Flavonol rhamnosylation indirectly modifies the cell wall defects of RHAMNOSE BIOSYNTHESIS1 mutants by altering rhamnose flux

FtMYB163 Gene Encodes SG7 R2R3-MYB Transcription Factor from Tartary Buckwheat (Fagopyrum tataricum Gaertn.) to Promote Flavonol Accumulation in Transgenic Arabidopsis thaliana

Tartary buckwheat (Fagopyrum tataricum Gaertn.) is a coarse grain crop rich in flavonoids that are beneficial to human health because they function as anti-inflammatories and provide protection against cardiovascular disease and diabetes. Flavonoid biosynthesis is a complex process, and relatively little is known about the regulatory pathways involved in Tartary buckwheat. Here, we cloned and characterized the FtMYB163 gene from Tartary buckwheat, which encodes a member of the R2R3-MYB transcription factor family. Amino acid sequence and phylogenetic analysis indicate that FtMYB163 is a member of subgroup 7 (SG7) and closely related to FeMYBF1, which regulates flavonol synthesis in common buckwheat (F. esculentum). We demonstrated that FtMYB163 localizes to the nucleus and has transcriptional activity. Expression levels of FtMYB163 in the roots, stems, leaves, flowers, and seeds of F. tataricum were positively correlated with the total flavonoid contents of these tissues. Overexpression of FtMYB163 in transgenic Arabidopsis enhanced the expression of several genes involved in early flavonoid biosynthesis (AtCHS, AtCHI, AtF3H, and AtFLS) and significantly increased the accumulation of several flavonoids, including naringenin chalcone, naringenin-7-O-glucoside, eriodictyol, and eight flavonol compounds. Our findings demonstrate that FtMYB163 positively regulates flavonol biosynthesis by changing the expression of several key genes in flavonoid biosynthetic pathways.

Integrated transcriptome and targeted metabolome analyses provide insights into flavonoid biosynthesis in kiwifruit (Actinidia chinensis)

So far, a variety of metabolite components of kiwifruit have been elucidated. However, the identification and analysis of flavonoids in different tissues of kiwifruit are rarely carried out. In this study, we performed transcriptome and metabolome analyses of roots (Gkf_R), stems (Gkf_T), leaves (Gkf_L), and fruits (Gkf_F) to provide insights into the differential accumulation and regulation mechanisms of flavonoids in kiwifruit. Results showed that a total of 301 flavonoids were identified, in four tissues with different accumulation trends, and a large proportion of flavonoids had high accumulation in Gkf_L and Gkf_R. A total of 84 genes have been identified involved in the flavonoid biosynthesis pathway, and the expression levels of five LAR, two DFR, and one HCT were significantly correlated with the accumulation of 16 flavonoids and co-localized in the flavonoid biosynthesis pathway. In addition, a total of 2362 transcription factor genes were identified, mainly MYBs, bHLHs, ERFs, bZIPs and WRKYs, among which the expression level of bHLH74, RAP2.3L/4L/10L, MYB1R1, and WRKY33 were significantly correlated with 25, 56, 43, and 24 kinds of flavonoids. Our research will enrich the metabolomic data and provide useful information for the directed genetic improvement and application in the pharmaceutical industry of kiwifruit.

TON1 recruiting motif 21 positively regulates the flavonoid metabolic pathway at the translational level in Arabidopsis thaliana

MAIN CONCLUSION

This study reveals that TRM21 acts as a positive regulator of flavonoid biosynthesis at the translational level in Arabidopsis, impacting both secondary metabolites and genes associated with root hair growth. TRM (TONNEAU1-recruiting motif) superfamily proteins are reported to be involved in microtubule assembly. However, the functions of this protein family are just beginning to be uncovered. Here, we provide metabolomic and genetic evidence that 1 of the 34 TRM members, TRM21, positively regulates the biosynthesis of flavonoids at the translational level in Arabidopsis thaliana. A loss-of-function mutation in TRM21 led to root hair growth defects and stunted plant growth, accompanied by significant alterations in secondary metabolites, particularly a marked reduction in flavonoid content. Interestingly, our study revealed that the transcription levels of genes involved in the flavonoid biosynthesis pathway remained unchanged in the trm21 mutants, but there was a significant downregulation in the translation levels of certain genes [flavanone 3-hydroxylase (F3H), dihydroflavonol-4-reductase (DFR), anthocyanidin reductase (ANR), flavanone 3'-hydroxylase (F3'H), flavonol synthase (FLS), chalcone synthase (CHS)]. Additionally, the translation levels of some genes related to root hair growth [RHO-related GTPases of plant 2 (ROP2), root hair defective 6 (RHD6), root hair defective 2 (RHD2)] were also reduced in the trm21 mutants. Taken together, these results indicate that TRM21 functions as a positive regulator of flavonoid biosynthesis at the translational level in Arabidopsis.

