The chalcone synthase multigene family of Petunia hybrida (V30): differential, light-regulated expression during flower development and UV light induction

Chalcone-Synthase-Encoding RdCHS1 Is Involved in Flavonoid Biosynthesis in Rhododendron delavayi

Flower color is an important ornamental feature that is often modulated by the contents of flavonoids. Chalcone synthase is the first key enzyme in the biosynthesis of flavonoids, but little is known about the role of R. delavayi CHS in flavonoid biosynthesis. In this paper, three CHS genes (RdCHS1-3) were successfully cloned from R. delavayi flowers. According to multiple sequence alignment and a phylogenetic analysis, only RdCHS1 contained all the highly conserved and important residues, which was classified into the cluster of bona fide CHSs. RdCHS1 was then subjected to further functional analysis. Real-time PCR analysis revealed that the transcripts of RdCHS1 were the highest in the leaves and lowest in the roots; this did not match the anthocyanin accumulation patterns during flower development. Biochemical characterization displayed that RdCHS1 could catalyze p-coumaroyl-CoA and malonyl-CoA molecules to produce naringenin chalcone. The physiological function of RdCHS1 was checked in Arabidopsis mutants and tobacco, and the results showed that RdCHS1 transgenes could recover the color phenotypes of the tt4 mutant and caused the tobacco flower color to change from pink to dark pink through modulating the expressions of endogenous structural and regulatory genes in the tobacco. All these results demonstrate that RdCHS1 fulfills the function of a bona fide CHS and contributes to flavonoid biosynthesis in R. delavayi.

VviKFB07 F-box E3 ubiquitin ligase promotes stilbene accumulation by ubiquitinating and degrading VviCHSs protein in grape

Stilbene and flavonoid are phytochemicals in plants and play an important role in plant disease resistance and human health. The regulation of stilbene and flavonoid synthesis in plants has been extensively studied at the transcriptional level, but translational and post-translational controls of stilbene and flavonoid biosynthesis are still poorly understood. In this study, a grape F-box E3 ubiquitin ligase VviKFB07 associated with the metabolism of stilbene and flavonoid was screened out with transcriptome. Overexpression of VviKFB07 in the Nicotiana tabacum resulted in a decrease in flavonol and anthocyanin content in corolla, and stable overexpression assays of VviKFB07 in grape callus promoted the accumulation of resveratrol. Subsequently, Yeast two-hybrid and bimolecular fluorescence complementation assays identified the physical interaction between VviKFB07 and VviCHSs proteins. In vivo experiments verified that VviKFB07 was involved in the ubiquitination and degradation of VviCHSs protein. Taken together, our findings clarify the role of ubiquitin ligase VviKFB07 in the synthesis of stilbene and flavonoid in grapes.

Multi-omics analysis reveals the mechanism of bHLH130 responding to low-nitrogen stress of apple rootstock

Nitrogen is critical for plant growth and development. With the increase of nitrogen fertilizer application, nitrogen use efficiency decreases, resulting in wasted resources. In apple (Malus domestica) rootstocks, the potential molecular mechanism for improving nitrogen uptake efficiency to alleviate low-nitrogen stress remains unclear. We utilized multi-omics approaches to investigate the mechanism of nitrogen uptake in two apple rootstocks with different responses to nitrogen stress, Malus hupehensis and Malus sieversii. Under low-nitrogen stress, Malus sieversii showed higher efficiency in nitrogen uptake. Multi-omics analysis revealed substantial differences in the expression of genes involved in flavonoid and lignin synthesis pathways between the two materials, which were related to the corresponding metabolites. We discovered that basic helix-loop-helix 130 (bHLH130) transcription factor was highly negatively associated with the flavonoid biosynthetic pathway. bHLH130 may directly bind to the chalcone synthase gene (CHS) promoter and inhibit its expression. Overexpressing CHS increased flavonoid accumulation and nitrogen uptake. Inhibiting bHLH130 increased flavonoid biosynthesis while decreasing lignin accumulation, thus improving nitrogen uptake efficiency. These findings revealed the molecular mechanism by which bHLH130 regulates flavonoid and lignin biosyntheses in apple rootstocks under low-nitrogen stress.

A transcriptional complex of FtMYB102 and FtbHLH4 coordinately regulates the accumulation of rutin in Fagopyrum tataricum

Tartary buckwheat is rich in flavonoids, which not only play an important role in the plant-environment interaction, but are also beneficial to human health. Rutin is a therapeutic flavonol which is massively accumulated in Tartary buckwheat. It has been demonstrated that transcription factors control rutin biosynthesis. However, the transcriptional regulatory network of rutin is not fully clear. In this study, through transcriptome and target metabolomics, we validated the role of FtMYB102 and FtbHLH4 TFs at the different developmental stages of Tartary buckwheat. The elevated accumulation of rutin in the sprout appears to be closely associated with the expression of FtMYB102 and FtbHLH4. Yeast two-hybrid, transient luciferase activity and co-immunoprecipitation demonstrated that FtMYB102 and FtbHLH4 can interact and form a transcriptional complex. Moreover, yeast one-hybrid showed that both FtMYB102 and FtbHLH4 directly bind to the promoter of chalcone isomerase (CHI), and they can coordinately induce CHI expression as shown by transient luciferase activity assay. Finally, we transferred FtMYB102 and FtbHLH4 into the hairy roots of Tartary buckwheat and found that they both can promote the accumulation of rutin. Our results indicate that FtMYB102 and FtbHLH4 can form a transcriptional complex by inducing CHI expression to coordinately promote the accumulation of rutin.

Pedoclimatic Conditions Influence the Morphological, Phytochemical and Biological Features of Mentha pulegium L

In this study, Mentha pulegium leaves and flowers harvested in three different Sicilian areas were investigated from a micromorphological, phytochemical and biological point of view. Light and scanning electron microscopy showed the presence of spherocrystalline masses of diosmin both in the leaf epidermal cells and in thin flower petals. Two different chemotypes were identified (I, kaempferide/rosmarinic acid; II, jaceidin isomer A). Phytochemical screening identified plant from collection site II as the richest in total phenolics (16.74 g GAE/100 g DE) and that from collection site I as the richest in flavonoids (46.56 g RE/100 g DE). Seventy-seven metabolites were identified both in flower and leaf extracts. Plant from site II showed the best antioxidant (0.90-83.72 µg/mL) and anti-inflammatory (27.44-196.31 µg/mL) activity expressed as half-maximal inhibitory concentration (IC₅₀) evaluated by DPPH, TEAC, FRAP, ORAC, BSA denaturation and protease inhibition assays. These data were also corroborated by in vitro cell-based assays on lymphocytes and erythrocytes. Moreover, plant of site II showed the best antiangiogenic properties (IC₅₀ 33.43-33.60 µg/mL) in vivo on a chick chorioallantoic membrane. In conclusion, pedoclimatic conditions influence the chemotype and the biological activity of M. pulegium, with chemotype I showing the most promising biological properties.

Impact of Growth Sites on the Phenolic Contents and Antioxidant Activities of Three Algerian Mentha Species (M. pulegium L., M. rotundifolia (L.) Huds., and M. spicata L.)

Research studies about the effect of environmental agents on the accumulation of phenolic compounds in medicinal plants are required to establish a set of optimal growth conditions. Hence, in this work, we considered the impact of habitat types, soil composition, climatic factors, and altitude on the content of phenolics in Mentha species [M. pulegium L. (MP), M. rotundifolia (L.) Huds. (MR), and M. spicata L. (MS)] grown in different regions of Algeria. The phenolic contents and antioxidant activities were analyzed using spectrophotometric and HPTLC methods. The harvesting localities differ by their altitudes and climates, but their soils are quite similar, characterized by slight alkalinity, moderate humidity, no-salinity, and high levels in organic matter. Both the contents in total phenolics (TPC), total flavonoids (TFC), and rosmarinic acid (RAC), and the antioxidant activities of Mentha samples collected from these Algerian localities are affected by the geographical regions of origin. The samples of MS and MP from the Khemis–Miliana region showed the highest concentration in TPC (MS, 7853 ± 265 mg GAE/100 g DW; MP, 5250 ± 191 mg GAE/100 g DW), while in Chemini, the MR samples were the richest in these compounds (MR, 3568 ± 195 mg GAE/100 g DW). Otherwise, the MP (from Tichy), MR (from Tajboudjth), and MS (from Khemis–Miliana) specimens exhibited the highest levels of TFC and RAC. The antioxidant levels in a total activity test (reduction of phosphomolybdate) appear correlated with the total phenolic contents, but this was not the case for most of the important ROS-scavenging and iron-chelating capacities for which the quality of polyphenols is probably more important than their amounts. A principal component analysis (PCA) score plot indicates that all of the Mentha samples can be divided into four groups. These discriminated groups appear comparatively similar in phenolic contents and antioxidant activities. As for the harvest localities, the Mentha samples were divided into four groups in which the phenolic contents and antioxidant activities were comparatively equivalent.

