A phenylalanine ammonia lyase from Fritillaria unibracteata promotes drought tolerance by regulating lignin biosynthesis and SA signaling pathway

Understanding the ternary interaction of crop plants, fungal pathogens, and rhizobacteria in response to global warming

Climate change is altering the equilibrium of the Earth's biosphere, imposing unpredictable survival dynamics on terrestrial organisms. This includes the intricate interactions between fungal pathogens and crop plants, which are pivotal for global food security. Rising temperatures are expected to exacerbate the prevalence of crop-pathogenic fungi worldwide, yet research on how crops respond to this imminent threat remains limited. Here, we identified predominant potential pathogens and antagonistic bacteria in vegetable fields in Shandong Province, China, revealing the near-ubiquitous presence of Fusarium oxysporum and Bacillus species in sampled soils of cucumber, tomato, chili, and ginger. Through simulated warming experiments within a temperature range of 20-40 °C and an experimental period of 3 days, we investigated the ternary interaction among vegetables and isolated F. oxysporum strain 05, and Bacillus sp. strain 31. Elevated temperatures enhanced F. oxysporum biomass and virulence, yet also stimulated vegetables to allocate more nutrients via root exudates. This enriched rhizospheric antagonistic Bacillus populations, it also boosted the expression of antifungal lipopeptide biosynthetic genes (bamb and ItuA) and auxin production in Bacillus sp. strain 31. This enrichment promoted plant growth and maintained a relatively stable level of pathogenic fungi. Our study unveiled a nuanced and complex interplay among crop plants, fungal pathogens, and rhizobacteria, that could inform future agricultural practices, and advance our understanding of crop survival strategies to bolster crop resilience and safeguard global food security under ongoing climate change.

Modulation of morphogenesis and metabolism by plant cell biomechanics: from model plants to traditional herbs

The quality of traditional herbs depends on organ morphogenesis and the accumulation of active pharmaceutical ingredients. While recent research highlights the significance of cell mechanobiology in model plant morphogenesis, our understanding of mechanical signal initiation and transduction in traditional herbs remains incomplete. Recent studies reveal a close correlation between cell wall (CW) biosynthesis and active ingredient production, yet the role of cell mechanics in balancing morphogenesis and secondary metabolism is often overlooked. This review explores how the cell wall, plasma membrane, cytoskeleton, and vacuole collaborate to regulate cell mechanics and respond to mechanical changes. We propose CW biosynthesis as a hub in connecting cell mechanics with secondary metabolism and emphasize that understanding the relationship between mechanical remodeling and secondary metabolism could provide new insights into plant cell mechanobiology and the breeding of high-quality herbs.

NAC transcription factors as biological macromolecules responded to abiotic stress: A comprehensive review

NAC transcription factors (NAC TFs) represent a large and vital family of transcription factors in the plant kingdom, playing a central role in regulating plant growth, developmental processes, and responses to abiotic stresses. As key regulators, NAC TFs fine-tune the expression of downstream genes, thereby actively contributing to the adaptation of crops to various abiotic stresses. The functions of NAC TFs are controlled by several complex signaling pathways, including those involving phytohormones (such as abscisic acid (ABA) and ethylene (ET)), reactive oxygen species (ROS), and mitogen-activated protein kinases (MAPKs). This review highlights recent advances in the biological functions and signaling pathways of NAC TFs in crops under abiotic stress conditions, such as drought, salinity, and extreme temperatures. It also offers prospects for further exploration of the complex mechanisms by which NAC TFs operate within signaling networks, with the aim of developing food crops with enhanced physiological traits.

Transcriptome analyses for revealing leaf abscission of Cyclocarya paliurus stem segments in vitro

Leaf abscission of Cyclocarya paliurus stem segments in vitro is very serious, and more than 90% of the leaves gradually fall off with prolonged culture time, which hinders breeding. This study investigated the molecular mechanism of leaf abscission. The emerged leaves of C. paliurus stem segments were cultured for 22 days (T0) in vitro; leaves at 27 days (T1) and leaves that had fallen after ≥ 32 days (T2) were used as materials for analysis of the physiological characteristics and transcriptome data. During the leaf abscission process of C. paliurus, the Indole-3-acetic acid (IAA) content gradually decreased, whereas the carotenoid, 1-aminocyclopropane-1-carboxylic acid (ACC) and lignin contents and pectinase and cellulase activities significantly increased; 1807 and 10,908 DEGs were obtained in T0 vs T1 and T1 vs T2, respectively. The plant hormone signal transduction pathway, phenylpropanoid biosynthesis pathway and flavonoid biosynthesis pathway were significantly enriched in the KEGG metabolic pathway analysis. The differential expression of related genes affected AUX and Ethylene (ETH) biosynthesis and signal transduction, lignin synthesis, ROS metabolism, leaf color changes. Weighted gene coexpression network analysis (WGCNA) identified 10 hub genes (U-box protein, ERF5, ERF109, ERF4, SAUR36, CML19, MYC2-like,SPHK1, TOE3, POD55) that interact to activate abscission signaling, which subsequently influences the genes expression involved in the biosynthesis and signal transduction of auxin and ethylene; this resulted in an imbalance of endogenous hormone levels in the leaves, leading to the upregulation of pectinase, cellulase, and lignin biosynthesis genes and acceleration of the rupture of the abscission zone (AZ) cell and vascular cell wall, which ultimately led to leaf abscission. The present study illustrates a regulatory mechanism of leaf abscission of C. paliurus stem segments in vitro, which provides potential application value for guiding the inhibition of leaf abscission in vitro.

