Genome-wide identification and characterization of DIRIGENT gene family (CcDIR) in pigeonpea (Cajanus cajan L.) provide insights on their spatial expression pattern and relevance to stress response

This study is a thorough characterization of pigeonpea dirigent gene (CcDIR) family, an important component of the lignin biosynthesis pathway. Genome-wide analysis identified 25 CcDIR genes followed by a range of analytical approaches employed to unravel their structural and functional characteristics. Structural examination revealed a classic single exon and no intron arrangement in CcDIRs contributing to our understanding on evolutionary dynamics. Phylogenetic analysis elucidated evolutionary relationships among CcDIR genes with six DIR sub-families, while motif distribution analysis displayed and highlighted ten conserved protein motifs in CcDIRs. Promoter analyses of all the dirigent genes detected 18 stress responsive cis-acting elements offering insights into transcriptional regulation. While spatial expression analyses across six plant tissues showed preferential expression of CcDIR genes, exposure to salt (CcDIR2 and CcDIR9) and herbivory (CcDIR1, CcDIR2, CcDIR3 and CcDIR11), demonstrated potential roles of specific DIRs in plant defense. Interestingly, increased gene expression during herbivory, also correlated with increased lignin content authenticating the specific response. Furthermore, exogenous application of stress hormones, SA and MeJA on leaves significantly induced the expression of CcDIRs that responded to herbivory. Taken together, these findings contribute to a comprehensive understanding of CcDIR genes impacting development and stress response in the important legume pigeonpea.

Genome editing of wood for sustainable pulping

Wood is an abundant and renewable feedstock for pulping and biorefining, but the aromatic polymer lignin greatly limits its efficient use. Sulis et al. recently reported a multiplex CRISPR editing strategy targeting multiple lignin biosynthetic genes to achieve combined lignin modifications, improve wood properties, and make pulping more sustainable.

Genotyping SNPs in lignin biosynthesis gene (CAD1) and transcription factors (MYB1 and MYB2) exhibits association with wood density in teak (Tectona grandis L.f.)

BACKGROUND

Teak (Tectona grandis L.f.), an important source of tropical timber with immense economic value, is a highly outcrossing forest tree species. 150 unrelated accessions of teak (Tectona grandis L.f.) plus trees assembled as clones at National Teak Germplasm Bank, Chandrapur, Maharashtra, India was investigated for association mapping of candidate lignin biosynthesis gene (CAD1) and transcription factors (MYB1 and MYB2).

METHODS AND RESULTS

The CAD1, MYB1 and MYB2 were amplified using specifically designed primers. The amplified sequences were then sequenced and genotyped for 112 SNPs/11 indels. We evaluated the association between SNPs and wood density in teak accessions using GLM and MLM statistical models, with Bonferroni correction applied. The teak accessions recorded an average wood density of 416.69 kg.m-3 (CV 4.97%) and comprised of three loosely structured admixed sub-populations (K = 3), containing 72.05% genetic variation within sub-populations with low intragenic LD (0-21% SNP pairs) at P < 0.05 and high LD decay (33-934 bp) at R2 = 0.1. GLM and MLM models discounting systematic biases (Q and K matrices) to avoid false discovery revealed five loci at rare variants (MAF 0.003) and three loci at common variants (MAF 0.05) to be significantly (P < 0.05) associated with the wood density. However, the stringent Bonferroni correction (4.06-7.04 × 10-4) yielded only a single associated locus (B1485C/A) from exon of MYB1 transcription factor, contributing to about 10.35% phenotypic variation in wood density trait.

CONCLUSION

Scored SNP locus (B1485C/A) can be developed as a molecular probe for selection of improved planting stock with proven wood density trait for a large-scale teak plantation.

VAMP726 from maize and Arabidopsis confers pollen resistance to heat and UV radiation by influencing lignin content of sporopollenin

Sporopollenin in the pollen cell wall protects male gametophytes from stresses. Phenylpropanoid derivatives, including guaiacyl (G) lignin units, are known to be structural components of sporopollenin, but the exact composition of sporopollenin remains to be fully resolved. We analyzed the phenylpropanoid derivatives in sporopollenin from maize and Arabidopsis by thioacidolysis coupled with nuclear magnetic resonance (NMR) and gas chromatography-mass spectrometry (GC-MS). The NMR and GC-MS results confirmed the presence of p-hydroxyphenyl (H), G, and syringyl (S) lignin units in sporopollenin from maize and Arabidopsis. Strikingly, H units account for the majority of lignin monomers in sporopollenin from these species. We next performed a genome-wide association study to explore the genetic basis of maize sporopollenin composition and identified a vesicle-associated membrane protein (ZmVAMP726) that is strongly associated with lignin monomer composition of maize sporopollenin. Genetic manipulation of VAMP726 affected not only lignin monomer composition in sporopollenin but also pollen resistance to heat and UV radiation in maize and Arabidopsis, indicating that VAMP726 is functionally conserved in monocot and dicot plants. Our work provides new insight into the lignin monomers that serve as structural components of sporopollenin and characterizes VAMP726, which affects sporopollenin composition and stress resistance in pollen.

Biochemical and in silico molecular study of caffeic acid-O-methyltransferase enzyme associated with lignin deposition in tall fescue

Caffeic acid-O-methyltransferase (COMT), an important enzyme governing the process of lignification in plants, functions at the level of caffeic acid methylation along with 3-O-methylation of monolignol precursors. The present investigation was carried out to decipher the role of COMT in tall fescue lignification and to clone and characterize the COMT gene. The study on COMT activity variation at different growth stages of tall fescue exhibited a significant increase in activity over all the growth stages of tall fescue. A significant relative increase of 47.8% was observed from the first vegetative to reproductive stage. COMT activity exhibited a strong positive correlation with lignin content suggesting it to be an important enzyme of tall fescue lignification. Amplification and sequencing of tall fescue COMT gene resulted in an amplicon of size 1662 (Accession No.-MW442832) and an ORF of 346 amino acids. The deduced protein was hydrophobic, thermally stable and acidic with molecular formula C1679H2623N445O482S20, molecular mass 37.4 kDa and theoretical pI of 6.12. The protein possesses a conserved dimerization domain with a highly conserved SAM binding site. The COMT protein was found to be a homo-dimer with 1 catalytic SAH/SAM ligand per monomer interacting with 14 amino acid residues within 4 Å region.

Seasonal Developing Xylem Transcriptome Analysis of Pinus densiflora Unveils Novel Insights for Compression Wood Formation

Wood is the most important renewable resource not only for numerous practical utilizations but also for mitigating the global climate crisis by sequestering atmospheric carbon dioxide. The compressed wood (CW) of gymnosperms, such as conifers, plays a pivotal role in determining the structure of the tree through the reorientation of stems displaced by environmental forces and is characterized by a high content of lignin. Despite extensive studies on many genes involved in wood formation, the molecular mechanisms underlying seasonal and, particularly, CW formation remain unclear. This study examined the seasonal dynamics of two wood tissue types in Pinus densiflora: CW and opposite wood (OW). RNA sequencing of developing xylem for two consecutive years revealed comprehensive transcriptome changes and unique differences in CW and OW across seasons. During growth periods, such as spring and summer, we identified 2255 transcripts with differential expression in CW, with an upregulation in lignin biosynthesis genes and significant downregulation in stress response genes. Notably, among the laccases critical for monolignol polymerization, PdeLAC17 was found to be specifically expressed in CW, suggesting its vital role in CW formation. PdeERF4, an ERF transcription factor preferentially expressed in CW, seems to regulate PdeLAC17 activity. This research provides an initial insight into the transcriptional regulation of seasonal CW development in P. densiflora, forming a foundation for future studies to enhance our comprehension of wood formation in gymnosperms.

Morpho-physiological traits and SSR markers-based analysis of relationships and genetic diversity among fodder maize landraces in India

BACKGROUND

Maize is an excellent fodder crop due to its high biomass, better palatability, succulency, and nutrition. Studies on morpho-physiological and biochemical characterization of fodder maize are limited. The present study aimed to explore the genetic variation in fodder maize landraces for various morpho-physiological traits and estimation of genetic relationship and population structure.

