Lignin Biosynthetic Genes Research Articles

The PtobZIP55-PtoMYB170 module regulates the wood anatomical and chemical properties of Populus tomentosa in acclimation to low nitrogen availability.

Poplar plantations are often established on nitrogen-poor land, and poplar growth and wood formation are constrained by low nitrogen (LN) availability. However, the molecular mechanisms by which specific genes regulate wood formation in acclimation to LN availability remain unclear. Here, we report a previously unrecognized module, basic region/leucine zipper 55 (PtobZIP55)-PtoMYB170, which regulates the wood formation of Populus tomentosa in acclimation to LN availability. PtobZIP55 was highly expressed in poplar wood and induced by LN. Altered wood anatomical properties and increased lignification were detected in PtobZIP55-overexpressing poplars, whereas the opposite results were detected in PtobZIP55-knockout poplars. Molecular and transgenic analyses revealed that PtobZIP55 directly binds to the promoter sequence of PtoMYB170 to activate its transcription. The phenotypes of PtoMYB170 transgenic poplars were similar to those of PtobZIP55 transgenic poplars under LN conditions. Further molecular analyses revealed that PtoMYB170 directly bound the promoter sequences of lignin biosynthetic genes to activate their transcription to increase lignin concentrations in LN-treated poplar wood. These results suggest that PtobZIP55 activates PtoMYB170 transcription, which in turn positively regulates lignin biosynthetic genes, increasing lignin deposition in the wood of P. tomentosa in the context of acclimation to LN availability.

Unveiling Key Genes and Unique Transcription Factors Involved in Secondary Cell Wall Formation in Pinus taeda.

Pinus taeda is a key timber species, and extensive research has been conducted on its wood formation. However, a comprehensive investigation into the biosynthetic pathways of lignin, cellulose, and hemicellulose in P. taeda is lacking, resulting in an incomplete understanding of secondary cell wall (SCW) formation in this species. In this study, we systematically analyzed transcriptomic data from previously published sources and constructed detailed pathways for lignin, cellulose, and hemicellulose biosynthesis. We identified 188 lignin-related genes and 78 genes associated with cellulose and hemicellulose biosynthesis. An RT-qPCR highlighted 15 key lignin biosynthesis genes and 13 crucial genes for cellulose and hemicellulose biosynthesis. A STEM analysis showed that most essential enzyme-coding genes clustered into Profile 14, suggesting their significant role in SCW formation. Additionally, we identified seven NAC and six MYB transcription factors (TFs) from atypical evolutionary clades, with distinct expression patterns from those of the previously characterized NAC and MYB genes, indicating potentially unique functions in SCW formation. This research provides the first comprehensive overview of lignin, cellulose, and hemicellulose biosynthetic genes in P. taeda and underscores the importance of non-canonical NAC and MYB TFs, laying a genetic foundation for future studies on SCW regulatory mechanisms.

Investigating the Variation between Lignin Content and the Fracture Characteristics in Capsicum annuum Mutant Stems

The cultivation of horticultural plants in controlled greenhouse environments is a pivotal practice in modern agriculture, offering the potential to enhance crop productivity and mitigate climate change effects. This study investigates the biomechanical properties and lignin content of various Capsicum annuum mutant lines—‘fragile-plant’ (frx), ‘tortuous internodi’ (tti), and ‘puffy-structured stem’ (pfi)—in comparison to a commercially established variety, ‘Garai Fehér’. We employed the acetyl bromide method to quantify lignin content and conducted three-point bending tests to assess rigidity in three distinct regions of the stem. Gene expression analysis of key lignin biosynthetic pathway genes (PAL, C4H, 4CL, CCoAOMT, CAD) was performed using qRT-PCR. The results revealed significant differences in lignin content and breaking force among the genotypes and stem regions. The tti mutants exhibited similar lignin content to the control but lower breaking strength, likely due to elongated internodes. The frx mutants showed uniformly reduced lignin content, correlating with their fragile stems. The pfi mutants displayed abnormally high lignin content in the top region yet demonstrated the lowest stem rigidity in every region. Overexpression of CAD and CCoAOMT was detected in the mutants in specific regions of the stem, suggesting alterations in lignin biosynthesis; however, we could not confirm the correlation between them. Our findings indicate that while lignin content generally correlates with stem rigidity, this trait is complex and influenced by more factors.

