Sorghum CCoAOMT and CCoAOMT-like gene evolution, structure, expression and the role of conserved amino acids in protein activity

Functional analysis of the CCoAOMT gene in Populus deltoides for enhancing tolerance to Alternaria burnsii

Alternaria blight (Alternaria burnsii ) causes significant economic losses due to defoliation, reduced yields, and poor-quality produce in various crops. Consequently, effective strategies for managing this disease are critical. In this study, the caffeoyl-CoA O-methyltransferase (PdCCoAOMT ) gene, which plays a key role in lignin biosynthesis and plant defense, was isolated from Populus deltoides and investigated for its potential to enhance resistance against A. burnsii , the causal agent of blight of various crop species. The PdCCoAOMT gene (741bp) was cloned, characterised, and expressed in the model plant Nicotiana tabacum via Agrobacterium -mediated transformation. Sequencing of the amplicon followed by BLAST analysis revealed 100% query coverage and 98.52% identity of CCoAOMT with the Populus tomentosa and Populus trichocarpa mRNA. Histochemical GUS staining of the putative transformed leaves displayed a distinct blue colour, predominantly in the veins. Gene expression analysis via real time quantitative PCR of 11 T1 plants showed the highest expression in T1 -6 plant. Overexpression of PdCCoAOMT gene showed a positive correlation with lignin deposition in the transformed plants compared to the control plants. A detached leaf assay for A. burnsii resistance demonstrated a significant negative correlation between lignin deposition and disease severity, suggesting that higher lignin accumulation in the leaf was associated with reduced disease symptoms. This highlights the effectiveness of the gene in mitigating the disease in the transformed tobacco plants. These findings suggest that PdCCoAOMT could be a valuable tool in developing crop varieties resistant to Alternaria blight, providing a promising strategy to combat this economically devastating pathogen.

Genetic improvement of low-lignin poplars: a new strategy based on molecular recognition, chemical reactions and empirical breeding

As an important source of pollution in the papermaking process, the presence of lignin in poplar can seriously affect the quality and process of pulping. During lignin synthesis, Caffeoyl-CoA-O methyltransferase (CCoAOMT), as a specialized catalytic transferase, can effectively regulate the methylation of caffeoyl-coenzyme A (CCoA) to feruloyl-coenzyme A. Targeting CCoAOMT, this study investigated the substrate recognition mechanism and the possible reaction mechanism, the key residues of lignin binding were mutated and the lignin content was validated by deep convolutional neural-network model based on genome-wide prediction (DCNGP). The molecular mechanics results indicate that the binding of S-adenosyl methionine (SAM) and CCoA is sequential, with SAM first binding and inducing inward constriction of the CCoAOMT; then CCoA binds to the pocket, and this process closes the outer channel, preventing contamination by impurities and ensuring that the reaction proceeds. Next, the key residues in the recognition process of SAM (F69 and D91) and CCoA (I40, N170, Y188 and D218) were analyzed, and we identified that K146 as a base catalyst is important for inducing the methylation reaction. Immediately after that, the possible methylation reaction mechanism was deduced by the combination of Restrained Electrostatic Potential (RESP) and Independent Gradient Model (IGM) analysis, focusing on the catalytic center electron cloud density and RESP charge distribution. Finally, the DCNGP results verified that the designed mutant groups were all able to effectively reduce the lignin content and increase the S-lignin content/ G-lignin content ratio, which was beneficial for the subsequent lignin removal. Multifaceted consideration of factors that reduce lignin content and combined deep learning to screen for favorable mutations in target traits provides new ideas for targeted breeding of low-lignin poplars.

Genome-Wide Characterization of Solanum tuberosum CCoAOMT Gene Family and Identification of StCCoAOMT Genes Involved in Anthocyanin Biosynthesis

BACKGROUND

The caffeoyl-CoA-O methyltransferase (CCoAOMT) family plays essential roles in the methylation of various secondary metabolites, including anthocyanins. Despite the wide identification of the CCoAOMT family in plants, the characterization and function of CCoAOMT protein members in Solanum tuberosum remain poorly understood.

