The 4-coumarate:CoA ligase gene family in Arabidopsis thaliana comprises one rare, sinapate-activating and three commonly occurring isoenzymes

Phenolic amides (avenanthramides) in oats - an update review

Oats (Avena sativa L.) are one of the worldwide cereal crops. Avenanthramides (AVNs), the unique plant alkaloids of secondary metabolites found in oats, are nutritionally important for humans and animals. Numerous bioactivities of AVNs have been investigated and demonstrated in vivo and in vitro. Despite all these, researchers from all over the world are taking efforts to learn more knowledge about AVNs. In this work, we highlighted the recent updated findings that have increased our understanding of AVNs bioactivity, distribution, and especially the AVNs biosynthesis. Since the limits content of AVNs in oats strictly hinders the demand, understanding the mechanisms underlying AVN biosynthesis is important not only for developing a renewable, sustainable, and environmentally friendly source in both plants and microorganisms but also for designing effective strategies for enhancing their production via induction and metabolic engineering. Future directions for improving AVN production in native producers and heterologous systems for food and feed use are also discussed. This summary will provide a broad view of these specific natural products from oats.

Duplication and sub-functionalization of flavonoid biosynthesis genes plays important role in Leguminosae root nodule symbiosis evolution

Gene innovation plays an essential role in trait evolution. Rhizobial symbioses, the most important N2-fixing agent in agricultural systems that exists mainly in Leguminosae, is one of the most attractive evolution events. However, the gene innovations underlying Leguminosae root nodule symbiosis (RNS) remain largely unknown. Here, we investigated the gene gain event in Leguminosae RNS evolution through comprehensive phylogenomic analyses. We revealed that Leguminosae-gain genes were acquired by gene duplication and underwent a strong purifying selection. Kyoto Encyclopedia of Genes and Genomes analyses showed that the innovated genes were enriched in flavonoid biosynthesis pathways, particular downstream of chalcone synthase (CHS). Among them, Leguminosae-gain type Ⅱ chalcone isomerase (CHI) could be further divided into CHI1A and CHI1B clades, which resulted from the products of tandem duplication. Furthermore, the duplicated CHI genes exhibited exon-intron structural divergences evolved through exon/intron gain/loss and insertion/deletion. Knocking down CHI1B significantly reduced nodulation in Glycine max (soybean) and Medicago truncatula; whereas, knocking down its duplication gene CHI1A had no effect on nodulation. Therefore, Leguminosae-gain type Ⅱ CHI participated in RNS and the duplicated CHI1A and CHI1B genes exhibited RNS functional divergence. This study provides functional insights into Leguminosae-gain genetic innovation and sub-functionalization after gene duplication that contribute to the evolution and adaptation of RNS in Leguminosae.

Deep quantitative proteomics of North American Pacific coast star tunicate (Botryllus schlosseri)

Botryllus schlosseri, is a model marine invertebrate for studying immunity, regeneration, and stress-induced evolution. Conditions for validating its predicted proteome were optimized using nanoElute® 2 deep-coverage LCMS, revealing up to 4930 protein groups and 20,984 unique peptides per sample. Spectral libraries were generated and filtered to remove interferences, low-quality transitions, and only retain proteins with >3 unique peptides. The resulting DIA assay library enabled label-free quantitation of 3426 protein groups represented by 22,593 unique peptides. Quantitative comparisons of single systems from a laboratory-raised with two field-collected populations revealed (1) a more unique proteome in the laboratory-raised population, and (2) proteins with high/low individual variabilities in each population. DNA repair/replication, ion transport, and intracellular signaling processes were distinct in laboratory-cultured colonies. Spliceosome and Wnt signaling proteins were the least variable (highly functionally constrained) in all populations. In conclusion, we present the first colonial tunicate's deep quantitative proteome analysis, identifying functional protein clusters associated with laboratory conditions, different habitats, and strong versus relaxed abundance constraints. These results empower research on B. schlosseri with proteomics resources and enable quantitative molecular phenotyping of changes associated with transfer from in situ to ex situ and from in vivo to in vitro culture conditions.

Ocimum kilimandscharicum 4CL11 negatively regulates adventitious root development via accumulation of flavonoid glycosides

4-Coumarate-CoA Ligase (4CL) is an important enzyme in the phenylpropanoid biosynthesis pathway. Multiple 4CLs are identified in Ocimum species; however, their in planta functions remain enigmatic. In this study, we independently overexpressed three Ok4CL isoforms from Ocimum kilimandscharicum (Ok4CL7, -11, and -15) in Nicotiana benthamiana. Interestingly, Ok4CL11 overexpression (OE) caused a rootless or reduced root growth phenotype, whereas overexpression of Ok4CL15 produced normal adventitious root (AR) growth. Ok4CL11 overexpression in N. benthamiana resulted in upregulation of genes involved in flavonoid biosynthesis and associated glycosyltransferases accompanied by accumulation of specific flavonoid-glycosides (kaempferol-3-rhamnoside, kaempferol-3,7-O-bis-alpha-l-rhamnoside [K3,7R], and quercetin-3-O-rutinoside) that possibly reduced auxin levels in plants, and such effects were not seen for Ok4CL7 and -15. Docking analysis suggested that auxin transporters (PINs/LAXs) have higher binding affinity to these specific flavonoid-glycosides, and thus could disrupt auxin transport/signaling, which cumulatively resulted in a rootless phenotype. Reduced auxin levels, increased K3,7R in the middle and basal stem sections, and grafting experiments (intra and inter-species) indicated a disruption of auxin transport by K3,7R and its negative effect on AR development. Supplementation of flavonoids and the specific glycosides accumulated by Ok4CL11-OE to the wild-type N. benthamiana explants delayed the AR emergence and also inhibited AR growth. While overexpression of all three Ok4CLs increased lignin accumulation, flavonoids, and their specific glycosides were accumulated only in Ok4CL11-OE lines. In summary, our study reveals unique indirect function of Ok4CL11 to increase specific flavonoids and their glycosides, which are negative regulators of root growth, likely involved in inhibition of auxin transport and signaling.

Impacts of in-vitro zebularine treatment on genome-wide DNA methylation and transcriptomic profiles in Salix purpurea L

Renewable energy resources such as biomass are crucial for a sustainable global society. Trees are a major source of lignocellulosic biomass, which can vary in response to different environmental factors owing to epigenetic regulation, such as DNA C-methylation. To investigate the effects of DNA methylation on plant development and wood formation, and its impacts on gene expression, with a focus on secondary cell wall (SCW)-associated genes, Salix purpurea plantlets were cloned from buds derived from a single hybrid tree for both treatment and control conditions. For the treatment condition, buds were exposed to 50 μM zebularine in vitro and a combined strategy of whole-genome bisulfite sequencing (WGBS) and RNA-seq was employed to examine the methylome and transcriptome profiles of different tissues collected at various time points under both conditions. Transcriptomic and methylome data revealed that most of the promoter and gene body demethylation had no marked effects on the expression profiles of genes. Nevertheless, gene expression tended to decrease with the increased methylation levels of genes with highly methylated promoters. Results indicated that demethylation is less evident in centromeric regions and sex chromosomes. Promoters of secondary cell wall-associated genes, such as 4-coumarate-CoA ligase-like and Rac-like GTP-binding protein RHO, were differentially methylated in the secondary xylem samples collected from two-month potted treated plants compared to control samples. Our results provide novel insights into DNA methylation and gene expression landscapes and a basis for investigating the epigenetic regulation of wood formation in S. purpurea as a model plant for bioenergy species.

The role of introgressive hybridization in shaping the geographically isolated gene pools of wax palm populations (genus Ceroxylon)

The speciation continuum is the process by which genetic groups diverge until they reach reproductive isolation. It has become common in the literature to show that this process is gradual and flickering, with possibly many instances of secondary contact and introgression after divergence has started. The level of divergence might vary among genomic regions due to, among others, the different forces and roles of selection played by the shared regions. Through hybrid capture, we sequenced ca. 4,000 nuclear regions in populations of six species of wax palms, five of which form a monophyletic group (genus Ceroxylon, Arecaceae: Ceroxyloideae). We show that in this group, the different populations show varying degrees of introgressive hybridization, and two of them are backcrosses of the other three 'pure' species. This is particularly interesting because these three species are dioecious, have a shared main pollinator, and have slightly overlapping reproductive seasons but highly divergent morphologies. Our work supports shows wax palms diverge under positive and background selection in allopatry, and hybridize due to secondary contact and inefficient reproductive barriers, which sustain genetic diversity. Introgressed regions are generally not under positive selection. Peripheral populations are backcrosses of other species; thus, introgressive hybridization is likely modulated by demographic effects rather than selective pressures. In general, these species might function as an 'evolutionary syngameon' where expanding, peripheral, small, and isolated populations maintain diversity by crossing with available individuals of other wax palms. In the Andean context, species can benefit from gained variation from a second taxon or the enhancement of population sizes by recreating a common genetic pool.