Transcription factors evolve faster than their structural gene targets in the flavonoid pigment pathway

Dissecting the relationship between gene function and substitution rates is key to understanding genome-wide patterns of molecular evolution. Biochemical pathways provide powerful systems for investigating this relationship because the functional role of each gene is often well characterized. Here, we investigate the evolution of the flavonoid pigment pathway in the colorful Petunieae clade of the tomato family (Solanaceae). This pathway is broadly conserved in plants, both in terms of its structural elements and its MYB, basic helix–loop–helix, and WD40 transcriptional regulators, and its function has been extensively studied, particularly in model species of petunia. We built a phylotranscriptomic data set for 69 species of Petunieae to infer patterns of molecular evolution across pathway genes and across lineages. We found that transcription factors exhibit faster rates of molecular evolution (dN/dS) than their targets, with the highly specialized MYB genes evolving fastest. Using the largest comparative data set to date, we recovered little support for the hypothesis that upstream enzymes evolve slower than those occupying more downstream positions, although expression levels do predict molecular evolutionary rates. Although shifts in floral pigmentation were only weakly related to changes affecting coding regions, we found a strong relationship with the presence/absence patterns of MYB transcripts. Intensely pigmented species express all three main MYB anthocyanin activators in petals, whereas pale or white species express few or none. Our findings reinforce the notion that pathway regulators have a dynamic history, involving higher rates of molecular evolution than structural components, along with frequent changes in expression during color transitions.

Metabolic Engineering of Isoflavones: An Updated Overview

Isoflavones are ecophysiologically active secondary metabolites derived from the phenylpropanoid pathway. They were mostly found in leguminous plants, especially in the pea family. Isoflavones play a key role in plant-environment interactions and act as phytoalexins also having an array of health benefits to the humans. According to epidemiological studies, a high intake of isoflavones-rich diets linked to a lower risk of hormone-related cancers, osteoporosis, menopausal symptoms, and cardiovascular diseases. These characteristics lead to the significant advancement in the studies on genetic and metabolic engineering of isoflavones in plants. As a result, a number of structural and regulatory genes involved in isoflavone biosynthesis in plants have been identified and characterized. Subsequently, they were engineered in various crop plants for the increased production of isoflavones. Furthermore, with the advent of high-throughput technologies, the regulation of isoflavone biosynthesis gains attention to increase or decrease the level of isoflavones in the crop plants. In the review, we begin with the role of isoflavones in plants, environment, and its benefits in human health. Besides, the main theme is to discuss the updated research progress in metabolic engineering of isoflavones in other plants species and regulation of production of isoflavones in soybeans.

Molecular cloning and characterization of chalcone synthase gene from Coelogyne ovalis Lindl. and its stress-dependent expression

Chalcone synthase (CHS, EC 2.3.1.74) is one of the key and rate-limiting enzymes of phenylpropanoid pathway which plays superior roles in the production of secondary metabolites. In the present study a full-length cDNA of CHS gene was isolated and characterized from Coelogyne ovalis, an orchid of ornamental and medicinal importance. The CHS gene sequence from C. ovalis (CoCHS) was found to be 1445 bp and comprised an open reading frame of 1182 bp, encoding for 394 amino acid residues. Further, the sequence alignment and phylogenetic analysis revealed that CoCHS protein shared high degree of similarity with CHS protein of other orchid species. It also confirmed that it contained all four motifs (I to IV) and signature sequence for the functionality of this gene. Structural modeling of CoCHS based on the crystallographic structure of Freesia hybrida indicated that CoCHS had a similar structure. Quantitative polymerase chain reaction (qPCR) disclosed that CoCHS was expressed in all tissues examined, with the highest transcript being in leaves, followed by pseudobulbs and roots. CoCHS expression was also evaluated in the in vitro-raised plantlets under the abiotic stress (dark, cold, UV-B, wounding, salinity). mRNA transcript expression of CHS gene was found to be positively enhanced and regulated by the different stress types. A correlation between the CoCHS transcript expression with flavonoid and anthocyanin contents revealed that a positive correlation existed between metabolites' content and CoCHS expression within the in vivo as well as in the in vitro-raised plant parts.

Chalcone synthases (CHSs): the symbolic type III polyketide synthases

Present review provides a thorough insight on some significant aspects of CHSs over a period of about past three decades with a better outlook for future studies toward comprehending the structural and mechanistic intricacy of this symbolic enzyme. Polyketide synthases (PKSs) form a large family of iteratively acting multifunctional proteins that are involved in the biosynthesis of spectrum of natural products. They exhibit remarkable versatility in the structural configuration and functional organization with an incredible ability to generate different classes of compounds other than the characteristic secondary metabolite constituents. Architecturally, chalcone synthase (CHS) is considered to be the simplest representative of Type III PKSs. The enzyme is pivotal for phenylpropanoid biosynthesis and is also well known for catalyzing the initial step of the flavonoid/isoflavonoid pathway. Being the first Type III enzyme to be discovered, CHS has been subjected to ample investigations which, to a greater extent, have tried to understand its structural complexity and promiscuous functional behavior. In this context, we vehemently tried to collect the fragmented information entirely focussed on this symbolic enzyme from about past three-four decades. The aim of this review is to selectively summarize data on some of the fundamental aspects of CHSs viz, its history and distribution, localization, structure and analogs in non-plant hosts, promoter analyses, and role in defense, with an emphasis on mechanistic studies in different species and vis-à-vis mutation-led changes, and evolutionary significance which has been discussed in detail. The present review gives an insight with a better perspective for the scientific community for future studies devoted towards delimiting the mechanistic and structural basis of polyketide biosynthetic machinery vis-à-vis CHS.

Transcriptome Sequencing and Metabolome Analysis Reveal Genes Involved in Pigmentation of Green-Colored Cotton Fibers

Green-colored fiber (GCF) is the unique raw material for naturally colored cotton textile but we know little about the pigmentation process in GCF. Here we compared transcriptomes and metabolomes of 12, 18 and 24 days post-anthesis (DPA) fibers from a green fiber cotton accession and its white-colored fiber (WCF) near-isogenic line. We found a total of 2047 non-redundant metabolites in GCF and WCF that were enriched in 80 pathways, including those of biosynthesis of phenylpropanoid, cutin, suberin, and wax. Most metabolites, particularly sinapaldehyde, of the phenylpropanoid pathway had a higher level in GCF than in WCF, consistent with the significant up-regulation of the genes responsible for biosynthesis of those metabolites. Weighted gene co-expression network analysis (WGCNA) of genes differentially expressed between GCF and WCF was used to uncover gene-modules co-expressed or associated with the accumulation of green pigments. Of the 16 gene-modules co-expressed with fiber color or time points, the blue module associated with G24 (i.e., GCF at 24 DPA) was of particular importance because a large proportion of its genes were significantly up-regulated at 24 DPA when fiber color was visually distinguishable between GCF and WCF. A total of 56 hub genes, including the two homoeologous Gh4CL4 that could act in green pigment biosynthesis, were identified among the genes of the blue module that are mainly involved in lipid metabolism, phenylpropanoid biosynthesis, RNA transcription, signaling, and transport. Our results provide novel insights into the mechanisms underlying pigmentation of green fibers and clues for developing cottons with stable green colored fibers.

