Identification and Functional Analysis of the Caffeic Acid O-Methyltransferase (COMT) Gene Family in Rice (Oryza sativa L.)

Metabolic Engineering of Yarrowia lipolytica for Enhanced De Novo Biosynthesis of Icaritin

Icaritin (ICT) is a naturally occurring flavonoid compound with notable anticancer properties, recently recognized for its efficacy in treating advanced hepatic carcinoma. Traditional methods of ICT production, including plant extraction and chemical synthesis, face challenges such as low yield and environmental concerns. This study leverages synthetic biology to construct a microbial cell factory using Yarrowia lipolytica for de novo ICT synthesis. We engineered the yeast by integrating the ICT synthesis pathway involving EsPT from Epimedium sagittatum and OsOMTm from Oryza sativa. By optimizing the metabolic pathways, including enhancing the supply of DMAPP via mevalonate pathway modifications, and fine-tuning the expression and catalytic efficiency of EsPT through truncation strategies, we significantly improved ICT yield to 247.02 mg/L─the highest microbial ICT titer reported to date. These findings lay a solid foundation for the large-scale industrial production of ICT and offer valuable insights into the biosynthesis of other flavonoid plant natural products.

Physiol-biochemical, transcriptome, and root microstructure analyses reveal the mechanism of salt shock recovery in sugar beet

Soil salinity substantially limits agricultural productivity, necessitating a sound understanding of salt-tolerance mechanisms in key crops for their improved breeding. Despite being a staple sugar crop with strong salt tolerance, sugar beet (Beta vulgaris L.), remains underexplored for its transcriptional responses to salt shock. This study compared the physiological traits, root structure, and full-length transcriptomes of salt-tolerant (T510) and salt-sensitive (S210) sugar beet varieties during stages of osmotic stress (0-24 h) and ionic stress (1-7 d) after incurring salt shock. The results show that T510 recovered faster, maintaining a higher water potential (WP), better osmotic regulation, lower reactive oxygen species (ROS) levels, and a balanced Na+/K+ ratio. Furthermore, while under osmotic stress, T510 exhibited extensive transcriptional reprogramming to enhance its photosynthetic efficiency and carbon assimilation via the C4-dicarboxylic acid (C4) cycle, which compensated for salt shock-induced disruptions to the Calvin-Benson (C3) cycle. Notably, elevated activity of ascorbate peroxidase (APX) and glutathione S-transferase (GST), driven by greater gene expression, enhanced the scavenging of ROS. In tandem, T510 synthesized more lignin than S210, and adapted its root microstructure to maintain water and nutrient transport functioning in the face of high salinity. Overall, these findings provide insights into the physiological, transcriptomic, and structural adaptations enabling salt tolerance in sugar beet plants, thus offering valuable strategies for strengthening crop resilience through molecular breeding.

Melatonin enhances salt tolerance by promoting CcCAD10-mediated lignin biosynthesis in pigeon pea

Melatonin plays a crucial role in enhancing plant resistance to salt stress by regulating biosynthesis of specialized metabolites. Phenylpropanoids, especially lignin, contribute to all aspects of plant responses toward biotic and abiotic stresses. However, the crosstalk between melatonin and lignin is largely unknown in pigeon pea under salt stress. In this study, the cinnamyl alcohol dehydrogenase CcCAD10 was identified to be involved in melatonin treatment and salt stress. The content of lignin was significantly increased in CcCAD10 over-expression (OE) lines, the enhanced antioxidant enzyme activities, indicating enhanced salt resistance. As a parallel branch of the lignin synthesis pathway, the content of flavonoids was further determined. The accumulations of luteolin, genistin, genistein, biochain A, apigenin and isovitexin were down-regulated in CcCAD10-OE hairy root. The results indicate that CcCAD10-OE mediated carbon flow from the phenylalanine pathway is redirected to the lignin pathway at the expense of less carbon flow in the flavonoid pathway, enhancing the salt-tolerance. Furthermore, we found the exogenous melatonin stimulated endogenous melatonin production mainly by upregulating the expression of CcASMT2 gene. This study reveals a novel mechanism by which melatonin enhances salt tolerance in pigeon pea, which laid a foundation for exploring the molecular mechanism of melatonin in salt stress response.

