PAL Genes Research Articles

Genome-Wide and Expression Pattern Analysis of the HIT4 Gene Family Uncovers the Involvement of GHHIT4_4 in Response to Verticillium Wilt in Gossypium hirsutum.

Chromatin remodelers are essential for regulating plant growth, development, and responses to environmental stresses. HIT4 (HEAT-INTOLERANT 4) is a novel stress-induced chromatin remodeling factor that has been less studied in abiotic stress and stress resistance, particularly in cotton. In this study, we conducted a comprehensive analysis of the members of the HIT4 gene family in Gossypium hirsutum using bioinformatics methods, including phylogenetic relationships, gene organization, transcription profiles, phylogenetic connections, selection pressure, and stress response. A total of 18 HIT4 genes were identified in four cotton species, with six HIT4 gene members in upland cotton. Based on the evolutionary relationships shown in the phylogenetic tree, the 18 HIT4 protein sequences were classified into four distinct subgroups. Furthermore, we conducted chromosome mapping to determine the genomic locations of these genes and visually represented the structural characteristics of HIT4 in G. hirsutum. In addition, we predicted the regulatory elements in HIT4 in G. hirsutum and conducted an analysis of repetitive sequences and gene collinearity among HIT4 in four cotton species. Moreover, we calculated the Ka/Ks ratio for homologous genes to assess the selection pressure acting on HIT4. Using RNA-seq, we explored the expression patterns of HIT4 genes in G. hirsutum and Gossypium barbadense. Through weighted gene co-expression network analysis (WGCNA), we found that GHHIT4_4 belonged to the MEblue module, which was mainly enriched in pathways such as DNA replication, phagosome, pentose and glucuronate interconversions, steroid biosynthesis, and starch and sucrose metabolism. This module may regulate the mechanism of upland cotton resistance to Verticillium wilt through DNA replication, phagosome, and various metabolic pathways. In addition, we performed heterologous overexpression of GH_D11G0591 (GHHIT4_4) in tobacco, and the results showed a significant reduction in disease index compared to the wild type, with higher expression levels of disease resistance genes in the transgenic tobacco. After conducting a VIGS (virus-induced gene silencing) experiment in cotton, the results indicated that silencing GHHIT4_4 had a significant impact, the resistance to Verticillium wilt weakened, and the internode length of the plants significantly decreased by 30.7% while the number of true leaves increased by 41.5%. qRT-PCR analysis indicated that GHHIT4_4 mainly enhanced cotton resistance to Verticillium wilt by indirectly regulating the PAL, 4CL, and CHI genes. The subcellular localization results revealed that GHHIT4_4 was predominantly distributed in the mitochondria and nucleus. This study offers preliminary evidence for the involvement of the GHHIT4_4 in cotton resistance to Verticillium wilt and lays the foundation for further research on the disease resistance mechanism of this gene in cotton.

Unveiling the role of vermicompost in modulating phenylpropanoid metabolism in basil (Ocimum basilicum L.): A single-cell type PGT approach

This research delves into phenylpropanoid metabolism, focusing on phenylpropene biosynthesis in the methyleugenol chemotype of basil (Ocimum basilicum L.). We isolated peltate glandular trichomes (PGTs) from basil leaves to eliminate primary metabolic influences, offering a unique perspective into these complex processes. Vermicompost, chosen for its eco-friendly composition and superiority in invigorating phenylpropanoid metabolism. In this study, we investigated the impacts of solid and tea-form vermicompost applications at 0%, 10%, and 25% doses on the methyleugenol chemotype of basil, focusing on the expression levels of PAL, 4CL, EGS, EOMT, and CVOMT genes and phenylpropene accumulation in the peltate glandular trichomes. Results showed that 10% solid vermicompost (SV) application increased 4CL expression level at 236%, while 25% SV application further enhanced EOMT and CVOMT expressions to towering values by 7,494-fold and 19,643-fold, respectively. SV applications did not significantly impact eugenol accumulation but suppressed chavicol biosynthesis. Methyleugenol and methylchavicol accumulation rose in a dose-dependent manner, with significant increases observed in the 25% SV application. A positive correlation was found between CVOMT expression and accumulation rates of methyleugenol and methylchavicol phenylpropenes following SV applications. Conversely, vermicompost tea (VT) applications led to mixed gene expression patterns and reduced eugenol and methyleugenol ratios in peltate glandular trichomes compared to control. In summary, the notably high gene expressions observed in the results of our preliminary study offer a new perspective in the field of phenylpropanoid metabolism. This underscores the value of utilizing single-cell type PGTs for examining secondary metabolic pathways in plants and demonstrates the impact of vermicompost on phenylpropene production.

