Molecular domains of the cellulose/xyloglucan network in the cell walls of higher plants

Characterization and antioxidant properties of three exopolysaccharides produced by the Cyclocarya paliurus endophytic fungus

In recent years, the considerable potential of endophytic bacteria and fungi as prolific producers of exopolysaccharides (EPSs) have attracted interest. In this study, 56 endophytes were isolated from Cyclocarya paliurus, and the secondary metabolites of EPSs were extracted from Monascus purpureus, Penicillium citrinum and Aspergillus versicolor, screened, and named MPE, PCE and AVE, respectively. In this work, the physicochemical properties and antioxidant activities of three EPSs, their cell proliferation activity on IEC-6 and RAW264.7 were investigated. The three EPSs were mainly composed of neutral sugar and differ in microstructure. However, MPE had a loose structure, and PCE exhibited a dense and sheet-like structure. In addition, the three EPSs performed ordinary antioxidant activity in vitro but showed excellent cell proliferation activity on IEC-6 and RAW264.7. The cell proliferation activity of PCE was 1.4-fold that of the controls at a concentration of 800 μg/mL on IEC-6, and MPE exhibited 1.3-fold increase on RAW264.7. This study provided scientific evidence and insights into the application of endophytes as a novel plant resource possessing huge application potential.

Structure and growth of plant cell walls

Plant cells build nanofibrillar walls that are central to plant growth, morphogenesis and mechanics. Starting from simple sugars, three groups of polysaccharides, namely, cellulose, hemicelluloses and pectins, with very different physical properties are assembled by the cell to make a strong yet extensible wall. This Review describes the physics of wall growth and its regulation by cellular processes such as cellulose production by cellulose synthase, modulation of wall pH by plasma membrane H+-ATPase, wall loosening by expansin and signalling by plant hormones such as auxin and brassinosteroid. In addition, this Review discusses the nuanced roles, properties and interactions of cellulose, matrix polysaccharides and cell wall proteins and describes how wall stress and wall loosening cooperatively result in cell wall growth.

Spaceflight impacts xyloglucan oligosaccharide abundance in Arabidopsis thaliana root cell walls

Over the course of more than a decade, space biology investigations have consistently indicated that cell wall remodeling occurs in a variety of spaceflight-grown plants. Here, we describe a mass spectrometric method to study the fundamental composition of xyloglucan, the most abundant hemicellulose in dicot cell walls, in space-grown plants. Four representative Arabidopsis root samples, from a previously conducted spaceflight experiment - Advanced Plant EXperiment - 04 (APEX-04), were used to investigate changes in xyloglucan oligosaccharides abundances in spaceflight-grown plants compared to ground controls. In situ localized enzymatic digestions and surface sampling mass spectrometry analysis provided spatial resolution of the changes in xyloglucan oligosaccharides abundances. Overall, the results showed that oligosaccharide XXLG/XLXG and XXFG branching patterns were more abundant in the lateral roots of spaceflight-grown plants, while XXXG, XLFG, and XLFG/XLFG were more abundant in the lateral roots of ground control plants. In the primary roots, XXFG had a higher abundance in ground controls than in spaceflight plants. This methodology of analyzing the basic components of the cell wall in this paper highlights two important findings. First, that are differences in the composition of xyloglucan oligosaccharides in spaceflight root cell walls compared to ground controls and, second, most of these differences are observed in the lateral roots. Thus, the methodology described in this paper provides insights into spaceflight cell wall modifications for future investigations.

Creating a novel genetic diversity of Trichoderma afroharzianum by γ-radiation for xylanase-cellulase production

Creating novel sources of a microbial strain using induced mutation can increase enzyme production for industrial use. According to this, we have developed a mutant strain of Trichoderma afroharzianum by Co60 gamma irradiation. Trichoderma mutants were isolated from an optimum dose of 250 Gy. The qualitative and quantitative screening were used for evaluating their enzyme production and the DNA barcoding method was used to identify the best Trichoderma mutant isolates. The highest cellulase (exo-glucanase, endoglucanase, β-glucosidase, and total cellulase) and xylanase activities were observed in superior mutant isolates of Trichoderma afroharzianum NAS107-M44 and Trichoderma afroharzianum NAS107-M82, which is approximately 1.6-2.5 times higher than its parent strain, respectively. The electrophoretic pattern of proteins showed that the exo-glucanase I, endo-glucanase III, and the xylanase I enzymes hydrolyzed the corn bran, synergistically. Overall, gamma irradiation-induced mutation could be an expedient technique to access such superior mutants for the bioconversion of corn bran wastes.

Identification and validation of seed dormancy loci and candidate genes and construction of regulatory networks by WGCNA in maize introgression lines

KEY MESSAGE

Seventeen PHS-QTLs and candidate genes were obtained, including eleven major loci, three under multiple environments and two with co-localization by the other mapping methods; The functions of three candidate genes were validated using mutants; nine target proteins and five networks were filtered by joint analysis of GWAS and WGCNA. Seed dormancy (SD) and pre-harvest sprouting (PHS) affect yield, as well as grain and hybrid quality in seed production. Therefore, identification of genetic and regulatory pathways underlying PHS and SD is key to gene function analysis, allelic variation mining and genetic improvement. In this study, 78,360 SNPs by SLAF-seq of 230 maize chromosome segment introgression lines (ILs), PHS under five environments were used to conduct GWAS (genome wide association study) (a threshold of 1/n), and seventeen unreported PHS QTLs were obtained, including eleven QTLs with PVE > 10% and three QTLs under multiple environments. Two QTL loci were co-located between the other two genetic mapping methods. Using differential gene expression analyses at two stages of grain development, gene functional analysis of Arabidopsis mutants, and gene functional analysis in the QTL region, seventeen PHS QTL-linked candidate genes were identified, and their five molecular regulatory networks constructed. Based on the Arabidopsis T-DNA mutations, three candidate genes were shown to regulate for SD and PHS. Meanwhile, using RNA-seq of grain development, the weighted correlation network analysis (WGCNA) was performed, deducing five regulatory pathways and target genes that regulate PHS and SD. Based on the conjoint analysis of GWAS and WGCNA, four pathways, nine target proteins and target genes were revealed, most of which regulate cell wall metabolism, cell proliferation and seed dehydration tolerance. This has important theoretical and practical significance for elucidating the genetic basis of maize PHS and SD, as well as mining of genetic resources and genetic improvement of traits.

