Main conclusion
DcMYB11, an R2R3 MYB gene associated with petiole anthocyanin pigmentation in carrot, was functionally characterized. A putative enhancer sequence is able to increase DcMYB11 activity.
Abstract
The accumulation of anthocyanin pigments can exhibit different patterns across plant tissues and crop varieties. This variability allowed the investigation of the molecular mechanisms behind the biosynthesis of these pigments in several plant species. Among crops, carrots have a well-defined anthocyanin pigmentation pattern depending on the genic background. In this work, we report on the discovery of DNA structural differences affecting the activity of an R2R3 MYB (encoded by DcMYB11) involved in anthocyanin regulation in carrot petiole. To this end, we first verified the function of DcMYB11 using heterologous systems and identified three different alleles which may explain differences in petiole pigmentation. Characterization of the DcMYB11 alleles at the 5' upstream sequence unveiled a sequence that functions as a putative enhancer. In conclusion, this study provides novel insight into the molecular mechanisms controlling anthocyanin accumulation in carrot. By these outcomes, we expanded our knowledge on the cis-regulatory sequences in plants.
Similar content being viewed by others
Data availability
Detailed data that support the findings of this study are available from the corresponding author upon reasonable request.
Abbreviations
- Gp:
-
Green petiole
- Pp:
-
Purple petiole
References
Agati G, Guidi L, Landi M, Tattini M (2021) Anthocyanins in photoprotection: knowing the actors in play to solve this complex ecophysiological issue. New Phytol 232:2228–2235. https://doi.org/10.1111/nph.17648
Albert NW, Lewis DH, Zhang H, Schwinn KE, Jameson PE, Davies KM (2011) Members of an R2R3-MYB transcription factor family in Petunia are developmentally and environmentally regulated to control complex floral and vegetative pigmentation patterning. Plant J 65:771–784. https://doi.org/10.1111/j.1365-313X.2010.04465.x
Albert NW, Davies KM, Lewis DH, Zhang H, Montefiori M, Brendolise C, Boase MR, Ngo H, Jameson PE, Schwinn KE (2014) A conserved network of transcriptional activators and repressors regulates anthocyanin pigmentation in eudicots. Plant Cell 26:962–980. https://doi.org/10.1105/tpc.113.122069
Bai C, Elledge SJ (1997) Gene identification using the yeast two-hybrid system. Meth Enzymol 283:141–156. https://doi.org/10.1016/s0076-6879(97)83013-3
Bannoud F, Ellison S, Paolinelli M, Horejsi T, Senalik D, Fanzone M, Iorizzo M, Simon PW, Cavagnaro PF (2019) Dissecting the genetic control of root and leaf tissue-specific anthocyanin pigmentation in carrot (Daucus carota L.). Theor Appl Genet 132:2485–2507. https://doi.org/10.1007/s00122-019-03366-5
Baudry A, Heim MA, Dubreucq B, Caboche M, Weisshaar B, Lepiniec L (2004) TT2, TT8, and TTG1 synergistically specify the expression of BANYULS and proanthocyanidin biosynthesis in Arabidopsis thaliana. Plant J 39:366–380. https://doi.org/10.1111/j.1365-313X.2004.02138.x
Brendolise C, Espley RV, Lin-Wang K, Laing W, Peng Y, McGhie T, Dejnoprat S, Tomes S, Hellens RP, Allan AC (2017) Multiple copies of a simple MYB-binding site confers trans-regulation by specific flavonoid-related R2R3 MYBs in diverse species. Front Plant Sci 8:1864. https://doi.org/10.1111/10.3389/fpls.2017.01864
Butelli E, Licciardello C, Zhang Y, Liu J, Mackay S, Bailey P, Reforgiato-Recupero G, Martin C (2012) Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges. Plant Cell 24:1242–1255. https://doi.org/10.1105/tpc.111.095232
