Transcriptional machineries in jasmonate-elicited plant secondary metabolism

CRISPR/Cas9-mediated knockout of NtMYC2a gene involved in resistance to bacterial wilt in tobacco

MYC2 is a class of bHLH family transcription factors and a major regulatory factor in the JA signaling pathway, and its molecular function in tobacco has not been reported. In this study, CRISPR/Cas9-mediated MYC2 gene NtMYC2a knockout mutants at tobacco was obtained and its agronomic traits, disease resistance, and chemical composition were identified. Comparing with the WT, the leaf width of the KO-NtMYC2a was narrowed, the nornicotine content and mecamylamine content increased significantly and the resistance to Ralstonia solanacearum significantly decreased. The transcriptome sequencing results showed that DEGs related to immunity, signal transduction and growth and development were enriched between KO-NtMYC2a and WT. NtJAR1 and NtCOI1 in KO-NtMYC2a were down-regulated to regulating the JA signaling pathway, result in a significant decrease in tobacco's resistance to R. solanacearum. Our research provides theoretical support for the functional research of MYC2 and the study of the mechanism of tobacco bacterial wilt resistance.

The MdNAC72-MdABI5 module acts as an interface integrating jasmonic acid and gibberellin signals and undergoes ubiquitination-dependent degradation regulated by MdSINA2 in apple

Jasmonic acid (JA) and gibberellin (GA) coordinately regulate plant developmental programs and environmental cue responses. However, the fine regulatory network of the cross-interaction between JA and GA remains largely elusive. In this study, we demonstrate that MdNAC72 together with MdABI5 positively regulates anthocyanin biosynthesis through an exquisite MdNAC72-MdABI5-MdbHLH3 transcriptional cascade in apple. MdNAC72 interacts with MdABI5 to promote the transcriptional activation of MdABI5 on its target gene MdbHLH3 and directly activates the transcription of MdABI5. The MdNAC72-MdABI5 module regulates the integration of JA and GA signals in anthocyanin biosynthesis by combining with JA repressor MdJAZ2 and GA repressor MdRGL2a. MdJAZ2 disrupts the MdNAC72-MdABI5 interaction and attenuates the transcriptional activation of MdABI5 by MdNAC72. MdRGL2a sequesters MdJAZ2 from the MdJAZ2-MdNAC72 protein complex, leading to the release of MdNAC72. The E3 ubiquitin ligase MdSINA2 is responsive to JA and GA signals and promotes ubiquitination-dependent degradation of MdNAC72. The MdNAC72-MdABI5 interface fine-regulates the integration of JA and GA signals at the transcriptional and posttranslational levels by combining MdJAZ2, MdRGL2a, and MdSINA2. In summary, our findings elucidate the fine regulatory network connecting JA and GA signals with MdNAC72-MdABI5 as the core in apple.

Co-expression analyses reveal key Cd stress response-related metabolites and transcriptional regulators in Kentucky bluegrass

Kentucky bluegrass (Poa pratensis) is known for its high cadmium (Cd) tolerance and accumulation, and it is therefore considered to have the potential for phytoremediation of Cd-contaminated soil. However, the mechanisms underlying the accumulation and tolerance of Cd in Kentucky bluegrass are largely unknown. In this study, we examined variances in the transcriptome and metabolome of a Cd-tolerant variety (Midnight, M) and a Cd-sensitive variety (Rugby II, R) to pinpoint crucial regulatory genes and metabolites associated with Cd response. We also validated the role of the key metabolite, l-phenylalanine, in Cd transport and alleviation of Cd stress by applying it to the Cd-tolerant variety M. Metabolites of the M and R varieties under Cd stress were subjected to co-expression analysis. The results showed that shikimate-phenylpropanoid pathway metabolites (phenolic acids, phenylpropanoids, and polyketides) were highly induced by Cd treatment and were more abundant in the Cd-tolerant variety. Gene co-expression network analysis was employed to further identify genes closely associated with key metabolites. The calcium regulatory genes, zinc finger proteins (ZAT6 and PMA), MYB transcription factors (MYB78, MYB62, and MYB33), ONAC077, receptor-like protein kinase 4, CBL-interacting protein kinase 1, and protein phosphatase 2A were highly correlated with the metabolism of phenolic acids, phenylpropanoids, and polyketides. Exogenous l-phenylalanine can significantly increase the Cd concentration in the leaves (22.27%-55.00%) and roots (7.69%-35.16%) of Kentucky bluegrass. The use of 1 mg/L of l-phenylalanine has been demonstrated to lower malondialdehyde levels and higher total phenols, flavonoids, and anthocyanins levels, while also significantly enhancing the uptake of Cd and its translocation from roots to shoots. Our results provide insights into the response mechanisms to Cd stress and offer a novel l-phenylalanine-based phytoremediation strategy for Cd-containing soil.

The methyl jasmonate-responsive transcription factor SmERF106 promotes tanshinone accumulation in Salvia miltiorrhiza

Understanding the regulatory biosynthesis mechanisms of active compounds in herbs is vital for the preservation and sustainable use of natural medicine resources. Diterpenoids, which play a key role in plant growth and resistance, also serve as practical products for humans. Tanshinone, a class of abietane-type diterpenes unique to the Salvia genus, such as Salvia miltiorrhiza, is an excellent model for studying diterpenoids. In this study, we discovered that a transcription factor, SmERF106, responds to MeJA induction and is located in the nucleus. It exhibits a positive correlation with the expression of SmKSL1 and SmIDI1, which are associated with tanshinone biosynthesis. We performed DNA affinity purification sequencing (DAP-seq) to predict genes that may be transcriptionally regulated by SmERF106. Our cis-elements analysis suggested that SmERF106 might bind to GCC-boxes in the promoters of SmKSL1 and SmIDI1. This indicates that SmKSL1 and SmIDI1 could be potential target genes regulated by SmERF106 in the tanshinone biosynthesis pathway. Their interaction was then demonstrated through a series of in vitro and in vivo binding experiments, including Y1H, EMSA, and Dual-LUC. Overexpression of SmERF106 in the hairy root of S. miltiorrhiza led to a significant increase in tanshinone content and the transcriptional levels of SmKSL1 and SmIDI1. In summary, we found that SmERF106 can activate the transcription of SmKSL1 and SmIDI1 in response to MeJA induction, thereby promoting tanshinone biosynthesis. This discovery provides new insights into the regulatory mechanisms of tanshinones in response to JA and offers a potential gene tool for tanshinone metabolic engineering strategy.

The OsMYC2-JA feedback loop regulates diurnal flower-opening time via cell wall loosening in rice

Diurnal flower-opening time (DFOT), the time of spikelet opening during the day, is an important trait for hybrid rice (Oryza sativa L.) seed production. Hybrids between indica and japonica rice varieties have strong heterosis, but the parental lines usually have different, nonoverlapping DFOTs. This reduces the success of hybrid seed production in crosses between indica and japonica subspecies, thus hindering the utilization of indica and japonica inter-subspecies heterosis. However, little is known about the molecular mechanisms regulating DFOT in rice. Here, we obtained japonica rice lines with a DFOT 1.5 h earlier than the wild type by overexpressing OsMYC2, a gene encoding a key transcription factor in the jasmonate (JA) signaling pathway. OsMYC2 is activated by JA signaling and directly regulates the transcription of genes related to JA biosynthesis and cell wall metabolism. Overexpressing OsMYC2 led to significantly increased JA contents and decreased cellulose and hemicellulose contents in lodicule cells, as well as the softening of lodicule cell walls. This may facilitate the swelling of lodicules, resulting in early diurnal flower-opening. These results suggest that the OsMYC2-JA feedback loop regulates DFOT in rice via cell wall remodeling. These findings shed light on the understanding of regulatory mechanism of the DFOT of plants, which should promote the development of indica and japonica varieties suitable for hybrid rice breeding.

EpMYB2 positively regulates chicoric acid biosynthesis by activating both primary and specialized metabolic genes in purple coneflower

Chicoric acid is the major active ingredient of the world-popular medicinal plant purple coneflower (Echinacea purpurea (L.) Menoch). It is recognized as the quality index of commercial hot-selling Echinacea products. While the biosynthetic pathway of chicoric acid in purple coneflower has been elucidated recently, its regulatory network remains elusive. Through co-expression and phylogenetic analysis, we found EpMYB2, a typical R2R3-type MYB transcription factor (TF) responsive to methyl jasmonate (MeJA) simulation, is a positive regulator of chicoric acid biosynthesis. In addition to directly regulating chicoric acid biosynthetic genes, EpMYB2 positively regulates genes of the upstream shikimate pathway. We also found that EpMYC2 could activate the expression of EpMYB2 by binding to its G-box site, and the EpMYC2-EpMYB2 module is involved in the MeJA-induced chicoric acid biosynthesis. Overall, we identified an MYB TF that positively regulates the biosynthesis of chicoric acid by activating both primary and specialized metabolic genes. EpMYB2 links the gap between the JA signaling pathway and chicoric acid biosynthesis. This work opens a new direction toward engineering purple coneflower with higher medicinal qualities.

