Arg-type dihydroflavonol 4-reductase genes from the fern Dryopteris erythrosora play important roles in the biosynthesis of anthocyanins

Biosynthesis and differential spatial distribution of the 3-deoxyanthocyanidins apigenidin and luteolinidin at the interface of a plant-cyanobacteria symbiosis exposed to cold

Aquatic ferns of the genus Azolla (Azolla) form highly productive symbioses with filamentous cyanobacteria fixing N2 in their leaf cavities, Nostoc azollae. Stressed symbioses characteristically turn red due to 3-deoxyanthocyanidin (DA) accumulation, rare in angiosperms and of unknown function. To understand DA accumulation upon cold acclimation and recovery, we integrated laser-desorption-ionization mass-spectrometry-imaging (LDI-MSI), a new Azolla filiculoides genome-assembly and annotation, and dual RNA-sequencing into phenotypic analyses of the symbioses. Azolla sp. Anzali recovered even when cold-induced DA-accumulation was inhibited by abscisic acid. Cyanobacterial filaments generally disappeared upon cold acclimation and Nostoc azollae transcript profiles were unlike those of resting stages formed in cold-resistant sporocarps, yet filaments re-appeared in leaf cavities of newly formed green fronds upon cold-recovery. The high transcript accumulation upon cold acclimation of AfDFR1 encoding a flavanone 4-reductase active in vitro suggested that the enzyme of the first step in the DA-pathway may regulate accumulation of DAs in different tissues. However, LDI-MSI highlighted the necessity to describe metabolite accumulation beyond class assignments as individual DA and caffeoylquinic acid metabolites accumulated differentially. For example, luteolinidin accumulated in epithelial cells, including those lining the leaf cavity, supporting a role for the former in the symbiotic interaction during cold acclimation.

Comparative Genomics of Lotus japonicus Reveals Insights into Proanthocyanidin Accumulation and Abiotic Stress Response

Lotus japonicus, is an important perennial model legume, has been widely used for studying biological processes such as symbiotic nitrogen fixation, proanthocyanidin (PA) biosynthesis, and abiotic stress response. High-quality L. japonicus genomes have been reported recently; however, the genetic basis of genes associated with specific characters including proanthocyanidin distribution in most tissues and tolerance to stress has not been systematically explored yet. Here, based on our previous high-quality L. japonicus genome assembly and annotation, we compared the L. japonicus MG-20 genome with those of other legume species. We revealed the expansive and specific gene families enriched in secondary metabolite biosynthesis and the detection of external stimuli. We suggested that increased copy numbers and transcription of PA-related genes contribute to PA accumulation in the stem, petiole, flower, pod, and seed coat of L. japonicus. Meanwhile, According to shared and unique transcription factors responding to five abiotic stresses, we revealed that MYB and AP2/ERF play more crucial roles in abiotic stresses. Our study provides new insights into the key agricultural traits of L. japonicus including PA biosynthesis and response to abiotic stress. This may provide valuable gene resources for legume forage abiotic stress resistance and nutrient improvement.

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.

Cloning and functional analysis of GhDFR1, a key gene of flavonoid synthesis pathway in naturally colored cotton

BACKGROUND

The naturally colored brown cotton fiber is the most widely used environmentally friendly textile material, which primarily contains proanthocyanidins and their derivatives. Many structural genes in the flavonoid synthesis pathway are known to improve the genetic resources of naturally colored cotton. Among them, DFR is a crucial late enzyme to synthesis both anthocyanins and proanthocyanidins in the plant flavonoid pathway.

METHODS

The protein sequences of GhDFRs were analyzed using bioinformatic tools. The expression levels of GhDFRs in various tissues and organs of upland cotton Zongxu1 (ZX1), were analyzed by quantitative real-time PCR, and the expression pattern of GhDFR1 during fiber development of white cotton and brown cotton was analyzed further. The function of GhDFR1 in NCC ZX1 was preliminarily analyzed by virus induced gene silencing (VIGS) technology.