Papiliotrema flavescens, a plant growth-promoting fungus, alters root system architecture and induces systemic resistance through its volatile organic compounds in Arabidopsis

The current trend in agricultural development is the establishment of sustainable agricultural systems. This involves utilizing and implementing eco-friendly biofertilizers and biocontrol agents as alternatives to conventional fertilizers and pesticides. A plant growth-promoting fungal strain, that could alter root system architecture and promote the growth of Arabidopsis seedlings in a non-contact manner by releasing volatile organic compounds (VOCs) was isolated in this study. 26S rDNA sequencing revealed that the strain was a yeast-like fungus, Papiliotrema flavescens. Analysis of plant growth-promoting traits revealed that the fungus could produce indole-3-acetic acid and ammonia and fix nitrogen. Transcriptome analysis in combination with inhibitor experiments revealed that P. flavescens VOCs triggered metabolic alterations, promoted auxin accumulation and distribution in the roots, and coordinated ethylene signaling, thus inhibiting primary root elongation and inducing lateral root formation in Arabidopsis. Additionally, transcriptome analysis and fungal infection experiments confirmed that pretreatment with P. flavescens stimulated the defense response of Arabidopsis to boost its resistance to the pathogenic fungus Botrytis cinerea. Solid-phase microextraction, which was followed by gas chromatography-mass spectrometry analysis, identified three VOCs (acetoin, naphthalene and indole) with significant plant growth-promoting attributes. Their roles were confirmed using further pharmacological experiments and upregulated expression of auxin- and ethylene-related genes. Our study serves as an essential reference for utilizing P. flavescens as a potential biological fertilizer and biocontrol agent.

Reconstructing curcumin biosynthesis in yeast reveals the implication of caffeoyl-shikimate esterase in phenylpropanoid metabolic flux

Curcumin is a polyphenolic natural product from the roots of turmeric (Curcuma longa). It has been a popular coloring and flavoring agent in food industries with known health benefits. The conventional phenylpropanoid pathway is known to proceed from phenylalanine via p-coumaroyl-CoA intermediate. Although hydroxycinnamoyl-CoA: shikimate hydroxycinnamoyl transferase (HCT) plays a key catalysis in the biosynthesis of phenylpropanoid products at the downstream of p-coumaric acid, a recent discovery of caffeoyl-shikimate esterase (CSE) showed that an alternative pathway exists. Here, the biosynthetic efficiency of the conventional and the alternative pathway in producing feruloyl-CoA was examined using curcumin production in yeast. A novel modular multiplex genome-edit (MMG)-CRISPR platform was developed to facilitate rapid integrations of up to eight genes into the yeast genome in two steps. Using this MMG-CRISPR platform and metabolic engineering strategies, the alternative CSE phenylpropanoid pathway consistently showed higher titers (2-19 folds) of curcumin production than the conventional pathway in engineered yeast strains. In shake flask cultures using a synthetic minimal medium without phenylalanine, the curcumin production titer reached up to 1.5 mg/L, which is three orders of magnitude (∼4800-fold) improvement over non-engineered base strain. This is the first demonstration of de novo curcumin biosynthesis in yeast. Our work shows the critical role of CSE in improving the metabolic flux in yeast towards the phenylpropanoid biosynthetic pathway. In addition, we showcased the convenience and reliability of modular multiplex CRISPR/Cas9 genome editing in constructing complex synthetic pathways in yeast.

Integrated transmission electron microscopy and proteomic analyses reveal the cytoarchitectural response to cucumber mosaic virus infection in tobacco

Cucumber mosaic virus (CMV) causes huge economic losses to agriculture every year; thus, understanding the mechanism of plant resistance to CMV is imperative. In this study, an integrated analysis of transmission electron microscopy (TEM) observations and proteomic results was used to identify cytoarchitectural differences in Nicotiana tabacum cv. NC82 (susceptible) and cv. Taiyan 8 (T.T.8; resistant) following infection with CMV. The TEM observations showed that the structure of the chloroplasts and mitochondria was severely damaged at the late stage of infection in NC82. Moreover, the chloroplast stroma and mitochondrial cristae were reduced and disaggregated. However, in T.T.8, organelle structure remained largely intact Selective autophagy predominated in T.T.8, whereas non-selective autophagy dominated in NC82, resembling cellular disorder. Proteomic analysis of T.T.8 revealed differentially expressed proteins (DEPs) mostly associated with photosynthesis, respiration, reactive oxygen species (ROS) scavenging, and cellular autophagy. Biochemical analyses revealed that ROS-related catalase, autophagy-related disulfide isomerase, and jasmonic acid and antioxidant secondary metabolite synthesis-related 4-coumarate:CoA ligase (Nt4CL) exhibited different trends and significant differences in expression in the two cultivars after CMV inoculation. Furthermore, mutant phenotyping verified that reduced Nt4CL expression impaired resistance in T.T.8. The identified DEPs are crucial for maintaining intracellular homeostatic balance and likely contribute to the mechanism of CMV resistance in tobacco. These findings increase our understanding of plant cytological mechanisms conferring resistance to CMV infection.

Molecular cloning and functional analysis of 4-coumarate: CoA ligases from Marchantia paleacea and their roles in lignin and flavanone biosynthesis

Phenylpropanoids play important roles in plant physiology and the enzyme 4-coumarate: coenzyme A ligase (4CL) catalyzes the formation of thioesters. Despite extensive characterization in various plants, the functions of 4CLs in the liverwort Marchantia paleacea remain unknown. Here, four 4CLs from M. paleacea were isolated and functionally analyzed. Heterologous expression in Escherichia coli indicated the presence of different enzymatic activities in the four enzymes. Mp4CL1 and Mp4CL2 were able to convert caffeic, p-coumaric, cinnamic, ferulic, dihydro-p-coumaric, and 5-hydroxyferulic acids to their corresponding CoA esters, while Mp4CL3 and Mp4CL4 catalyzed none. Mp4CL1 transcription was induced when M. paleacea thalli were treated with methyl jasmonate (MeJA). The overexpression of Mp4CL1 increased the levels of lignin in transgenic Arabidopsis. In addition, we reconstructed the flavanone biosynthetic pathway in E. coli. The pathway comprised Mp4CL1, co-expressed with chalcone synthase (CHS) from different plant species, and the efficiency of biosynthesis was optimal when both the 4CL and CHS were obtained from the same species M. paleacea.

Gibberellin signaling regulates lignin biosynthesis to modulate rice seed shattering

The elimination of seed shattering was a key step in rice (Oryza sativa) domestication. In this paper, we show that increasing the gibberellic acid (GA) content or response in the abscission region enhanced seed shattering in rice. We demonstrate that SLENDER RICE1 (SLR1), the key repressor of GA signaling, could physically interact with the rice seed shattering-related transcription factors quantitative trait locus of seed shattering on chromosome 1 (qSH1), O. sativa HOMEOBOX 15 (OSH15), and SUPERNUMERARY BRACT (SNB). Importantly, these physical interactions interfered with the direct binding of these three regulators to the lignin biosynthesis gene 4-COUMARATE: COENZYME A LIGASE 3 (4CL3), thereby derepressing its expression. Derepression of 4CL3 led to increased lignin deposition in the abscission region, causing reduced rice seed shattering. Importantly, we also show that modulating GA content could alter the degree of seed shattering to increase harvest efficiency. Our results reveal that the "Green Revolution" phytohormone GA is important for regulating rice seed shattering, and we provide an applicable breeding strategy for high-efficiency rice harvesting.

GERDH: an interactive multi-omics database for cross-species data mining in horticultural crops

Horticultural plants contribute immensely to the quality of human's life. The rapid development of omics studies on horticultural plants has resulted in large volumes of valuable growth- and development-related data. Genes that are essential for growth and development are highly conserved in evolution. Cross-species data mining reduces the impact of species heterogeneity and has been extensively used for conserved gene identification. Owing to the lack of a comprehensive database for cross-species data mining using multi-omics data from all horticultural plant species, the current resources in this field are far from satisfactory. Here, we introduce GERDH (https://dphdatabase.com), a database platform for cross-species data mining among horticultural plants, based on 12 961 uniformly processed publicly available omics libraries from more than 150 horticultural plant accessions, including fruits, vegetables and ornamental plants. Important and conserved genes that are essential for a specific biological process can be obtained by cross-species analysis module with interactive web-based data analysis and visualization. Moreover, GERDH is equipped with seven online analysis tools, including gene expression, in-species analysis, epigenetic regulation, gene co-expression, enrichment/pathway and phylogenetic analysis. By interactive cross-species analysis, we identified key genes contributing to postharvest storage. By gene expression analysis, we explored new functions of CmEIN3 in flower development, which was validated by transgenic chrysanthemum analysis. We believe that GERDH will be a useful resource for key gene identification and will allow for omics big data to be more available and accessible to horticultural plant community members.

Plant terpene specialized metabolism: complex networks or simple linear pathways?

From the perspectives of pathway evolution, discovery and engineering of plant specialized metabolism, the nature of the biosynthetic routes represents a critical aspect. Classical models depict biosynthesis typically from an end-point angle and as linear, for example, connecting central and specialized metabolism. As the number of functionally elucidated routes increased, the enzymatic foundation of complex plant chemistries became increasingly well understood. The perception of linear pathway models has been severely challenged. With a focus on plant terpenoid specialized metabolism, we review here illustrative examples supporting that plants have evolved complex networks driving chemical diversification. The completion of several diterpene, sesquiterpene and monoterpene routes shows complex formation of scaffolds and their subsequent functionalization. These networks show that branch points, including multiple sub-routes, mean that metabolic grids are the rule rather than the exception. This concept presents significant implications for biotechnological production.

