Characterization of the cis elements in the proximal promoter regions of the anthocyanin pathway genes reveals a common regulatory logic that governs pathway regulation

Zhu, Zhi‐Xin; Wang, Hailong; Wang, Yiting; Guan, Shaokang; Wang, Fang; Tang, Jingyu; Zhang, Ruijuan; Xie, Lulu; Lu, Yao-Ping

doi:10.1093/jxb/erv173

Cited by 92 publications

(82 citation statements)

References 76 publications

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“…Promoter regions were analysed using the SoftBerry suite (http://www.softberry.com/) and screened for cis ‐acting elements using the New PLACE database (http://www.dna.affrc.go.jp/htdocs/PLACE/; Higo et al ., ). Specific binding sites corresponding to consensus sequences for MYB (ANCNNCC), bHLH (CACNH(G/T)) recognition elements (Wang et al ., ; Zhu et al ., ), and WRKY ((T)(T)TGACY) recognition elements (W‐boxes, Eulgem et al ., ; Pesch et al ., ) were found and then localized using PlantPAN 2.0 database (http://plantpan2.itps.ncku.edu.tw/; Chow et al ., ; Figure S5).…”

Section: Methodsmentioning

confidence: 99%

The MYB5‐driven MBW complex recruits a WRKY factor to enhance the expression of targets involved in vacuolar hyper‐acidification and trafficking in grapevine

et al. 2019

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† These authors contributed equally to this work. SUMMARYThe accumulation of secondary metabolites and the regulation of tissue acidity contribute to the important traits of grape berry and influence plant performance in response to abiotic and biotic factors. In several plant species a highly conserved MYB-bHLH-WD (MBW) transcriptional regulatory complex controls flavonoid pigment synthesis and transport, and vacuolar acidification in epidermal cells. An additional component, represented by a WRKY-type transcription factor, physically interacts with the complex increasing the expression of some target genes and adding specificity for other targets. Here we investigated the function of MBW(W) complexes involving two MYBs (VvMYB5a and VvMYB5b) and the WRKY factor VvWRKY26 in grapevine (Vitis vinifera L.). Using transgenic grapevine plants we showed that these complexes affected different aspects of morphology, plant development, pH regulation, and pigment accumulation. Transcriptomic analysis identified a core set of putative target genes controlled by VvMYB5a, VvMYB5b, and VvWRKY26 in different tissues. Our data indicated that VvWRKY26 enhances the expression of selected target genes induced by VvMYB5a/b. Among these targets are genes involved in vacuolar hyper-acidification, such as the P-type ATPases VvPH5 and VvPH1, and trafficking, and genes involved in the biosynthesis of flavonoids. In addition, VvWRKY26 is recruited specifically by VvMYB5a, reflecting the functional diversification of VvMYB5a and VvMYB5b. The expression of MBWW complexes in vegetative organs, such as leaves, indicates a possible function of vacuolar hyper-acidification in the repulsion of herbivores and/or in developmental processes, as shown by defects in transgenic grape plants where the complex is inactivated.

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Section: Methodsmentioning

confidence: 99%

The MYB5‐driven MBW complex recruits a WRKY factor to enhance the expression of targets involved in vacuolar hyper‐acidification and trafficking in grapevine

et al. 2019

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“…UGT75C1 is also upregulated by PAP1, encoding an MYB transcription factor [47]. As a whole, the TF complex (TT2, TT8, and TTG1) and SmMYB1, an R2R3 MYB transcription factor, can regulate all anthocyanin pathway genes [73,75]. In this study, we identified thousands of TFs, including TFs for TAC synthesis, which might be involved in the regulation of genes in the TAC metabolic pathway.…”

Section: Discussionmentioning

confidence: 98%

“…The TFs include MYB, bHLH, and WDR. In Arabidopsis thaliana, the PAP1-GL3-TTG1 complex can regulate the TFs of MYB and bHLH [73]. In addition, the reduction of MYB expression can reduce the expression levels of DFR, LDOX, GST12, F3'H and UGT75C1 in the TAC pathway [74].…”

Section: Discussionmentioning

confidence: 99%

iTRAQ-based comparative proteomic analysis in mature leaves of Ethiopian mustard (Brassica carinata) provides insights into the whole-proteomic profiles and the role of anthocyanin biosynthesis in leaf color diversity