RESULTS

Bioinformatic analysis revealed that GhDFRs sequences in upland cotton genome were extremely conserved. Furthermore, evolutionary tree analysis revealed that the functions of GhDFR1 and GhDFR2, and GhDFR3 and GhDFR4, presented different and shared some similarities. Our study showed GhDFR1 and GhDFR2 were specifically expressed in fibers, while GhDFR3 and GhDFR4 were specifically expressed in petals. GhDFR1 was exclusively expressed in brown cotton fiber at various stages of development and progressively increased with the growth of fiber, but the trend of expression in white cotton was quite the opposite. We silenced GhDFR1 expression in brown cotton fiber using VIGS technology, and observed the VIGS-interference plants. After reducing the expression level of GhDFR1, the period for significant GhDFR1 expression in the developing fibers changed, reducing the content of anthocyanins, and lightening the color of mature cotton fibers.

CONCLUSION

GhDFR1 was preferentially expressed in brown cotton during fiber development. The timing of GhDFR1 expression for flavonoid synthesis altered, resulting in anthocyanin contents reduced and the fiber color of the GhDFR1i lines lightened. These findings showed the role of GhDFR1 in fiber coloration of NCC and provided a new candidate for NCC genetic improvement.

Integrated Transcriptomic and Metabolomic Analysis of the Mechanism of Foliar Application of Hormone-Type Growth Regulator in the Improvement of Grape (Vitis vinifera L.) Coloration in Saline-Alkaline Soil

(1) Background: To solve the problems of incomplete coloration and quality decline caused by unreasonable use of regulators in grapes, this study clarified the differences in the effects of a hormone-type growth regulator (AUT) and two commercial regulators on grape coloration and quality through field experiments. (2) Methods: The color indexes (brightness (L*), red/green color difference (a*), yellow/blue color difference (b*), and color index for red grapes (CIRG)) of grape fruit were measured using a CR-400 handheld color difference meter. The titratable acid content, total phenol content, and total sugar content were measured using anthrone colorimetry, folinol colorimetry, and NaOH titration, respectively, and the chalcone isomerase activity, phenylalanine ammoniase activity, dihydroflavol reductase activity, and anthocyanin content were measured using a UV spectrophotometer. (3) Results: The a*, total sugar and total phenol contents, and chalcone isomerase (CHI) and phenylalanine ammoniase (PAL) activities of grape fruit in the AUT treatment significantly increased, while the titratable acid content significantly decreased, compared to those in the CK treatment. The expressions of the differentially expressed genes (DEGs) trpB and argJ in AUT treatment were significantly up-regulated. The expressions of the differentially expressed metabolites (DEMs) phenylalanine and 4-oxoproline were significantly up-regulated, while those of 3,4-dihydroxybenzaldehyde and N-acetyl glutamate were significantly down-regulated. The CIRG significantly increased by 36.4% compared to that in the CK, indicating improved fruit coloration. (4) Conclusion: The AUT could shorten the color conversion period of grape fruit and improve the coloration, taste, and tolerance to saline and alkaline stresses.

Transcriptome analysis reveals cell cycle-related transcripts as key determinants of varietal differences in seed size of Brassica juncea

Brassica juncea is an important oilseed crop, widely grown as a source of edible oil. Seed size is a pivotal agricultural trait in oilseed Brassicas. However, the regulatory mechanisms underlying seed size determination are poorly understood. To elucidate the transcriptional dynamics involved in the determination of seed size in B. juncea, we performed a comparative transcriptomic analysis using developing seeds of two varieties, small-seeded Early Heera2 (EH2) and bold-seeded Pusajaikisan (PJK), at three distinct stages (15, 30 and 45 days after pollination). We detected 112,550 transcripts, of which 27,186 and 19,522 were differentially expressed in the intra-variety comparisons and inter-variety comparisons, respectively. Functional analysis using pathway, gene ontology, and transcription factor enrichment revealed that cell cycle- and cell division-related transcripts stay upregulated during later stages of seed development in the bold-seeded variety but are downregulated at the same stage in the small-seeded variety, indicating that an extended period of cell proliferation in the later stages increased seed weight in PJK as compared to EH2. Further, k-means clustering and candidate genes-based analyses unravelled candidates for employing in seed size improvement of B. juncea. In addition, candidates involved in determining seed coat color, oil content, and other seed traits were also identified.

