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Journal ArticleDOI

Recent advances in the transcriptional regulation of the flavonoid biosynthetic pathway

01 May 2011-Journal of Experimental Botany (Oxford University Press)-Vol. 62, Iss: 8, pp 2465-2483
TL;DR: A better knowledge of the regulatory mechanisms of the flavonoids pathway is likely to favour the development of new biotechnological tools for the generation of value-added plants with optimized flavonoid content.
Abstract: Flavonoids are secondary metabolites involved in several aspects of plant development and defence. They colour fruits and flowers, favouring seed and pollen dispersal, and contribute to plant adaptation to environmental conditions such as cold or UV stresses, and pathogen attacks. Because they affect the quality of flowers (for horticulture), fruits and vegetables, and their derivatives (colour, aroma, stringency, etc.), flavonoids have a high economic value. Furthermore, these compounds possess pharmaceutical properties extremely attractive for human health. Thanks to easily detectable mutant phenotypes, such as modification of petal pigmentation and seeds exhibiting transparent testa, the enzymes involved in the flavonoid biosynthetic pathway have been characterized in several plant species. Conserved features as well as specific differences have been described. Regulation of structural gene expression appears tightly organized in a spatial and temporal way during plant development, and is orchestrated by a ternary complex involving transcription factors from the R2R3-MYB, basic helix-loop-helix (bHLH), and WD40 classes. This MYB-bHLH-WD40 (MBW) complex regulates the genes that encode enzymes specifically involved in the late steps of the pathway leading to the biosynthesis of anthocyanins and condensed tannins. Although several genes encoding transcription factors from these three families have been identified, many gaps remain in our understanding of the regulation of this biosynthetic pathway, especially about the respective roles of bHLH and WD40 proteins. A better knowledge of the regulatory mechanisms of the flavonoid pathway is likely to favour the development of new biotechnological tools for the generation of value-added plants with optimized flavonoid content.

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Citations
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Journal ArticleDOI
TL;DR: Different strategies and achievements through the genetic engineering of flavonoid biosynthesis with implication in the industry and the combinatorial biosynthesis in microorganisms by the reconstruction of the pathway to obtain high amounts of specific compounds are discussed.
Abstract: Flavonoids are widely distributed secondary metabolites with different metabolic functions in plants. The elucidation of the biosynthetic pathways, as well as their regulation by MYB, basic helix-loop-helix (bHLH), and WD40-type transcription factors, has allowed metabolic engineering of plants through the manipulation of the different final products with valuable applications. The present review describes the regulation of flavonoid biosynthesis, as well as the biological functions of flavonoids in plants, such as in defense against UV-B radiation and pathogen infection, nodulation, and pollen fertility. In addition, we discuss different strategies and achievements through the genetic engineering of flavonoid biosynthesis with implication in the industry and the combinatorial biosynthesis in microorganisms by the reconstruction of the pathway to obtain high amounts of specific compounds.

1,260 citations


Cites background from "Recent advances in the transcriptio..."

  • ...…(Fragaria x ananassa), apple (Malus domestica), cauliflower (Brassica oleracea var botrytis), potato (Solanum tuberosum L.), bayberry (Myrica rubra), mangosteen (Garcinia mangostana L.), pear (Pyrus pyrifolia), and purple kale (Brassica oleracea var. acephala f. tricolor) (Hichri et al., 2011)....

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Journal ArticleDOI
TL;DR: Recent advances in the characterization of the underlying regulatory mechanisms of flavonoid biosynthesis are reviewed, with a special focus on the MBW (MYB-bHLH-WDR) protein complexes.

1,032 citations

Journal ArticleDOI
TL;DR: In the rhizosphere, increasing evidence suggests that root specific chemicals (exudates) might initiate and manipulate biological and physical interactions between roots and soil organisms, and one-way signals that relate the nature of chemical and physical soil properties to the roots.

855 citations


Cites background from "Recent advances in the transcriptio..."

  • ...The PA-related R2R3MYBs (sub-group 5) were first described for A. thaliana, with the R2R3MYB TT2 interacting with TT8 (bHLH) and TTG1 (WDR) to form the MBW complex [70,74]....

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  • ...The R2R3MYBs regulating anthocyanin production in grape have been extensively studied over the last decade [74], butmore recently those for the PA [78e80] and flavonol [117] pathway branches have been identified, as well as the phenylpropanoid-related bHLHs and WDR [74,118]....

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  • ...thaliana, with the R2R3MYB TT2 interacting with TT8 (bHLH) and TTG1 (WDR) to form the MBW complex [70,74]....

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  • ..., there have also been significant advances in the depth of understanding of regulation of phenylpropanoid biosynthesis in important horticultural species, in particular grape and apple [74,116]....

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  • ...The use of TFs as transgenes for modification of the biosynthesis of polyphenolics is now well proven, with many different genes shown to be effective and a large number of species successfully targeted [74,81]....

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Journal ArticleDOI
TL;DR: A simplified model for the different regulatory networks involved with anthocyanin production in fruit is proposed and shows clear links between the developmental regulatory network and the specific regulators of anthcyanin biosynthesis during fruit ripening.

