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Rapid High-Resolution Analysis of Polysaccharide-Lignin Interactions in Secondary Plant Cell Walls Using Proton-Detected Solid-State NMR
The plant secondary cell wall, a complex matrix composed of cellulose, hemicellulose, and lignin, is crucial for the mechanical strength and water-proofing properties of plant tissues, and serves as a primary source of biomass for biorenewable energy and biomaterials. Structural analysis of these polymers and their interactions within the secondary cell wall has been heavily relying on 13 C-based solid-state NMR techniques. In this study, we explore the application of 1 H-detected solid-state NMR techniques for rapid, high-resolution structural characterization of polysaccharides and lignin, demonstrated on the stems of hardwood eucalyptus. We explored the use of synthesized 2D spectra to resolve central 1 H resonances and the combined application of 3D hCCH and hCHH experiments for complete resonance assignment and unambiguous identification of lignin-carbohydrate interactions. Our findings emphasize the central role of acetylated three-fold xylan conformers, rather than two-fold, in stabilizing the carbohydrate-lignin interface, with glucuronic acid sidechains in eucalyptus glucuronoxylan colocalizing with lignin, revised cellulose-lignin interactions involving uncoated microfibril surfaces, and pectin-lignin interactions indicative of early-stage lignification. These results present a novel approach for rapid structural analysis of lignocellulosic biomaterials without the need for solubilization or extraction.
Microfibril orientation and compositional heterogeneity in fiber and vessel cell walls of poplar xylem studied by AFM-IR and SFG spectroscopy
Understanding the structural organization of cellulose microfibrils (CMFs) within individual plant cell walls is essential for connecting cell wall architecture to its mechanical and physiological functions. However, due to the complex hierarchical structure and nanoscale heterogeneity of cell walls, it remains technically challenging to resolve detailed compositional and orientational information at subcellular levels of individual cell walls. This study investigates the internal 3D structure, chemical composition, and sublayer organization of fiber and vessel cell walls in the xylem tissue of a two-year-old field-grown hybrid poplar tree (Populus alba × P. glandulosa) using photothermal atomic force microscopy coupled with infrared spectroscopy (AFM-IR) and sum frequency generation (SFG) hyperspectral microscopy. AFM-IR provided nanoscale chemical imaging, revealing localized compositional heterogeneity, including variations between adjacent cell walls and transitional layers beyond the traditional S1, S2, and S3 sublayers. SFG microscopy revealed that CMFs in fiber walls are highly aligned along the stem axis, consistent with their role in mechanical support, while vessel cell walls exhibited slightly tilted CMFs, reflecting their function in hydraulic transport. Together, these results offer new insights into cell-type-specific CMF organization and compositional gradients in hybrid poplar xylem. These findings highlight the structural and chemical complexity of secondary cell walls in woody plants and demonstrate the value of AFM-IR and SFG spectroscopy in elucidating plant cell wall architecture.
Cellulose synthesis complexes are homo-oligomeric and hetero-oligomeric in Physcomitrium patens
The common ancestor of seed plants and mosses contained homo-oligomeric cellulose synthesis complexes (CSCs) composed of identical subunits encoded by a single CELLULOSE SYNTHASE (CESA) gene. Seed plants use different CESA isoforms for primary and secondary cell wall deposition. Both primary and secondary CESAs form hetero-oligomeric CSCs that assemble and function in planta only when all the required isoforms are present. The moss Physcomitrium (Physcomitrella) patens has seven CESA genes that can be grouped into two functionally and phylogenetically distinct classes. Previously, we showed that PpCESA3 and/or PpCESA8 (class A) together with PpCESA6 and/or PpCESA7 (class B) form obligate hetero-oligomeric complexes required for normal secondary cell wall deposition. Here, we show that gametophore morphogenesis requires a member of class A, PpCESA5, and is sustained in the absence of other PpCESA isoforms. Further, PpCESA5 also differs from the other class A PpCESAs as it is able to self-interact and does not co-immunoprecipitate with other PpCESA isoforms. These results are consistent with the hypothesis that homo-oligomeric CSCs containing only PpCESA5 subunits synthesize cellulose required for gametophore morphogenesis. Analysis of mutant phenotypes also revealed that, like secondary cell wall deposition, normal protonemal tip growth requires class B isoforms (PpCESA4 or PpCESA10), along with a class A partner (PpCESA3, PpCESA5, or PpCESA8). Thus, P. patens contains both homo-oligomeric and hetero-oligomeric CSCs.