Biocontrol and Growth Promotion Potential of Bacillus subtilis CTXW 7-6-2 against Rhizoctonia solani that Causes Tobacco Target Spot Disease.

Fungal diseases form perforated disease spots in tobacco plants, resulting in a decline in tobacco yield and quality. The present study investigated the antagonistic effect of Bacillus subtilis CTXW 7-6-2 against Rhizoctonia solani, its ability to promote the growth of tobacco seedlings, and the expression of disease resistance-related genes for efficient and eco-friendly plant disease control. Our results showed that CTXW 7-6-2 had the most vigorous growth after being cultured for 96 h, and its rate of inhibition of R. solani growth in vitro was 94.02%. The volatile compounds produced by CTXW 7-6-2 inhibited the growth of R. solani significantly (by 96.62%). The fungal growthinhibition rate of the B. subtilis CTXW 7-6-2 broth obtained after high-temperature and no-high-temperature sterile fermentation was low, at 50.88% and 54.63%, respectively. The lipopeptides extracted from the B. subtilis CTXW 7-6-2 fermentation broth showed a 74.88% fungal growth inhibition rate at a concentration of 100 mg/l. Scanning and transmission electron microscopy showed some organelle structural abnormalities, collapse, shrinkage, blurring, and dissolution in the R. solani mycelia. In addition, CTXW 7-6-2 increased tobacco seedling growth and improved leaf and root weight compared to the control. After CTXW 7-6-2 inoculation, tobacco leaves showed the upregulation of the PDF1.2, PPO, and PAL genes, which are closely related to target spot disease resistance. In conclusion, B. subtilis CTXW 7-6-2 may be an efficient biological control agent in tobacco agriculture and enhance plant growth potential.

Engineering styrene biosynthesis: designing a functional trans-cinnamic acid decarboxylase in Pseudomonas

We are interested in converting second generation feedstocks into styrene, a valuable chemical compound, using the solvent-tolerant Pseudomonas putida DOT-T1E as a chassis. Styrene biosynthesis takes place from L-phenylalanine in two steps: firstly, L-phenylalanine is converted into trans-cinnamic acid (tCA) by PAL enzymes and secondly, a decarboxylase yields styrene. This study focuses on designing and synthesizing a functional trans-cinnamic acid decarboxylase in Pseudomonas putida. To achieve this, we utilized the “wholesale” method, involving deriving two consensus sequences from multi-alignments of homologous yeast ferulate decarboxylase FDC1 sequences with > 60% and > 50% identity, respectively. These consensus sequences were used to design Pseudomonas codon-optimized genes named psc1 and psd1 and assays were conducted to test the activity in P. putida. Our results show that the PSC1 enzyme effectively decarboxylates tCA into styrene, whilst the PSD1 enzyme does not. The optimal conditions for the PSC1 enzyme, including pH and temperature were determined. The L-phenylalanine DOT-T1E derivative Pseudomonas putida CM12-5 that overproduces L-phenylalanine was used as the host for expression of pal/psc1 genes to efficiently convert L-phenylalanine into tCA, and the aromatic carboxylic acid into styrene. The highest styrene production was achieved when the pal and psc1 genes were co-expressed as an operon in P. putida CM12-5. This construction yielded styrene production exceeding 220 mg L−1. This study serves as a successful demonstration of our strategy to tailor functional enzymes for novel host organisms, thereby broadening their metabolic capabilities. This breakthrough opens the doors to the synthesis of aromatic hydrocarbons using Pseudomonas putida as a versatile biofactory.

Phenylpropane biosynthesis and alkaloid metabolism pathways involved in resistance of Amorphophallus spp. against soft rot disease.