Butelli E, Garcia-Lor A, Licciardello C, Las Casas G, Hill L, Recupero GR, Keremane ML, Ramadugu C, Krueger R, Xu Q, Deng X (2017) Changes in anthocyanin production during domestication of Citrus. Plant Physiol 173:2225–2242. https://doi.org/10.1104/pp.16.01701
Cavagnaro PF, Iorizzo M, Yildiz M, Senalik D, Parsons J, Ellison S, Simon P (2014) A gene-derived SNP-based high resolution linkage map of carrot including the location of QTL conditioning root and leaf anthocyanin pigmentation. BMC Genom 15:1118. https://doi.org/10.17660/10.1186/1471-2164-15-1118
Cavagnaro PF, Bannoud F, Senalik D, Ellison SL, Simon PW (2019) Carrot anthocyanins: nutrition, diversity and genetics. Acta Hortic 2019:101–106. https://doi.org/10.17660/ActaHortic.2019.1264.11
Chagné D, Lin-Wang K, Espley RV et al (2013) An ancient duplication of apple MYB transcription factors is responsible for novel red fruit-flesh phenotypes. Plant Physiol 161:225–239. https://doi.org/10.1104/pp.112.206771
Colanero S, Perata P, Gonzali S (2020a) What’s behind purple tomatoes? Insight into the mechanisms of anthocyanin synthesis in tomato fruits. Plant Physiol 182:1841–1853. https://doi.org/10.1104/pp.19.01530
Colanero S, Tagliani A, Perata P, Gonzali S (2020b) Alternative splicing in the anthocyanin fruit gene encoding an R2R3 MYB transcription factor affects anthocyanin biosynthesis in tomato fruits. Plant Commun 1:100006. https://doi.org/10.1016/j.xplc.2019.100006
D’Amelia V, Villano C, Batelli G, Çobanoğlu Ö, Carucci F, Melito S, Chessa M, Chiaiese P, Aversano R, Carputo D (2020) Genetic and epigenetic dynamics affecting anthocyanin biosynthesis in potato cell culture. Plant Sci 298:110597. https://doi.org/10.1016/j.plantsci.2020.110597
D’Amelia V, Aversano R, Batelli G, Caruso I, Castellano Moreno M, Castro-Sanz AB, Chiaiese P, Fasano C, Palomba F, Carputo D (2014) High AN1 variability and interaction with basic helix-loop-helix co-factors related to anthocyanin biosynthesis in potato leaves. Plant J 80:527–540. https://doi.org/10.1111/tpj.12653
D’Amelia V, Aversano R, Ruggiero A, Batelli G, Appelhagen I, Dinacci C, Hill L, Martin C, Carputo D (2018) Subfunctionalization of duplicate MYB genes in Solanum commersonii generated the cold-induced ScAN2 and the anthocyanin regulator ScAN1. Plant Cell Environ 41:1038–1051. https://doi.org/10.1111/pce.12966
Davies KM, Albert NW, Zhou Y, Schwinn KE (2018) Functions of flavonoid and betalain pigments in abiotic stress tolerance in plants. In: Roberts JA (ed) Annual plant reviews online, https://doi.org/10.1002/9781119312994.apr0604
Dubos C, Stracke R, Grotewold E, Weisshaar B, Martin C, Lepiniec L (2010) MYB transcription factors in Arabidopsis. Trends Plant Sci 15:573–581
Ellison SL, Luby CH, Corak KE, Coe KM, Senalik D, Iorizzo M, Goldman IL, Simon PW, Dawson JC (2018) Carotenoid presence is associated with the Or gene in domesticated carrot. Genetics 210:1497–1508. https://doi.org/10.1534/genetics.118.301299
Gel B, Serra E (2017) karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data. Bioinformatics 33:3088–3090. https://doi.org/10.1093/bioinformatics/btx346
Giusti MM, Wrolstad RE (2001) Characterization and measurement of anthocyanins by UV-visible spectroscopy. Curr Protoc Food Anal Chem 1:F1-2. https://doi.org/10.1002/0471142913.faf0102s00
Gonzalez A, Zhao M, Leavitt JM, Lloyd AM (2008) Regulation of the anthocyanin biosynthetic pathway by the TTG1/bHLH/Myb transcriptional complex in Arabidopsis seedlings. Plant J 53:814–827. https://doi.org/10.1111/j.1365-313X.2007.03373.x