Biochemical and Transcriptome Analyses Reveal a Stronger Capacity for Photosynthate Accumulation in Low-Tillering Rice Varieties

Moderate control of rice tillering and the development of rice varieties with large panicles are important topics for future high-yield rice breeding. Herein, we found that low-tillering rice varieties stopped tillering earlier and had a larger leaf area of the sixth leaf. Notably, at 28 days after sowing, the rice seedlings of the low-tillering group had an average single-culm above-ground biomass of 0.84 g, significantly higher than that of the multi-tillering group by 56.26%, and their NSC (non-structural carbohydrate) and starch contents in sheaths were increased by 43.34% and 97.75%, respectively. These results indicated that the low-tillering group of rice varieties had a stronger ability to store photosynthetic products in the form of starch in their sheaths, which was thus more beneficial for their large panicle development. The results of carbon and nitrogen metabolism analyses showed that the low-tillering group had a relatively strong carbon metabolism activity, which was more favorable for the accumulation of photosynthesis products and the following development of large panicles, while the multi-tillering group showed relatively strong nitrogen metabolism activity, which was more beneficial for the development and formation of new organs, such as tillers. Accordingly, in the low-tillering rice varieties, the up-regulated genes were enriched in the pathways mainly related to the synthesis of carbohydrates, while the down-regulated genes were mainly enriched in the nitrogen metabolism pathways. This study provides new insights into the mechanism of rice tillering regulation and promotes the development of new varieties with ideal plant types.

Cellulose assembles into helical bundles of uniform handedness in cell walls with abnormal pectin composition

Plant cells and organs grow into a remarkable diversity of shapes, as directed by cell walls composed primarily of polysaccharides such as cellulose and multiple structurally distinct pectins. The properties of the cell wall that allow for precise control of morphogenesis are distinct from those of the individual polysaccharide components. For example, cellulose, the primary determinant of cell morphology, is a chiral macromolecule that can self-assemble in vitro into larger-scale structures of consistent chirality, and yet most plant cells do not display consistent chirality in their growth. One interesting exception is the Arabidopsis thaliana rhm1 mutant, which has decreased levels of the pectin rhamnogalacturonan-I and causes conical petal epidermal cells to grow with a left-handed helical twist. Here, we show that in rhm1 the cellulose is bundled into large macrofibrils, unlike the evenly distributed microfibrils of the wild type. This cellulose bundling becomes increasingly severe over time, consistent with cellulose being synthesized normally and then self-associating into macrofibrils. We also show that in the wild type, cellulose is oriented transversely, whereas in rhm1 mutants, the cellulose forms right-handed helices that can account for the helical morphology of the petal cells. Our results indicate that when the composition of pectin is altered, cellulose can form cellular-scale chiral structures in vivo, analogous to the helicoids formed in vitro by cellulose nano-crystals. We propose that an important emergent property of the interplay between rhamnogalacturonan-I and cellulose is to permit the assembly of nonbundled cellulose structures, providing plants flexibility to orient cellulose and direct morphogenesis.

Natural variation of warm temperature-induced raffinose accumulation identifies TREHALOSE-6-PHOSPHATE SYNTHASE 1 as a modulator of thermotolerance