METHODS AND RESULTS

In this study, a total of 12 StCCoAOMT members were identified in the genome of S. tuberosum using the Blastp and HMM search and were unevenly located on eight chromosomes. Collinearity analysis revealed that four tandem duplicated gene pairs and two segmental duplicated gene pairs existed in the S. tuberosum genome, demonstrating that duplication events play a key role in the expansion of the CCoAOMT family. All StCCoAOMTs were clustered into group I and group II based on phylogenetic analysis, which was further verified by the conserved motifs and gene structures analysis. The cis-acting elements analysis illustrated that StCCoAOMTs might be important for photosynthesis, hormone responses, and abiotic stress. Expression analysis demonstrated that StCCoAOMT genes have diverse transcript levels in various tissues and that StCCoAOMT10 was significantly expressed in purple potatoes with abundant anthocyanin content according to RNA-seq data and qRT-PCR assays. In addition, the subcellular localization assay validated that the StCCoAOMT10 protein was mainly localized in the cytoplasm and nucleus.

CONCLUSIONS

These results will be of great importance for a better understanding of the features of CCoAOMT family members, especially of the candidate genes involved in the methylation of anthocyanins in S. tuberosum, and also for improving the nutritional quality of S. tuberosum.

Genome-Wide Analysis of Caffeoyl-CoA-O-methyltransferase (CCoAOMT) Family Genes and the Roles of GhCCoAOMT7 in Lignin Synthesis in Cotton

Caffeoyl coenzyme A-O-methyltransferase (CCoAOMT) has a critical function in the lignin biosynthesis pathway. However, its functions in cotton are not clear. In this research, we observed 50 CCoAOMT genes from four cotton species, including two diploids (Gossypium arboretum, 9, and Gossypium raimondii, 8) and two tetraploids (Gossypium hirsutum, 16, and Gossypium barbadense, 17), performed bioinformatic analysis, and focused on the involvement and functions of GhCCoAOMT7 in lignin synthesis of Gossypium hirsutum. CCoAOMT proteins were divided into four subgroups based on the phylogenetic tree analysis. Motif analysis revealed that all CCoAOMT proteins possess conserved Methyltransf_3 domains, and conserved structural features were identified based on the genes' exon-intron organization. A synteny analysis suggested that segmental duplications were the primary cause in the expansion of the CCoAOMT genes family. Transcriptomic data analysis of GhCCoAOMTs revealed that GhCCoAOMT2, GhCCoAOMT7, and GhCCoAOMT14 were highly expressed in stems. Subcellular localization experiments of GhCCoAOMT2, GhCCoAOMT7, and GhCCoAOMT14 showed that GhCCoAOMT2, GhCCoAOMT7, and GhCCoAOMT14 were localized in the nucleus and plasma membrane. However, there are no cis-regulatory elements related to lignin synthesis in the GhCCoAOMT7 gene promoter. GhCCoAOMT7 expression was inhibited by virus-induced gene silencing technology to obtain gene silencing lines, the suppression of GhCCoAOMT7 expression resulted in a 56% reduction in the lignin content in cotton stems, and the phloroglucinol staining area corresponding to the xylem was significantly decreased, indicating that GhCCoAOMT7 positively regulates lignin synthesis. Our results provided fundamental information regarding CCoAOMTs and highlighted their potential functions in cotton lignin biosynthesis and lignification.

Engineered reduction of S-adenosylmethionine alters lignin in sorghum

BACKGROUND

Lignin is an aromatic polymer deposited in secondary cell walls of higher plants to provide strength, rigidity, and hydrophobicity to vascular tissues. Due to its interconnections with cell wall polysaccharides, lignin plays important roles during plant growth and defense, but also has a negative impact on industrial processes aimed at obtaining monosaccharides from plant biomass. Engineering lignin offers a solution to this issue. For example, previous work showed that heterologous expression of a coliphage S-adenosylmethionine hydrolase (AdoMetase) was an effective approach to reduce lignin in the model plant Arabidopsis. The efficacy of this engineering strategy remains to be evaluated in bioenergy crops.