Overexpression of SlALC Increases Drought and Salt Tolerance and Affects Fruit Dehiscence in Tomatoes.

The bHLH transcription factors are important plant regulators against abiotic stress and involved in plant growth and development. In this study, SlALC, a gene coding for a prototypical DNA-binding protein in the bHLH family, was isolated, and SlALC-overexpression tomato (SlALC-OE) plants were generated by Agrobacterium-mediated genetic transformation. SlALC transgenic lines manifested higher osmotic stress tolerance than the wild-type plants, estimated by higher relative water content and lower water loss rate, higher chlorophyll, reducing sugar, starch, proline, soluble protein contents, antioxidant enzyme activities, and lower MDA and reactive oxygen species contents in the leaves. In SlALC-OE lines, there were more significant alterations in the expression of genes associated with stress. Furthermore, SlALC-OE fruits were more vulnerable to dehiscence, with higher water content, reduced lignin content, SOD/POD/PAL enzyme activity, and lower phenolic compound concentrations, all of which corresponded to decreased expression of lignin biosynthetic genes. Moreover, the dual luciferase reporter test revealed that SlTAGL1 inhibits SlALC expression. This study revealed that SlALC may play a role in controlling plant tolerance to drought and salt stress, as well as fruit lignification, which influences fruit dehiscence. The findings of this study have established a foundation for tomato tolerance breeding and fruit quality improvement.

Identification and analysis of gibberellin 2-oxidase (GA2ox) members in Cunninghamia lanceolate and the negative regulatory character of ClGA2ox12 in tree stature and xylem lignin deposits

Cunninghamia lanceolata (Lamb.) Hook (C. lanceolate) is a fast-growing evergreen coniferous tree species with high wood yield and fantabulous timber quality. To date, numerous studies have revealed that gibberellins (GAs) regulate the formation of plant wood (secondary xylem). Moreover, GA 2-oxidases (GA2oxs) are known as the major enzymes that deactivate GAs. However, a small or no number of the GA2oxs involved in xylem development and lignin biosynthesis mediated by the GA pathway in woody plants have been identified previously. In this study, 5 GA2oxs members were identified in C. lanceolate, including 4 ClGA2ox12s and one ClGA2ox8-like. Exogenous gibberellin not only promoted lignin deposition in the stem of C. lanceolate but also up-regulated the expression of the lignin biosynthesis gene ClCAD1 by 2–3 folds and one of ClGA2ox12s (designated ClGA2ox12) by 4 folds, suggesting that ClGA2ox12 may be involved in the modulation of lignin deposition by the gibberellin signaling pathway in C. lanceolate. Furthermore, transgenic Populus tomentosa overexpressing ClGA2ox12 exhibited growth retardation and a typical dwarfing phenotype, with a reduction of approximately 40 % in the number of xylem cell layers and a decrease of approximately 16.7 %-26.9 % in lignin content relative to wild-type plants. At the same time, the expression level of lignin biosynthetic genes and lignin content were down-regulated in transgenic plants. Together, these results suggested that ClGA2ox12 functioned as a GA 2oxs catabolic enzyme that plays pivotal roles in plant growth processes, xylem development, and lignin biosynthesis, which gives insights into producing dwarf and low-lignin varieties of C. lanceolate.

Spatial accumulation of lignin monomers and cellulose underlying stalk strength in maize

Lodging largely affects yield, quality and mechanical harvesting of maize. Stalk strength is one of the major factors that affect maize lodging. Although plant cell wall components including lignin and cellulose were known to be associated with stalk strength and lodging resistance, spatial accumulation of specific lignin monomers and cellulose in different tissues and their association with stalk strength in maize was not clearly understood. In this study, we found that both G and S lignin monomers accumulate highest in root, stem rind and leaf vein. Consistently, most lignin biosynthetic genes were expressed higher in root and stem than in other tissues. However, cellulose appears to be lowest in root. There are only mild changes of G lignin and cellulose in different internodes. Instead, we noticed a dramatic decrease of S-lignin accumulation and lignin biosynthetic gene expression in 2nd to 4th internodes wherein stem breakage usually occurs, thereby revealing a few candidate lignin biosynthetic genes associated with stalk strength. Moreover, stalk strength is positively correlated with G, S lignin, and cellulose, but negatively correlated with S/G ratio based on data of maize lines with high or low stalk strength. Loss-of-function of a caffeic acid o-methyltransferase (COMT), which is involved in S lignin biosynthesis, in the maize bm3 mutant, leads to lower stalk strength. Our data collectively suggest that stalk strength is determined by tissue-specific accumulation of lignin monomers and cellulose, and manipulation of the cell wall components by genetic engineering is vital to improve maize stalk strength and lodging resistance.