Caffeic acid O-methyltransferase-dependent flavonoid defenses promote sorghum resistance to fall armyworm infestation

Sorghum (Sorghum bicolor), one of the world's most important monocot crops, suffers severe yield losses due to attack by a polyphagous insect pest, fall armyworm (FAW; Spodoptera frugiperda). Here, we show that the Brown midrib 12 (Bmr12) gene, which encodes the caffeic acid O-methyltransferase (COMT) enzyme, promotes sorghum defense against FAW. Loss of Bmr12 function resulted in increased susceptibility, but enhanced resistance to FAW was observed in Bmr12-overexpression (OE) plants compared with wild-type (RTx430) plants. Although COMT is associated with modulating lignin levels, FAW infestation resulted in comparable lignin levels between bmr12 and Bmr12-OE sorghum plants. On the contrary, evidence presented here indicates that FAW feeding induced the accumulation of flavonoids, which was previously shown to have a negative impact on FAW growth and survival in Bmr12-OE plants compared with bmr12 and RTx430 plants. Furthermore, a combination of phytohormone profiling and transcriptomic analysis uncovered that COMT-mediated resistance to FAW depends on jasmonic acid (JA) and oxidative stress-associated pathways. Exogenous application of FAW oral secretions stimulated flavonoid accumulation in Bmr12-OE plants compared with bmr12 and RTx430 plants, indicating that COMT has an essential function in perceiving FAW oral cues. Taken together, the critical role of COMT in sorghum defense against FAW hinges upon the interplay between JA and its derivatives and hydrogen peroxide, which potentially helps to mount a robust flavonoid-based host defense upon caterpillar attack.

Cloning and bioinformatics analysis of key gene ShOMT3 of podophyllotoxin biosynthesis pathway in Sinopodophyllum hexandrum

Sinopodophyllum hexandrum (S. hexandrum) is an endangered traditional Chinese medicine as abundant podophyllotoxin with powerful anticancer activity. In this study, the rootstalks of S. hexandrum from different geographical locations in China [S1 (Gansu) and S2 (Shaanxi)] were used as research materials to clone the key gene pluviatolide O-methyltransferase 3 (ShOMT3) in the podophyllotoxin biosynthetic pathway. Subsequently, bioinformatics analysis of the ShOMT3 gene and its encoded protein was subjected to bioinformatics analysis using various analysis software including ProtParam, DeepTMHMM, SubLoc, Signal-P 5.0, and Swiss-model. The results of the analysis revealed that the CDS region of the ShOMT3 gene is 1119 bp long, encoding 372 amino acids. The theoretical molecular weight of the ShOMT3 protein is 41.32784 kD, and the theoretical isoelectric point (pI) is 5.27. The instability coefficient of the protein is 46.05, the aliphatic index is 93.58, and the grand average of hydropathicity (GRAVY) is 0.037, indicating that it is an unstable hydrophobic protein. The protein does not contain transmembrane domains or signal peptides, indicating that it is a non-secreted protein. Secondary structure prediction results suggests that the protein consists of alpha helices, random coils, extended strands, and beta-turns. Tertiary structure prediction results suggests that the protein functions as a monomer. In the phylogenetic tree, the ShOMT3 protein has the highest homology with Podophyllum peltatum (P. peltatum). The successful cloning and bioinformatics analysis of the ShOMT3 gene provide theoretical basis and excellent genetic resources for the molecular regulatory mechanism analysis of the podophyllotoxin biosynthetic pathway and molecular breeding in S. hexandrum.

A functional cascading of lignin modification via repression of caffeic acid O-methyltransferase for bioproduction and anti-oxidation in rice

INTRODUCTION

Crop straws provide substantial biomass resources that are transformable for sustainable biofuels and valuable bioproducts. However, the natural lignocellulose recalcitrance results in an expensive biomass process and secondary waste liberation. As lignin is a major recalcitrant factor, genetic engineering of lignin biosynthesis is increasingly being implemented in bioenergy crops, but much remains unclear about the desired lignocellulose alteration and resulting function.

OBJECTIVES

This study attempted to explore the mechanisms of lignin modification responsible for efficient lignocellulose conversion in vitro and an effective plant anti-oxidation response in vivo.

METHODS

We initially selected specific rice mutants by performing modern CRISPR/cas9 editing with caffeic acid O-methyltransferase involved in the synthetic pathways of monolignols (G, S) and ferulic acid (FA), and then explored lignocellulose conversion and plant cadmium (Cd) accumulation using advanced chemical, biochemical and thermal-chemical analyses.

RESULTS

Notable lignin modification was achieved from the predominately synergistic down-regulation of S-monomer synthesis in three mutants. This consequently upgraded lignocellulose porosity by up to 1.8 folds to account for significantly enhanced biomass saccharification and bioethanol production by 20 %-26 % relative to the wild-type. The modified lignin also favors the dissection of diverse lignin nanoparticles with dimensions reduced by 1.5-1.9 folds, applicable for thermal-chemical conversion into the carbon quantum dots with increased yields by 15 % and 31 %. The proportions of G-monomers and FA were significantly increased in the mutants, and the lignin extractions were further assayed with higher activities for two standard antioxidants (DPPH and ABTS) in vitro compared to the wild-type, revealing a distinctively enhanced plant antioxidative capacity in the mutants. Water culture showed that young mutant seedlings accumulated more Cd than wild-type did (p < 0.01, n = 3), suggesting effective heavy metal phytoremediation in the mutants.