BcVQ11A-BcWRKY23-BcWRKY25 Module Is Involved in Thermotolerance by Regulating Phenylalanine Ammonia-Lyase Activity in Non-Heading Chinese Cabbage

High temperature can significantly affect the quality and yield of plants. However, there has been limited research investigating the thermotolerance of non-heading Chinese cabbage (NHCC). This study, identified BcWRKY23 through transcriptome analysis in NHCC with varying levels of thermotolerance. Overexpression and silencing experiments demonstrated that BcWRKY23 positively regulates the thermotolerance of NHCC by activating its own expression under short-term heat stress (HS). Additionally, BcWRKY23 was found to bind to the promoter of BcWRKY25 and activate its expression, which also enhanced thermotolerance. BcWRKY23 and BcWRKY25 enhanced the expression of HSR genes to improve thermotolerance. Furthermore, BcPAL1 was shown to be activated by BcWRKY23, while BcPAL2 was activated by both BcWRKY23 and BcWRKY25. Overexpression of BcPAL1 and BcPAL2 in NHCC significantly increased thermotolerance, accompanied by an enhancement of phenylalanine ammonia-lyase (PAL) activity. Moreover, under long-term HS, the significant accumulation of BcVQ11A was observed, and the interaction between BcVQ11A and BcWRKY23 as well as BcWRKY25 inhibited the activation of them to target genes, resulting in decreased PAL activity. This study proposes a HS response pathway involving BcVQ11A-BcWRKY23-BcWRKY25-BcPAL1/BcPAL2, providing valuable insights into the molecular mechanisms underlying thermotolerance in plants.

Ornithine enantiomers modulate essential oil yield and constituents and gene expression of monoterpenes synthase in Salvia officinalis under well-watered and drought stress conditions

The impact of drought stress on plant growth, development, and productivity presents a significant challenge in various environments worldwide. The exogenous application of polyamines as osmotically active materials plays a crucial role in enhancing plant tolerance to environmental stress. In this study, we examined the effects of L- and D-enantiomers of ornithine (0 and 1 mM) under both well-watered and drought stress conditions on the growth traits, essential oil (EO) yield, and composition, gene expression, and total phenolic and flavonoid content of Salvia officinalis. The experiment was designed as a factorial experiment using a completely randomized design with three replications. The results demonstrated that drought stress led to a decrease in plant biomass and an increase in EO content, chemical profiles of the EO, and total phenolic and flavonoid content compared to the respective control values. However, the exogenous supplementation of ornithine particularly D-ornithine resulted in enhanced stem, leaf, and total plant biomass, a 20% increase in EO content, and a 75% increase in yield. Additionally, these were increases of 11.76% in total phenol and 70%, 105.66%, and 114.28% in flavonoid content when compared to well-watered plants without ornithine supplementation. These improvements were strongly linked to growth enhancement, as evidenced by principal component analysis (PCA). The EO extracted from S. officinalis consisted of 22 compounds, primarily monoterpenes, including α-thujone (18.47-41.65%), camphor (15.05-25.17%), 1,8-cineole (10.12-21.6%), and β-thujone (6.23-21.2%). The percentage of these volatile compounds was found to be highest in D-ornithine-treated stressed plants compared to control conditions. The interaction between water availability and the application of D-ornithine and L-ornithine significantly influenced the expression of borneol diphosphate synthase (BS), sabinene synthase (SS), and cineole synthase (CS) under drought stress, with notable upregulation observed compared to normal growth conditions. Specifically, D-ornithine enhanced the expression of BS and SS by 45.29% and 113.63%, respectively, under drought stress, while both D-ornithine and DL-ornithine significantly increased CS expression. The present results suggest that D-ornithine may serve as a stress-protecting compound, increasing total phenol and flavonoids content, thereby enhancing the capacity of the antioxidant system and increasing EO compounds under drought stress.

Physiological and metabolome characterization of Amaranthus hybridus L. grown under cypermethrin stress: an insight of Jasmonic acid treatment

The indiscriminate use of pesticides compromises physiology and metabolism in crops, posing health risks through residue accumulation in edible tissues. Amaranthus hybridus L., a fast growing, nutritionally and medicinally valuable crop was studied here to assess the impact of cypermethrin (CYP) at recommended (R1, 100 ppm) and double dose (R2, 200 ppm) alongside foliar application of jasmonic acid (JA) at 50 µM, 100 µM, and 200 µM concentrations. CYP at R1 dose induced hormesis, while R2 was toxic, elevating the production of ROS molecules (H2O2, SOR, MDA). JA application upregulated the antioxidant activity of SOD, POD, APX, GST, DHAR, GSH, and proline to alleviate oxidative stress and improve growth indicators, including shoot length, leaf area, chlorophyll content, Fv/Fm ratio, and biomass. JA at 100 µM yielded the highest increase in biomass, 11.52% and 13.7% for R1 and R2 treated plants, respectively and also led to reduced accumulation of CYP residues. The UHPLC-MS analysis of leaf tissue revealed increase in the contents of carotenoids, flavonoids, phenolics, phenylpropanoids, steroids content in the plant group combinedly treated with JA and CYP compared to those treated with CYP alone, indicating a protective and growth-promoting role of JA under pesticide stress conditions. Overall, 100 µM concentration of JA proved to be effective against the stress induced by the either dose of CYP in the study. These insights could offer strategies to reduce pesticide-induced damage in vegetable crops, advancing sustainable agriculture.

Identification and characteristics of differentially expressed genes under UV-B stress in Gossypium hirsutum

Objective

This study aimed to screen the differentially expressed genes (DEGs) of Gossypium hirsutum under UV-B stress and identify the significant pathways based on gene enrichment analysis results.

Methods

In this study, the allotetraploid crop G. hirsutum was used to examine changes in various physiological indexes under UV-B stress, and screened out all DEGs under UV-B stress (16 kJ m-2 d-1) based on six leaf transcriptomes. The main enrichment pathways of DEGs were analyzed according to gene annotation. Finally, we predicted the regulatory genes of phenylpropanoid pathway under UV-B stress by co-expression network analysis, and selected GhMYB4 for verification.

