Advances in the MYB-bHLH-WD Repeat (MBW) Pigment Regulatory Model: Addition of a WRKY Factor and Co-option of an Anthocyanin MYB for Betalain Regulation.
TL;DR: The history of the MBW model spanning the last three decades is surveyed, highlighting the major findings that have contributed to current understanding, and recent discoveries regarding WRKY protein control of the flavonoid pigment pathway and its relationship to theMBW complex will be emphasized.
Abstract: Flavonoids are secondary metabolites derived from the general phenylpropanoid pathway and are widespread throughout the plant kingdom The functions of flavonoids are diverse, including defense against phytopathogens, protection against UV light damage and oxidative stress, regulation of auxin transport and allelopathy One of the most conspicuous functions of flavonoids has long attracted the attention of pollinators and scientist alike: the vivid shades of red, pink, orange, blue and purple on display in the flowers of angiosperms Thus, flavonoid pigments have perhaps been the most intensely studied phenylpropanoids From Mendel to McClintock and up to the present, studies centered on flavonoid pigments have resulted in some of the most important scientific discoveries of the last 150 years, including the first examples of transcriptional regulation in plants Here we focus on the highly conserved MYB-bHLH-WD repeat (MBW) transcriptional complex model for the regulation of the flavonoid pigment pathway We will survey the history of the MBW model spanning the last three decades, highlighting the major findings that have contributed to our current understanding In particular, recent discoveries regarding WRKY protein control of the flavonoid pigment pathway and its relationship to the MBW complex will be emphasized In addition, we will discuss recent findings about the regulation of the beet betalain pigment pathway, and how a MYB member of the MBW complex was co-opted to regulate this chemically unrelated but functionally equivalent pathway
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Fujian Agriculture and Forestry University1, University of Florida2, International Crops Research Institute for the Semi-Arid Tropics3, National Cheng Kung University4, North China University of Science and Technology5, University of Western Australia6, Agricultural Research Service7, Crops Research Institute8, Zhongkai University of Agriculture and Engineering9, Tsinghua University10, Shenzhen University11, Tuskegee University12, Osmania University13, National Tsing Hua University14, Plant Genome Mapping Laboratory15, University of Illinois at Urbana–Champaign16
TL;DR: High-quality genome sequence of cultivated peanut provides insights into genome evolution and the genetic mechanisms underlying seed size and leaf resistance in peanut, providing a cornerstone for functional genomics and peanut improvement.
Abstract: High oil and protein content make tetraploid peanut a leading oil and food legume. Here we report a high-quality peanut genome sequence, comprising 2.54 Gb with 20 pseudomolecules and 83,709 protein-coding gene models. We characterize gene functional groups implicated in seed size evolution, seed oil content, disease resistance and symbiotic nitrogen fixation. The peanut B subgenome has more genes and general expression dominance, temporally associated with long-terminal-repeat expansion in the A subgenome that also raises questions about the A-genome progenitor. The polyploid genome provided insights into the evolution of Arachis hypogaea and other legume chromosomes. Resequencing of 52 accessions suggests that independent domestications formed peanut ecotypes. Whereas 0.42–0.47 million years ago (Ma) polyploidy constrained genetic variation, the peanut genome sequence aids mapping and candidate-gene discovery for traits such as seed size and color, foliar disease resistance and others, also providing a cornerstone for functional genomics and peanut improvement.
320 citations
TL;DR: An integrated regulatory network of anthocyanin biosynthesis controlled by MYB repressors and MBW activation complex is built based on the significant progress into the role of MYB Repressors.
121 citations
Cites background from "Advances in the MYB-bHLH-WD Repeat ..."
...The anthocyanin biosynthesis pathway is conserved in higher plants (Koes et al., 2005; Hichri et al., 2011; Lloyd et al., 2017; Naing and Kim, 2018)....
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TL;DR: This review considers current knowledge of the flavonoid pathway in the bryophytes, consisting of the liverworts, hornwort, and mosses, and the apparent complete absence of flavonoids from the hornworts.
Abstract: The flavonoid pathway is one of the best characterized specialized metabolite pathways of plants. In angiosperms, the flavonoids have varied roles in assisting with tolerance to abiotic stress and are also key for signaling to pollinators and seed dispersal agents. The pathway is thought to be specific to land plants and to have arisen during the period of land colonization around 550-470 million years ago. In this review we consider current knowledge of the flavonoid pathway in the bryophytes, consisting of the liverworts, hornworts, and mosses. The pathway is less characterized for bryophytes than angiosperms, and the first genetic and molecular studies on bryophytes are finding both commonalities and significant differences in flavonoid biosynthesis and pathway regulation between angiosperms and bryophytes. This includes biosynthetic pathway branches specific to each plant group and the apparent complete absence of flavonoids from the hornworts.