CONCLUSION

A hypothetical model of characteristic lignin modification for specific S-monomer reduction, accountable for improved lignocellulose recalcitrance, was proposed. It provides a powerful strategy for achieving high-yield biofuels and value-added bioproducts or enhancing plant antioxidative capacity for heavy metal phytoremediation.

Views and perspectives on the indoleamines serotonin and melatonin in plants: past, present and future

In the decades since their discovery in plants in the mid-to-late 1900s, melatonin (N-acetyl-5-methoxytryptamine) and serotonin (5-methoxytryptamine) have been established as their own class of phytohormone and have become popular targets for examination and study as stress ameliorating compounds. The indoleamines play roles across the plant life cycle from reproduction to morphogenesis and plant environmental perception. There is growing interest in harnessing the power of these plant neurotransmitters in applied and agricultural settings, particularly as we face increasingly volatile climates for food production; however, there is still a lot to learn about the mechanisms of indoleamine action in plants. A recent explosion of interest in these compounds has led to exponential growth in the field of melatonin research in particular. This concept paper aims to summarize the current status of indoleamine research and highlight some emerging trends.

Identification of GiOMT gene family in Glycyrrhiza inflata bat and expression analysis under UV-B stresses

BACKGROUND

O-Methyltransferase (OMTs) is a class of conserved multifunctional enzymes that play important roles in plant developmental regulation, hormone signaling, secondary metabolite synthesis and abiotic stress response. The GiOMT gene family has been identified and analyzed in species such as citrus, alfalfa, Populus and grape, but has not been reported in Glycyrrhiza inflata Bat.

RESULTS

In this study, we systematically identified and analyzed the GiOMT gene family of G. inflata by bioinformatics, and analyzed their physicochemical properties, conserved motifs, conserved structural domains, gene structures, phylogenetic relationships, chromosomal localization and fragment duplications, and the expression patterns of GiOMT genes in combination with transcriptomic data and qRT-PCR. The results showed that a total of 41 GiOMTs were identified in G. inflata, which were named GiOMT1 ~ GiOMT41 based on their chromosomal locations. Protein characterization showed that 29 GiOMT proteins were hydrophilic and 12 GiOMT proteins were hydrophobic. Subcellular predicted localization revealed that most GiOMT proteins localized in the cytoplasm and chloroplasts. Phylogenetic relationships showed that the OMT genes of three species, G. inflata, Arabidopsis and alfalfa, were distributed in three taxa, while the GiOMT genes were distributed in taxa I and II. Promoters of GiOMT genes contained light responsive element and many hormone responsive elements. The expression levels of GiOMT genes under UV-B stress were varied, indicating that GiOMT gene was in response to abiotic stresses in G. inflata.

CONCLUSION

In this study, we investigated the genome-wide identification, structure, evolution and expression analysis of the GiOMT gene in G. inflata. The basal sequence of GiOMT genes was highly conserved throughout the evolutionary history of G. inflata. Most of the GiOMT genes were highly expressed in roots and were involved in the response to UV-B stress. The GiOMT genes may lead to the accumulation of flavonoids and enhancement of G. inflata quality and drug activity in G. inflata under UV-B radiation.

A Novel Single Base Mutation in OsSPL42 Leads to the Formation of Leaf Lesions in Rice

Rice spotted-leaf mutants serve as valuable resources for studying plant programmed cell death (PCD) and disease resistance mechanisms, making them crucial for research on disease resistance in rice. Map-based cloning was used to identify and clone the spotted-leaf gene OsSPL42. Then, functional complementation and CRISPR/Cas9 techniques were also employed to further validate the function of this gene. By applying leaf clippings for bacterial blight (BB) inoculation, the BB resistance of different rice lines was assessed. The results in this study were as follows: The OsSPL42 behaved as a recessive nuclear gene and was narrowed down to a 111 kb region on chromosome 8. All T0 transgenic rice plants in the complementation experiments exhibited a wild-type phenotype, without any lesion spots on the rice leaves. This suggests that the LOC_Os08g06100 encoding O-methyltransferase is the candidate gene for the mutant spl42. The OsSpl42 is widely expressed and the OsSPL42-GFP protein is mainly localized in the cytoplasm. OsSPL42 overexpression lines are more susceptible to BBs, which indicates that OsSPL42 may act as a negative regulator of rice resistance to BB. In summary, we speculate that OsSPL42 plays an important role in the regulation of pathogen response, providing new insights into plant defense mechanisms.