RESULTS

We studied the impact of expressing AdoMetase on lignin synthesis in sorghum (Sorghum bicolor L. Moench). Lignin content, monomer composition, and size, as well as biomass saccharification efficiency were determined in transgenic sorghum lines. The transcriptome and metabolome were analyzed in stems at three developmental stages. Plant growth and biomass composition was further evaluated under field conditions. Results evidenced that lignin was reduced by 18% in the best transgenic line, presumably due to reduced activity of the S-adenosylmethionine-dependent O-methyltransferases involved in lignin synthesis. The modified sorghum features altered lignin monomer composition and increased lignin molecular weights. The degree of methylation of glucuronic acid on xylan was reduced. These changes enabled a ~20% increase in glucose yield after biomass pretreatment and saccharification compared to wild type. RNA-seq and untargeted metabolomic analyses evidenced some pleiotropic effects associated with AdoMetase expression. The transgenic sorghum showed developmental delay and reduced biomass yields at harvest, especially under field growing conditions.

CONCLUSIONS

The expression of AdoMetase represents an effective lignin engineering approach in sorghum. However, considering that this strategy potentially impacts multiple S-adenosylmethionine-dependent methyltransferases, adequate promoters for fine-tuning AdoMetase expression will be needed to mitigate yield penalty.

Duplication and sub-functionalization of flavonoid biosynthesis genes plays important role in Leguminosae root nodule symbiosis evolution

Gene innovation plays an essential role in trait evolution. Rhizobial symbioses, the most important N2-fixing agent in agricultural systems that exists mainly in Leguminosae, is one of the most attractive evolution events. However, the gene innovations underlying Leguminosae root nodule symbiosis (RNS) remain largely unknown. Here, we investigated the gene gain event in Leguminosae RNS evolution through comprehensive phylogenomic analyses. We revealed that Leguminosae-gain genes were acquired by gene duplication and underwent a strong purifying selection. Kyoto Encyclopedia of Genes and Genomes analyses showed that the innovated genes were enriched in flavonoid biosynthesis pathways, particular downstream of chalcone synthase (CHS). Among them, Leguminosae-gain type Ⅱ chalcone isomerase (CHI) could be further divided into CHI1A and CHI1B clades, which resulted from the products of tandem duplication. Furthermore, the duplicated CHI genes exhibited exon-intron structural divergences evolved through exon/intron gain/loss and insertion/deletion. Knocking down CHI1B significantly reduced nodulation in Glycine max (soybean) and Medicago truncatula; whereas, knocking down its duplication gene CHI1A had no effect on nodulation. Therefore, Leguminosae-gain type Ⅱ CHI participated in RNS and the duplicated CHI1A and CHI1B genes exhibited RNS functional divergence. This study provides functional insights into Leguminosae-gain genetic innovation and sub-functionalization after gene duplication that contribute to the evolution and adaptation of RNS in Leguminosae.

Transcriptome analysis provides insights into the cell wall and aluminum toxicity related to rusty root syndrome of Panax ginseng

Rusty root syndrome is a common and serious disease in the process of Panax ginseng cultivation. This disease greatly decreases the production and quality of P. ginseng and causes a severe threat to the healthy development of the ginseng industry. However, its pathogenic mechanism remains unclear. In this study, Illumina high-throughput sequencing (RNA-seq) technology was used for comparative transcriptome analysis of healthy and rusty root-affected ginseng. The roots of rusty ginseng showed 672 upregulated genes and 526 downregulated genes compared with the healthy ginseng roots. There were significant differences in the expression of genes involved in the biosynthesis of secondary metabolites, plant hormone signal transduction, and plant-pathogen interaction. Further analysis showed that the cell wall synthesis and modification of ginseng has a strong response to rusty root syndrome. Furthermore, the rusty ginseng increased aluminum tolerance by inhibiting Al entering cells through external chelating Al and cell wall-binding Al. The present study establishes a molecular model of the ginseng response to rusty roots. Our findings provide new insights into the occurrence of rusty root syndrome, which will reveal the underlying molecular mechanisms of ginseng response to this disease.