Polysaccharide assemblies in fungal and plant cell walls explored by solid-state NMR

Structural analysis of macromolecular complexes within their natural cellular environment presents a significant challenge. Recent applications of solid-state NMR (ssNMR) techniques on living fungal cells and intact plant tissues have greatly enhanced our understanding of the structure of extracellular matrices. Here, we selectively highlight the most recent progress in this field. Specifically, we discuss how ssNMR can provide detailed insights into the chemical composition and conformational structure of pectin, and the consequential impact on polysaccharide interactions and cell wall organization. We elaborate on the use of ssNMR data to uncover the arrangement of the lignin-polysaccharide interface and the macrofibrillar structure in native plant stems or during degradation processes. We also comprehend the dynamic structure of fungal cell walls under various morphotypes and stress conditions. Finally, we assess how the combination of NMR with other techniques can enhance our capacity to address unresolved structural questions concerning these complex macromolecular assemblies.

Genome-Wide Identification and Expression Analysis of the Xyloglucan Endotransglucosylase/Hydrolase Gene Family in Sweet Potato [Ipomoea batatas (L.) Lam]

The xyloglucan endotransglucosylase/hydrolase (XET/XEH, also named XTH) family is a multigene family, the function of which plays a significant role in cell-wall rebuilding and stress tolerance in plants. However, the specific traits of the XTH gene family members and their expression pattern in different tissues and under stress have not been carried out in sweet potato. Thirty-six XTH genes were identified in I. batatas, all of which had conserved structures (Glyco_hydro_16). Based on Neighbor-Joining phylogenetic analysis the IbXTHs can be divided into three subfamilies-the I/II, IIIA, and IIIB subfamilies, which were unevenly distributed on 13 chromosomes, with the exception of Chr9 and Chr15. Multiple cis-acting regions related to growth and development, as well as stress responses, may be found in the IbXTH gene promoters. The segmental duplication occurrences greatly aided the evolution of IbXTHs. The results of a collinearity analysis showed that the XTH genes of sweet potato shared evolutionary history with three additional species, including A. thaliana, G. max, and O. sativa. Additionally, based on the transcriptome sequencing data, the results revealed that the IbXTHs have different expression patterns in leaves, stems, the root body (RB), the distal end (DE), the root stock (RS), the proximal end (PE), the initiative storage root (ISR), and the fibrous root (FR), and many of them are well expressed in the roots. Differentially expressed gene (DEG) analysis of FRs after hormone treatment of the roots indicated that IbXTH28 and IbXTH30 are up-regulated under salicylic acid (SA) treatment but down-regulated under methyl jasmonate (MeJA) treatment. Attentionally, there were only two genes showing down-regulation under the cold and drought treatment. Collectively, all of the findings suggested that genes from the XTH family are crucial for root specificity. This study could provide a theoretical basis for further research on the molecular function of sweet potato XTH genes.

Acetyl Group Migration in Xylan and Glucan Model Compounds as Studied by Experimental and Computational Methods

It was recently demonstrated by us that acetyl groups in oligosaccharides can migrate not only within one saccharide unit but also between two different saccharide units. Kinetics of this phenomenon were previously investigated in both mannan model compounds and a naturally occurring polysaccharide. In addition to mannans, there are also several other naturally acetylated polysaccharides, such as xyloglucans and xylans. Both xyloglucans and xylans are some of the most common acetylated polysaccharides in nature, displaying important roles in the plant cells. Considering the various biological roles of natural polysaccharides, it could be hypothesized that the intramolecular migration of acetyl groups might also be associated with regulation of the biological activity of polysaccharides in nature. Consequently, a better understanding of the overall migration phenomenon across the glycosidic bonds could help to understand the potential role of such migrations in the context of the biological activity of polysaccharides. Here, we present a detailed investigation on acetyl group migration in the synthesized xylan and glucan trisaccharide model compounds by a combination of experimental and computational methods, showing that the migration between the saccharide units proceeds from a secondary hydroxyl group of one saccharide unit toward a primary hydroxyl group of the other unit.

Building an Artificial Plant Cell Wall on a Lipid Bilayer by Assembling Polysaccharides and Engineered Proteins

The cell wall constitutes a fundamental structural component of plant cells, providing them with mechanical resistance and flexibility. Mimicking this wall is a critical step in the conception of an experimental model of the plant cell. The assembly of cellulose/hemicellulose in the form of cellulose nanocrystals and xyloglucans as a representative model of the plant cell wall has already been mastered; however, these models lacked the pectin component. In this work, we used an engineered chimeric protein designed for bridging pectin to the cellulose/hemicellulose network, therefore achieving the assembly of complete cell wall mimics. We first engineered a carbohydrate-binding module from Ruminococcus flavefaciens able to bind oligogalacturonan, resulting in high-affinity polygalacturonan receptors with K_d in the micromolar range. A Janus protein, with cell wall gluing property, was then designed by assembling this carbohydrate-binding module with a Ralstonia solanacearum lectin specific for fucosylated xyloglucans. The resulting supramolecular architecture is able to bind fucose-containing xyloglucans and homogalacturonan, ensuring high affinity for both. A two-dimensional assembly of an artificial plant cell wall was then built first on synthetic polymer and then on the supported lipid bilayer. Such an artificial cell wall can serve as a basis for the development of plant cell mechanical models and thus deepen the understanding of the principles underlying various aspects of plant cells and tissues.