Two monolignoid biosynthetic genes 4-coumarate:coenzyme A ligase (4CL) and p-coumaric acid 3-hdroxylase (C3H) involved in lignin accumulation in pear fruits

One of the most important factors impacting the quality of pear fruit is the presence of stone cells and lignin. Lignin is the main component of stone cells in pear fruits. Two monolignoid biosynthetic genes 4-coumarate:coenzyme A ligase (4CL) and p-coumaric acid 3-hdroxylase (C3H) are involved in lignin accumulation in pear fruits. However, the functions of these genes in lignin biosynthesis were excluded in pear. In our study, we isolated and cloned Pb4CL11 (GenBank: KM455955.1) and PbC3H1 (GenBank: KM373790.1) from pear, which contained 1644 bp encoded 54 amino acids (AA), and 1539 bp encoded 513 AA, respectively. The expression of Pb4CL11 and PbC3H1 in Arabidopsis thaliana led to an increase in cell wall thickness for intervascular fibers and xylem cells and lignin content. Overexpression of Pb4CL11 and PbC3H1 in A. thaliana can significantly increase the expression of AtPAL, AtC4H, AtHCT, AtC3H, AtCCOMT, AtCCR, AtF5H, AtCOMT, AtCAD4 and AtCAD5 with promotion of lignin biosynthesis. Taken together, our study's findings not only demonstrated the probable function of Pb4CL11 and PbC3H1 in lignin biosynthesis but also laid the groundwork for future studies using molecular biological methods to control lignin production and the formation of stone cells in pear fruits.

Rapid Biocatalytic Synthesis of Aromatic Acid CoA Thioesters by Using Microbial Aromatic Acid CoA Ligases

Chemically labile ester linkages can be introduced into lignin by incorporation of monolignol conjugates, which are synthesized in planta by acyltransferases that use a coenzyme A (CoA) thioester donor and a nucleophilic monolignol alcohol acceptor. The presence of these esters facilitates processing and aids in the valorization of renewable biomass feedstocks. However, the effectiveness of this strategy is potentially limited by the low steady-state levels of aromatic acid thioester donors in plants. As part of an effort to overcome this, aromatic acid CoA ligases involved in microbial aromatic degradation were identified and screened against a broad panel of substituted cinnamic and benzoic acids involved in plant lignification. Functional fingerprinting of this ligase library identified four robust, highly active enzymes capable of facile, rapid, and high-yield synthesis of aromatic acid CoA thioesters under mild aqueous reaction conditions mimicking in planta activity.

Molecular module of CmMYB15-like-Cm4CL2 regulating lignin biosynthesis of chrysanthemum (Chrysanthemum morifolium) in response to aphid (Macrosiphoniella sanborni) feeding

Lignin is a major component of plant cell walls and a conserved basic defense mechanism in higher plants deposited in response to aphid infection. However, the molecular mechanisms of lignin biosynthesis in response to aphid infection and the effect of lignin on aphid feeding behavior remain unclear. We report that 4-Coumarate:coenzyme A ligase 2 (Cm4CL2), a gene encoding a key enzyme in the lignin biosynthesis pathway, is induced by aphid feeding, resulting in lignin deposition and reduced aphid attack. Upstream regulator analysis showed that the expression of Cm4CL2 in response to aphid feeding was directly upregulated by CmMYB15-like, an SG2-type R2R3-MYB transcription factor. CmMYB15-like binds directly to the AC cis-element in the promoter region of Cm4CL2. Genetic validation demonstrated that CmMYB15-like was induced by aphid infection and contributed to lignin deposition and cell wall thickening, which consequently enhanced aphid resistance in a Cm4CL2-dependent manner. This study is the first to show that the CmMYB15-like-Cm4CL2 module regulates lignin biosynthesis in response to aphid feeding.

Genome-wide analysis of MYB family in Nicotiana benthamiana and the functional role of the key members in resistance to Bemisia tabaci

MYB transcription factors (TFs) play a key role in plant resistance to abiotic and biotical stresses. However, little is currently known about their involvement in the plant defense to piercing-sucking insects. Here, we studied the MYB TFs that responded to and resisted Bemisia tabaci whitefly in the model plant Nicotiana benthamiana. Firstly, a total of 453 NbMYB TFs in N. benthamiana genome were identified and 182 R2R3-MYB TFs were analyzed for molecular characteristics, phylogenetic analysis, genetic structure, motif composition, and cis-elements. Then, six stress-related NbMYB genes were selected for further study. The expression pattern shows they were highly expressed in mature leaves and intensively induced upon whitefly attack. Combined with bioinformatic analysis, overexpression, β-Glucuronidase (GUS) assay, and virus-induced silencing tests, we determined the transcriptional regulation of these NbMYBs on the genes in lignin biosynthesis and SA-signaling pathways. Meanwhile, we tested the performance of whitefly on plants with increased or silenced NbMYB genes expression and found that NbMYB42, NbMYB107, NbMYB163, and NbMYB423 were resistant to whitefly. Our results contribute to a comprehensive understanding of the MYB TFs in N. benthamiana. Furthermore, our findings will facilitate further studies on the role of MYB TFs in the interaction between plants and piercing-sucking insects.

Transcriptional Analysis of Tea Plants (Camellia sinensis) in Response to Salicylic Acid Treatment

Salicylic acid (SA) is an important plant hormone and signal required for establishing resistance to diverse pathogens and plant diseases. The abundant polyphenols in tea plants also defend plants from biotic and abiotic stresses. However, whether exogenous SA would increase the resistance of tea plants to adversity and the relationship between SA and polyphenols are still poorly understood. Here, we carried out SA treatment on tea seedlings and performed transcriptome sequencing. SA treatment inhibited the phenylpropanoid and flavonoid metabolic pathways but promoted the lignin metabolic pathways. The increased accumulation of lignin in tea leaves after treating with SA indicated that lignin might coordinate SA, enhance, and improve plant defense and disease resistance. Simultaneously, an SA-inducible flavonoid glucosyltransferase (CsUGT0554) specifically involved in 7-OH site glycosylation was characterized in vitro. These results provided valuable information about the effects of SA on tea seedlings and the molecular basis for SA-mediated immune responses.

Chromosomal-level genome and multi-omics dataset provides new insights into leaf pigmentation in Acer palmatum

Acer palmatum (A. palmatum), a deciduous shrub or small arbour which belongs to Acer of Aceraceae, is an excellent greening species as well as a beautiful ornamental plant. In this study, a high-quality chromosome-level reference genome for A. palmatum was constructed using Oxford Nanopore sequencing and Hi-C technology. The assembly genome was ∼745.78 Mb long with a contig N50 length of 3.20 Mb, and 95.30 % (710.71 Mb) of the assembly was anchored into 13 pseudochromosomes. A total of 28,559 protein-coding genes were obtained, ∼90.02 % (25,710) of which could be functionally annotated. The genomic evolutionary analysis revealed that A. palmatum is most closely related to A. yangbiense and A. truncatum, and underwent only an ancient gamma whole-genome duplication event. Despite lacking a recent independent WGD, 25,795 (90.32 %) genes of A. palmatum were duplicated, and the unique/expanded gene families were linked with genes involved in plant-pathogen interaction and several metabolic pathways, which might underpin adaptability. A combined genomic, transcriptomic, and metabolomic analysis related to the biosynthesis of anthocyanin in leaves during the different season were characterized. The results indicate that the dark-purple colouration of the leaves in spring was caused by a high amount of anthocyanins, especially delphinidin and its derivatives; and the red colouration of the leaves in autumn by a high amount of cyanidin 3-O-glucoside. In conclusion, these valuable multi-omic resources offer important foundations to explore the molecular regulation mechanism in leaf colouration and also provide a platform for the scientific and efficient utilization of A. palmatum.

Production of various phenolic aldehyde compounds using the 4CL-FCHL biosynthesis platform

Vanillin (3-methoxy-4-hydroxybenzaldehyde) is one of the most important flavoring substances used in the cosmetic and food industries. Feruloyl-CoA hydratase/lyase (FCHL) is an enzyme that catalyzes the production of vanillin from feruloyl-CoA. In this study, we report kinetic parameters and biochemical properties of FCHL from Sphingomonas paucimobilis SYK-6 (SpFCHL). Also, the crystal structures of an apo-form of SpFCHL and two complexed forms with acetyl-CoA and vanillin/CoA was present. Comparing the apo structure to its complexed forms of SpFCHL, a gate loop with an "open and closed" role was observed at the entrance of the substrate-binding site. With vanillin and CoA complexed to SpFCHL, we captured a conformational change in the feruloyl moiety-binding pocket that repositions the catalytic SpFCHL^E146 and other key residues. This binding pocket does not tightly fit the vanillin structure, suggesting substrate promiscuity of this enzyme. This observation is in good agreement with assay results for phenylpropanoid-CoAs and indicates important physicochemical properties of the substrate for the hydratase/lyase reaction mechanism. In addition, we showed that various phenolic aldehydes could be produced using the 4CL-FCHL biosynthesis platform.