METHODS AND RESULTS

The study on 47 fodder maize landraces revealed significant variation for all morpho-physiological traits except leaf-stem ratio. Plant height, stem girth, leaf-width and number of leaves showed positive correlation with green fodder yield. Morpho-physiological traits-based clustering grouped the landraces into three major clusters, whereas neighbour joining cluster and population structure analysis using 40 SSR markers revealed four and five major groups, respectively. Most landraces of Northern Himalaya-Kashmir and Ludhiana fall into a single group, whereas rest groups mainly had landraces from North-Eastern Himalaya. A total of 101 alleles were generated with mean polymorphic information content value of 0.36 and major allele frequency of 0.68. The pair wise genetic dissimilarity between genotypes ranged from 0.21 to 0.67. Mantel test revealed weak but significant correlation between morphological and molecular distance. Biochemical characterisation of superior landraces revealed significant variation for neutral detergent fibre, acid detergent fibre, cellulose and lignin content.

CONCLUSION

Interestingly, significant, and positive correlation of SPAD with lignin content can be explored to bypass the costly affair of invitro quality assessment for digestibility parameters. The study identified superior landraces and demonstrated the use of molecular markers in genetic diversity assessment and grouping of genotypes for fodder maize improvement.

Multiplex CRISPR editing of wood for sustainable fiber production

The domestication of forest trees for a more sustainable fiber bioeconomy has long been hindered by the complexity and plasticity of lignin, a biopolymer in wood that is recalcitrant to chemical and enzymatic degradation. Here, we show that multiplex CRISPR editing enables precise woody feedstock design for combinatorial improvement of lignin composition and wood properties. By assessing every possible combination of 69,123 multigenic editing strategies for 21 lignin biosynthesis genes, we deduced seven different genome editing strategies targeting the concurrent alteration of up to six genes and produced 174 edited poplar variants. CRISPR editing increased the wood carbohydrate-to-lignin ratio up to 228% that of wild type, leading to more-efficient fiber pulping. The edited wood alleviates a major fiber-production bottleneck regardless of changes in tree growth rate and could bring unprecedented operational efficiencies, bioeconomic opportunities, and environmental benefits.

Genetic editing of wood for sustainability

Trees engineered to have less lignin could make paper production less polluting.

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.

The MYB transcription factor Seed Shattering 11 controls seed shattering by repressing lignin synthesis in African rice

African cultivated rice (Oryza glaberrima Steud.) was domesticated from its wild progenitor species (Oryza barthii) about 3000 years ago. Seed shattering is one of the main constraints on grain production in African cultivated rice, which causes severe grain losses during harvest. By contrast, Asian cultivated rice (Oryza sativa) displays greater resistance to seed shattering, allowing higher grain production. A better understanding in regulation of seed shattering would help to improve harvesting efficiency in African cultivated rice. Here, we report the map-based cloning and characterization of OgSH11, a MYB transcription factor controlling seed shattering in O. glaberrima. OgSH11 represses the expression of lignin biosynthesis genes and lignin deposition by binding to the promoter of GH2. We successfully developed a new O. glaberrima material showing significantly reduced seed shattering by knockout of SH11 in O. glaberrima using CRISPR-Cas9 mediated approach. Identification of SH11 not only supplies a new target for seed shattering improvement in African cultivated rice, but also provides new insights into the molecular mechanism of abscission layer development.

Acibenzolar-S-methyl activates calcium signalling to mediate lignin synthesis in the exocarp of Docteur Jules Guyot pears

'Docteur Jules Guyot' pears were immersed in acibenzolar-S-methyl (ASM) and 0.01 mol L^-1 ethyl glycol tetra acetic acid (EGTA) to investigate the changes of Ca²⁺ receptor proteins and phenylpropanoid pathway. Results showed that ASM treatment increased the activities of phenylalanine ammonia-lyase (PAL), cinnamate-4-hydroxylase (C4H), 4-coumarate coenzyme A ligase (4CL), polyphenol oxidase (PPO), and cinnamyl alcohol dehydrogenase (CAD) in the exocarp of pears, whereas EGTA pre-treatment inhibited the activities of these enzymes. ASM treatment also enhanced the transcription of PcPAL, PcC4H, Pc4CL, PcC3H, PcCOMT, PcCCoAOMT, PcCCR, PcPOD, PcCDPK1, PcCDPK2, PcCDPK5, PcCDPK11, PcCDPK13, PcCBL1, PcCBL9, PcCIPK14, and PcCML27 in pears. EGTA + ASM treatments inhibited the transcription of PcPAL, PcC4H, Pc4CL, PcC3H, PcCCR, PcF5H, PcCAD, PcCDPK11, PcCDPK26, PcCDPK32, PcCBL1, PcCIPK14, PcCIPK23, and PcCaM in the fruit. All these results indicated that ASM induced the gene expressions of Ca²⁺ receptor proteins, the key enzyme activities and gene expressions in phenylpropanoid pathway; Ca²⁺ mediated phenylpropane metabolism in pears after ASM treatment.

The Larix kaempferi genome reveals new insights into wood properties

Here, through single-molecule real-time sequencing, we present a high-quality genome sequence of the Japanese larch (Larix kaempferi), a conifer species with great value for wood production and ecological afforestation. The assembled genome is 10.97 Gb in size, harboring 45,828 protein-coding genes. Of the genome, 66.8% consists of repeat sequences, of which long terminal repeat retrotransposons are dominant and make up 69.86%. We find that tandem duplications have been responsible for the expansion of genes involved in transcriptional regulation and stress responses, unveiling their crucial roles in adaptive evolution. Population transcriptome analysis reveals that lignin content in L. kaempferi is mainly determined by the process of monolignol polymerization. The expression values of six genes (LkCOMT7, LkCOMT8, LkLAC23, LkLAC102, LkPRX148, and LkPRX166) have significantly positive correlations with lignin content. These results indicated that the increased expression of these six genes might be responsible for the high lignin content of the larches' wood. Overall, this study provides new genome resources for investigating the evolution and biological function of conifer trees, and also offers new insights into wood properties of larches.

Transcriptome Analysis Reveals Candidate Lignin-Related Genes and Transcription Factors during Fruit Development in Pomelo (Citrus maxima)

Juice sac granulation (a physiological disorder) leads to large postharvest losses of pomelo (Citrus maxima). Previous studies have shown that juice sac granulation is closely related to lignin accumulation, while the molecular mechanisms underlying this disorder remain elusive in pomelo. Our results showed that the lignin content in NC (near the core) and FC (far away from the core) juice sacs overall increased from 157 DPA (days post anthesis) to 212 DPA and reached a maximum at 212 DPA. Additionally, the lignin content of NC juice sacs was higher than that of FC juice sacs. In this study, we used transcriptome-based weighted gene co-expression network analysis (WGCNA) to address how lignin formation in NC and FC juice sacs is generated during the development of pomelo. After data assembly and bioinformatic analysis, we found a most correlated module (black module) to the lignin content, then we used the 11 DEGs in this module as hub genes for lignin biosynthesis. Among these DEGs, PAL (phenylalanine ammonia lyase), HCT (hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase), 4CL2 (4-coumarate: CoA ligase), C4H (cinnamate 4-hydroxylase), C3'H (p-coumarate 3-hydroxylase), and CCoAOMT1 (caffeoyl CoA 3-Omethyltransferase) were the most distinct DEGs in granulated juice sacs. Co-expression analysis revealed that the expression patterns of several transcription factors such as MYB, NAC, OFP6, and bHLH130 are highly correlated with lignin formation. In addition, the expression patterns of the DEGs related to lignin biosynthesis and transcription factors were validated by qRT-PCR, and the results were highly concordant with the RNA-seq results. These results would be beneficial for further studies on the molecular mechanism of lignin accumulation in pomelo juice sacs and would help with citrus breeding.