114 citations
TL;DR: The results demonstrate that MdWRKY40 is a key modulator in the wounding- induced anthocyanin biosynthesis, which provides new insights into the regulation of wounding-induced anthocianin bios synthesis at both transcriptional and post-translational levels in apple.
Abstract: Wounding stress leads to anthocyanin accumulation. However, the underlying molecular mechanism remains elusive. In this study, MdWRKY40 was found to promote wounding-induced anthocyanin biosynthesis in association with MdMYB1 and undergo MdBT2-mediated degradation in apple. We found that MdMYB1, a positive regulator of anthocyanin biosynthesis, was essential for the wounding-induced anthocyanin biosynthesis in apple. MdWRKY40 was identified as an MdMYB1-interacting protein, and enhanced the binding of MdMYB1 to its target genes in response to wounding. We found that MdBT2 interacted physically with MdWRKY40 and was involved in its degradation through the 26S proteasome pathway. Our results demonstrate that MdWRKY40 is a key modulator in the wounding-induced anthocyanin biosynthesis, which provides new insights into the regulation of wounding-induced anthocyanin biosynthesis at both the transcriptional and post-translational levels in apple.
105 citations
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TL;DR: The elucidation ofMYB protein function and regulation that is possible in Arabidopsis will provide the foundation for predicting the contributions of MYB proteins to the biology of plants in general.
3,542 citations
"Advances in the MYB-bHLH-WD Repeat ..." refers background in this paper
...Accordingly, MYB proteins function in a diverse array of processes including the regulation of plant form, the cell cycle, cell differentiation, metabolism and stress response (for a general review of plant MYB transcription factors, see Dubos et al. 2010, Feller et al. 2011)....
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TL;DR: In this paper, two cDNAs were isolated whose dimerized products bind specifically to a DNA sequence, kappa E2, located in the immunoglobulin kappa chain enhancer.
2,418 citations
TL;DR: The helix-loop-helix (HLH) family of transcriptional regulatory proteins are key players in a wide array of developmental processes, including neurogenesis, myogenesis, hematopoiesis, and pancreatic development and the structure and functional properties are examined.
Abstract: The helix-loop-helix (HLH) family of transcriptional regulatory proteins are key players in a wide array of developmental processes. Over 240 HLH proteins have been identified to date in organisms ranging from the yeast Saccharomyces cerevisiae to humans (6). Studies in Xenopus laevis, Drosophila melanogaster, and mice have convincingly demonstrated that HLH proteins are intimately involved in developmental events such as cellular differentiation, lineage commitment, and sex determination. In yeast, HLH proteins regulate several important metabolic pathways, including phosphate uptake and phospholipid biosynthesis (19, 67, 112). In multicellular organisms, HLH factors are required for a multitude of important developmental processes, including neurogenesis, myogenesis, hematopoiesis, and pancreatic development (12, 86, 127, 179). The purpose of this review is to examine the structure and functional properties of HLH proteins.
E-box sites: elements mediating cell-type-specific gene transcription.
Gene transcription of the immunoglobulin heavy-chain (IgH) gene has long been known to be regulated, in part, by a cis-acting DNA element known as the IgH intronic enhancer (109, 156). By in vivo methylation protection assays, a number of sites were identified in both the IgH and the kappa light-chain gene enhancers which were specifically protected in B cells but not in nonlymphoid cells (41). These elements shared a signature motif which consisted of the core hexanucleotide sequence, CANNTG, and were subsequently dubbed E boxes (41). A total of five E-box elements are present in the IgH gene enhancer: μE1, μE2, μE3, μE4, and μE5. The Ig kappa enhancer also contains three cannonical E boxes, designated κE1, κE2, and κE3. E-box sites have been subsequently found in B-cell-specific promoter and enhancer elements, including a subset of Ig light-chain gene promoters, the IgH and Ig light-chain 3′ enhancers, and, more recently, the λ5 promoter (110, 118, 156).
E-box elements have also been identified in promoter and enhancer elements that regulate muscle-, neuron-, and pancreas-specific gene expression. For example, in muscle, the muscle creatine kinase gene, acetylcholine receptor genes α and δ, and the myosin light-chain gene all require E-box elements for full activity (27, 51, 85). A number of genes whose expression is limited to the pancreas also require E-box sites for proper expression. The insulin and somatostatin genes, for example, contain E-box sites that, when multimerized, are sufficient to regulate pancreatic β-cell-specific gene expression (168). More recently, E-box regulatory sites have been identified in a number of neuron-specific genes, including the opsin, hippocalcin, beta 2 subunit of the neuronal nicotinic acetylcholine receptor, and muscarinic acetylcholine receptor genes (1, 21, 52, 125).
E-box sites: cognate recognition sequence for HLH proteins.