He J, Ye S, Correia P, Fernandes I, Zhang R, Wu M, Freitas V, Mateus N, Oliveira H (2022) Dietary polyglycosylated anthocyanins, the smart option? A comprehensive review on their health benefits and technological applications. Compr Rev Food Sci Food Saf 21:3096–3128. https://doi.org/10.1111/1541-4337.12970
Heim MA, Jakoby M, Werber M, Martin C, Weisshaar B, Bailey PC (2003) The basic helix–loop–helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity. Mol Biol Evol 20:735–747. https://doi.org/10.1093/molbev/msg088
Huang D, Wang X, Tang Z, Yuan Y, Xu Y, He J, Jiang X, Peng SA, Li L, Butelli E, Deng X (2018) Subfunctionalization of the Ruby2–Ruby1 gene cluster during the domestication of citrus. Nature Plants 4:930–941. https://doi.org/10.1038/s41477-018-0287-6
Iorizzo M, Ellison S, Senalik D et al (2016) A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution. Nat Genet 48:657–666. https://doi.org/10.1038/ng.3565
Iorizzo M, Cavagnaro PF, Bostan H, Zhao Y, Zhang J, Simon PWA (2019) Cluster of MYB transcription factors regulates anthocyanin biosynthesis in carrot (Daucus carota L.) root and petiole. Front Plant Sci 9:1927. https://doi.org/10.3389/fpls.2018.01927
Iorizzo M, Curaba J, Pottorff M, Ferruzzi MG, Simon P, Cavagnaro PF (2020) Carrot anthocyanins genetics and genomics: Status and perspectives to improve its application for the food colorant industry. Genes 11:906. https://doi.org/10.3390/genes11080906
Jung CS, Griffiths HM, De Jong DM, Cheng S, Bodis M, Kim TS, De Jong WS (2009) The potato developer (D) locus encodes an R2R3 MYB transcription factor that regulates expression of multiple anthocyanin structural genes in tuber skin. Theor Appl Genet 120:45–57
Kobayashi S, Ishimaru M, Hiraoka K, Honda C (2002) Myb-related genes of the Kyoho grape (Vitis labruscana) regulate anthocyanin biosynthesis. Planta 215:924–933. https://doi.org/10.1007/s00425-002-0830-5
Koes R, Verweij W, Quattrocchio F (2005) Flavonoids: a colorful model for the regulation and evolution of biochemical pathways. Trends Plant Sci 10:236–242. https://doi.org/10.1016/j.tplants.2005.03.002
Koressaar T, Lepamets M, Kaplinski L, Raime K, Andreson R, Remm M (2018) Primer3_masker: integrating masking of template sequence with primer design software. Bioinformatics 34:1937–1938. https://doi.org/10.1093/bioinformatics/bty036
Laimbeer FPE, Bargmann BO, Holt SH, Pratt T, Peterson B, Doulis AG, Buell CR, Veilleux RE (2020) Characterization of the f locus responsible for floral anthocyanin production in potato. G3. https://doi.org/10.1534/g3.120.401684
Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, Rouzé P, Rombauts S (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res 30:325–327. https://doi.org/10.1093/nar/30.1.325
Lin-Wang K, Bolitho K, Grafton K, Kortstee A, Karunairetnam S, McGhie TK, Espley RV, Hellens RP, Allan AC (2010) An R2R3 MYB transcription factor associated with regulation of the anthocyanin biosynthetic pathway in Rosaceae. BMC Plant Biol 10:50. https://doi.org/10.1186/1471-2229-10-50
Montefiori M, Brendolise C, Dare AP, Lin-Wang K, Davies KM, Hellens RP, Allan A (2015) In the Solanaceae, a hierarchy of bHLHs confer distinct target specificity to the anthocyanin regulatory complex. J Exp Bot 66:427–1436. https://doi.org/10.1093/jxb/eru494
Passeri V, Koes R, Quattrocchio FM (2016) New challenges for the design of high value plant products: stabilization of anthocyanins in plant vacuoles. Front Plant Sci 7:153. https://doi.org/10.3389/fpls.2016.00153