Overexpression of REDUCED WALL ACETYLATION C increases xylan acetylation and biomass recalcitrance in Populus
Abstract Plant lignocellulosic biomass, i.e. secondary cell walls of plants, is a vital alternative source for bioenergy. However, the acetylation of xylan in secondary cell walls impedes the conversion of biomass to biofuels. Previous studies have shown that REDUCED WALL ACETYLATION (RWA) proteins are directly involved in the acetylation of xylan but the regulatory mechanism of RWAs is not fully understood. In this study, we demonstrate that overexpression of a Populus trichocarpa PtRWA-C gene increases the level of xylan acetylation and increases the lignin content and S/G ratio, ultimately yielding poplar woody biomass with reduced saccharification efficiency. Furthermore, through gene coexpression network and expression quantitative trait loci (eQTL) analysis, we found that PtRWA-C was regulated not only by the secondary cell wall hierarchical regulatory network but also by an AP2 family transcription factor HARDY (HRD). Specifically, HRD activates PtRWA-C expression by directly binding to the PtRWA-C promoter, which is also the cis-eQTL for PtRWA-C. Taken together, our findings provide insights into the functional roles of PtRWA-C in xylan acetylation and consequently saccharification and shed light on synthetic biology approaches to manipulate this gene and alter cell wall properties. These findings have substantial implications for genetic engineering of woody species, which could be used as a sustainable source of biofuels, valuable biochemicals, and biomaterials.
Direct Measurement of Plant Cellulose Microfibril and Bundles in Native Cell Walls
Not Available
Mitogen-activated protein kinase 6 negatively regulates secondary wall biosynthesis by modulating MYB46 protein stability in Arabidopsis thaliana
The R2R3-MYB transcription factor MYB46 functions as a master switch for secondary cell wall biosynthesis, ensuring the exquisite expression of the secondary wall biosynthetic genes in the tissues where secondary walls are critical for growth and development. At the same time, suppression of its function is needed when/where formation of secondary walls is not desirable. Little is known about how this opposing control of secondary cell wall formation is achieved. We used both transient and transgenic expression of MYB46 and mitogen-activated protein kinase 6 (MPK6) to investigate the molecular mechanism of the post-translational regulation of MYB46. We show that MYB46 is phosphorylated by MPK6, leading to site specific phosphorylation-dependent degradation of MYB46 by the ubiquitin-mediated proteasome pathway. In addition, the MPK6-mediated MYB46 phosphorylation was found to regulate in planta secondary wall forming function of MYB46. Furthermore, we provide experimental evidences that MYB83, a paralog of MYB46, is not regulated by MPK6. The coupling of MPK signaling to MYB46 function provides insights into the tissue- and/or condition-specific activity of MYB46 for secondary wall biosynthesis.
De novo transcriptome analysis of white teak (Gmelina arborea Roxb) wood reveals critical genes involved in xylem development and secondary metabolism
Gmelina arborea Roxb is a fast-growing tree species of commercial importance for tropical countries due to multiple industrial uses of its wood. Wood is primarily composed of thick secondary cell walls of xylem cells which imparts the strength to the wood. Identification of the genes involved in the secondary cell wall biosynthesis as well as their cognate regulators is crucial to understand how the production of wood occurs and serves as a starting point for developing breeding strategies to produce varieties with improved wood quality, better paper pulping or new potential uses such as biofuel production. In order to gain knowledge on the molecular mechanisms and gene regulation related with wood development in white teak, a de novo sequencing and transcriptome assembly approach was used employing secondary cell wall synthesizing cells from young white teak trees. For generation of transcriptome, RNA-seq reads were assembled into 110,992 transcripts and 49,364 genes were functionally annotated using plant databases; 5071 GO terms and 25,460 SSR markers were identified within xylem transcripts and 10,256 unigenes were assigned to KEGG database in 130 pathways. Among transcription factor families, C2H2, C3H, bLHLH and MYB were the most represented in xylem. Differential gene expression analysis using leaves as a reference was carried out and a total of 20,954 differentially expressed genes were identified including monolignol biosynthetic pathway genes. The differential expression of selected genes (4CL, COMT, CCoAOMT, CCR and NST1) was validated using qPCR. We report the very first de novo transcriptome of xylem-related genes in this tropical timber species of commercial importance and constitutes a valuable extension of the publicly available transcriptomic resource aimed at fostering both basic and breeding studies.