Plant YABBY transcription factors: a review of gene expression, biological functions, and prospects

Transcription factors often contain several different functional regions, including DNA-binding domains, and play an important regulatory role in plant growth, development, and the response to external stimuli. YABYY transcription factors are plant-specific and contain two special domains (N-terminal C2C2 zinc-finger and C-terminal helix-loop-helix domains) that are indispensable. Specifically, YABBY transcription factors play key roles in maintaining the polarity of the adaxial-abaxial axis of leaves, as well as in regulating: vegetative and reproductive growth, hormone response, stress resistance, and secondary metabolite synthesis in plants. Recently, the identification and functional verification of YABBY transcription factors in different plants has increased. On this basis, we summarize recent advances in the: identification, classification, expression patterns, and functions of the YABBY transcription factor family. The normal expression and function of YABBY transcription factors rely on a regulatory network that is established through the interaction of YABBY family members with other genes. We discuss the interaction network of YABBY transcription factors during leaf polarity establishment and floral organ development. This article provides a reference for research on YABBY function, plant genetic improvement, and molecular breeding.

A signaling cascade mediating fruit trait development via phosphorylation-modulated nuclear accumulation of JAZ repressor

It is generally accepted that jasmonate-ZIM domain (JAZ) repressors act to mediate jasmonate (JA) signaling via CORONATINE-INSENSITIVE1 (COI1)-mediated degradation. Here, we report a cryptic signaling cascade where a JAZ repressor, FvJAZ12, mediates multiple signaling inputs via phosphorylation-modulated subcellular translocation rather than the COI1-mediated degradation mechanism in strawberry (Fragaria vesca). FvJAZ12 acts to regulate flavor metabolism and defense response, and was found to be the target of FvMPK6, a mitogen-activated protein kinase that is capable of responding to multiple signal stimuli. FvMPK6 phosphorylates FvJAZ12 at the amino acid residues S179 and T183 adjacent to the PY residues, thereby attenuating its nuclear accumulation and relieving its repression for FvMYC2, which acts to control the expression of lipoxygenase 3 (FvLOX3), an important gene involved in JA biosynthesis and a diverse array of cellular metabolisms. Our data reveal a previously unreported mechanism for JA signaling and decipher a signaling cascade that links multiple signaling inputs with fruit trait development.

ApCPS2 contributes to medicinal diterpenoid biosynthesis and defense against insect herbivore in Andrographis paniculata

Kalmegh (Andrographis paniculata) spatiotemporally produces medicinally-important ent-labdane-related diterpenoids (ent-LRDs); andrographolide (AD), 14-deoxy-11,12-didehydroandrographolide (DDAD), neoandrographolide (NAD). ApCPS1 and ApCPS2, the ent-copalyl pyrophosphate (ent-CPP)-producing class II diterpene synthases (diTPSs) were identified, but their contributions to ent-CPP precursor supply for ent-LRD biosynthesis were not well understood. Here, we characterized ApCPS4, an additional ent-CPP-forming diTPS. Further, we elucidated in planta function of the ent-CPP-producing diTPSs (ApCPS1,2,4) by integrating transcript-metabolite co-profiles, biochemical analysis and gene functional characterization. ApCPS1,2,4 localized to the plastids, where diterpenoid biosynthesis occurs in plants, but ApCPS1,2,4 transcript expression patterns and ent-LRD contents revealed a strong correlation of ApCPS2 expression and ent-LRD accumulation in kalmegh. ApCPS1,2,4 upstream sequences differentially activated β-glucuronidase (GUS) in Arabidopsis and transiently-transformed kalmegh. Similar to higher expression of ApCPS1 in kalmegh stem, ApCPS1 upstream sequence activated GUS in stem/hypocotyl of Arabidopsis and kalmegh. However, ApCPS2,4 upstream sequences weakly activated GUS expression in Arabidopsis, which was not well correlated with ApCPS2,4 transcript expression in kalmegh tissues. Whereas, ApCPS2,4 upstream sequences could activate GUS expression at a considerable level in kalmegh leaf and roots/calyx, respectively, suggesting the involvement of transcriptional regulator(s) of ApCPS2,4 that might participate in kalmegh-specific diterpenoid pathway. Interestingly, ApCPS2-silenced kalmegh showed a drastic reduction in AD, DDAD and NAD contents and compromised defense against insect herbivore Spodoptera litura. However, ent-LRD contents and herbivore defense in ApCPS1 or ApCPS4-silenced plants remained largely unaltered. Overall, these results suggested an important role of ApCPS2 in producing ent-CPP for medicinal ent-LRD biosynthesis and defense against insect herbivore.

The Emerging Role of 2OGDs as Candidate Targets for Engineering Crops with Broad-Spectrum Disease Resistance

Plant diseases caused by pathogens result in a marked decrease in crop yield and quality annually, greatly threatening food production and security worldwide. The creation and cultivation of disease-resistant cultivars is one of the most effective strategies to control plant diseases. Broad-spectrum resistance (BSR) is highly preferred by breeders because it confers plant resistance to diverse pathogen species or to multiple races or strains of one species. Recently, accumulating evidence has revealed the roles of 2-oxoglutarate (2OG)-dependent oxygenases (2OGDs) as essential regulators of plant disease resistance. Indeed, 2OGDs catalyze a large number of oxidative reactions, participating in the plant-specialized metabolism or biosynthesis of the major phytohormones and various secondary metabolites. Moreover, several 2OGD genes are characterized as negative regulators of plant defense responses, and the disruption of these genes via genome editing tools leads to enhanced BSR against pathogens in crops. Here, the recent advances in the isolation and identification of defense-related 2OGD genes in plants and their exploitation in crop improvement are comprehensively reviewed. Also, the strategies for the utilization of 2OGD genes as targets for engineering BSR crops are discussed.

Defense strategies and associated phytohormonal regulation in Brassica plants in response to chewing and sap-sucking insects

Plants have evolved distinct defense strategies in response to a diverse range of chewing and sucking insect herbivory. While chewing insect herbivores, exemplified by caterpillars and beetles, cause visible tissue damage and induce jasmonic acid (JA)-mediated defense responses, sucking insects, such as aphids and whiteflies, delicately tap into the phloem sap and elicit salicylic acid (SA)-mediated defense responses. This review aims to highlight the specificity of defense strategies in Brassica plants and associated underlying molecular mechanisms when challenged by herbivorous insects from different feeding guilds (i.e., chewing and sucking insects). To establish such an understanding in Brassica plants, the typical defense responses were categorized into physical, chemical, and metabolic adjustments. Further, the impact of contrasting feeding patterns on Brassica is discussed in context to unique biochemical and molecular modus operandi that governs the resistance against chewing and sucking insect pests. Grasping these interactions is crucial to developing innovative and targeted pest management approaches to ensure ecosystem sustainability and Brassica productivity.

Hormonal regulation of plant primary metabolism under drought

Phytohormones are essential signalling molecules globally regulating many processes of plants, including their growth, development, and stress responses. The promotion of growth and the enhancement of stress resistance have to be balanced, especially under adverse conditions such as drought stress, because of limited resources. Plants cope with drought stress via various strategies, including the transcriptional regulation of stress-responsive genes and the adjustment of metabolism, and phytohormones play roles in these processes. Although abscisic acid (ABA) is an important signal under drought, less attention has been paid to other phytohormones. In this review, we summarize progress in the understanding of phytohormone-regulated primary metabolism under water-limited conditions, especially in Arabidopsis thaliana, and highlight recent findings concerning the amino acids associated with ABA metabolism and signalling. We also discuss how phytohormones function antagonistically and synergistically in order to balance growth and stress responses.

Methyl jasmonate inducible UGT79A18 is a novel glycosyltransferase involved in the bacoside biosynthetic pathway in Bacopa monnieri

Bacosides are dammarane-type triterpenoidal saponins in Bacopa monnieri and have various pharmacological applications. All the bacosides are diversified from two isomers, i.e., jujubogenin and pseudojujubogenin. The biosynthetic pathway of bacoside is not well elucidated. In the present study, we characterized a UDP-glycosyltransferase, UGT79A18, involved in the glycosylation of pseudojujubogenin. UGT79A18 shows higher expression in response to 5 h of wounding, and 3 h of MeJA treatment. The recombinant UGT79A18 shows in vitro activity against a wide range of flavonoids and triterpenes and has a substrate preference for protopanaxadiol, a dammarane-type triterpene. Secondary metabolite analysis of overexpression and knockdown lines of UGT79A18 in B. monnieri identify bacopasaponin D, bacopaside II, bacopaside N2 and pseudojujubogenin glucosyl rhamnoside as the major bacosides that were differentially accumulated. In the overexpression lines of UGT79A18, we found 1.7-fold enhanced bacopaside II, 8-fold enhanced bacopasaponin D, 3-fold enhanced pseudojujubogenin glucosyl rhamnoside, and 1.6-fold enhanced bacopaside N2 content in comparison with vector control plant, whereas in the knockdown lines of UGT79A18, we found 1.4-fold reduction in bacopaside II content, 3-fold reduction in the bacopasaponin D content, 2-fold reduction in the pseudojujubogenin glucosyl rhamnoside content, and 1.5-fold reduction in bacopaside N2 content in comparison with vector control. These results suggest that UGT79A18 is a significant UDP glycosyltransferase involved in glycosylating pseudojujubogenin and enhancing the pseudojujubogenin-derived bacosides.