Biorefinery of apple pomace: New insights into xyloglucan building blocks

Within the apple pomace biorefinery cascade processing framework aiming at adding value to an agroindustrial waste, after pectin recovery, this study focused on hemicellulose. The structure of the major apple hemicellulose, xyloglucan (XyG), was assessed as a prerequisite to potential developments in industrial applications. DMSO-LiCl and 4 M KOH soluble hemicelluloses from pectin-extracted apple pomace were purified by anion exchange chromatography. XyG structure was assessed by coupling xyloglucanase and endo-β-1,4-glucanase digestions to HPAEC and MALDI-TOF MS analyses. 71.9% of pomaces hemicellulose were recovered with starch. DMSO-LiCl and 4 M KOH soluble XyG exhibited Mw of 19 and 140 kDa, respectively. Besides the XXXG, XLXG, XXLG, XXFG, XLFG and XLLG structures, novel oligosaccharides with degree of polymerization of 6-10 were observed after xyloglucanase digestion. Cellobiose and cellotriose were revealed randomly distributed in XyG backbone and were more present in DMSO-LiCl soluble XyG. Residual pomace remains a potential source of other materials.

Building an extensible cell wall

This article recounts, from my perspective of four decades in this field, evolving paradigms of primary cell wall structure and the mechanism of surface enlargement of growing cell walls. Updates of the structures, physical interactions, and roles of cellulose, xyloglucan, and pectins are presented. This leads to an example of how a conceptual depiction of wall structure can be translated into an explicit quantitative model based on molecular dynamics methods. Comparison of the model's mechanical behavior with experimental results provides insights into the molecular basis of complex mechanical behaviors of primary cell wall and uncovers the dominant role of cellulose-cellulose interactions in forming a strong yet extensible network.

Dynamics of pectic homogalacturonan in cellular morphogenesis and adhesion, wall integrity sensing and plant development

Homogalacturonan (HG) is the most abundant pectin subtype in plant cell walls. Although it is a linear homopolymer, its modification states allow for complex molecular encoding. HG metabolism affects its structure, chemical properties, mobility and binding capacity, allowing it to interact dynamically with other polymers during wall assembly and remodelling and to facilitate anisotropic cell growth, cell adhesion and separation, and organ morphogenesis. HGs have also recently been found to function as signalling molecules that transmit information about wall integrity to the cell. Here we highlight recent advances in our understanding of the dual functions of HG as a dynamic structural component of the cell wall and an initiator of intrinsic and environmental signalling. We also predict how HG might interconnect the cell wall, plasma membrane and intracellular components with transcriptional networks to regulate plant growth and development.

Broad Specific Xyloglucan:Xyloglucosyl Transferases Are Formidable Players in the Re-Modelling of Plant Cell Wall Structures

Plant xyloglucan:xyloglucosyl transferases, known as xyloglucan endo-transglycosylases (XETs) are the key players that underlie plant cell wall dynamics and mechanics. These fundamental roles are central for the assembly and modifications of cell walls during embryogenesis, vegetative and reproductive growth, and adaptations to living environments under biotic and abiotic (environmental) stresses. XET enzymes (EC 2.4.1.207) have the β-sandwich architecture and the β-jelly-roll topology, and are classified in the glycoside hydrolase family 16 based on their evolutionary history. XET enzymes catalyse transglycosylation reactions with xyloglucan (XG)-derived and other than XG-derived donors and acceptors, and this poly-specificity originates from the structural plasticity and evolutionary diversification that has evolved through expansion and duplication. In phyletic groups, XETs form the gene families that are differentially expressed in organs and tissues in time- and space-dependent manners, and in response to environmental conditions. Here, we examine higher plant XET enzymes and dissect how their exclusively carbohydrate-linked transglycosylation catalytic function inter-connects complex plant cell wall components. Further, we discuss progress in technologies that advance the knowledge of plant cell walls and how this knowledge defines the roles of XETs. We construe that the broad specificity of the plant XETs underscores their roles in continuous cell wall restructuring and re-modelling.

Solid-State Nuclear Magnetic Resonance as a Tool to Probe the Impact of Mechanical Preprocessing on the Structure and Arrangement of Plant Cell Wall Polymers

Efficient separation of the plant cell wall polymers during lignocellulose processing has been historically challenging due to insolubility of the polymers and their propensity for recalcitrant reassembly. Methods, such as "lignin first" extraction techniques, have advanced efficient biomass use, but the molecular mechanisms for recalcitrance remain enigmatic. Here, we discuss how solid-state Nuclear Magnetic Resonance (NMR) approaches report on the 3D organization of cellulose, xylan, and lignin in the plant cell wall. Recent results illustrate that the organization of these polymers varies across biomass sources and sample preparation methods, with even minimal physical processing causing significant effects. These structural differences contribute to variable extraction efficiencies for bioproducts after downstream processing. We propose that solid-state NMR methods can be applied to follow biomass processing, providing an understanding of the polymer rearrangements that can lead to poor yields for the desired bioproducts. The utility of the technique is illustrated for mechanical processing using lab-scale vibratory ball milling of Sorghum bicolor.