Integrated Degradome and Srna Sequencing Revealed miRNA-mRNA Regulatory Networks between the Phloem and Developing Xylem of Poplar

Lignin and cellulose are the most abundant natural organic polymers in nature. MiRNAs are a class of regulatory RNAs discovered in mammals, plants, viruses, and bacteria. Studies have shown that miRNAs play a role in lignin and cellulose biosynthesis by targeting key enzymes. However, the specific miRNAs functioning in the phloem and developing xylem of Populus deltoides are still unknown. In this study, a total of 134 miRNAs were identified via high-throughput small RNA sequencing, including 132 known and two novel miRNAs, six of which were only expressed in the phloem. A total of 58 differentially expressed miRNAs (DEmiRNAs) were identified between the developing xylem and the phloem. Among these miRNAs, 21 were significantly upregulated in the developing xylem in contrast to the phloem and 37 were significantly downregulated. A total of 2431 target genes of 134 miRNAs were obtained via high-throughput degradome sequencing. Most target genes of these miRNAs were transcription factors, including AP2, ARF, bHLH, bZIP, GRAS, GRF, MYB, NAC, TCP, and WRKY genes. Furthermore, 13 and nine miRNAs were involved in lignin and cellulose biosynthesis, respectively, and we validated the miRNAs via qRT-PCR. Our study explores these miRNAs and their regulatory networks in the phloem and developing xylem of P.deltoides and provides new insight into wood formation.

Identification of a novel laccase gene EuLAC1 and its potential resistance against Botrytis cinerea

In this study, a novel laccase gene, EuLAC1, was cloned from Eucommia ulmoides Oliver (E. ulmoides). An overexpression vector harboring the EuLAC1 was constructed and introduced into the tobacco (Nicotiana tabacum cv. Xanthi). The laccase activity, resistance to Botrytis cinerea (B. cinerea) and lignin level in wild-type and transgenic plants were thereafter investigated. Interestingly, the transgenic tobacco displayed a significantly higher laccase activity and resistance to gray mold as compared to the wild-type tobacco. Additionally, the lignin contents in the leaves and stems of the transgenic tobacco were significantly higher in comparison to the wild-type tobacco. Scanning electron microscopy was used to observe the cross sections of wild-type and transgenic tobacco stems and it was noted that the cell wall near the xylem catheter of the transgenic tobacco was substantially thicker and the outline clearer than that of the wild-type. Thus, the EuLAC1 gene can significantly increase laccase activity and lignin content in tobacco, leading to an increase in the physical defenses, thereby increasing tobacco resistance to gray mold.

Genome-wide association study for lignocellulosic compounds and fermentable sugar in rice straw

Cellulose and lignin are the two main components of secondary plant cell walls with substantial impact on stalk in the field and on straw during industrial processing. The amount of fermentable sugar that can be accessed is another important parameter affecting various industrial applications. In the present study, genetic variability of rice (Oryza sativa L.) genotypes for cellulose, lignin, and fermentable sugars contents was analyzed in rice straw. A genome-wide association study of 33,484 single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) >0.05 was performed. The genome-wide association study identified seven, three, and three genomic regions to be significantly associated with cellulose, lignin, and fermentable sugar contents, respectively. Candidate genes in the associated genomic regions were enzymes mainly involved in cell wall metabolism. Novel SNP markers associated with cellulose were tagged to GH16, peroxidase, GT6, GT8, and CSLD2. For lignin content, Villin protein, OsWAK1/50/52/53, and GH16 were identified. For fermentable sugar content, UTP-glucose-1-phosphate uridylyltransferase, BRASSINOSTEROID INSENSITIVE 1, and receptor-like protein kinase 5 were found. The results of this study should improve our understanding of the genetic basis of the factors that might be involved in biosynthesis, turnover, and modification of major cell wall components and saccharides in rice straw.

Lignin Synthesis, Affected by Sucrose in Lotus (Nelumbo nucifera) Seedlings, Was Involved in Regulation of Root Formation in the Arabidopsis thanliana

Adventitious roots (ARs) have an unmatched status in plant growth and metabolism due to the degeneration of primary roots in lotuses. In the present study, we sought to assess the effect of sucrose on ARs formation and observed that lignin synthesis was involved in ARs development. We found that the lignification degree of the ARs primordium was weaker in plants treated with 20 g/L sucrose than in 50 g/L sucrose treatment and control plants. The contents of lignin were lower in plants treated with 20 g/L sucrose and higher in plants treated with 50 g/L sucrose. The precursors of monomer lignin, including p-coumaric acid, caffeate, sinapinal aldehyde, and ferulic acid, were lower in the GL50 library than in the GL20 library. Further analysis revealed that the gene expression of these four metabolites had no novel difference in the GL50/GL20 libraries. However, a laccase17 gene (NnLAC17), involved in polymer lignin synthesis, had a higher expression in the GL50 library than in the GL20 library. Therefore, NnLAC17 was cloned and the overexpression of NnLAC17 was found to directly result in a decrease in the root number in transgenic Arabidopsis plants. These findings suggest that lignin synthesis is probably involved in ARs formation in lotus seedlings.

Characterization and Interaction Analysis of the Secondary Cell Wall Synthesis-Related Transcription Factor PmMYB7 in Pinus massoniana Lamb

In vascular plants, the importance of R2R3-myeloblastosis (R2R3-MYB) transcription factors (TFs) in the formation of secondary cell walls (SCWs) has long been a controversial topic due to the lack of empirical evidence of an association between TFs and downstream target genes. Here, we found that the transcription factor PmMYB7, which belongs to the R2R3-MYB subfamily, is involved in lignin biosynthesis in Pinus massoniana. PmMYB7 was highly expressed in lignified tissues and upon abiotic stress. As a bait carrier, the PmMYB7 protein had no toxicity or autoactivation in the nucleus. Forty-seven proteins were screened from the P. massoniana yeast library. These proteins were predicted to be mainly involved in resistance, abiotic stress, cell wall biosynthesis, and cell development. We found that the PmMYB7 protein interacted with caffeoyl CoA 3-O-methyltransferase-2 (PmCCoAOMT2)—which is involved in lignin biosynthesis—but not with beta-1, 2-xylosyltransferase (PmXYXT1) yeast two-hybrid (Y2H) studies. Our in vivo coimmunoprecipitation (Co-IP) assay further showed that the PmMYB7 and PmCCoAOMT2 proteins could interact. Therefore, we concluded that PmMYB7 is an upstream TF that can interact with PmCCoAOMT2 in plant cells. These findings lay a foundation for further research on the function of PmMYB7, lignin biosynthesis and molecular breeding in P. massoniana.

pHBMT1, a BAHD-family monolignol acyltransferase, mediates lignin acylation in poplar

Poplar (Populus) lignin is naturally acylated with p-hydroxybenzoate ester moieties. However, the enzyme(s) involved in the biosynthesis of the monolignol-p-hydroxybenzoates have remained largely unknown. Here, we performed an in vitro screen of the Populus trichocarpa BAHD acyltransferase superfamily (116 genes) using a wheatgerm cell-free translation system and found five enzymes capable of producing monolignol-p-hydroxybenzoates. We then compared the transcript abundance of the five corresponding genes with p-hydroxybenzoate concentrations using naturally occurring unrelated genotypes of P. trichocarpa and revealed a positive correlation between the expression of p-hydroxybenzoyl-CoA monolig-nol transferase (pHBMT1, Potri.001G448000) and p-hydroxybenzoate levels. To test whether pHBMT1 is responsible for the biosynthesis of monolignol-p-hydroxybenzoates, we overexpressed pHBMT1 in hybrid poplar (Populus alba × P. grandidentata) (35S::pHBMT1 and C4H::pHBMT1). Using three complementary analytical methods, we showed that there was an increase in soluble monolignol-p-hydroxybenzoates and cell-wall-bound monolignol-p-hydroxybenzoates in the poplar transgenics. As these pendent groups are ester-linked, saponification releases p-hydroxybenzoate, a precursor to parabens that are used in pharmaceuticals and cosmetics. This identified gene could therefore be used to engineer lignocellulosic biomass with increased value for emerging biorefinery strategies.

