Flavonoids Metabolomics in Arabidopsis Research

the_flowers_of_Arabidopsis_plantIn our previous blog, we offered an introductory exploration of flavonoid classification, synthesis pathways, and their functional roles. However, it's essential to recognize that the functions of flavonoids are more intricate than previously discussed. In the forthcoming sections, we will meticulously delve into the extensive research on flavonoids across various species. This issue, our primary focus centers on the in-depth examination of the model plant, Arabidopsis thaliana.


Advancements in Flavonoid Biosynthesis Regulatory Gene Research in Arabidopsis

Arabidopsis thaliana stands as one of the most well-established model plants for molecular biology studies pertaining to flavonoid metabolism (Debeaujon et al., 2003; Pourcel et al., 2005; Yonekura-Sakakibara et al., 2008; Nakabayashi et al., 2009; Stracke et al., 2010; Saito et al., 2013). Genes associated with the biosynthesis of flavonoid skeletons have been comprehensively characterized in this species. A multitude of genes responsible for flavonoid modifications, encompassing eight glycosyltransferases, four acyltransferases, and one methyltransferase, have been meticulously isolated (Saito et al., 2013). Additionally, various transcription factors, including those governing flavonol (PFG1/MYB11, PFG2/MYB12, and PFG3/MYB111), anthocyanin (PAP1/MYB75, PAP2/MYB90, MYB113, and MYB114), and proanthocyanidin (TT2/MYB123) biosynthesis, along with other transcription factors such as bHLH and WD, have been well-defined (Koes et al., 2005; Dubus et al., 2010).





Functional mechanisms




Binds to bHLH and affects MBW activity; Inhibits expression of ADT6 (Arogenate Dehydratase 6, the final step in phenylalanine synthesis);

Wang XC., et al., 2020


Binds to bHLH and affects MBW activity


Binds to bHLH and affects MBW activity

CPC (Single-repeat R3 MYB)

Inhibits anthocyanin synthesis, competing with PAP1/2 (R2R3-MYB transcription factor that activates expression of anthocyanin synthesis genes) Promotes flavonol synthesis

Zhu H F., et al., 2009


Promotion of flavonol synthesis


(bHLH) basic helix-loop-helix





Significantly enhanced transcriptional activation of R2R3MYBs bound by the bHLH protein TT8; negatively regulates hormone transport;

Li S., Zachgo S., 2013

WD-repeat proteins






Directly chelate MYBL2 and JAZ deterrents, leading to the release of bHLH/MYB subunits and subsequent formation of ac                    

Xie Y., et al., 2016



Involved in glycosidic transfer processes such as the synthesis of cornflowerin into cornflowerin 3-O-glucoside;        Li P., et al., 2017


Exploring the Functions of Flavonoids in Arabidopsis

Numerous studies have delved into how flavonoid biosynthesis plays a pivotal role in various life processes within Arabidopsis. For example, the identification of UVR8 (UV RESISTANCE LOCUS 8) as the primary UV-B light receptor (Rizzini et al., 2011) has significantly enriched our comprehension of how plants respond to UV-B radiation. Further research has unveiled that quercetin and kaempferol glycosides accumulate in response to UV-B exposure, facilitating the maintenance of normal growth under moderate UV-B conditions. Additionally, in the face of cold stress, Arabidopsis regulates the accumulation of anthocyanins to bolster cold resistance. It is imperative to recognize that the same flavonoid substances may have distinct regulatory mechanisms under varying environmental conditions.


Existing research underscores that flavonols, which represent the most abundant subgroup of flavonoids, play a pivotal role in diverse life processes. Their functional mechanisms can be succinctly summarized into three primary aspects: shielding plants from damage to the photosynthetic electron transport chain, safeguarding DNA from harm, and acting as substrates for peroxidases in vacuoles to scavenge H2O2 that diffuses from chloroplasts. This, in turn, establishes them as crucial buffering agents for regulating H2O2 levels within plant cells. Therefore, when analyzing flavonoid outcomes, it is prudent to accord priority to flavonols, considering their multifaceted functions in deciphering the plant's response mechanisms.


