Genome-Wide Identification and Characterization of Caffeic Acid O-Methyltransferase Gene Family in Soybean

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.

Identification and virus-induced gene silencing (VIGS) analysis of methyltransferase affecting tomato (Solanum lycopersicum) fruit ripening

MAIN CONCLUSION

Six methyltransferase genes affecting tomato fruit ripening were identified through genome-wide screening, VIGS assay, and expression pattern analysis. The data provide the basis for understanding new mechanisms of methyltransferases. Fruit ripening is a critical stage for the formation of edible quality and seed maturation, which is finely modulated by kinds of factors, including genetic regulators, hormones, external signals, etc. Methyltransferases (MTases), important genetic regulators, play vital roles in plant development through epigenetic regulation, post-translational modification, or other mechanisms. However, the regulatory functions of numerous MTases except DNA methylation in fruit ripening remain limited so far. Here, six MTases, which act on different types of substrates, were identified to affect tomato fruit ripening. First, 35 MTase genes with relatively high expression at breaker (Br) stage of tomato fruit were screened from the tomato MTase gene database encompassing 421 genes totally. Thereafter, six MTase genes were identified as potential regulators of fruit ripening via virus-induced gene silencing (VIGS), including four genes with a positive regulatory role and two genes with a negative regulatory role, respectively. The expression of these six MTase genes exhibited diverse patterns during the fruit ripening process, and responded to various external ripening-related factors, including ethylene, 1-methylcyclopropene (1-MCP), temperature, and light exposure. These results help to further elaborate the biological mechanisms of MTase genes in tomato fruit ripening and enrich the understanding of the regulatory mechanisms of fruit ripening involving MTases, despite of DNA MTases.

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.

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.

Transcriptomic analysis of alternative splicing events for different stages of growth and development in Sistan Yaghooti grape clusters

Sistan Yaghooti grape variety, despite characteristics such as early ripening, is vulnerable to cluster rot due to small berries and dense clusters. In this regard, AS may serve as a regulatory mechanism during developmental processes and in response to environmental signals. RNA-Seq analysis was performed to measure gene expression and the extent of AS events in the cluster growth and development stages of Sistan Yaghooti grape. The number of AS events increased during stages, suggesting that it contributes to the grapevine's adaptability to various stresses. In addition, DEG and DAS genes showed little overlap in cluster growth stages. Functional analysis of 19,194 DAS -gene sets showed that VIT_06s0004g06670 gene is involved in the activation of calcium channels (Ca2+) through the activation of 5 PLC biosynthetic pathways. Among the 27,229 DEG -sets, VIT_07s0005g05320 gene showed higher expression. Interestingly, this gene is involved in the synthesis of an EF -hand domain-containing protein capable of binding to Ca2+ by activating 4 biochemical pathways. These genes increase cytosolic Ca2+ concentration, enhancing plant stress tolerance and resistance to cracking. These results show that AS can respond independently to different types of stress. Among the other DAS genes, the GA2ox gene (VvGA2ox) showed an increase in AS events during cluster development. This gene is critical for initiating the degradation process of GA and plays a crucial role in different stages of seed development. Therefore, it is very likely that this gene is one of the main factors responsible for the density and seedlessness of Sistan Yaghooti grape.

Characterization of sugarcane mutants developed through gamma irradiations for their lignin content and caffeic acid-O-methyl transferase (COMT) gene mutations

PURPOSE

Bagasse, the residue left after extracting juice from sugarcane stalks, is rich in lignocellulosic biomass. The lignin present in this plant biomass is the key factor that hinders the efficient extraction of ethanol from the bagasse. In the current study, γ-irradiated sugarcane mutants were evaluated for variation in lignin content and its corresponding caffeic acid-O-methyl transferase (COMT) gene.