REPRISAL: mapping lignification dynamics using chemistry, data segmentation, and ratiometric analysis

This article describes a methodology for detailed mapping of the lignification capacity of plant cell walls that we have called "REPRISAL" for REPorter Ratiometrics Integrating Segmentation for Analyzing Lignification. REPRISAL consists of the combination of three separate approaches. In the first approach, H*, G*, and S* monolignol chemical reporters, corresponding to p-coumaryl alcohol, coniferyl alcohol, and sinapyl alcohol, are used to label the growing lignin polymer in a fluorescent triple labeling strategy based on the sequential use of three main bioorthogonal chemical reactions. In the second step, an automatic parametric and/or artificial intelligence segmentation algorithm is developed that assigns fluorescent image pixels to three distinct cell wall zones corresponding to cell corners, compound middle lamella and secondary cell walls. The last step corresponds to the exploitation of a ratiometric approach enabling statistical analyses of differences in monolignol reporter distribution (ratiometric method [RM] 1) and proportions (RM 2) within the different cell wall zones. We first describe the use of this methodology to map developmentally related changes in the lignification capacity of wild-type Arabidopsis (Arabidopsis thaliana) interfascicular fiber cells. We then apply REPRISAL to analyze the Arabidopsis peroxidase (PRX) mutant prx64 and provide further evidence for the implication of the AtPRX64 protein in floral stem lignification. In addition, we also demonstrate the general applicability of REPRISAL by using it to map lignification capacity in poplar (Populus tremula × Populus alba), flax (Linum usitatissimum), and maize (Zea mays). Finally, we show that the methodology can be used to map the incorporation of a fucose reporter into noncellulosic cell wall polymers.

Exogenous chalcone synthase expression in developing poplar xylem incorporates naringenin into lignins

Lignin, a polyphenolic polymer, is a major chemical constituent of the cell walls of terrestrial plants. The biosynthesis of lignin is a highly plastic process, as highlighted by an increasing number of noncanonical monomers that have been successfully identified in an array of plants. Here, we engineered hybrid poplar (Populus alba x grandidentata) to express chalcone synthase 3 (MdCHS3) derived from apple (Malus domestica) in lignifying xylem. Transgenic trees displayed an accumulation of the flavonoid naringenin in xylem methanolic extracts not inherently observed in wild-type trees. Nuclear magnetic resonance analysis revealed the presence of naringenin in the extract-free, cellulase-treated xylem lignin of MdCHS3-poplar, indicating the incorporation of this flavonoid-derived compound into poplar secondary cell wall lignins. The transgenic trees also displayed lower total cell wall lignin content and increased cell wall carbohydrate content and performed significantly better in limited saccharification assays than their wild-type counterparts.

Homeostatic regulation of flavonoid and lignin biosynthesis in phenylpropanoid pathway of transgenic tobacco

Flavonoids and lignin consist of a large number of secondarymetabolites which are derived from the phenylpropanoid pathway, and they act as a significant role in plant growth, development, and stress response. However, few reports have documented that how different subbranches of phenylpropanoid metablolic pathway mutually interact. In Arabidopsis, AtCPC (AtCAPRICE) is known to play a negative role in anthocyanin accumulation. Nonetheless, whether AtCPC could control the biosynthesis of lignin is largely unknown. Additionally, whether the RrFLS and RrANR, flavonol synthase and anthocyanidin reductase, from Rosa rugosa regulate different branches of phenylpropanoid pathway is unclear. Here, we performed a series of transgenic experiments with short life cycle tobacco and RNA-Seq analysis. Finally, a series of assays related to biological, physiological, and phenotypic characteristics were undertaken. Our results indicated that ectopic expression of AtCPC in tobacco not only decreased the flavonoid compound accumulation, but also up-regulated several lignin biosynthetic genes, and significantly increased the accumulation of lignin. Our results also revealed that although they respectively improved the flavonol and proanthocyanidin contents, the overexpression of RrFLS and RrANR plays positive roles in lignin biosynthesis in transgenic tobacco plants. Our findings provide a novel insight into the mechanism underlying homeostatic regulation of flavonoid and lignin biosynthesis in phenylpropanoid pathway of plants.

Molecular cloning and characterization of two distinct caffeoyl CoA O-methyltransferases (CCoAOMTs) from the liverwort Marchantia paleacea

Caffeoyl CoA O-methyltransferases (CCoAOMTs) catalyze the transfer of a methyl group from S-adenosylmethionine to a hydroxyl moiety of caffeoyl-CoA as part of the lignin biosynthetic pathway. CCoAOMT-like proteins also catalyze to a variety of flavonoids, coumarins, and phenylpropanoids. Several CCoAOMTs that prefer flavonoids as substrates have been characterized from liverworts. Here, we cloned two CCoAOMT genes, MpalOMT2 and MpalOMT3, from the liverwort Marchantia paleacea. MpalOMT3 has a second ATG codon downstream and the truncated version that lacks 11 amino acids was named MpalOMT3-Tr. Phylogenetic analysis placed MpalOMT3 at the root of the clade with true CCoAOMTs from vascular plants and placed MpalOMT2 between the CCoAOMT and CCoAOMT-like proteins. Recombinant OMTs methylated caffeoyl CoA, phenylpropanoids, and flavonoids containing two or three vicinal hydroxyl groups. MpalOMT3 showed higher catalytic activity for phenylpropanoids than MpalOMT2, but MpalOMT2 showed more promiscuous towards eriodictyol and myricetin. The lignin content in Arabidopsis thaliana stems increased with constitutive heterologous expression of MpalOMT3-Tr, but not MpalOMT2. Subcellular localization experiments indicated that the N-terminus of MpalOMT3 probably served as a chloroplast transit peptide and inhibited its enzymatic activity. Combining the phylogenetic analysis and functional characterization, we conclude that the liverwort M. paleacea harbors true CCoAOMT and CCoAOMT-like genes.

Systematic Analysis and Biochemical Characterization of the Caffeoyl Shikimate Esterase Gene Family in Poplar

Caffeoyl shikimate esterase (CSE) hydrolyzes caffeoyl shikimate into caffeate and shikimate in the phenylpropanoid pathway. In this study, we performed a systematic analysis of the CSE gene family and investigated the possible roles of CSE and CSE-like genes in Populus. We conducted a genome-wide analysis of the CSE gene family, including functional and phylogenetic analyses of CSE and CSE-like genes, using the poplar (Populus trichocarpa) genome. Eighteen CSE and CSE-like genes were identified in the Populus genome, and five phylogenetic groups were identified from phylogenetic analysis. CSEs in Group Ia, which were proposed as bona fide CSEs, have probably been lost in most monocots except Oryza sativa. Primary functional classification showed that PoptrCSE1 and PoptrCSE2 had putative function in lignin biosynthesis. In addition, PoptrCSE2, along with PoptrCSE12, might also respond to stress with a function in cell wall biosynthesis. Enzymatic assay of PoptoCSE1 (Populus tomentosa), -2 and -12 showed that PoptoCSE1 and -2 maintained CSE activity. PoptoCSE1 and 2 had similar biochemical properties, tissue expression patterns and subcellular localization. Most of the PoptrCSE-like genes are homologs of AtMAGL (monoacylglycerol lipase) genes in Arabidopsis and may function as MAG lipase in poplar. Our study provides a systematic understanding of this novel gene family and suggests the function of CSE in monolignol biosynthesis in Populus.

The SlHB8 Acts as a Negative Regulator in Stem Development and Lignin Biosynthesis

The stem is an important organ in supporting plant body, transporting nutrients and communicating signals for plant growing. However, studies on the regulation of stem development in tomato are rather limited. In our study, we demonstrated that SlHB8 negatively regulated tomato stem development. SlHB8 belongs to homeo domain-leucine zipper Class III gene family transcription factors and expressed in all the organs examined including root, stem, leaves, flower, and fruit. Among these tissues, SlHB8 showed stable high expression level during tomato stem development. Overexpression of SlHB8 gene decreased stem diameter with inhibited xylem width and xylem cell layers, while loss of function of SlHB8gene increased the stem diameter and xylem width. The contents of lignin were decreased both in leaves and stems of SlHB8 overexpression plants. RNA-seq analysis on the stems of wild type and SlHB8 transgenic plants showed that the 116 DEGs (differential expressed genes) with reversible expression profiles in SlHB8-ox and SlHB8-cr plants were significantly enriched in the phenylpropanoid biosynthesis pathway and plant-pathogen pathway which were related to lignin biosynthesis and disease resistance. Meanwhile, the key genes involved in the lignin biosynthesis pathway such as SlCCR (cinnamoyl-CoA reductase), SlCYP73A14/C4H (cinnamate 4-hydroxylase), SlC3H (coumarate 3-hydroxylase) and SlCAD (cinnamoyl alcohol dehydrogenase) were down-regulated in both stem and leaves of SlHB8 overexpression plants, indicating a negative regulatory role of SlHB8 in the lignin biosynthesis and stem development.