GhCOMT33D modulates melatonin synthesis, impacting plant response to Cd2+ in cotton via ROS

Caffeic acid-3-O-methyltransferase (COMT) serves as the final pivotal enzyme in melatonin biosynthesis and plays a crucial role in governing the synthesis of melatonin in plants. This research used bioinformatics to analyze the phylogenetic relationships, gene structure, and promoter cis-acting elements of the upland cotton COMT gene family members， which it identified as the key gene GhCOMT33D to promote melatonin synthesis and responding to Cd2+ stress. After silencing GhCOMT33D through virus-induced gene silencing (VIGS), cotton seedlings showed less resistance to Cd2+ stress. Under Cd2+ stress, the melatonin content in the silenced plants significantly decreased, while ROS, MDA, and proline accumulated in the plant cells. The stomatal aperture of the leaves was reduced, hindering normal photosynthesis, leading to cotton leaves withering and yellowing, and epidermal cells becoming twisted and deformed, with a large number of gaps appearing. The non-silenced plants had a significantly higher melatonin content and were in better condition, providing important evidence for further research on how plant melatonin enhances the Cd2+ resistance of cotton and its regulatory mechanisms.

Genome-Wide Identification of COMT Gene Family in Maize and its Function in Response to Light

Maize is a major crop, feed, and industrial material. Caffeic acid-O-methyltransferase (COMT) is a methylase closely associated with lignin biosynthesis and plant growth and resistance. In this study, we identified the COMT gene (ZmCOMT) family in maize and further analyzed its phylogenetic evolution, subcellular localization, and its function in response to light. Thirty-one ZmCOMT genes were identified in the maize genome, which were distributed across eight chromosomes and mainly clustered on chromosome 4. Most ZmCOMT proteins were predicted to localize in the cytoplasm. Ten different conserved motifs were present in most ZmCOMT proteins, and motif1, motif6, and motif7 were highly conserved and present in all ZmCOMT proteins. The photoresponsivity elements were conserved among all members, and ZmCOMT22 and ZmCOMT10 genes responsive to light. This result suggests a potential function for these two genes in lignin biosynthesis which a previous study had linked to light regulation. Jasmonic acid responsive and abscisic acid cis-acting elements were present in the promoter regions of family members, thus the family may be regulated by hormone signaling pathways of maize. In summary, ZmCOMT genes are ancient, and the highly conserved motifs may be significant in survival and evolution of maize. Furthermore, light may influence lignin biosynthesis and photosynthesis through ZmCOMT genes. This research provided theoretical basis for lignin biosynthesis of maize and the potential value of ZmCOMT22 and ZmCOMT10 genes to enhance plant photosynthesis for facing global warming.

How lignin biosynthesis responds to nitrogen in plants: a scoping review

Nitrogen (N) plays a critical role in the functioning of key amino acids and synthetic enzymes responsible for the various stages of lignin biosynthesis. However, the precise mechanisms through which N influences lignin biosynthesis have not been fully elucidated. This scoping review explores how lignin biosynthesis responds to N in plants. A systematic search of the literature in several databases was conducted using relevant keywords. Only 44 of the 1842 selected studies contained a range of plant species, experimental conditions, and research approaches. Lignin content, structure, and biosynthetic pathways in response to N are discussed, and possible response mechanisms of lignin under low N are proposed. Among the selected studies, 64.52% of the studies reter to lignin content found a negative correlation between N availability and lignin content. Usually, high N decreases the lignin content, delays cell lignification, increases p-hydroxyphenyl propane (H) monomer content, and regulates lignin synthesis through the expression of key genes (PAL, 4CL, CCR, CAD, COMT, LAC, and POD) encoding miRNAs and transcription factors (e.g., MYB, bHLH). N deficiency enhances lignin synthesis through the accumulation of phenylpropanoids, phenolics, and soluble carbohydrates, and indirect changes in phytohormones, secondary metabolites, etc. This review provides new insights and important references for future studies on the regulation of lignin biosynthesis.