Soft rot of konjac (Amorphophallus spp.) is a devastating disease caused by the bacterium Pectobacterium carotovorum subsp. carotovorum (Pcc) with serious adverse effects on plantation development, corm quality and crop yield due to the current lack of effective control measures. The main objective of the present study was to elucidate the mechanisms underlying plant resistance to soft rot disease. A combination of transcriptomic and metabolomic analyses demonstrated significant enrichment of differentially expressed genes (DEG) and differentially accumulated metabolites (DAM) associated with plant hormones, phenylpropanoid biosynthesis and, in particular, alkaloid metabolism, in Amorphophallus muelleri following Pcc infection compared with A. konjac, these data implicate alkaloid metabolism as the dominant mechanism underlying disease resistance of A. muelleri. Quantitative real-time polymerase chain reaction analysis further revealed involvement of PAL, CYP73A16, CCOAOMT1, RBOHD and CDPK20 genes in the response of konjac to Pcc. Analysis of the bacteriostatic activities of total alkaloid from A. muelleri validated the assumption that alkaloid metabolism positively regulates disease resistance of konjac. Our collective results provide a foundation for further research on the resistance mechanisms of konjac against soft rot disease.

Effects of nano silicon fertilizer on the lodging resistance characteristics of wheat basal second stem node

The application of nano fertilizers is one of the hotspots in current agricultural production. In this study, nano silicon materials were mixed with compound fertilizers to make nano silicon fertilizer. The effects of different amounts of nano silicon application on the breaking-resistance strength, lodging-resistance index, lignin accumulation, lignin synthesis related enzymes, and the relative expression of lignin synthesis related genes in the second stem node of wheat were mainly studied. Four treatments were set up: CK (750 kg·ha−1 compound fertilizer), T1 (750 kg·ha−1 compound fertilizer + 0.9 kg·ha−1 nano silicon), T2 (750 kg·ha−1 compound fertilizer + 1.8 kg·ha−1 nano silicon), T3 (750 kg·ha−1 compound fertilizer + 2.7 kg·ha−1 nano silicon). The results of the two-year experiment showed that the breaking-resistance strength, lodging-resistance index, lignin accumulation in the second stem node of wheat treated with nano silicon fertilizer were higher than CK. In the first year of the experiment, the lignin accumulation of T2 was 130.73%, 5.14% and 7.25% higher than that of CK, T1 and T3 respectively at the maturity stage. In the second year of the experiment, the lignin accumulation of T2 was 20.33%, 11.19% and 9.89% higher than that of CK, T1 and T3 respectively at the maturity stage. And the activities of PAL, 4CL, CAD, and related gene expression levels were also higher than CK. And among them, T2 performed the best, indicating that the application of nano silicon fertilizer is beneficial for improving the lodging resistance of wheat stems and is of great significance for improving the quality of wheat.

In silico characterization of GbPAL, GbCHS, GbDFR and GbANS structural genes involved in the biosynthesis of flavonoids in Gynura bicolor DC

Gynura bicolor is a member of the Asteraceae family, possessing important pharmaceutical compounds such as flavonoids, anthocyanins, and terpenoids. Genetic and molecular studies focusing on the biosynthesis of flavonoids are indispensable to determining their regulation. GbPAL, GbCHS, GbDFR, and GbANS are genes encoding Phenylalanine ammonia lyase, Chalcone synthase, Dihydroflavonol reductase, and Anthocyanidin synthase enzymes, resepectively and are involved in the biosynthesis of flavonoids in G. bicolor, resepectively. There are still a few studies concerning the characterization of these genes. In this study, the structural enzyme sequences were selected to be characterized in silico using bioinformatics software. The phylogenetic analysis demonstrated that the genes in question were closely related to several species of the Asteraceae family. Our data revealed that the G. bicolor PAL, CHS, DFR and ANS genes are closely related to the sequence of genes found in Chrysanthemum morifolium. Furthermore, the CHS, DFR and ANS of G. bicolor also tightly correlated with sequence from Callistephus chinensis. Further analysis also demonstrated that all conserved motifs contain active functional and catalytic domain supporting the flavonoid-related enzyme functions. All physicochemical parameters used in this study also meet the prediction criteria. The investigation of secondary structure prediction using two instruments (PSIPRED and SOPMA) revealed that all enzymes tested possess similar α-helix (H), β-sheet (E), and coil (C) composition. GbPAL showed a secondary structure dominated by helix (mainly alpha), GbCHS and GbDFR (Alpha-beta), and GbANS (mainly beta). Each enzyme was modeled, with RMSD values superimposed on the template: 0.125 Å (GbPAL), 0.061 Å (GbCHS), 0.065 Å (GbDFR), and 0.089 Å (GbANS). The 3D model evaluation was checked using four parameters, including PROCHECK, Verify3D, ERRAT, and QMEAN-Z score. All the parameters verified that the model showed a high quality (more than 90 % of the favored region), high ressemblence of the 3D and 1D amino acid sequence, the 3D modeles were acceptable since they possesed high resolution of the protein structure (2.5 – 3 Å), and the enzyme models have Z-Score values in the permissible range. The accuracy and reliability of the generated models met Ramachandran value in comparison to experimentally resolved protein templates. The molecular docking analysis showed that each substrate compound docked at the real binding site in every tested enzyme. Furthermore, they also showed similar results compared to other experimentally observed proteins. The overall findings provide an insight into the molecular characteristics of flavonoid-related genes, which might enrich our understanding for further genomic application of the Gynura bicolor.