Multi-omics analysis of small RNA, transcriptome, and degradome to identify putative miRNAs linked to MeJA regulated and oridonin biosynthesis in Isodon rubescens

Isodon rubescens has garnered much attention due to its anti-tumor or anti-cancer properties. However, little is known about the molecular mechanism of oridonin biosynthesis leveraging the regulatory network between small RNAs and mRNAs. In this study, the regulatory networks of miRNAs and targets were examined by combining mRNA, miRNA, and degradome. A total of 348 miRNAs, including 287 known miRNAs and 61 novel miRNAs, were identified. Among them, 51 miRNAs were significantly expressed, and 36 miRNAs responded to MeJA. A total of 3066 target genes were associated with 228 miRNAs via degradome sequencing. Multi-omics analysis demonstrated that 27 miRNA-mRNA pairs were speculated to be involved in MeJA regulation, and 36 miRNA-mRNA pairs were hypothesized to be involved in the genotype-dependence of I. rubescens. Furthermore, 151 and 7 miRNA-mRNA modules were likely engaged in oridonin biosynthesis as identified by psRNATarget and degradome sequencing, respectively. Some miRNA-mRNA modules were confirmed via RT-qPCR. Moreover, miRNAs targeting plant hormone signal transduction pathway genes were identified, such as miR156, miR167, miR393, and PC-3p-19822_242. Collectively, our results demonstrate for the first time that miRNAs are identified in I. rubescens, and laid a solid foundation for further research on the molecular mechanism of oridonin biosynthesis mediated by miRNA.

Genome-wide identification and integrated analysis of TCP genes controlling ginsenoside biosynthesis in Panax ginseng

Panax ginseng is an important medicinal plant, and ginsenosides are the main bioactive molecules of ginseng. The TCP (TBI, CYC, PCF) family is a group of transcription factors (TFs) that play an important role in plant growth and development, hormone signalling and synthesis of secondary metabolites. In our study, 78 PgTCP transcripts were identified from the established ginseng transcriptome database. A phylogenetic tree analysis showed that the 67 PgTCP transcripts with complete open reading frames were classified into three subfamilies, including CIN, PCF, and CYC/TB1. Protein structure analysis showed that PgTCP genes had bHLH structures. Chromosomal localization analysis showed that 63 PgTCP genes were localized on 17 of the 24 chromosomes of the Chinese ginseng genome. Expression pattern analysis showed that PgTCP genes differed among different lineages and were spatiotemporally specific. Coexpression network analysis indicated that PgTCP genes were coexpressed and involved in plant activities or metabolic regulation in ginseng. The expression levels of PgTCP genes from class I (PCF) were significantly downregulated, while the expression levels of PgTCP genes from class II (CIN and CYC/TB1) were upregulated, suggesting that TCP genes may be involved in the regulation of secondary metabolism in ginseng. As the PgTCP26-02 gene was found to be related to ginsenoside synthesis, its predicted protein structure and expression pattern were further analysed. Our results provide new insights into the origin, differentiation, evolution and function of the PgTCP gene family in ginseng, as well as the regulation of plant secondary metabolism.

Plant disease resistance outputs regulated by AP2/ERF transcription factor family

Plants have evolved a complex and elaborate signaling network to respond appropriately to the pathogen invasion by regulating expression of defensive genes through certain transcription factors. The APETALA2/ethylene response factor (AP2/ERF) family members have been determined as key regulators in growth, development, and stress responses in plants. Moreover, a growing body of evidence has demonstrated the critical roles of AP2/ERFs in plant disease resistance. In this review, we describe recent advances for the function of AP2/ERFs in defense responses against microbial pathogens. We summarize that AP2/ERFs are involved in plant disease resistance by acting downstream of mitogen activated protein kinase (MAPK) cascades, and regulating expression of genes associated with hormonal signaling pathways, biosynthesis of secondary metabolites, and formation of physical barriers in an MAPK-dependent or -independent manner. The present review provides a multidimensional perspective on the functions of AP2/ERFs in plant disease resistance, which will facilitate the understanding and future investigation on the roles of AP2/ERFs in plant immunity.

PatWRKY71 transcription factor regulates patchoulol biosynthesis and plant defense response

Patchoulol, a valuable compound belonging to the sesquiterpenoid family, is the primary component of patchouli oil produced by Pogostemon cablin (P. cablin). It has a variety of pharmacological and biological activities and is widely used in the medical and cosmetic industries. However, despite its significance, there is a lack of research on the transcriptional modulation of patchoulol biosynthesis.Salicylic acid (SA), is a vital plant hormone that serves as a critical signal molecule and plays an essential role in plant growth and defense. However, to date, no studies have explored the modulation of patchoulol biosynthesis by SA. In our study, we discovered that the application of SA can enhance the production of patchoulol. Utilizing transcriptome analysis of SA-treated P. cablin, we identified a crucial downstream transcription factor, PatWRKY71. The transcription level of PatWRKY71 was significantly increased with the use of SA. Furthermore, our research has revealed that PatWRKY71 was capable of binding to the promoter of PatPTS, ultimately leading to an increase in its expression. When PatWRKY71 was silenced by a virus, the expression of both PatWRKY71 and PatPTS was reduced, resulting in the down-regulation of patchoulol production. Through our studies, we discovered that heterologous expression of PatWRKY71 leads to an increase in the sensitivity of Arabidopsis to salt and Cd, as well as an outbreak of reactive oxygen species (ROS). Additionally, we uncovered the regulatory role of PatWRKY71 in both patchoulol biosynthesis and plant defense response. This discovery provided a theoretical basis for the improvement of the content of patchoulol and the resistance of P. cablin through genetic engineering.

Transcriptomics and Physiological Analyses Reveal Changes in Paclitaxel Production and Physiological Properties in Taxus cuspidata Suspension Cells in Response to Elicitors

In this research, the cell growth, physiological, and biochemical reactions, as well as the paclitaxel production, of Taxus cuspidata suspension cells after treatment with polyethylene glycol (PEG), cyclodextrin (CD), or salicylic acid (SA) (alone or in combination) were investigated. To reveal the paclitaxel synthesis mechanism of T. cuspidata suspension cells under elicitor treatment, the transcriptomics of the Control group and P + C + S group (PEG + CD + SA) were compared. The results show that there were no significant differences in cell biomass after 5 days of elicitor treatments. However, the content of hydrogen peroxide (H2O2) and malondialdehyde (MDA), and the activities of phenylalanine ammonia-lyase (PAL) and polyphenol oxidase (PPO) after elicitor combination treatments were decreased compared with the single-elicitor treatment. Meanwhile, the antioxidant enzyme activity (superoxide dismutase (SOD), catalase (CAT), and peroxidase (PO)) and the contents of soluble sugar and soluble protein were increased after combination elicitor treatments. Additionally, the paclitaxel yield after treatment with the combination of all three elicitors (P + C + S) was 6.02 times higher than that of the Control group, thus indicating that the combination elicitor treatments had a significant effect on paclitaxel production in T. cuspidata cell suspension culture. Transcriptomics analysis revealed 13,623 differentially expressed genes (DEGs) between the Control and P + C + S treatment groups. Both GO and KEGG analyses showed that the DEGs mainly affected metabolic processes. DEGs associated with antioxidant enzymes, paclitaxel biosynthesis enzymes, and transcription factors were identified. It can be hypothesized that the oxidative stress of suspension cells occurred with elicitor stimulation, thereby leading to a defense response and an up-regulation of the gene expression associated with antioxidant enzymes, paclitaxel synthesis enzymes, and paclitaxel synthesis transcription factors; this ultimately increased the production of paclitaxel.

Deciphering triterpenoid saponin biosynthesis by leveraging transcriptome response to methyl jasmonate elicitation in Saponaria vaccaria

Methyl jasmonate (MeJA) is a known elicitor of plant specialized metabolism, including triterpenoid saponins. Saponaria vaccaria is an annual herb used in traditional Chinese medicine, containing large quantities of oleanane-type triterpenoid saponins with anticancer properties and structural similarities to the vaccine adjuvant QS-21. Leveraging the MeJA-elicited saponin biosynthesis, we identify multiple enzymes catalyzing the oxidation and glycosylation of triterpenoids in S. vaccaria. This exploration is aided by Pacbio full-length transcriptome sequencing and gene expression analysis. A cellulose synthase-like enzyme can not only glucuronidate triterpenoid aglycones but also alter the product profile of a cytochrome P450 monooxygenase via preference for the aldehyde intermediate. Furthermore, the discovery of a UDP-glucose 4,6-dehydratase and a UDP-4-keto-6-deoxy-glucose reductase reveals the biosynthetic pathway for the rare nucleotide sugar UDP-D-fucose, a likely sugar donor for fucosylation of plant natural products. Our work enables the production and optimization of high-value saponins in microorganisms and plants through synthetic biology approaches.