Field of Research

Related Flavonoids

Functional mechanisms



p-coumaroylagmatine; kaempferol 3-O-glucoside 7-O-rhamnoside; kaempferol 3-O-[2''-O-(glucosyl) rhamnoside] 7-O-rhamnoside; quercetin 3-O-rhamnoside 7-O-rhamnoside; quercetin 3-O-glucoside 7-O-Rhamnoside;


Kusano M., et al., 2011

Fasano R., et al., 2014


quercetin; kaempferol glycosides;


Ballaré CL., 2012; 

Emiliani J., et al., 2013

Dwarf Plant

kaempferol 3-O-rhamno-side-7-O-rhamnoside

Negative regulation of IAA transport

Yin R., et al., 2013


Quercetin 3-O-glucoside (Q3G); cyanidin 3-O-glucoside (C3G);

Scavenging H2O2; Preventing water loss;

Nakabayashi R., et al., 2014


quercetins, scopolin


Petridis A., et al., 2016


quercetin; Moracin M; Formononetin; Eriodictyol; Medicagol; Erythrinin A; 5-Hydroxy-6'', 6''-dimethylpyranoflavone; Alpinumisoflavone; Psoralidin; Lupinalbin H; Semilicoisoflavone B; Sigmoidin H; Eriodictin; Phlorizin; Orotinichalcone; Erythbigenone A; Epigallocatechin 3-(4-methyl-gallate); 6-Methoxyluteolin 7-glucuronide; 6''-O-Malonyldaidzin; Formononetin 7-(6''-malonylglucoside); 6''-Malonylgenistin; 5,2'-Dihydroxy-7,8,6'-trimethoxyflavone 2'-glucuronide; Biochanin A 7-(6-malonylglucoside); 6''-O-Malonylglycitin; 2'-Hydroxygenistein 7-(6''-malonylglucoside); Procyanidin; Poncirin; Kaempferol 3-rhamnoside 7-galacturonide; Pinocembrin 7-O-neohesperidoside 6''-O-acetate; Myricetin 3-sambubioside; Prunin 4'',6''-di-O-gallate


Bian X., et al., 2020


In this blog, we have provided a concise overview of the functions of flavonoids and the associated regulatory genes within Arabidopsis thaliana. Our next installment will delve into the extensive body of research on flavonoids in crop plants.



Wang, Xiao‐Chen, Wu J , Guan, Meng‐Ling, et al. Arabidopsis MYB4 plays dual roles in flavonoid biosynthesis[J]. The Plant Journal, 2020.

Zhu H F , Fitzsimmons K , Khandelwal A , et al. CPC, a Single-Repeat R3 MYB, Is a Negative Regulator of Anthocyanin Biosynthesis in Arabidopsis[J]. Molecular Plant, 2009, 2(004):790-802.

Li S , Zachgo S . TCP3 interacts with R2R3-MYB proteins, promotes flavonoid biosynthesis and negatively regulates the auxin response in Arabidopsis thaliana.[J]. Plant Journal, 2013, 76(6):901-913.

Ye, Xie, Huijuan, et al. DELLA Proteins Promote Anthocyanin Biosynthesis via Sequestering MYBL2 and JAZ Suppressors of the MYB/bHLH/WD40 Complex in Arabidopsis thaliana.[J]. Molecular Plant, 2016.

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.

Kusano M , Tohge T , Fukushima A , et al. Metabolomics reveals comprehensive reprogramming involving two independent metabolic responses of Arabidopsis to UV-B light[J]. The Plant Journal, 2011, 67(2):354-369.

Fasano R , Gonzalez N , Tosco A , et al. Role of Arabidopsis UV RESISTANCE LOCUS 8 in Plant Growth Reduction under Osmotic Stress and Low Levels of UV-B[J]. Molecular Plant, 2014(5):773-791.

CL Ballaré. UVR8 Mediates UV-B-Induced Arabidopsis Defense Responses against Botrytis cinerea by Controlling Sinapate Accumulation[J]. Molecular Plant, 2012, 5(3):642-652.

Emiliani J , Grotewold E , Ferreyra M , et al. Flavonols Protect Arabidopsis Plants against UV-B Deleterious Effects[J]. Molecular Plant, 2013, 6(004):1376-1379.

Yin R , Han K , Heller W , et al. Kaempferol 3-O-rhamnoside-7-O-rhamnoside is an endogenous flavonol inhibitor of polar auxin transport in Arabidopsis shoots[J]. New Phytologist, 2013, 201(2).

Nakabayashi R , Yonekura-Sakakibara K , Urano K , et al. Enhancement of oxidative and drought tolerance in Arabidopsis by overaccumulation of antioxidant flavonoids[J]. Plant Journal, 2014, 77(3):367-379.

Petridis A , Dll S , Nichelmann L , et al. Arabidopsis thaliana G2㎜IKE FLAVONOID REGULATOR and BRASSINOSTEROID ENHANCED EXPRESSION1 are low‐temperature regulators of flavonoid accumulation[J]. New Phytologist, 2016, 211.

Bian X , Li W , Niu C , et al. A class B heat shock factor selected for during soybean domestication contributes to salt tolerance by promoting flavonoid biosynthesis[J]. New Phytologist, 2020.



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