Results

Gene annotation analysis revealed that DEGs were predominantly enriched in pathways related to photosynthesis and secondary metabolism. Further analysis revealed that UV-B stress impaired photosynthesis mainly by damaging photosystem II (PSII) and inhibiting electron transport, whereas G. hirsutum responded to UV-B stress by synthesizing secondary metabolites such as anthocyanins and lignin. We selected the regulatory genes GhMYB4 for verification. It was found to be an anthocyanin negative regulator in response to UV-B stress.

Conclusions

UV-B stress impaired photosynthesis mainly by damaging photosystem II (PSII) and inhibiting electron transport, whereas G. hirsutum responded to UV-B stress by synthesizing secondary metabolites such as anthocyanins and lignin.

Spermidine-induced improvements in water relations and antioxidant defense enhance drought tolerance in yarrow (Achillea millefolium L.)

Drought stress poses a serious threat to agricultural productivity worldwide. This study investigated the mitigative effects of exogenous spermidine on drought stressed yarrow (Achillea millefolium L.). Plants were subjected to three drought levels (25 %, 50 % and 75 % field capacity) and foliar sprayed with 0, 1.5 and 3 μM spermidine. Drought significantly reduced relative water content, photosynthetic pigments (chlorophyll, carotenoids), osmolyte (proline, soluble sugars) accumulation and antioxidant enzyme activities such as catalase (CAT), peroxidase (POD) and ascorbate peroxidase (APX), indicating oxidative damage. Spermidine treatment attenuated drought injury by improving the above parameters. Maximum responses were observed at 1.5 μM for photosynthetic pigments and osmolytes, while 3 μM performed best for secondary metabolites (phenolics, flavonoids, anthocyanins) and antioxidant enzymes. Drought also upregulated secondary metabolites like phenolics, while spermidine further augmented their levels. Moreover, spermidine maintained membrane integrity and osmotic adjustment under water deficit. Overall, spermidine enhanced yarrow's drought tolerance by modulating physiological and biochemical processes. Our findings provide insights into spermidine-induced adaptation mechanisms in plants combating water scarcity. Optimization of spermidine concentration may help develop drought-resilient crops.

A hierarchical ubiquitination-mediated regulatory module controls bamboo lignin biosynthesis

The lignocellulosic feedstock of woody bamboo shows promising potential as an alternative to conventional wood, attributed to its excellent properties. The content and distribution of lignin serve as the foundation of these properties. While the regulation of lignin biosynthesis in bamboo has been extensively studied at the transcriptional level, its posttranslational control has remained poorly understood. This study provides a ubiquitinome dataset for moso bamboo (Phyllostachys edulis), identifying 13,015 ubiquitinated sites in 4,849 unique proteins. We further identified Kelch repeat F-box protein 9 (PeKFB9) that plays a negative role in lignin biosynthesis. Heterologous expression of PeKFB9 resulted in reduced accumulation of lignin and decreased phenylalanine ammonia lyase (PAL) activities. Both in vitro and in vivo assays identified interaction between PeKFB9 and PePAL10. Further examination revealed that SCFPeKFB9 mediated the ubiquitination and degradation of PePAL10 via the 26S proteasome pathway. Moreover, PebZIP28667 could bind to the PePAL10 promoter to significantly inhibit its transcription, and ubiquitination of PebZIP28667 weakened this inhibition. Collectively, our findings reveal a PeKFB9-PePAL10/PebZIP28667-PePAL10 module that acts as a negative regulator of lignin biosynthesis. This study advances our understanding of posttranslational regulation in plant lignification, which will facilitate the improvement of the properties of bamboo wood and the breeding of varieties.

Antifungal mechanisms and characteristics of Pseudomonas fluorescens: Promoting peanut growth and combating Fusarium oxysporum-induced root rot

Continuous cropping of peanuts presents significant challenges to sustainable production due to soil-borne diseases like root rot caused by Fusarium species. In this study, field inoculation experiments treatments and in vitro agar plate confrontation tests were conducted, including non-inoculated controls (CK), inoculation with Pseudomonas fluorescens (PF), Fusarium oxysporum (FO), and co-inoculation with both (PF + FO). The aim was to explore the antifungal mechanisms of Pseudomonas fluorescens in mitigating root rot and enhancing peanut yield. The results indicated that PF and PF + FO significantly enhanced peanut root activity, as well as superoxide dismutase, catalase, and glutathione S-transferase activities, while simultaneously decreasing the accumulation of reactive oxygen species and malondialdehyde contents, compared to FO treatment. Additionally, PF treatment notably increased lignin content through enhanced phenylalanine ammonia lyase, cinnamate 3-hydroxylase, and peroxidase activity compared to CK and FO treatment. Moreover, PF treatment resulted in longer roots and a higher average diameter and surface area, potentially due to increased endogenous levels of auxin and zeatin riboside, coupled with decreased abscisic acid content. PF treatment significantly elevated chlorophyll content and the maximum photochemical efficiency of PSII in the light-adapted state, the actual photochemical efficiency and the proportion of PSII reaction centers open, leading to improved photosynthetic performance. Confrontation culture assays revealed PF's notable inhibitory effects on Fusarium oxysporum growth, subsequently reducing rot disease incidence in the field. Ultimately, PF treatment led to increased peanut yield by enhancing plant numbers and pod weight compared to FO treatment, indicating its potential in mitigating Fusarium oxysporum-induced root rot disease under continuous cropping systems.

