The phenylalanine ammonia-lyase gene family in Isatis indigotica Fort.: molecular cloning, characterization, and expression analysis

Insights to Phenylalanine Ammonia Lyase (PAL) and Secondary Metabolism in Orchids: An in silico Approach

The phenylalanine ammonia lyase (PAL) catalyses the first step of phenylpropanoid metabolic pathway which leads to the biosynthesis of a diverse group of secondary metabolites. Orchids serve as a rich source of metabolites and the availability of genome or transcriptome for selected orchid species provides an opportunity to analyse the PAL genes in orchids. In the present study, 21 PAL genes were characterized using bioinformatics tools in nine orchid species (Apostasia shenzhenica, Cypripedium formosanum, Dendrobium catenatum, Phalaenopsis aphrodite, Phalaenopsis bellina, Phalaenopsis equestris, Phalaenopsis lueddemanniana, Phalaenopsis modesta and Phalaenopsis schilleriana). Multiple sequence alignment confirmed the presence of PAL-specific conserved domains (N-terminal, MIO, core, shielding and C-terminal domain). All these proteins were predicted to be hydrophobic in nature and to have cytoplasmic localisation. Structural modelling depicted the presence of alpha helices, extended strands, beta turns and random coils in their structure. Ala-Ser-Gly triad known for substrate binding and catalysis of MIO-domain was found to be completely conserved in all the proteins. Phylogenetic study showed that the PALs of pteridophytes, gymnosperms and angiosperms clustered together in separate clades. Expression profiling showed tissue-specific expression for all the 21 PAL genes in the various reproductive and vegetative tissues which suggested their diverse role in growth and development. This study provides insights to the molecular characterization of PAL genes which may help in developing biotechnological strategies to enhance the synthesis of phenylpropanoids in orchids and other heterologous systems for pharmaceutical applications.

Rapid identification of chemical constituents in Hugan tablets by ultra-performance liquid chromatography-quadrupole-exactive orbitrap mass spectrometry

Hugan tablet is a Chinese medicine preparation. It is composed of Bupleuri Radix, Artemisiae Scopariae Herba, Isatidis Radix, Schisandrae Chinensis Fructus, Suis Fellis Pulvis, and Vigna radiata L. It has the effects of dispersing stagnated liver qi, strengthening the spleen and eliminating food to be used for the treatment of chronic hepatitis and early cirrhosis. However, the chemical composition of Hugan tablet is complex and not fully understood, which hampers the research in pharmacology. In this study, a reliable method for the rapid analysis and identification of the chemical components in Hugan tablet by their characteristic fragments and neutral losses using ultra-performance liquid chromatography-quadrupole-exactive orbitrap mass spectrometry was developed. A total of 144 chemical components were tentatively identified, including 57 organic acids, 19 flavonoids, 23 alkaloids, 18 lignans, 7 saponins, and 20 others. These components may be the active ingredients of Hugan tablet. The established method can systematically and rapidly analyze the chemical components in Hugan tablet, which provides a basis for the pharmacodynamic substance study and is meaningful for the quality control of Hugan tablet.

Functional Characterization of UDP-Glycosyltransferases Involved in Anti-viral Lignan Glycosides Biosynthesis in Isatis indigotica

Isatis indigotica is a popular herbal medicine with its noticeable antiviral properties, which are primarily due to its lignan glycosides such as lariciresinol-4-O-β-D-glucoside and lariciresinol-4,4'-bis-O-β-D-glucosides (also called clemastanin B). UDP-glucose-dependent glycosyltransferases are the key enzymes involved in the biosynthesis of these antiviral metabolites. In this study, we systematically characterized the UGT72 family gene IiUGT1 and two UGT71B family genes, IiUGT4 and IiUGT71B5a, with similar enzymatic functions. Kinetic analysis showed that IiUGT4 was more efficient than IiUGT1 or IiUGT71B5a for the glycosylation of lariciresinol. Further knock-down and overexpression of these IiUGTs in I. indigotica's hairy roots indicates that they play different roles in planta: IiUGT71B5a primarily participates in the biosynthesis of coniferin not pinoresinol diglucoside, and IiUGT1 primarily participates in the biosynthesis of pinoresinol diglucoside, while IiUGT4 is responsible for the glycosylation of lariciresinol and plays a dominant role in the biosynthesis of lariciresinol glycosides in I. indigotica. Analysis of the molecular docking and site-mutagenesis of IiUGT4 have found that key residues for its catalytic activity are H373, W376, E397, and that F151 could be associated with substrate preference. This study elucidates the biosynthetic route of anti-viral lignan glycosides in I. indigotica, and provides the foundation for the production of anti-viral lignan glycosides via synthetic biology under the heterologous model.