Genome-Wide Identification of the COMT Gene Family in Juglans regia L. and Response to Drought Stress

Caffeic acid O-methyltransferase (COMT), as a multifunctional enzyme involved in various physiological and biochemical processes in lignin metabolism, plays an important role in a plant's response to stress. In this study, we isolated COMT family members from the walnut genome by bioinformatics and analyzed their physicochemical properties and their expression under drought stress to provide gene resources for drought resistance in walnut. The results showed that 33 COMT genes were identified from walnuts and distributed on different chromosomes. The molecular weight of proteins varies greatly. According to the phylogenetic tree, the family can be divided into seven subgroups, which are relatively conservative in evolution and closely related to Arabidopsis thaliana. Promoter analysis showed that the promoter of the walnut COMT gene contains rich cis-elements of plant hormone response and stress response, and the real-time fluorescence scale name can be significantly induced by drought stress. Compared with wild-type Arabidopsis, overexpression JrCOMT19 significantly increased the enzyme activity (SOD, POD, and CAT) and proline content. Meanwhile, overexpression of JrCOMT19 significantly increased the lignin content and expression of related genes. Therefore, JrCOMT plays an important role in responding to drought in walnuts, and overexpression JrCOMT19 can improve the resistance to drought stress by increasing lignin content, antioxidant enzyme activity, and osmotic substance content.

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.

Exploring Lignin Biosynthesis Genes in Rice: Evolution, Function, and Expression

Lignin is nature's second most abundant vascular plant biopolymer, playing significant roles in mechanical support, water transport, and stress responses. This study identified 90 lignin biosynthesis genes in rice based on phylogeny and motif constitution, and they belong to PAL, C4H, 4CL, HCT, C3H, CCoAOMT, CCR, F5H, COMT, and CAD families. Duplication events contributed largely to the expansion of these gene families, such as PAL, CCoAOMT, CCR, and CAD families, mainly attributed to tandem and segmental duplication. Microarray data of 33 tissue samples covering the entire life cycle of rice suggested fairly high PAL, HCT, C3H, CCoAOMT, CCR, COMT, and CAD gene expressions and rather variable C4H, 4CL, and F5H expressions. Some members of lignin-related genes (OsCCRL11, OsHCT1/2/5, OsCCoAOMT1/3/5, OsCOMT, OsC3H, OsCAD2, and OsPAL1/6) were expressed in all tissues examined. The expression patterns of lignin-related genes can be divided into two major groups with eight subgroups, each showing a distinct co-expression in tissues representing typically primary and secondary cell wall constitutions. Some lignin-related genes were strongly co-expressed in tissues typical of secondary cell walls. Combined HPLC analysis showed increased lignin monomer (H, G, and S) contents from young to old growth stages in five genotypes. Based on 90 genes' microarray data, 27 genes were selected for qRT-PCR gene expression analysis. Four genes (OsPAL9, OsCAD8C, OsCCR8, and OsCOMTL4) were significantly negatively correlated with lignin monomers. Furthermore, eleven genes were co-expressed in certain genotypes during secondary growth stages. Among them, six genes (OsC3H, OsCAD2, OsCCR2, OsCOMT, OsPAL2, and OsPAL8) were overlapped with microarray gene expressions, highlighting their importance in lignin biosynthesis.

Genome-Wide Association Analysis Identified Quantitative Trait Loci (QTLs) Underlying Drought-Related Traits in Cultivated Peanut (Arachis hypogaea L.)

Drought is a destructive abiotic stress that affects all critical stages of peanut growth such as emergence, flowering, pegging, and pod filling. The development of a drought-tolerant variety is a sustainable strategy for long-term peanut production. The U.S. mini-core peanut germplasm collection was evaluated for drought tolerance to the middle-season drought treatment phenotyping for pod weight, pod count, relative water content (RWC), specific leaf area (SLA), leaf dry matter content (LDMC), and drought rating. A genome-wide association study (GWAS) was performed to identify minor and major QTLs. A total of 144 QTLs were identified, including 18 significant QTLs in proximity to 317 candidate genes. Ten significant QTLs on linkage groups (LGs) A03, A05, A06, A07, A08, B04, B05, B06, B09, and B10 were associated with pod weight and pod count. RWC stages 1 and 2 were correlated with pod weight, pod count, and drought rating. Six significant QTLs on LGs A04, A07, B03, and B04 were associated with RWC stages 1 and 2. Drought rating was negatively correlated with pod yield and pod count and was associated with a significant QTL on LG A06. Many QTLs identified in this research are novel for the evaluated traits, with verification that the pod weight shared a significant QTL on chromosome B06 identified in other research. Identified SNP markers and the associated candidate genes provide a resource for molecular marker development. Verification of candidate genes surrounding significant QTLs will facilitate the application of marker-assisted peanut breeding for drought tolerance.