Genome-Wide Identification and Expression Analysis of the 4-Coumarate: CoA Ligase Gene Family in Solanum tuberosum

4-coumarate: CoA ligase (4CL) is not only involved in the biosynthetic processes of flavonoids and lignin in plants but is also closely related to plant tolerance to abiotic stress. UV irradiation can activate the expression of 4CL genes in plants, and the expression of 4CL genes changed significantly in response to different phytohormone treatments. Although the 4CL gene has been cloned in potatoes, there have been fewer related studies of the 4CL gene family on the potato genome-wide scale. In this study, a total of 10 potato 4CL genes were identified in the potato whole genome. Through multiple sequence alignment, phylogenetic analysis as well as gene structure analysis indicated that the potato 4CL gene family could be divided into two subgroups. Combined with promoter cis-acting element analysis, transcriptome data, and RT-qPCR results indicated that potato 4CL gene family was involved in potato response to white light, UV irradiation, ABA treatment, MeJA treatment, and PEG simulated drought stress. Abiotic stresses such as UV, ABA, MeJA, and PEG could promote the up-regulated expression of St4CL6 and St4CL8 but inhibits the expression of St4CL5. The above results will increase our understanding of the evolution and expression regulation of the potato 4CL gene family and provide reference value for further research on the molecular biological mechanism of 4CL participating in response to diverse environmental signals in potatoes.

Comparative transcriptomic analysis provides insights into the molecular basis underlying pre-harvest sprouting in rice

BACKGROUND

Pre-harvest sprouting (PHS) is one of the most serious rice production constraints in areas where prolonged rainfall occurs during harvest. However, the molecular mechanisms of transcriptional regulation underlying PHS remain largely unknown.

RESULTS

In the current study, comparative transcriptome analyses were performed to characterize the similarities and differences between two rice varieties: PHS-sensitive Jiuxiangzhan (JXZ) and PHS-resistant Meixiangxinzhan (MXXZ). The physiological experimental results indicated that PHS causes a significant decrease in starch content and, in contrast, a significant increase in soluble sugar content and amylase activity. The extent of change in these physiological parameters in the sensitive variety JXZ was greater than that in the resistant variety MXXZ. A total of 9,602 DEGs were obtained from the transcriptome sequencing data, and 5,581 and 4,021 DEGs were identified in JXZ and MXXZ under high humidity conditions, respectively. The KEGG pathway enrichment analysis indicated that many DEGs under high humidity treatment were mainly linked to plant hormone signal transduction, carbon metabolism, starch and sucrose metabolism, and phenylpropanoid biosynthesis. Furthermore, the number of upregulated genes involved in these pathways was much higher in JXZ than in MXXZ, while the number of downregulated genes was higher in MXXZ than in JXZ. These results suggest that the physiological and biochemical processes of these pathways are more active in the PHS-sensitive JXZ than in the PHS-resistant MXXZ.

CONCLUSION

Based on these results, we inferred that PHS in rice results from altered phytohormone regulation, more active carbon metabolism and energy production, and enhanced phenylpropanoid biosynthesis. Our study provides a theoretical foundation for further elucidation of the complex regulatory mechanism of PHS in rice and the molecular breeding of PHS-resistant rice varieties.

Physiological and Metabolic Responses of Gac Leaf (Momordica cochinchinensis (Lour.) Spreng.) to Salinity Stress

Gac is a carotenoid-rich, healthful tropical fruit; however, its productivity is limited by soil salinity, a growing environmental stress. This study aimed to evaluate the effects of salinity stress on key physiological traits and metabolites in 30-day-old gac seedling leaves, treated with 0, 25-, 50-, 100-, and 150-mM sodium chloride (NaCl) for four weeks to identify potential alarm, acclimatory, and exhaustion responses. Electrolyte leakage increased with increasing NaCl concentrations (p < 0.05) indicating loss of membrane permeability and conditions that lead to reactive oxygen species production. At 25 and 50 mM NaCl, superoxide dismutase (SOD) activity, starch content, and total soluble sugar increased. Chlorophyll a, and total chlorophyll increased at 25 mM NaCl but decreased at higher NaCl concentrations indicating salinity-induced thylakoid membrane degradation and chlorophyllase activity. Catalase (CAT) activity decreased (p < 0.05) at all NaCl treatments, while ascorbate peroxidase (APX) and guaiacol peroxidase (GPX) activities were highest at 150 mM NaCl. GC-MS-metabolite profiling showed that 150 mM NaCl induced the largest changes in metabolites and was thus distinct. Thirteen pathways and 7.73% of metabolites differed between the control and all the salt-treated seedlings. Salinity decreased TCA cycle intermediates, and there were less sugars for growth but more for osmoprotection, with the latter augmented by increased amino acids. Although 150 mM NaCl level decreased SOD activity, the APX and GPX enzymes were still active, and some carbohydrates and metabolites also accumulated to promote salinity resistance via multiple mechanisms.

Proteomic and Metabolomic Revealed Differences in the Distribution and Synthesis Mechanism of Aroma Precursors in Yunyan 87 Tobacco Leaf, Stem, and Root at the Seedling Stage

Tobacco, as an important cash crop and model plant, has been the subject of various types of research. The quality of flue-cured tobacco products depends on the compound collection of tobacco leaves, including pigments, carbohydrates, amino acids, polyphenols, and alkaloid aroma precursors. The present study investigates tobacco seedling organs (leaf, stem, and root) with the assistance of label-free proteomic technology and untargeted metabonomic technology. We analyzed 4992 proteins and 298 metabolites obtained in the leaf, stem, and root groups and found that there were significant differences in both primary and secondary metabolism processes involved in aroma precursor biosynthesis, such as carbohydrate metabolism, energy metabolism, and amino acid biosynthesis, and phenylpropanoid, flavonoid, and alkaloid biosynthesis. The findings showed that the contents of alkaloid metabolites such as nornicotine, anatabine, anatalline, and myosmine were significantly higher in tobacco roots than in leaves and stems at the seedling stage.

Proteomic and metabolic disturbances in lignin-modified Brachypodium distachyon

Lignin biosynthesis begins with the deamination of phenylalanine and tyrosine (Tyr) as a key branch point between primary and secondary metabolism in land plants. Here, we used a systems biology approach to investigate the global metabolic responses to lignin pathway perturbations in the model grass Brachypodium distachyon. We identified the lignin biosynthetic protein families and found that ammonia-lyases (ALs) are among the most abundant proteins in lignifying tissues in grasses. Integrated metabolomic and proteomic data support a link between lignin biosynthesis and primary metabolism mediated by the ammonia released from ALs that is recycled for the synthesis of amino acids via glutamine. RNA interference knockdown of lignin genes confirmed that the route of the canonical pathway using shikimate ester intermediates is not essential for lignin formation in Brachypodium, and there is an alternative pathway from Tyr via sinapic acid for the synthesis of syringyl lignin involving yet uncharacterized enzymatic steps. Our findings support a model in which plant ALs play a central role in coordinating the allocation of carbon for lignin synthesis and the nitrogen available for plant growth. Collectively, these data also emphasize the value of integrative multiomic analyses to advance our understanding of plant metabolism.

Tartary buckwheat FtF3'H1 as a metabolic branch switch to increase anthocyanin content in transgenic plant

Tartary buckwheat (TB) is a pseudocereal rich in flavonoids, mainly including flavonols and anthocyanins. The flavonoid 3'-hydroxylase (F3'H) is a key enzyme in flavonoid biosynthesis and is encoded by two copies in TB genome. However, its biological function and effects on flavonol and anthocyanin synthesis in TB have not been well validated yet. In this study, we cloned the full-length FtF3'H1 gene highly expressed in all tissues (compared with FtF3'H2) according to TB flowering transcriptome data. The corresponding FtF3'H1 protein contains 534 amino acids with the molecular properties of the typical plant F3'H and belongs to the CYP75B family. During the flowering stage, the FtF3'H1 expression was highest in flowers, and its expression pattern showed a significant and positive correlation with the total flavonoids (R ² > 0.95). The overexpression of FtF3'H1 in Arabidopsis thaliana, Nicotiana tabacum and TB hairy roots resulted in a significant increase in anthocyanin contents (p < 0.05) but a decrease in rutin (p < 0.05). The average anthocyanin contents were 2.94 mg/g (fresh weight, FW) in A. thaliana (about 135% increase), 1.18 mg/g (FW) in tobacco (about 17% increase), and 1.56 mg/g (FW) TB hairy roots (about 44% increase), and the rutin contents were dropped to about 53.85, 14.99, 46.31%, respectively. However, the expression of genes involved in anthocyanin (DFRs and ANSs) and flavonol (FLSs) synthesis pathways were significantly upregulated (p < 0.05). In particular, the expression level of DFR, a key enzyme that enters the anthocyanin branch, was upregulated thousand-fold in A. thaliana and in N. tabacum. These results might be attributed to FtF3'H1 protein with a higher substrate preference for anthocyanin synthesis substrates. Altogether, we identified the basic biochemical activity of FtF3'H1 in vivo and investigated its involvement in anthocyanin and flavonol metabolism in plant.

