Plant Secondary Metabolism


Plants synthesise an extraordinary array of natural products that usually do not play a role in their growth and development, and thus are traditionally referred to as secondary metabolites. However, recent advances in plant sciences have revealed that these compounds not only function in response to environmental stimuli, but also play more basic roles in plant growth. Secondary metabolites have several important roles in plants: they protect against herbivores and microbial infection and act as signals for symbiotic bacteria and mycorrhiza, attractants for pollinators and seed‚Äźdispersing animals, allelopathic agents in natural habitats, physical and chemical barriers to abiotic stressors such as UV and evaporation and endogenous regulators of plant growth hormones. Many secondary metabolites are also useful for mankind as dyes, essential oils, flavouring agents, pesticides, pharmaceuticals, tanning agents and so on. Rapid advances in the metabolic engineering and synthetic biology of secondary metabolites have revealed novel physiological roles of these secondary metabolites in plants.

Key Concepts:

  • Plants synthesise a vast array of natural products (secondary metabolites) in response to environmental stimuli.

  • Secondary metabolites have several important roles: they protect against herbivores and microbial infection and act as attractants for pollinators and seed‚Äźdispersing animals, allelopathic agents in natural environments and endogeneous regulators of plant growth.

  • Secondary metabolites are synthesised from primary metabolites such as acetate, pyruvate, and amino acids, and are mainly classified into three major groups; the terpenoids, the phenolics (mainly phenylpropanoids) and alkaloids.

Keywords: secondary metabolites; natural products; biosynthesis; accumulation; taxonomy; raison d'etre; metabolic engineering; environmental response

Figure 1.

Some terpenoid compounds from plants.

Figure 2.

Biosynthesis of isopentenyl pyrophosphate and dimethylallyl pyrophosphate; the biological equivalents of ‘isoprene’.

Figure 3.

The cinnamyl alcohols: precursors of lignins.

Figure 4.

Some simple plant phenolics derived from the ‘hydroxycinnamate pool’. Glc, glucose.

Figure 5.

Tetrahydrocannabinol is synthesised from two building units.

Figure 6.

Plant phenolics derived from ‘acetate’ and ‘hydroxycinnamate pool’ precursors. Glc, glucose.

Figure 7.

Some plant alkaloids; biosynthetic origins shown in parentheses.

Figure 8.

Miscellaneous classes of plant secondary metabolites – polyacetylenes, polyenes, cyanogenic glycosides, glucosinolates, nonprotein amino acids – and their biosynthetic precursors. Glc, glucose.

Figure 9.

Taxol biosynthesis: the role of oxygenation reactions (broken arrows). Ac, acetyl; Bz, benzoyl; Ph, phenyl.

Figure 10.

Plant secondary metabolites that act as hormones and signalling agents.

Figure 11.

Plant secondary metabolites in defence and allelopathy.



Arimura G, Matsui K and Takabayashi J (2009) Chemical and molecular ecology of herbivore induced plant volatiles: proximate factors and their ultimate functions. Plant and Cell Physiology 50: 911–923.

Bartwal A, Mall R, Lohani P, Guru SK and Arora S (2013) Role of secondary metabolites and brassinosteroids in plant defense against environmental stresses. Journal of Plant Growth Regulation 32: 216–232.

Butelli E, Titta L, Giorgio M et al. (2008) Enrichment of tomato fruit with health‐promoting anthocyanins by expression of select transcription factors. Nature Biotechnology 26: 1301–1308.

Chu HY, Wegel E and Osbourn A (2011) From hormones to secondary metabolism: the emergence of metabolic gene clusters in plants. Plant Journal 66: 66–79.

Croteau R, Kutchan TM and Lewis NG (2000) Natural products (secondary metabolites). In: Buchanan BB, Gruissem W and Jones RL (eds) Biochemistry & Molecular Biology of Plants, pp. 1250–1318. Rockville, MD, USA: American Society of Plant Biologists.

DeLuca V, Salim V, Atsumi SM and Yu F (2012) Mining the biodiversity of plants: a revolution in the making. Science 336: 1658–1661.

Fraenkel G (1959) The raison d'être of secondary plant substances. Science 129: 1466–1470.

Hagel JM and Facchini PJ (2013) Benzylisoquinoline alkaloid metabolism: a century of discovery and a brave new world. Plant and Cell Physiology 54: 647–672.

Hagimori M, Matsumoto T and Obi Y (1982) Studies on the production of Digitalis cardenolides by plant tissue culture: II. effect of light and plant growth substances on digitoxin formation by undifferentiated cells and shoot‐forming cultures of Digitalis purpurea l. grown in liquid media. Plant Physiology 69: 653–656.

Hartmann T (2007) From waste products to ecochemicals: fifty years research of plant secondary metabolism. Phytochemistry 68: 2831–2846.

Hashimoto T, Hayashi A, Amano Y et al. (1991) Hyoscyamine 6 beta‐hydroxylase, an enzyme involved in tropane alkaloid biosynthesis, is localized at the pericycle of the root. Journal of Biological Chemistry 266: 4648–4653.

Itkin M, Heining U, Tzfadia O et al. (2013) Biosynthesis of antinutritional alkaloids in Solanaceous crops is mediated by clustered genes. Science 341: 175–179.

Jenke‐Kodama H, Sandmann A, Müller R and Dittmann E (2005) Evolutionary implications of bacterial polyketidesynthases. Molecular Biology and Evolution 22(10): 2027–2039.