Genome-Wide Identification and Expression Analysis of Dendrocalamus farinosus CCoAOMT Gene Family and the Role of DfCCoAOMT14 Involved in Lignin Synthesis

As the main component of plant cell walls, lignin can not only provide mechanical strength and physical defense for plants, but can also be an important indicator affecting the properties and quality of wood and bamboo. Dendrocalamus farinosus is an important economic bamboo species for both shoots and timber in southwest China, with the advantages of fast growth, high yield and slender fiber. Caffeoyl-coenzyme A-O-methyltransferase (CCoAOMT) is a key rate-limiting enzyme in the lignin biosynthesis pathway, but little is known about it in D. farinosus. Here, a total of 17 DfCCoAOMT genes were identified based on the D. farinosus whole genome. DfCCoAOMT1/14/15/16 were homologs of AtCCoAOMT1. DfCCoAOMT6/9/14/15/16 were highly expressed in stems of D. farinosus; this is consistent with the trend of lignin accumulation during bamboo shoot elongation, especially DfCCoAOMT14. The analysis of promoter cis-acting elements suggested that DfCCoAOMTs might be important for photosynthesis, ABA/MeJA responses, drought stress and lignin synthesis. We then confirmed that the expression levels of DfCCoAOMT2/5/6/8/9/14/15 were regulated by ABA/MeJA signaling. In addition, overexpression of DfCCoAOMT14 in transgenic plants significantly increased the lignin content, xylem thickness and drought resistance of plants. Our findings revealed that DfCCoAOMT14 can be a candidate gene that is involved in the drought response and lignin synthesis pathway in plants, which could contribute to the genetic improvement of many important traits in D. farinosus and other species.

Evolution and expression analysis of the caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) gene family in jute (Corchorus L.)

BACKGROUND

Jute is considered one of the most important crops for fiber production and multipurpose usages. Caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) is a crucial enzyme involved in lignin biosynthesis in plants. The potential functions of CCoAOMT in lignin biosynthesis of jute have been reported in several studies. However, little is known about the evolution of the CCoAOMT gene family, and either their expression level at different developing stages in different jute cultivars, as well as under abiotic stresses including salt and drought stress.

RESULTS

In the present study, 66 CCoAOMT genes from 12 species including 12 and eight CCoAOMTs in Corchorus olitorius and C. capsularis were identified. Phylogenetic analysis revealed that CCoAOMTs could be divided into six groups, and gene expansion was observed in C. olitorius. Furthermore, gene expression analysis of developing jute fibers was conducted at different developmental stages (15, 30, 45, 60, and 90 days after sowing [DAS]) in six varieties (Jute-179 [J179], Lubinyuanguo [LB], and Qiongyueqing [QY] for C. capsularis; Funong No.5 [F5], Kuanyechangguo [KY], and Cvlv [CL] for C. olitorius). The results showed that CCoAOMT1 and CCoAOMT2 were the dominant genes in the CCoAOMT family. Of these two dominant CCoAOMTs, CCoAOMT2 showed a constitutive expression level during the entire growth stages, while CCoAOMT1 exhibited differential expression patterns. These two genes showed higher expression levels in C. olitorius than in C. capsularis. The correlation between lignin content and CCoAOMT gene expression levels indicated that this gene family influences the lignin content of jute. Using real-time quantitative reverse transcription PCR (qRT-PCR), a substantial up-regulation of CCoAOMTs was detected in stem tissues of jute 24 h after drought treatment, with an up to 17-fold increase in expression compared to that of untreated plants.

CONCLUSIONS

This study provides a basis for comprehensive genomic studies of the entire CCoAOMT gene family in C. capsularis and C. olitorius. Comparative genomics analysis among the CCoAOMT gene families of 12 species revealed the close evolutionary relationship among Corchorus, Theobroma cacao and Gossypium raimondii. This study also shows that CCoAOMTs are not only involved in lignin biosynthesis, but also are associated with the abiotic stress response in jute, and suggests the potential use of these lignin-related genes to genetically improve the fiber quality of jute.

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.

Identification and analysis of lignin biosynthesis genes related to fruit ripening and stress response in banana (Musa acuminata L. AAA group, cv. Cavendish)

BACKGROUND

Lignin is a key component of the secondary cell wall of plants, providing mechanical support and facilitating water transport as well as having important impact effects in response to a variety of biological and abiotic stresses.

RESULTS

In this study, we identified 104 genes from ten enzyme gene families related to lignin biosynthesis in Musa acuminata genome and found the number of MaCOMT gene family was the largest, while MaC3Hs had only two members. MaPALs retained the original members, and the number of Ma4CLs in lignin biosynthesis was significantly less than that of flavonoids. Segmental duplication existed in most gene families, except for MaC3Hs, and tandem duplication was the main way to expand the number of MaCOMTs. Moreover, the expression profiles of lignin biosynthesis genes during fruit development, postharvest ripening stages and under various abiotic and biological stresses were investigated using available RNA-sequencing data to obtain fruit ripening and stress response candidate genes. Finally, a co-expression network of lignin biosynthesis genes was constructed by weighted gene co-expression network analysis to elucidate the lignin biosynthesis genes that might participate in lignin biosynthesis in banana during development and in response to stresses.