Metabolome and transcriptome analyses identify the plant immunity systems that facilitate sesquiterpene and lignan biosynthesis in Syringa pinnatifolia Hemsl

BACKGROUND

Syringa pinnatifolia Hemsl. is a shrub belonging to the Oleaceae family. The peeled woody stems and roots of S. pinnatifolia are used in Chinese traditional medicine. This plant has been used for centuries, and modern pharmacological research has revealed its medicinal value. However, the wild populations of S. pinnatifolia have been decreasing, and it has been listed as an endangered plant in China. To elucidate the molecular mechanism leading to the synthesis of the major components of S. pinnatifolia for its further development and sustainable use, this study compared peeled stems and twigs at the metabolic and molecular levels.

RESULTS

Peeled stems with the purple substance visible (SSP) and peeled twigs without the purple substance (TSP) were compared at different levels. Microscopic observation showed resin-like fillers in SSP and wood fiber cell walls approximately 1.0 μm thicker than those in TSP (wood fiber cell thickness approximately 2.7 μm). In addition, 104 volatile organic compounds and 870 non-volatile metabolites were detected in the non-targeted and widely-targeted metabolome analyses, respectively. Among the 76 differentially accumulated metabolites (DAMs) detected, 62 were up-accumulated in SSP. Most of these DAMs were terpenes, of which 90% were identified as sesquiterpenes in the volatile organic compound analysis. In the analysis of the non-volatile metabolites, 21 differentially accumulated lignans were identified, of which 18, including five subtypes, were accumulated in SSP. RNA sequencing revealed 4,421 upregulated differentially expressed genes (DEGs) and 5,522 downregulated DEGs in SSP compared with TSP, as well as 33,452 genes that were not differentially expressed. Analysis of the DEGs suggested that sesquiterpenes and lignans were mostly biosynthesized via the mevalonate and phenylpropanoid pathways, respectively. Additionally, in SSP, the enriched Gene Ontology terms included response to biotic stimulus and defense response, while the enriched Kyoto Encyclopedia of Genes and Genomes pathways included plant-pathogen interaction and many other pathways related to plant immunity.

CONCLUSIONS

This study provides metabolome and transcriptome information for S. pinnatifolia, suggesting that biotic stimuli, including pathogens, are potential and valuable approaches to promoting the biosynthesis of the metabolites linked to the medicinal properties of this plant.

Isatis indigotica: from (ethno) botany, biochemistry to synthetic biology

Isatis indigotica Fort. (Chinese woad) is a species with an ancient and well-documented history as an indigo dye and medicinal plant. It is often confused with Isatis tinctoria L. (European woad), a medicinal plant in Europe. Here, the differences between I. indigotica and I. tinctoria are systematically described. The usage development history, clinical applications and pharmacological activities, and chemical components of I. indigotica are also summarized. Lignans, indole alkaloids, and their corresponding derivatives have been identified as the major active ingredients of I. indigotica and are associated with anti-viral, anti-inflammatory, anti-cancer, and other health-promoting activities. Notable progress has been made in understanding the biosynthetic pathway and regulation mechanism of lignans and indole alkaloids in I. indigotica, the results from which should facilitate the process of targeted metabolic engineering or synthetic biology. Moreover, multiple biotechnology methods such as polyploid breeding and genetic engineering have been used with I. indigotica to result in, for example, greater yields, higher levels of bioactive component accumulation, and enhanced stress tolerance to salt, drought, and insects. Some issues require additional analyses, and suggestions for future research on I. indigotica are also discussed.

Quality, Bioactive Compounds, Antioxidant Capacity, and Enzymes of Raspberries at Different Maturity Stages, Effects of Organic vs. Conventional Fertilization

Raspberries are important sources of bioactive compounds, whose synthesis is influenced by the fertilization system and the maturity stage. This study evaluated the effect of organic and conventional fertilization systems on raspberries at three maturity stages, pink, ripe, and overripe. Physicochemical characteristics, bioactive compounds (phenolic profile, vitamin C), antioxidant capacity (DPPH, FRAP, TEAC, and ORAC), phenolic-associated enzyme, phenylalanine ammonia lyase (PAL), and antioxidant enzymes (SOD, CAT, GPx, and APX) were evaluated. The physicochemical determination of the fruit did not reveal differences between fertilization systems. Regarding bioactive compounds, higher content of anthocyanins was found in organic raspberries at all maturity stages. Organic fertilization increased the content of ellagic acid and gallic acid at all stages of maturity. Higher content of caffeic, hydroxybenzoic, protocatechuic acid, and vitamin C was observed in organic raspberry at the overripe stage. Raspberries grown with organic fertilization exhibited higher values of antioxidant capacity by the DPPH, FRAP, and TEAC methods at all maturity stages. Raspberries under organic fertilization showed significantly greater activity of CAT, SOD, APX, GPX, and PAL. The present study suggests that organic fertilization induces oxidative stress causing an increase in antioxidant defense mechanisms, enhancing bioactive compound production, and improving antioxidant capacity in raspberries.