Molecular and biochemical characterization of two 4-coumarate: CoA ligase genes in tea plant (Camellia sinensis)

Two 4-coumarate: CoA ligase genes in tea plant involved in phenylpropanoids biosynthesis and response to environmental stresses. Tea plant is rich in flavonoids benefiting human health. Lignin is essential for tea plant growth. Both flavonoids and lignin defend plants from stresses. The biosynthesis of lignin and flavonoids shares a key intermediate, 4-coumaroyl-CoA, which is formed from 4-coumaric acid catalyzed by 4-coumaric acid: CoA ligase (4CL). Herein, we report two 4CL paralogs from tea plant, Cs4CL1 and Cs4CL2, which are a member of class I and II of this gene family, respectively. Cs4CL1 was mainly expressed in roots and stems, while Cs4CL2 was mainly expressed in leaves. The promoter of Cs4CL1 had AC, nine types of light sensitive (LSE), four types of stress-inducible (SIE), and two types of meristem-specific elements (MSE). The promoter of Cs4CL2 also had AC and nine types of LSEs, but only had two types of SIEs and did not have MSEs. In addition, the LSEs varied in the two promoters. Based on the different features of regulatory elements, three stress treatments were tested to understand their expression responses to different conditions. The resulting data indicated that the expression of Cs4CL1 was sensitive to mechanical wounding, while the expression of Cs4CL2 was UV-B-inducible. Enzymatic assays showed that both recombinant Cs4CL1 and Cs4CL2 transformed 4-coumaric acid (CM), ferulic acid (FR), and caffeic acid (CF) to their corresponding CoA ethers. Kinetic analysis indicated that the recombinant Cs4CL1 preferred to catalyze CF, while the recombinant Cs4CL2 favored to catalyze CM. The overexpression of both Cs4CL1 and Cs4CL2 increased the levels of chlorogenic acid and total lignin in transgenic tobacco seedlings. In addition, the overexpression of Cs4CL2 consistently increased the levels of three flavonoid compounds. These findings indicate the differences of Cs4CL1 and Cs4CL2 in the phenylpropanoid metabolism.

Insights into the Regulation of Rice Seed Storability by Seed Tissue-Specific Transcriptomic and Metabolic Profiling

Non-dormant seeds are continuously aging and deteriorating during storage, leading to declining seed vigor, which is a challenge for the rice seed industry. Improving the storability of seeds is of great significance to ensure the quality of rice and national food security. Through a set of chromosome segment substitution lines population constructed using japonica rice NIP as donor parent and indica rice ZS97 as recurrent parent, we performed seed storability QTL analysis and selected four non-storable NILs to further investigate the storability regulatory mechanisms underlying it. The seeds were divided into four tissues, which were the embryo, endosperm, aleurone layer, and hull, and tissue-specific transcriptome and metabolome analyses were performed on them. By exploring the common differentially expressed genes and differentially accumulated metabolites, as well as the KEGG pathway of the four non-storable NILs, we revealed that the phenylpropanoid biosynthesis pathway and diterpenoid biosynthesis pathway played a central role in regulating seed storability. Integrated analysis pinpointed 12 candidate genes that may take part in seed storability. The comprehensive analysis disclosed the divergent and synergistic effect of different seed tissues in the regulation of rice storability.

Systematic Analysis and Expression Profiles of the 4-Coumarate: CoA Ligase (4CL) Gene Family in Pomegranate (Punica granatum L.)

4-Coumarate:CoA ligase (4CL, EC6.2.1.12), located at the end of the phenylpropanoid metabolic pathway, regulates the metabolic direction of phenylpropanoid derivatives and plays a pivotal role in the biosynthesis of flavonoids, lignin, and other secondary metabolites. In order to understand the molecular characteristics and potential biological functions of the 4CL gene family in the pomegranate, a bioinformatics analysis was carried out on the identified 4CLs. In this study, 12 Pg4CLs were identified in the pomegranate genome, which contained two conserved amino acid domains: AMP-binding domain Box I (SSGTTGLPKGV) and Box II (GEICIRG). During the identification, it was found that Pg4CL2 was missing Box II. The gene cloning and sequencing verified that this partial amino acid deletion was caused by genome sequencing and splicing errors, and the gene cloning results corrected the Pg4CL2 sequence information in the ‘Taishanhong’ genome. According to the phylogenetic tree, Pg4CLs were divided into three subfamilies, and each subfamily had 1, 1, and 10 members, respectively. Analysis of cis-acting elements found that all the upstream sequences of Pg4CLs contained at least one phytohormone response element. An RNA-seq and protein interaction network analysis suggested that Pg4CL5 was highly expressed in different tissues and may participate in lignin synthesis of pomegranate. The expression of Pg4CL in developing pomegranate fruits was analyzed by quantitative real-time PCR (qRT-PCR), and the expression level of Pg4CL2 demonstrated a decreasing trend, similar to the trend of flavonoid content, indicating Pg4CL2 may involve in flavonoid synthesis and pigment accumulation. Pg4CL3, Pg4CL7, Pg4CL8, and Pg4CL10 were almost not expressed or lowly expressed, the expression level of Pg4CL4 was higher in the later stage of fruit development, suggesting that Pg4CL4 played a crucial role in fruit ripening. The expression levels of 4CL genes were significantly different in various fruit development stages. The results laid the foundation for an in-depth analysis of pomegranate 4CL gene functions.

Transgenic manipulation of triacylglycerol biosynthetic enzymes in B. napus alters lipid-associated gene expression and lipid metabolism

Oilseed rape (Brassica napus) is an important crop that is cultivated for the oil (mainly triacylglycerol; TAG) it produces in its seeds. TAG synthesis is controlled mainly by key enzymes in the Kennedy pathway, such as glycerol 3-phosphate acyltransferase (GPAT), lysophosphatidate acyltransferase (LPAT) and diacylglycerol acyltransferase (DGAT) but can also be produced from phosphoglycerides such as phosphatidylcholine (PC) by the activity of the enzyme phospholipid: diacylglycerol acyltransferase (PDAT). To evaluate the potential for these enzymes to alter oil yields or composition, we analysed transgenic B. napus lines which overexpressed GPAT, LPAT or PDAT using heterologous transgenes from Arabidopsis and Nasturtium and examined lipid profiles and changes in gene expression in these lines compared to WT. Distinct changes in PC and TAG abundance and spatial distribution in embryonic tissues were observed in some of the transgenic lines, together with altered expression of genes involved generally in acyl-lipid metabolism. Overall our results show that up-regulation of these key enzymes differentially affects lipid composition and distribution as well as lipid-associated gene expression, providing important information which could be used to improve crop properties by metabolic engineering.

Investigating the Mechanism of Unilateral Cross Incompatibility in Longan (Dimocarpus longan Lour.) Cultivars (Yiduo × Shixia)

Longan (Dimocarpus longan Lour.) is an important subtropical fruit tree in China. Nearly 90% of longan fruit imports from Thailand are from the cultivar Yiduo. However, we have observed that there exists a unilateral cross incompatibility (UCI) when Yiduo is used as a female parent and Shixia (a famous Chinese cultivar) as a male parent. Here, we performed a comparative transcriptome analysis coupled with microscopy of pistils from two reciprocal pollination combinations [Shixia♂ × Yiduo♀(SY) and Yiduo♀ × Shixia♂(YS)] 4, 8, 12, and 24 h after pollination. We also explored endogenous jasmonic acid (JA) and jasmonyl isoleucine (JA-Ile) levels in pistils of the crosses. The microscopic observations showed that the UCI was sporophytic. The endogenous JA and JA-Ile levels were higher in YS than in SY at the studied time points. We found 7,251 differentially expressed genes from the transcriptome analysis. Our results highlighted that genes associated with JA biosynthesis and signaling, pollen tube growth, cell wall modification, starch and sucrose biosynthesis, and protein processing in endoplasmic reticulum pathways were differentially regulated between SY and YS. We discussed transcriptomic changes in the above-mentioned pathways regarding the observed microscopic and/or endogenous hormone levels. This is the first report on the elaboration of transcriptomic changes in longan reciprocal pollination combination showing UCI. The results presented here will enable the longan breeding community to better understand the mechanisms of UCI.

Bibenzyl synthesis in Cannabis sativa L

This study focuses on the biosynthesis of a suite of specialized metabolites from Cannabis that are known as the 'bibenzyls'. In planta, bibenzyls accumulate in response to fungal infection and various other biotic stressors; however, it is their widely recognized anti-inflammatory properties in various animal cell models that have garnered recent therapeutic interest. We propose that these compounds are synthesized via a branch point from the core phenylpropanoid pathway in Cannabis, in a three-step sequence. First, various hydroxycinnamic acids are esterified to acyl-coenzyme A (CoA) by a member of the 4-coumarate-CoA ligase family (Cs4CL4). Next, these CoA esters are reduced by two double-bond reductases (CsDBR2 and CsDBR3) that form their corresponding dihydro-CoA derivatives from preferred substrates. Finally, the bibenzyl backbone is completed by a polyketide synthase that specifically condenses malonyl-CoA with these dihydro-hydroxycinnamoyl-CoA derivatives to form two bibenzyl scaffolds: dihydropiceatannol and dihydroresveratrol. Structural determination of this 'bibenzyl synthase' enzyme (CsBBS2) indicates that a narrowing of the hydrophobic pocket surrounding the active site evolved to sterically favor the non-canonical and more flexible dihydro-hydroxycinnamoyl-CoA substrates in comparison with their oxidized relatives. Accordingly, three point mutations that were introduced into CsBBS2 proved sufficient to restore some enzymatic activity with an oxidized substrate, in vitro. Together, the identification of this set of Cannabis enzymes provides a valuable contribution to the growing 'parts prospecting' inventory that supports the rational metabolic engineering of natural product therapeutics.