789 citations

Journal ArticleDOI
TL;DR: MYB TFs are reviewed with particular emphasis on their role in controlling different biological processes to provide valuable insights in understanding regulatory networks and associated functions to develop strategies for crop improvement.
Abstract: Regulation of gene expression at the level of transcription controls many crucial biological processes. Transcription factors (TFs) play a great role in controlling cellular processes and MYB TF family is large and involved in controlling various processes like responses to biotic and abiotic stresses, development, differentiation, metabolism, defense etc. Here, we review MYB TFs with particular emphasis on their role in controlling different biological processes. This will provide valuable insights in understanding regulatory networks and associated functions to develop strategies for crop improvement.

700 citations


Cites background from "Recent advances in the transcriptio..."

  • ...1994; Hichri et al. 2011), biotic and abiotic stress (Segarra et al. 2009; Lippold et al. 2009), cell shape such as Am MIXTA (Noda et al. 1994), differentiation (Oppenheimer et al. 1991; Kang et al. 2009; Xie et al. 2010), hormone responses i.e. AtMYB2 (Urao et al. 1993), GAMYB and CpMYB (Gubler et…...

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References
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Journal ArticleDOI
TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
Abstract: A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.

57,055 citations


"Recent advances in the transcriptio..." refers background or methods in this paper

  • ...Full-length protein sequences were aligned with Muscle (Edgar, 2004), and the phylogenetic tree was constructed according to the Neighbor–Joining method (Saitou and Nei, 1987)....

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  • ...The bHLH domain is constituted of nearly 60 amino acids, and is characterized by the presence of 19 conserved amino acids, five in the basic region, five in the first helix, one in the loop, and finally eight amino acids in the second helix (Fig....

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Journal ArticleDOI
TL;DR: The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies and shows significant evidence for a group if it is defined by three or more characters.
Abstract: The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.

40,349 citations


"Recent advances in the transcriptio..." refers methods in this paper

  • ...3) (Toledo-Ortiz et al., 2003)....

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  • ...The bootstrap consensus tree inferred from 2000 replicates is taken to represent the evolutionary history of the proteins (Felsenstein, 1985)....

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Journal ArticleDOI
TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
Abstract: We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the logexpectation score, and refinement using treedependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.

37,524 citations


Additional excerpts

  • ...Edgar RC. 2004....

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Journal ArticleDOI
TL;DR: Version 4 of MEGA software expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses.
Abstract: We announce the release of the fourth version of MEGA software, which expands on the existing facilities for editing DNA sequence data from autosequencers, mining Web-databases, performing automatic and manual sequence alignment, analyzing sequence alignments to estimate evolutionary distances, inferring phylogenetic trees, and testing evolutionary hypotheses. Version 4 includes a unique facility to generate captions, written in figure legend format, in order to provide natural language descriptions of the models and methods used in the analyses. This facility aims to promote a better understanding of the underlying assumptions used in analyses, and of the results generated. Another new feature is the Maximum Composite Likelihood (MCL) method for estimating evolutionary distances between all pairs of sequences simultaneously, with and without incorporating rate variation among sites and substitution pattern heterogeneities among lineages. This MCL method also can be used to estimate transition/transversion bias and nucleotide substitution pattern without knowledge of the phylogenetic tree. This new version is a native 32-bit Windows application with multi-threading and multi-user supports, and it is also available to run in a Linux desktop environment (via the Wine compatibility layer) and on Intel-based Macintosh computers under the Parallels program. The current version of MEGA is available free of charge at (http://www.megasoftware.net).

29,021 citations


Additional excerpts

  • ...MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0....

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  • ...Phylogenetic analyses were conducted using MEGA4 (Tamura et al., 2007)....

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Journal ArticleDOI
TL;DR: Some of the recent advances in flavonoid research are reviewed and the role of anthocyanins and flavones in providing stable blue flower colours in the angiosperms is outlined.

3,465 citations


"Recent advances in the transcriptio..." refers background or methods in this paper

  • ...…accumulate in leaf epidermal cells, waxes, and trichomes, where they act as UV-B filters, but can also complex with DNA and protect it from oxidative damage (Sarma and Sharma, 1999; Harborne and Williams, 2000; Dixon, 2005; Dixon et al., 2005; Aron and Kennedy, 2008; Albert et al., 2009)....

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  • ...All flavonoids display a C6–C3–C6 skeleton structure, except for the aurones (C6–C2–C6) (Harborne and Williams, 2000; Marais et al., 2006)....

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  • ...Flavonoids also play a role in the interaction between plants and animals, as exemplified in leaves, where the concentration and nature of PAs determine the bitter taste and thus prevent feeding by herbivores (Harborne and Williams, 2000; Aron and Kennedy, 2008)....

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  • ...Published by Oxford University Press [on behalf of the Society for Experimental Biology]....

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  • ...Flavonoids also have demonstrated neuroprotective, anti-inflammatory, analgesic, bactericidal, fungicidal, and spasmolytic properties (Harborne and Williams, 2000; Sun et al., 2002)....

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