CONCLUSION

This study systematically identified the lignin biosynthesis genes in the Musa acuminata genome, providing important candidate genes for further functional analysis. The identification of the major genes involved in lignin biosynthesis in banana provides the basis for the development of strategies to improve new banana varieties tolerant to biological and abiotic stresses with high yield and high quality.

Caffeoyl-CoA 3-O-methyltransferase gene family in jute: Genome-wide identification, evolutionary progression and transcript profiling under different quandaries

Jute (Corchorus sp.), is a versatile, naturally occurring, biodegradable material that holds the promising possibility of diminishing the extensive use of plastic bags. One of the major components of the cell wall, lignin plays both positive and negative roles in fiber fineness and quality. Although it gives mechanical strength to plants, an excess amount of it is responsible for the diminution of fiber quality. Among various gene families involved in the lignin biosynthesis, Caffeoyl-CoA 3-O-methyltransferase (CCoAOMT) is the most significant and has remained mostly unexplored. In this study, an extensive in-silico characterization of the CCoAOMT gene family was carried out in two jute species (C. capsularis L. and C. olitoroius L.) by analyzing their structural, functional, molecular and evolutionary characteristics. A total of 6 CCoAOMT gene members were identified in each of the two species using published reference genomes. These two jute species showed high syntenic conservation and the identified CCoAOMT genes formed four clusters in the phylogenetic tree. Histochemical assay of lignin in both jute species could shed light on the deposition pattern in stems and how it changes in response to abiotic stresses. Furthermore, expression profiling using qPCR showed considerable alteration of CCoAOMT transcripts under various abiotic stresses and hormonal treatment. This study will lay a base for further analysis and exploration of target candidates for overexpression of gene silencing using modern biotechnological techniques to enhance the quality of this economically important fiber crop.

Genome-wide identification and characterization of caffeoyl-coenzyme A O-methyltransferase genes related to the Fusarium head blight response in wheat

Background

Lignin is one of the main components of the cell wall and is directly associated with plant development and defence mechanisms in plants, especially in response to Fusarium graminearum (Fg) infection. Caffeoyl-coenzyme A O-methyltransferase (CCoAOMT) is the main regulator determining the efficiency of lignin synthesis and composition. Although it has been characterized in many plants, to date, the importance of the CCoAOMT family in wheat is not well understood.

Results

Here, a total of 21 wheat CCoAOMT genes (TaCCoAOMT) were identified through an in silico genome search method and they were classified into four groups based on phylogenetic analysis, with the members of the same group sharing similar gene structures and conserved motif compositions. Furthermore, the expression patterns and co-expression network in which TaCCoAOMT is involved were comprehensively investigated using 48 RNA-seq samples from Fg infected and mock samples of 4 wheat genotypes. Combined with qRT-PCR validation of 11 Fg-responsive TaCCoAOMT genes, potential candidates involved in the FHB response and their regulation modules were preliminarily suggested. Additionally, we investigated the genetic diversity and main haplotypes of these CCoAOMT genes in bread wheat and its relative populations based on resequencing data.

Conclusions

This study identified and characterized the CCoAOMT family in wheat, which not only provided potential targets for further functional analysis, but also contributed to uncovering the mechanism of lignin biosynthesis and its role in FHB tolerance in wheat and beyond.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07849-y.

Transcriptomics of Biostimulation of Plants Under Abiotic Stress

Plant biostimulants are compounds, living microorganisms, or their constituent parts that alter plant development programs. The impact of biostimulants is manifested in several ways: via morphological, physiological, biochemical, epigenomic, proteomic, and transcriptomic changes. For each of these, a response and alteration occur, and these alterations in turn improve metabolic and adaptive performance in the environment. Many studies have been conducted on the effects of different biotic and abiotic stimulants on plants, including many crop species. However, as far as we know, there are no reviews available that describe the impact of biostimulants for a specific field such as transcriptomics, which is the objective of this review. For the commercial registration process of products for agricultural use, it is necessary to distinguish the specific impact of biostimulants from that of other legal categories of products used in agriculture, such as fertilizers and plant hormones. For the chemical or biological classification of biostimulants, the classification is seen as a complex issue, given the great diversity of compounds and organisms that cause biostimulation. However, with an approach focused on the impact on a particular field such as transcriptomics, it is perhaps possible to obtain a criterion that allows biostimulants to be grouped considering their effects on living systems, as well as the overlap of the impact on metabolism, physiology, and morphology occurring between fertilizers, hormones, and biostimulants.