Wang

Guo

Yu³

et al. 2019

Preprint

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Background Anthocyanins are the main pigments in leaves, flowers and fruits, performing diverse biological functions in plants and exhibiting benefits for human health. The purple-leaved accession of B. carinata was used to study the biosynthetic mechanism of anthocyanins in this study. To elucidate the mechanisms of anthocyanin accumulation in the purple-leaved line, we employed a proteomic approach based on an isobaric tags for relative and absolute quantification (iTRAQ)-based technique to investigate the protein expression profile of the purple-leaved line of B. carinata in comparison with that of the green-leaved line.Results In total, 4,631 proteins were identified, of which 285 exhibited significant changes in abundance between BC-G01 and BC-P01. Of the 285 DEPs, 175 are upregulated and 110 are downregulated in the leaves of the purple-leaved line compared with the leaves of the green-leaved line. Bioinformatics analysis indicated that anthocyanin biosynthesis was the most significantly elevated metabolic process, containing three DEPs corresponding to two genes UGT75C1 and UGT79B1 . UGT75C1 and UGT79B1 , encoding anthocyanin 3-O-glucoside: 2’’-O-xylosyltransferase and anthocyanin 5-O-glucosyltransferase, respectively, play an important role in the biosynthesis of anthocyanins.Conclusions The exact functions of these proteins remain to be examined. Nevertheless, our study paves the way for understanding the genetic regulatory mechanisms of anthocyanin biosynthesis and accumulation in B. carinata .

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“…The same candidate regions appear in the results of different ΔSNP-indexes, and the intersection of these regions was selected as the final candidate region. In the genomic candidate region, it is preferred to use the rice genome annotation site MSU-RGAP (http://rice.plantbiology.msu.edu/) to annotate the genes in the candidate region, and the genes related to plant anthocyanin synthesis (Zhu et al, 2015); secondly, the candidate region containing candidate gene or adjacent to the known gene related to anthocyanin synthesis in rice were taken as a candidate gene; finally, the homozygous variation site with a sequencing depth of not less than 4× and ΔSNP-index=1 was selected as a candidate gene. At the same time, by referring to the method of Yano et al(Yano et al, 2016), all the polymorphisms in the candidate region were classified into three types.…”

Section: Construction Of Genomic Dna Poolsmentioning

confidence: 99%

Pair-wise Comparison Analysis for Multiple Pool-seq: an efficient method identified anthocyanin biosynthesis genes in rice pericarp

Yang

Xia

Zhang

et al. 2019

Preprint

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The complex traits are derived from multiple genes and exhibit a large variety of phenotypes. High-throughput sequencing technologies have become the new strategies for mapping the important traits of crops. However, these methods have their own disadvantages and limitations. Here we introduced Pair-wise Comparison Analysis for Multiple Pool-seq (PCAMP) for mapping the candidate genomic regions involved in anthocyanin biosynthesis in rice pericarp. In this protocol, the second filial generation (F2) populations obtained by crossing two parents with different target traits were divided into n (n>=3) subpopulations according to their phenotypes. Thirty phenotypically identical individuals were selected from each subpopulation and DNA samples were extracted to form a pool for sequencing. Finally, we compared the SNP-index between every two Pool-seqs to map the candidate genomic regions. We applied PCAMP to analyse F2 populations and successfully identified five known genes and five new candidate genomic regions for anthocyanin biosynthesis in rice pericarp. These results demonstrate that PCAMP is an efficient new method for dissecting the complex traits of crops.

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Characterization of the cis elements in the proximal promoter regions of the anthocyanin pathway genes reveals a common regulatory logic that governs pathway regulation

Abstract: HighlightMYB and bHLH bind to two identifiable syntaxes present in target gene promoters, and the anthocyanin pathway is regulated as one unit as in other branches of the flavonoid network.

Cited by 92 publications

References 76 publications

The MYB5‐driven MBW complex recruits a WRKY factor to enhance the expression of targets involved in vacuolar hyper‐acidification and trafficking in grapevine

The MYB5‐driven MBW complex recruits a WRKY factor to enhance the expression of targets involved in vacuolar hyper‐acidification and trafficking in grapevine

iTRAQ-based comparative proteomic analysis in mature leaves of Ethiopian mustard (Brassica carinata) provides insights into the whole-proteomic profiles and the role of anthocyanin biosynthesis in leaf color diversity

Pair-wise Comparison Analysis for Multiple Pool-seq: an efficient method identified anthocyanin biosynthesis genes in rice pericarp

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