Assessing Anthocyanin Biosynthesis in Solanaceae as a Model Pathway for Secondary Metabolism

Solanaceae have played an important role in elucidating how flower color is specified by the flavonoid biosynthesis pathway (FBP), which produces anthocyanins and other secondary metabolites. With well-established reverse genetics tools and rich genomic resources, Solanaceae provide a robust framework to examine the diversification of this well-studied pathway over short evolutionary timescales and to evaluate the predictability of genetic perturbation on pathway flux. Genomes of eight Solanaceae species, nine related asterids, and four rosids were mined to evaluate variation in copy number of the suite of FBP enzymes involved in anthocyanin biosynthesis. Comparison of annotation sources indicated that the NCBI annotation pipeline generated more and longer FBP annotations on average than genome-specific annotation pipelines. The pattern of diversification of each enzyme among asterids was assessed by phylogenetic analysis, showing that the CHS superfamily encompasses a large paralogous family of ancient and recent duplicates, whereas other FBP enzymes have diversified via recent duplications in particular lineages. Heterologous expression of a pansy F3′5′H gene in tobacco changed flower color from pink to dark purple, demonstrating that anthocyanin production can be predictably modified using reverse genetics. These results suggest that the Solanaceae FBP could be an ideal system to model genotype-to-phenotype interactions for secondary metabolism.

The light-induced transcription factor FtMYB116 promotes accumulation of rutin in Fagopyrum tataricum

Tartary buckwheat (Fagopyrum tataricum) not only provides a supplement to primary grain crops in China but also has high medicinal value, by virtue of its rich content of flavonoids possessing antioxidant, anti-inflammatory, and anticancer properties. Light is an important environmental factor that can regulate the synthesis of plant secondary metabolites. In this study, we treated tartary buckwheat seedlings with different wavelengths of light and found that red and blue light could increase the content of flavonoids and the expression of genes involved in flavonoid synthesis pathways. Through coexpression analysis, we identified a new MYB transcription factor (FtMYB116) that can be induced by red and blue light. Yeast one-hybrid assays and an electrophoretic mobility shift assay showed that FtMYB116 binds directly to the promoter region of flavonoid-3'-hydroxylase (F3'H), and a transient luciferase activity assay indicated that FtMYB116 can induce F3'H expression. After transforming FtMYB116 into the hairy roots of tartary buckwheat, we observed significant increases in the content of rutin and quercetin. Collectively, our results indicate that red and blue light promote an increase in flavonoid content in tartary buckwheat seedlings; we also identified a new MYB transcription factor, FtMYB116, that promotes the accumulation of rutin via direct activation of F3'H expression.

Light induces petal color change in Quisqualis indica (Combretaceae)

Petal color change, a common phenomenon in angiosperms, is induced by various environmental and endogenous factors. Interestingly, this phenomenon is important for attracting pollinators and further reproductive success. Quisqualis indica L. (Combretaceae) is a tropical Asian climber that undergoes sequential petal color change from white to pink to red. This color changing process is thought to be a good strategy to attract more pollinators. However, the underlying physiological and biochemical mechanisms driving this petal color change phenomenon is still underexplored. In this context, we investigated whether changes in pH, pollination, light, temperature or ethylene mediate petal color change. We found that the detected changes in petal pH were not significant enough to induce color alterations. Additionally, pollination and temperatures of 20-30 °C did not alter the rate of petal color change; however, flowers did not open when exposed to constant temperatures at 15 °C or 35 °C. Moreover, the application of ethylene inhibitor, i.e., silver thiosulphate, did not prevent color change. It is worth mentioning here that in our study we found light as a strong factor influencing the whole process of petal color change, as petals remained white under dark conditions. Altogether, the present study suggests that petal color change in Q. indica is induced by light and not by changes in petal pH, pollination, ethylene, or temperature, while extremely low or high temperatures affect flower anthesis. In summary, our findings represent the probable mechanism underlying the phenomenon of petal color change, which is important for understanding flower color evolution.

Response of miR156-SPL Module during the Red Peel Coloration of Bagging-Treated Chinese Sand Pear (Pyrus pyrifolia Nakai)

MicroRNA156 is an evolutionarily highly conserved plant micro-RNA (miRNA) that controls an age-dependent flowering pathway. miR156 and its target SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes regulate anthocyanin accumulation in plants, but it is unknown whether this process is affected by light. Red Chinese sand pear (Pyrus pyrifolia) fruits exhibit a unique coloration pattern in response to bagging treatments, which makes them appropriate for studying the molecular mechanism underlying light-induced anthocyanin accumulation in fruit. Based on high-throughput miRNA and degradome sequencing data, we determined that miR156 was expressed in pear fruit peels, and targeted four SPL genes. Light-responsive elements were detected in the promoter regions of the miR156a and miR156ba precursors. We identified 19 SPL genes using the “Suli” pear (Pyrus pyrifolia Chinese White Pear Group) genome database, of which seven members were putative miR156 targets. The upregulated expression of anthocyanin biosynthetic and regulatory genes and downregulated expression of PpSPL2, PpSPL5, PpSPL7, PpSPL9, PpSPL10, PpSPL13, PpSPL16, PpSPL17, and PpSPL18 were observed in pear fruits after bags were removed from plants during the anthocyanin accumulation period. Additionally, miR156a/ba/g/s/sa abundance increased after bags were removed. Yeast two-hybrid results suggested that PpMYB10, PpbHLH, and PpWD40 could form a protein complex, probably involved in anthocyanin biosynthesis. Additionally, PpSPL10 and PpSPL13 interacted with PpMYB10. The results obtained in this study are helpful in understanding the possible role of miR156 and its target PpSPL genes in regulating light-induced red peel coloration and anthocyanin accumulation in pear.

Molecular and functional characterization of two isoforms of chalcone synthase and their expression analysis in relation to flavonoid constituents in Grewia asiatica L

Chalcone synthase constitutes a functionally diverse gene family producing wide range of flavonoids by catalyzing the initial step of the phenylpropanoid pathway. There is a pivotal role of flavonoids in pollen function as they are imperative for pollen maturation and pollen tube growth during sexual reproduction in flowering plants. Here we focused on medicinally important fruit-bearing shrub Grewia asiatica. It is a rich repository of flavonoids. The fruits are highly acclaimed for various putative health benefits. Despite its importance, full commercial exploitation is hampered due to two drawbacks which include short shelf life of its fruits and larger seed volume. To circumvent these constraints, seed abortion is one of the viable options. Molecular interventions tested in a number of economic crops have been to impair male reproductive function by disrupting the chalcone synthase (CHS) gene activity. Against this backdrop the aim of the present study included cloning and characterization of two full-length cDNA clones of GaCHS isoforms from the CHS multigene family. These included GaCHS1 (NCBI acc. KX129910) and GaCHS2 (NCBI acc. KX129911) with an ORF of 1176 and 1170 bp, respectively. GaCHSs were heterologously expressed and purified in E. coli to validate their functionality. Functionality of CHS isoforms was also characterized via enzyme kinetic studies using five different substrates. We observed differential substrate specificities in terms of their Km and Vmax values. Accumulation of flavonoid constituents naringenin and quercetin were also quantified and their relative concentrations corroborated well with the expression levels of GaCHSs. Further, our results demonstrate that GaCHS isoforms show differential expression patterns at different reproductive phenological stages. Transcript levels of GaCHS2 were more than its isoform GaCHS1 at the anthesis stage of flower development pointing towards its probable role in male reproductive maturity.

Genome-wide identification and phylogenetic analysis of the chalcone synthase gene family in rice

The enzymes of the chalcone synthase family are also known as type III polyketide synthases (PKS), and produce a series of secondary metabolites in bacteria, fungi and plants. In a number of plants, genes encoding PKS comprise a large multigene family. Currently, detailed reports on rice (Oryza sativa) PKS (OsPKS) family genes and tissue expression profiling are limited. Here, 27 candidate OsPKS genes were identified in the rice genome,and 23 gene structures were confirmed by EST and cDNA sequencing; phylogenetic analysis has indicated that these 23 OsPKS members could be clustered into three groups (I-III). Comparative analysis has shown OsPKS08 and OsPKS26 could be classified with the CHS genes of other species. Two members OsPKS10 and OsPKS21 were grouped into anther specific chalcone synthase-like (ASCL) clade. Intron/exon structure analysis revealed that nearly all of the OsPKS members contained one phase-1 intron at a conserved Cys. Analysis of chromosomal localization and genome distribution showed that some of the members were distributed on a chromosome as a cluster. Expression data exhibited widespread distribution of the rice OsPKS gene family within plant tissues, suggesting functional diversification of the OsPKS genes. Our results will contribute to future study of the complexity of the OsPKS gene family in rice.