Jørgensen K, Rasmussen AV, Morant M et al. (2005) Metabolon formation and metabolic channeling in the biosynthesis of plant natural products. Current Opinion in Plant Biology 8(3): 280–291.

Katsumoto Y, Fukuchi‐Mizutani M, Fukui Y et al. (2007) Engineering of the rose flavonoid biosynthetic pathway successfully generated blue‐hued flowers accumulating delphinidin. Plant and Cell Physiology 48: 1589–1600.

Kim Y‐S, Uefuji H, Ogita S and Sano H (2006) Transgenic tobacco plants producing caffeine: a potential new strategy for insect pest control. Transgenic Research 15: 667–672.

Liscombe DK, Louie GV and Noel JP (2012) Architectures, mechanisms and molecular evolution of natural product methyltransferases. Natural Product Reports 29: 1238–1250.

Matsuba Y, Nguyen TTH, Wiegert K et al. (2013) Evolution of a complex locus for terpene biosynthesis in Solanum. Plant Cell 25: 2022–2036.

Minami H, Kim J‐S, Ikezawa N et al. (2008) Microbial production of plant benzylisoquinoline alkaloids. Proceedings of the National Academy of Sciences of the USA 105: 7393–7398.

Mizutani M and Sato F (2011) Unusual P450 reactions in plant secondary metabolism. Archives of Biochemistry and Biophysics 507(1): 194–203.

Nielsen KA and Møller BL (2005) Cytochrome P450s in plants. In: Ortiz de Montellano P (ed.) Cytochrome P450: Structure, Mechanism, and Biochemistry, pp. 553–583. New York, NY: Springer.

Ro DK, Paradise EM, Ouellet M et al. (2006) Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440(7086): 940–943.

Sato F, Hashimoto T, Hachiya A et al. (2001) Metabolic engineering of plant alkaloid biosynthesis. Proceedings of the National Academy of Sciences of the USA 98(1): 367–372.

Sato F and Matsui K (2011) Engineering the biosynthesis of low molecular weight metabolites for quality traits (essential nutrients, health‐promoting phytochemicals, volatiles, and aroma compounds). In: Altman A and Hasegawa PM (eds) Plant Biotechnology and Agriculture, pp. 443–462. Oxford: Academic Press.

Sato F and Yamada Y (2008) Engineering formation of medicinal compounds in cell cultures. In: Bohnert HJ, Nguyen H and Lewis NG (eds) Advances in Plant Biochemistry and Molecular Biology: Vol. 1, pp. 311–345. Amsterdam: Elsevier.

Stahl E (1888) Pflanzen und Schnecken. Biologische Studie uber die Schutzmittel der Pflanzen gegen Schneckenfraas. Jenaische Zeitschrift fuer Naturwissenschaften und Medizin 22: 557–684.

Tanaka Y, Sasaki N and Ohmiya A (2008) Biosynthesis of plant pigments: anthocyanins, betalains and carotenoids. Plant Journal 54: 733–749.

Taylor LP and Grotewold E (2005) Flavonoids as developmental regulators. Current Opinion in Plant Biology 8: 317–323.

Waterman PG (1992) Roles for secondary metabolites in plants. In: Davies J (ed.) Secondary Metabolites: Their Evolution and Function. Ciba Foundation Symposium 171, pp. 255–275. Chichester: Ciba Foundation, Wiley.

Weng J‐K, Philippe RN and Noel JP (2012) The rise of chemodiversity in plants. Science 336: 1667–1670.

Winkel BSJ (2004) Metabolic channeling in plants. Annual Review of Plant Biology 55: 85–107.

Winzer T, Gazda V, He Z et al. (2012) A Papaver somniferum 10‐gene cluster for synthesis of the anticancer alkaloid noscapine. Science 336: 1704–1708.

Yamada Y and Sato F (2013) Transcription factors in alkaloid biosynthesis. International Review of Cell and Molecular Biology 305: 339–382.

Further Reading

Altman A and Hasegawa PM (eds) (2011) Plant Biotechnology and Agriculture: Prospects for the 21st Century. Oxford: Academic Press.

Chandra S, Lata H and Varma A (eds) (2013) Biotechnology for Medicinal Plants: Micropropagation and Improvement. Heidelberg: Springer‐Verlag.

Giglioli‐Guivarc'h N (ed.) (2013) Advances in Botanical Research. Vol. 68. New Light on Alkaloid Biosynthesis and Future Prospects. London: Academic Press.

Harborne JB (1993) Introduction to Ecological Biochemistry, 4th edn. London: Academic Press.

Haslam E (1994/1995) Secondary metabolism – evolution and function: products or processes? Chemoecology 5/6: 89–95.

Luckner M (1990) Secondary Metabolism in Micro‐organisms, Plants and Animals. Berlin: Springer‐Verlag.

Mann J (1992) Murder, Magic and Medicine. Oxford: Oxford University Press.

Ramawat KG and Merillon JM (eds) (2013) Handbook of Natural Products. Berlin: Springer‐Verlag.

Verpoorte R, Alfermann AW and Johnson TS (eds) (2007) Applications of Plant Metabolic Engineering. Dordrecht: Springer‐Verlag.

Wink M (ed.) (2010) Biochemistry of Plant Secondary Metabolism, Annual Plant Reviews 2nd edn, vol. 40. Oxford: Wiley‐Blackwell.

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Sato, Fumihiko(Aug 2014) Plant Secondary Metabolism. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0001812.pub2]