A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit

BACKGROUND

Stone cells in fruits of pear (Pyrus pyrifolia) negatively influence fruit quality because their lignified cell walls impart a coarse and granular texture to the fruit flesh.

RESULTS

We generate RNA-seq data from the developing fruits of 206 pear cultivars with a wide range of stone cell contents and use a systems genetics approach to integrate co-expression networks and expression quantitative trait loci (eQTLs) to characterize the regulatory mechanisms controlling lignocellulose formation in the stone cells of pear fruits. Our data with a total of 35,897 expressed genes and 974,404 SNPs support the identification of seven stone cell formation modules and the detection of 139,515 eQTLs for 3229 genes in these modules. Focusing on regulatory factors and using a co-expression network comprising 39 structural genes, we identify PbrNSC as a candidate regulator of stone cell formation. We then verify the function of PbrNSC in regulating lignocellulose formation using both pear fruit and Arabidopsis plants and further show that PbrNSC can transcriptionally activate multiple target genes involved in secondary cell wall formation.

CONCLUSIONS

This study generates a large resource for studying stone cell formation and provides insights into gene regulatory networks controlling the formation of stone cell and lignocellulose.

Application of CRISPR/Cas9 Tools for Genome Editing in the White-Rot Fungus Dichomitus squalens

Dichomitus squalens is an emerging reference species that can be used to investigate white-rot fungal plant biomass degradation, as it has flexible physiology to utilize different types of biomass as sources of carbon and energy. Recent comparative (post-) genomic studies on D. squalens resulted in an increasingly detailed knowledge of the genes and enzymes involved in the lignocellulose breakdown in this fungus and showed a complex transcriptional response in the presence of lignocellulose-derived compounds. To fully utilize this increasing amount of data, efficient and reliable genetic manipulation tools are needed, e.g., to characterize the function of certain proteins in vivo and facilitate the construction of strains with enhanced lignocellulolytic capabilities. However, precise genome alterations are often very difficult in wild-type basidiomycetes partially due to extremely low frequencies of homology directed recombination (HDR) and limited availability of selectable markers. To overcome these obstacles, we assessed various Cas9-single guide RNA (sgRNA) ribonucleoprotein (RNP) -based strategies for selectable homology and non-homologous end joining (NHEJ) -based gene editing in D. squalens. We also showed an induction of HDR-based genetic modifications by using single-stranded oligodeoxynucleotides (ssODNs) in a basidiomycete fungus for the first time. This paper provides directions for the application of targeted CRISPR/Cas9-based genome editing in D. squalens and other wild-type (basidiomycete) fungi.

Bm-miR172c-5p Regulates Lignin Biosynthesis and Secondary Xylem Thickness by Altering the Ferulate 5 Hydroxylase Gene in Bacopa monnieri

MicroRNAs (miRNAs) are small non-coding, endogenous RNAs containing 20-24 nucleotides that regulate the expression of target genes involved in various plant processes. A total of 1,429 conserved miRNAs belonging to 95 conserved miRNA families and 12 novel miRNAs were identified from Bacopa monnieri using small RNA sequencing. The Bm-miRNA target transcripts related to the secondary metabolism were further selected for validation. The Bm-miRNA expression in shoot and root tissues was negatively correlated with their target transcripts. The Bm-miRNA cleavage sites were mapped within the coding or untranslated region as depicted by the modified RLM-RACE. In the present study, we validate three miRNA targets, including asparagine synthetase, cycloartenol synthase and ferulate 5 hydroxylase (F5H) and elucidate the regulatory role of Bm-miR172c-5p, which cleaves the F5H gene involved in the lignin biosynthesis. Overexpression (OE) of Bm-miR172c-5p precursor in B. monnieri suppresses F5H gene, leading to reduced lignification and secondary xylem thickness under control and drought stress. By contrast, OE of endogenous target mimics (eTMs) showed enhanced lignification and secondary xylem thickness leading to better physiological response under drought stress. Taken together, we suggest that Bm-miRNA172c-5p might be a key player in maintaining the native phenotype of B. monnieri under control and different environmental conditions.

An aptamer highly specific to cellulose enables the analysis of the association of cellulose with matrix cell wall polymers in vitro and in muro

The current toolbox of cell wall-directed molecular probes has been pivotal for advancing basic and application-oriented plant carbohydrate research; however, it still exhibits limitations regarding target diversity and specificity. Scarcity of probes targeting intramolecular associations between cell wall polymers particularly hinders our understanding of the cell wall microstructure and affects the development of effective means for its efficient deconstruction for bioconversion. Here we report a detailed characterization of a cellulose-binding DNA aptamer CELAPT MINI using a combination of various in vitro biochemical, biophysical, and molecular biology techniques. Our results show evidence for its high specificity towards long non-substituted β-(1-4)-glucan chains in both crystalline and amorphous forms. Fluorescent conjugates of CELAPT MINI are applicable as in situ cellulose probes and are well suited for various microscopy techniques, including super-resolution imaging. Compatibility of fluorescent CELAPT MINI variants with immunodetection of cell wall matrix polymers enabled them simultaneously to resolve the fibrillar organization of complex cellulose-enriched pulp material and to quantify the level of cellulose masking by xyloglucan and xylan. Using enzymatically, chemically, or genetically modulated Brachypodium internode sections we showed the diversity in cell wall packing among various cell types and even cell wall microdomains. We showed that xylan is the most prominent, but not the only, cellulose-masking agent in Brachypodium internode tissues. These results collectively highlight the hitherto unexplored potential to expand the cell wall probing toolbox with highly specific and versatile in vitro generated polynucleotide probes.

Monolignol acyltransferase for lignin p-hydroxybenzoylation in Populus

Plant lignification exhibits notable plasticity. Lignin in many species, including Populus spp., has long been known to be decorated with p-hydroxybenzoates. However, the molecular basis for such structural modification remains undetermined. Here, we report the identification and characterization of a Populus BAHD family acyltransferase that catalyses monolignol p-hydroxybenzoylation, thus controlling the formation of p-hydroxybenzoylated lignin structures. We reveal that Populus acyltransferase PHBMT1 kinetically preferentially uses p-hydroxybenzoyl-CoA to acylate syringyl lignin monomer sinapyl alcohol in vitro. Consistently, disrupting PHBMT1 in Populus via CRISPR-Cas9 gene editing nearly completely depletes p-hydroxybenzoates of stem lignin; conversely, overexpression of PHBMT1 enhances stem lignin p-hydroxybenzoylation, suggesting PHBMT1 functions as a prime monolignol p-hydroxybenzoyltransferase in planta. Altering lignin p-hydroxybenzoylation substantially changes the lignin solvent dissolution rate, indicative of its structural significance on lignin physiochemical properties. Identification of monolignol p-hydroxybenzoyltransferase offers a valuable tool for tailoring lignin structure and physiochemical properties and for engineering the industrially important platform chemical in woody biomass.

Pathogen and drought stress affect cell wall and phytohormone signaling to shape host responses in a sorghum COMT bmr12 mutant

BACKGROUND

As effects of global climate change intensify, the interaction of biotic and abiotic stresses increasingly threatens current agricultural practices. The secondary cell wall is a vanguard of resistance to these stresses. Fusarium thapsinum (Fusarium stalk rot) and Macrophomina phaseolina (charcoal rot) cause internal damage to the stalks of the drought tolerant C4 grass, sorghum (Sorghum bicolor (L.) Moench), resulting in reduced transpiration, reduced photosynthesis, and increased lodging, severely reducing yields. Drought can magnify these losses. Two null alleles in monolignol biosynthesis of sorghum (brown midrib 6-ref, bmr6-ref; cinnamyl alcohol dehydrogenase, CAD; and bmr12-ref; caffeic acid O-methyltransferase, COMT) were used to investigate the interaction of water limitation with F. thapsinum or M. phaseolina infection.