Isolation of CHS Gene from Brunfelsia acuminata Flowers and Its Regulation in Anthocyanin Biosysthesis

Chalcone synthase gene (BaCHS) from Brunfelsia acuminata flowers was isolated using RT-PCR and RACE. The coding region of the gene is 1425-bp with an open reading frame of 1170-bp, 73-bp 5'UTR, and 172-bp 3'UTR. Its deduced protein does not have a signal peptide but does contain a cond_enzyme superfamily domain, and consists of 389 amino acids with a predicted molecular mass of 42,699 Da and a pI of 6.57. The deduced amino acid sequence of BaCHS shares 90%, 88%, 85%, 84% and 79% identity with CHS from Petunia hybrida, Nicotiana tabacum, Solanum lycopersicum, Capsicum annuum and Camellia sinensis, respectively. The striking color change from dark purple to light purple and ultimately lead to pure white resulted from a decline in anthocyanin content of the petals and was preceded by a decrease in the expression of BaCHS. Its gene expression was positively correlated with the contents of anthocyanin (p ≤ 0.01).

Evolutionary correlations in flavonoid production across flowers and leaves in the Iochrominae (Solanaceae)

Plant reproductive and vegetative tissues often use the same biochemical pathways to produce specialized metabolites. In such cases, selection acting on the synthesis of specific products in a particular tissue could result in correlated changes in other products of the pathway, both in the same tissue and in other tissues. This study examined how changes in floral anthocyanin pigmentation affect the production of other compounds of the flavonoid pathway in flowers and in leaves. Focusing on the Iochrominae, a clade of Solanaceae with a wide range of flower colors, liquid chromatography coupled with mass spectrometry and UV detection was used to profile and quantify the variation in two classes of flavonoids, anthocyanins and flavonols. Purple, red, orange and white-flowered Iochrominae produced all of the six common anthocyanidin types, as well as several classes of flavonols. Differences in anthocyanin and flavonol production were significantly correlated in flowers, particularly with respect to B ring hydroxylation pattern. However, these differences in floral flavonoids were not strongly related to differences in leaf chemistry. Specifically, most species made only flavonols (not anthocyanins) in leaves, and these comprised the two most common flavonols, quercetin and kaempferol, regardless of the color of the flower. These results suggest that shifts in flower color may occur without significant pleiotropic consequences for flavonoid production in vegetative tissues. Similar studies in other systems will be important for testing the generality of this pattern in other groups of flowering plants.

Phylogeny and Expression Analyses Reveal Important Roles for Plant PKS III Family during the Conquest of Land by Plants and Angiosperm Diversification

Polyketide synthases (PKSs) utilize the products of primary metabolism to synthesize a wide array of secondary metabolites in both prokaryotic and eukaryotic organisms. PKSs can be grouped into three distinct classes, types I, II, and III, based on enzyme structure, substrate specificity, and catalytic mechanisms. The type III PKS enzymes function as homodimers, and are the only class of PKS that do not require acyl carrier protein. Plant type III PKS enzymes, also known as chalcone synthase (CHS)-like enzymes, are of particular interest due to their functional diversity. In this study, we mined type III PKS gene sequences from the genomes of six aquatic algae and 25 land plants (1 bryophyte, 1 lycophyte, 2 basal angiosperms, 16 core eudicots, and 5 monocots). PKS III sequences were found relatively conserved in all embryophytes, but not exist in algae. We also examined gene expression patterns by analyzing available transcriptome data, and identified potential cis-regulatory elements in upstream sequences. Phylogenetic trees of dicots angiosperms showed that plant type III PKS proteins fall into three clades. Clade A contains CHS/STS-type enzymes coding genes with diverse transcriptional expression patterns and enzymatic functions, while clade B is further divided into subclades b1 and b2, which consist of anther-specific CHS-like enzymes. Differentiation regions, such as amino acids 196-207 between clades A and B, and predicted positive selected sites within α-helixes in late appeared branches of clade A, account for the major diversification in substrate choice and catalytic reaction. The integrity and location of conserved cis-elements containing MYB and bHLH binding sites can affect transcription levels. Potential binding sites for transcription factors such as WRKY, SPL, or AP2/EREBP may contribute to tissue- or taxon-specific differences in gene expression. Our data shows that gene duplications and functional diversification of plant type III PKS enzymes played a critical role in the ancient conquest of the land by early plants and angiosperm diversification.

Genome-Wide Identification, Characterization and Expression Analysis of the Chalcone Synthase Family in Maize

Members of the chalcone synthase (CHS) family participate in the synthesis of a series of secondary metabolites in plants, fungi and bacteria. The metabolites play important roles in protecting land plants against various environmental stresses during the evolutionary process. Our research was conducted on comprehensive investigation of CHS genes in maize (Zea mays L.), including their phylogenetic relationships, gene structures, chromosomal locations and expression analysis. Fourteen CHS genes (ZmCHS01-14) were identified in the genome of maize, representing one of the largest numbers of CHS family members identified in one organism to date. The gene family was classified into four major classes (classes I-IV) based on their phylogenetic relationships. Most of them contained two exons and one intron. The 14 genes were unevenly located on six chromosomes. Two segmental duplication events were identified, which might contribute to the expansion of the maize CHS gene family to some extent. In addition, quantitative real-time PCR and microarray data analyses suggested that ZmCHS genes exhibited various expression patterns, indicating functional diversification of the ZmCHS genes. Our results will contribute to future studies of the complexity of the CHS gene family in maize and provide valuable information for the systematic analysis of the functions of the CHS gene family.

A De novo Transcriptomic Approach to Identify Flavonoids and Anthocyanins "Switch-Off" in Olive (Olea europaea L.) Drupes at Different Stages of Maturation

Highlights A de novo transcriptome reconstruction of olive drupes was performed in two genotypesGene expression was monitored during drupe development in two olive cultivarsTranscripts involved in flavonoid and anthocyanin pathways were analyzed in Cassanese and Leucocarpa cultivarsBoth cultivar and developmental stage impact gene expression in Olea europaea fruits. During ripening, the fruits of the olive tree (Olea europaea L.) undergo a progressive chromatic change characterized by the formation of a red-brown "spot" which gradually extends on the epidermis and in the innermost part of the mesocarp. This event finds an exception in the Leucocarpa cultivar, in which we observe a destabilized equilibrium between the metabolisms of chlorophyll and other pigments, particularly the anthocyanins whose switch-off during maturation promotes the white coloration of fruits. Despite its importance, genomic information on the olive tree is still lacking. Different RNA-seq libraries were generated from drupes of "Leucocarpa" and "Cassanese" olive genotypes, sampled at 100 and 130 days after flowering (DAF), and were used in order to identify transcripts involved in the main phenotypic changes of fruits during maturation and their corresponding expression patterns. A total of 103,359 transcripts were obtained and 3792 and 3064 were differentially expressed in "Leucocarpa" and "Cassanese" genotypes, respectively, during 100-130 DAF transition. Among them flavonoid and anthocyanin related transcripts such as phenylalanine ammonia lyase (PAL), cinnamate 4-hydroxylase (C4H), 4-coumarate-CoA ligase (4CL), chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavonol 3'-hydrogenase (F3'H), flavonol 3'5 '-hydrogenase (F3'5'H), flavonol synthase (FLS), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS), UDP-glucose:anthocianidin: flavonoid glucosyltransferase (UFGT) were identified. These results contribute to reducing the current gap in information regarding metabolic processes, including those linked to fruit pigmentation in the olive.

Two showy traits, scent emission and pigmentation, are finely coregulated by the MYB transcription factor PH4 in petunia flowers

The mechanism underlying the emission of phenylpropanoid volatiles is poorly understood. Here, we reveal the involvement of PH4, a petunia MYB-R2R3 transcription factor previously studied for its role in vacuolar acidification, in floral volatile emission. We used the virus-induced gene silencing (VIGS) approach to knock down PH4 expression in petunia, measured volatile emission and internal pool sizes by GC-MS, and analyzed transcript abundances of scent-related phenylpropanoid genes in flowers. Silencing of PH4 resulted in a marked decrease in floral phenylpropanoid volatile emission, with a concurrent increase in internal pool levels. Expression of scent-related phenylpropanoid genes was not affected. To identify putative scent-related targets of PH4, we silenced PH5, a tonoplast-localized H(+) -ATPase that maintains vacuolar pH homeostasis. Suppression of PH5 did not yield the reduced-emission phenotype, suggesting that PH4 does not operate in the context of floral scent through regulation of vacuolar pH. We conclude that PH4 is a key floral regulator that integrates volatile production and emission processes and interconnects two essential floral traits - color and scent.