Lignin’s Indispensable role in orchestrating seed stone formation: Insights from jujuba, peach and pear with future prospective on pitless fruits
A hard endocarp (i.e., stone) inside fruit is a characteristic of drupe fruits such as jujube, peach, mango, etc. Hard stone significantly affects the quality and downstream processing of fruits. The complex aromatic polymer lignin deposition in the secondary cell wall determines stone hardness. Lignin comprises phenylpropanoid units formed by hydroxycinnamoyl alcohol, which includes coniferyl, sinapyl, and p-coumaroyl alcohols. Lignin biosynthesis pathway involves a series of complex enzymatic reactions initiated from phenylalanine ammonia lyase and ends up polymerizing lignin monomers by laccase and peroxidase enzymes. Phytohormones, particularly auxin, gibberellins, and Ca²⁺ signaling, further modulate endocarp lignification by regulating transcriptional networks and lignin biosynthetic genes, thereby fine-tuning secondary cell wall thickening and stone hardness in drupe fruits. Lignin biosynthesis is controlled by both structural genes and transcriptional regulators. The structural genes encoding lignin biosynthetic enzymes include LAC12–1, PAL2, C4H, C3H, CSE, CCoAOMT, F5H, CAD, and PRX1. In addition, several transcription factors regulating secondary cell wall and lignin deposition, such as MYB24, bZIP48, and bZIP33 play key regulatory roles. Conversely, delignification or suppression of stone formation is associated with transcription factors (Pistillata, MYB32, FUL, and REPLUMLESS) and post-transcriptional regulators, including miR397a, miR31-3p, and miR8-5p. Accurate alteration in the expression of these genes will result in the attainment of stoneless fruits for cheap and hazel-free downstream processing.
Morphological changes in woody stem of Prunus jamasakura under simulated microgravity
When the four-week-old woody stem of Prunus jamasakura was grown under simulated microgravity condition on a three-dimensional clinostat, it bent at growth, and width of its secondary xylem decreased due to the reduction of fiber cell numbers and a smaller microfibril angle in the secondary cell wall, as reported in our previous paper. Gravity induces the development of the secondary xylem that supports the stem upward against the action of gravity. In this study, morphological changes of the tissues and cells were microscopically observed. Disorder was found in the concentric structure of tissues that organize the stem. The radial arrangement of the cells was also disturbed in the secondary xylem, and in the secondary phloem secondary cell walls of the bast fiber cells were undeveloped. These findings suggest that differentiation and development of the secondary xylem and the bast fiber cells are strongly controlled by terrestrial gravity. These tissue and cells functions to support the stem under the action of gravity. Furthermore, clinorotation induced disorder in the straight joint of vessel elements and the lattice-like structure of radial parenchyma cells, which is responsible for water transportation and storage, respectively. Gravity is an essential factor for keeping the division and differentiation normal in woody stem.