Quattrocchio F, Wing J, van der Woude K, Souer E, de Vetten N, Mol J, Koes R (1999) Molecular analysis of the anthocyanin2 gene of petunia and its role in the evolution of flower color. Plant Cell 11:1433–1444. https://doi.org/10.1105/tpc.11.8.1433
Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 6:841–842. https://doi.org/10.1093/bioinformatics/btq033
Ramsay NA, Glover BJ (2005) MYB–bHLH–WD40 protein complex and the evolution of cellular diversity. Trends Plant Sci 10:63–70. https://doi.org/10.1016/j.tplants.2004.12.011
Schwinn K, Venail J, Shang Y, Mackay S, Alm V, Butelli E, Oyama R, Bailey P, Davies K, Martin C (2006) A small family of MYB-regulatory genes controls floral pigmentation intensity and patterning in the genus Antirrhinum. Plant Cell 18:831–851. https://doi.org/10.1105/tpc.105.039255
Spelt C, Quattrocchio F, Mol JN, Koes R (2000) anthocyanin1 of petunia encodes a basic helix-loop-helix protein that directly activates transcription of structural anthocyanin genes. Plant Cell 12:1619–1631. https://doi.org/10.1105/tpc.12.9.1619
Stracke R, Werber M, Weisshaar B (2001) The R2R3-MYB gene family in Arabidopsis thaliana. Curr Opin Plant Biol 4:447–456. https://doi.org/10.1016/s1369-5266(00)00199-0
Weber B, Zicola J, Oka R, Stam M (2016) Plant enhancers: a call for discovery. Trends Plant Sci 21:974–987. https://doi.org/10.1016/j.tplants.2016.07.013
Xu ZS, Feng K, Que F, Wang F, Xiong AS (2017) A MYB transcription factor, DcMYB6, is involved in regulating anthocyanin biosynthesis in purple carrot taproots. Sci Rep 7:1–9. https://doi.org/10.1038/srep45324
Xu ZS, Yang QQ, Feng K, Xiong AS (2019) Changing carrot color: insertions in DcMYB7 alter the regulation of anthocyanin biosynthesis and modification. Plant Physiol 181:195–207. https://doi.org/10.1104/pp.19.00523
Zhang P, Chopra S, Peterson T (2000) A segmental gene duplication generated differentially expressed myb-homologous genes in maize. Plant Cell 12:2311–3232. https://doi.org/10.1105/tpc.12.12.2311
Zhang H, Koes R, Shang H, Fu Z, Wang L, Dong X, Zhang J, Passeri V, Li Y, Jiang H, Gao J (2019) Identification and functional analysis of three new anthocyanin R2R3-MYB genes in Petunia. Plant Direct 3:1–13. https://doi.org/10.1002/pld3.114
Zhu B, Zhang W, Zhang T, Liu B, Jiang J (2015) Genome-wide prediction and validation of intergenic enhancers in Arabidopsis using open chromatin signatures. Plant Cell 27:2415–2426
Zimmermann IM, Heim MA, Weisshaar B, Uhrig JF (2004) Comprehensive identification of Arabidopsis thaliana MYB transcription factors interacting with R/B-like BHLH proteins. Plant J 40:22–34
Acknowledgements
The authors would like to thank Changqing Zhang from N.C. State University Plants for Human Health Institute for providing us the plasmid vectors (pF35SE and pFAGM) used in this study.
Funding
This work was supported by the United States Department of Agriculture National Institute of Food and Agriculture, Hatch Project 1008691 and Award No. 2022–67013-36389. VDA was supported by ExPoPe-STAR-Line 1, 2017-Unina-Intesa San Paolo and Short Mobility of program of University of Naples Federico II.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors have no competing interest to declare.
Additional information
Communicated by Dorothea Bartels.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
D’Amelia, V., Curaba, J., Abid, M.A. et al. Functional characterization of DcMYB11, an R2R3 MYB associated with the purple pigmentation of carrot petiole. Planta 258, 50 (2023). https://doi.org/10.1007/s00425-023-04200-5
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s00425-023-04200-5