Metabolomics in Plants

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Metabolomic studies in plants help to understand plant biology and physiology from the perspective of small chemical molecules. The role of metabolomics has found its way in plant biotechnology, transgenic research, improved tolerance to stress, and plant breeding.

Arabidopsis thaliana (model plant). Credit: SINITAR/Shutterstock.com

Approaches for determining metabolomes in plants

Chromatography, high performance chromatography coupled with mass spectroscopy, nuclear magnetic resonance spectroscopy (NMR), near infrared resonance (NIR) Raman spectroscopy, and Fourier transformed infrared spectroscopy (FT-IR) are some of the metabolomic approaches used to determine plant metabolites.

A combination of capillary electrophoresis with mass spectroscopy (CE-MS) aids in the characterization of the amino acid profile in the cell culture of plants, demonstrates the metabolome in the orange leaves infected by bacteria, and in the metabolite profile identification in Illicium anisatum.
Metabolic fingerprinting procedure has been introduced in plant sciences using FT-IR.
Microscopy coupled with Raman spectroscopy has been found to be successful in identifying and quantifying phytochemicals and their distribution straight away from the tissues of plants.
NMR has been used to describe metabolites that are produced when maize plants are exposed to salt stress.
NMR approach has differentiated transgenic and non-transgenic Arabidopsis thaliana plants
NMR methods have proved to improve anticancer indole alkaloids production by overexpression of G10H and ORCA3 in Catharanthus roseus plants.
Gas chromatography coupled with mass spectrometry has shown a rise in the levels of monolignol analog and phenolic acids with more deconstruction in the facile cell wall of the organism Panicum virgatum. The same approach has shown increased drought tolerance in Solanum tuberosum (L) by Trehalose-6-phosphate synthase 1 expression.

Usage of liquid chromatography coupled with mass spectrometry methods (LC-MS) is on the increasing trend.

Plant species databases

To explain the function of genes in Arabidopsis (member of the family, Brassicaceae), the Plant metabolomics initiative was started. Metabolites recognized by LC-MS is contained in Metabolome Tomato Database. Terpmed has information about terpenoid plants.

It also contains data on other secondary metabolites and natural products that are essential in therapeutic drugs application. The Armec Repository Project has information about potato, Arabidopsis and on more species that are focused toward food crops.

Data about ions found in tomato are available in MotoDB and KOMICS. Resources such as MetaCyc have information on over 1,800 pathways that integrate with metabolite data from above 2,000 plant organisms.

KEGG PLANT of the KEGG Pathway database has data on secondary metabolites. Data from a variety of plant species such as wheat, rice, Arabidopsis, and pear are found to be present in MS2T. AraCyc, RiceCyc, Solanacea Genomics Network, HumanCyc, Mapman, Arabidopsis Reactome, PlantCyc, and KaPPA-View are other associated databases. These databases help to validate metabolome data and are available as a source of reference for metabolomic researches.

Metabolic pathway identification

To improve the health of human beings, food metabolite production is important. To achieve this objective, metabolomics help in identifying pathways. In fact, studies have already shown that modifying certain pathways can increase the nutritional value in plant production.

Metabolomic research on Golden Rice (GR) has addressed the global nutritional issue—deficiency of Vitamin A. In the endosperm of genetically altered rice, β-carotene (vitamin A) is accumulated. In GR2 rice variety, 84% of β-carotene is accumulated.

Patrick Moore, PhD Ecologist, Allow Golden Rice Now, Canada

Anthocyanins, which give color and antioxidant qualities to plants, are enhanced with plant engineering. These metabolites are helpful to protect against many diseases in humans; however, the natural anthocyanin levels in plants are not sufficient to give optimal benefits. Metabolomic research on tomato has shown anthocyanins accumulation in higher quantities; concentrations are matched with plants such as blueberries and blackberries, which have higher antocyanin levels.

The antioxidant capacity was enhanced to three times in the new purple color tomato variety. Also, when this new tomato variety was given as a diet supplement to mice, suspected with cancer, the life span of the mice also increased.

Another study has found that the transgenic tomato variety has shown a higher level of polyamines such as spermine and spermidine. This has led to a rise in lycopene (metabolite) at the onset of fruit ripening, which extends the vine life, improves the nutritional quality, and produces superior fruit juice. Studies have proved that with HP1/LeDDB1 gene mutation, flavanoids accumulation was higher in Solanum Lycopersicum, leading to higher nutritional value in the plant.

Role in crop yield

Plant metabolites play a role in providing color, scent, taste in flowers and fruits while involving in stress and resistance responses. Several metabolomic studies are focused to reduce yield loss when crops are exposed to biotic or abiotic stress or a combination of stresses.

Metabolomic studies on the floral organs of rice have found that drought and heat stress causes sugar starvation resulting in reproductive failure in the grain. Another study has found that phenylalanine and glutamine—the 2 amino acids, and 16 other fatty acids play a role in rice varieties that are resistant to gall midge.