Integrated Transcriptomics and Metabolomics Analysis Promotes the Understanding of Adventitious Root Formation in Eucommia ulmoides Oliver.

As a primary approach to nutrient propagation for many woody plants, cutting roots is essential for the breeding and production of Eucommia ulmoides Oliver. In this study, hormone level, transcriptomics, and metabolomics analyses were performed on two E. ulmoides varieties with different adventitious root (AR) formation abilities. The higher JA level on the 0th day and the lower JA level on the 18th day promoted superior AR development. Several hub genes executed crucial roles in the crosstalk regulation of JA and other hormones, including F-box protein (EU012075), SAUR-like protein (EU0125382), LOB protein (EU0124232), AP2/ERF transcription factor (EU0128499), and CYP450 protein (EU0127354). Differentially expressed genes (DEGs) and metabolites of AR formation were enriched in phenylpropanoid biosynthesis, flavonoid biosynthesis, and isoflavonoid biosynthesis pathways. The up-regulated expression of PAL, CCR, CAD, DFR, and HIDH genes on the 18th day could contribute to AR formation. The 130 cis-acting lncRNAs had potential regulatory functions on hub genes in the module that significantly correlated with JA and DEGs in three metabolism pathways. These revealed key molecules, and vital pathways provided more comprehensive insight for the AR formation mechanism of E. ulmoides and other plants.

Comparative analyses reveal a phenylalanine ammonia lyase dependent and salicylic acid mediated host resistance in Zingiber zerumbet against the necrotrophic soft rot pathogen Pythium myriotylum

Little is known about the molecular basis of host defense in resistant wild species Zingiber zerumbet (L.) Smith against the soil-borne, necrotrophic oomycete pathogen Pythium myriotylum Drechsler, which causes the devastating soft rot disease in the spice crop ginger (Zingiber officinale Roscoe). We investigated the pattern of host defense between Z. zerumbet and ginger in response to P. myriotylum inoculation. Analysis of gene expression microarray data revealed enrichment of phenylpropanoid biosynthetic genes, particularly lignin biosynthesis genes, in pathogen-inoculated Z. zerumbet compared to ginger. RT-qPCR analysis showed the robust activation of phenylpropanoid biosynthesis genes in Z. zerumbet, including the core genes PAL, C4H, 4CL, and the monolignol biosynthesis and polymerization genes such as CCR, CAD, C3H, CCoAOMT, F5H, COMT, and LAC. Additionally, Z. zerumbet exhibited the accumulation of the phenolic acids including p-coumaric acid, sinapic acid, and ferulic acid that are characteristic of the cell walls of commelinoid monocots like Zingiberaceae and are involved in cell wall strengthening by cross linking with lignin. Z. zerumbet also had higher total lignin and total phenolics content compared to pathogen-inoculated ginger. Phloroglucinol staining revealed the enhanced fortification of cell walls in Z. zerumbet, specifically in xylem vessels and surrounding cells. The trypan blue staining indicated inhibition of pathogen growth in Z. zerumbet at the first leaf whorl, while ginger showed complete colonization of the pith within 36 h post inoculation (hpi). Accumulation of salicylic acid (SA) and induction of SA regulator NPR1 and the signaling marker PR1 were observed in Z. zerumbet. Silencing of PAL in Z. zerumbet through VIGS suppressed downstream genes, leading to reduced phenylpropanoid accumulation and SA level, resulting in the susceptibility of plants to P. myriotylum. These findings highlight the essential role of PAL-dependent mechanisms in resistance against P. myriotylum in Z. zerumbet. Moreover, our results suggest an unconventional role for SA in mediating host resistance against a necrotroph. Targeting the phenylpropanoid pathway could be a promising strategy for the effective management of P. myriotylum in ginger.