PbARF19-mediated auxin signaling regulates lignification in pear fruit stone cells

The stone cells in pear fruits cause rough flesh and low juice, seriously affecting the taste. Lignin has been demonstrated as the main component of stone cells. Auxin, one of the most important plant hormone, regulates most physiological processes in plants including lignification. However, the concentration effect and regulators of auxin on pear fruits stone cell formation remains unclear. Here, endogenous indole-3-acetic acid (IAA) and stone cells were found to be co-localized in lignified cells by immunofluorescence localization analysis. The exogenous treatment of different concentrations of IAA demonstrated that the application of 200 µM IAA significantly reduced stone cell content, while concentrations greater than 500 µM significantly increased stone cell content. Besides, 31 auxin response factors (ARFs) were identified in pear genome. Putative ARFs were predicted as critical regulators involved in the lignification of pear flesh cells by phylogenetic relationship and expression analysis. Furthermore, the negative regulation of PbARF19 on stone cell formation in pear fruit was demonstrated by overexpression in pear fruitlets and Arabidopsis. These results illustrated that the PbARF19-mediated auxin signal plays a critical role in the lignification of pear stone cell by regulating lignin biosynthetic genes. This study provides theoretical and practical guidance for improving fruit quality in pear production.

Exogenous applications of brassinosteroids promote secondary xylem differentiation in Eucalyptus grandis.

Brassinosteroids (BRs) play many pivotal roles in plant growth and development, especially in cell elongation and vascular development. Although its biosynthetic and signal transduction pathway have been well characterized in model plants, their biological roles in Eucalyptus grandis, a major hardwood tree providing fiber and energy worldwide, remain unclear. Here, we treated E. grandis plantlets with 24-epibrassinolide (EBL), the most active BR and/or BR biosynthesis inhibitor brassinazole. We recorded the plant growth and analyzed the cell structure of the root and stem with histochemical methods; then, we performed a secondary growth, BR synthesis, and signaling-related gene expression analysis. The results showed that the BRs dramatically increased the shoot length and diameter, and the exogenous BR increased the xylem area of the stem and root. In this process, EgrBRI1, EgrBZR1, and EgrBZR2 expression were induced by the BR treatment, and the expressions of HD-ZIPIII and cellulose synthase genes were also altered. To further verify the effect of BRs in secondary xylem development in Eucalyptus, we used six-month-old plants as the material and directly applied EBL to the xylem and cambium of the vertical stems. The xylem area, fiber cell length, and cell numbers showed considerable increases. Several key BR-signaling genes, secondary xylem development-related transcription factor genes, and cellulose and lignin biosynthetic genes were also considerably altered. Thus, BR had regulatory roles in secondary xylem development and differentiation via the BR-signaling pathway in this woody plant.

The effect of nitrogen source and levels on hybrid aspen tree physiology and wood formation.

Nitrogen can be taken up by trees in the form of nitrate, ammonium and amino acids, but the influence of the different forms on tree growth and development is poorly understood in angiosperm species like Populus. We studied the effects of both organic and inorganic forms of nitrogen on growth and wood formation of hybrid aspen trees in experimental conditions that allowed growth under four distinct steady-state nitrogen levels. Increased nitrogen availability had a positive influence on biomass accumulation and the radial dimensions of both xylem vessels and fibers, and a negative influence on wood density. An optimal level of nitrogen availability was identified where increases in biomass accumulation outweighed decreases in wood density. None of these responses depended on the source of nitrogen except for shoot biomass accumulation, which was stimulated more by treatments complemented with nitrate than by ammonium alone or the organic source arginine. The most striking difference between the nitrogen sources was the effect on lignin composition, whereby the abundance of H-type lignin increased only in the presence of nitrate. The differential effect of nitrate is possibly related to the well-known role of nitrate as a signaling compound. RNA-sequencing revealed that while the lignin-biosynthetic genes did not significantly (FDR <0.01) respond to added NO3 - , the expression of several laccases, catalysing lignin polymerization, was dependent on N-availability. These results reveal a unique role of nitrate in wood formation and contribute to the knowledge basis for decision-making in utilizing hybrid aspen as a bioresource.

