Secondary metabolites – an overview

Have you ever heard of plant-based ingredients? They are often found in the cosmetic, food, and pharmaceutical industries. Essentially, these plant-based components are compounds synthesized by plants that fulfill many purposes. They are known as 'secondary metabolites' in plant science and are produced not just by plants, but also by bacteria and fungi. They have important implications in the production of plant-based cosmetics, drugs, and horticultural/agricultural industries.

In this article, we will describe what secondary metabolites are, their uses, and their relation to plant tissue culture!

What is a secondary metabolite?

Plants produce hundreds of thousands of low molecular weight organic compounds that are divided into three groups based on their role in the plant’s metabolic processes:

  1. Primary metabolites, which are essential for plant growth and development;
  2. Hormones, which regulate metabolism; and
  3. Secondary metabolites.

Secondary metabolites (SMs) are compounds produced by plants through subsidiary pathways that are not directly involved in basic plant life functions. This means that they are not essential for the plant. However, they mediate plant-environment interactions and might be crucial for its survival and reproduction. Secondary metabolites are often species-specific and exert a wide range of effects on the plant itself and other living organisms.

Their functionality was first related to their effect on human health and many years later, they became the focus of plant science for commercial and academic research purposes. At present, secondary metabolites are a constant in our lives. As an example, we have caffeine, a plant secondary metabolite found in coffee, tea, or chocolate, which not only helps us start the day on the right foot but is also a therapeutic tool against degenerative diseases!

Why do plants produce them?

It was over a thousand years ago when we, humans, first started using plants as a source of medicine. At that time, we did not even know what a metabolite was and they were just considered as “accessory” products that happen to serve us. However, as interest in them expanded, two questions arose: why do plants produce them? And how do they produce them?

First, plants, unlike animals, are sessile organisms that cannot move when facing biotic or abiotic stress. Therefore, they need to adapt to survive, and secondary metabolites were the response. These chemicals, although being generated in little quantities at a significant energy cost, govern the plant's defensive system. They are also in charge of the plant’s response to changing environmental circumstances.

To produce them, plants use by-products or intermediates of primary metabolism as the basis of most of the secondary metabolites. They tend to be synthesized in specialized cell types, in selected plant life stages. The different reactions and pathways that plants use to produce SMs are called the plant secondary metabolism. This metabolism is only activated under certain periods and conditions, with stress signals being the ones that trigger it.

Diversity of plant secondary metabolites

A single plant can produce hundreds of secondary metabolites under appropriate conditions and stimulation. Each secondary metabolite differs from the others in its chemical structure and bioactivity. The main classes of secondary metabolites are:

  1. Phenolics such as salicylic acid (used in the cosmetic industry) and flavonoids (known as pigments);
  2. Alkaloids such as nicotine (from tobacco plants), morphine (from poppy straw); and
  3. Terpenes such as menthol and limonene.

Plant secondary metabolites are numerous and diverse. If we look at the examples, they are compounds that are part of different products that we use in our daily life, and each of them is used for different purposes.


It is estimated that the plant kingdom produces over 200,000 different secondary metabolites.

Commercial and ecological implications

In nature, there are still more secondary metabolites to identify with functions that are still unknown.  So, the search for new SMs in plants comes with the hope of discovering new products and formulations. Secondary metabolites are high-value chemicals with several uses that are important for both ecology and economy.

In natural systems, secondary metabolites make plants competitive in their own environment. The ecological implications and functions of SMs are:

  1. Induce flowering, fruit set, and abscission;
  2. Maintain perennial growth;
  3. Signal deciduous behavior;
  4. Attracting or repelling other organisms;
  5. Defense against herbivores, fungi, bacteria, viruses, and other plants;
  6. Signaling to attract pollinating and seed dispersing animals;
  7. Stimulation in processes like symbiosis and nutrient sequestration;
  8. Protection from UV light, evaporation, temperature extremes, drought; and
  9. Plant to plant communication.

Aside from their ecological role, secondary metabolites have a wide range of potential applications in different industries. They can be used as:

  1. Pigments, dyes, flavors, and fragrances in food and cosmetic industries;
  2. Ingredients in food supplements and nutraceuticals;
  3. Antioxidant agents;
  4. Anti-inflammatory, antihypertensive, anticancer, antidepressant, and neuroprotective agents in pharmaceutical formulations; 
  5. Anthelmintic and antimicrobial agents in the veterinary field;
  6. Tanning agents in the leather industry;
  7. Psychotropic and toxicological drugs; and
  8. Chemo-preventive, antifungal, antiviral, analgesic, biopesticide, and antiparasitic agents in agriculture.

In other words, secondary metabolites are crucial for pharmaceutical, food, cosmetic, perfumery, and agricultural industries. Therefore, we can consider plants as bio factories that provide us with many ingredients!

Plant tissue culture in the production of secondary metabolites

Secondary metabolites have been gaining popularity for over three decades. Due to their applications in different industries, there is an intense growing demand. Even more so now with the trend towards eco-friendly, greener, natural, and organic products. However, SMs are produced in small quantities, have structural complexity, and are quite difficult and expensive to extract from the plant.

How do we meet the rising demand for these plant-based ingredients? Plant cell and tissue culture has been the answer. From the manipulation of culture conditions to the use of stress signaling chemicals, there are now different techniques available to stimulate and enhance the production of secondary metabolites within the plant.  

If you want to know more about this and other interesting plant science topics, stay tuned to our news!

By Valeria Franco Franklin | 8-March-2022

About the author

Valeria Franco is from Colombia, the land of orchids. She is a focused and passionate biologist who specializes in biotechnology and molecular biology. Valeria has prior laboratory and research experience. She is presently employed as a content creator at Lab Associates and is always looking for new challenges. Valeria is enthusiastic about plant science themes and reading as a tool for lifelong learning. Her hobbies include studying foreign languages, traveling, and archery.


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