Genome-wide analysis of general phenylpropanoid and monolignol-specific metabolism genes in sugarcane

Lignin is the main component of secondary cell walls and is essential for plant development and defense. However, lignin is recognized as a major recalcitrant factor for efficiency of industrial biomass processing. Genes involved in general phenylpropanoid and monolignol-specific metabolism in sugarcane have been previously analyzed at the transcriptomic level. Nevertheless, the number of genes identified in this species is still very low. The recently released sugarcane genome sequence has allowed the genome-wide characterization of the 11 gene families involved in the monolignol biosynthesis branch of the phenylpropanoid pathway. After an exhaustive analysis of sugarcane genomes, 438 haplotypes derived from 175 candidate genes from Saccharum spontaneum and 144 from Saccharum hybrid R570 were identified as associated with this biosynthetic route. The phylogenetic analyses, combined with the search for protein conserved residues involved in the catalytic activity of the encoded enzymes, were employed to identify the family members potentially involved in developmental lignification. Accordingly, 15 candidates were identified as bona fide lignin biosynthesis genes: PTAL1, PAL2, C4H4, 4CL1, HCT1, HCT2, C3'H1, C3'H2, CCoAOMT1, COMT1, F5H1, CCR1, CCR2, CAD2, and CAD7. For this core set of lignin biosynthetic genes, we searched for the chromosomal location, the gene expression pattern, the promoter cis-acting elements, and microRNA targets. Altogether, our results present a comprehensive characterization of sugarcane general phenylpropanoid and monolignol-specific genes, providing the basis for further functional studies focusing on lignin biosynthesis manipulation and biotechnological strategies to improve sugarcane biomass utilization.

Identification and expression analysis of caffeoyl-coenzyme A O-methyltransferase family genes related to lignin biosynthesis in tea plant (Camellia sinensis)

Tea plant, an economically important crop, is used in producing tea, which is a non-alcoholic beverage. Lignin, the second most abundant component of the cell wall, reduces the tenderness of tea leaves and affects tea quality. Caffeoyl-coenzyme A O-methyltransferase (CCoAOMT) involved in lignin biosynthesis affects the efficiency of lignin synthesis and lignin composition. A total of 10 CsCCoAOMTs were identified based on tea plant genome. Systematic analysis of CCoAOMTs was conducted for its physicochemical properties, phylogenetic relationships, conserved motifs, gene structure, and promoter cis-element prediction. Phylogenetic analysis suggested that all the CsCCoAOMT proteins can be categorized into three clades. The promoters of six CsCCoAOMT genes possessed lignin-specific cis-elements, indicating they are possibly essential for lignin biosynthesis. According to the distinct tempo-spatial expression profiles, five genes were substantially expressed in eight tested tissues. Most CsCCoAOMT genes were expressed in stems and leaves in three tea plant cultivars 'Longjing 43,' 'Anjibaicha,' and 'Fudingdabai' by RT-qPCR detection and analysis. The expression levels of two genes (CsCCoAOMT5 and CsCCoAOMT6) were higher than those of the other genes. The expression levels of most CsCCoAOMT genes in 'Longjing 43' were significantly higher than that those in 'Anjibaicha' and 'Fudingdabai.' Correlation analysis revealed that only the expression levels of CsCCoAOMT6 were positively correlated with lignin content in the leaves and stems. These results lay a foundation for the future exploration of the roles of CsCCoAOMTs in lignin biosynthesis in tea plant.