A GhLac1-centered transcriptional regulatory cascade mediates cotton resistance to Verticillium dahliae through the lignin biosynthesis pathway

The lignin biosynthesis pathway plays a crucial role in the defense response against V. dahliae in cotton, and it is essential to identify the key regulators in this pathway for disease-resistant breeding. In a previous study, the cotton laccase gene GhLac1 was identified as mediating plant broad-spectrum biotic stress tolerance by manipulating phenylpropanoid metabolism. However, the upstream master regulators and regulatory mechanism of lignin are still largely unknown. This study aims to identify the upstream regulators of GhLac1 and explore the molecular mechanism underlying cotton's disease resistance response to V. dahliae. Through the study, three WRKY, three MYB, and one APETALA2/ETHYLENE RESPONSIVE FACTOR (ERF) TFs were identified as differentially responding to V. dahliae infection in cotton. Among these TFs, GhWRKY30, GhWRKY41, GhMYB42, and GhTINY2 were found to directly bind to the GhLac1 promoter and activate its expression. Transient overexpression of these four TFs in cotton led to increased expression of GhLac1 and other the laccase family members, while knockdown of these TFs resulted in reduced lignin accumulation and increased susceptibility to V. dahliae. Additionally, GhWRKY30 and GhWRKY41 were observed to interact with themselves and with each other, synergistically transactivating the GhLac1 promoter. This study reveals a GhLac1-centered transcriptional regulatory cascade of lignin synthesis that contributes to cotton's defense response by modulating lignin metabolism.

Genome-wide identification of AP2/ERF gene family in Coptis Chinensis Franch reveals its role in tissue-specific accumulation of benzylisoquinoline alkaloids

BACKGROUND

The Plant-specific AP2/ERF gene family encodes proteins involved in various biological and physiological processes. Although the genome of Coptis chinensis Franch, a plant producing benzylisoquinoline alkaloids (BIAs), has been sequenced at the chromosome level, studies on the AP2/ERF gene family in C. chinensis are lacking. Thus, a genome-wide identification of AP2/ERF gene family in C. chinensis was conducted to explore its role in BIAs biosynthesis.

RESULTS

A total of 96 CcAP2/ERF genes were identified and categorized into five subfamilies, including 43 ERFs, 32 DREBs, 17 AP2s, 3 RAVs, and 1 Soloist, based on their structural domains. These CcAP2/ERF genes were unevenly distributed across nine chromosomes. Analysis of gene duplication events identified 17 CcAP2/ERF gene pairs in the genome, with 7 involved in tandem duplication events and 10 involved in segmental duplicate events, indicating that both types of duplications contributed to the expansion of the AP2/ERF gene family. The Ka/Ks ratio analysis suggested that the CcAP2/ERF gene family underwent strong purifying selection. Two phytohormones, methyl jasmonate and abscisic acid, were identified as potential key inducers of BIAs biosynthesis due to the cis-acting element prediction. Analysis of the spatial transcriptomic data revealed that 28 differentially expressed AP2/ERF genes had the highest or relatively higher expression levels in the rhizome, 17 of which positively correlated with the tissue-specific accumulation of BIAs. Further real-time PCR verification and protein-protein interaction analysis indicated that DREB1B might be one of the central regulators in a highly complex BIAs biosynthesis network.

CONCLUSION

These findings provide significant insight into the function of AP2/ERF genes in C. chinensis, particularly in the regulatory network of BIAs biosynthesis in C. chinensis. This study also identifies candidate genes for metabolic engineering to increase BIAs content in C. chinensis.

Caffeic acid O-methyltransferase from Ligusticum chuanxiong alleviates drought stress, and improves lignin and melatonin biosynthesis

Drought stress is a major constraint on plant growth and agricultural productivity. Caffeic acid O-methyltransferase (COMT), an enzyme involved in the methylation of various substrates, plays a pivotal role in plant responses to abiotic stress. The involvement of COMTs in drought response, particularly through the enhancement of lignin and melatonin biosynthesis, remains poorly understood. In this study, LcCOMT was firstly proposed to be associated with the biosynthesis of both lignin and melatonin, as demonstrated through sequence comparison, phylogenetic analysis, and conserved motif identification. In vitro enzymatic assays revealed that LcCOMT effectively methylates N-acetylserotonin to melatonin, albeit with a higher Km value compared to caffeic acid. Site-directed mutagenesis of residues Phe171 and Asp269 resulted in a significant reduction in catalytic activity for caffeic acid, with minimal impact on N-acetylserotonin, underscoring the specificity of these residues in substrate binding and catalysis. Under drought conditions, LcCOMT expression was significantly upregulated. Overexpression of LcCOMT gene in Arabidopsis plants conferred enhanced drought tolerance, characterized by elevated lignin and melatonin levels, increased chlorophyll and carotenoid content, heightened activities of antioxidant enzymes peroxidase (POD), catalase (CAT), and superoxide dismutase (SOD), and reduced malondialdehyde (MDA) and hydrogen peroxide (H2O2) accumulation. This study is among the few to demonstrate that COMT-mediated drought tolerance is achieved through the simultaneous promotion of lignin and melatonin biosynthesis. LcCOMT represents the first functionally characterized COMT in Apiaceae family, and it holds potential as a target for genetic enhancement of drought tolerance in future crop improvement strategies.

Enzymatic Characterization of SpPAL Genes in S. polyrhiza and Overexpression of the SpPAL3

Phenylalanine ammonia-lyase (PAL, EC 4.3.1.5) catalyzes the deamination of phenylalanine, which is the initial step in the biosynthesis of phenylpropanoids. It serves as a crucial enzyme that facilitates the transfer of carbon from primary to secondary metabolism in plants. Duckweed is regarded as a promising chassis plant in synthetic biology research and application, due to its being rich in secondary metabolites and other advantages. The genes encoding PAL in Spirodela polyrhiza (L.) Schleid, the giant duckweed, were investigated in this study. Three SpPAL genes (SpPAL1-SpPAL3) were identified and cloned. All of them were successfully expressed in E. coli, and their recombinant proteins all showed PAL activity. In addition, SpPAL1 and SpPAL2 proteins could also utilize tyrosine as substrate, although the activity was low. A qRT-PCR analysis demonstrated that the expression of SpPAL3 was most pronounced in young fronds. It was found that the expression of SpPAL1 and SpPAL3 was significantly induced by MeJA treatment. Overexpression of SpPAL3 in Lemna turionifera inhibited the growth of fronds and adventitious roots in the transgenic plants, indicating the importance of SpPAL3 in duckweed besides its involvement in the secondary metabolism.