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.

Integrated transcriptomic and metabolomic analysis reveals the effects of polyploidization on the lignin content and metabolic pathway in Eucalyptus

BackgroundLignin is a major restriction factor for the industrial production of biomass resources, such as pulp and bioenergy. Eucalyptus is one of the most important sources of pulp and bioenergy. After polyploidization, the lignin content of forest trees is generally reduced, which is considered a beneficial genetic improvement. However, the differences in the lignin content between triploid and diploid Eucalyptus and the underlying regulatory mechanism are still unclear.ResultsWe conducted a comprehensive analysis at the phenotypic, transcriptional and metabolite levels between Eucalyptus urophylla triploids and diploids to reveal the effects of polyploidization on the lignin content and lignin metabolic pathway. The results showed that the lignin content of Eucalyptus urophylla triploid stems was significantly lower than that of diploids. Lignin-related metabolites were differentially accumulated between triploids and diploids, among which coniferaldehyde, p-coumaryl alcohol, sinapaldehyde and coniferyl alcohol had significant positive correlations with lignin content, indicating that they might be primarily contributing metabolites. Most lignin biosynthetic genes were significantly downregulated, among which 11 genes were significantly positively correlated with the lignin content and above metabolites. Furthermore, we constructed a co-expression network between lignin biosynthetic genes and transcription factors based on weighted gene co-expression network analysis. The network identified some putative orthologues of secondary cell wall (SCW)-related transcription factors, among which MYB52, MYB42, NAC076, and LBD15 were significantly downregulated in Eucalyptus urophylla triploids. In addition, potential important transcription factors, including HSL1, BEE3, HHO3, and NAC046, also had high degrees of connectivity and high edge weights with lignin biosynthetic genes, indicating that they might also be involved in the variation of lignin accumulation between triploid and diploid Eucalyptus urophylla.ConclusionsThe results demonstrated that some lignin-related metabolites, lignin biosynthetic genes and transcription factors in Eucalyptus urophylla triploids may be relatively sensitive in response to the polyploidization effect, significantly changing their expression levels, which ultimately correlated with the varied lignin content. The analysis of the underlying formation mechanism could provide beneficial information for the development and utilization of polyploid biomass resources, which will be also valuable for genetic improvement in other bioenergy plants.

Homoeologous non-reciprocal translocation explains a major QTL for seed lignin content in oilseed rape (Brassica napus L.)

Key messageA homoeologous non-reciprocal translocation was identified in the major QTL for seed lignin content in the low lignin line SGDH14. The lignin biosynthetic gene PAL4 was deleted.Oilseed rape is a major oil crop and a valuable protein source for animal and human nutrition. Lignin is a non-digestible, major component of the seed coat with negative effect on sensory quality, bioavailability and usage of oilseed rape’s protein. Hence, seed lignin reduction is of economic and nutritional importance. In this study, the major QTL for reduced lignin content found on chromosome C05 in the DH population SGDH14 x Express 617 was further examined. SGDH14 had lower seed lignin content than Express 617. Harvested seeds from a F2 population of the same cross were additionally field tested and used for seed quality analysis. The F2 population showed a bimodal distribution for seed lignin content. F2 plants with low lignin content had thinner seed coats compared to high lignin lines. Both groups showed a dark seed colour with a slightly lighter colour in the low lignin group indicating that a low lignin content is not necessarily associated with yellow seed colour. Mapping of genomic long-reads from SGDH14 against the Express 617 genome assembly revealed a homoeologous non-reciprocal translocation (HNRT) in the confidence interval of the major QTL for lignin content. A homologous A05 region is duplicated and replaced the C05 region in SGDH14. As consequence several genes located in the C05 region were lost in SGDH14. Thus, a HNRT was identified in the major QTL region for reduced lignin content in the low lignin line SGDH14. The most promising candidate gene related to lignin biosynthesis on C05, PAL4, was deleted.