Identification of genes from the general phenylpropanoid and monolignol-specific metabolism in two sugarcane lignin-contrasting genotypes

The phenylpropanoid pathway is an important route of secondary metabolism involved in the synthesis of different phenolic compounds such as phenylpropenes, anthocyanins, stilbenoids, flavonoids, and monolignols. The flux toward monolignol biosynthesis through the phenylpropanoid pathway is controlled by specific genes from at least ten families. Lignin polymer is one of the major components of the plant cell wall and is mainly responsible for recalcitrance to saccharification in ethanol production from lignocellulosic biomass. Here, we identified and characterized sugarcane candidate genes from the general phenylpropanoid and monolignol-specific metabolism through a search of the sugarcane EST databases, phylogenetic analysis, a search for conserved amino acid residues important for enzymatic function, and analysis of expression patterns during culm development in two lignin-contrasting genotypes. Of these genes, 15 were cloned and, when available, their loci were identified using the recently released sugarcane genomes from Saccharum hybrid R570 and Saccharum spontaneum cultivars. Our analysis points out that ShPAL1, ShPAL2, ShC4H4, Sh4CL1, ShHCT1, ShC3H1, ShC3H2, ShCCoAOMT1, ShCOMT1, ShF5H1, ShCCR1, ShCAD2, and ShCAD7 are strong candidates to be bona fide lignin biosynthesis genes. Together, the results provide information about the candidate genes involved in monolignol biosynthesis in sugarcane and may provide useful information for further molecular genetic studies in sugarcane.

The lignin toolbox of the model grass Setaria viridis

The core set of biosynthetic genes potentially involved in developmental lignification was identified in the model C4 grass Setaria viridis. Lignin has been recognized as a major recalcitrant factor negatively affecting the processing of plant biomass into bioproducts. However, the efficient manipulation of lignin deposition in order to generate optimized crops for the biorefinery requires a fundamental knowledge of several aspects of lignin metabolism, including regulation, biosynthesis and polymerization. The current availability of an annotated genome for the model grass Setaria viridis allows the genome-wide characterization of genes involved in the metabolic pathway leading to the production of monolignols, the main building blocks of lignin. Here we performed a comprehensive study of monolignol biosynthetic genes as an initial step into the characterization of lignin metabolism in S. viridis. A total of 56 genes encoding bona fide enzymes catalyzing the consecutive ten steps of the monolignol biosynthetic pathway were identified in the S. viridis genome. A combination of comparative phylogenetic studies, high-throughput expression analysis and quantitative RT-PCR analysis was further employed to identify the family members potentially involved in developmental lignification. Accordingly, 14 genes clustered with genes from closely related species with a known function in lignification and showed an expression pattern that correlates with lignin deposition. These genes were considered the "core lignin toolbox" responsible for the constitutive, developmental lignification in S. viridis. These results provide the basis for further understanding lignin deposition in C4 grasses and will ultimately allow the validation of biotechnological strategies to produce crops with enhanced processing properties.

Overexpression of the Sorghum bicolor SbCCoAOMT alters cell wall associated hydroxycinnamoyl groups

Sorghum (Sorghum bicolor) is a drought tolerant crop, which is being developed as a bioenergy feedstock. The monolignol biosynthesis pathway is a major focus for altering the abundance and composition of lignin. Caffeoyl coenzyme-A O-methyltransferase (CCoAOMT) is an S-adenosyl methionine (SAM)-dependent O-methyltransferase that methylates caffeoyl-CoA to generate feruloyl-CoA, an intermediate required for the biosynthesis of both G- and S-lignin. SbCCoAOMT was overexpressed to assess the impact of increasing the amount of this enzyme on biomass composition. SbCCoAOMT overexpression increased both soluble and cell wall-bound (esterified) ferulic and sinapic acids, however lignin concentration and its composition (S/G ratio) remained unaffected. This increased deposition of hydroxycinnamic acids in these lines led to an increase in total energy content of the stover. In stalk and leaf midribs, the increased histochemical staining and autofluorescence in the cell walls of the SbCCoAOMT overexpression lines also indicate increased phenolic deposition within cell walls, which is consistent with the chemical analyses of soluble and wall-bound hydroxycinnamic acids. The growth and development of overexpression lines were similar to wild-type plants. Likewise, RNA-seq and metabolite profiling showed that global gene expression and metabolite levels in overexpression lines were also relatively similar to wild-type plants. Our results demonstrate that SbCCoAOMT overexpression significantly altered cell wall composition through increases in cell wall associated hydroxycinnamic acids without altering lignin concentration or affecting plant growth and development.