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Flavonoids Metabolomics: Structure and Functions

Flavonoids, owing to their versatile functionalities, have emerged as prominent molecules in the realm of plant material research. In this article, our focus lies on elucidating the classification, synthesis pathways, and functional aspects pertinent to flavonoids.



I. Classification and Structural Characteristics of Flavonoids

metabolomics_Core_structure_of_FlavonoidsFlavonoids represent the most extensive category of polyphenolic compounds known to date, estimated to encompass over 8000 distinct flavonoid metabolites1. These compounds share a common structural framework characterized by a diphenylpropane A (C6-C3-C6) skeleton, wherein two aromatic rings are interconnected by a three-carbon chain (Figure 1). The A-ring is typically biosynthesized through the acetate pathway, stemming from either resorcinol or pyrogallol molecules and exhibiting distinct hydroxylation patterns at the C5 and C7 positions. In contrast, the B-ring originates from the more comprehensive cinnamic acid pathway and frequently bears hydroxylation at positions 3', 4' and 5'.

Flavonoids are mainly classified into chalcones, flavones, flavonols, flavanones, isoflavones, dihydroflavonols, flavanols, anthocyanins, flavonoid glycosides, and proanthocyanidins.



II. Biosynthesis Pathways of Flavonoids: An In-Depth Exploration

The biosynthetic journey of flavonoid compounds commences with phenylalanine, whereby phenylalanine ammonia-lyase (PAL), cinnamic acid 4-hydroxylase (C4H), and 4-coumaroyl CoA ligase (4CL), enzymes encoded by core phenylalanine-related biosynthetic genes, orchestrate the conversion of phenylalanine. This process serves as a pivotal precursor for the biosynthesis of major secondary metabolites within higher plants. Despite their remarkable diversity, the core biosynthetic pathway for flavonoids remains evolutionarily conserved.

Table 1. Structural genes in the flavonoid synthesis pathway




chalcone synthase


chalcone isomerase


flavone synthase


flavanone 3-hydroxylase


flavonol synthase


flavonoid 3′-hydroxylase


dihydroflavonol reductase


leucoanthocyanidin dioxygenase/anthocyanidin synthase




glutathione S-transferase


rhamnose synthase


Anthocyanidin reductase


Leucocyanidin reductase


Flavonoid compounds exhibit extensive variability across diverse taxa, exemplified by the synthesis of isoflavones in soybeans2, anthocyanins in Arabidopsis and alfalfa3, flavone-C-glycoside synthesis in kudzu4, and flavonoid biosynthesis in monocotyledonous maize5. Intriguingly, distinct accumulation patterns are discernible among different species and even within specific genotypes, tissues, and developmental stages.


III. Multifaceted Functions of Flavonoids in Plants

Flavonoids play multifaceted roles within extant plant systems.

1. They actively participate in pivotal growth and developmental processes. Notably, in Arabidopsis flavonoids exert influence over cell wall synthesis. The abrogation of flavonol synthesis ensures the unimpeded transport of quercetin to the cell wall6. Furthermore, flavonols intricately regulate root phototropism and root growth through intricate interactions with phytohormones such as auxins, cytokinins, and reactive oxygen species (ROS)7. Gibberellins, on the other hand, promote root growth by directly curtailing flavonol biosynthesis8. Additionally, in cabbage, the downregulation of flavonoid synthesis within the stigma promotes self-pollination9.


2. Flavonoids are pivotal in pigment formation, exemplified by the striking coloration of grape skins attributable to the accumulation of anthocyanins10.


3. Flavonoids contribute significantly to abiotic stress responses. For instance, the synthesis of quercetin glucosides heightens cold resistance in Arabidopsis11. In rice, the extent of flavonoid accumulation correlates directly with ultraviolet (UV) resistance12.


4. Flavonoids are integral components of biotic stress resistance mechanisms. Elevated levels of flavonoids in rice enhance resistance against brown planthoppers13, with hesperetin demonstrating enhanced effectiveness against bacterial pathogens and cyanidin exhibiting superior antifungal properties14. An augmentation in isoflavone content bolsters soybean leaf resistance to soybean mosaic virus15.