Enhanced accumulation of pinosylvin stilbenes and related gene expression in Pinus strobus after infection of pine wood nematode

Pine wood nematodes (PWNs; Bursaphelenchus xylophilus) infect pine trees and cause serious pine wilt disease. Eastern white pine (Pinus strobus) has resistance to PWN. However, the detailed defense mechanisms of P. strobus against PWN are not well known. When P. strobus plants were infected with PWNs, the accumulation of stilbenoids, dihydropinosylvin monomethyl ether (DPME) and pinosylvin monomethyl ether (PME) was increased remarkably. Both DPME and PME had high nematicidal activity. The nematicidal activity of the two compounds was resulted in a developmental stage-dependent manner. Pinosylvin monomethyl ether was more toxic to adult PWNs than juveniles, whereas DPME was found more toxic to juvenile PWNs than the adults. The genes involved in PME and DPME biosynthesis such as phenylalanine ammonia-lyase (PAL), 4-coumarate-CoA ligase (4CL), pinosylvin synthase (STS) and pinosylvin O-methyltransferase (PMT) were isolated using de novo sequencing of the transcriptome in P. strobus. In addition, transcription factors (TFs; bHLH, MYB and WRKY) related to stilbene biosynthesis were isolated. qPCR analyses of the selected genes (PAL, 4CL, STS and PMT) including TFs (bHLH, MYB and WRKY) revealed that the expression level of the selected genes highly enhanced after PWN infection. Our results suggest that pinosylvin-type stilbenoid biosynthesis is highly responsive to PWN infection and plays an important role in PWN resistance of P. strobus trees.

Transcriptomic, Proteomic and Metabolomic Analysis of Flavonoid Biosynthesis During Fruit Maturation in Rubus chingii Hu

Rubus chingii HU, is a medicinal and nutritious fruit, which is very rich in flavonoids. However, the biosynthesis of its flavonoids is poorly understood. This study examined flavonoids and the genes/proteins at four fruit ripening phases using LC-MS/MS and qPCR. Six major kinds of anthocyanins, primarily consisted of flavanol-anthocyanins, which differed in form or concentration from other Rubus species. In contrast to other known raspberries species, R. chingii had a decline in flavonoids during fruit ripening, which was due to down-regulation of genes and proteins involved in phenylpropanoid and flavonoid biosynthesis. Unexpectedly, anthocyanin also continuously decreased during fruit maturation. This suggests that anthocyanins are not responsible for the fruit's reddish coloration. Flavanol-anthocyanins were derived from the proanthocyanidin pathway, which consumed two flavonoid units both produced through the same upstream pathway. Their presence indicates a reduction in the potential biosynthesis of anthocyanin production. Also, the constantly low expression of RchANS gene resulted in low levels of anthocyanin biosynthesis. The lack of RchF3'5'H gene/protein hindered the production of delphinidin glycosides. Flavonoids primarily comprising of quercetin/kaempferol-glycosides were predominately located at fruit epidermal-hair and placentae. The proportion of receptacle/drupelets changes with the maturity of the fruit and may be related to a decrease in the content of flavonoids per unit mass as the fruit matures. The profile and biosynthesis of R. chingii flavonoids are unique to Rubus. The unique flavonol pathways of R. chingii could be used to broaden the genetic diversity of raspberry cultivars and to improve their fruit quality.

Transcriptome-Wide Identification and Quantification of Caffeoylquinic Acid Biosynthesis Pathway and Prediction of Its Putative BAHDs Gene Complex in A. spathulifolius

The phenylpropanoid pathway is a major secondary metabolite pathway that helps plants overcome biotic and abiotic stress and produces various byproducts that promote human health. Its byproduct caffeoylquinic acid is a soluble phenolic compound present in many angiosperms. Hydroxycinnamate-CoA shikimate/quinate transferase is a significant enzyme that plays a role in accumulating CQA biosynthesis. This study analyzed transcriptome-wide identification of the phenylpropanoid to caffeoylquinic acid biosynthesis candidate genes in A. spathulifolius flowers and leaves. Transcriptomic analyses of the flowers and leaves showed a differential expression of the PPP and CQA biosynthesis regulated unigenes. An analysis of PPP-captive unigenes revealed a major duplication in the following genes: PAL, 120 unigenes in leaves and 76 in flowers; C3′H, 169 unigenes in leaves and 140 in flowers; 4CL, 41 unigenes in leaves and 27 in flowers; and C4H, 12 unigenes in leaves and 4 in flowers. The phylogenetic analysis revealed 82 BAHDs superfamily members in leaves and 72 in flowers, among which five unigenes encode for HQT and three for HCT. The three HQT are common to both leaves and flowers, whereas the two HQT were specialized for leaves. The pattern of HQT synthesis was upregulated in flowers, whereas HCT was expressed strongly in the leaves of A. spathulifolius. Overall, 4CL, C4H, and HQT are expressed strongly in flowers and CAA and HCT show more expression in leaves. As a result, the quantification of HQT and HCT indicates that CQA biosynthesis is more abundant in the flowers and synthesis of caffeic acid in the leaves of A. spathulifolius.

Amide Bond Formation Using 4-Coumarate: CoA Ligase from Arabidopsis thaliana

Amide bond formation is one of the most fundamental reactions in organic chemistry, and amide bonds constitute the key functional groups in natural products, peptides, and pharmaceuticals. Here we demonstrate the chemoenzymatic syntheses of 4-coumaroyl- and hexanoyl-amino acids, using 4-coumarate: CoA ligase from the model plant Arabidopsis thaliana (At4CL2). At4CL2 accepts 4-coumaric acid and hexanoic acid as the carboxylate substrates to generate acyl adenylates, which are captured by the amino group of amino acids to afford a series of N-acyl amides. This study shows the potential of 4CL for application as a biocatalyst to generate a series of biologically active amide compounds.

Seasonal Variations of Rosmarinic Acid and Its Glucoside and Expression of Genes Related to Their Biosynthesis in Two Medicinal and Aromatic Species of Salvia subg. Perovskia

Simple Summary

Here, we studied two closely related medicinal and aromatic plants from Asia, called Russian sage or from their previously used Latin name–Perovskia. These plants contain various specialized metabolites called phenylpropanoids that contribute to their medicinal uses. In our experiments, several different specialized phytochemicals were traced down in the roots and leaves with the major metabolite called rosmarinic acid, known for health beneficial properties. In order to check if the composition of these plants is regulated by specific genes encoding proteins that assemble these phytochemicals, we analyzed their expression during the growth season (spring, summer and fall). Despite being the closest kin, the two species of Russian sage displayed different seasonal changes in the composition of bioactive metabolites and the activity of genes responsible for their production. The genes’ activity was correlated with rosmarinic acid content in the roots but not in the green parts of the plants. Two genes pointed out were linked to the regulation of rosmarinic acid biosynthesis, called RAS (for Rosmarinic Acid-Synthase) and a newly reported version of an oxidizing enzyme called Cyp98A14. These discoveries broaden our understanding of relationships between the genes’ activity and production of bioactive constituents in herbs such as the two studied species of Russian sages.

Abstract

Salvia abrotanoides Kar. and Salvia yangii B.T. Drew are medicinal and aromatic plants belonging to the subgenus Perovskia and used as herbal medicines in Asia. Derivatives of caffeic acid, mainly rosmarinic acid (RA), are the major phenolic compounds identified in these plants. Understanding the factors and molecular mechanisms regulating the accumulation of pharmacologically and ecologically relevant phenolic metabolites is essential for future biotechnological and medical applications. Up to date, no studies of phenylpropanoid biosynthetic pathway at the transcriptional level has been performed in the Perovskia subgenus. Using a combined qRT-PCR transcriptional activity analysis with LC-MS based metabolic profiling of roots and leaves at the beginning, in the middle and at the end of vegetation season, we have identified the following gene candidates with properties correlating to phenolic acid biosynthesis in S. abrotanoides and S. yangii: PAL, C4H, 4CL, TAT, HPPR, RAS1, RAS2 and Cyp98A14. A comparison of phenolic acid profiles with gene transcript levels revealed the transcriptional regulation of RA biosynthesis in the roots but not the leaves of the studied species. Additionally, RAS1 and Cyp98A14 were identified as rate-limiting steps regulating phenylpropanoid biosynthesis on a transcription level. In the future, this will facilitate the gene-based metabolic enhancement of phenolic compounds production in these promising medicinal herbs.

Integrated metabolome and transcriptome revealed the flavonoid biosynthetic pathway in developing Vernonia amygdalina leaves

Background

Vernonia amygdalina as a tropical horticultural crop has been widely used for medicinal herb, feed, and vegetable. Recently, increasing studies revealed that this species possesses multiple pharmacological properties. Notably, V. amygdalina leaves possess an abundance of flavonoids, but the specific profiles of flavonoids and the mechanisms of fl avonoid bi osynthesis in developing leaves are largely unknown.