Identification of Flowering Regulatory Networks and Hub Genes Expressed in the Leaves of Elymus sibiricus L. Using Comparative Transcriptome Analysis

Flowering is a significant stage from vegetative growth to reproductive growth in higher plants, which impacts the biomass and seed yield. To reveal the flowering time variations and identify the flowering regulatory networks and hub genes in Elymus sibiricus, we measured the booting, heading, and flowering times of 66 E. sibiricus accessions. The booting, heading, and flowering times varied from 136 to 188, 142 to 194, and 148 to 201 days, respectively. The difference in flowering time between the earliest- and the last-flowering accessions was 53 days. Furthermore, transcriptome analyses were performed at the three developmental stages of six accessions with contrasting flowering times. A total of 3,526 differentially expressed genes (DEGs) were predicted and 72 candidate genes were identified, including transcription factors, known flowering genes, and plant hormone-related genes. Among them, four candidate genes (LATE, GA2OX6, FAR3, and MFT1) were significantly upregulated in late-flowering accessions. LIMYB, PEX19, GWD3, BOR7, PMEI28, LRR, and AIRP2 were identified as hub genes in the turquoise and blue modules which were related to the development time of flowering by weighted gene co-expression network analysis (WGCNA). A single-nucleotide polymorphism (SNP) of LIMYB found by multiple sequence alignment may cause late flowering. The expression pattern of flowering candidate genes was verified in eight flowering promoters (CRY, COL, FPF1, Hd3, GID1, FLK, VIN3, and FPA) and four flowering suppressors (CCA1, ELF3, Ghd7, and COL4) under drought and salt stress by qRT-PCR. The results suggested that drought and salt stress activated the flowering regulation pathways to some extent. The findings of the present study lay a foundation for the functional verification of flowering genes and breeding of new varieties of early- and late-flowering E. sibiricus.

Enhancing Flavan-3-ol Biosynthesis in Saccharomyces cerevisiae

Flavan-3-ols are a group of flavonoids that exert beneficial effects. This study aimed to enhance key metabolic processes related to flavan-3-ols biosynthesis. The engineered Saccharomyces cerevisiae strain E32 that produces naringenin from glucose was further engineered for de novo production of two basic flavan-3-ols, afzelechin (AFZ) and catechin (CAT). Through introduction of flavonoid 3-hydroxylase, flavonoid 3'-hydroxylase, dihydroflavonol 4-reductase (DFR), and leucoanthocyanidin reductase (LAR), de novo production of AFZ and CAT can be achieved. The combination of FaDFR from Fragaria × ananassa and VvLAR from Vitis vinifera was optimal. (GGGGS)₂ and (EAAAK)₂ linkers between DFR and LAR proved optimal for the production of AFZ and CAT, respectively. Optimization of promoters and the enhanced supply of NADPH further increased the production. By combining the best engineering strategies, the optimum strains produced 500.5 mg/L AFZ and 321.3 mg/L CAT, respectively, after fermentation for 90 h in a 5 L bioreactor. The strategies presented could be applied for a more efficient production of flavan-3-ols by various microorganisms.

Functional analysis of a dihydroflavonol 4-reductase gene in Ophiorrhiza japonica (OjDFR1) reveals its role in the regulation of anthocyanin

Dihydroflavonol 4-reductase (DFR), a key regulatory enzyme, participated in the biosynthesis of anthocyanins, proanthocyanidins and other flavonoids that essential for plant survival and human health. However, the role of this enzyme in Ophiorrhiza japonica is still unknown. Here, three putative DFR-like genes were firstly isolated from O. japonica. Phylogenetic analysis indicated that OjDFR1 was classified into DFR subgroup, while the rest two were clustered into other NADPH-dependent reductases. Then, functions of the three genes were further characterized. Expression analysis showed that OjDFR1 transcripts had strong correlations with the accumulation pattern of anthocyanin during the flower developmental, whereas other two were not, this suggested the potential roles of OjDFR1 in anthocyanin biosynthesis. Subsequently, all three clones were functionally expressed in Escherichia coli, but confirming that only OjDFR1 encode active DFR proteins that catalyzed the reduction of dihydroflavonols to leucoanthocyanidin. Consistant with the biochemical assay results, overexpressing OjDFR1 in Arabidopsis tt3-1 mutant successfully restored the deficiency of anthocyanin and proanthocyanidin, hinting its function as DFR in planta. Additionally, heterologous expression of OjDFR1 in transgenic tobacco contributed to darker flower color via up-regulating the expressions of endogenous NtANS and NtUFGT, which suggested that OjDFR1 was involved in flower color development. In summary, this study validates the functions of OjDFR1 and expands our understanding of anthocyanin biosynthesis in O. japonica.