MATERIALS AND METHODS

The acetyl bromide method was used to estimate lignin content in sugarcane mutants. PCR-based cloning of the COMT gene was performed in low lignin mutants as well as control plants in E. coli (strain DH5α) to understand the mechanism of variation at the molecular level. The Sanger sequencing for cloned gene was performed to check variation in gene sequence.

RESULTS

In comparison to the control (21.5%), the mutant plants' lignin content ranged from 13 to 28%. The Sanger sequencing revealed approximately the same length of the gene from mutants as well as a control plant. In comparison to the reference gene, the mutated gene showed SNPs and indels in different regions, which may have an impact on lignin content.

CONCLUSIONS

Therefore, γ-irradiated mutagenesis is an acceptable approach to develop novel mutants of sugarcane with low lignin content to enhance bioethanol production from waste material using bioprocess technology.

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.

In-silico identification and characterization of O-methyltransferase gene family in peanut (Arachis hypogaea L.) reveals their putative roles in development and stress tolerance

Cultivated peanut (Arachis hypogaea) is a leading protein and oil-providing crop and food source in many countries. At the same time, it is affected by a number of biotic and abiotic stresses. O-methyltransferases (OMTs) play important roles in secondary metabolism, biotic and abiotic stress tolerance. However, the OMT genes have not been comprehensively analyzed in peanut. In this study, we performed a genome-wide investigation of A. hypogaea OMT genes (AhOMTs). Gene structure, motifs distribution, phylogenetic history, genome collinearity and duplication of AhOMTs were studied in detail. Promoter cis-elements, protein-protein interactions, and micro-RNAs targeting AhOMTs were also predicted. We also comprehensively studied their expression in different tissues and under different stresses. We identified 116 OMT genes in the genome of cultivated peanut. Phylogenetically, AhOMTs were divided into three groups. Tandem and segmental duplication events played a role in the evolution of AhOMTs, and purifying selection pressure drove the duplication process. AhOMT promoters were enriched in several key cis-elements involved in growth and development, hormones, light, and defense-related activities. Micro-RNAs from 12 different families targeted 35 AhOMTs. GO enrichment analysis indicated that AhOMTs are highly enriched in transferase and catalytic activities, cellular metabolic and biosynthesis processes. Transcriptome datasets revealed that AhOMTs possessed varying expression levels in different tissues and under hormones, water, and temperature stress. Expression profiling based on qRT-PCR results also supported the transcriptome results. This study provides the theoretical basis for further work on the biological roles of AhOMT genes for developmental and stress responses.

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.

Effects of Date Palm Waste Compost Application on Root Proteome Changes of Barley (Hordeum vulgare L.)

Proteomic analysis was performed to investigate the differentially abundant proteins (DAPs) in barley roots during the tillering stage. Bioinformatic tools were used to interpret the biological function, the pathway analysis and the visualisation of the network amongst the identified proteins. A total of 72 DAPs (33 upregulated and 39 downregulated) among a total of 2580 proteins were identified in response to compost treatment, suggesting multiple pathways of primary and secondary metabolism, such as carbohydrates and energy metabolism, phenylpropanoid pathway, glycolysis pathway, protein synthesis and degradation, redox homeostasis, RNA processing, stress response, cytoskeleton organisation, and phytohormone metabolic pathways. The expression of DAPs was further validated by qRT-PCR. The effects on barley plant development, such as the promotion of root growth and biomass increase, were associated with a change in energy metabolism and protein synthesis. The activation of enzymes involved in redox homeostasis and the regulation of stress response proteins suggest a protective effect of compost, consequently improving barley growth and stress acclimation through the reduction of the environmental impact of productive agriculture. Overall, these results may facilitate a better understanding of the molecular mechanism of compost-promoted plant growth and provide valuable information for the identification of critical genes/proteins in barley as potential targets of compost.