Genetic basis for a rare floral mutant in an Andean species of Solanaceae

PREMISE OF THE STUDY

White forms of typically pigmented flowers are one of the most common polymorphisms in flowering plants. Although the range of genetic changes that give rise to white phenotypes is well known from model systems, few studies have identified causative mutations in natural populations.

METHODS

Here we combine genetic studies, in vitro enzyme assays, and biochemical analyses to identify the mechanism underlying the loss of anthocyanin pigment production in the naturally occurring white-flowered morph of Iochroma calycinum (Solanaceae).

KEY RESULTS

Comparison of anthocyanin gene sequences revealed a putative loss-of-function mutation, an 11 amino-acid deletion in dihydroflavonol 4-reductase (DFR), in the white morph. Functional assays of Dfr alleles from blue and white morphs demonstrated that this deletion results in a loss of enzymatic activity, indicating that the deletion could be solely responsible for the lack of pigment production. Consistent with this hypothesis, quantitative PCR showed no significant differences in expression of anthocyanin genes between the morphs. Also, thin layer chromatography confirmed that the white morph continues to accumulate compounds upstream of the DFR enzyme.

CONCLUSIONS

Collectively, these experiments indicate that the structural mutation at Dfr underlies the rare white flower morph of I. calycinum. This study is one of only a few examples where a flower color polymorphism is due to a loss-of-function mutation in the coding region of an anthocyanin enzyme. The rarity of such mutations in nature suggests that negative consequences prevent fixation across populations.

The velamen protects photosynthetic orchid roots against UV-B damage, and a large dated phylogeny implies multiple gains and losses of this function during the Cenozoic

UV-B radiation damage in leaves is prevented by epidermal UV-screening compounds that can be modulated throughout ontogeny. In epiphytic orchids, roots need to be protected against UV-B because they photosynthesize, sometimes even replacing the leaves. How orchid roots, which are covered by a dead tissue called velamen, avoid UV-B radiation is currently unknown. We tested for a UV-B protective function of the velamen using gene expression analyses, mass spectrometry, histochemistry, and chlorophyll fluorescence in Phalaenopsis × hybrida roots. We also investigated its evolution using comparative phylogenetic methods. Our data show that two paralogues of the chalcone synthase (CHS) gene family are UV-B-induced in orchid root tips, triggering the accumulation of two UV-B-absorbing flavonoids and resulting in effective protection of the photosynthetic root cortex. Phylogenetic and dating analyses imply that the two CHS lineages duplicated c. 100 million yr before the rise of epiphytic orchids. These findings indicate an additional role for the epiphytic orchid velamen previously thought to function solely in absorbing water and nutrients. This new function, which fundamentally differs from the mechanism of UV-B avoidance in leaves, arose following an ancient duplication of CHS, and has probably contributed to the family's expansion into the canopy during the Cenozoic.

Undesired small RNAs originate from an artificial microRNA precursor in transgenic petunia (Petunia hybrida)

Although artificial microRNA (amiRNA) technology has been used frequently in gene silencing in plants, little research has been devoted to investigating the accuracy of amiRNA precursor processing. In this work, amiRNAchs1 (amiRchs1), based on the Arabidopsis miR319a precursor, was expressed in order to suppress the expression of CHS genes in petunia. The transgenic plants showed the CHS gene-silencing phenotype. A modified 5′ RACE technique was used to map small-RNA-directed cleavage sites and to detect processing intermediates of the amiRchs1 precursor. The results showed that the target CHS mRNAs were cut at the expected sites and that the amiRchs1 precursor was processed from loop to base. The accumulation of small RNAs in amiRchs1 transgenic petunia petals was analyzed using the deep-sequencing technique. The results showed that, alongside the accumulation of the desired artificial microRNAs, additional small RNAs that originated from other regions of the amiRNA precursor were also accumulated at high frequency. Some of these had previously been found to be accumulated at low frequency in the products of ath-miR319a precursor processing and some of them were accompanied by 3′-tailing variant. Potential targets of the undesired small RNAs were discovered in petunia and other Solanaceae plants. The findings draw attention to the potential occurrence of undesired target silencing induced by such additional small RNAs when amiRNA technology is used. No appreciable production of secondary small RNAs occurred, despite the fact that amiRchs1 was designed to have perfect complementarity to its CHS-J target. This confirmed that perfect pairing between an amiRNA and its targets is not the trigger for secondary small RNA production. In conjunction with the observation that amiRNAs with perfect complementarity to their target genes show high efficiency and specificity in gene silencing, this finding has an important bearing on future applications of amiRNAs in gene silencing in plants.

A molecular assessment of the genetic model of spathe color inheritance in Anthurium andraeanum (Hort.)

Past genetic studies have shown three independent loci designated O, R and M control spathe color in Anthurium andraeanum (Hort.). To evaluate the genetic model and to understand the control of anthocyanin biosynthesis at the molecular level, the expression of the anthocyanin biosynthetic genes, CHS, F3H, DFR, ANS and F3'H, was examined at the mRNA and protein levels and correlated to anthocyanin content and spathe color in eight genetically characterized anthurium cultivars representing different states of the O, R and M loci. The results showed that the expression of F3H and ANS was co-regulated by a putative transcription factor encoded by the R locus, and the expression of DFR was regulated by a putative transcription factor encoded by the O locus. White cultivars, which were in the homozygous recessive state for either O or R or both, exhibited reduced expression of the anthocyanin biosynthetic genes and hence had negligible levels of anthocyanin. Cultivars that were mm displayed reduced expression of F3'H suggesting that it may either encode a defective form of the F3'H gene or a regulator that controls its expression. Additionally, a correlation between anthocyanin abundance and the expression of F3'H in the red cultivars suggested that F3'H expression may be a key control point in the regulation of anthocyanin biosynthesis in anthurium and hence plays a major role in influencing the shade intensity in red cultivars. These findings provide evidence in support of the genetic model for color inheritance in the spathe.

A cis-element responsible for cGMP in the promoter of the soybean chalcone synthase gene

The cyclic nucleotides cGMP and cAMP have been reported to play key roles in the regulation of plant processes and responses. We have previously reported that several genes encoding flavonoid biosynthetic enzymes, including chalcone synthase (CHS) in soybean (Glycine max L.), were induced by cGMP but not cAMP. The soybean genome contains nine CHS gene copies (GmCHS1-9). We investigated the responsiveness of several GmCHS genes to cGMP, cAMP, NO, and white light. Quantitative RT-PCR analysis showed that the transcript levels of GmCHS7 and GmCHS8 were increased by 3.6- and 3.8-fold, respectively, with cGMP whereas the transcript levels of GmCHS2 remained constant. Although cAMP had no effect on the transcript levels of the three genes, NO had an activation effect on all three. White light activated the three genes in a transient manner, with GmCHS2, GmCHS7, and GmCHS8 transcript levels increasing 3-fold after 3 h and decreasing to basal levels after 9 h. The GmCHS8 promoter contains several important cis-elements, including the G-box and H-box forming the Unit-I-like sequence and the MYB binding sequence, a target of the GmMYB176 transcription factor regulating the expression of GmCHS8. A transient gene expression assay revealed the activation of the Unit-I-like sequence, but not of the MYB binding sequence, by cGMP. The combination of G-box and H-box was necessary for cGMP responsiveness. Taken together, these results suggest that the Unit-I-like sequence in the promoters of GmCHS7 and GmCHS8 is a cGMP responsive cis-element in these genes and that NO exerts its effect via cis-elements other than the Unit-I-like sequence.

Chalcone synthase family genes have redundant roles in anthocyanin biosynthesis and in response to blue/UV-A light in turnip (Brassica rapa; Brassicaceae)

PREMISE OF THE STUDY

The epidermis of Brassica rapa (turnip) cv. Tsuda contains light-induced anthocyanins, visible signs of activity of chalcone synthase (CHS), a key anthocyanin biosynthetic enzyme, which is encoded by the CHS gene family. To elucidate the regulation of this light-induced pigmentation, we isolated Brassica rapa CHS1-CHS6 (BrCHS1-CHS6) and characterized their cis-elements and expression patterns.

