Characterization of the cis elements in the proximal promoter regions of the anthocyanin pathway genes reveals a common regulatory logic that governs pathway regulation.
Cellular activities such as compound synthesis often require the transcriptional activation of an entire pathway; however, the molecular mechanisms underlying pathway activation have rarely been explained. Here, the cis regulatory architecture of the anthocyanin pathway genes targeted by the transcription factor (TF) complex including MYB, bHLH, and WDR was systematically analysed in one species and the findings extended to others. In Ipomoea purpurea, the IpMYB1-IpbHLH2-IpWDR1 (IpMBW) complex was found to be orthologous to the PAP1-GL3-TTG1 (AtPGT) complex of Arabidopsis thaliana, and interacted with a 7-bp MYB-recognizing element (MRE) and a 6-bp bHLH-recognizing element (BRE) at the proximal promoter region of the pathway genes. There was little transcription of the gene in the absence of the MRE or BRE. The cis elements identified experimentally converged on two syntaxes, ANCNNCC for MREs and CACN(A/C/T)(G/T) for BREs, and our bioinformatic analysis showed that these were present within anthocyanin gene promoters in at least 35 species, including both gymnosperms and angiosperms. For the anthocyanin pathway, IpMBW and AtPGT recognized the interspecific promoters of both early and later genes. In A. thaliana, the seed-specific TF complex (TT2, TT8, and TTG1) may regulate all the anthocyanin pathway genes, in addition to the proanthocyanidin-specific BAN. When multiple TF complexes in the anthocyanin pathway were compared, the cis architecture played a role larger than the TF complex in determining the variation in promoter activity. Collectively, a cis logic common to the pathway gene promoters was found, and this logic is essential for the trans factors to regulate the pathway.
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China.
Zhixin
Z
Zhu
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China.
Hailong
H
Wang
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China.
Yiting
Y
Wang
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China.
Shan
S
Guan
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China.
Fang
F
Wang
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China.
Jingyu
J
Tang
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China.
Ruijuan
R
Zhang
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China.
Lulu
L
Xie
State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, 20 Nan Xin Cun, Beijing 100093, China University of Chinese Academy of Sciences, Beijing 100049, China yqlu@ibcas.ac.cn.
Yingqing
Y
Lu
D000704:Analysis of Variance; D000872:Anthocyanins / Q000235:genetics*; D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D051792:Basic Helix-Loop-Helix Proteins; D053898:Biosynthetic Pathways / Q000235:genetics*; D024202:Electrophoretic Mobility Shift Assay; D005419:Flavonoids / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D017343:Genes, Plant; D027741:Ipomoea / Q000235:genetics*; D008969:Molecular Sequence Data; D000073718:Pancreatitis-Associated Proteins; D011401:Promoter Regions, Genetic; D020218:Response Elements / Q000235:genetics; D013045:Species Specificity
D000872:Anthocyanins; D051792:Basic Helix-Loop-Helix Proteins; D005419:Flavonoids; D000073718:Pancreatitis-Associated Proteins; C000612141:REG3A protein, human
Anthocyanin pathway; Arabidopsis; Ipomoea; MBW complex; MYB; WDR.; bHLH; cis element; promoter activity; promoter architecture; regulatory module; trans factor; transcription initiation