RESULTS

The bmr12 plants inoculated with either of these pathogens had increased levels of salicylic acid (SA) and jasmonic acid (JA) across both watering conditions and significantly reduced lesion sizes under water limitation compared to adequate watering, which suggested that drought may prime induction of pathogen resistance. RNA-Seq analysis revealed coexpressed genes associated with pathogen infection. The defense response included phytohormone signal transduction pathways, primary and secondary cell wall biosynthetic genes, and genes encoding components of the spliceosome and proteasome.

CONCLUSION

Alterations in the composition of the secondary cell wall affect immunity by influencing phenolic composition and phytohormone signaling, leading to the action of defense pathways. Some of these pathways appear to be activated or enhanced by drought. Secondary metabolite biosynthesis and modification in SA and JA signal transduction may be involved in priming a stronger defense response in water-limited bmr12 plants.

Transcriptome Reveals Roles of Lignin-Modifying Enzymes and Abscisic Acid in the Symbiosis of Mycena and Gastrodia elata

Gastrodia elata is a well-known medicinal and heterotrophic orchid. Its germination, limited by the impermeability of seed coat lignin and inhibition by abscisic acid (ABA), is triggered by symbiosis with fungi such as Mycena spp. However, the molecular mechanisms of lignin degradation by Mycena and ABA biosynthesis and signaling in G. elata remain unclear. In order to gain insights into these two processes, this study analyzed the transcriptomes of these organisms during their dynamic symbiosis. Among the 25 lignin-modifying enzyme genes in Mycena, two ligninolytic class II peroxidases and two laccases were significantly upregulated, most likely enabling Mycena hyphae to break through the lignin seed coats of G. elata. Genes related to reduced virulence and loss of pathogenicity in Mycena accounted for more than half of annotated genes, presumably contributing to symbiosis. After coculture, upregulated genes outnumbered downregulated genes in G. elata seeds, suggesting slightly increased biological activity, while Mycena hyphae had fewer upregulated than downregulated genes, indicating decreased biological activity. ABA biosynthesis in G. elata was reduced by the downregulated expression of 9-cis-epoxycarotenoid dioxygenase (NCED-2), and ABA signaling was blocked by the downregulated expression of a receptor protein (PYL12-like). This is the first report to describe the role of NCED-2 and PYL12-like in breaking G. elata seed dormancy by reducing the synthesis and blocking the signaling of the germination inhibitor ABA. This study provides a theoretical basis for screening germination fungi to identify effective symbionts and for reducing ABA inhibition of G. elata seed germination.

Targeted plant improvement through genome editing: from laboratory to field

This review illustrates how far we have come since the emergence of GE technologies and how they could be applied to obtain superior and sustainable crop production. The main challenges of today's agriculture are maintaining and raising productivity, reducing its negative impact on the environment, and adapting to climate change. Efficient plant breeding can generate elite varieties that will rapidly replace obsolete ones and address ongoing challenges in an efficient and sustainable manner. Site-specific genome editing in plants is a rapidly evolving field with tangible results. The technology is equipped with a powerful toolbox of molecular scissors to cut DNA at a pre-determined site with different efficiencies for designing an approach that best suits the objectives of each plant breeding strategy. Genome editing (GE) not only revolutionizes plant biology, but provides the means to solve challenges related to plant architecture, food security, nutrient content, adaptation to the environment, resistance to diseases and production of plant-based materials. This review illustrates how far we have come since the emergence of these technologies and how these technologies could be applied to obtain superior, safe and sustainable crop production. Synergies of genome editing with other technological platforms that are gaining significance in plants lead to an exciting new, post-genomic era for plant research and production. In previous months, we have seen what global changes might arise from one new virus, reminding us of what drastic effects such events could have on food production. This demonstrates how important science, technology, and tools are to meet the current time and the future. Plant GE can make a real difference to future sustainable food production to the benefit of both mankind and our environment.

GhWRKY1-like enhances cotton resistance to Verticillium dahliae via an increase in defense-induced lignification and S monolignol content

Cotton is one of the most important economic crops and is cultivated globally. Verticillium wilt, caused by the soil-borne hemibiotrophic fungus Verticillium dahliae, is the most destructive disease in cotton production for its infection strategies and great genetic plasticity. Recent studies have identified the accumulation of lignin is a general and basal defense reaction in plant immunity and cotton resistance to V. dahliae. However, the functions and regulatory mechanisms of transcription factors in cotton defense-induced lignification and lignin composition alteration were less reported. Here, we identified a WRKY transcription factor GhWRKY1-like from upland cotton (Gossypium hirsutum) as a positive regulator in resistance to V. dahliae via directly manipulating lignin biosynthesis. Further analysis revealed that GhWRKY1-like interacts with the promoters of lignin biosynthesis related genes GhPAL6 and GhCOMT1, and activates the expression of GhPAL6 and GhCOMT1, which led to enhanced total lignin especially S monomers biosynthesis. These results demonstrate that GhWRKY1-like enhances Verticillium wilt resistance via an increase in defense-induced lignification and broaden our knowledge of the roles of lignification and the lignin composition in plant defense responses.

GhMYB4 downregulates lignin biosynthesis and enhances cotton resistance to Verticillium dahliae

GhMYB4 acts as a negative regulator in lignin biosynthesis, which results in alteration of cell wall integrity and activation of cotton defense response. Verticillium wilt of cotton (Gossypium hirsutum) caused by the soil-borne fungus Verticillium dahliae (V. dahliae) represents one of the most important constraints of cotton production worldwide. Mining of the genes involved in disease resistance and illuminating the molecular mechanisms that underlie this resistance is of great importance in cotton breeding programs. Defense-induced lignification in plants is necessary for innate immunity, and there are reports of a correlation between increased lignification and disease resistance. In this study, we present an example in cotton whereby plants with reduced lignin content also exhibit enhanced disease resistance. We identified a negative regulator of lignin synthesis, in cotton encoded in GhMYB4. Overexpression of GhMYB4 in cotton and Arabidopsis enhanced resistance to V. dahliae  with reduced lignin deposition. Moreover, GhMYB4 could bind the promoters of several genes involved in lignin synthesis, such as GhC4H-1, GhC4H-2, Gh4CL-4, and GhCAD-3, and impair their expression. The reduction of lignin content in GhMYB4-overexpressing cotton led to alterations of cell wall integrity (CWI) and released more oligogalacturonides (OGs) which may act as damage-associated molecular patterns (DAMPs) to stimulate plant defense responses. In support of this hypothesis, exogenous application with polygalacturonic acid (PGA) in cotton activated biosynthesis of jasmonic acid (JA) and JA-mediated defense against V. dahliae, similar to that described for cotton plants overexpressing GhMYB4. This study provides a new candidate gene for cotton disease-resistant breeding and an increased understanding of the relationship between lignin synthesis, OG release, and plant immunity.

The Cotton Lignin Biosynthetic Gene Gh4CL30 Regulates Lignification and Phenolic Content and Contributes to Verticillium Wilt Resistance

Verticillium wilt is a vascular disease causing tremendous damage to cotton production worldwide. However, our knowledge of the mechanisms of cotton resistance or susceptibility to this disease is very limited. In this study, we compared the defense transcriptomes of cotton (Gossypium hirsutum) cultivars Shidalukang 1 (Verticillium dahliae resistant, HR) and Junmian 1 (V. dahliae susceptible, HS) before and after V. dahliae infection, identified hub genes of the network associated with responses to V. dahliae infection, and functionally characterized one of the hub genes involved in biosynthesis of lignin and phenolics. We identified 6,831 differentially expressed genes (DEGs) between the basal transcriptomes of HR and HS; 3,685 and 3,239 of these DEGs were induced in HR and HS, respectively, at different time points after V. dahliae infection. KEGG pathway analysis indicated that DEGs were enriched for genes involved in lignin biosynthesis. In all, 23 hub genes were identified based on a weighted gene coexpression network analysis of the 6,831 DEGs and their expression profiles at different time points after V. dahliae infection. Knockdown of Gh4CL30, one of the hub genes related to the lignin biosynthesis pathway, by virus-induced gene silencing, led to a decreased content of flavonoids, lignin, and S monomer but an increased content of G monomer, G/S lignin monomer, caffeic acid, and ferulic acid, and enhanced cotton resistance to V. dahliae. These results suggest that Gh4CL30 is a key gene modulating the outputs of different branches of the lignin biosynthesis pathway, and provide new insights into cotton resistance to V. dahliae.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Drought-induced ABA, H2O2 and JA positively regulate CmCAD genes and lignin synthesis in melon stems

BACKGROUND

Cinnamyl alcohol dehydrogenase (CAD) is an important enzyme functions at the last step in lignin monomer synthesis pathway. Our previous work found that drought induced the expressions of CmCAD genes and promoted lignin biosynthesis in melon stems.