Expression and functional analysis of NAC transcription factors under five diverse growth stages reveal their regulatory roles during wood formation in Chinese cedar (Cryptomeria fortunei Hooibrenk)

NAC transcription factor (TF), the most prominent plant-specific gene family, is involved in various metabolic pathways during the growth and development of the plant. However, few reports have been published concerning the NAC gene family in gymnosperms such as Cryptomeria fortunei Hooibrenk. As an essential native coniferous timber tree, C. fortunei is widely cultivated in southern China due to its significant economic and ecological value. Here, we aimed to identify and characterize the CfNACs in C. fortunei vascular development. A total of 33 CfNACs were identified from C. fortunei vascular cambium. They all shared the conserved NAC motifs. Phylogenetic evolutionary indicated that CfNACs were classified into various evolutionary branches, including secondary xylem development, lignin and secondary cell wall (SCW) biosynthesis, and various stress response. In addition, the expression profiles of CfNACs under diverse developmental stages suggested that several CfNACs were involved in multiple metabolic pathways during C. fortunei cambium development. Moreover, the co-expression network revealed that numerous CfNACs were involved in vascular and xylem development, and lignin biosynthesis as key upstream regulators. There were significant correlations between CfNACs and lignin biosynthetic genes, phytohormone synthase genes. Transient expression analysis implied that CfNAC5 and CfNAC16, targeted to the nucleus, acted as activators. Genetic transformation analysis demonstrated that overexpression of CfNAC5 dramatically affected the secondary xylem development and elevated the lignin biosynthesis and SCW thickness in transgenic plants. Furthermore, the expression levels of lignin biosynthetic genes were markedly increased in transgenic plants. In conclusion, these findings would help provide insight into the functional differentiation and evolutionary relationships of CfNACs and elucidate the regulatory roles of CfNACs during C. fortunei vascular development and wood formation.

Integrated analysis of transcriptomics and metabolomics of peach under cold stress.

Low temperature is one of the environmental factors that restrict the growth and geographical distribution of peach (Prunus persica L. Batsch). To explore the molecular mechanisms of peach brunches in response to cold, we analyzed the metabolomics and transcriptomics of 'Donghe No.1' (cold-tolerant, CT) and '21st Century' (cold-sensitive, CS) treated by different temperatures (-5 to -30°C) for 12 h. Some cold-responsive metabolites (e.g., saccharides, phenolic acids and flavones) were identified with upregulation only in CT. Further, we identified 1991 cold tolerance associated genes in these samples and they were significantly enriched in the pathways of 'galactose metabolism', 'phenylpropanoid biosynthesis' and 'flavonoids biosynthesis'. Weighted gene correlation network analysis showed that soluble sugar, flavone, and lignin biosynthetic associated genes might play a key role in the cold tolerance of peach. In addition, several key genes (e.g., COMT, CCR, CAD, PER and F3'H) were substantially expressed more in CT than CS under cold stress, indicating that they might be major factors during the adaptation of peach to low temperature. This study will not only improve our understanding towards the molecular mechanisms of peach trees under cold stress but also contribute to the screening and breeding program of peach in the future.

Chitosan triggers tolerance to Pythium myriotylum infection in ginger (Zingiber officinale) by modulating multiple defense signaling pathways

In this study, we evaluated the potential of abscisic acid, brassinolide, isoxaben, hexanoic acid, β-aminobutyric acid, oligogalacturonic acid, flagellin 22, chitosan, methyl salicylate and pipecolic acid in suppressing the soft rot disease in ginger (Zingiber officinale) caused by the necrotrophic oomycete pathogen Pythium myriotylum. Of the ten elicitors tested, the treatment with 100 μM chitosan curtailed the disease severity in ginger to ∼36%. We examined the differential modulation in different parameters between the chitosan treated P. myriotylum inoculated (CTI) and the untreated inoculated (UTI) ginger plants. The ROS generator RBOHD was induced in CTI plants whereas the different ROS scavengers were modulated variously between the two regimens. While the biosynthetic and signaling genes of the jasmonic acid and ethylene were induced in CTI plants, salicylic acid signaling genes were suppressed. The chitosan treatment induced the HR marker gene HSR203J in ginger and suppressed the expression of cell death markers HIN1, AIF1 and AIF2. Similarly, while the lignin biosynthetic genes were mostly upregulated, the cell wall homeostasis genes EXLA2, INV3 and WAK2-LIKE were suppressed. Total phenylpropanoids declined in both the regimens, but the level of decline was less in the CTI plants. The histopathology showed retarded pathogen ingress in CTI plants. Well diffusion assays revealed non-toxicity of chitosan to the pathogen. The data highlight that the orchestration pattern of defense pathways in chitosan primed ginger and the pathogen induced basal defense pathways operated in a resistant plant host are loosely parallel. The results demonstrate the ability of chitosan to prime standing ginger plants against soft rot disease and implicate the potential of integrating chitosan for the sustainable management of ginger soft rot.