Comparative transcriptome analysis and Arabidopsis thaliana overexpression reveal key genes associated with cadmium transport and distribution in root of two Capsicum annuum cultivars

The molecular mechanisms underlying high and low cadmium (Cd) accumulation in hot pepper cultivars remain unclear. In this study, comparative transcriptome analysis of root between high-Cd (J) and low-Cd (Z) cultivars was conducted under hydroponic cultivation with 0 and 0.4 mg/L Cd, respectively. The results showed that J enhanced the root uptake of Cd by elevating the expression of Nramp5 and counteracting Cd toxicity by increasing the expression of genes, such as NIR1, GLN1, and IAA9. Z reduced Cd accumulation by enhancing the cell wall lignin synthesis genes PAL, COMT, 4CL, LAC, and POD and the Cd transporters ABC, MTP1, and DTX1. Elevated expression of genes related to sulfur metabolism was observed in Z, potentially contributing to its ability to detoxify Cd. To investigate the function of CaCOMT1, an Arabidopsis thaliana overexpression line (OE-CaCOMT1) was constructed. The results revealed that OE-CaCOMT1 drastically increased the lignin content by 38–42% and reduced the translocation of Cd to the aboveground parts by 32%. This study provides comprehensive insights into the mechanisms underlying Cd accumulation in hot pepper cultivars using transcriptome analysis. Moreover, this study elucidates the critical function of CaCOMT1, providing a theoretical foundation for the production of low-Cd vegetables for food safety.

NtERF4 promotes the biosynthesis of chlorogenic acid and flavonoids by targeting PAL genes in Nicotiana tabacum.

Chlorogenic acid (CGA) and flavonoids are important secondary metabolites, which modulate plant growth and development, and contribute to plant resistance to various environmental stresses. ERF4 has been shown to be a repressor of anthocyanin accumulation in grape, but its full roles in regulating the biosynthesis of other phenylpropanoid compounds still needs to be further studied. In the present study, two NtERF4 genes were identified from N. tabacum genome. The expression level of NtERF4a was higher than that of NtERF4b in all the tobacco tissues examined. Over-expression of NtERF4a significantly promoted the accumulation of CGA and flavonoids in tobacco leaves, while silencing of NtERF4a significantly repressed the biosynthesis of CGA and flavonoids. RNA-seq analysis of NtERF4a-OE and WT plants revealed 8 phenylpropanoids-related differentially expressed genes (DEGs), including 4 NtPAL genes that encode key enzymes in the phenylpropanoid pathway. Activation of NtERF4a-GR fusion protein in tobacco significantly induced the transcription of NtPAL1 and NtPAL2 in the presence of protein synthesis inhibitor. Chromatin immunoprecipitation and Dual-Luc assays further indicated that NtERF4a could bind to the GCC box presented in the promoters of NtPAL1 and NtPAL2, thereby activating their transcription. Moreover, ectopic expression of NtERF4a induced the transcription of NtGSK1, NtMYC2, and NtJAZ3 genes, and enhanced the resistance of tobacco seedlings to salt and drought stresses, indicating multiple roles of NtERF4a in plants. Our findings revealed new roles of NtERF4a in modulating the accumulation of phenylpropanoid compounds in tobacco, and provided a putative target for improving phenylpropanoids synthesis and stress resistance in plants.

β-Aminobutyric Acid and Powdery Mildew Infection Enhanced the Activation of Defense-Related Genes and Salicylic Acid in Cucumber (Cucumis sativus L.).

Powdery mildew disease, caused by Sphaerotheca fusca, is a major disease affecting cucumbers cultivated in greenhouses. This study was conducted to find defense genes induced by β-aminobutyric acid (BABA) and powdery mildew in cucumber. Disease severities of 25% and 5% were exhibited by the 2000 and 5000 mg/L BABA-treated cucumber, respectively. BABA did not affect the spore germination of the powdery mildew pathogen, showing that BABA is not an antifungal agent against the pathogen. In quantitative real-time PCR analysis, BABA-treated cucumber upregulated the transcriptional levels of the defense genes CsPAL, CsPR3, CsPR1, CsLOX1, CsLOX23, Cs LecRK6.1, CsWRKY20, and Cupi4 in cucumber to maximum levels at 48 h, whereas CsLecRK6.1 reached maximum expression after 24 h, and further, salicylic acid (SA) levels were significantly increased in BABA-treated cucumber plants. In addition, the cucumber infected with powdery mildew underwent a 1.6- to 47.3-fold enhancement in the defense genes PAL, PR3, PR1, Lox1, Lox 23, LecRK6.1, WRKY20, and Cupi4 compared to heathy cucumber. These results suggest that the BABA-induced defense response is associated with SA signaling pathway-dependent systemic acquired resistance (SAR) in cucumber, which is involved in plant resistance mechanisms.