PcENO3 interacts with patchoulol synthase to positively affect the enzymatic activity and patchoulol biosynthesis in Pogostemon cablin

Patchouli alcohol, a significant bioactive component of the herbal plant Pogostemon cablin, has considerable medicinal and commercial potential. Several genes and transcription factors involved in the biosynthesis pathway of patchouli alcohol have been identified. However, so far, regulatory factors directly interacting with patchouli synthase (PTS) have not been reported. This study was conducted to analyze the interaction between PcENO3 and PcPTS to explore the molecular regulation effect of PcENO3 on patchouli alcohol biosynthesis. PcENO3, a homologous protein of Arabidopsis ENO3 belonging to the enolase family, was identified and characterized. Subcellular localization experiments in Arabidopsis protoplast cells indicated that the PcENO3 protein was localized in both the cytoplasm and nucleus. The physical interaction between PcENO3 and PcPTS was confirmed through yeast two-hybrid (Y2H), GST pull-down, and bimolecular fluorescence complementation assays. Furthermore, the Y2H assay demonstrated that PcENO3 could also interact with JAZ proteins in the JA pathway. Enzymatic assays showed that the interaction with PcENO3 increased the catalytic activity of patchoulol synthase. Additionally, suppression of PcENO3 expression with VIGS (virus-induced gene silencing) decreased patchouli alcohol content compared to the control. These findings suggest that PcENO3 interacts with patchoulol synthase and modulates patchoulol biosynthesis by enhancing the enzymatic activity of PcPTS.

An Investigation of the JAZ Family and the CwMYC2-like Protein to Reveal Their Regulation Roles in the MeJA-Induced Biosynthesis of β-Elemene in Curcuma wenyujin

β-Elemene (C15H24), a sesquiterpenoid compound isolated from the volatile oil of Curcuma wenyujin, has been proven to be effective for multiple cancers and is widely used in clinical treatment. Unfortunately, the β-elemene content in C. wenyujin is very low, which cannot meet market demands. Our previous research showed that methyl jasmonate (MeJA) induced the accumulation of β-elemene in C. wenyujin. However, the regulatory mechanism is unclear. In this study, 20 jasmonate ZIM-domain (JAZ) proteins in C. wenyujin were identified, which are the core regulatory factors of the JA signaling pathway. Then, the conservative domains, motifs composition, and evolutionary relationships of CwJAZs were analyzed comprehensively and systematically. The interaction analysis indicated that CwJAZs can form homodimers or heterodimers. Fifteen out of twenty CwJAZs were significantly induced via MeJA treatment. As the master switch of the JA signaling pathway, the CwMYC2-like protein has also been identified and demonstrated to interact with CwJAZ2/3/4/5/7/15/17/20. Further research found that the overexpression of the CwMYC2-like gene increased the accumulation of β-elemene in C. wenyujin leaves. Simultaneously, the expressions of HMGR, HMGS, DXS, DXR, MCT, HDS, HDR, and FPPS related to β-elemene biosynthesis were also up-regulated by the CwMYC2-like protein. These results indicate that CwJAZs and the CwMYC2-like protein respond to the JA signal to regulate the biosynthesis of β-elemene in C. wenyujin.

Common environmental stress responses in a model marine diatom

Marine planktonic diatoms are among the most important contributors to phytoplankton blooms and marine net primary production. Their ecological success has been attributed to their ability to rapidly respond to changing environmental conditions. Here, we report common molecular mechanisms used by the model marine diatom Thalassiosira pseudonana to respond to 10 diverse environmental stressors using RNA-Seq analysis. We identify a specific subset of 1076 genes that are differentially expressed in response to stressors that induce an imbalance between energy or resource supply and metabolic capacity, which we termed the diatom environmental stress response (d-ESR). The d-ESR is primarily composed of genes that maintain proteome homeostasis and primary metabolism. Photosynthesis is strongly regulated in response to environmental stressors but chloroplast-encoded genes were predominantly upregulated while the nuclear-encoded genes were mostly downregulated in response to low light and high temperature. In aggregate, these results provide insight into the molecular mechanisms used by diatoms to respond to a range of environmental perturbations and the unique role of the chloroplast in managing environmental stress in diatoms. This study facilitates our understanding of the molecular mechanisms underpinning the ecological success of diatoms in the ocean.

The phenotypic variation mechanisms of Atractylodes lancea post-cultivation revealed by conjoint analysis of rhizomic transcriptome and metabolome

The wild Atractylodes lancea rhizomes have been traditionally used as herbal medicine. As the increasingly exhaustion of wild A. lancea, the artificial cultivation mainly contributed to the medicinal material production. However, besides the phenotypic variation of rhizome phenotypic trait alteration, the qualities of cultivated A. lancea decrease compared with the wild counterpart. To unveil the physiological and molecular mechanism beneath the phenotypic variation, GC-MS-based volatile organic compounds (VOCs) profiling and RNAseq-based transcriptome analysis were conducted. The volatile metabolomics profiling revealed 65 differentially accumulated metabolites (DAMs) while the transcriptomic profiling identified 12 009 differentially expressed unigenes (DEGs) post-cultivation. The volatile active compounds including atractylone, and eudesmol accumulated more in wild rhizome than in the cultivated counterpart, and several unigenes in terpene synthesis were downregulated under cultivated condition. Compared with the wild A. lancea rhizome, the contents of bioactive Jasmonic Acid (JAs) in cultivated A. lancea rhizome were higher, and evidences that JAs negatively regulate the terpenes biosynthesis in the cultivated A. lancea rhizome were also provided. The combinational omics analysis further indicated the high correlation between the ten cultivation-suppressed VOCs and the cultivation-altered genes for sesquiterpenoids biosynthesis in A. lancea. The network of the cultivation-altered transcription factors (TFs) and the ten VOCs suggested TFs (e.g. Arabidopsis ERF13 homologs and WRKY50) are involved in the regulation of terpenes biosynthesis. These results laid a theoretical basis for developing geo-herbalism medicinal plants with "high quality and optimal shape".

The R2R3-MYB transcription factor OfMYB21 positively regulates linalool biosynthesis in Osmanthus fragrans flowers

Osmanthus fragrans is a well-known landscape ornamental tree species for its pleasing floral fragrance and abundance of flowers. Linalool, the core floral volatiles of O. fragrans, has tremendous economic value in the pharmaceuticals, cleaning products and cosmetics industries. However, the transcriptional regulatory network for the biosynthesis of linalool in O. fragrans remains unclear. Here, OfMYB21, a potential transcription factor regulating the linalool synthetase OfTPS2, was identified using RNA-seq data and qRT-PCR analysis. Yeast one-hybrid, dual-luciferase and EMSA showed that OfMYB21 directly binds to the promoter of OfTPS2 and activates its expression. Overexpression of OfMYB21 in the petals of O. fragrans led to up-regulation of OfTPS2 and increased accumulation of linalool, while silencing of OfMYB21 led to down-regulation of OfTPS2 and decreased biosynthesis of linalool. Subsequently, yeast two-hybrid, pull-down and BiFC experiments showed that OfMYB21 interacts with JA signaling factors OfJAZ2/3 and OfMYC2. Interestingly, the interaction between OfMYC2 and OfMYB21 further enhanced the transcription of OfTPS2, whereas OfJAZ3 attenuated this effect. Overall, our studies provided novel finding on the regulatory mechanisms responsible for the biosynthesis of the volatile monoterpenoid linalool in O. fragrans.

Jasmonates Coordinate Secondary with Primary Metabolism

Jasmonates (JAs), including jasmonic acid (JA), its precursor 12-oxo-phytodienoic acid (OPDA) and its derivatives jasmonoyl-isoleucine (JA-Ile), methyl jasmonate (MeJA), cis-jasmone (CJ) and other oxylipins, are important in the regulation of a range of ecological interactions of plants with their abiotic and particularly their biotic environments. Plant secondary/specialized metabolites play critical roles in implementing these ecological functions of JAs. Pathway and transcriptional regulation analyses have established a central role of JA-Ile-mediated core signaling in promoting the biosynthesis of a great diversity of secondary metabolites. Here, we summarized the advances in JAs-induced secondary metabolites, particularly in secondary metabolites induced by OPDA and volatile organic compounds (VOCs) induced by CJ through signaling independent of JA-Ile. The roles of JAs in integrating and coordinating the primary and secondary metabolism, thereby orchestrating plant growth-defense tradeoffs, were highlighted and discussed. Finally, we provided perspectives on the improvement of the adaptability and resilience of plants to changing environments and the production of valuable phytochemicals by exploiting JAs-regulated secondary metabolites.