Evolution and Analysis of Caffeic Acid Transferase (COMT) in Seed Plants

Caffeic acid transferase (COMT) is a key enzyme in the lignin and melatonin synthesis pathways and plays an important role in plant growth and development. All seed plants have two characteristics: they have vascular tissues, phloem, and xylem, and they can produce and reproduce seeds. In order to understand the distribution and evolution of COMTs in seed plants, we performed physicochemical property analysis, subcellular localization, phylogenetic analysis, conserved motif analysis, and protein interaction network analysis of 44 COMT homologs from 26 seed plants through in silico. The results showed that in seed plants, the structure of COMT genes tends to be stable in different plant taxa, while the relationship between the chromosomal positions of different COMT genes in the same plant was more intricate. The conserved distribution of COMT in seed plants reflected its highly specialized function.

Genetic linkage mapping and quantitative trait locus (QTL) analysis of sweet basil (Ocimum basilicum L.) to identify genomic regions associated with cold tolerance and major volatiles

Chilling sensitivity is one of the greatest challenges affecting the marketability and profitability of sweet basil (Ocimum basilicum L.) in the US and worldwide. Currently, there are no sweet basils commercially available with significant chilling tolerance and traditional aroma profiles. This study was conducted to identify quantitative trait loci (QTLs) responsible for chilling tolerance and aroma compounds in a biparental mapping population, including the Rutgers advanced breeding line that served as a chilling tolerant parent, 'CB15', the chilling sensitive parent, 'Rutgers Obsession DMR' and 200 F2 individuals. Chilling tolerance was assessed by percent necrosis using machine learning and aroma profiling was evaluated using gas chromatography (GC) mass spectrometry (MS). Single nucleotide polymorphism (SNP) markers were generated from genomic sequences derived from double digestion restriction-site associated DNA sequencing (ddRADseq) and converted to genotype data using a reference genome alignment. A genetic linkage map was constructed and five statistically significant QTLs were identified in response to chilling temperatures with possible interactions between QTLs. The QTL on LG24 (qCH24) demonstrated the largest effect for chilling response and was significant in all three replicates. No QTLs were identified for linalool, as the population did not segregate sufficiently to detect this trait. Two significant QTLs were identified for estragole (also known as methyl chavicol) with only qEST1 on LG1 being significant in the multiple-QTL model (MQM). QEUC26 was identified as a significant QTL for eucalyptol (also known as 1,8-cineole) on LG26. These QTLs may represent key mechanisms for chilling tolerance and aroma in basil, providing critical knowledge for future investigation of these phenotypic traits and molecular breeding.

Whole genome identification, molecular docking and expression analysis of enzymes involved in the selenomethionine cycle in Cardamine hupingshanensis

BACKGROUND

The selenomethionine cycle (SeMTC) is a crucial pathway for the metabolism of selenium. The basic bioinformatics and functions of four enzymes involved in the cycle including S-adenosyl-methionine synthase (MAT), SAM-dependent methyltransferase (MTase), S-adenosyl-homocysteine hydrolase (SAHH) and methionine synthase (MTR), have been extensively reported in many eukaryotes. The identification and functional analyses of SeMTC genes/proteins in Cardamine hupingshanensis and their response to selenium stress have not yet been reported.

RESULTS

In this study, 45 genes involved in SeMTC were identified in the C. hupingshanensis genome. Phylogenetic analysis showed that seven genes from ChMAT were clustered into four branches, twenty-seven genes from ChCOMT were clustered into two branches, four genes from ChSAHH were clustered into two branches, and seven genes from ChMTR were clustered into three branches. These genes were resided on 16 chromosomes. Gene structure and homologous protein modeling analysis illustrated that proteins in the same family are relatively conserved and have similar functions. Molecular docking showed that the affinity of SeMTC enzymes for selenium metabolites was higher than that for sulfur metabolites. The key active site residues identified for ChMAT were Ala269 and Lys273, while Leu221/231 and Gly207/249 were determined as the crucial residues for ChCOMT. For ChSAHH, the essential active site residues were found to be Asn87, Asp139 and Thr206/207/208/325. Ile204, Ser111/329/377, Asp70/206/254, and His329/332/380 were identified as the critical active site residues for ChMTR. In addition, the results of the expression levels of four enzymes under selenium stress revealed that ChMAT3-1 genes were upregulated approximately 18-fold, ChCOMT9-1 was upregulated approximately 38.7-fold, ChSAHH1-2 was upregulated approximately 11.6-fold, and ChMTR3-2 genes were upregulated approximately 28-fold. These verified that SeMTC enzymes were involved in response to selenium stress to varying degrees.

CONCLUSIONS

The results of this research are instrumental for further functional investigation of SeMTC in C. hupingshanensis. This also lays a solid foundation for deeper investigations into the physiological and biochemical mechanisms underlying selenium metabolism in plants.