Modulation of morpho-physiological attributes and in situ analysis of secondary metabolites using Raman spectroscopy in response to red and blue light exposure in Artemisia annua

Differential light conditions, such as variations in photoperiod, light quality, and light intensity, play a crucial role as external factors that can influence plant morphogenesis and secondary metabolism. However, there is still a lack of understanding of how Artemisia annua responds to monochromatic and dichromatic light regimes in terms of the different physiological mechanisms that control plant growth and secondary metabolite production. Therefore, the primary aim of this study was to investigate and assess the various physiological parameters, biochemical analysis, and molecular aspects in detail. Therefore, the plantlets were exposed to LED lighting such as monochromatic red light (R), monochromatic blue light (B), white light (W), and a combination of red and blue light (RB, 1:1) at a PPFD (photosynthetic photon flux density) of 200 mol. m−2. s−1 for 10 days. Our results indicate that exposure to RB light resulted in an immense increase in ROS accumulation, flavonoids, lignin, and artemisinin by 4.7-fold, 44%, and 53.4%, respectively, in contrast to W light. Whereas blue light led to increments of 160.2% in phenolic and 107.9% in anthocyanin content. RB and B light also influence the parameters of chlorophyll fluorescence, as well as leaf area, stomatal density, trichome size, antioxidant enzyme activity, and the production of more secondary metabolites to combat oxidative stress. Real-time PCR analysis of biosynthetic pathway-associated genes HMGR, DXR, DXS, FPS, ADS, CYP71AVI, DBR2, ALDH1, and flavonoid key biosynthesis pathway genes PAL, C4H, 4CL, CHS, and F3′H showed the highest increment under RB, light followed by B and R light exposure. Further, RB LED light has significant potential for enhancing natural bio-active compounds as revealed by Raman spectroscopy, such as camphor, limonene, terpene-4-ol, α pinene, 1,8-cineole, β-caryophyllene, artemisinin, kaempferol, luteolin, rutin, and caffeic acid in A. annua. Taken together, red and blue LEDs can serve as significant elicitors for the production of commercially important metabolites.

A Biocontrol Strain of Serratia plymuthica MM Promotes Growth and Controls Fusarium Wilt in Watermelon

Fusarium wilt, caused by Fusarium oxysporum f. sp. niveum (FON), is a predominant and devastating soil-borne disease that results in significant yield losses in watermelon cultivation. In this study, a strain MM isolated from the herbage rhizosphere soil, exhibited an inhibition rate of 65.46% against FON, leading to mycelial collapse, atrophy, and deformation. In pot experiments, strain MM effectively controlled Fusarium wilt of watermelon, showing a control efficacy of 74.07%. Through morphological observation and 16S rDNA gene sequencing, strain MM was identified as Serratia plymuthica. Additionally, S. plymuthica MM demonstrated antagonistic activity against eight plant pathogens, indicating that MM had broad-spectrum antifungal activity. The strain also exhibited the ability to synthesize siderophores and indole acetic acid (IAA), both of which are growth-promoting compounds. Moreover, strain MM secreted various extracellular enzymes, including protease, chitinase, β-glucanase, and cellulase. This ability allowed S. plymuthica MM to readily colonize watermelon roots and promote seedling growth. Inoculation with S. plymuthica MM increased the activity of PAL, POD, PPO, and CAT enzymes associated with watermelon defense. Furthermore, qRT-PCR analysis revealed up-regulation of LOX, POD, PAL, ClPR3, and C4H genes, which are related to plant disease resistance. The results indicated that S. plymuthica MM enhances watermelon plants’ resistance to FON by activating the JA, SA, and shikimic acid phenylpropanoid–lignin synthesis pathways. Gas chromatography–mass spectrometry (GC-MS) analysis of S. plymuthica MM culture supernatant identified piperazinedione, pyrrolo[1,2-a]pyrazine-1,4-dione, and octadecenamide as the main antimicrobial substances. Overall, S. plymuthica MM shows promise as a biocontrol agent against Fusarium wilt of watermelon, suggesting its potential for the development of a new biocontrol agent.