Structural Profiling of Xyloglucans from Food Plants by High-Performance Anion-Exchange Chromatography with Parallel Pulsed Amperometric and Mass Spectrometric Detection

Xyloglucans are the dominant hemicelluloses in the primary cell wall of dicotyledonous plants, fulfilling numerous functions. However, routine methods of cell wall analytical chemistry such as methylation analysis are time-consuming and often not adequate to capture the structural diversity of xyloglucans. Here, a xyloglucan profiling method based on the enzymatic release of xyloglucan oligosaccharides by a xyloglucan-specific endo-β-(1→4)-glucanase and subsequent analysis of these oligosaccharides by high-performance anion-exchange chromatography (HPAEC) with parallel pulsed amperometric and mass spectrometric detection was developed. For this purpose, a set of 23 authentic xyloglucan oligosaccharides was generated, structurally characterized by mass spectrometry and NMR spectroscopy, and established as analytical standard compounds. Coupling of HPAEC with parallel electrochemical and MS detection was demonstrated to be an excellent tool to analyze xyloglucan-derived oligosaccharides. The applicability of the method was demonstrated by characterizing the xyloglucan architecture from a set of nine economically relevant food plants from the botanical orders Caryophyllales (rhubarb, buckwheat, amaranth, and quinoa), Cucurbitales (Hokkaido squash), Laurales (avocado), Myrtales (pomegranate), and Sapindales (mango and orange) for the first time. In future studies, this method can ideally be used to monitor structural alterations of xyloglucans as a result of genetic engineering, plant/tissue maturation, and processing of plant material.

Molecular self-organization of wood lignin-carbohydrate matrix

The analysis of the state of research on the chemical composition, functional nature and structure of the main components of the lignin-carbohydrate matrix allows considering the wood substance as a thermodynamically self-organizing nanobiocomposite system. Features of biosynthesis of the wood matrix main biopolymers, the formation of their functional nature and structure determine the complex hierarchical organization of cell walls. The supramolecular level of biosynthesis considers the interaction of cell wall components. On the one hand, these are questions of dynamics of cell walls synthesis and processes of self-organization that control the formation of chaotic objects of biological origin; on the other hand, it is the question of thermodynamic compatibility of plant tissue components. Various models of structural organization are currently being considered, focusing on various features (biological, chemical, structural) of wood substance. At the same time, the lignin-carbohydrate matrix is a three-component system of natural polymers: lignin-hemicelluloses-cellulose, the state of which is described by specific values of thermodynamic parameters that characterize the degree of its stability. The new approach proposed in this paper allows considering the plant lignin-carbohydrate matrix from the standpoint of physical chemistry of polymer as quasi-equilibrium, thermodynamically limited ordered system of biopolymers. Thus, the biochemical processes of synthesis and self-organization lead to the formation of a complex multicomponent system of wood substance, considered as a nanobiocomposite. This determines the need to study the applicability of the fundamental cycle "structure-functional nature-properties" from the standpoint of physical chemistry of biopolymers both for the investigation of plant objects and for the development of modern technologies for complex processing based on the principles of "green chemistry".

Bioconversion of Renewable Plant Biomass. Second-Generation Biofuels: Raw Materials, Biomass Pretreatment, Enzymes, Processes, and Cost Analysis

The review discusses various aspects of renewable plant biomass conversion and production of the second-generation biofuels, including the types of plant biomass, its composition and reaction ability in the enzymatic hydrolysis, and various pretreatment methods for increasing the biomass reactivity. Conversion of plant biomass into sugars requires the use of a complex of enzymes, the composition of which should be adapted to the biomass type and the pretreatment method. The efficiency of enzymatic hydrolysis can be increased by optimizing the composition of the enzymatic complex and by increasing the catalytic activity and operational stability of its constituent enzymes. The availability of active enzyme producers also plays an important role. Examples of practical implementation and scaling of processes for the production of second-generation biofuels are presented together with the cost analysis of bioethanol production.

Characterization of pectin-xylan-glucan-arabinogalactan proteins complex from Siberian fir Abies sibirica Ledeb

Polysaccharide AS_K was isolated from the Abies sibirica foliage by extraction with an aqueous KOH solution. AS_K was shown to contain structurally different polymers such as arabinoglucuronoxylans, xyloglucans, glucomannans, arabinogalactan-proteins (AGPs). The pectic polysaccharides were also found in the alkaline extract of AS_K and were represented by regions of homogalactorunan and rhamnogalactouronan-I whose side sugar chains were made up chiefly of highly branched 1,5-α-l-arabinan. The potential couplings between those polysaccharides were examined. Our studies showed simultaneous elution of pectin, xyloglucans, arabinoglucuronoxylans and AGPs, indicating that pectins can be covalently bound to the other cell-wall polysaccharides. NMR spectroscopy results revealed that the polysaccharides obtained by ion-exchange chromatography almost had no free reducing ends. These findings corroborate the conclusion that pectin, AGPs, glucan and xylan are bound together. The existence of the covalently bound complex of pectin-xylan-xyloglucan-AGP is suggested herein. Pectin and xylan are hypothesized to be covalently linked through RG-I regions.

Rational engineering of xylanase hyper-producing system in Trichoderma reesei for efficient biomass degradation

BACKGROUND

Filamentous fungus Trichoderma reesei has been widely used as a workhorse for cellulase and xylanase productions. Xylanase has been reported as the crucial accessory enzyme in the degradation of lignocellulose for higher accessibility of cellulase. In addition, the efficient hydrolysis of xylan needs the co-work of multiple xylanolytic enzymes, which rise an increasing demand for the high yield of xylanase for efficient biomass degradation.