High-temperature stress limits plant growth and reproduction. Exposure to high temperature, however, also elicits a physiological response, which protects plants from the damage evoked by heat. This response involves a partial reconfiguration of the metabolome including the accumulation of the trisaccharide raffinose. In this study, we explored the intraspecific variation of warm temperature-induced raffinose accumulation as a metabolic marker for temperature responsiveness with the aim to identify genes that contribute to thermotolerance. By combining raffinose measurements in 250 Arabidopsis thaliana accessions following a mild heat treatment with genome-wide association studies, we identified five genomic regions that were associated with the observed trait variation. Subsequent functional analyses confirmed a causal relationship between TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1) and warm temperature-dependent raffinose synthesis. Moreover, complementation of the tps1-1 null mutant with functionally distinct TPS1 isoforms differentially affected carbohydrate metabolism under more severe heat stress. While higher TPS1 activity was associated with reduced endogenous sucrose levels and thermotolerance, disruption of trehalose 6-phosphate signalling resulted in higher accumulation of transitory starch and sucrose and was associated with enhanced heat resistance. Taken together, our findings suggest a role of trehalose 6-phosphate in thermotolerance, most likely through its regulatory function in carbon partitioning and sucrose homoeostasis.

Metabolite Profiling and Transcriptome Analysis Explain the Difference in Accumulation of Bioactive Constituents in Taxilli Herba from Two Hosts

Taxilli Herba (TH) is a semi-parasitic herb and the host is a key factor affecting its quality. Flavonoids are the main bioactive constituents in TH. However, studies on the difference in accumulation of flavonoids in TH from different hosts are vacant. In this study, integrated transcriptomic and metabolomic analyses were performed on TH from Morus alba L. (SS) and Liquidambar formosana Hance (FXS) to investigate the relationship between the regulation of gene expression and the accumulation of bioactive constituents. The results showed that a total of 3319 differentially expressed genes (DEGs) were screened in transcriptomic analysis, including 1726 up-regulated genes and 1547 down-regulated genes. In addition, 81 compounds were identified using ultra-fast performance liquid chromatography coupled with triple quadrupole-time of flight ion trap tandem mass spectrometry (UFLC-Triple TOF-MS/MS) analysis, and the relative contents of flavonol aglycones and glycosides were higher in TH from SS group than those from the FXS group. A putative biosynthesis network of flavonoids was created, combined with structural genes, and the expression patterns of genes were mostly consistent with the variation of bioactive constituents. It was noteworthy that the UDP-glycosyltransferase genes might participate in downstream flavonoid glycosides synthesis. The findings of this work will provide a new way to understand the quality formation of TH from the aspects of metabolite changes and molecular mechanism.

Molecular identification of phenylalanine ammonia lyase-encoding genes EfPALs and EfPAL2-interacting transcription factors in Euryale ferox

Flavonoids are one of the most important secondary metabolites in plants, and phenylalanine ammonia-lyase (PAL) is the first rate-limiting enzyme for their biosynthesis. However, detailed information on the regulation of PAL in plants is still little. In this study, PAL in E. ferox was identified and functionally analyzed, and its upstream regulatory network was investigated. Through genome-wide identification, we obtained 12 putative PAL genes from E. ferox. Phylogenetic tree and synteny analysis revealed that PAL in E. ferox was expanded and mostly preserved. Subsequently, enzyme activity assays demonstrated that EfPAL1 and EfPAL2 both catalyzed the production of cinnamic acid from phenylalanine only, with EfPAL2 exhibiting a superior enzyme activity. Overexpression of EfPAL1 and EfPAL2 in Arabidopsis thaliana, respectively, both enhanced the biosynthesis of flavonoids. Furthermore, two transcription factors, EfZAT11 and EfHY5, were identified by yeast one-hybrid library assays as binding to the promoter of EfPAL2, and further luciferase (LUC) activity analysis indicated that EfZAT11 promoted the expression of EfPAL2, while EfHY5 repressed the expression of EfPAL2. These results suggested that EfZAT11 and EfHY5 positively and negatively regulate flavonoid biosynthesis, respectively. Subcellular localization revealed that EfZAT11 and EfHY5 were localized in the nucleus. Our findings clarified the key EfPAL1 and EfPAL2 of flavonoid biosynthesis in E. ferox and established the upstream regulatory network of EfPAL2, which would provide novel information for the study of flavonoid biosynthesis mechanism.