RESULTS

Here we studied the effects of abscisic acid (ABA), hydrogen peroxide (H2O2) and jasmonic acid (JA) to CmCADs under drought stress. Results discovered that drought-induced ABA, H2O2 and MeJA were prevented efficiently from increasing in melon stems pretreated with fluridone (Flu, ABA inhibitor), imidazole (Imi, H2O2 scavenger) and ibuprofen (Ibu, JA inhibitor). ABA and H2O2 are involved in the positive regulations to CmCAD1, 2, 3, and 5, and JA is involved in the positive regulations to CmCAD2, 3, and 5. According to the expression profiles of lignin biosynthesis genes, ABA, H2O2 and MeJA all showed positive regulations to CmPAL2-like, CmPOD1-like, CmPOD2-like and CmLAC4-like. In addition, positive regulations were also observed with ABA to CmPAL1-like, CmC4H and CmCOMT, with H2O2 to CmPAL1-like, CmC4H, CmCCR and CmLAC17-like, and with JA to CmCCR, CmCOMT, CmLAC11-like and CmLAC17-like. As expected, the signal molecules positively regulated CAD activity and lignin biosynthesis under drought stress. Promoter::GUS assays not only further confirmed the regulations of the signal molecules to CmCAD1~3, but also revealed the important role of CmCAD3 in lignin synthesis due to the strongest staining of CmCAD3 promoter::GUS.

CONCLUSIONS

CmCADs but CmCAD4 are positively regulated by ABA, H2O2 and JA under drought stress and participate in lignin synthesis.

Structural analysis of rice Os4BGlu18 monolignol β-glucosidase

Monolignol glucosides are storage forms of monolignols, which are polymerized to lignin to strengthen plant cell walls. The conversion of monolignol glucosides to monolignols is catalyzed by monolignol β-glucosidases. Rice Os4BGlu18 β-glucosidase catalyzes hydrolysis of the monolignol glucosides, coniferin, syringin, and p-coumaryl alcohol glucoside more efficiently than other natural substrates. To understand more clearly the basis for substrate specificity of a monolignol β-glucosidase, the structure of Os4BGlu18 was determined by X-ray crystallography. Crystals of Os4BGlu18 and its complex with δ-gluconolactone diffracted to 1.7 and 2.1 Å resolution, respectively. Two protein molecules were found in the asymmetric unit of the P212121 space group of their isomorphous crystals. The Os4BGlu18 structure exhibited the typical (β/α)8 TIM barrel of glycoside hydrolase family 1 (GH1), but the four variable loops and two disulfide bonds appeared significantly different from other known structures of GH1 β-glucosidases. Molecular docking studies of the Os4BGlu18 structure with monolignol substrate ligands placed the glycone in a similar position to the δ-gluconolactone in the complex structure and revealed the interactions between protein and ligands. Molecular docking, multiple sequence alignment, and homology modeling identified amino acid residues at the aglycone-binding site involved in substrate specificity for monolignol β-glucosides. Thus, the structural basis of substrate recognition and hydrolysis by monolignol β-glucosidases was elucidated.

Wood transcriptome analysis and expression variation of lignin biosynthetic pathway transcripts in Ailanthus excelsa Roxb., a multi-purpose tropical tree species

Safety matches are an essential consumer commodity which faces considerable shortage of raw material due to specific requirements like color, wax stability, consistent burning and splinting ability in wood. Ailanthus excelsa Roxb. is a multi-purpose tropical tree species which is predominantly used for production of match splints. It is a data deficient species with no information on molecular regulation governing the wood phenotypes. Hence, with the aim to identify the lignin biosynthetic pathway transcripts, transcriptome sequencing of pooled developing secondary wood tissues of a 22-month-old tree was conducted. The processed reads were de novo assembled and 48,493 unigenes were annotated. Quantitative real time PCR was conducted in six even-aged trees to document the natural expression profiles of nine major transcripts from the monolignol pathway. Significant differential expression of Phenylalanine ammonia-lyase (AePAL), Cinnamate 4-hydroxylase (AeC4H), Cinnamyl-alcohol dehydrogenase (AeCAD), Laccase (AeLACI) and Caffeic Acid 3-O-Methyl Transferase (AeCOMT) was documented across all genotypes studied. Transcriptome-wise microsatellites were also mined and is the first co-dominant marker resource in this species. The genomic resource generated in A. excelsa will facilitate understanding the molecular mechanisms of wood formation and accelerate trait-based breeding program through diversity assessment, population structure analysis, clonal discrimination and marker assisted selection.

Hevea brasiliensis coniferaldehyde-5-hydroxylase (HbCAld5H) regulates xylogenesis, structure and lignin chemistry of xylem cell wall in Nicotiana tabacum

KEY MESSAGE

The HbCAld5H1 gene cloned from Hevea brasiliensis regulates the cambial activity, xylem differentiation, syringyl-guaiacyl ratio, secondary wall structure, lignification pattern and xylan distribution in xylem fibres of transgenic tobacco plants. Molecular characterization of lignin biosynthesis gene coniferaldehyde-5-hydroxylase (CAld5H) from Hevea brasiliensis and its functional validation was performed. Both sense and antisense constructs of HbCAld5H1 gene were introduced into tobacco through Agrobacterium-mediated genetic transformation for over expression and down-regulation of this key enzyme to understand its role affecting structural and cell wall chemistry. The anatomical studies of transgenic tobacco plants revealed the increase of cambial activity leading to xylogenesis in sense lines and considerable reduction in antisense lines. The ultra-structural studies showed that the thickness of secondary wall (S2 layer) of fibre had been decreased with non-homogenous lignin distribution in antisense lines, while sense lines showed an increase in S2 layer thickness. Maule color reaction revealed that syringyl lignin distribution in the xylem elements was increased in sense and decreased in antisense lines. The immunoelectron microscopy revealed a reduction in LM 10 and LM 11 labelling in the secondary wall of antisense tobacco lines. Biochemical studies showed a radical increase in syringyl lignin in sense lines without any significant change in total lignin content, while S/G ratio decreased considerably in antisense lines. Our results suggest that CAld5H gene plays an important role in xylogenesis stages such as cambial cell division, secondary wall thickness, xylan and syringyl lignin distribution in tobacco. Therefore, CAld5H gene could be considered as a promising target for lignin modification essential for timber quality improvement in rubber.

Os4BGlu14, a monolignol β-Glucosidase, negatively affects seed longevity by influencing primary metabolism in rice

Os4BGlu14, a monolignol β-glucosidase, plays a negative role in seed longevity by affecting primary metabolism during seed development and aging. Seed longevity is a crucial trait in agriculture and in the conservation of germplasm resources. β-Glucosidases (BGlus) are multifunctional enzymes that affect plant growth and their adaptation to the environment. The function of rice BGlus in seed longevity, however, remains unknown. We report here that Os4BGlu14, a rice β-Glucosidase, negatively affected seed longevity during accelerated aging. Os4BGlu14 was highly expressed in rice embryos and induced by accelerated aging. Compared to the wild type, rice lines overexpressing Os4BGlu14 had significantly greater grain length, but smaller grain width and thickness. Overexpressing (OE) lines also showed lower starch but higher glucose contents. After accelerated aging treatment, OE lines displayed a significantly lower germination percentage than the wild type. Additionally, these lines had higher lignin accumulation before and after accelerated aging. Metabolome analysis detected 217 metabolites in untreated and aged rice seeds. Comparison of the differential metabolites between WT and OE5 revealed that ten key metabolites, four of which (e.g., uridine 5'-diphosphoglucose-glucose, UDPG) were increased, while the other six (e.g., γ-aminobutyric acid and methionine) were decreased, might be the crucial factors that lead to seed deterioration. Further analysis confirmed higher UDPG levels and more severe programmed cell death in OE lines than in the wild type. Furthermore, OE lines presented a lower germination rate after abscisic acid and paclobutrazol treatment during germination, compared to the wild type. Our study provides a basis for understanding the function of Os4BGlu14 in seed longevity in rice.