Two proteins, termed E12 and E47, were originally identified as binding to the κE2/μE5 site (65, 102). They have a region of homology with the Drosophila Daughterless protein, the myogenic differentiation factor MyoD, members of the achaete-scute gene complex, and the Myc family of transcription factors (102). This stretch of conserved residues, known as the Myc homology region, appeared to be critical for the DNA binding properties of E12 and E47 (102). The E12 and E47 proteins, which differ only within this Myc homology region, arise by alternative splicing of the E2A gene (157). This conserved sequence, which was modeled as two amphipathic alpha helices separated by a flexible loop structure, was named the HLH motif and shown to function as a dimerization domain.
The HLH structure.
The solution structure of the basic HLH (bHLH)-leucine zipper (LZ) factor Max first confirmed the existence of the HLH motif (44). Subsequently, the three-dimensional structure of the E47 bHLH polypeptide bound to its E-box recognition site, CACCTG, has been solved at 2.8-Å resolution (38). A number of interesting features were revealed from analysis of the E47 crystal structure. The E47 dimer forms a parallel, four-helix bundle which allows the basic region to contact the major groove (38). In addition to the basic region, residues in the loop and helix 2 also make contact with DNA (38). Stable interaction of the HLH domain is favored by van der Waals interactions between conserved hydrophobic residues (38). The E47 dimer is centered over the E box, with each monomer interacting with either a CAC or CAG half-site. A glutamate present in the basic region of each subunit makes contact with the cytosine and adenine bases in the E-box half-site. An adjacent arginine residue stabilizes the position of the glutamate by direct interaction with these nucleotides and additionally the phosphodiester backbone. Both the glutamate and the arginine residues are conserved in most bHLH proteins, consistent with a role in specific DNA binding (6, 38, 102).
Classification of the HLH proteins.
Owing to the large number of HLH proteins that have been described, a classification scheme that was based upon tissue distribution, dimerization capabilities, and DNA-binding specificities was devised (Fig. (Fig.1)1) (101). Class I HLH proteins, also known as the E proteins, include E12, E47, HEB, E2-2, and Daughterless. These proteins are expressed in many tissues and capable of forming either homo- or heterodimers (103). The DNA-binding specificity of class I proteins is limited to the E-box site. Class II HLH proteins, which include members such as MyoD, myogenin, Atonal, NeuroD/BETA2, and the achaete-scute complex, show a tissue-restricted pattern of expression. With few exceptions, they are incapable of forming homodimers and preferentially heterodimerize with the E proteins. Class I-class II heterodimers can bind both canonical and noncanonical E-box sites (103). Class III HLH proteins include the Myc family of transcription factors, TFE3, SREBP-1, and the microphthalmia-associated transcription factor, Mi. Proteins of this class contain an LZ adjacent to the HLH motif (66, 177). Class IV HLH proteins define a family of molecules, including Mad, Max, and Mxi, that are capable of dimerizing with the Myc proteins or with one another (7, 22, 174). A group of HLH proteins that lack a basic region, including Id and emc, define the class V HLH proteins (18, 39, 47). Class V members are negative regulators of class I and class II HLH proteins (18, 39, 47). Class VI HLH proteins have as their defining feature a proline in their basic region. This group includes the Drosophila proteins Hairy and Enhancer of split (76, 141). Finally, the class VII HLH proteins are categorized by the presence of the bHLH-PAS domain and include members such as the aromatic hydrocarbon receptor (AHR), the AHR nuclear-translocator (Arnt), hypoxia-inducible factor 1α, and the Drosophila Single-minded and Period proteins (34).
FIG. 1
Multiple sequence alignment and classification of some representative members of the HLH family of transcription factors. Shown is a dendrogram created by aligning the sequences of the indicated HLH proteins by the Clustal W algorithm (160).
Recently, another classification method of HLH proteins has been described (6). Based on the amino acid sequences of 242 HLH proteins, a phylogenetic tree was created to group family members according to evolutionary relationships (6). Four major groups, A through D, which comprise more than 24 protein families were identified (6). The groupings were based upon DNA-binding specificity as well as conservation of amino acids at certain positions (6). As the number of HLH proteins continues to grow, this evolutionary or “natural” classification may provide a more accurate and convenient means of categorization.
1,710 citations
"Advances in the MYB-bHLH-WD Repeat ..." refers background in this paper
...Functionally, the basic region is important for making DNA contacts while the HLH region allows dimerization between bHLH proteins (Massari and Murre 2000)....
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TL;DR: A novel approach for enhancing the accumulation of natural products based on activation tagging by Agrobacterium-mediated transformation with a T-DNA that carries cauliflower mosaic virus 35S enhancer sequences at its right border is reported.