Heterologous expression of Arabidopsis laccase2, laccase4 and peroxidase52 driven under developing xylem specific promoter DX15 improves saccharification in populus
Secondary cell wall holds considerable potential as it has gained immense momentum to replace the lignocellulosic feedstock into fuels. Lignin one of the components of secondary cell wall tightly holds the polysaccharides thereby enhancing the recalcitrance and complexity in the biomass. Laccases (LAC) and peroxidases (PRX) are the major phenyl-oxidases playing key functions during the polymerization of monolignols into lignin. Yet, the functions of laccase and peroxidases gene families remained largely unknown. Hence, the objective of this conducted study is to understand the role of specific LAC and PRX in Populus wood formation and to further investigate how the altered Lac and Prx expression affects biomass recalcitrance and plant growth. This study of heterologous expression of Arabidopsis Lac and Prx genes was conducted in poplar to avoid any otherwise occurring co-suppression mechanism during the homologous overexpression of highly expressed native genes. In the pursuit of optimizing lignocellulosic biomass for biofuel production, the present study focuses on harnessing the enzymatic potential of Arabidopsis thaliana Laccase2, Laccase4, and Peroxidase52 through heterologous expression. We overexpressed selected Arabidopsis laccase2 (AtLac2), laccase4 (AtLac4), and peroxidase52 (AtPrx52) genes, based on their high transcript expression respective to the differentiating xylem tissues in the stem, in hybrid poplar (cv. 717) expressed under the developing xylem tissue-specific promoter, DX15 characterized the transgenic populus for the investigation of growth phenotypes and recalcitrance efficiency. Bioinformatics analyses conducted on AtLac2 and AtLac4 and AtPrx52, revealed the evolutionary relationship between the laccase gene and peroxidase gene homologs, respectively. Transgenic poplar plant lines overexpressing the AtLac2 gene (AtLac2-OE) showed an increase in plant height without a change in biomass yield as compared to the controls; whereas AtLac4-OE and AtPrx52-OE transgenic lines did not show any such observable growth phenotypes compared to their respective controls. The changes in the levels of lignin content and S/G ratios in the transgenic poplar resulted in a significant increase in the saccharification efficiency as compared to the control plants. Overall, saccharification efficiency was increased by 35–50%, 21–42%, and 8–39% in AtLac2-OE, AtLac4-OE, and AtPrx52-OE transgenic poplar lines, respectively, as compared to their controls. Moreover, the bioengineered plants maintained normal growth and development, underscoring the feasibility of this approach for biomass improvement without compromising overall plant fitness. This study also sheds light on the potential of exploiting regulatory elements of DX15 to drive targeted expression of lignin-modifying enzymes, thereby providing a promising avenue for tailoring biomass for improved biofuel production. These findings contribute to the growing body of knowledge in synthetic biology and plant biotechnology, offering a sustainable solution to address the challenges associated with lignocellulosic biomass recalcitrance.
Growth–defense trade‐offs and yield loss in plants with engineered cell walls
Summary As a major component of plant secondary cell walls, lignin provides structural integrity and rigidity, and contributes to primary defense by providing a physical barrier to pathogen ingress. Genetic modification of lignin biosynthesis has been adopted to reduce the recalcitrance of lignified cell walls to improve biofuel production, tree pulping properties and forage digestibility. However, lignin‐modification is often, but unpredictably, associated with dwarf phenotypes. Hypotheses suggested to explain this include: collapsed vessels leading to defects in water and solute transport; accumulation of molecule(s) that are inhibitory to plant growth or deficiency of metabolites that are critical for plant growth; activation of defense pathways linked to cell wall integrity sensing. However, there is still no commonly accepted underlying mechanism for the growth defects. Here, we discuss recent data on transcriptional reprogramming in plants with modified lignin content and their corresponding suppressor mutants, and evaluate growth‐defense trade‐offs as a factor underlying the growth phenotypes. New approaches will be necessary to estimate how gross changes in transcriptional reprogramming may quantitatively affect growth. Better understanding of the basis for yield drag following cell wall engineering is important for the biotechnological exploitation of plants as factories for fuels and chemicals.
UDP-glucuronic acid decarboxylase in alfalfa: a target to improve ruminal digestibility of stems
Alfalfa (Medicago sativa) has a high nutritional value, but poor digestibility of the stems limits its value as an energy source in ruminant diets. Xylan and lignin negatively affect cell wall digestibility, whereas pectins have high digestibility in the rumen. In plants, UDP-xylose synthase (UXS) catalyses the decarboxylation of UDP-glucuronic acid to form UDP-xylose in an irreversible step that is key for xylan synthesis. Here, we functionally characterized two UXS genes in alfalfa, namely MsaUXS2 and MsaUXS4, and investigated their impact on ruminal digestibility. Both genes are more highly expressed in stems than leaves, and the enzymes have UDP-glucuronic acid decarboxylase activity in vitro. Silencing of MsaUXS2 and MsaUXS4 via RNAi altered plant growth and resulted in a 40% decrease in xylose, a 115% increase in arabinose, and a 60% increase in galacturonic acid in the polysaccharide matrix as well as a 20% decrease in lignin in the cell wall. Together, our results show a major role for UXS2 and UXS4 in xylan synthesis and secondary cell wall deposition in alfalfa. Additionally, in vitro rumen digestibility assays for the silenced lines had on average 30% increased gas production at 24 h, demonstrating the potential of targeting UXS genes to increase stem digestibility.