Transcriptomic responses of 'Huping jujube' (Zizyphus jujuba mill. cv. Huping) fruit to combined treatment of acidic electrolyzed water and high-voltage electrostatic field

The molecular mechanism underlying the preserving superior quality attributes of postharvest Huping jujube fruit by combining acidic electrolyzed water and high-voltage electrostatic field (AH) treatment remained unclear. The high-throughput sequencing analysis revealed a total of 3590 common differentially expressed genes (DEGs) in the T-W-CK0 vs T-W-CK75 and T-W-CK75 vs T-W-AH75 groups. AH treatment down-regulated most genes associated with respiratory metabolism, as well as lignin and anthocyanin biosynthesis, thereby maintaining lower physiological activities, improving taste and color quality of mature-white jujube. Additionally, AH treatment downregulated the genes involved in reactive oxygen species (ROS) generation and disease resistance, while simultaneously upregulating the genes associated with ROS elimination. This suggested that AH treatment could inhibit pathogen infection to prevent the activation of plants' active defense and reduce the ROS-induced damage. In sum, the present study provided a comprehension explanation that AH treatment improved the storage quality attributes of jujube fruit at the genetic level.

Effects of melatonin on inhibiting quality deterioration of postharvest water bamboo shoots

Water bamboo shoots (Zizania latifolia) is prone to quality deterioration during cold storage after harvest, which causes the decline of commodity value. Chlorophyll synthesis and lignin deposition are the major reasons for quality degradation. This paper studied the influence of exogenous melatonin (MT) on the cold storage quality of water bamboo shoots. MT treatment could delay the increase in skin browning, hardness and weight loss rate, inhibit chlorophyll synthesis and color change of water bamboo shoots, while maintain the content of total phenols and flavonoids, and inhibit lignin deposition by inhibiting the activity and gene expression of phenylpropanoid metabolism related enzymes as PAL, C4H, 4CL, CAD, and POD. The results indicate that exogenous MT treatment can effectively inhibit the quality degradation of cold stored water bamboo shoots.

Multifaceted insights into the environmental adaptability of Arnebia guttata under drought stress

Introduction

Global warming has led to increased environmental stresses on plants, notably drought. This affects plant distribution and species adaptability, with some medicinal plants showing enhanced drought tolerance and increased medicinal components. In this pioneering study, we delve into the intricate tapestry of Arnebia guttata, a medicinal plant renowned for its resilience in arid environments. By fusing a rich historical narrative with cutting-edge analytical methodologies, this research endeavors to demystify the plant's intricate response to drought stress, illuminating its profound implications for medicinal valorization.

Methods

The methodology includes a comprehensive textual research and resource investigation of A. guttata, regionalization studies, field sample distribution analysis, transcriptome and metabolome profiling, rhizosphere soil microbiome analysis, and drought stress experiments. Advanced computational tools like ArcGIS, MaxEnt, and various bioinformatics software were utilized for data analysis and modeling.

Results

The study identified significant genetic variations among A. guttata samples from different regions, correlating with environmental factors, particularly precipitation during the warmest quarter (BIO18). Metabolomic analysis revealed marked differences in metabolite profiles, including shikonin content, which is crucial for the plant's medicinal properties. Soil microbial community analysis showed variations that could impact plant metabolism and stress response. Drought stress experiments demonstrated A. guttata's resilience and its ability to modulate metabolic pathways to enhance drought tolerance.

Discussion

The findings underscore the complex interplay between genetic makeup, environmental factors, and microbial communities in shaping A. guttata's adaptability and medicinal value. The study provides insights into how drought stress influences the synthesis of active compounds and suggests that moderate stress could enhance the plant's medicinal properties. Predictive modeling indicates future suitable growth areas for A. guttata, aiding in resource management and conservation efforts. The research contributes to the sustainable development of medicinal resources and offers strategies for improving the cultivation of A. guttata.

Genome-Wide Identification and Expression Profile Analysis of the Phenylalanine Ammonia-Lyase Gene Family in Hevea brasiliensis

The majority of the world's natural rubber comes from the rubber tree (Hevea brasiliensis). As a key enzyme for synthesizing phenylpropanoid compounds, phenylalanine ammonia-lyase (PAL) has a critical role in plant satisfactory growth and environmental adaptation. To clarify the characteristics of rubber tree PAL family genes, a genome-wide characterization of rubber tree PALs was conducted in this study. Eight PAL genes (HbPAL1-HbPAL8), which spread over chromosomes 3, 7, 8, 10, 12, 13, 14, 16, and 18, were found to be present in the genome of H. brasiliensis. Phylogenetic analysis classified HbPALs into groups I and II, and the group I HbPALs (HbPAL1-HbPAL6) displayed similar conserved motif compositions and gene architectures. Tissue expression patterns of HbPALs quantified by quantitative real-time PCR (qPCR) proved that distinct HbPALs exhibited varying tissue expression patterns. The HbPAL promoters contained a plethora of cis-acting elements that responded to hormones and stress, and the qPCR analysis demonstrated that abiotic stressors like cold, drought, salt, and H2O2-induced oxidative stress, as well as hormones like salicylic acid, abscisic acid, ethylene, and methyl jasmonate, controlled the expression of HbPALs. The majority of HbPALs were also regulated by powdery mildew, anthracnose, and Corynespora leaf fall disease infection. In addition, HbPAL1, HbPAL4, and HbPAL7 were significantly up-regulated in the bark of tapping panel dryness rubber trees relative to that of healthy trees. Our results provide a thorough comprehension of the characteristics of HbPAL genes and set the groundwork for further investigation of the biological functions of HbPALs in rubber trees.

Identification and characterization of PAL genes involved in the regulation of stem development in Saccharum spontaneum L

BACKGROUND

Saccharum spontaneum L. is a closely related species of sugarcane and has become an important genetic component of modern sugarcane cultivars. Stem development is one of the important factors for affecting the yield, while the molecular mechanism of stem development remains poorly understanding in S. spontaneum. Phenylalanine ammonia-lyase (PAL) is a vital component of both primary and secondary metabolism, contributing significantly to plant growth, development and stress defense. However, the current knowledge about PAL genes in S. spontaneum is still limited. Thus, identification and characterization of the PAL genes by transcriptome analysis will provide a theoretical basis for further investigation of the function of PAL gene in sugarcane.