Plant immune inducer ZNC promotes rutin accumulation and enhances resistance to Botrytis cinerea in tomato

Gray mold is a destructive disease caused by Botrytis cinerea, a pervasive plant pathogen, which poses a threat to both tomato growth and postharvest storage. The utilization of induced resistance presents a potential strategy for combating plant pathogenic attacks. ZNC (zhinengcong), an extract derived from the endophytic fungus Paecilomyces variotii, has been discovered to play a vital role in preventing diverse forms of bacterial infections. Nevertheless, the precise mechanism behind its ability to enhance tomato resistance to fungi remains unclear. In this study, we found that the exogenous spraying of ZNC could significantly improve the resistance of tomato plants to B. cinerea. The results of both the metabolomic analysis and high-performance liquid chromatography (HPLC) demonstrated that tomato plants responded to ZNC treatment by accumulating high levels of rutin. Additional transcriptome analysis uncovered that rutin enhances tomato resistance possible by initiating the generation of reactive oxygen species (ROS) and phosphorylation of mitogen-activated protein kinases (MPKs) related genes expression during the initial phase of invasion by B. cinerea. In addition, we also found that rutin might activate plant immunity by eliciting ethylene (ET) and jasmonic acid (JA)-mediated pathways. Therefore, plant immune inducer ZNC and rutin has bright application prospects and high utilization value to control gray mold.

Multiomics analysis reveals the molecular mechanisms underlying virulence in Rhizoctonia and jasmonic acid-mediated resistance in Tartary buckwheat (Fagopyrum tataricum)

Rhizoctonia solani is a devastating soil-borne pathogen that seriously threatens the cultivation of economically important crops. Multiple strains with a very broad host range have been identified, but only 1 (AG1-IA, which causes rice sheath blight disease) has been examined in detail. Here, we analyzed AG4-HGI 3 originally isolated from Tartary buckwheat (Fagopyrum tataricum), but with a host range comparable to AG1-IA. Genome comparison reveals abundant pathogenicity genes in this strain. We used multiomic approaches to improve the efficiency of screening for disease resistance genes. Transcriptomes of the plant-fungi interaction identified differentially expressed genes associated with virulence in Rhizoctonia and resistance in Tartary buckwheat. Integration with jasmonate-mediated transcriptome and metabolome changes revealed a negative regulator of jasmonate signaling, cytochrome P450 (FtCYP94C1), as increasing disease resistance probably via accumulation of resistance-related flavonoids. The integration of resistance data for 320 Tartary buckwheat accessions identified a gene homolog to aspartic proteinase (FtASP), with peak expression following R. solani inoculation. FtASP exhibits no proteinase activity but functions as an antibacterial peptide that slows fungal growth. This work reveals a potential mechanism behind pathogen virulence and host resistance, which should accelerate the molecular breeding of resistant varieties in economically essential crops.

Effects of LPS from Rhodobacter sphaeroides, a Purple Non-Sulfur Bacterium (PNSB), on the Gene Expression of Rice Root

The effects of lipopolysaccharide (LPS) from Rhodobacter sphaeroides, a purple non-sulfur bacterium (PNSB), on the gene expression of the root of rice (Oryza sativa) were investigated by next generation sequencing (NGS) RNA-seq analysis. The rice seeds were germinated on agar plates containing 10 pg/mL of LPS from Rhodobacter sphaeroides NBRC 12203 (type culture). Three days after germination, RNA samples were extracted from the roots and analyzed by RNA-seq. The effects of dead (killed) PNSB cells of R. sphaeroides NBRC 12203^T at the concentration of 10¹ cfu/mL (ca. 50 pg cell dry weight/mL) were also examined. Clean reads of NGS were mapped to rice genome (number of transcript ID: 44785), and differentially expressed genes were analyzed by DEGs. As a result of DEG analysis, 300 and 128 genes, and 86 and 8 genes were significantly up- and down-regulated by LPS and dead cells of PNSB, respectively. The plot of logFC (fold change) values of the up-regulated genes of LPS and PNSB dead cells showed a significant positive relationship (r² = 0.6333, p < 0.0001), indicating that most of the effects of dead cell were attributed to those of LPS. Many genes related to tolerance against biotic (fungal and bacterial pathogens) and abiotic (cold, drought, and high salinity) stresses were up-regulated, and the most strikingly up-regulated genes were those involved in the jasmonate signaling pathway, and the genes of chalcone synthase isozymes, indicating that PNSB induced defense response against biotic and abiotic stresses via the jasmonate signaling pathway, despite the non-pathogenicity of PNSB.

Engineering the plant metabolic system by exploiting metabolic regulation

Plants are the most sophisticated biofactories and sources of food and biofuels present in nature. By engineering plant metabolism, the production of desired compounds can be increased and the nutritional or commercial value of the plant species can be improved. However, this can be challenging because of the complexity of the regulation of multiple genes and the involvement of different protein interactions. To improve metabolic engineering (ME) capabilities, different tools and strategies for rerouting the metabolic pathways have been developed, including genome editing and transcriptional regulation approaches. In addition, cutting-edge technologies have provided new methods for understanding uncharacterized biosynthetic pathways, protein degradation mechanisms, protein-protein interactions, or allosteric feedback, enabling the design of novel ME approaches.

Genome-Wide Identification and Expression Analysis of WRKY Gene Family in Neolamarckia cadamba

The WRKY transcription factor family plays important regulatory roles in multiple biological processes in higher plants. They have been identified and functionally characterized in a number of plant species, but very little is known in Neolamarckia cadamba, a 'miracle tree' for its fast growth and potential medicinal resource in Southeast Asia. In this study, a total of 85 WRKY genes were identified in the genome of N. cadamba. They were divided into three groups according to their phylogenetic features, with the support of the characteristics of gene structures and conserved motifs of protein. The NcWRKY genes were unevenly distributed on 22 chromosomes, and there were two pairs of segmentally duplicated events. In addition, a number of putative cis-elements were identified in the promoter regions, of which hormone- and stress-related elements were shared in many NcWRKYs. The transcript levels of NcWRKY were analyzed using the RNA-seq data, revealing distinct expression patterns in various tissues and at different stages of vascular development. Furthermore, 16 and 12 NcWRKY genes were confirmed to respond to various hormone treatments and two different abiotic stress treatments, respectively. Moreover, the content of cadambine, the active metabolite used for the various pharmacological activities found in N. cadamba, significantly increased after Methyl jasmonate treatment. In addition, expression of NcWRKY64/74 was obviously upregulated, suggesting that they may have a potential function of regulating the biosynthesis of cadambine in response to MeJA. Taken together, this study provides clues into the regulatory roles of the WRKY gene family in N. cadamba.

Comprehensive study of volatile compounds and transcriptome data providing genes for grape aroma

BACKGROUND

Fruit aroma is an important quality with respect to consumer preference, but the most important aroma compounds and their genetic regulatory mechanisms remain elusive.

RESULTS

In this study, we qualitatively analysed volatile compounds in the pulp and skin of five table grape cultivars with three aroma types (muscat, strawberry, and neutral) using solid-phase microextraction gas chromatography/mass spectrometry. We identified 215 aroma compounds, including 88 esters, 64 terpenes, and 29 alcohols, and found significant differences in the number of compounds between the pulp and skin, especially for terpenes. Skin transcriptome data for the five grape cultivars were generated and subjected to aroma compound-gene correlation analysis. The combined transcriptomic analysis and terpene profiling data revealed 20 candidate genes, which were assessed in terms of their involvement in aroma biosynthetic regulation, including 1 VvCYP (VIT_08s0007g07730), 2 VvCCR (VIT_13s0067g00620, VIT_13s0047g00940), 3 VvADH (VIT_00s0615g00010, VIT_00s0615g00030, VIT_ 00s0615g00020), and 1 VvSDR (VIT_08s0040g01200) in the phenylpropanoids synthesis pathway, and 1 VvDXS (VIT_05s0020g02130) and 6 VvTPS (VIT_13s0067g00370, Vitis_vinifera_newGene_3216, VIT_13s0067g00380, VIT_13s0084g00010, VIT_00s0271g00010, and VIT_13s0067g00050) in the methylerythritol phosphate pathway (involved in the production and accumulation of aromatic compounds). Additionally, 2 VvMYB (VIT_17s0000g07950, VIT_03s0063g02620) and 1 VvGATA (VIT_15s0024g00980) transcription factor played important regulatory roles in the accumulation of key biosynthetic precursors of these compounds in grapes. Our results indicated that downstream genes, specifically 1 VvBGLU (VIT_03s0063g02490) and 2 VvUGT (VIT_17s0000g07070, VIT_17s0000g07060) are involved in regulating the formation and volatilization of bound compounds in grapes.

CONCLUSIONS

The results of this study shed light on the volatile compounds and "anchor points" of synthetic pathways in the pulp and skin of muscat and strawberry grapes, and provide new insight into the regulation of different aromas in grapes.