RESULTS

In this study, a xylanase hyper-producing system in T. reesei was established by tailoring two transcription factors, XYR1 and ACE1, and homologous overexpression of the major endo-xylanase XYNII. The expressed xylanase cocktail contained 5256 U/mL xylanase activity and 9.25 U/mL β-xylosidase (pNPXase) activity. Meanwhile, the transcription level of the xylanolytic genes in the strain with XYR1 overexpressed was upregulated, which was well correlated with the amount of XYR1-binding sites. In addition, the higher expression of associated xylanolytic enzymes would result in more efficient xylan hydrolysis. Besides, 2310-3085 U/mL of xylanase activities were achieved using soluble carbon source, which was more efficient and economical than the traditional strategy of xylan induction. Unexpectedly, deletion of ace1 in C30OExyr1 did not give any improvement, which might be the result of the disturbed function of the complex formed between ACE1 and XYR1. The enzymatic hydrolysis of alkali pretreated corn stover using the crude xylanase cocktails as accessory enzymes resulted in a 36.64% increase in saccharification efficiency with the ratio of xylanase activity vs FPase activity at 500, compared to that using cellulase alone.

CONCLUSIONS

An efficient and economical xylanase hyper-producing platform was developed in T. reesei RUT-C30. The novel platform with outstanding ability for crude xylanase cocktail production would greatly fit in biomass degradation and give a new perspective of further engineering in T. reesei for industrial purposes.

Plant Xyloglucan Xyloglucosyl Transferases and the Cell Wall Structure: Subtle but Significant

Plant xyloglucan xyloglucosyl transferases or xyloglucan endo-transglycosylases (XET; EC 2.4.1.207) catalogued in the glycoside hydrolase family 16 constitute cell wall-modifying enzymes that play a fundamental role in the cell wall expansion and re-modelling. Over the past thirty years, it has been established that XET enzymes catalyse homo-transglycosylation reactions with xyloglucan (XG)-derived substrates and hetero-transglycosylation reactions with neutral and charged donor and acceptor substrates other than XG-derived. This broad specificity in XET isoforms is credited to a high degree of structural and catalytic plasticity that has evolved ubiquitously in algal, moss, fern, basic Angiosperm, monocot, and eudicot enzymes. These XET isoforms constitute gene families that are differentially expressed in tissues in time- and space-dependent manners during plant growth and development, and in response to biotic and abiotic stresses. Here, we discuss the current state of knowledge of broad specific plant XET enzymes and how their inherently carbohydrate-based transglycosylation reactions tightly link with structural diversity that underlies the complexity of plant cell walls and their mechanics. Based on this knowledge, we conclude that multi- or poly-specific XET enzymes are widespread in plants to allow for modifications of the cell wall structure in muro, a feature that implements the multifaceted roles in plant cells.

Pretreatment of Rapeseed Meal Increases Its Recalcitrant Fiber Fermentation and Alters the Microbial Community in an in vitro Model of Swine Large Intestine

The aim of current study was to investigate in an in vitro study how enzymatic and chemical pretreated rapeseed meal (RSM) influences the fiber fermentation and microbial community in the swine large intestine. RSM was processed enzymatically by a cellulase (CELL), two pectinases (PECT), or chemically by an alkaline (ALK) treatment. 16S rRNA gene sequencing data was performed to evaluate changes in the gut microbiota composition, whereas short-chain fatty acid (SCFA) production (ion-chromatography) and non-starch polysaccharides (NSP) composition (using monoclonal antibodies; mAbs) were used to assess fiber degradation. The results showed that ALK, CELL, PECT1, and PECT2 changed microbial community composition, increased the predicted abundance of microbial fiber-degrading enzymes and pathways, and increased acetic acid, propionic acid, butyric acid, and total SCFA production. The increased microbial genera positively correlated with SCFA production. Monoclonal antibody analyses showed that the cell wall polysaccharide structures of RSM shifted after ALK, CELL, PECT1, and PECT2 treatment. The degradation of NSP during the fermentation period was dynamic, and not continuous based on the epitope recognition by mAbs. This study provides the first detailed analysis of changes in the swine intestinal microbiota due to RSM modified by ALK, CELL, PECT1, and PECT2, which altered the microbial community structure, shifted the predicted functional metagenomic profile and subsequently increased total SCFA production. Our findings that ALK, CELL, PECT1, and PECT2 increased fiber degradability in RSM could help guide feed additive strategies to improve efficiency and productivity in swine industry. The current study gave insight into how enzymatic treatment of feed can alter microbial communities, which provides good opportunity to develop novel carbohydrase treatments, particularly in swine feed.

Three highly acidic Equisetum XTHs differ from hetero-trans-β-glucanase in donor substrate specificity and are predominantly xyloglucan homo-transglucosylases

Transglycanases are enzymes that remodel the primary cell wall in plants, potentially loosening and/or strengthening it. Xyloglucan endotransglucosylase (XET; EC 2.4.1.207), ubiquitous in land plants, is a homo-transglucanase activity (donor, xyloglucan; acceptor, xyloglucan) exhibited by XTH (xyloglucan endotransglucosylase/hydrolase) proteins. By contrast, hetero-trans-β-glucanase (HTG) is the only known enzyme that is preferentially a hetero-transglucanase. Its two main hetero-transglucanase activities are MLG : xyloglucan endotransglucosylase (MXE) and cellulose : xyloglucan endotransglucosylase (CXE). HTG is highly acidic and found only in the evolutionarily isolated genus of fern-allies, Equisetum. We now report genes for three new highly acidic HTG-related XTHs in E. fluviatile (EfXTH-A, EfXTH-H and EfXTH-I). We expressed them heterologously in Pichia and tested the encoded proteins' enzymic activities to determine whether their acidity and/or their Equisetum-specific sequences might confer high hetero-transglucanase activity. Untransformed Pichia was found to secrete MLG-degrading enzyme(s), which had to be removed for reliable MXE assays. All three acidic EfXTHs exhibited very predominantly XET activity, although low but measurable hetero-transglucanase activities (MXE and CXE) were also detected in EfXTH-H and EfXTH-I. We conclude that the extremely high hetero-transglucanase activities of Equisetum HTG are not emulated by similarly acidic Equisetum XTHs that share up to 55.5% sequence identity with HTG.