METHODS

Epidermises of light-exposed swollen hypocotyls (ESHS) were harvested to analyze transcription levels of BrCHS genes by real-time PCR. Different promoters for the genes were inserted into tobacco to examine pCHS-GUS activity by histochemistry. Yeast-one-hybridization was used to detect binding activity of BrCHS motifs to transcription factors.

KEY RESULTS

Transcript levels of BrCHS1, -4, and -5 and anthocyanin-biosynthesis-related genes F3H, DFR, and ANS were high, while those of BrCHS2, -3, and -6 were almost undetectable in pigmented ESHS. However, in leaves, CHS5, F3H, and ANS expression was higher than in nonpigmented ESHS, but transcription of DFR was not detected. In the analysis of BrCHS1 and BrCHS3 promoter activity, GUS activity was strong in pigmented flowers of BrPCHS1-GUS-transformed tobacco plants, but nearly absent in BrPCHS3-GUS-transformed plants. Transcript levels of regulators, BrMYB75 and BrTT8, were strongly associated with the anthocyanin content and were light-induced. Coregulated cis-elements were found in promoters of BrCHS1,-4, and -5, and BrMYB75 and BrTT8 had high binding activities to the BrCHS Unit 1 motif.

CONCLUSIONS

The chalcone synthase gene family encodes a redundant set of light-responsive, tissue-specific genes that are expressed at different levels and are involved in flavonoid biosynthesis in Tsuda turnip.

The flavonoid pathway regulates the petal colors of cotton flower

Although biochemists and geneticists have studied the cotton flower for more than one century, little is known about the molecular mechanisms underlying the dramatic color change that occurs during its short developmental life following blooming. Through the analysis of world cotton germplasms, we found that all of the flowers underwent color changes post-anthesis, but there is a diverse array of petal colors among cotton species, with cream, yellow and red colors dominating the color scheme. Genetic and biochemical analyses indicated that both the original cream and red colors and the color changes post-anthesis were related to flavonoid content. The anthocyanin content and the expression of biosynthesis genes were both increased from blooming to one day post-anthesis (DPA) when the flower was withering and undergoing abscission. Our results indicated that the color changes and flavonoid biosynthesis of cotton flowers were precisely controlled and genetically regulated. In addition, flavonol synthase (FLS) genes involved in flavonol biosynthesis showed specific expression at 11 am when the flowers were fully opened. The anthocyanidin reductase (ANR) genes, which are responsible for proanthocyanidins biosynthesis, showed the highest expression at 6 pm on 0 DPA, when the flowers were withered. Light showed primary, moderate and little effects on flavonol, anthocyanin and proanthocyanidin biosynthesis, respectively. Flavonol biosynthesis was in response to light exposure, while anthocyanin biosynthesis was involved in flower color changes. Further expression analysis of flavonoid genes in flowers of wild type and a flavanone 3-hydroxylase (F3H) silenced line showed that the development of cotton flower color was controlled by a complex interaction between genes and light. These results present novel information regarding flavonoids metabolism and flower development.

Phosphorus starvation induces post-transcriptional CHS gene silencing in Petunia corolla

The corolla of Petunia 'Magic Samba' exhibits unstable anthocyanin expression depending on its phosphorus content. Phosphorus deficiency enhanced post-transcriptional gene silencing of chalcone synthase - A in the corolla. Petunia (Petunia hybrida) 'Magic Samba' has unstable red-white bicolored corollas that respond to nutrient deficiency. We grew this cultivar hydroponically using solutions that lacked one or several nutrients to identify the specific nutrient related to anthocyanin expression in corolla. The white area of the corolla widened under phosphorus (P)-deficient conditions. When the P content of the corolla grown under P-deficient conditions dropped to <2,000 ppm, completely white corollas continued to develop in >40 corollas until the plants died. Other elemental deficiencies had no clear effects on anthocyanin suppression in the corolla. After phosphate was resupplied to the P-deficient plants, anthocyanin was restored in the corollas. The expression of chalcone synthase-A (CHS-A) was suppressed in the white area that widened under P-suppressed conditions, whereas the expression of several other genes related to anthocyanin biosynthesis was enhanced more in the white area than in the red area. Reddish leaves and sepals developed under the P-deficient condition, which is a typical P-deficiency symptom. Two genes related to anthocyanin biosynthesis were enhanced in the reddish organs. Small interfering RNA analysis of CHS-A showed that the suppression resulted from post-transcriptional gene silencing (PTGS). Thus, it was hypothesized that the enhancement of anthocyanin biosynthetic gene expression due to P-deficiency triggered PTGS of CHS-A, which resulted in white corolla development.

Deep sequencing uncovers commonality in small RNA profiles between transgene-induced and naturally occurring RNA silencing of chalcone synthase-A gene in petunia

Background

Introduction of a transgene that transcribes RNA homologous to an endogenous gene in the plant genome can induce silencing of both genes, a phenomenon termed cosuppression. Cosuppression was first discovered in transgenic petunia plants transformed with the CHS-A gene encoding chalcone synthase, in which nonpigmented sectors in flowers or completely white flowers are produced. Some of the flower-color patterns observed in transgenic petunias having CHS-A cosuppression resemble those in existing nontransgenic varieties. Although the mechanism by which white sectors are generated in nontransgenic petunia is known to be due to RNA silencing of the CHS-A gene as in cosuppression, whether the same trigger(s) and/or pattern of RNA degradation are involved in these phenomena has not been known. Here, we addressed this question using deep-sequencing and bioinformatic analyses of small RNAs.

Results

We analyzed short interfering RNAs (siRNAs) produced in nonpigmented sectors of petal tissues in transgenic petunia plants that have CHS-A cosuppression and a nontransgenic petunia variety Red Star, that has naturally occurring CHS-A RNA silencing. In both silencing systems, 21-nt and 22-nt siRNAs were the most and the second-most abundant size classes, respectively. CHS-A siRNA production was confined to exon 2, indicating that RNA degradation through the RNA silencing pathway occurred in this exon. Common siRNAs were detected in cosuppression and naturally occurring RNA silencing, and their ranks based on the number of siRNAs in these plants were correlated with each other. Noticeably, highly abundant siRNAs were common in these systems. Phased siRNAs were detected in multiple phases at multiple sites, and some of the ends of the regions that produced phased siRNAs were conserved.

Conclusions

The features of siRNA production found to be common to cosuppression and naturally occurring silencing of the CHS-A gene indicate mechanistic similarities between these silencing systems especially in the biosynthetic processes of siRNAs including cleavage of CHS-A transcripts and subsequent production of secondary siRNAs in exon 2. The data also suggest that these events occurred at multiple sites, which can be a feature of these silencing phenomena.

Methylation effect on chalcone synthase gene expression determines anthocyanin pigmentation in floral tissues of two Oncidium orchid cultivars

The anthocyanin-biosynthetic pathway was studied in flowers of Oncidium Gower Ramsey with yellow floral color and mosaic red anthocyanin in lip crests, sepals and petals, and compared with the anthocyanin biosynthesis in flowers of Oncidium Honey Dollp, a natural somatoclone derived from tissue culture of Gower Ramsey, with a yellow perianth without red anthocyanins in floral tissues. HPLC analysis revealed that the red anthocyanin in lip crests of the Gower Ramsey cultivar comprised peonidin-3-O-glucoside, delphinidin-3-O-glucoside and cyanidin-3-O-glucoside, whereas Honey Dollp was devoid of anthocyanin compounds. Among the five anthocyanin-biosynthetic genes, OgCHS was actively expressed in lip crests of Gower Ramsey flowers, but no transcripts of OgCHS were detected in Honey Dollp floral tissues. Transient expression of OgCHS by bombardment confirmed that recovery of the OgCHS gene expression completed the anthocyanin pathway and produced anthocyanin compounds in lip crests of Honey Dollp flowers. Transcription factor genes regulating anthocyanin biosynthesis showed no distinctive differences in the expression level of OgMYB1, OgbHLH and OgWD40 between the two cultivars. A methylation assay revealed that the promoter of OgCHS was not methylated in Gower Ramsey, while a positive methylation effect was present in the upstream promoter region of OgCHS in Honey Dollp. Overall, our results suggest that the failure of anthocyanin accumulation in Honey Dollp floral tissues may be attributed to inactivation of the OgCHS gene resulting from the epigenetic methylation of 5'-upstream promoter region.