Identification of QTL underlying the main stem related traits in a doubled haploid barley population

Lodging reduces grain yield in cereal crops. The height, diameter and strength of stem are crucial for lodging resistance, grain yield, and photosynthate transport in barley. Understanding the genetic basis of stem benefits barley breeding. Here, we evaluated 13 stem related traits after 28 days of heading in a barley DH population in two consecutive years. Significant phenotypic correlations between lodging index (LI) and other stem traits were observed. Three mapping methods using the experimental data and the BLUP data, detected 27 stable and major QTLs, and 22 QTL clustered regions. Many QTLs were consistent with previously reported traits for grain filling rate, internodes, panicle and lodging resistance. Further, candidate genes were predicted for stable and major QTLs and were associated with plant development and adverse stress in the transition from vegetative stage to reproductive stage. This study provided potential genetic basis and new information for exploring barley stem morphology, and laid a foundation for map-based cloning and further fine mapping of these QTLs.

Flavonoids in vegetables: improvement of dietary flavonoids by metabolic engineering to promote health

Flavonoids are the most abundant polyphenols in plants, and have antioxidant effects as well as other bioactivities (e.g., anti-inflammatory, anti-cancer, anti-allergic, and neuroprotective effects). Vegetables are rich in flavonoids and are indispensable in our daily diet. Moreover, the vegetables as chassis for producing natural products would emerge as a promising means for cost-effective and sustainable production of flavonoids. Understanding the metabolic engineering of flavonoids in vegetables allows us to improve their nutrient composition. In this review, a comprehensive overview of flavonoids in vegetables, including the characterized types and distribution, health-promoting effects, associated metabolic pathways, and applied metabolic engineering are provided. We also introduce breakthroughs in multi-omics approaches that pertain to the elucidation of flavonoids metabolism in vegetables, as well as prospective and potential genome-editing technologies. Based on the varied composition and content of flavonoids among vegetables, dietary suggestions are further provided for human health.

Proteomic analysis of Euryale ferox Salisb seeds at different developmental stages

The development of plant seeds is accompanied by changes in their internal substances. The edible part of E. ferox is the seed, and starch and flavonoids are the storage substances and functional substances in E. ferox seeds respectively. Herein, four time points of seed development, including after flowering T10 (10 days), T20 (20 days), T30 (30 days) and T40 (40 days), were investigated by using iTRAQ technology. A total of 2809 differential proteins were identified. The enrichment analysis of differential proteins found that they were mainly enriched in starch synthesis pathways and flavonoid biosynthesis pathways. The key candidate enzymes for starch synthesis, APS (c54069), APL (c55730), SBE (c56416), SSS (c54912) and GBSS (c53181), were identified. At the same time,PAL (c50934), CHS (c49212), F3H (c35949) and ANS (c54610) may be key enzymes in flavonoid biosynthesis. In addition, the ABA signal transduction pathway was analyzed and it was identified that PYL3 (c54854) and ABI5 (c56122) are up-regulated from T10 to T40, and it is speculated that they play an important regulatory role in the development of E. ferox seeds. Together, these results reveals the dynamic changes during the development of E. ferox seeds, which will provide guidance for the study of the molecular mechanism of starch and flavonoids.

Metabolomic Patterns of Septoria Canker Resistant and Susceptible Populus trichocarpa Genotypes 24 Hours Postinoculation

Sphaerulina musiva is an economically and ecologically important fungal pathogen that causes Septoria stem canker and leaf spot disease of Populus species. To bridge the gap between genetic markers and structural barriers previously found to be linked to Septoria canker disease resistance in poplar, we used hydrophilic interaction liquid chromatography and tandem mass spectrometry to identify and quantify metabolites involved with signaling and cell wall remodeling. Fluctuations in signaling molecules, organic acids, amino acids, sterols, phenolics, and saccharides in resistant and susceptible P. trichocarpa inoculated with S. musiva were observed. The patterns of 222 metabolites in the resistant host implicate systemic acquired resistance (SAR), cell wall apposition, and lignin deposition as modes of resistance to this hemibiotrophic pathogen. This pattern is consistent with the expected response to the biotrophic phase of S. musiva colonization during the first 24 h postinoculation. The fungal pathogen metabolized key regulatory signals of SAR, other phenolics, and precursors of lignin biosynthesis that were depleted in the susceptible host. This is the first study to characterize metabolites associated with the response to initial colonization by S. musiva between resistant and susceptible hosts.