Adsorption of xyloglucan and cellulose nanocrystals on natural fibres for the creation of hierarchically structured fibres

Green treatment of natural fibres is a major issue in paper, textile and biocomposites industries to design innovative and eco-friendly products. In this work, hierarchical structuring of flax woven fabrics by the adsorption of xyloglucan (XG) and cellulose nanocrystals (CNC) is studied. Indeed, CNC have high mechanical properties, high specific surface area and great potential for functionalization. The adsorption of XG and CNC has been investigated in terms of localization by confocal and scanning electron microscopy (SEM) and quantification through adsorption isotherms. Adhesion force measurements have also been performed by Atomic Force Microscopy (AFM). XG and CNC are homogeneously adsorbed on flax fabric and adsorption isotherms reach plateau values around 20 mg /g_fibres for both. The pre-adsorption of XG on flax fabric influences the amount of adsorbed CNC in the high concentrations and also creates entanglements and strong interactions between XG and CNC with the formation of an extensible network.

Fruit From Two Kiwifruit Genotypes With Contrasting Softening Rates Show Differences in the Xyloglucan and Pectin Domains of the Cell Wall

Fruit softening is controlled by hormonal and developmental cues, causing an upregulation of cell wall-associated enzymes that break down the complex sugar matrices in the cell wall. The regulation of this process is complex, with different genotypes demonstrating quite different softening patterns, even when they are closely related. Currently, little is known about the relationship between cell wall structure and the rate of fruit softening. To address this question, the softening of two Actinidia chinensis var. chinensis (kiwifruit) genotypes (a fast 'AC-F' and a slow 'AC-S' softening genotype) was examined using a range of compositional, biochemical, structural, and molecular techniques. Throughout softening, the cell wall structure of the two genotypes was fundamentally different at identical firmness stages. In the hemicellulose domain, xyloglucanase enzyme activity was higher in 'AC-F' at the firm unripe stage, a finding supported by differential expression of xyloglucan transglycosylase/hydrolase genes during softening. In the pectin domain, differences in pectin solubilization and location of methyl-esterified homogalacturonan in the cell wall between 'AC-S' and 'AC-F' were shown. Side chain analyses and molecular weight elution profiles of polyuronides and xyloglucans of cell wall extracts revealed fundamental differences between the genotypes, pointing towards a weakening of the structural integrity of cell walls in the fast softening 'AC-F' genotype even at the firm, unripe stage. As a consequence, the polysaccharides in the cell walls of 'AC-F' may be easier to access and hence more susceptible to enzymatic degradation than in 'AC-S', resulting in faster softening. Together these results suggest that the different rates of softening between 'AC-F' and 'AC-S' are not due to changes in enzyme activities alone, but that fundamental differences in the cell wall structure are likely to influence the rates of softening through differential modification and accessibility of specific cell wall polysaccharides during ripening.

Pectic galactan affects cell wall architecture during secondary cell wall deposition

β-(1,4)-galactan determines the interactions between different matrix polysaccharides and cellulose during the cessation of cell elongation. Despite recent advances regarding the role of pectic β-(1,4)-galactan neutral side chains in primary cell wall remodelling during growth and cell elongation, little is known about the specific function of this polymer in other developmental processes. We have used transgenic Arabidopsis plants overproducing chickpea βI-Gal β-galactosidase under the 35S CaMV promoter (35S::βI-Gal) with reduced galactan levels in the basal non-elongating floral stem internodes to gain insight into the role of β-(1,4)-galactan in cell wall architecture during the cessation of elongation and the beginning of secondary growth. The loss of galactan mediated by βI-Gal in 35S::βI-Gal plants is accompanied by a reduction in the levels of KOH-extracted xyloglucan and an increase in the levels of xyloglucan released by a cellulose-specific endoglucanase. These variations in cellulose-xyloglucan interactions cause an altered xylan and mannan deposition in the cell wall that in turn results in a deficient lignin deposition. Considering these results, we can state that β-(1,4)-galactan plays a key structural role in the correct organization of the different domains of the cell wall during the cessation of growth and the early events of secondary cell wall development. These findings reinforce the notion that there is a mutual dependence between the different polysaccharides and lignin polymers to form an organized and functional cell wall.

Insights from semi-oriented EPR spectroscopy studies into the interaction of lytic polysaccharide monooxygenases with cellulose

Probing the detailed interaction between lytic polysaccharide monooxygenases (LPMOs) and their polysaccharide substrates is key to revealing further insights into the mechanism of action of this class of enzymes on recalcitrant biomass. This investigation is somewhat hindered, however, by the insoluble nature of the substrates, which precludes the use of most optical spectroscopic techniques. Herein, we report a new semi-oriented EPR method which evaluates directly the binding of cellulose-active LPMOs to crystalline cellulose. We make use of the intrinsic order of cellulose fibres in Apium graveolens (celery) to orient the LPMO with respect to the magnetic field of an EPR spectrometer. The subsequent angle-dependent changes observed in the EPR spectra can then be related to the orientation of the g matrix principal directions with respect to the magnetic field of the spectrometer and, hence, to the binding of the enzyme onto the cellulose fibres. This method, which does not require specific modification of standard CW-EPR equipment, can be used as a general procedure to investigate LPMO-cellulose interactions.