Tandemly arranged chalcone synthase A genes contribute to the spatially regulated expression of siRNA and the natural bicolor floral phenotype in Petunia hybrida

The natural bicolor floral traits of the horticultural petunia (Petunia hybrida) cultivars Picotee and Star are caused by the spatial repression of the chalcone synthase A (CHS-A) gene, which encodes an anthocyanin biosynthetic enzyme. Here we show that Picotee and Star petunias carry the same short interfering RNA (siRNA)-producing locus, consisting of two intact CHS-A copies, PhCHS-A1 and PhCHS-A2, in a tandem head-to-tail orientation. The precursor CHS mRNAs are transcribed from the two CHS-A copies throughout the bicolored petals, but the mature CHS mRNAs are not found in the white tissues. An analysis of small RNAs revealed the accumulation of siRNAs of 21 nucleotides that originated from the exon 2 region of both CHS-A copies. This accumulation is closely correlated with the disappearance of the CHS mRNAs, indicating that the bicolor floral phenotype is caused by the spatially regulated post-transcriptional silencing of both CHS-A genes. Linkage between the tandemly arranged CHS-A allele and the bicolor floral trait indicates that the CHS-A allele is a necessary factor to confer the trait. We suppose that the spatially regulated production of siRNAs in Picotee and Star flowers is triggered by another putative regulatory locus, and that the silencing mechanism in this case may be different from other known mechanisms of post-transcriptional gene silencing in plants. A sequence analysis of wild Petunia species indicated that these tandem CHS-A genes originated from Petunia integrifolia and/or Petunia inflata, the parental species of P. hybrida, as a result of a chromosomal rearrangement rather than a gene duplication event.

[Progress in genes related to seed-coat color in soybean]

Seed-coat color has changed from black to yellow during natural and artificial selection of cultivated soybean from wild soybean, and it is also an important morphological marker. Therefore, discovering genes related to the soybean seed-coat color will play a very important role in breeding and evolutionary study. Different seed-coat colors caused by deposition of various anthocyanin pigments. Although pigmentation has been well dissected at molecular level in several plant species, the genes controlling natural variation of seed-coat color in soybean remain to be unknown. Genes related to seed-coat color in soybean were discussed in this paper, including 5 genetic loci (I, T, W1, R and O). Locus I is located in a region that riches in chalcone synthase (CHS) genes on chromosome 8. Gene CHS is a multi-gene family with highly conserved sequences in soybean. Locus T located on chromosome 6 has been cloned and verified, which encodes a flavon-oid-3'-hydroxylase. Mutant of F3'H can not interact with the heme-binding domain due to lack of conservative domain GGEK caused by a nucleotide deletion in the coding region of F3'H. Locus R is located between A668-1 and K387-1 on chromosome 9 (linkage group K). This locus may encode a R2R3 MYB transcription factor or a UDP flavonoid 3-O glyco-syltransferase. Locus O is located between Satt207 and Satt493 on chromosome 8 (linkage group A2) and its molecular characteristics has not been characterized. Locus W1 may be a homology of F3'5'H gene.

Coincident sequence-specific RNA degradation of linked transgenes in the plant genome

The expression of transgenes in plant genomes can be inhibited by either transcriptional gene silencing or posttranscriptional gene silencing (PTGS). Overexpression of the chalcone synthase-A (CHS-A) transgene triggers PTGS of CHS-A and thus results in loss of flower pigmentation in petunia. We previously demonstrated that epigenetic inactivation of CHS-A transgene transcription leads to a reversion of the PTGS phenotype. Although neomycin phosphotransferase II (nptII), a marker gene co-introduced into the genome with the CHS-A transgene, is not normally silenced in petunia, even when CHS-A is silenced, here we found that nptII was silenced in a petunia line in which CHS-A PTGS was induced, but not in the revertant plants that had no PTGS of CHS-A. Transcriptional activity, accumulation of short interfering RNAs, and restoration of mRNA level after infection with viruses that had suppressor proteins of gene silencing indicated that the mechanism for nptII silencing was posttranscriptional. Read-through transcripts of the CHS-A gene toward the nptII gene were detected. Deep-sequencing analysis revealed a striking difference between the predominant size class of small RNAs produced from the read-through transcripts (22 nt) and that from the CHS-A RNAs (21 nt). These results implicate the involvement of read-through transcription and distinct phases of RNA degradation in the coincident PTGS of linked transgenes and provide new insights into the destabilization of transgene expression.

Characterization of a chalcone synthase (CHS) flower-specific promoter from Lilium orential 'Sorbonne'

The first enzyme in the flavonoid pathway, chalcone synthase, is encoded by a gene (CHS) whose expression is normally under developmental control. In our previous studies, an 896-bp promoter region of a flower-specific CHS gene was isolated from Lilium orential 'Sorbonne', and designated as PLoCHS. Here, the PLoCHS promoter was fused to the β-glucuronidase (GUS) gene to characterize its spatial and temporal expression in Petunia hybrida 'Dreams Midnight' using an Agrobacterium-mediated leaf disc transformation method. Our results demonstrated that GUS expression was present in flowers, but reduced or absent in the other tissues (leaf and stem) examined. In petals, GUS activity reached its peak at flower developmental stage 4, and decreased at later stages. Deletion analysis indicated that even a 307-bp fragment of the PLoCHS promoter could still direct flower-specific expression. Further deletion of the region from -261 to -72 bp resulted in weak expression in different organs, including flowers, leaves and stems. This evidence combined with prediction of cis-acting elements in the PLoCHS promoter suggests that the TACPyAT box located in this promoter plays a key role in the regulation of organ-specific expression.

Chalcone synthase and its functions in plant resistance

Chalcone synthase (CHS, EC 2.3.1.74) is a key enzyme of the flavonoid/isoflavonoid biosynthesis pathway. Besides being part of the plant developmental program the CHS gene expression is induced in plants under stress conditions such as UV light, bacterial or fungal infection. CHS expression causes accumulation of flavonoid and isoflavonoid phytoalexins and is involved in the salicylic acid defense pathway. This review will discuss CHS and its function in plant resistance.

Sense and antisense transcripts of convergent gene pairs in Arabidopsis thaliana can share a common polyadenylation region

The Arabidopsis genome contains a large number of gene pairs that encode sense and antisense transcripts with overlapping 3′ regions, indicative for a potential role of natural antisense transcription in regulating sense gene expression or transcript processing. When we mapped poly(A) transcripts of three plant gene pairs with long overlapping antisense transcripts, we identified an unusual transcript composition for two of the three gene pairs. Both genes pairs encoded a class of long sense transcripts and a class of short sense transcripts that terminate within the same polyadenylation region as the antisense transcripts encoded by the opposite strand. We find that the presence of the short sense transcript was not dependent on the expression of an antisense transcript. This argues against the assumption that the common termination region for sense and antisense poly(A) transcripts is the result of antisense-specific regulation. We speculate that for some genes evolution may have especially favoured alternative polyadenylation events that shorten transcript length for gene pairs with overlapping sense/antisense transcription, if this reduces the likelihood for dsRNA formation and transcript degradation.

Genome-wide analysis of the chalcone synthase superfamily genes of Physcomitrella patens

Enzymes of the chalcone synthase (CHS) superfamily catalyze the production of a variety of secondary metabolites in bacteria, fungi and plants. Some of these metabolites have played important roles during the early evolution of land plants by providing protection from various environmental assaults including UV irradiation. The genome of the moss, Physcomitrella patens, contains at least 17 putative CHS superfamily genes. Three of these genes (PpCHS2b, PpCHS3 and PpCHS5) exist in multiple copies and all have corresponding ESTs. PpCHS11 and probably also PpCHS9 encode non-CHS enzymes, while PpCHS10 appears to be an ortholog of plant genes encoding anther-specific CHS-like enzymes. It was inferred from the genomic locations of genes comprising it that the moss CHS superfamily expanded through tandem and segmental duplication events. Inferred exon-intron architectures and results from phylogenetic analysis of representative CHS superfamily genes of P. patens and other plants showed that intron gain and loss occurred several times during evolution of this gene superfamily. A high proportion of P. patens CHS genes (7 of 14 genes for which the full sequence is known and probably 3 additional genes) are intronless, prompting speculation that CHS gene duplication via retrotransposition has occurred at least twice in the moss lineage. Analyses of sequence similarities, catalytic motifs and EST data indicated that a surprisingly large number (as many as 13) of the moss CHS superfamily genes probably encode active CHS. EST distribution data and different light responsiveness observed with selected genes provide evidence for their differential regulation. Observed diversity within the moss CHS superfamily and amenability to gene manipulation make Physcomitrella a highly suitable model system for studying expansion and functional diversification of the plant CHS superfamily of genes.

