#FlavonoidFriday

This repository provides additional background to the #FlavonoidFriday posts. #FlavonoidFriday is maintained by the PuckerLab.

Introduction

The flavonoid biosnythesis is one of the best studied specialized metabolism pathways in plants. Flavonoids are produced by almost all land plants, but specific branches of this pathway are not present in all species. Flavonol biosynthesis, flavone biosynthesis, anthocyanin biosnythesis, and proanthocyanidin biosynthesis are some branches of the flavonoid biosynthesis. Products of these branches have different functions and the enzymes might compete for substrate when branches are active at the same time. Therefore, the gene expression of all players in this pathway is tightly regulated by a number of transcription factors (see Transcriptional Regulation). Fig. 1 provides a simplified overview of the flavonoid biosynthesis (Pucker et al., 2020, Grünig et al., 2025).

Fig. 1: Simplified overview of the flavonoid biosynthesis. Source: Grünig et al., 2025.

Flavonoids are transported from the site of biosynthesis (ER) into the central vacuole. Two potential flavonoid transport routes have been proposed: (1) transport across the tonoplast mediated by membrane-bound transport proteins and (2) vesicle-mediated transport with or without an involvement of the Golgi apparatus (Fig. 2, Pucker & Selmar, 2022, Grünig et al., 2025).

Fig. 2: Simplified overview of the intracellular flavonoid transport. Source: Pucker & Selmar, 2022.

Transcriptional Regulation

The sophisticated regulatory network of the flavonoid biosnythesis contains members of numerous transcription factor families. Among the important families are MYBs, bHLHs, WD40s, NACs, and WRKYs. Some MYBs, bHLHs, and WD40s form a complex which is called MBW. More information about the MYBs is available through the MybMonday.

Mutual Exclusion of Anthocyanins and Betalains

While the flavonoid biosynthesis is present in (almost) all land plants, certain branches are not. One famemous example is the mutual exclusion of anthocyanins and betalains in the Caryophyllales. The yellow to red betalains are tyrosine-derived pigment group which replaced anthocyanins in several families of the Caryophyllales. Both pigments have never reported together in the same tissue and the same species. Please see Timoneda et al., 2019 for a recent review of the complex pigment evolution in the Caryophyllales. Our latest publication on the topic explains why there are no anthocyanins in the betalain-pigmented Caryophyllales: Pucker et al., 2024.

Automatic annotation of the flavonoid biosynthesis

Do you have a new transcriptome and genome assembly of a plant species? If you are interested in studying the flavonoid biosynthesis, KIPEs (Pucker et al., 2020) could be helpful. KIPEs produces an annotation of the flavonoid biosynthesis players based on knowledge about the flavonoid biosynthesis in other species (Fig. 3). A table of the involved genes and phylogenetic trees of all players in the pathways can serve as basis to investigate the flavonoid biosynthesis in a new species. KIPEs is freely available for download via github. Additionally, we operate a web server for convenient use: KIPEs web server. The latest version also enables the annotation of the carotenoid biosynthesis: Rempel et al., 2023.

Fig. 3: KIPEs workflow. Source: Rempel et al., 2023.

Anthocyanin loss - a frequent event during evolution

Accessions of many plant species lack anthocyanin pigmentation. This is often visible when flowers of individual plants appear white instead of red or blue. These evolutionary color changes are not randomly affecting genes in the anthocyanin biosynthesis, but are mostly affecting transcription factors. The most frequently affected transcription factor in the anthocyanin activating R2R3-MYB. Read more about this topic in a systematic assessment of available studies: Recinos & Pucker, 2024.

Fig. 4: Phylogenetic distribution of anthocyanin loss events. Source: Marin-Recinos & Pucker, 2024.

Recommended reviews about the flavonoid biosynthesis

There are several excellent resources to get an overview of the flavonoid biosynthesis. This is an incomplete list:

Winkel-Shirley, 2001: Flavonoid Biosynthesis. A Colorful Model for Genetics, Biochemistry, Cell Biology, and Biotechnology. doi:10.1104/pp.126.2.485

Grotewold, 2006: The Science of Flavonoids. Book published by Springer

Tohge et al., 2017: Current understanding of the pathways of flavonoid biosynthesis in model and crop plants. doi:10.1093/jxb/erx177

Davies et al., 2024: The evolution of flavonoid biosynthesis. doi: 10.1098/rstb.2023.0361.

Grünig et al., 2025: Diversity and Ecological Functions of Anthocyanins. doi: 10.1186/s12870-025-08006-3.

Social media posts with addtional background

(1) General Flavonoid Biosynthesis Overview

Post: Flavonoids are a large group of phenylalanine-derived specialized metabolites in plants. Branches of the biosynthesis lead to flavonols, anthocyanins, proanthocyanins, flavones, and others. #FlavonoidFriday

<img alt="Flavonoid biosynthesis pathway overview (Tweet #1)" src="https://pbs.twimg.com/media/Eu4yOCfWYAIMKxJ?format=jpg&name=4096x4096" width="400"> (Figure source: [Pucker et al., 2020](https://doi.org/10.3390/plants9091103))

The background about this tweet is described above in the general introduction to the flavonoid biosynthesis.

(2) Flavonol biosynthesis is an old branch of the flavonoid biosynthesis

Post: Flavonols are an evolutionary old group of flavonoids. Their functions include UV & ROS protection, but also signaling & regulation of developmental processes. Flavonol production is triggered by biotic and abiotic factors #FlavonoidFriday

(3) Anthocyanins are colourful pigments

Post: Anthocyanins (Greek: 'blue flower') are pigments with pH-dependent colours ranging from red to blue. Their functions include attraction of animals for pollination & seed dispersal, but also protection against abiotic stressors. #FlavonoidFriday

While anthocyanins are well known for their colour, it is likely that additional functions in stress response might be even more important (reviewed by Landi et al., 2015).

(4) Proanthocyanidins are responsible for seed coat colouration

Post: Proanthocyanidins (PA) are responsible for a dark appearance of seed coats. The biosynthesis of PAs is not completely understood and probably differs between species #FlavonoidFriday

LAR and ANR are involved in the PA biosynthesis in many species. However, A. thaliana lacks LAR, but is still able to produce proanthocyanidins which provide a dark colouration to the seed coat. This indicates that there must be a PA biosynthesis pathway which does not require LAR.

(5) Dietary Flavonoids

Post: Flavonoids are abundant phytochemicals in fruits and vegetables. Health and nutritional benefits were reported for several flavonoids including antioxidant and anti-inflammatory functions #FlavonoidFriday

<img alt="Dietary Flavonoids (Tweet #5)" src="https://pbs.twimg.com/media/ExYtlWkWEAEworj?format=jpg&name=4096x4096" width="400"> (Figure source: [Ahn-Jarvis et al., 2019](https://doi.org/10.3390/antiox8070202))

Flavonoids are not just responsible for beautiful flower phenotypes. These molecules can also be beneficial for human health. Flavonoids in the human diet and the potential for biomedical/biotechnological applications in the future were recently reviewed by Ahn-Jarvis et al.. They discus the releveance of increasing the bioavailability of flavonoids through agricultural engineering and tar

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