM; PEPTIDES; GLUTATHIONE; MASS-SPECTROMETRY; HPLC; ROLES; Mathematical & Computational Biology
• Research Categories: Health Sciences, Medicine and Surgery; Health Sciences, Nutrition

Abstract

Phytochelatins (PyCs) are a diverse set of plant compounds that chelate metals, protect against metal toxicity and function in metal homeostasis. PyCs are present in plants consumed as food by humans and could, in principle, impact absorption and utilization of essential and toxic metals such as selenium and cadmium, respectively. PyCs vary in terminal amino acid composition and chain length, exist in multiple oxidation states and reversibly bind multiple metals; consequently, PyCs include a large set of possible structures. Although individual PyC-metal complexes have been studied, no resource exists to characterize the diversity of PyCs and PyC-metal complexes. We used the scientific literature to develop a database of elemental formulas for polymer forms varying in chain length from 2 to 11 glutamyl-cysteine repeats. Using elemental formulas, we calculated monoisotopic masses using the most abundant isotopes of each element and calculated masses for complexes with 13 metals of nutritional and toxicological significance. The resulting phytochelatin database (PyCDB) contains 46 260 unique elemental formulas for PyC and PyC-metal complexes. The database is available online for download as well as for direct mass queries for mass spectrometry using an accurate mass annotation tool for user-selected PyC types, metals and adducts of interest. We performed studies of a commonly consumed food-onion-to validate the database and test utility of the tool. Onion samples were analyzed using ultra-high resolution mass spectrometry-based metabolomics. Mass spectral features were annotated using the PyCDB web tool and the R package, xMSannotator; annotated features were further validated by collision-induced dissociation mass spectrometry. The results establish use and a workflow for PyCDB as a resource for characterization of PyCs and PyC-metal complexes.