Populus PtrbHLH011 Is a Transcriptional Co‐Regulator Involved in the Activation of Cell Wall Biosynthesis by Iron Deprivation
The lack of a mechanistic understanding of the environmental plasticity of secondary cell wall (SCW) biosynthesis restricts large-scale biomass and bioenergy production on marginal lands. Using Populus (poplar), a key bioenergy crop, we discovered that iron deprivation, a prevalent abiotic stress on marginal lands, stimulates SCW biosynthesis in stems. We identified the transcription factor PtrbHLH011 as a critical regulator underlying this response. Through integrated analyses involving phenotypic characterisation of PtrbHLH011 knockout and overexpression plants, functional genomics and molecular investigations, we established that PtrbHLH011 functions as a central regulator of SCW biosynthesis, iron homeostasis and flavonoid biosynthesis by directly repressing essential genes in these pathways. Iron deprivation downregulates PtrbHLH011 expression, subsequently activating these biosynthetic pathways. Notably, cytosine base editing-based knockout of PtrbHLH011 significantly enhanced plant growth, yielding up to a 110% increase in stem diameter and a 300% increase in leaf iron content. These findings present a novel regulatory mechanism linking environmental iron availability to SCW biosynthesis and illustrate a practical strategy to improve biomass yield on iron-deficient marginal lands. Furthermore, our mechanistic insights into PtrbHLH011 target recognition and regulation provide a valuable foundation for precise manipulation of gene regulatory networks, facilitating the development of high-performance bioenergy crops adapted to marginal environments.
Functional characterization of a cellulose synthase, CtCESA1, from the marine red alga Calliarthron tuberculosum (Corallinales)
In land plants and algae, cellulose is important for strengthening cell walls and preventing breakage due to physical forces. Though our understanding of cellulose production by cellulose synthases (CESAs) has seen significant advances for several land plant and bacterial species, functional characterization of this fundamental protein is absent in red algae. Here we identify CESA gene candidates in the calcifying red alga Calliarthron tuberculosum using sequence similarity-based approaches, and elucidate their phylogenetic relationship with other CESAs from diverse taxa. One gene candidate, CtCESA1, was closely related to other putative red algal CESA genes. To test if CtCESA1 encoded a true cellulose synthase, CtCESA1 protein was expressed and purified from insect and yeast expression systems. CtCESA1 showed glucan synthase activity in glucose tracer assays. CtCESA1 activity was relatively low when compared with plant and bacterial CESA activity. In an in vitro assay, a predicted N-terminal starch-binding domain from CtCESA1 bound red algal floridean starch extracts, representing a unique domain in red algal CESAs not present in CESAs from other lineages. When the CtCESA1 gene was introduced into Arabidopsis thaliana cesa mutants, the red algal CtCESA1 partially rescued the growth defects of the primary cell wall cesa6 mutant, but not cesa3 or secondary cell wall cesa7 mutants. A fluorescently tagged CtCESA1 localized to the plasma membrane in the Arabidopsis cesa6 mutant background. This study presents functional evidence validating the sequence annotation of red algal CESAs. Furthermore, the relatively low activity of CtCESA1, partial complementation in Arabidopsis, and presence of unique protein domains suggest that there are probably functional differences between the algal and land plant CESAs.