Methods

The total flavonoids of V. amygdalina leaves were detected using ultraviolet spectrophotometer. The temporal flavonoid profiles of V. amygdalina leaves were analyzed by LC-MS. The transcriptome analysis of V. amygdalina leaves was performed by Illumina sequencing. Functional annotation and differential expression analysis of V. amygdalina genes were performed by Blast2GO v2.3.5 and RSEM v1.2.31, respectively. qRT-PCR analysis was used to verify the gene expressions in developing V. amygdalina leaves.

Results

By LC-MS analysis, three substrates (p-coumaric acid, trans-cinnamic acid, and phenylalanine) for flavonoid biosynthesis were identified in V. amygdalina leaves. Additionally, 42 flavonoids were identified from V. amygdalina leaves, including six dihydroflavones, 14 flavones, eight isoflavones, nine flavonols, two xanthones, one chalcone, one cyanidin, and one dihydroflavonol. Glycosylation and methylation were common at the hydroxy group of C3, C7, and C4’ positions. Moreover, dynamic patterns of different flavonoids showed diversity. By Illumina sequencing, the obtained over 200 million valid reads were assembled into 60,422 genes. Blast analysis indicated that 31,872 genes were annotated at least in one of public databases. Greatly increasing molecular resources makes up for the lack of gene information in V. amygdalina. By digital expression profiling and qRT-PCR, we specifically characterized some key enzymes, such as Va-PAL1, Va-PAL4, Va-C4H1, Va-4CL3, Va-ACC1, Va-CHS1, Va-CHI, Va-FNSII, and Va-IFS3, involved in flavonoid biosynthesis. Importantly, integrated metabolome and transcriptome data of V. amygdalina leaves, we systematically constructed a flavonoid biosynthetic pathway with regards to material supplying, flavonoid scaffold biosynthesis, and flavonoid modifications. Our findings contribute significantly to understand the underlying mechanisms of flavonoid biosynthesis in V. amygdalina leaves, and also provide valuable information for potential metabolic engineering.

Constitutive expression of Ribosomal Protein L6 modulates salt tolerance in rice transgenic plants

We have functionally characterized the RPL6, a Ribosomal Protein Large subunit gene for salt stress tolerance in rice. The overexpression of RPL6 resulted in tolerance to moderate (150 mM) to high (200 mM) levels of salt (NaCl). The transgenic rice plants expressing RPL6 constitutively showed better phenotypic and physiological responses with high quantum efficiency, accumulation of higher chlorophyll and proline contents, and an overall increase in seed yield compared with the wild type in salt stress treatments. An iTRAQ-based comparative proteomic analysis revealed the high expression of about 333 proteins among the 4378 DAPs in a selected overexpression line of RPL6 treated with 200 mM of NaCl. The functional analysis showed that these highly accumulated proteins (HAPs) are involved in photosynthesis, ribosome and chloroplast biogenesis, ion transportation, transcription and translation regulation, phytohormone and secondary metabolite signal transduction. An in silico network analysis of HAPs predicted that RPL6 binds with translation-related proteins and helicases, which coordinately affect the activities of a comprehensive signaling network, thereby inducing tolerance and promoting growth and productivity in response to salt stress. Our overall findings identified a novel candidate, RPL6, whose characterization contributed to the existing knowledge on the complexity of salt tolerance mechanism in plants.

Functional insights into two Ocimum kilimandscharicum 4-coumarate-CoA ligases involved in phenylpropanoid biosynthesis

Plant 4-coumarate-CoA ligase (4CL) catalyzes the ligation of CoA to cinnamic acid and its derivatives. Activated CoA esters are utilized for the biosynthesis of phenolic metabolites and lignin that play essential function in plants. Here, we characterize the diversity of Ocimum kilimandscharicum 4CLs (Ok4CLs). Phylogenetic analysis suggest that Ok4CLs could be grouped into three classes, class I - enzymes mostly involved in lignin biosynthesis, class II - non-structural phenylpropanoid biosynthesis and class III - yet to be characterized for specific role(s). We selected two Ok4CLs namely Ok4CL7 and Ok4CL15 for further characterization. Gene expression analysis suggested that Ok4CL7 is highly expressed in leaf trichomes, whereas Ok4CL15 is abundant in the roots. The recombinant Ok4CL7 and Ok4CL15 had optimal enzyme activities at 40 °C in pH 8 and 7, respectively. Ok4CL7 showed substrate preference towards p-coumaric acid, ferulic acid and caffeic acid. While, Ok4CL15 preferred p-coumaric acid, ferulic acid and sinapic acid. Feruloyl adenylate showed higher number of contacts and lowers binding energy with Ok4CL7 and 15 compared to cinnamoyl adenylate. Based on root-specific expression and preference for sinapic acid, Ok4CL15 might be involved in lignin biosynthesis. Further exploration is needed to unravel the role of diverse Ok4CLs in O. kilimandscharicum.

Exploiting Spermidine N-Hydroxycinnamoyltransferase Diversity and Substrate Promiscuity to Produce Various Trihydroxycinnamoyl Spermidines and Analogues in Engineered Yeast

Trihydroxycinnamoyl spermidines (THCSpd) are plant specialized metabolites with promising pharmacological activities as antifungals, antibacterial, antiviral, and antidepressant drugs. However, their characterization and potential pharmaceutical exploitation are greatly impaired by the sourcing of these compounds, restricted to the pollen of core Eudicot plant species. In this work, we developed a precursor-directed biosynthesis of THCSpd in yeast using a dual enzymatic system based on 4-coumarate-CoA ligases (4CL) and spermidine N-hydroxycinnamoyltransferases (SHT). The system relies on the yeast endogenous spermidine pool and only requires hydroxycinnamic acids as exogenous precursors. By exploring 4CL isoforms and SHT diversity among plants, we have driven the production of 8 natural THCSpd, using single or mixed hydroxycinnamic acid precursors. Substrate promiscuities of 4CL and SHT were genuinely exploited to produce 8 new-to-nature THCSpd from exotic hydroxycinnamic and dihydrohydroxycinnamic acids, together with 3 new-to-nature THCSpd containing halogenated hydroxycinnamoyl moieties. In this work, we established a versatile and modular biotechnological production platform allowing the tailor-made THCSpd synthesis, constituting pioneer metabolic engineering for access to these valuable natural products.

Comparative transcriptome analysis of Rheum australe, an endangered medicinal herb, growing in its natural habitat and those grown in controlled growth chambers

Rheum australe is an endangered medicinal herb of high altitude alpine region of Himalayas and is known to possess anti-cancerous properties. Unlike many herbs of the region, R. australe has broad leaves. The species thrives well under the environmental extremes in its niche habitat, therefore an understanding of transcriptome of R. australe to environmental cues was of significance. Since, temperature is one of the major environmental variables in the niche of R. australe, transcriptome was studied in the species growing in natural habitat and those grown in growth chambers maintained at 4 °C and 25 °C to understand genes associated with different temperatures. A total of 39,136 primarily assembled transcripts were obtained from 10,17,74,336 clean read, and 21,303 unigenes could match to public databases. An analysis of transcriptome by fragments per kilobase of transcript per million, followed by validation through qRT-PCR showed 22.4% up- and 22.5% down-regulated common differentially expressed genes in the species growing under natural habitat and at 4 °C as compared to those at 25 °C. These genes largely belonged to signaling pathway, transporters, secondary metabolites, phytohormones, and those associated with cellular protection, suggesting their importance in imparting adaptive advantage to R. australe in its niche.

Genetic analysis of phenylpropanoids and antioxidant capacity in strawberry fruit reveals mQTL hotspots and candidate genes

Phenylpropanoids are a large class of plant secondary metabolites, which play essential roles in human health mainly associated with their antioxidant activity. Strawberry (Fragaria × ananassa) is a rich source of phytonutrients, including phenylpropanoids, which have been shown to have beneficial effects on human health. In this study, using the F. × ananassa '232' × '1392' F₁ segregating population, we analyzed the genetic control of individual phenylpropanoid metabolites, total polyphenol content (TPC) and antioxidant capacity (TEAC) in strawberry fruit over two seasons. We have identified a total of 7, 9, and 309 quantitative trait loci (QTL) for TPC, TEAC and for 77 polar secondary metabolites, respectively. Hotspots of stable QTL for health-related antioxidant compounds were detected on linkage groups LG IV-3, LG V-2 and V-4, and LG VI-1 and VI-2, where associated markers represent useful targets for marker-assisted selection of new varieties with increased levels of antioxidant secondary compounds. Moreover, differential expression of candidate genes for major and stable mQTLs was studied in fruits of contrasting lines in important flavonoids. Our results indicate that higher expression of FaF3'H, which encodes the flavonoid 3'-hydroxylase, is associated with increased content of these important flavonoids.