Plant Cell Walls: Impact on Nutrient Bioaccessibility and Digestibility

Cell walls are important structural components of plants, affecting both the bioaccessibility and subsequent digestibility of the nutrients that plant-based foods contain. These supramolecular structures are composed of complex heterogeneous networks primarily consisting of cellulose, and hemicellulosic and pectic polysaccharides. The composition and organization of these different polysaccharides vary depending on the type of plant tissue, imparting them with specific physicochemical properties. These properties dictate how the cell walls behave in the human gastrointestinal tract, and how amenable they are to digestion, thereby modulating nutrient release from the plant tissue. This short narrative review presents an overview of our current knowledge on cell walls and how they impact nutrient bioaccessibility and digestibility. Some of the most relevant methods currently used to characterize the food matrix and the cell walls are also described.

Functional and chemical characterization of XAF: a heat-stable plant polymer that activates xyloglucan endotransglucosylase/hydrolase (XTH)

BACKGROUND AND AIMS

Xyloglucan endotransglucosylase/hydrolase (XTH) proteins that possess xyloglucan endotransglucosylase (XET) activity contribute to cell-wall assembly and remodelling, orchestrating plant growth and development. Little is known about in-vivo XET regulation, other than at the XTH transcriptional level. Plants contain 'cold-water-extractable, heat-stable polymers' (CHPs) which are XTH-activating factors (XAFs) that desorb and thereby activate wall-bound XTHs. Because XAFs may control cell-wall modification in vivo, we have further explored their nature.

METHODS

Material was cold-water-extracted from 25 plant species; proteins were precipitated by heat-denaturation, then CHP was ethanol-precipitated. For XAF assays, CHP (or sub-fractions thereof) was applied to washed Arabidopsis thaliana cell walls, and the enzymes thus solubilized were assayed radiochemically for XET activity. In some experiments, the CHP was pre-treated with trifluoroacetic acid (TFA), alkali (NaOH) or glycanases.

KEY RESULTS

CHP specifically desorbed wall-bound XTHs, but not β-glucosidases, phosphatases or peroxidases. CHP preparations from 25 angiosperms all possessed XAF activity but had no consistent monosaccharide composition. Of 11 individual plant polymers tested, only gum arabic and tamarind xyloglucan were XAF-active, albeit less so than CHP. On gel-permeation chromatography, XAF-active cauliflower CHP eluted with a molecular weight of ~7000-140 000, although no specific sugar residue(s) co-eluted exactly with XAF activity. Cauliflower XAF activity survived cold alkali and warm dilute TFA (which break ester and glycofuranosyl linkages, respectively), but was inactivated by hot 2 m TFA (which breaks glycopyranosyl linkages). Cauliflower XAF activity was remarkably stable to diverse glycanases and glycosidases.

CONCLUSIONS

XAFs are naturally occurring heat-stable polymers that specifically desorb (thereby activating) wall-bound XTHs. Their XAF activity considerably exceeds that of gum arabic and tamarind xyloglucan, and they were not identifiable as any major plant polysaccharide. We propose that XAF is a specific, minor, plant polymer that regulates xyloglucan transglycosylation in vivo, and thus wall assembly and restructuring.

Substrate specificity, regiospecificity, and processivity in glycoside hydrolase family 74

Glycoside hydrolase family 74 (GH74) is a historically important family of endo-β-glucanases. On the basis of early reports of detectable activity on cellulose and soluble cellulose derivatives, GH74 was originally considered to be a "cellulase" family, although more recent studies have generally indicated a high specificity toward the ubiquitous plant cell wall matrix glycan xyloglucan. Previous studies have indicated that GH74 xyloglucanases differ in backbone cleavage regiospecificities and can adopt three distinct hydrolytic modes of action: exo, endo-dissociative, and endo-processive. To improve functional predictions within GH74, here we coupled in-depth biochemical characterization of 17 recombinant proteins with structural biology-based investigations in the context of a comprehensive molecular phylogeny, including all previously characterized family members. Elucidation of four new GH74 tertiary structures, as well as one distantly related dual seven-bladed β-propeller protein from a marine bacterium, highlighted key structure-function relationships along protein evolutionary trajectories. We could define five phylogenetic groups, which delineated the mode of action and the regiospecificity of GH74 members. At the extremes, a major group of enzymes diverged to hydrolyze the backbone of xyloglucan nonspecifically with a dissociative mode of action and relaxed backbone regiospecificity. In contrast, a sister group of GH74 enzymes has evolved a large hydrophobic platform comprising 10 subsites, which facilitates processivity. Overall, the findings of our study refine our understanding of catalysis in GH74, providing a framework for future experimentation as well as for bioinformatics predictions of sequences emerging from (meta)genomic studies.

EXPANSIN A1-mediated radial swelling of pericycle cells positions anticlinal cell divisions during lateral root initiation

In plants, postembryonic formation of new organs helps shape the adult organism. This requires the tight regulation of when and where a new organ is formed and a coordination of the underlying cell divisions. To build a root system, new lateral roots are continuously developing, and this process requires the tight coordination of asymmetric cell division in adjacent pericycle cells. We identified EXPANSIN A1 (EXPA1) as a cell wall modifying enzyme controlling the divisions marking lateral root initiation. Loss of EXPA1 leads to defects in the first asymmetric pericycle cell divisions and the radial swelling of the pericycle during auxin-driven lateral root formation. We conclude that a localized radial expansion of adjacent pericycle cells is required to position the asymmetric cell divisions and generate a core of small daughter cells, which is a prerequisite for lateral root organogenesis.