Transcriptome analysis of Taraxacum kok-saghyz reveals the role of exogenous methyl jasmonate in regulating rubber biosynthesis and drought tolerance

Taraxacum kok-saghyz has been identified as one of the most promising alternative rubber crops, with laticifer cells that produce high-quality rubber. To uncover the underlying molecular mechanisms regulating natural rubber biosynthesis under MeJA induction, a reference transcriptome was constructed from nine samples of T. kok-saghyz. MeJA treatment was applied for 0 h (control), 6 h, and 24 h. A total of 7452 differentially expressed genes (DEGs) were identified in response to MeJA stress, relative to the control. Functional enrichment showed that these DEGs were primarily related to hormone signaling, defensive responses, and secondary metabolism. Combined analysis of the DEGs induced by MeJA and high-expression genes in laticifer cells further identified seven DEGs related to natural rubber biosynthesis that were upregulated in latex tissue, suggesting that these candidate genes could prove valuable in studying the mechanism of MeJA-mediated natural rubber biosynthesis. In addition, 415 MeJA-responsive DEGs were from several transcription factor families associated with drought resistance. This study helps to elucidate the mechanism of natural rubber biosynthesis in T. kok-saghyz in response to MeJA stress and identifies key candidate MeJA-induced DEGs in laticifer tissue, as well as a candidate drought-response target gene, whose knowledge will promote the breeding of T. kok-saghyz in the aspect of rubber yields and quality, and drought tolerance.

Cloning and functional analysis of the root-knot nematode resistance gene NtRk1 in tobacco

Tobacco (Nicotiana tabacum L.) is an economically important crop worldwide. Root-knot nematodes (RKNs) are responsible for yield losses in tobacco and other crops, such as tomato, potato, peanut, and soybean. Therefore, screening for resistance genes that can prevent RKN infestation and the associated damage is crucial. However, there is no report of cloning tobacco RKN resistance genes to date. Here, we cloned the tobacco RKN resistance gene NtRk1 from the resistant variety TI706, using rapid amplification of cDNA ends. NtRk1 has high homology with other RKN resistance genes (CaMi in pepper, Mi-1.1 and Mi-1.2 in tomato). Under normal conditions, NtRk1 was barely expressed in the roots; however, following RKN infection, its expression level rapidly increased. Overexpression of NtRk1 in the susceptible cultivar "Changbohuang" enhanced its resistance to Meloidogyne incognita, while RNA interference of NtRk1 in the resistant cultivar K326 resulted in its susceptibility to M. incognita. Moreover, compared with resistant variety K326, we found the salicylic acid and jasmonic acid contents of RNAi plants decreased after inoculation with M. incognita, and confirmed that the function of NtRk1 is related to these phytohormones. These findings indicate that NtRk1 is an RKN resistance gene, which is abundantly expressed in response to RKN infection and may enhance host defense responses by elevating salicylic acid and jasmonic acid levels.

Cell type matters: competence for alkaloid metabolism differs in two seed-derived cell strains of Catharanthus roseus

Since the discovery of the anticancer drugs vinblastine and vincristine, Catharanthus roseus has been intensively studied for biosynthesis of several terpene indole alkaloids (TIAs). Due to their low abundance in plant tissues at a simultaneously high demand, modes of production alternative to conventional extraction are mandatory. Plant cell fermentation might become one of these alternatives, yet decades of research have shown limited success to certain product classes, leading to the question: how to preserve the intrinsic ability to produce TIAs (metabolic competence) in cell culture? We used the strategy to use the developmental potency of mature embryos to generate such strains. Two cell strains (C1and C4) from seed embryos of Catharanthus roseus were found to differ not only morphologically, but also in their metabolic competence. This differential competence became manifest not only under phytohormone elicitation, but also upon feeding with alkaloid pathway precursors. The more active strain C4 formed larger cell aggregates and was endowed with longer mitochondria. These cellular features were accompanied by higher alkaloid accumulation in response to methyl jasmonate (MeJA) elicitation. The levels of catharanthine could be increased significantly, while the concurrent vindoline branch of the pathway was blocked, such that no bisindole alkaloids were detectable. By feeding vindoline to MeJA-elicited C4 cells, vincristine became detectable; however, only to marginal amounts. In conclusion, these results show that cultured cells are not "de-differentiated", but can differ in metabolic competence. In addition to elicitation and precursor feeding, the cellular properties of the "biomatter" are highly relevant for the success of plant cell fermentation.

The Conserved Cysteine-Rich Secretory Protein MaCFEM85 Interacts with MsWAK16 to Activate Plant Defenses

Metarhizium anisopliae is an entomopathogenic fungus which may enhance plant growth and resistance when acting as an endophyte in host plants. However, little is known about the protein interactions nor their activating mechanisms. Common in fungal extracellular membrane (CFEM) proteins have been identified as plant immune regulators that suppress or activate plant resistance responses. Here, we identified a CFEM domain-containing protein, MaCFEM85, which was mainly localized in the plasma membrane. Yeast two-hybrid (Y2H), glutathione-S-transferase (GST) pull-down, and bimolecular fluorescence complementation assays demonstrated that MaCFEM85 interacted with the extracellular domain of a Medicago sativa (alfalfa) membrane protein, MsWAK16. Gene expression analyses showed that MaCFEM85 and MsWAK16 were significantly upregulated in M. anisopliae and M. sativa, respectively, from 12 to 60 h after co-inoculation. Additional yeast two-hybrid assays and amino acid site-specific mutation indicated that the CFEM domain and 52th cysteine specifically were required for the interaction of MaCFEM85 with MsWAK16. Defense function assays showed that JA was up-regulated, but Botrytis cinerea lesion size and Myzus persicae reproduction were suppressed by transient expression of MaCFEM85 and MsWAK16 in the model host plant Nicotiana benthamiana. Collectively, these results provide novel insights into the molecular mechanisms underlying interactions of M. anisopliae with host plants.

AabHLH113 integrates jasmonic acid and abscisic acid signaling to positively regulate artemisinin biosynthesis in Artemisia annua

Artemisinin, a sesquiterpene lactone isolated from Artemisia annua, is in huge market demand due to its efficient antimalarial action, especially after the COVID-19 pandemic. Many researchers have elucidated that phytohormones jasmonic acid (JA) and abscisic acid (ABA) positively regulate artemisinin biosynthesis via types of transcription factors (TFs). However, the crosstalk between JA and ABA in regulating artemisinin biosynthesis remains unclear. Here, we identified a novel ABA- and JA-induced bHLH TF, AabHLH113, which positively regulated artemisinin biosynthesis by directly binding to the promoters of artemisinin biosynthetic genes, DBR2 and ALDH1. The contents of artemisinin and dihydroartemisinic acid increased by 1.71- to 2.06-fold and 1.47- to 2.23-fold, respectively, in AabHLH1113 overexpressed A. annua, whereas they decreased by 14-36% and 26-53%, respectively, in RNAi-AabHLH113 plants. Furthermore, we demonstrated that AabZIP1 and AabHLH112, which, respectively, participate in ABA and JA signaling pathway to regulate artemisinin biosynthesis, directly bind to and activate the promoter of AabHLH113. Collectively, we revealed a complex network in which AabHLH113 plays a key interrelational role to integrate ABA- and JA-mediated regulation of artemisinin biosynthesis.

MeJA regulates the accumulation of baicalein and other 4'-hydroxyflavones during the hollowed root development in Scutellaria baicalensis

The dried roots of Scutellaria baicalensis are important traditional Chinese medicine used to treat liver and lung inflammation. An anomalous structure, hollowed root, was discovered in perennial cultivated Scutellaria baicalensis. The presence of the hollow may change the contents of bioactive metabolites, such as baicalein, and other 4'-hydroxyflavones in Scutellaria baicalensis roots, but the relationship between the hollowed root and bioactive metabolite contents is poorly understood. In this study, we identified the anatomical structure of the hollowed root and detected differentially accumulating flavonoid metabolites and enzymes related to 4'-hydroxyflavone biosynthesis in 3-year-old roots with a hollow. We confirmed that methyl jasmonate (MeJA) induced the accumulation of 4'-hydroxyflavones and the expression of enzymes related to 4'-hydroxyflavone biosynthesis in hydroponically cultured Scutellaria baicalensis roots. The development of the hollowed root were divided into 4 stages. The 4'-hydroxyflavone contents and expression of enzymes related to 4'-hydroxyflavone biosynthesis increased synchronously with the content of MeJA during the development of hollowed root. Pathogen and programed-cell-death related genes were induced during hollowed root development. Taken together, our results provide novel insight into the importance of MeJA in the development of hollowed root and the accumulation of 4'-hydroxyflavones in Scutellaria baicalensis roots. Our results suggest that a pathogen and senescence are the two major causes for the development of hollowed root in Scutellaria baicalensis roots.