Fraxinus mandshurica 4-coumarate-CoA ligase 2 enhances drought and osmotic stress tolerance of tobacco by increasing coniferyl alcohol content

4-Coumarate-CoA ligase (4CL) is an important branch point in the phenylpropane pathway and plays important roles in plant growth and development. In this study, the 4CL2 gene from Fraxinus mandshurica (designated Fm4CL2) was identified and isolated. Sequence analysis revealed that Fm4CL2 is a type I 4CL gene involved in lignin biosynthesis. Analysis of cell wall components revealed that Fm4CL2-overexpressing (OE-Fm4CL2) tobacco showed increased lignin content (by 58.9%) and decreased hemicellulose content (by 41.2%). Detection of small-molecule metabolites in the lignin pathway revealed that coumaric acid content decreased by 48% and coniferyl alcohol content increased by 250% compared with the control values. Compared with wild type, OE-Fm4CL2 tobacco showed increased xylem cell layer number (by 120%) and cell wall thickness (by 54.5%). Under osmotic stress, transgenic tobacco showed higher growth than wild-type tobacco. The germination rate of transgenic tobacco was higher than that of wild type. Reactive oxygen species accumulation and malondialdehyde content were significantly lower in transgenic tobacco than in wild type. Under drought, the expression of stress-related genes was higher in 35S-Fm4CL2-infected Fraxinus mandshurica plants than in control plants. These results indicate that Fm4CL2 overexpression can enhance drought and osmotic stress tolerance of plants.

Quantitative metabolome and transcriptome analysis reveals complex regulatory pathway underlying photoinduced fiber color formation in cotton

As an important plant single cell model and textile application materials, poorly known about fiber color formation in cotton, which is sensitively regulated by environmental signals. Our studies underline the importance of photo signal on sensitive fiber color formation and characterize fiber color early initiation (15 DPA) and late accumulated metabolites (45 DPA) in different lighting condition. The results revealed 236 differential metabolites between control and shading, of which phenylpropanoids metabolites accounted for 20%, including uncharacterized novel metabolites and pathways. Furthermore, the early initiation specific genes respond to the absence of light are highly correlated with phenylpropanoid metabolites related to pigmentation. The current study reveals the complex pathways involving early initiation regulation and late metabolic pathways. In addition, the collection composed of uncharacterized photoinduced metabolites and early initiation signaling/regulatory genes were identified, which are important resources for understanding fiber color formation. This report provides new insight into molecular regulatory and biochemical basis underlying photoinduced fiber color formation in cotton.

Structural insight of two 4-Coumarate CoA ligase (4CL) isoforms in Leucaena suggests targeted genetic manipulations could lead to better lignin extractability from the pulp

4-Coumarate: coenzyme A ligase (4CL) is a key enzyme involved in the early steps of the monolignol biosynthetic pathway. It is hypothesized to modulate S and G monolignol content in the plant. Lignin removal is imperative to the paper industry and higher S/G ratio governs better extractability of lignin and economics of the pulping process. This background prompted us to predict 3D structure of two isoforms of 4CL in Leucaena leucocephala and evaluate their substrate preferences. The 3D structure of Ll4CL1 and Ll4CL2 protein were created by homology modeling and further refined by loop refinement. Molecular docking studies suggested differential substrate preferences of both the isoforms. Ll4CL1 preferred sinapic acid (- 4.91 kcal/mole), ferulic acid (- 4.84 kcal/mole), hydroxyferulic acid (- 4.72 kcal/mole), and caffeic acid (- 4.71 kcal/mole), in their decreasing order. Similarly, Ll4CL2 preferred caffeic acid (- 6.56 kcal/mole, 4 H bonds), hydroxyferulic acid (- 6.56 kcal/mole, 3 H bonds), and ferulic acid (- 6.32 kcal/mole) and sinapic acid (- 5.00 kcal/mole) in their decreasing order. Further, active site residues were identified in both the isoforms and in silico mutation and docking analysis was performed. Our analysis suggested that ASP228, TYR262, and PRO326 for Ll4CL1 and SER165, LYS247 and PRO315 for Ll4CL2 were important for their functional activity. Based on differential substrate preferences of the two isoforms, as a first step towards genetically modified Leuaena having the desired phenotype, it can be proposed that over-expression of Ll4CL1 gene and/or down-regulation of Ll4CL2 gene could yield higher S/G ratio leading to better extractability of lignin.

Integrated metabolomic and transcriptomic profiling reveals the tissue-specific flavonoid compositions and their biosynthesis pathways in Ziziphora bungeana

Background

Ziziphora bungeana Juz. is a folk medicine from the Xinjiang Uygur Autonomous Region. The herb or the aerial parts of it have been used to medicinally treat cardiovascular diseases. Flavonoids are the main pharmacologically active ingredients in Z. bungeana. Identification of the tissue-specific distribution of flavonoids in Z. bungeana is crucial for effective and sustainable medicinal use of the plant. Furthermore, understanding of the biosynthesis pathways of these flavonoids in Z. bungeana is of great biological significance.

Methods

The flavonoids from different tissues of Z. bungeana were identified using liquid chromatography-tandem mass spectrometry (LC–MS/MS). The full-length transcriptome of Z. bungeana was determined using a strategy based on a combination of Illumina and PacBio sequencing techniques. The functions of differentially expressed unigenes were predicted using bioinformatics methods and further investigated by real-time quantitative PCR and phylogenetic relationship analysis.

Results

Among the 12 major flavonoid components identified from Z. bungeana extracts, linarin was the most abundant component. Nine flavonoids were identified as characteristic components of specific tissues. Transcriptome profiling and bioinformatic analysis revealed that 18 genes were putatively involved in flavonoid biosynthesis. The gene expression and phylogenetic analysis results indicated that ZbPALs, Zb4CL3, ZbCHS1, and ZbCHI1 may be involved in the biosynthesis of the main flavonoid intermediate. ZbFNSII, ZbANS, and ZbFLS may be involved in the biosynthesis of flavones, anthocyanins, and flavonols, respectively. A map of the biosynthesis pathways of the 12 major flavonoids in Z. bungeana is proposed.

Conclusions

The chemical constituent analysis revealed the compositions of 9 characteristic flavonoids in different tissues of Z. bungeana. Linarin can be hydrolysed into acacetin to exert a pharmaceutical role. Apigenin-7-O-rutinoside is hypothesised to be the precursor of linarin in Z. bungeana. There was greater content of linarin in the aerial parts of the plant than in the whole herb, which provides a theoretical basis for using the aerial parts of Z. bungeana for medicine. These results provide a valuable reference for further research on the flavonoid biosynthesis pathways of Z. bungeana and will be significant for the effective utilisation and ecological protection of Z. bungeana.

Comparative analysis of drought-responsive transcriptomes of sugarcane genotypes with differential tolerance to drought

Water stress causes considerable yield losses in sugarcane. To investigate differentially expressed genes under water stress, two sugarcane genotypes were subjected to three water-deficit levels (mild, moderate, and severe) and subsequent recovery and leaf transcriptome was generated using Illumina NextSeq sequencing. Among the differentially expressed genes, the tolerant genotype Co 06022 generated 2970 unigenes (p ≤ 0.05, functionally known, non-redundant DEGs) at 2-day stress, and there was a progressive decrease in the expressed genes as the stress period increased with 2109 unigenes at 6-day stress and 2307 unigenes at 10-day stress. There was considerable reduction at recovery with 1334 unigenes expressed at 10 days after recovery. However, in the susceptible genotype Co 8021, the number of unigenes expressed at 2 days was lower (2025) than the tolerant genotype and a further reduction was seen at 6-day stress (1552). During recovery, more differentially expressed genes were observed in the susceptible cultivar indicating that the cultivar has to activate more functions/processes to recover from the damage caused by stress. Comparison of DEGs between all stages of stress and recovery in both genotypes revealed that, the commonly up- and down-regulated genes across different stages were approximately double in the tolerant genotype. The most enriched gene ontology classes were heme binding, peroxidase activity and metal ion binding in the biological process and response to oxidative stress, hydrogen peroxide catabolic process and response to stress in the molecular function category. The cellular component was enriched with DEGs involved in extracellular region followed by integral component of membrane. The KEGG pathway analysis revealed important metabolic activities and functionally important genes involved in mitigating water-deficit stress in both the varieties. In addition, several unannotated genes in important pathways were detected and together may provide novel insights into water-deficit tolerance mechanisms in sugarcane. The reliability of the observed expression patterns was confirmed by qRT-PCR. The results of this study will help to identify useful genes for improving drought tolerance in sugarcane.

Functional analysis of 4-coumarate: CoA ligase from Dryopteris fragrans in transgenic tobacco enhances lignin and flavonoids

4-Coumaric acid: coenzyme A ligase (4CL) is a key enzyme in the phenylpropanoid metabolic pathway that regulates the biosynthesis of lignin and flavonoids. Therefore, the study of 4CL is important to explore the accumulation and regulation of metabolites. This study investigated the role that the 4CL2 gene from Dryopteris fragrans (Df4CL2) plays in the metabolite synthesis. Changes in gene expression, enzyme activity, and the content of lignin and flavonoids were measured in different tissues of tobacco as model plant that was successfully transferred with Df4CL2. Tobacco plants with Df4CL2 (transgenic tobacco, TT) were successfully obtained via the Agrobacterium-transformation method. This TT tended to be thicker and had an earlier flowering period than wild type tobacco (WT). The expression levels of Df4CL2 were higher in the stem, leaf, and root in TT compared to WT. In addition, compared to WT, TT had higher 4CL enzyme activity and higher lignin and flavonoids contents. This suggests that Df4CL2 is involved in the synthesis of lignin and flavonoids in D. fragrans. This research provides important evidence toward understanding the phenylpropanoid metabolic pathway in ferns.