The role of light on foliage colour development in coleus (Solenostemon scutellarioides (L.) Codd)

Many coleus (Solenostemon scutellarioides (L). Codd) varieties change pigmentation when exposed to high light intensity: they increase anthocyanin amount and decrease chlorophyll content. The physiological and molecular mechanisms involved in this phenomenon have been investigated in two independent experiments using two related coleus varieties 'Royal Glissade' (RG) and 'UF06-1-06' (UF). The developmental stage of a leaf had a minimum effect on colouration. Light intensity affected the rate of colour transition, anthocyanin and chlorophyll concentrations, and plant growth. Foliage colour was affected by a complex interaction between anthocyanin and chlorophyll. The isolation and expression analysis of several structural and regulatory genes involved in the anthocyanin biosynthetic pathway, and the genes Lchb2 and CBS, an indicator of cellular energy status are reported. Results indicate a close similarity between transcript amount and anthocyanin accumulation and its rate was tightly associated with light intensity. Differences in foliage colour between RG and UF are due to different sensitivity to light, probably affecting chlorophyll content and F3H and UFGT expression.

Altered trans-regulatory control of gene expression in multiple anthocyanin genes contributes to adaptive flower color evolution in Mimulus aurantiacus

A fundamental goal in evolutionary biology is to identify the molecular changes responsible for adaptive evolution. In this study, we describe a genetic analysis to determine whether the molecular changes contributing to adaptive flower color divergence in Mimulus aurantiacus affect gene expression or enzymatic activity. High performance liquid chromatography analysis confirms that flower color differences are caused by the presence versus absence of anthocyanin pigments. Cosegregation analysis and in vitro enzymatic assays rule out mutations that affect enzymatic function in the anthocyanin pathway genes. By contrast, cosegregation of gene expression with flower color suggests that tissue-specific differences in pigment production are caused by the coordinated regulatory control of three anthocyanin pathway genes. We provide evidence indicating that these expression differences are caused by a locus that acts in trans- and explains 45% of the phenotypic variance in flower color. A second locus with sequence similarity to the R2R3 MYB family of transcription factors explains 9% of the variation but does so in a complex fashion. These results demonstrate one of only two examples where we have clear evidence of both the adaptive nature of a flower color transition and evidence for its genetic basis. In both cases, mutations appear to affect expression of the anthocyanin structural genes. Future studies will allow us to determine whether these differences represent a real bias in favor of mutations that affect gene expression.

Tomato leaf curl virus satellite DNA as a gene silencing vector activated by helper virus infection

Tomato leaf curl virus (TLCV) satellite DNA (sat-DNA) constructs containing functional segments of the cauliflower mosaic virus (CaMV) 35S promoter, replicate in tobacco in the presence of helper TLCV and silence GUS activity in transgenic tobacco plants containing a CaMV 35S-GUS expression cassette. We have analysed these plants for evidence of the hallmarks of silencing. The GUS transcript was not detectable in the leaves of GUS-silenced tobacco plants. These plants contained siRNAs of approximately 23 nt in length homologous to both the 35S promoter region and the GUS ORF. The absence of GUS expression and the existence of siRNAs in transgenic plants show that the silencing induced by TLCV sat-DNA is due to RNA silencing. To test the utility of this silencing system, a 341 nucleotide promoter sequence of the petunia chalcone synthase A (ChsA) was inserted into the sat-DNA and inoculated into petunia plants, together with the helper TLCV, and found to markedly reduce pigmentation of flowers and the level of ChsA transcript. This DNA-based silencing system has the potential to introduce epigenetic traits via short DNA inserts to a variety of plants that are hosts to different geminiviruses supporting the sat-DNA.

Altering expression of the flavonoid 3'-hydroxylase gene modified flavonol ratios and pollen germination in transgenic Mitchell petunia plants

Antisense technology was successfully used to reduce flavonoid 3'-hydroxylase (F3'H) gene expression and enzyme activity and to promote the accumulation of monohydroxylated flavonols in petunia flower tissue. The hydroxylation pattern of specific flavonoid groups is a target for modification because of the possible associated changes in a range of factors including colour, stress tolerance and reproductive viability. Petunia (cv. Mitchell) plants were transformed to express in the antisense orientation the sequences encoding the F3'H (asF3'H). Transformants showed a range of responses, in terms of the level of endogenous F3'H gene expression and the relative proportion of the monohydroxylated flavonol (kaempferol) glycosides that accumulated. Kaempferol glycosides increased from 7% of the total flavonols in flower limb tissue of the wild type plants, to 45% in the flower limb tissue of line 114, the transgenic line that also showed the greatest decrease in F3'H expression in flower tissue. In leaf tissue, the trend was for a decrease in total flavonol concentration, with the relative proportion of kaempferol glycosides varying from ~40 to 80% of the total flavonols. The changes in leaf tissue were not consistent with the changes observed in flower tissue of the same lines. Endogenous F3'H activity in flower limb tissue was not completely shut down, although an 80% decrease in enzyme activity was recorded for line 114. The residual F3'H activity was still sufficient that quercetin glycosides remained as the major flavonol form. Alteration of F3'H activity appears to have affected overall flavonoid biosynthesis. A decrease in total flavonol concentration was observed in leaf tissue and two other flavonoid biosynthetic genes were down-regulated. No morphological changes were observed in the transgenic plants; however, up to a 60% decrease in pollen germination was observed in line 13. Thus, the relatively small change in flavonoid biosynthesis induced by the asF3'H transgene, correlated with several other effects beyond just the specific biosynthetic step regulated by this enzyme.

Molecular evolution and functional specialization of chalcone synthase superfamily from Phalaenopsis Orchid

Plant genomes appear to exploit the process of gene duplication as a primary means of acquiring biochemical and developmental flexibility. The best example is the gene encoding chalcone synthase (CHS, EC2.3.1.74), the first committed step in flavonoid biosynthesis. In this study, we examined the molecular evolution of three CHS family members of Phalaenopsis including a novel chs gene (phchs5), which is slowly evolved. The inferred phylogeny of the chs genes of Phalaenopsis with other two orchid plants, Bromoheadia finlaysoniana and Dendrobium hybrid, suggested that gene duplication and divergence have occurred before divergence of these three genera. Relatively quantitative RT-PCR analysis identified expression patterns of these three chs genes in different floral tissues at different developmental stages. Phchs5 was the most abundantly expressed chs gene in floral organs and it was specifically transcribed in petal and lip at the stages when anthocyanin accumulated (stage1-4). Phchs3 and phchs4 were expressed at much lower levels than phchs5. Phchs3 was expressed in pigmented tissue (including lip, petal and sepal) at middle stages (stages 2-4) and in colorless reproductive tissue at late stage (stage 5). Phchs4 was only expressed in petal at earlier stages (stage 1-3) and in lip at middle stage (stage 4). These results present new data on differentiation of gene expression among duplicate copies of chs genes in Phalaenopsis.

Cryptochrome 2 is involved in betacyanin decomposition induced by blue light in Suaeda salsa

Seeds of the halophyte Suaeda salsa (L.) Pall. were cultured in 24 h dark and 14 h blue light / 10 h dark to examine the role of blue light and the blue-light-absorbing photoreceptor cryptochrome 2 (CRY2) in betacyanin accumulation, hypocotyl elongation and cotyledon opening in S. salsa seedlings. Darkness significantly promoted betacyanin accumulation and hypocotyl elongation but inhibited cotyledon opening. Blue light suppressed betacyanin accumulation and hypocotyl elongation but stimulated cotyledon opening. Betacyanin in S. salsa seedlings decomposed with time in blue light. Western blot analysis showed that CRY2 protein accumulated both in hypocotyls and cotyledons of S. salsa seedlings grown in dark, but degraded with time in blue light, which was paralleled by a decrease of tyrosine hydroxylation activity of tyrosinase, a key enzyme involved in the betalain biosynthesis pathway. These results suggest that CRY2 protein mediates betacyanin decomposition via inactivation of tyrosinase in S. salsa seedlings, and the blue-light-dependent degradation of CRY2 protein is crucial to its function.