Lignin Removal in Subcellular Location of Poplar Cell Wall During Pretreatment Significantly Impacts Cellulose Digestibility
The γ-valerolactone (GVL) pretreatment is one of the leading solvent-based methods for producing high-quality lignin under mild conditions. However, the glucan conversion yield from GVL pretreated biomass remains unsatisfactory. To explore the discrepancies between the relatively low glucan conversion and high lignin extraction, we conducted GVL−HCl and NaOH pretreatments on poplar and investigated their effects on lignin content and location, as well as on enzymatic hydrolysis of poplar cell walls at the subcellular level. Under designated pretreatment conditions of GVL−HCl (90% GVL, 0.1 M HCl, 100 °C, 1 h) and NaOH (1 M, 121 °C, 2 h), the glucan conversion yields were 69.4% and 95.8%, with lignin removal rates of 67.8% and 47.7%, respectively. Four types of GFP-labeled carbohydrate binding modules were used to identify different forms of cellulose in the pretreated cell walls. The overall binding intensities to pretreated poplar were stronger for NaOH compared to GVL−HCl pretreatment. Stimulated Raman scattering microscopy imaging revealed that GVL−HCl preferentially extracted lignin from the compound middle lamella and cell corner areas, while NaOH effectively dissolved lignin in the secondary cell walls. Real-time imaging of cellulase degradation of pretreated cell walls further indicated that digestion started from both the cell lumen and the compound middle lamella areas for GVL, whereas it occurred uniformly across the secondary cell walls for NaOH. Our findings suggest that the location of lignin removal during pretreatment is crucial for enzymatic cellulose degradation, in addition to the total amount of lignin extraction.
Visualizing plant cell wall changes proves the superiority of hydrochloric acid over sulfuric acid catalyzed γ-valerolactone pretreatment
Thermochemical pretreatment is one of the key steps to process lignocellulosic biomass for production of biofuels and biomaterials. γ-valerolactone (GVL) has been used as a green and renewable solvent to efficiently dissolve lignin under acidic conditions and enhance subsequent enzyme digestibility. Further improvement is still required to lower the pretreatment temperature in order to reduce sugar degradation and irreversible lignin condensation, as well as the capital cost. In this study, we compared the use of HCl and H 2 SO 4 as catalysts during GVL pretreatment, and found the performance of GVL-HCl at 100 °C was comparable to that of GVL-H 2 SO 4 at 120 °C in terms of xylan and lignin removal and enzyme digestibility. We further monitored the lignin removal and cellulose accessibility in the cell walls at different pretreatment time points by imaging the changes in lignin auto-fluorescence and in CtCBM3-GFP binding with confocal laser scanning microscopy (CLSM), respectively. We found GVL-HCl pretreatment at a relative low temperature (100 °C) could rapidly remove lignin in the compound middle lamella and cell corner areas, which concurred with the increase of CtCBM3-GFP binding in these areas. Real-time imaging of cell wall degradation by cellulases further revealed that the secondary cell walls could be digested from both cell lumen and CML sides, and eventually fully deconstructed within 24 h. Furthermore, our results provide new insight into the effects of chloride anions on plant cell wall structure during GVL pretreatment, and offer potential routes to further optimize and enhance the efficiency of GVL-based pretreatment.
Native Architecture of Wheat Straw Cell Walls: A Unified Model from X-ray Scattering and Solid-State NMR
Plant secondary cell walls constitute the dominant reservoir of renewable biomass, comprising tightly packed cellulose, hemicellulose, and lignin at the nanoscale. Recent advances in solid-state NMR spectroscopy and the availability of small-angle X-ray scattering for biomass characterization have led to an accumulation of experimental data on cell wall organization, yet no explicit structure model has simultaneously satisfied both Xray and NMR observations. Using wheat straw as a model system, we propose a structural framework consistent with current knowledge of cellulose biosynthesis, X-ray scattering data, and one- and two-dimensional 13 C solid-state NMR spectra. In this model, 18-chain elementary fibrils align in parallel and populate the cross-section at random. Arabinose-substituted xylan shows no conformational dependence for cellulose-binding in wheat, and only a minor fraction of 2-fold xylan appears in close proximity to cellulose, unlike in Arabidopsis, where xylan is more tightly attached to the cellulose surface. While NMR data cannot unambiguously resolve the internal arrangement of the 18 glucan chains, X-ray scattering profiles uniquely constrain the fibril size and exclude the possibility of tight bundling in the intact walls. The specific interaction between the matrix polymers and the cellulose elementary fibrils must be reconsidered in light of the small interfibril spaces, which bring the matrix components into spatial proximity with cellulose even in the absence of attractive interactions. These findings provide fundamental molecular-level insight into cellulose fibril architecture and matrix−polymer interactions, resolving longstanding discrepancies between spectroscopic and scattering data and advancing our understanding of biopolymer assembly into structurally and functionally versatile lignocellulosic biomaterials.