Bacillus cereus G2 alleviate salt stress in Glycyrrhiza uralensis Fisch. by balancing the downstream branches of phenylpropanoids and activating flavonoid biosynthesis

The salinity environment is one of the biggest threats to Glycyrrhiza uralensis Fisch. (G. uralensis) growth, resulting from the oxidative stress caused by excess reactive oxygen species (ROS). Flavonoids are the main pharmacodynamic composition and help maintain ROS homeostasis and mitigate oxidative damage in G. uralensis in the salinity environment. To investigate whether endophytic Bacillus cereus G2 can improve the salt-tolerance of G. uralensis through controlling flavonoid biosynthesis, the transcriptomic and physiological analysis of G. uralensis treated by G2 in the saline environment was conducted, focused on flavonoid biosynthesis-related pathways. Results uncovered that salinity inhibited flavonoids synthesis by decreasing the activities of phenylalanine ammonialyase (PAL) and 4-coumarate-CoA ligase (4CL) (42% and 39%, respectively) due to down-regulated gene Glyur000910s00020578 at substrate level, and then decreasing the activities of chalcone isomerase (CHI) and chalcone synthase (CHS) activities (50% and 42%, respectively) due to down-regulated genes Glyur006062s00044203 and Glyur000051s00003431, further decreasing isoliquiritigenin content by 53%. However, salt stress increased liquiritin content by 43%, which might be a protective mechanism of salt-treated G. uralensis seedlings. Interestingly, G2 enhanced PAL activity by 27% whereas reduced trans-cinnamate 4-monooxygenase (C4H) activity by 43% which could inhibit lignin biosynthesis but promote flavonoid biosynthesis of salt-treated G. uralensis at the substrate level. G2 decreased shikimate O-hydroxycinnamoyltransferase (HCT) activity by 35%, increased CHS activity by 54% through up-regulating the gene Glyur000051s00003431 encoding CHS, and increased CHI activity by 72%, thereby decreasing lignin (34%) and liquiritin (24%) content, but increasing isoliquiritigenin content (35%), which could mitigate oxidative damage and changed salt-tolerance mechanism of G. uralensis.

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.

Caffeic Acid O-Methyltransferase Gene Family in Mango (Mangifera indica L.) with Transcriptional Analysis under Biotic and Abiotic Stresses and the Role of MiCOMT1 in Salt Tolerance

Caffeic acid O-methyltransferase (COMT) participates in various physiological activities in plants, such as positive responses to abiotic stresses and the signal transduction of phytohormones. In this study, 18 COMT genes were identified in the chromosome-level reference genome of mango, named MiCOMTs. A phylogenetic tree containing nine groups (I-IX) was constructed based on the amino acid sequences of the 71 COMT proteins from seven species. The phylogenetic tree indicated that the members of the MiCOMTs could be divided into four groups. Quantitative real-time PCR showed that all MiCOMT genes have particularly high expression levels during flowering. The expression levels of MiCOMTs were different under abiotic and biotic stresses, including salt and stimulated drought stresses, ABA and SA treatment, as well as Xanthomonas campestris pv. mangiferaeindicae and Colletotrichum gloeosporioides infection, respectively. Among them, the expression level of MiCOMT1 was significantly up-regulated at 6-72 h after salt and stimulated drought stresses. The results of gene function analysis via the transient overexpression of the MiCOMT1 gene in Nicotiana benthamiana showed that the MiCOMT1 gene can promote the accumulation of ABA and MeJA, and improve the salt tolerance of mango. These results are beneficial to future researchers aiming to understand the biological functions and molecular mechanisms of MiCOMT genes.

Genome-wide characterization of COMT family and regulatory role of CsCOMT19 in melatonin synthesis in Camellia sinensis

BACKGROUND

Caffeic acid O-methyltransferase (COMT) is a key enzyme that regulates melatonin synthesis and is involved in regulating the growth, development, and response to abiotic stress in plants. Tea plant is a popular beverage consumed worldwide, has been used for centuries for its medicinal properties, including its ability to reduce inflammation, improve digestion, and boost immune function. By analyzing genetic variation within the COMT family, while helping tea plants resist adversity, it is also possible to gain a deeper understanding of how different tea varieties produce and metabolize catechins, then be used to develop new tea cultivars with desired flavor profiles and health benefits.

