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Plant Primary and Secondary Metabolites

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Plant primary metabolism provides energy and some small molecule compound raw materials for secondary metabolism through photosynthesis, citric acid cycle, etc. Secondary metabolism also has an impact on primary metabolism. Primary metabolism occurs throughout the life of the plant, and secondary metabolism tends to occur at a certain stage in the life process.

Primary and secondary metabolism in plantsFig 1. Primary and secondary metabolism in plants (Sinha et al., 2019).

Primary metabolism

Primary metabolism is a metabolic process that involves the synthesis of substances essential for life activities in plants, the products of which mainly include organic substances such as proteins, fats, sugars and nucleic acids. The products of primary metabolism are the plant morphological building blocks that we can see (roots, stems, leaves, flowers, fruits, seeds).

Primary metabolism is directly related to plant growth, development and reproduction, providing energy and intermediate products for plant survival, growth, development and reproduction. Green plants and algae synthesize carbon dioxide and water into sugars through photosynthesis, and further produce ATP, NADH, endoneic acid, phosphoenolpyruvate, 4-phosphate─erythrose, ribose and other substances indispensable for maintaining the vital activities of plant muscles through different pathways. Phosphoenolpyruvate and 4-phosphate─erythrose can further synthesize mangiferous acid (the starting material of plant secondary metabolism). And the endo-keto acid is hydrogenated and decarboxylated to produce acetyl coenzyme A (the starting material of plant secondary metabolism), and then enters the citric acid cycle to produce a series of organic acids and malonic acid monoacyl coenzyme A, etc., and through the nitrogen fixation reaction to obtain a series of amino acids (the substrate for the synthesis of nitrogenous compounds), these processes are primary metabolic processes.

Secondary metabolism

Secondary metabolism is a metabolic process influenced by the interaction between the plant and the environment, and its products are substances produced by further reactions of primary metabolites. The products of secondary metabolism, such as endogenous plant hormones like growth hormone and gibberellin, participate in the regulation of life activities, terpenoids like carotenoids participate in the photosynthesis process as photosynthetic pigments, and chemosensory substances like alkaloids, phenolic derivatives, flavonoids, organic acids, terpenoids and steroids participate in the defense process while forming the quality and flavor of fruits. The secondary metabolites accumulated in plants are the products of long-term struggle against various adversities.

Metabolomics analysis of plant primary and secondary metabolites

A cell usually relies on many metabolic regulatory pathways. Moreover, multiple metabolic pathways undergo various changes at all times, generating a variety of secondary metabolites. The research and application of metabolomics meet the need for simultaneous studies of multiple metabolic pathways.

Metabolomics is the science of the types and amounts of endogenous metabolites in biological systems and their variation patterns. It is the study of endogenous metabolites and their influence by intrinsic or extrinsic factors in the whole life, system or organ, with the goal of elucidating the overall metabolic network of plants and its regulatory mechanisms.

The study of plant metabolomics does not aim to isolate and identify a single component in plants, but to study all secondary metabolites in plants systematically and comprehensively from a holistic perspective, and to study the spatial and temporal relationships.

Plant metabolomics research techniques include instrumental analysis and data analysis. In plant metabolomics studies, multiple techniques are often applied in combination to obtain more information about metabolites, including GC-MS, LC-MS, NMR and so on. It is necessary to analyze and mine the acquired large amount of multidimensional information to obtain potential information. The analysis of the data requires a chemometric approach, mainly by mathematical algorithms to designate and group peaks. The analysis of the whole process is non-discriminatory and allows to identify any substance, either endogenous or exogenous, that causes differences in grouping, such as principal component analysis and neural networks.


  1. Sinha, S., Sandhu, K., Bisht, N., Naliwal, T., Saini, I., & Kaushik, P. (2019). Ascertaining the paradigm of secondary metabolism enhancement through gene level modification in therapeutic plants. Journal of Young Pharmacists, 11(4), 337.

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