Abstract: Plants produce a wide array of natural products, many of which are likely to be useful bioactive structures. Unfortunately, these complex natural products usually occur at very low abundance and with restricted tissue distribution, thereby hindering their evaluation. Here, we report a novel approach for enhancing the accumulation of natural products based on activation tagging by Agrobacterium-mediated transformation with a T-DNA that carries cauliflower mosaic virus 35S enhancer sequences at its right border. Among ∼5000 Arabidopsis activation-tagged lines, we found a plant that exhibited intense purple pigmentation in many vegetative organs throughout development. This upregulation of pigmentation reflected a dominant mutation that resulted in massive activation of phenylpropanoid biosynthetic genes and enhanced accumulation of lignin, hydroxycinnamic acid esters, and flavonoids, including various anthocyanins that were responsible for the purple color. These phenotypes, caused by insertion of the viral enhancer sequences adjacent to an MYB transcription factor gene, indicate that activation tagging can overcome the stringent genetic controls regulating the accumulation of specific natural products during plant development. Our findings suggest a functional genomics approach to the biotechnological evaluation of phytochemical biodiversity through the generation of massively enriched tissue sources for drug screening and for isolating underlying regulatory and biosynthetic genes.
1,345 citations
"Advances in the MYB-bHLH-WD Repeat ..." refers background in this paper
...…(RNAi) approaches helped identify four partially redundant Arabidopsis MYB genes (PAP1, PAP2, MYB113 and MYB114, collectively known as PAP MYBs for production of anthocyanin pigment) dedicated to the regulation of the anthocyanin pathway in the shoot (Borevitz et al. 2000, Gonzalez et al. 2008)....
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TL;DR: It is demonstrated that overexpression of Myb113 or Myb114 results in substantial increases in pigment production similar to those previously seen as a result of over-expression of PAP1, and pigment production in these overexpressors remains TTG1- and bHLH-dependent.
Abstract: In all higher plants studied to date, the anthocyanin pigment pathway is regulated by a suite of transcription factors that include Myb, bHLH and WD-repeat proteins. However, in Arabidopsis thaliana, the Myb regulators remain to be conclusively identified, and little is known about anthocyanin pathway regulation by TTG1-dependent transcriptional complexes. Previous overexpression of the PAP1 Myb suggested that genes from the entire phenylpropanoid pathway are targets of regulation by Myb/bHLH/WD-repeat complexes in Arabidopsis, in contrast to other plants. Here we demonstrate that overexpression of Myb113 or Myb114 results in substantial increases in pigment production similar to those previously seen as a result of over-expression of PAP1, and pigment production in these overexpressors remains TTG1- and bHLH-dependent. Also, plants harboring an RNAi construct targeting PAP1 and three Myb candidates (PAP2, Myb113 and Myb114) showed downregulated Myb gene expression and obvious anthocyanin deficiencies. Correlated with these anthocyanin deficiencies is downregulation of the same late anthocyanin structural genes that are downregulated in ttg1 and bHLH anthocyanin mutants. Expression studies using GL3:GR and TTG1:GR fusions revealed direct regulation of the late biosynthetic genes only. Functional diversification between GL3 and EGL3 with regard to activation of gene targets was revealed by GL3:GR studies in single and double bHLH mutant seedlings. Expression profiles for Myb and bHLH regulators are also presented in the context of pigment production in young seedlings.
1,275 citations
"Advances in the MYB-bHLH-WD Repeat ..." refers background in this paper
...In addition, it was shown that the TTG2 gene is regulated by the MBW complex in the context of trichome and seed coat development (Johnson et al. 2002, Lepiniec et al. 2006, Ishida et al. 2007, Gonzalez et al. 2008, Zhao et al, 2008)....
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...As discussed elsewhere, the duplicated Arabidopsis PAP MYBs differentially regulate the anthocyanin pathway in varied environmental and developmental contexts (Lea et al. 2007, Gonzalez et al. 2008, Shan et al. 2009, Luo et al. 2012, Shin et al. 2013)....
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...…(RNAi) approaches helped identify four partially redundant Arabidopsis MYB genes (PAP1, PAP2, MYB113 and MYB114, collectively known as PAP MYBs for production of anthocyanin pigment) dedicated to the regulation of the anthocyanin pathway in the shoot (Borevitz et al. 2000, Gonzalez et al. 2008)....
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...Depicted on the right are Arabidopsis wild-type dry seed showing the brownish orange PA pigments expressed in the seed coat. regulation of late flavonoid biosynthetic genes (Baudry et al. 2004, Gonzalez et al. 2008, Xu et al. 2014)....
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...…of the sets differ between species and even tissues (Taylor and Briggs 1991, Martin et al. 1991, Quattrocchio et al. 1993, Deboo et al. 1995, Winkel-Shirley et al. 1995, Pelletier and Winkel Shirley 1996, Pelletier et al. 1997, Zhang et al. 2003, Morita et al. 2006, Gonzalez et al. 2008)....
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