RESULTS

In this study, a total of 25 CsCOMT genes were identified based on the high-quality tea (Camellia sinensis) plant genome database. Phylogenetic tree analysis of CsCOMTs with COMTs from other species showed that COMTs divided into four subfamilies (Class I, II, III, IV), and CsCOMTs was distributed in Class I, Class II, Class III. CsCOMTs not only undergoes large-scale gene recombination in pairs internally in tea plant, but also shares 2 and 7 collinear genes with Arabidopsis thaliana and poplar (Populus trichocarpa), respectively. The promoter region of CsCOMTs was found to be rich in cis-acting elements associated with plant growth and stress response. By analyzing the previously transcriptome data, it was found that some members of CsCOMT family exhibited significant tissue-specific expression and differential expression under different stress treatments. Subsequently, we selected six CsCOMTs to further validated their expression levels in different tissues organ using qRT-PCR. In addition, we silenced the CsCOMT19 through virus-induced gene silencing (VIGS) method and found that CsCOMT19 positively regulates the synthesis of melatonin in tea plant.

CONCLUSION

These results will contribute to the understanding the functions of CsCOMT gene family and provide valuable information for further research on the role of CsCOMT genes in regulating tea plant growth, development, and response to abiotic stress.

Genome-wide identification of the OMT gene family in Cucumis melo L. and expression analysis under abiotic and biotic stress

Background

O-methyltransferase (OMT)-mediated O-methylation is a frequent modification that occurs during natural product biosynthesis, and it increases the diversity and stability of secondary metabolites. However, detailed genome-wide identification and expression analyses of OMT gene family members have not been performed in melons. In this study, we aimed to perform the genome-wide identification of OMT gene family members in melon to identify and clarify their actions during stress.

Methods

Genome-wide identification of OMT gene family members was performed using data from the melon genome database. The Cucumis melo OMT genes (CmOMTs) were then compared with the genes from two representative monocotyledons and three representative dicotyledons. The basic information, cis-regulatory elements in the promoter, predicted 3-D-structures, and GO enrichment results of the 21 CmOMTs were analyzed.

Results

In our study, 21 CmOMTs (named CmOMT1-21) were obtained by analyzing the melon genome. These genes were located on six chromosomes and divided into three groups composed of nine, six, and six CmOMTs based on phylogenetic analysis. Gene structure and motif descriptions were similar within the same classes. Each CmOMT gene contains at least one cis-acting element associated with hormone transport regulation. Analysis of cis-acting elements illustrated the potential role of CmOMTs in developmental regulation and adaptations to various abiotic and biotic stresses. The RNA-seq and quantitative real-time PCR (qRT-PCR) results indicated that NaCl stress significantly induced CmOMT6/9/14/18 and chilling and high temperature and humidity (HTH) stresses significantly upregulated CmOMT14/18. Furthermore, the expression pattern of CmOMT18 may be associated with Fusarium oxysporum f. sp. melonis race 1.2 (FOM1.2) and powdery mildew resistance. Our study tentatively explored the biological functions of CmOMT genes in various stress regulation pathways and provided a conceptual basis for further detailed studies of the molecular mechanisms.

The regulation of plant cell wall organisation under salt stress

Plant cell wall biosynthesis is a complex and tightly regulated process. The composition and the structure of the cell wall should have a certain level of plasticity to ensure dynamic changes upon encountering environmental stresses or to fulfil the demand of the rapidly growing cells. The status of the cell wall is constantly monitored to facilitate optimal growth through the activation of appropriate stress response mechanisms. Salt stress can severely damage plant cell walls and disrupt the normal growth and development of plants, greatly reducing productivity and yield. Plants respond to salt stress and cope with the resulting damage by altering the synthesis and deposition of the main cell wall components to prevent water loss and decrease the transport of surplus ions into the plant. Such cell wall modifications affect biosynthesis and deposition of the main cell wall components: cellulose, pectins, hemicelluloses, lignin, and suberin. In this review, we highlight the roles of cell wall components in salt stress tolerance and the regulatory mechanisms underlying their maintenance under salt stress conditions.

Genetic and evolutionary dissection of melatonin response signaling facilitates the regulation of plant growth and stress responses

The expansion of gene families during evolution could generate functional diversity among their members to regulate plant growth and development. Melatonin, a phylogenetically ancient molecule, is vital for many aspects of a plant's life. Understanding the functional diversity of the molecular players involved in melatonin biosynthesis, signaling, and metabolism will facilitate the regulation of plant phenotypes. However, the molecular mechanism of melatonin response signaling elements in regulating this network still has many challenges. Here, we provide an in-depth analysis of the functional diversity and evolution of molecular components in melatonin signaling pathway. Genetic analysis of multiple mutants in plant species will shed light on the role of gene families in melatonin regulatory pathways. Phylogenetic analysis of these genes was performed, which will facilitate the identification of melatonin-related genes for future study. Based on the abovementioned signal networks, the mechanism of these genes was summarized to provide reference for studying the regulatory mechanism of melatonin in plant phenotypes. We hope that this work will facilitate melatonin research in higher plants and finely tuned spatio-temporal regulation of melatonin signaling.