Carex rigescens caffeic acid O-methyltransferase gene CrCOMT confer melatonin-mediated drought tolerance in transgenic tobacco

Melatonin is an important, multifunctional protective agent against a variety of abiotic and biotic stressors in plants. Caffeic acid O-methyltransferase (COMT) catalyzes the last step of melatonin synthesis in plants and reportedly participates in the regulation of stress response and tolerance. However, few studies have reported its function in melatonin-mediated drought resistance. In this study, CrCOMT was identified and was strongly induced by drought stress in Carex rigescens. CrCOMT overexpression in transgenic tobacco increased tolerance to drought stress with high levels of seed germination, relative water content, and survival rates. CrCOMT overexpression in tobacco improved membrane stability, and plants exhibited lower relative electrolytic leakage and malondialdehyde content, as well as higher photochemical efficiency than the wildtype (WT) under drought stress. The transgenic plants also had higher levels of proline accumulation and antioxidant enzyme activity, which decreased oxidative stress damage due to reactive oxygen species (ROS) hyperaccumulation under drought stress. The transcription of drought stress response and ROS scavenging genes was significantly higher in the CrCOMT overexpression plants than in the WT plants. In addition, CrCOMT transgenic tobacco plants exhibited higher melatonin content under drought stress conditions. Exogenous melatonin was applied to C. rigescens under drought stress to confirm the function of melatonin in mediating drought tolerance; the relative water content and proline content were higher, and the relative electrolytic leakage was lower in melatonin-treated C. rigescens than in the untreated plants. In summary, these results show that CrCOMT plays a positive role in plant drought stress tolerance by regulating endogenous melatonin content.

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

Caffeic acid O-methyltransferase (COMT) is one of the core enzymes involved in lignin synthesis. However, there is no systematic study on the rice COMT gene family. We identified 33 COMT genes containing the methyltransferase-2 domain in the rice genome using bioinformatic methods and divided them into Group I (a and b) and Group II. Motifs, conserved domains, gene structure and SNPs density are related to the classification of OsCOMTs. The tandem phenomenon plays a key role in the expansion of OsCOMTs. The expression levels of fourteen and thirteen OsCOMTs increased or decreased under salt stress and drought stress, respectively. OsCOMTs showed higher expression levels in the stem. The lignin content of rice was measured in five stages; combined with the expression analysis of OsCOMTs and multiple sequence alignment, we found that OsCOMT8, OsCOMT9 and OsCOMT15 play a key role in the synthesis of lignin. Targeted miRNAs and gene ontology annotation revealed that OsCOMTs were involved in abiotic stress responses. Our study contributes to the analysis of the biological function of OsCOMTs, which may provide information for future rice breeding and editing of the rice genome.

Genome-Wide Identification, Characterization and Expression Analysis of Lipoxygenase Gene Family in Artemisia annua L

Lipoxygenase (LOX) is a ubiquitous oxygenase found in animals and plants and plays a pivotal role in diverse biological processes, including defense and development. Artemisinin, which can only be obtained from Artemisia annua L., is the most effective therapeutic drug for malaria without serious side effects. This study identified and analyzed LOX gene family members in the A. annua genome at the chromosomal level. Twenty LOX genes with various molecular weights, isoelectric points, and amino acid numbers were identified and named AaLOX, which were located in the cytoplasm or chloroplast. The average protein length of all AaLOX was 850 aa. Phylogenetic tree analysis revealed that the AaLOX was divided into two major groups, 9-LOX and 13-LOX. The exon numbers ranged from 1 to 12, indicating that different AaLOX genes have different functions. The secondary structure was mainly composed of alpha helix and random coil, and the tertiary structure was similar for most AaLOX. Upstream promoter region analysis revealed that a large number of cis-acting elements were closely related to plant growth and development, light response, hormone, and other stress responses. Transcriptome data analysis of different tissues suggested that the gene family was differently expressed in the roots, stems, leaves, and flowers of two A. annua strains HAN1 and LQ9. qRT-PCR confirmed that AaLOX5 and AaLOX17 had the highest expression in flowers and leaves. This study provides a theoretical basis for the further functional analysis of the AaLOX gene family.