High-Quality Genome of the Medicinal Plant Strobilanthes cusia Provides Insights Into the Biosynthesis of Indole Alkaloids

Strobilanthes cusia (Nees) Kuntze is an important plant used to process the traditional Chinese herbal medicines "Qingdai" and "Nanbanlangen". The key active ingredients are indole alkaloids (IAs) that exert antibacterial, antiviral, and antitumor pharmacological activities and serve as natural dyes. We assembled the S. cusia genome at the chromosome level through combined PacBio circular consensus sequencing (CCS) and Hi-C sequencing data. Hi-C data revealed a draft genome size of 913.74 Mb, with 904.18 Mb contigs anchored into 16 pseudo-chromosomes. Contig N50 and scaffold N50 were 35.59 and 68.44 Mb, respectively. Of the 32,974 predicted protein-coding genes, 96.52% were functionally annotated in public databases. We predicted 675.66 Mb repetitive sequences, 47.08% of sequences were long terminal repeat (LTR) retrotransposons. Moreover, 983 Strobilanthes-specific genes (SSGs) were identified for the first time, accounting for ~2.98% of all protein-coding genes. Further, 245 putative centromeric and 29 putative telomeric fragments were identified. The transcriptome analysis identified 2,975 differentially expressed genes (DEGs) enriched in phenylpropanoid, flavonoid, and triterpenoid biosynthesis. This systematic characterization of key enzyme-coding genes associated with the IA pathway and basic helix-loop-helix (bHLH) transcription factor family formed a network from the shikimate pathway to the indole alkaloid synthesis pathway in S. cusia. The high-quality S. cusia genome presented herein is an essential resource for the traditional Chinese medicine genomics studies and understanding the genetic underpinning of IA biosynthesis.

Comparative genomic analysis of the PAL genes in five Rosaceae species and functional identification of Chinese white pear

Phenylalanine ammonia lyase (PAL) plays an important role in the biosynthesis of secondary metabolites regulating plant growth response. To date, the evolutionary history of the PAL family in Rosaceae plants remains unclear. In this study, we identified 16 PAL homologous genes in five Rosaceae plants (Pyrus bretschneideri, Fragaria vesca, Prunus mume, Prunus persica, and Malus × domestica). We classified these PALs into three categories based on phylogenetic analysis, and all PALs were distributed on 13 chromosomes. We tracked gene duplication events and performed sliding window analysis. These results revealed the evolution of PALs in five Rosaceae plants. We predicted the promoter of the PbPALs by PLANT CARE online software, and found that the promoter region of both PbPAL1 and PbPAL3 have at least one AC element. The results of qRT-PCR analysis found that PbPAL1 and PbPAL2 were highly expressed in the stems and roots, while expression level of PbPAL3 was relatively low in different tissues. The expression of PbPAL1 and PbPAL2 increased firstly and then decreased at different developmental periods of pear fruit. Among them, the expression of PbPAL1 reached the highest level 55 days after flowering. Three PbPALs were induced by abiotic stress to varying degrees. We transfected PbPAL1 and PbPAL2 into Arabidopsis thaliana, which resulted in an increase in lignin content and thickening of the cell walls of intervascular fibres and xylem cells. In summary, this research laid a foundation for better understanding the molecular evolution of PALs in five Rosaceae plants. Furthermore, the present study revealed the role of PbPALs in lignin synthesis, and provided basic data for regulating lignin synthesis and stone cells development in pear plants.

Genome-Wide Identification and Transcriptional Expression of the PAL Gene Family in Common Walnut (Juglans Regia L.)

Juglans regia L. is an economically important crop cultivated worldwide for its high quality and quantity of wood and nuts. Phenylalanine ammonia-lyase (PAL) is the first enzyme in the phenylpropanoid pathway that plays a critical role in plant growth, development, and adaptation, but there have been few reports of the PAL gene family in common walnut. Here, we report a genome-wide study of J. regiaPAL genes and analyze their phylogeny, duplication, microRNA, and transcriptional expression. A total of 12 PAL genes were identified in the common walnut and clustered into two subfamilies based on phylogenetic analysis. These common walnut PALs are distributed on eight different pseudo-chromosomes. Seven of the 12 PALs (JrPAL2-3, JrPAL4-2, JrPAL2-1, JrPAL4-1, JrPAL8, JrPAL9, and JrPAL6) were specific found in J. regia, and JrPAL3, JrPAL5, JrPAL1-2, JrPAL7, and JrPAL2-2 were found to be closely associated with the woody plant Populus trichocarpa. Additionally, the expression patterns of JrPAL3, JrPAL7, JrPAL9, and JrPAL2-1 showed that they had high expression in female and male flowers. The miRNA ath-miR830-5p regulates two genes, JrPAL5 and JrPAL1, such that they have low expression in the male and female flowers of the common walnut. Our research provides useful information for further research into the function of PAL genes in common walnut and Juglans.