Mutation of Os4BGlu18, monolignol β-glucosidase, improves salinity insensitivity in a rice

Rice is a salt-sensitive crop, and its development and yield are greatly affected by salinity. Using a forward genetics approach, the salt-insensitive line, sitl2, was selected from a core population (M 10 ) induced by gamma-ray irradiation. Under salt treatment, the sitl2 mutant showed greater fresh weight, chlorophyll content, and lower hydrogen peroxide (H 2 O 2 ) levels than the wild type (WT). In addition, the sitl2 mutant showed a lower Na+ content in the shoots and roots under salinity stress. A single-base guanine deletion of Os4BGlu18 , which hydrolyzes monolignol-glucoside by monolignol β-glucosidase, was found by whole genome re-sequencing. Subcellular localization of Os4BGlu18 and the mutant form (Os4BGlu18p.Gly115fs) GFP-tagged proteins were found in the cytosol of rice protoplasts. The expression levels of Os4BGlu18 and most UDP-glucosyltransferase genes examined were lower in the mutant than in the WT. Monolignols were extracted in higher amounts from WT shoots and roots than from the sitl2 mutant; however, monolignol glucoside was extracted in higher amounts in sitl2 . Phloroglucinol-HCl staining showed that sitl2 had more intense and higher lignin content than WT. These results suggest that sitl2 might confer salt tolerance caused by the mutation of Os4BGlu 18 and could be used as a new resource for breeding programs to enhance salt tolerance in rice. • Using a forward genetics approach, a salt-insensitive TILLING line ( sitl2 ) was selected, which could be useful as a new resource for breeding programs. • The sitl2 mutant exhibited a single-base guanine deletion in Os4BGlu18 and a frameshift with a premature stop. • Mutation of Os4BGlu18 affected the expression of lignin biosynthetic pathway genes and UDP-glucosyltransferase genes, and caused high accumulation of lignin in the vascular bundles of shoots and roots in sit2.

Overexpression of PtoMYB115 improves lignocellulose recalcitrance to enhance biomass digestibility and bioethanol yield by specifically regulating lignin biosynthesis in transgenic poplar

BackgroundWoody plants provide the most abundant biomass resource that is convertible for biofuels. Since lignin is a crucial recalcitrant factor against lignocellulose hydrolysis, genetic engineering of lignin biosynthesis is considered as a promising solution. Many MYB transcription factors have been identified to involve in the regulation of cell wall formation or phenylpropanoid pathway. In a previous study, we identified that PtoMYB115 contributes to the regulation of proanthocyanidin pathway, however, little is known about its role in lignocellulose biosynthesis and biomass saccharification in poplar.ResultsHere, we detected the changes of cell wall features and examined biomass enzymatic saccharification for bioethanol production under various chemical pretreatments in PtoMYB115 transgenic plants. We reported that PtoMYB115 might specifically regulate lignin biosynthesis to affect xylem development. Overexpression of PtoMYB115 altered lignin biosynthetic gene expression, resulting in reduced lignin deposition, raised S/G and beta-O-4 linkage, resulting in a significant reduction in cellulase adsorption with lignin and an increment in cellulose accessibility. These alterations consequently improved lignocellulose recalcitrance for significantly enhanced biomass saccharification and bioethanol yield in the PtoMYB115-OE transgenic lines. In contrast, the knockout of PtoMYB115 by CRISPR/Cas9 showed reduced woody utilization under various chemical pretreatments.ConclusionsThis study shows that PtoMYB115 plays an important role in specifically regulating lignin biosynthesis and improving lignocellulose features. The enhanced biomass saccharification and bioethanol yield in the PtoMYB115-OE lines suggests that PtoMYB115 is a candidate gene for genetic modification to facilitate the utilization of biomass.