Are cuproproteins part of the multi-protein framework for making the Casparian strip?

Casparian strip (CS) is a lignified structure localized on the cell wall between adjacent root endodermal cells and functions as an apoplastic diffusion barrier in the root. The polarly localized, lignin-based CS is an excellent system for studying peptide signaling and position recognition. In this short review, we summarize advances in the past decade on the molecular mechanism governing CS development. In addition to the multi-protein framework underlying the CS membrane domain, we discuss recently observed participation of cell wall located cuproproteins in CS formation. These new discoveries shed light on a potential CS wall domain that coordinates with the membrane domain to provide bidirectional positional information for guiding precise CS development.

The Cotton BEL1-Like Transcription Factor GhBLH7-D06 Negatively Regulates the Defense Response against Verticillium dahliae

Verticillium wilt will seriously affect cotton yield and fiber quality. BEL1-Like transcription factors are involved in the regulation of secondary cell wall (SCW) formation, especially the biosynthesis of lignin that also plays a key role in cotton disease resistance. However, there is no report on the role of BEL1-Like transcription factor in the regulation of plant biological stress. In this study, tissue expression pattern analysis showed that a BEL1-Like transcription factor GhBLH7-D06 was predominantly expressed in vascular tissues and the SCW thickening stage of fiber development, while its expression could also respond to Verticillium dahliae infection and the phytohormone MeJA treatment, which indicated that GhBLH7-D06 might be involved in the defense response of Verticillium wilt. Using virus-induced gene silencing (VIGS) technology, we found silencing the expression of GhBLH7-D06 could enhance the resistance of cotton plants to Verticillium wilt, and the acquisition of resistance might be mainly due to the significant overexpression of genes related to lignin biosynthesis and JA signaling pathway, which also proves that GhBLH7-D06 negatively regulates the resistance of cotton to Verticillium wilt. Based on the results of yeast two-hybrid (Y2H) library screening and confirmation by bimolecular fluorescence complementary (BiFC) experiment, we found an Ovate Family Protein (OFP) transcription factor GhOFP3-D13 which was also a negative regulator of cotton Verticillium wilt resistance could that interacts with GhBLH7-D06. Furthermore, the dual-luciferase reporter assay and yeast one-hybrid (Y1H) experiment indicated that GhBLH7-D06 could target binding to the promoter region of GhPAL-A06 to suppress its expression and eventually lead to the inhibition of lignin biosynthesis. In general, the GhBLH7-D06/GhOFP3-D13 complex can negatively regulate resistance to Verticillium wilt of cotton by inhibiting lignin biosynthesis and JA signaling pathway.

Functions and regulatory framework of ZmNST3 in maize under lodging and drought stress

The growth and development of maize are negatively affected by various abiotic stresses including drought, high salinity, extreme temperature, and strong wind. Therefore, it is important to understand the molecular mechanisms underlying abiotic stress resistance in maize. In the present work, we identified that a novel NAC transcriptional factor, ZmNST3, enhances maize lodging resistance and drought stress tolerance. ChIP-Seq and expression of target genes analysis showed that ZmNST3 could directly regulate the expression of genes related to cell wall biosynthesis which could subsequently enhance lodging resistance. Furthermore, we also demonstrated that ZmNST3 affected the expression of genes related to the synthesis of antioxidant enzyme secondary metabolites that could enhance drought resistance. More importantly, we are the first to report that ZmNST3 directly binds to the promoters of CESA5 and Dynamin-Related Proteins2A (DRP2A) and activates the expression of genes related to secondary cell wall cellulose biosynthesis. Additionally, we revealed that ZmNST3 directly binds to the promoters of GST/GlnRS and activates genes which could enhance the production of antioxidant enzymes in vivo. Overall, our work contributes to a comprehensive understanding of the regulatory network of ZmNST3 in regulating maize lodging and drought stress resistance.

MicroRNA comparison between poplar and larch provides insight into the different mechanism of wood formation

MiRNA transcriptome analysis of different tissues in poplar and larch suggests variant roles of miRNAs in regulating wood formation between two kinds of phyla. Poplar and larch belong to two different phyla. Both are ecological woody species and major resources for wood-related industrial applications. However, wood properties are different between these two species and the molecular basis is largely unknown. In this study, we performed high-throughput sequencing of microRNAs (miRNAs) in the three tissues, xylem, phloem and leaf of Populus alba × Populus glandulosa and Larix kaempferi. Differentially expressed miRNA (DEmiRNA) analysis identified 85 xylem-specific miRNAs in P. alba × P. glandulosa and 158 xylem-specific miRNAs in L. kaempferi. Among 36 common miRNAs, 12 were conserved between the two species. GO and KEGG analyses of the miRNA target genes showed similar metabolism in two species. Through KEGG and BLASTN, we predicted target genes of xylem differentially expressed (DEmiRNA) in the wood formation-related pathways and located DEmiRNAs in these pathways. A network was built for wood formation-related DEmiRNAs, their target genes and orthologous genes in Arabidopsis thaliana. Comparison of DEmiRNA and target gene annotation between P. alba × P. glandulosa and L. kaempferi suggested the different functions of DEmiRNAs and divergent mechanism in wood formation between two species, providing knowledge to understand wood formation mechanism in gymnosperm and angiosperm woody plants.

Xylem systems genetics analysis reveals a key regulator of lignin biosynthesis in Populus deltoides

Despite the growing resources and tools for high-throughput characterization and analysis of genomic information, the discovery of the genetic elements that regulate complex traits remains a challenge. Systems genetics is an emerging field that aims to understand the flow of biological information that underlies complex traits from genotype to phenotype. In this study, we used a systems genetics approach to identify and evaluate regulators of the lignin biosynthesis pathway in Populus deltoides by combining genome, transcriptome, and phenotype data from a population of 268 unrelated individuals of P. deltoides The discovery of lignin regulators began with the quantitative genetic analysis of the xylem transcriptome and resulted in the detection of 6706 and 4628 significant local- and distant-eQTL associations, respectively. Among the locally regulated genes, we identified the R2R3-MYB transcription factor MYB125 (Potri.003G114100) as a putative trans-regulator of the majority of genes in the lignin biosynthesis pathway. The expression of MYB125 in a diverse population positively correlated with lignin content. Furthermore, overexpression of MYB125 in transgenic poplar resulted in increased lignin content, as well as altered expression of genes in the lignin biosynthesis pathway. Altogether, our findings indicate that MYB125 is involved in the control of a transcriptional coexpression network of lignin biosynthesis genes during secondary cell wall formation in P. deltoides.

Identification and Functional Characterization of PtoMYB055 Involved in the Regulation of the Lignin Biosynthesis Pathway in Populus tomentosa

Wood, which is mainly composed of lignified secondary cell wall, is the most abundant biomass in woody plants. Previous studies have revealed that R2R3-type MYB transcription factors are important regulators of the formation of the secondary cell wall in vascular plants. In this study, we isolated the R2R3-type MYB transcription factor gene PtoMYB055, which is mainly expressed in xylem and phloem tissue, from Populus tomentosa and demonstrate that PtoMYB055 is a key regulator of lignin biosynthesis. PtoMYB055 as a transcriptional activator is localized to the nucleus. Overexpression of PtoMYB055 upregulates expression of lignin biosynthetic genes in transgenic poplar plants, resulting in ectopic deposition of lignin in phloem tissue and an increase in thickness of the secondary cell wall. In sum, PtoMYB055 is a transcriptional activator that is involved in regulating lignin biosynthesis during the formation of the secondary cell wall in poplar.