RESULTS

In this study, 42 of PAL genes were identified, including 26 SsPAL genes from S. spontaneum, 8 ShPAL genes from sugarcane cultivar R570, and 8 SbPAL genes from sorghum. Phylogenetic analysis showed that SsPAL genes were divided into three groups, potentially influenced by long-term natural selection. Notably, 20 SsPAL genes were existed on chromosomes 4 and 5, indicating that they are highly conserved in S. spontaneum. This conservation is likely a result of the prevalence of whole-genome replications within this gene family. The upstream sequence of PAL genes were found to contain conserved cis-acting elements such as G-box and SP1, GT1-motif and CAT-box, which collectively regulate the growth and development of S. spontaneum. Furthermore, quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis showed that SsPAL genes of stem had a significantly upregulated than that of leaves, suggesting that they may promote the stem growth and development, particularly in the + 6 stem (The sixth cane stalk from the top to down) during the growth stage.

CONCLUSIONS

The results of this study revealed the molecular characteristics of SsPAL genes and indicated that they may play a vital role in stem growth and development of S. spontaneum. Altogether, our findings will promote the understanding of the molecular mechanism of S. spontaneum stem development, and also contribute to the sugarcane genetic improving.

Blue light regulated lignin and cellulose content of soybean petioles and stems under low light intensity

To improve light harvest and plant structural support under low light intensity, it is useful to investigate the effects of different ratios of blue light on petiole and stem growth. Two true leaves of soybean seedlings were exposed to a total light intensity of 200μmolm-2 s-1 , presented as either white light or three levels of blue light (40μmolm-2 s-1 , 67μmolm-2 s-1 and 100μmolm-2 s-1 ) for 15days. Soybean petioles under the low blue light treatment upregulated expression of genes relating to lignin metabolism, enhancing lignin content compared with the white light treatment. The low blue light treatment had high petiole length, increased plant height and improved petiole strength arising from high lignin content, thus significantly increasing leaf dry weight relative to the white light treatment. Compared with white light, the treatment with the highest blue light ratio reduced plant height and enhanced plant support through increased cellulose and hemicellulose content in the stem. Under low light intensity, 20% blue light enhanced petiole length and strength to improve photosynthate biomass; whereas 50% blue light lowered plants' centre of gravity, preventing lodging and conserving carbohydrate allocation.

Systematic Analysis of the MIO-forming Residues of Aromatic Ammonia Lyases

Aromatic ammonia lyases (AALs) and tyrosine/phenylalanine ammonia mutases (TAM/PAM) are 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO)-dependent enzymes. Usually, the MIO moiety is autocatalytically formed from the tripeptide Ala-Ser-Gly (ASG) and acts as an electrophile during the enzymatic reaction. However, the MIO-forming residues (ASG) have some diversity in this enzyme class. In this work, a systematic investigation on the variety of MIO-forming residues was carried out using in-depth sequence analyses. Several protein clusters of AAL-like enzymes with unusual MIO-forming residues such as ACG, TSG, SSG, and CSG were identified, including two novel histidine ammonia lyases and one PAM with CSG and TSG residues, respectively, as well as three novel ergothioneine trimethylammonia lyases without MIO motif. The mutagenesis of common MIO-groups confirmed the function of these MIO variants, which provides good starting points for future functional prediction and mutagenesis research of AALs.

Bioinformatic Analysis of Codon Usage Bias of HSP20 Genes in Four Cruciferous Species

Heat shock protein 20 (HSP20) serves as a chaperone and plays roles in numerous biological processes, but the codon usage bias (CUB) of its genes has remained unexplored. This study identified 140 HSP20 genes from four cruciferous species, Arabidopsis thaliana, Brassica napus, Brassica rapa, and Camelina sativa, that were identified from the Ensembl plants database, and we subsequently investigated their CUB. As a result, the base composition analysis revealed that the overall GC content of HSP20 genes was below 50%. The overall GC content significantly correlated with the constituents at three codon positions, implying that both mutation pressure and natural selection might contribute to the CUB. The relatively high ENc values suggested that the CUB of the HSP20 genes in four cruciferous species was relatively weak. Subsequently, ENc exhibited a negative correlation with gene expression levels. Analyses, including ENc-plot analysis, neutral analysis, and PR2 bias, revealed that natural selection mainly shaped the CUB patterns of HSP20 genes in these species. In addition, a total of 12 optimal codons (ΔRSCU > 0.08 and RSCU > 1) were identified across the four species. A neighbor-joining phylogenetic analysis based on coding sequences (CDS) showed that the 140 HSP20 genes were strictly and distinctly clustered into 12 subfamilies. Principal component analysis and cluster analysis based on relative synonymous codon usage (RSCU) values supported the fact that the CUB pattern was consistent with the genetic relationship at the gene level and (or) species levels. These results will not only enrich the HSP20 gene resource but also advance our understanding of the CUB of HSP20 genes, which may underlie the theoretical basis for exploration of their genetic and evolutionary pattern.

Molecular mechanism overview of metabolite biosynthesis in medicinal plants

Medicinal plants are essential and rich resources for plant-based medicines and new drugs. Increasing attentions are paid to the secondary metabolites of medicinal plants due to their unique biological activity, pharmacological action, and high utilization value. However, the development of medicinal plants is constrained by limited natural resources and an unclear understanding of the mechanisms underlying active medicinal ingredients, thereby rendering the utilization and exploration of secondary metabolites more challenging. Besides, with the advancement of research on biosynthesis and molecular metabolism of natural products from medicinal plants, the methods for studying the biological activity and pharmacological effects of these products are constantly evolving. In recent years, significant progress has been made in the biosynthetic pathways and related regulatory genes of secondary metabolites in medicinal plants, which has greatly advanced both basic research and the development of clinical applications for medicinal plants. In this review, we discuss the past two decades of international research on the development of medicinal plant resources, mainly focusing on the biosynthetic pathway of secondary metabolites, intracellular signal transduction processes, multi-omics applications, and the application of gene editing technology in related research progress. We also discuss future development trends to promote the deep mining and development of natural products from medicinal plants, providing a useful reference.