Mechanisms of Control by <i>Pseudomonas fluorescens</i> of Barley Root Rot Caused by <i>Fusarium culmorum</i>

In this paper, we found out why in the presence of the rhizobacterium Pseudomonas fluorescens 2137, the intensity of barley fusarium root rot caused by Fusarium culmorum 30 decreases, if there is no obvious decrease in the amount of fungus in the roots in the presence of the bacterium. It has been suggested that (1) the presence of rhizobacteria stimulates the defence reactions in barley, (2) rhizobacteria reduces the production of trichothecene toxins by F. culmorum 30, a known factor of aggressiveness of the fungus. The responses of barley to the colonization of its roots by fungus and bacteria were studied in sterile vermiculite for 11 days by the intensity of expression of the LOX, PAL, PR4 and PR1 genes. The production of F. culmorum 30 trichothecene toxins was evaluated by the expression level of the TRI13 gene. As a result, it was found that P. fluorescens 2137 induced the expression of all studied defence genes already in diurnal barley roots, but only in the presence of F. culmorum 30. In the presence of the bacterium, the expression level of the TRI13 gene did not decrease, however, a decrease in the number of diseased plants suggests that P. fluorescens 2137 is capable of detoxifying trichothecene toxins produced by the fungus or inducing this ability in barley.

Exogenous melatonin delays strawberry fruit ripening by suppressing endogenous ABA signaling

Ripening as a physico-chemical change is part of a continuous developmental process and hormones play a major role in this processes. The present study was carried out to investigate the effect of external melatonin (0 and 10 μM) injection at the light green stage on the ripening of strawberry fruit. The fruit was sampled for morphological, biochemical, and gene expression analysis during (0, 5, 10, and 15 days after treatment). The results showed a lower accumulation of anthocyanin content was observed in fruits treated with 10 μM. The injection of 10 μM melatonin caused a lower total soluble solid content and fruit color, and higher titratable acidity and softening. The total phenol content was higher in fruit treated with 10 µM melatonin, accompanied by increased PAL enzyme activity and gene expression, increased DPPH scavenging capacity, and higher content of quercetin, gallic, caffeic, and chlorogenic acids. The delay in fruit ripening was associated with suppression of H2O2 level and endogenous ABA accumulation caused by lower expression of NCEDs genes. In general, it is concluded that activating the melatonin ROS scavenging cascade might be responsible for the delayed ripening and development of strawberry fruit. Therefore, our study demonstrates that the exogenous application of 10 μM melatonin can slow the ripening of strawberry fruit.

Potential regulatory genes of light induced anthocyanin accumulation in sweet cherry identified by combining transcriptome and metabolome analysis.

Anthocyanins exist widely in various plant tissues and organs, and they play an important role in plant reproduction, disease resistance, stress resistance, and protection of human vision. Most fruit anthocyanins can be induced to accumulate by light. Here, we shaded the "Hong Deng" sweet cherry and performed an integrated analysis of its transcriptome and metabolome to explore the role of light in anthocyanin accumulation. The total anthocyanin content of the fruit and two of its anthocyanin components were significantly reduced after the shading. Transcriptome and metabolomics analysis revealed that PAL, 4CL, HCT, ANS and other structural genes of the anthocyanin pathway and cyanidin 3-O-glucoside, cyanidin 3-O-rutinoside, and other metabolites were significantly affected by shading. Weighted total gene network analysis and correlation analysis showed that the upstream and middle structural genes 4CL2, 4CL3, and HCT2 of anthocyanin biosynthesis may be the key genes affecting the anthocyanin content variations in fruits after light shading. Their expression levels may be regulated by transcription factors such as LBD, ERF4, NAC2, NAC3, FKF1, LHY, RVE1, and RVE2. This study revealed for the first time the possible role of LBD, FKF1, and other transcription factors in the light-induced anthocyanin accumulation of sweet cherry, thereby laying a preliminary foundation for further research on the role of light in anthocyanin accumulation of deep red fruit varieties and the genetic breeding of sweet cherry.