Genome-Wide Identification of SnRK1 Catalytic α Subunit and FLZ Proteins in Glycyrrhiza inflata Bat. Highlights Their Potential Roles in Licorice Growth and Abiotic Stress Responses

Sucrose non-fermenting-1-related protein kinase-1 (SnRK1) and its scaffolding proteins, FCS-like zinc finger proteins (FLZs), are well conserved in land plants and involved in various processes of plant growth and stress responses. Glycyrrhiza inflata Bat. is a widely used licorice species with strong abiotic stress resistance, in which terpenoids and flavonoids are the major bioactive components. Here, we identified 2 SnRK1 catalytic α subunit encoding genes (GiSnRK1α1 and GiSnRK1α2) and 21 FLZ genes in G. inflata. Polygenetic analysis showed that the 21 GiFLZs could be divided into three groups. A total of 10 representative GiFLZ proteins interact with GiSnRK1α1, and they display overlapped subcellular localization (mainly in the nucleus and the cytoplasm) when transiently expressed in Nicotiana benthamiana leaf cells. Coinciding with the existence of various phytohormone-responsive and stress-responsive cis-regulatory elements in the GiSnRK1α and GiFLZ gene promoters, GiFLZs are actively responsive to methyl jasmonic acid (MeJA) and abscisic acid (ABA) treatments, and several GiFLZs and GiSnRK1α1 are regulated by drought and saline-alkaline stresses. Interestingly, GiSnRK1α and 20 of 21 GiFLZs (except for GiFLZ2) show higher expression in the roots than in the leaves. These data provide comprehensive information on the SnRK1 catalytic α subunit and the FLZ proteins in licorice for future functional characterization.

Systematic Identification of Methyl Jasmonate-Responsive Long Noncoding RNAs and Their Nearby Coding Genes Unveils Their Potential Defence Roles in Tobacco BY-2 Cells

Long noncoding RNAs (lncRNAs) are distributed in various species and play critical roles in plant growth, development, and defence against stimuli. However, the lncRNA response to methyl jasmonate (MeJA) treatment has not been well characterized in Nicotiana tabacum Bright Yellow-2 (BY-2) cells, and their roles in plant defence remain elusive. Here, 7848 reliably expressed lncRNAs were identified in BY-2 cells, of which 629 differentially expressed (DE) lncRNAs were characterized as MeJA-responsive lncRNAs. The lncRNAs in BY-2 cells had a strong genus specificity in Nicotiana. The combined analysis of the cis-regulated lncRNAs and their target genes revealed the potential up- and downregulated target genes that are responsible for different biological functions and metabolic patterns. In addition, some lncRNAs for response-associated target genes might be involved in plant defence and stress resistance via their MeJA- and defence-related cis-regulatory elements. Moreover, some MeJA-responsive lncRNA target genes were related to quinolinate phosphoribosyltransferase, lipoxygenases, and endopeptidase inhibitors, which may contribute to nicotine synthesis and disease and insect resistance, indicating that MeJA-responsive lncRNAs regulate nicotine biosynthesis and disease resistance by regulating their potential target genes in BY-2 cells. Therefore, our results provide more targets for genetically engineering the nicotine content and plant defence in tobacco plants.

Distinct chemical resistance-inducing stimuli result in common transcriptional, metabolic, and nematode community signatures in rice root and rhizosphere

Induced resistance (IR), a phenotypic state induced by an exogenous stimulus and characterized by enhanced resistance to future (a)biotic challenge, is an important component of plant immunity. Numerous IR-inducing stimuli have been described in various plant species, but relatively little is known about 'core' systemic responses shared by these distinct IR stimuli and the effects of IR on plant-associated microbiota. In this study, rice (Oryza sativa) leaves were treated with four distinct IR stimuli (β-aminobutyric acid, acibenzolar-S-methyl, dehydroascorbic acid, and piperonylic acid) capable of inducing systemic IR against the root-knot nematode Meloidogyne graminicola and evaluated their effect on the root transcriptome and exudome, and root-associated nematode communities. Our results reveal shared transcriptional responses-notably induction of jasmonic acid and phenylpropanoid metabolism-and shared alterations to the exudome that include increased amino acid, benzoate, and fatty acid exudation. In rice plants grown in soil from a rice field, IR stimuli significantly affected the composition of rhizosphere nematode communities 3 d after treatment, but by 14 d after treatment these changes had largely reverted. Notably, IR stimuli did not reduce nematode diversity, which suggests that IR might offer a sustainable option for managing plant-parasitic nematodes.

Plagiodera versicolora feeding induces systemic and sexually differential defense responses in poplars

Dioecious plants have evolved effective defense strategies to deal with various biotic and abiotic stresses. However, little is known regarding sexual differences in their defense against herbivores. In this study, we investigated the mechanism of systemic defense responses in male and female Populus cathayana attacked by Plagiodera versicolora Laicharting. The results revealed that P. cathayana exhibits sexually differential responses to a defoliator. The percentage of damaged leaf area was greater in males than in females. Furthermore, the observed saccharide changes imply that males and females exhibit different response times to defoliators. The contents of flavonoids and anthocyanins were significantly increased in both sexes but were higher in females. Specifically, the jasmonic acid (JA) pathway plays an important role. Expression of pest-related genes further revealed that hormones induce changes in downstream genes and metabolites, and upregulation of JA ZIM-domain (JAZ) and CORONATINE INSENSITIVE 1 (COI1) was more significant in females. In the undamaged adjacent leaves, metabolite and gene changes displayed similar patterns to the damaged local leaves, but levels of JA, JAZ1, and COI1 were higher in females. Therefore, our data confirmed that plants initiate the JA pathway to defend against herbivores, that there is systematic signal transduction, and that this ability is stronger in females than in males. This study provides new insights into the resistance of dioecious plants to herbivory and adds a new theoretical basis for the systemic signal transduction of plants in response to biotic stress.

The basic helix-loop-helix transcription factors MYC1 and MYC2 have a dual role in the regulation of constitutive and stress-inducible specialized metabolism in tomato

Plants produce specialized metabolites to protect themselves from biotic enemies. Members of the Solanaceae family accumulate phenylpropanoid-polyamine conjugates (PPCs) in response to attackers while also maintaining a chemical barrier of steroidal glycoalkaloids (SGAs). Across the plant kingdom, biosynthesis of such defense compounds is promoted by jasmonate signaling in which clade IIIe basic helix-loop-helix (bHLH) transcription factors play a central role. By characterizing hairy root mutants obtained through Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR associated protein 9 (CRISPR-Cas9) genome editing, we show that the tomato clade IIIe bHLH transcription factors, MYC1 and MYC2, redundantly control jasmonate-inducible PPC and SGA production, and are also essential for constitutive SGA biosynthesis. Double myc1 myc2 loss-of-function tomato hairy roots displayed suppressed constitutive expression of SGA biosynthesis genes, and severely reduced levels of the main tomato SGAs α-tomatine and dehydrotomatine. In contrast, basal expression of genes involved in PPC biosynthesis was not affected. CRISPR-Cas9(VQR) genome editing of a specific cis-regulatory element, targeted by MYC1/2, in the promoter of a SGA precursor biosynthesis gene led to decreased constitutive expression of this gene, but did not affect its jasmonate inducibility. Our results demonstrate that clade IIIe bHLH transcriptional regulators have evolved under the control of distinct regulatory cues to specifically steer constitutive and stress-inducible specialized metabolism.

TcJAV3-TcWRKY26 Cascade Is a Missing Link in the Jasmonate-Activated Expression of Taxol Biosynthesis Gene DBAT in Taxus chinensis

Jasmonates (JAs) are the most effective inducers for the biosynthesis of various secondary metabolites. Currently, jasmonate ZIM domain (JAZ) and its interactors, such as MYC2, constitute the main JA signal transduction cascade, and such a cascade fails to directly regulate all the taxol biosynthesis genes, especially the rate-limit gene, DBAT. Another JA signaling branch, JAV and WRKY, would probably fill the gap. Here, TcJAV3 was the closest VQ-motif-containing protein in Taxus chinensis to AtJAV1. Although TcJAV3 was overexpressed in AtJAV1 knockdown mutant, JAVRi17, the enhanced disease resistance to Botrytis cinerea caused by silencing AtJAV1 was completely recovered. The results indicated that TcJAV3 indeed transduced JA signal as AtJAV1. Subsequently, TcWRKY26 was screened out to physically interact with TcJAV3 by using a yeast two-hybrid system. Furthermore, bimolecular fluorescence complementation and luciferase complementary imaging also confirmed that TcJAV3 and TcWRKY26 could form a protein complex in vivo. Our previous reports showed that transient TcWRKY26 overexpression could remarkably increase DBAT expression. Yeast one-hybrid and luciferase activity assays revealed that TcWRKY26 could directly bind with the wa-box of the DBAT promoter to activate downstream reporter genes. All of these results indicated that TcWRKY26 acts as a direct regulator of DBAT, and the TcJAV3−TcWRKY26 complex is actually another JA signal transduction mode that effectively regulates taxol biosynthesis in Taxus. Our results revealed that JAV−WRKY complexes directly regulated DBAT gene in response to JA stimuli, providing a novel model for JA-regulated secondary metabolism. Moreover, JAV could also transduce JA signal and function non-redundantly with JAZ during the regulation of secondary metabolisms.