A chromosome-level genome assembly of Styphnolobium japonicum combined with comparative genomic analyses offers insights on the evolution of flavonoid and lignin biosynthesis

Styphnolobium japonicum is an important industrial crop that is widely used as a source of flavonoids. In this study, the first chromosome-scale reference genome of S. japonicum was provided by combining Illumina and nanopore sequencing and high-throughput chromatin conformation capture technology. The genome of S. japonicum is 520 Mb and has an N50 contig that is 4.77 Mb. The contig could be clustered into 14 pseudochromosomes. A total of 32,551 genes that encode proteins were annotated in the genome. Comparative and phylogenetic analyses of the genome revealed the phylogenetic placement of this plant, which indicates that S. japonicum experienced two whole-genome duplication (WGD) events. The genes retained after the WGD were shared by members of the papilionoideae. A comparative genomic analysis revealed that the expansion and contraction of the flavonoid pathway gene families was the reason that the production of flavonoids was enhanced. This reference genome enabled the prediction of 17 genes that are involved in the flavonoid and lignin biosynthetic gene families. Collectively, S. japonicum could have undergone adaptive evolution to promote its growth by enhancing the production of flavonoids and altering the composition of lignin.

Hrip1 mediates rice cell wall fortification and phytoalexins elicitation to confer immunity against Magnaporthe oryzae.

Magnaporthe oryzae is a potent fungus that adversely affects rice yield. Combinatorial techniques of prevention, toxic chemicals, and fungicide are used to remedy rice blast infection. We reported the role of Hrip1 in cell death elicitation and expression of systematic acquired resistance that could potentially stifle M. oryzae infection. In this study, transcriptome and metabolomic techniques were used to investigate the mechanism by which Hrip1 reprogramed the transcriptome of rice seedlings to confer immunity against M. oryzae. Our results showed that Hrip1 induces cell wall thickening and phytoalexin elicitation to confer immunity against M. oryzae infection. Hrip1 activates key lignin biosynthetic genes and myeloblastosis transcription factors that act as molecular switches for lignin production. Lignin content was increased by 68.46% and more after 48 h onwards in Hrip1-treated seedlings compared to the control treatment. Further analysis of cell wall morphology using the transmission electron microscopy technique revealed over 100% cell wall robustness. Hrip1 also induced the expression of 24 diterpene synthases. These include class I and II terpene synthases, cytochrome P450 subfamilies (OsCYP76M and OsCYP71Z), and momilactones synthases. The relationship between the expression of these genes and metabolic elicitation was analyzed using ultra-performance liquid chromatography–tandem mass spectrometry. Enhanced amounts of momilactones A and B, oryzalactone, and phytocassane A and G were detected in the Hrip1-treated leaves. We also identified seven benzoxazinoid genes (BX1-BX7) that could improve rice immunity. Our findings show that Hrip1 confers dual immunity by leveraging lignin and phytoalexins for physical and chemical resistance. This study provides novel insights into the mechanisms underlying Hrip1-treated plant immunity.

Transcription factor OsNAC055 regulates GA-mediated lignin biosynthesis in rice straw

Crop straws represent enormous biomass resource that mainly contain secondary cell walls (SCWs) consisting of cellulose, hemicelluloses and lignin. Nevertheless, the regulatory mechanism of SCW biosynthesis still needs to be well understood. In this study, we identified a rice NAC (NAM, ATAF1/2, CUC2) transcription factor OsNAC055 that regulates GA-mediated lignin biosynthesis. As a nucleus-localized transcription factor, OsNAC055 exhibits the transcriptional activation activity. Overexpression of OsNAC055 increases the lignin content in rice straw. Transcriptomic analyses showed that the expression of multiple lignin biosynthetic genes was increased in OsNAC055-overexpressing plants. Further ChIP-qPCR analysis and transient transactivation assays indicated that OsNAC055 directly activates rice lignin biosynthetic genes CINNAMOYL-CoA REDUCTASE 10 (OsCCR10) and CINNAMYL ALCOHOL DEHYDROGENASE 2 (OsCAD2) by binding to their promoters. On the other hand, phytohormone measurement showed that OsNAC055 overexpression significantly increased exogenous GA3 levels in rice plants by regulating GA biosynthetic gene OsGA20ox2. Moreover, yeast two-hybrid and bimolecular fluorescence complement (BiFC) assays indicated that OsNAC055 interacts with SLENDER RICE1 (SLR1), the repressor in GA signaling. More importantly, exogenous GA treatment markedly enhanced the transcription of OsCCR10 and OsCAD2, suggesting the role of GA in lignin biosynthesis. Together, our results provide the evidence that OsNAC055 functions as an essential transcription factor to regulate the GA-mediated lignin biosynthesis, which provides a strategy for manipulating lignin production.