In through the out door: Biochemical mechanisms affecting flavonoid glycoside catabolism in plants

Plants are the sole source of flavonoids, a chemical category that includes flavonols. For the most part, flavonols occur as glycosides with numerous postulated biological roles in plants, including photoprotection, modulation of hormone translocation, and sequestration of reactive oxygen species. Flavonol glycosides are often considered as dead-end metabolites because related flavonoids (i.e., anthocyanins) occur in terminal tissues such as flowers and fruit, but recent evidence points to their turnover in planta, including developing photosynthetic tissues. Although microbial degradation pathways for flavonol glycosides of plant origin are well described, plant catabolic pathways are little studied by comparison. This review will address our current understanding of biochemical processes leading to the loss of flavonol glycosides in plants, with a specific emphasis on the evidence for flavonol-specific β-glucosidases. Complete elucidation of these catabolic pathways is dependent on the identification of regiospecific modifying steps, including enzymes associated with the hydrolysis of rhamnosylated flavonols, as well as flavonol peroxidation and their encoding genes. Herein, we highlight challenges for the identification of hypothetical plant α-rhamnosidases and peroxidases involved in flavonol glycoside degradation, and the potential biological role of this catabolism in mitigating oxidative stress in developing and postharvest plant tissues.

NDP-rhamnose biosynthesis and rhamnosyltransferases: building diverse glycoconjugates in nature

Rhamnose is an important 6-deoxy sugar present in many natural products, glycoproteins, and structural polysaccharides. Whilst predominantly found as the l-enantiomer, instances of d-rhamnose are also found in nature, particularly in the Pseudomonads bacteria. Interestingly, rhamnose is notably absent from humans and other animals, which poses unique opportunities for drug discovery targeted towards rhamnose utilizing enzymes from pathogenic bacteria. Whilst the biosynthesis of nucleotide-activated rhamnose (NDP-rhamnose) is well studied, the study of rhamnosyltransferases that synthesize rhamnose-containing glycoconjugates is the current focus amongst the scientific community. In this review, we describe where rhamnose has been found in nature, as well as what is known about TDP-β-l-rhamnose, UDP-β-l-rhamnose, and GDP-α-d-rhamnose biosynthesis. We then focus on examples of rhamnosyltransferases that have been characterized using both in vivo and in vitro approaches from plants and bacteria, highlighting enzymes where 3D structures have been obtained. The ongoing study of rhamnose and rhamnosyltransferases, in particular in pathogenic organisms, is important to inform future drug discovery projects and vaccine development.

Directional phyllotactic bias in calatheas (Goeppertia, Marantaceae): A citizen science approach

Lateral organs arranged in spiral phyllotaxy are separated by the golden angle, ≈137.5°, leading to chirality: either clockwise or counter-clockwise. In some species, leaves are asymmetric such that they are smaller and curved towards the side ascending the phyllotactic spiral. As such, these asymmetries lead to mirroring of leaf shapes in plants of opposite phyllotactic handedness. Previous reports had suggested that the pin-stripe calathea (Goeppertia ornata) may be exclusively of one phyllotactic direction, counter-clockwise, but had limited sampling to a single population. Here, we use a citizen science approach leveraging a social media poll, internet image searches, in-person verification at nurseries in four countries and digitally-curated, research-grade observations to demonstrate that calatheas (Goeppertia spp.) around the world are biased towards counter-clockwise phyllotaxy. The possibility that this bias is genetic and its implications for models of phyllotaxy that assume handedness is stochastically specified in equal proportions is discussed.

Rhamnose in plants - from biosynthesis to diverse functions

In plants, the deoxy sugar l-rhamnose is widely present as rhamnose-containing polymers in cell walls and as part of the decoration of various specialized metabolites. Here, we review the current knowledge on the distribution of rhamnose, highlighting the differences between what is known in dicotyledoneuos compared to commelinid monocotyledoneous (grasses) plants. We discuss the biosynthesis and transport of UDP-rhamnose, as well as the transfer of rhamnose from UDP-rhamnose to various primary and specialized metabolites. This is carried out by rhamnosyltransferases, enzymes that can use a large variety of substrates. Some unique characteristics of rhamnose synthases, the multifunctional enzymes responsible for the conversion of UDP-glucose into UDP-rhamnose, are considered, particularly from the perspective of their ability to convert glucose present in flavonoids. Finally, we discuss how little is still known with regards to how plants rescue rhamnose from the many compounds to which it is linked, or how rhamnose is catabolized.