In summary, flavonoids occupy a prominent position within the sphere of plant research. At Metware lab in Boston, we offer Flavonoids Metabolomics service which can detect more than 3700 flavonoids in plant samples, contact us to speed up your research!


[1] Wen W, Alseekh S, Fernie AR. Conservation and diversification of flavonoid metabolism in the plant kingdom. Curr Opin Plant Biol. 2020 Jun;55:100-108. 

[2] Sukumaran A , Mcdowell T , Chen L , et al. Isoflavonoid‐specific prenyltransferase gene family in soybean: GmPT01, a pterocarpan 2‐dimethylallyltransferase involved in glyceollin biosynthesis[J]. The Plant Journal, 2018, 96(5).

[3] Jun J H , X Xiao, X Rao, et al. Proanthocyanidin subunit composition determined by functionally diverged dioxygenases[J]. Nature Plants, 2018.

[4] Xin W , Li C , Chen Z , et al. Molecular characterization of the C‐glucosylation for puerarin biosynthesis in Pueraria lobata[J]. The Plant Journal, 2017, 90(3).

[5] Xu G , Cao J , Wang X , et al. Evolutionary Metabolomics Identifies Substantial Metabolic Divergence between Maize and Its Wild Ancestor, Teosinte[J]. The Plant Cell, 2019, 31(9):tpc.00111.2019.

[6] Saffer A M , Irish V F . Flavonol rhamnosylation indirectly modifies the cell wall defects of RHAMNOSE BIOSYNTHESIS1 mutants by altering rhamnose flux[J]. Plant Journal, 2018.

[7] Tohge T , Fernie A R . Specialized Metabolites of the Flavonol Class Mediate Root Phototropism and Growth[J]. Molecular Plant, 2016, 9(012):1554-1555.

[8] Tan H , Man C , Xie Y , et al. A Crucial Role of GA-Regulated Flavonol Biosynthesis in Root Growth of Arabidopsis[J]. Molecular Plant, 2019.

[9] Lan X , Jia Y , Kumar A , et al. Flavonoids and ROS Play Opposing Roles in Mediating Pollination in Ornamental Kale ( Brassica oleracea var. acephala)[J]. Molecular Plant, 2017, 10(10):1361-1364.

[10] The role of VvMYBA2r and VvMYBA2w alleles of the MYBA2 locus in the regulation of anthocyanin biosynthesis for molecular breeding of grape (Vitis spp.) skin coloration[J]. Plant Biotechnology Journal, 2021.

[11] Li P , Li Y J , Zhang F J , et al. The Arabidopsis UDP‐glycosyltransferases UGT79B2 and UGT79B3, contribute to cold, salt and drought stress tolerance via modulating anthocyanin accumulation[J]. Plant Journal, 2017.

[12]  Peng M , Shahzad R , Gul A , et al. Differentially evolved glucosyltransferases determine natural variation of rice flavone accumulation and UV-tolerance[J]. Nature Communications, 2017.

[13] Dai Z , J Tan, Zhou C , et al. The OsmiR396–OsGRF8–OsF3H‐flavonoid pathway mediates resistance to the brown planthopper in rice (Oryza sativa).

[14] Natural variation in the expression and catalytic activity of a naringenin 7㎡﹎ethyltransferase influences antifungal defenses in diverse rice cultivars[J]. The Plant Journal, 2020, 101.

[15] Zhang, Peipei; Du, Hongyang; Wang, Jiao; Pu, Yixiang; Yang, Changyun; Yan, Rujuan; Yang, Hui; Cheng, Hao; Yu, Deyue (2019). Multiplex CRISPR/Cas9‐mediated metabolic engineering increases soybean isoflavone content and resistance to soybean mosaic virus. Plant Biotechnology Journal, (), pbi.13302–.


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