MYC transcription factors coordinate tryptophan-dependent defence responses and compromise seed yield in Arabidopsis

Robust plant immunity negatively affects other fitness traits, including growth and seed production. Jasmonate (JA) confers broad-spectrum protection against plant consumers by stimulating the degradation of JASMONATE ZIM-DOMAIN (JAZ) proteins, which in turn relieves repression on transcription factors (TFs) coincident with reduced growth and fecundity. The molecular mechanisms underlying JA-mediated decreases in fitness remain largely unknown. To assess the contribution of MYC TFs to growth and reproductive fitness at high levels of defence, we mutated three MYC genes in a JAZ-deficient mutant (jazD) of Arabidopsis thaliana that exhibits strong defence and low seed yield. Genetic epistasis analysis showed that de-repression of MYC TFs in jazD not only conferred strong resistance to insect herbivory but also reduced shoot and root growth, fruit size and seed yield. We also provided evidence that the JAZ-MYC module coordinates the supply of tryptophan with the production of indole glucosinolates and the proliferation of endoplasmic reticulum bodies that metabolise glucosinolates through the action of β-glucosidases. Our results establish MYCs as major regulators of growth- and reproductive-defence trade-offs and further indicate that these factors coordinate tryptophan availability with the production of amino acid-derived defence compounds.

Interplay of transcription factors orchestrating the biosynthesis of plant alkaloids

Plants produce a range of secondary metabolites primarily as defence molecules. A plant has to invest considerable energy to synthesise alkaloids, and sometimes they are even toxic to themselves. Hence, the biosynthesis of alkaloids is a spatiotemporally regulated process under quantitative feedback regulation which is accomplished by the signal reception, transcriptional/translational regulation, transport, storage and accumulation. The transcription factors (TFs) initiate the biosynthesis of alkaloids after appropriate cues. The present study recapitulates last decade understanding of the role of TFs in alkaloid biosynthesis. The present review discusses TF families, viz. AP2/ERF, bHLH, WRKY, MYB involved in the biosynthesis of various types of alkaloids. It also highlights the role of the jasmonic acid cascade and post-translational modifications of TF proteins. A thorough understanding of TFs will help us to decide a strategy to facilitate successful pathway manipulation and in vitro production.

Arbuscular mycorrhizal fungi: Effects on secondary metabolite accumulation of traditional Chinese medicines

Traditional Chinese medicine (TCM) has played a pivotal role in maintaining the health of people, and the intrinsic quality of TCM is directly related to the clinical efficacy. The medicinal ingredients of TCM are derived from the secondary metabolites of plant metabolism and are also the result of the coordination of various physiological activities in plants. Arbuscular mycorrhizal fungi (AMF) are among the most ubiquitous plant mutualists that enhance the growth and yield of plants by facilitating the uptake of nutrients and water. Symbiosis of AMF with higher plants promotes growth and helps in the accumulation of secondary metabolites. However, there is still no systematic analysis and summation of their roles in the application of TCM, biosynthesis and accumulation of active substances of herbs, as well as the mechanisms. AMF directly or indirectly affect the accumulation of secondary metabolites of TCM, which is the focus of this review. First, in this review, the effects of AMF symbiosis on the content of different secondary metabolites in TCM, such as phenolic acids, flavonoids, alkaloids and terpenoids, are summarized. Moreover, the mechanism of AMF regulating the synthesis of secondary metabolites was also considered, in combination with the establishment of mycorrhizal symbionts, response mechanisms of plant hormones, nutritional elements and expression of key enzyme their activities. Finally, combined with the current application prospects for AMF in TCM, future in-depth research is planned, thus providing a reference for improving the quality of TCM. In this manuscript, we review the research status of AMF in promoting the accumulation of secondary metabolites in TCM to provide new ideas and methods for improving the quality of TCM.

Interference between ER stress-related bZIP-type and jasmonate-inducible bHLH-type transcription factors in the regulation of triterpene saponin biosynthesis in Medicago truncatula

Triterpene saponins (TS) are a structurally diverse group of metabolites that are widely distributed in plants. They primarily serve as defense compounds and their production is often triggered by biotic stresses through signaling cascades that are modulated by phytohormones such as the jasmonates (JA). Two JA-modulated basic helix-loop-helix (bHLH) transcription factors (TFs), triterpene saponin biosynthesis activating regulator 1 (TSAR1) and TSAR2, have previously been identified as direct activators of TS biosynthesis in the model legume Medicago truncatula. Here, we report on the involvement of the core endoplasmic reticulum (ER) stress-related basic leucine zipper (bZIP) TFs bZIP17 and bZIP60 in the regulation of TS biosynthesis. Expression and processing of M. truncatula bZIP17 and bZIP60 proteins were altered in roots with perturbed TS biosynthesis or treated with JA. Accordingly, such roots displayed an altered ER network structure. M. truncatula bZIP17 and bZIP60 proteins were shown to localize in the nucleus and appeared to be capable of interfering with the TSAR-mediated transactivation of TS biosynthesis genes. Furthermore, interference between ER stress-related bZIP and JA-modulated bHLH TFs in the regulation of JA-dependent terpene biosynthetic pathways may be widespread in the plant kingdom, as we demonstrate that it also occurs in the regulation of monoterpene indole alkaloid biosynthesis in the medicinal plant Catharanthus roseus.

Jasmonates in plant growth and development and elicitation of secondary metabolites: An updated overview

Secondary metabolites are incontestably key specialized molecules with proven health-promoting effects on human beings. Naturally synthesized secondary metabolites are considered an important source of pharmaceuticals, food additives, cosmetics, flavors, etc., Therefore, enhancing the biosynthesis of these relevant metabolites by maintaining natural authenticity is getting more attention. The application of exogenous jasmonates (JAs) is well recognized for its ability to trigger plant growth and development. JAs have a large spectrum of action that covers seed germination, hypocotyl growth regulation, root elongation, petal expansion, and apical hook growth. This hormone is considered as one of the key regulators of the plant's growth and development when the plant is under biotic or abiotic stress. The JAs regulate signal transduction through cross-talking with other genes in plants and thereby deploy an appropriate metabolism in the normal or stressed conditions. It has also been found to be an effective chemical elicitor for the synthesis of naturally occurring secondary metabolites. This review discusses the significance of JAs in the growth and development of plants and the successful outcomes of jasmonate-driven elicitation of secondary metabolites including flavonoids, anthraquinones, anthocyanin, xanthonoid, and more from various plant species. However, as the enhancement of these metabolites is essentially measured via in vitro cell culture or foliar spray, the large-scale production is significantly limited. Recent advancements in the plant cell culture technology lay the possibilities for the large-scale manufacturing of plant-derived secondary metabolites. With the insights about the genetic background of the metabolite biosynthetic pathway, synthetic biology also appears to be a potential avenue for accelerating their production. This review, therefore, also discussed the potential manoeuvres that can be deployed to synthesis plant secondary metabolites at the large-scale using plant cell, tissue, and organ cultures.

Overcoming Metabolic Constraints in the MEP-Pathway Enrich Salvia sclarea Hairy Roots in Therapeutic Abietane Diterpenes

Abietane diterpenoids (e.g., carnosic acid, aethiopinone, 1-oxoaethiopinone, salvipisone, and ferruginol) synthesized in the roots of several Salvia species have proved to have promising biological activities, but their use on a large scale is limited by the very low content extracted from in vivo roots. In this review, we summarized our efforts and the achieved results aimed at optimizing the synthesis of these diterpenes in Salvia sclarea hairy roots by either elicitation or by modifying the expression of genes encoding enzymes of the MEP-pathway, the biosynthetic route from which they derive. Stable S. sclarea hairy roots (HRs) were treated with methyl jasmonate or coronatine, or genetically engineered, by tuning the expression of genes controlling enzymatic rate-limiting steps (DXS, DXR, GGPPS, CPPS alone or in combination), by silencing of the Ent-CPPS gene, encoding an enzyme acting at gibberellin lateral competitive route or by coordinate up-regulation of biosynthetic genes mediated by transcription factors (WRKY and MYC2). Altogether, these different approaches successfully increased the amount of abietane diterpenes in S. sclarea HRs from to 2 to 30 times over the content found in the control HR line.

PatDREB Transcription Factor Activates Patchoulol Synthase Gene Promoter and Positively Regulates Jasmonate-Induced Patchoulol Biosynthesis

The production of patchoulol in the patchouli (Pogostemon cablin) plant determines its application value, as it is the principal active sesquiterpene of essential oil extracted from this plant. Here, the promoter of patchoulol synthase gene (PatPTS_pro) was isolated and found to be methyl jasmonate (MeJA)-induced. A nucleus-localized AP2/ERF transcription factor PatDREB was identified as a transcription activator binding to PatPTS_pro, regulating patchoulol biosynthesis through modulating the gene expression. PatDREB also interacts with jasmonate ZIM-domain 4 (JAZ4). Furthermore, PatDREB could physically interact with the MYB-related transcription factor PatSWC4 and synergistically facilitate patchoulol biosynthesis. However, the transcriptional activation activity of the PatDREB-PatSWC4 complex could be inhibited by PatJAZ4, and JA could reverse this interference. Overall, we demonstrated the positive roles of PatDREB and the PatDREB-PatSWC4 complex in regulating patchoulol production, which advance our understanding of the regulatory network of patchoulol biosynthesis.