Comprehensive physiological, transcriptomic, and metabolomic analysis of the key metabolic pathways in millet seedling adaptation to drought stress

Drought is one of the leading environmental constraints that affect the growth and development of plants and, ultimately, their yield and quality. Foxtail millet (Setaria italica) is a natural stress-resistant plant and an ideal model for studying plant drought resistance. In this study, two varieties of foxtail millet with different levels of drought resistance were used as the experimental material. The soil weighing method was used to simulate drought stress, and the differences in growth, photosynthetic physiology, metabolite metabolism, and gene transcriptional expression under drought stress were compared and analyzed. We aimed to determine the physiological and key metabolic regulation pathways of the drought-tolerant millet in resistance to drought stress. The results showed that drought-tolerant millet exhibited relatively stable growth and photosynthetic parameters under drought stress while maintaining a relatively stable level of photosynthetic pigments. The metabolomic, transcriptomic, and gene co-expression network analysis confirmed that the key to adaptation to drought by millet was to enhance lignin metabolism, promote the metabolism of fatty acids to be transformed into cutin and wax, and improve ascorbic acid circulation. These findings provided new insights into the metabolic regulatory network of millet adaptation to drought stress.

Biomod2 modeling for predicting the potential ecological distribution of three Fritillaria species under climate change

The Fritillaria species ranked as a well-known traditional medicine in China and has become rare due to excessive harvesting. To find reasonable strategy for conservation and cultivation, identification of new ecological distribution of Fritillaria species together with prediction of those responses to climate change are necessary. In terms of current occurrence records and bioclimatic variables, the suitable habitats for Fritillaria delavayi, Fritillaria taipaiensis, and Fritillaria wabuensis were predicted. In comparison with Maxent and GARP, Biomod2 obtained the best AUC, KAPPA and TSS values of larger than 0.926 and was chosen to construct model. Temperature seasonality was indicated to put the greatest influence on Fritillaria taipaiensis and Fritillaria wabuensis, while isothermality was of most importance for Fritillaria delavayi. The current suitable areas for three Fritillaria species were distributed in south-west China, accounting for approximately 17.72%, 23.06% and 20.60% of China's total area, respectively. During 2021-2100 period, the suitable habitats of F. delavayi and F. wabuensis reached the maximum under SSP585 scenario, while that of F. taipaiensis reached the maximum under SSP126 scenario. The high niche overlap among three Fritillaria species showed correlation with the chemical composition (P ≤ 0.05), while no correlation was observed between niche overlap and DNA barcodes, indicating that spatial distribution had a major influence on chemical composition in the Fritillaria species. Finally, the acquisition of species-specific habitats would contribute to decrease in habitat competition, and future conservation and cultivation of Fritillaria species.

The power of magnesium: unlocking the potential for increased yield, quality, and stress tolerance of horticultural crops

Magnesium (Mg2+) is pivotal for the vitality, yield, and quality of horticultural crops. Central to plant physiology, Mg2+ powers photosynthesis as an integral component of chlorophyll, bolstering growth and biomass accumulation. Beyond basic growth, it critically affects crop quality factors, from chlorophyll synthesis to taste, texture, and shelf life. However, Mg2 + deficiency can cripple yields and impede plant development. Magnesium Transporters (MGTs) orchestrate Mg2+ dynamics, with notable variations observed in horticultural species such as Cucumis sativus, Citrullus lanatus, and Citrus sinensis. Furthermore, Mg2+ is key in fortifying plants against environmental stressors and diseases by reinforcing cell walls and spurring the synthesis of defense substances. A burgeoning area of research is the application of magnesium oxide nanoparticles (MgO-NPs), which, owing to their nanoscale size and high reactivity, optimize nutrient uptake, and enhance plant growth and stress resilience. Concurrently, modern breeding techniques provide insights into Mg2+ dynamics to develop crops with improved Mg2+ efficiency and resilience to deficiency. Effective Mg2+ management through soil tests, balanced fertilization, and pH adjustments holds promise for maximizing crop health, productivity, and sustainability. This review unravels the nuanced intricacies of Mg2+ in plant physiology and genetics, and its interplay with external factors, serving as a cornerstone for those keen on harnessing its potential for horticultural excellence.

Differential roles of Cassia tora 1-deoxy-D-xylulose-5-phosphate synthase and 1-deoxy-D-xylulose-5-phosphate reductoisomerase in trade-off between plant growth and drought tolerance

Due to global climate change, drought is emerging as a major threat to plant growth and agricultural productivity. Abscisic acid (ABA) has been implicated in plant drought tolerance, however, its retarding effects on plant growth cannot be ignored. The reactions catalyzed by 1-deoxy-D-xylulose-5-phosphate synthase (DXS) and 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR) proteins are critical steps within the isoprenoid biosynthesis in plants. Here, five DXS (CtDXS1-5) and two DXR (CtDXR1-2) genes were identified from Cassia tora genome. Based on multiple assays including the phylogeny, cis-acting element, expression pattern, and subcellular localization, CtDXS1 and CtDXR1 genes might be potential candidates controlling the isoprenoid biosynthesis. Intriguingly, CtDXS1 transgenic plants resulted in drought tolerance but retardant growth, while CtDXR1 transgenic plants exhibited both enhanced drought tolerance and increased growth. By comparison of β-carotene, chlorophyll, abscisic acid (ABA) and gibberellin 3 (GA3) contents in wild-type and transgenic plants, the absolute contents and (or) altered GA3/ABA levels were suggested to be responsible for the balance between drought tolerance and plant growth. The transcriptome of CtDXR1 transgenic plants suggested that the transcript levels of key genes, such as DXS, 9-cis-epoxycarotenoid dioxygenases (NCED), ent-kaurene synthase (KS) and etc, involved with chlorophyll, β-carotene, ABA and GA3 biosynthesis were induced and their contents increased accordingly. Collectively, the trade-off effect induced by CtDXR1 was associated with redesigning architecture in phytohormone homeostasis and thus was highlighted for future breeding purposes.