Role of Phenylpropanoids and Flavonoids in Plant Defense Mechanism

Phenylpropanoids and flavonoids are specialized metabolites that play a crucial role in plant defenses against biotic and abiotic stresses. Secondary metabolites in plants, such as phenylpropanoids, flavonoids, lignins, monolignols, phenolic acids, stilbenes and coumarins, play a significant role in biotic and abiotic stress responses and interactions with their environment. Under stress-free conditions, flavonoids influence pollen tube growth, seed maturation, dormancy, and the longevity of plant reproductive organs and seeds. Under adverse abiotic conditions, flavonoids can mediate defense responses, such as the accumulation of flavonoids in leaves and glandular trichomes. Metabolomics has identified specialized PPP metabolites correlated with plant resistance to fungi and oomycetes. However, the correlation can be in opposite directions depending on the pathogen and a systemic approach is required to achieve increased resistance without decreasing resistance to another pathogen. The PAL gene is located upstream in the PPP pathway and phenylpropanoids and flavonoids have antifungal activity against Fusarium oxysporum, Rhizoctonia solani and Alternaria alternata. Phenylpropanoids have been studied in vitro to develop biological alternatives to synthetic phytoprotectants but the host's defense system is the most effective mode of action. Post-inoculation transcriptomic shifts reveal that some genes encoding enzymes in the PPP are rapidly activated, while others are induced later in the infection response. Insects are the most problematic macroscopic pests on cultivated plants and plants' natural defense mechanisms against herbivores include releasing volatile organic compounds, attracting enemies and producing phenylpropanoids and flavonoids. Increasing the content of flavonoids in infested plants can reduce the population of insects that cause damage to plants and spread viruses. Plant-environment interaction, mediated by secondary metabolites like phenylpropanoids and flavonoids, leads to diversity in gene structures. Systemic biology approach will be realized through sequencing, structural elucidation, and analytical tools. Model plants and crops can be used for exploration.

Genome-Wide Identification of WRKY Gene Family and Functional Characterization of CcWRKY25 in Capsicum chinense.

Pepper is renowned worldwide for its distinctive spicy flavor. While the gene expression characteristics of the capsaicinoid biosynthesis pathway have been extensively studied, there are already a few reports regarding transcriptional regulation in capsaicin biosynthesis. In this study, 73 WRKYs were identified in the genome of Capsicum chinense, and their physicochemical traits, DNA, and protein sequence characteristics were found to be complex. Combining RNA-seq and qRT-PCR data, the WRKY transcription factor CA06g13580, which was associated with the accumulation tendency of capsaicinoid, was screened and named CcWRKY25. CcWRKY25 was highly expressed in the placenta of spicy peppers. The heterologous expression of CcWRKY25 in Arabidopsis promoted the expression of genes PAL, 4CL1, 4CL2, 4CL3, CCR, and CCoAOMT and led to the accumulation of lignin and flavonoids. Furthermore, the expression of the capsaicinoid biosynthesis pathway genes (CBGs) pAMT, AT3, and KAS was significantly reduced in CcWRKY25-silenced pepper plants, resulting in a decrease in the amount of capsaicin. However, there was no noticeable difference in lignin accumulation. The findings suggested that CcWRKY25 could be involved in regulating capsaicinoid synthesis by promoting the expression of genes upstream of the phenylpropanoid pathway and inhibiting CBGs' expression. Moreover, the results highlighted the role of CcWRKY25 in controlling the pungency of pepper and suggested that the competitive relationship between lignin and capsaicin could also regulate the spiciness of the pepper.

Bioinformatics and Expression Analysis of PAL Gene Family of Poplar Plant under Different Nitrogen Treatments

Phenylalanine ammonia lyase is the crucial enzyme and rate-limiting enzyme in the biosynthesis pathway of phenylpropane. Lignin, phytoalexin and many kinds of active substances produced in this pathway, such as flavonoids and phenols, play a key role in lignification, stress resistance, insect resistance and disease resistance of plant cells. In this study, five PAL gene sequences of Populus simonii × p.nigra were studied, and the basic characteristics of their genes and proteins were analyzed. The tissue expression pattern of PAL gene of Populus simonii × p.nigra were tested by real-time quantitative. PCR under different nitrogen forms and nitrogen concentrations. The results showed that the physicochemical property of five proteins were similar. All the proteins except PtrPAL4 and PtrPAL5 were stained on chromosome 10, PtrPAL1, PtrPAL2 and PtrPAL3 were on chromosome 6, 8 and 16, respectively. The five proteins were mainly distributed in chloroplasts, and the three-level structures of the five proteins were consistent, and they were all homologous tetramers. The evolutionary relationship results show that the PAL gene of poplar is highly homologous to rice and Arabidopsis. When poplar was treated with 0.1 mmol · L-1, 10 mmol · L-1 and 2 mmol · L-1, the relative expression of PAL genes in stem was the highest under low nitrogen level, and was most obviously induced by ammonium nitrogen. Key words: Poplar, PAL gene family, bioinformatics, Stem, Gene expression