Integrated transcriptomic and metabolomic analysis reveals the molecular basis of tissue-specific accumulation of bioactive steroidal alkaloids in Fritillaria unibracteata

Fritillaria unibracteata is an endangered medicinal plant whose bulb has been used as a Chinese herb to suppress cough, asthma and excessive phlegm for centuries. Steroidal alkaloids, which are synthesized via the steroid synthesis pathways, are their significant bioactive constituents. However, few studies on genes involved in steroidal alkaloid biosynthesis in F. unibracteata have been reported, mainly due to the lack of the F. unibracteata genome. In this paper, comparative transcriptomic and metabolomic analyses of four different tissues of F. unibracteata (leaves, flowers, stems, and bulbs) were performed. Imperialine, peiminine, and peimisine were among the significant bioactive compounds that were considerably abundant in bulb tissue, according to the metabolomic findings. Then, 83.60 Gb transcriptome sequencing of four different tissues was performed, of which one gene encoding phosphomevalonate kinase was directly functionally characterized to verify the accuracy of sequences obtained from the transcriptome. A total of 9217 differentially expressed unigenes (DEGs) were identified in four different tissues of F. unibracteata. GO and KEGG enrichments revealed that phenylpropanoid biosynthesis, MVA-mediated terpenoid backbone biosynthesis, and steroid biosynthesis were enriched in bulb tissue, whereas enrichment of MEP-mediated terpenoid backbone biosynthesis, photosynthesis, photosynthesis-antenna protein and carotenoid biosynthesis was observed in aerial tissues. Moreover, clustering analysis indicated that the downstream steroid biosynthesis pathway was more important in steroidal alkaloid biosynthesis compared to the upstream terpenoid backbone biosynthesis pathway. Hence, MVA-mediated biosynthesis of steroidal alkaloids was proposed, in which 15 bulb-clustered DEGs were positively correlated with a high accumulation of bioactive steroid alkaloids, further validating our proposal. In addition, 36 CYP450s showing a positive correlation with bioactive steroidal alkaloids provided candidate enzymes to catalyze the subsequent steps of steroidal alkaloid biosynthesis. In addition, the transcription factors and ABC transporters clustered in bulb tissue might be responsible for the regulation and transportation of steroidal alkaloid biosynthesis. Protein-protein interaction analysis implied a highly complex steroid alkaloid biosynthesis network in which delta (24)-sterol reductase might be one of the central catalysts. Based on the integrated transcriptome and metabolome, this current study is a first step in understanding the tissue-specific biosynthesis of steroidal alkaloids in F. unibracteata. Furthermore, key genes and regulators identified herein could facilitate metabolic engineering to improve steroidal alkaloids in F. unibracteata.

Global Responses of Autopolyploid Sugarcane Badila (Saccharum officinarum L.) to Drought Stress Based on Comparative Transcriptome and Metabolome Profiling

Sugarcane (Saccharum spp. hybrid) is frequently affected by seasonal drought, which causes substantial declines in quality and yield. To understand the drought resistance mechanisms of S. officinarum, the main species of modern sugarcane, at a molecular level, we carried out a comparative analysis of transcriptome and metabolome profiling of the sugarcane variety Badila under drought stress (DS). Compared with control group (CG) plants, plants exposed to DS had 13,744 (6663 up-regulated and 7081 down-regulated) differentially expressed genes (DEGs). GO and KEGG analysis showed that the DEGs were enriched in photosynthesis-related pathways and most DEGs had down-regulated expression. Moreover, the chlorophyll content, photosynthesis (Photo), stomatal conductance (Cond), intercellular carbon dioxide concentration (Ci) and transpiration rate (Trmmol) were sharply decreased under DS. These results indicate that DS has a significant negative influence on photosynthesis in sugarcane. Metabolome analysis identified 166 (37 down-regulated and 129 up-regulated) significantly regulated metabolites (SRMs). Over 50% of SRMs were alkaloids, amino acids and their derivatives, and lipids. The five most significantly enriched KEGG pathways among SRMs were Aminoacyl-tRNA biosynthesis, 2-Oxocarboxylic acid metabolism, Biosynthesis of amino acids, Phenylalanine metabolism, and Arginine and proline metabolism (p < 0.05). Comparing CG with DS for transcriptome and metabolome profiling (T_CG/DS and M_CG/DS, respectively), we found three of the same KEGG-enriched pathways, namely Biosynthesis of amino acids, Phenylalanine metabolism and Arginine and proline metabolism. The potential importance of Phenylalanine metabolism and Arginine and proline metabolism was further analyzed for response to DS in sugarcane. Seven SRMs (five up-regulated and two down-regulated) and 60 DEGs (17 up-regulated and 43 down-regulated) were enriched in Phenylalanine metabolism under DS, of which novel.31261, Sspon.04G0008060-1A, Sspon.04G0008060-2B and Sspon.04G0008060-3C were significantly correlated with 7 SRMs. In Arginine and proline metabolism, eight SRMs (seven up-regulated and one down-regulated) and 63 DEGs (32 up-regulated and 31 down-regulated) were enriched, of which Sspon.01G0026110-1A (OAT) and Sspon.03G0002750-3D (P5CS) were strongly associated with proline (r > 0.99). These findings present the dynamic changes and possible molecular mechanisms of Phenylalanine metabolism as well as Arginine and proline metabolism under DS and provide a foundation for future research and sugarcane improvement.