β-(1,4)-Galactan remodelling in Arabidopsis cell walls affects the xyloglucan structure during elongation

Galactan turnover occurs during cell elongation and affects the cell wall xyloglucan structure which is involved in the interaction between cellulose and xyloglucan. β-(1,4)-Galactan is one of the main side chains of rhamnogalacturonan I. Although the specific function of this polymer has not been completely established, it has been related to different developmental processes. To study β-(1,4)-galactan function, we have generated transgenic Arabidopsis plants overproducing chickpea βI-Gal β-galactosidase under the 35S CaMV promoter (35S::βI-Gal) to reduce galactan side chains in muro. Likewise, an Arabidopsis double loss-of-function mutant for BGAL1 and BGAL3 Arabidopsis β-galactosidases (bgal1/bgal3) has been obtained to increase galactan levels. The characterization of these plants has confirmed the role of β-(1,4)-galactan in cell growth, and demonstrated that the turnover of this pectic side chain occurs during cell elongation, at least in Arabidopsis etiolated hypocotyls and floral stem internodes. The results indicate that BGAL1 and BGAL3 β-galactosidases act in a coordinate way during cell elongation. In addition, this work indicates that galactan plays a role in the maintenance of the cell wall architecture during this process. Our results point to an involvement of the β-(1,4)-galactan in the xyloglucan structure and the interaction between cellulose and xyloglucan.

Interactions between pectin and cellulose in primary plant cell walls

To understand the architecture of the plant cell wall, it is of importance to understand both structural characteristics of cell wall polysaccharides and interactions between these polysaccharides. Interactions between polysaccharides were studied in the residue after water and chelating agent extraction by sequential extractions with H₂O and alkali. The 6 M alkali residue still represented 31%, 11% and 5% of all GalA present in carrot, tomato and strawberry, respectively, and these pectin populations were assumed to strongly interact with cellulose. Digestion of the carrot 6 M alkali residue by glucanases released ∼27% of the 6 M residue, mainly representing pectin. In tomato and strawberry alkali residues, glucanases were not able to release pectin populations. The ability of glucanases to release pectin populations suggests that the carrot cell wall contains unique, covalent interactions between pectin and cellulose.

Transcriptome analysis reveals potential mechanisms for different grain size between natural and resynthesized allohexaploid wheats with near-identical AABB genomes

BACKGROUND

Common wheat is a typical allohexaploid species (AABBDD) derived from the interspecific crossing between allotetraploid wheat (AABB) and Aegilops tauschii (DD). Wide variation in grain size and shape observed among Aegilops tauschii can be retained in synthetic allohexaploid wheats, but the underlying mechanism remains enigmatic. Here, the natural and resynthesized allohexaploid wheats with near-identical AB genomes and different D genomes (TAA10 and XX329) were employed for analysis.

RESULTS

Significant differences in grain size and weight between TAA10 and XX329 were observed at the early stages of development, which could be mainly attributed to the higher growth rates of the pericarp and endosperm cells in XX329 compared to TAA10. Furthermore, comparative transcriptome analysis identified that 8891 of 69,711 unigenes (12.75%) were differentially expressed between grains at 6 days after pollination (DAP) of TAA10 and XX329, including 5314 up-regulated and 3577 down-regulated genes in XX329 compared to TAA10. The MapMan functional annotation and enrichment analysis revealed that the differentially expressed genes were significantly enriched in categories of cell wall, carbohydrate and hormone metabolism. Notably, consistent with the up-regulation of sucrose synthase genes in resynthesized relative to natural allohexaploid wheat, the resynthesized allohexaploid wheat accumulated much higher contents of glucose and fructose in 6-DAP grains than those of the natural allohexaploid wheat.

CONCLUSIONS

These data indicated that the genetic variation of the D genome induced drastic alterations of gene expression in grains of the natural and resynthesized allohexaploid wheats, which may contribute to the observed differences in grain size and weight.

Xyloglucan in the primary cell wall: assessment by FESEM, selective enzyme digestions and nanogold affinity tags

Xyloglucan has been hypothesized to bind extensively to cellulose microfibril surfaces and to tether microfibrils into a load-bearing network, thereby playing a central role in wall mechanics and growth, but this view is challenged by newer results. Here we combined high-resolution imaging by field emission scanning electron microscopy (FESEM) with nanogold affinity tags and selective endoglucanase treatments to assess the spatial location and conformation of xyloglucan in onion cell walls. FESEM imaging of xyloglucanase-digested cell walls revealed an altered microfibril organization but did not yield clear evidence of xyloglucan conformations. Backscattered electron detection provided excellent detection of nanogold affinity tags in the context of wall fibrillar organization. Labelling with xyloglucan-specific CBM76 conjugated with nanogold showed that xyloglucans were associated with fibril surfaces in both extended and coiled conformations, but tethered configurations were not observed. Labelling with nanogold-conjugated CBM3, which binds the hydrophobic surface of crystalline cellulose, was infrequent until the wall was predigested with xyloglucanase, whereupon microfibril labelling was extensive. When tamarind xyloglucan was allowed to bind to xyloglucan-depleted onion walls, CBM76 labelling gave positive evidence for xyloglucans in both extended and coiled conformations, yet xyloglucan chains were not directly visible by FESEM. These results indicate that an appreciable, but still small, surface of cellulose microfibrils in the onion wall is tightly bound with extended xyloglucan chains and that some of the xyloglucan has a coiled conformation.

Comprehensive functional characterization of the glycoside hydrolase family 3 enzymes from Cellvibrio japonicus reveals unique metabolic roles in biomass saccharification

Lignocellulose degradation is central to the carbon cycle and renewable biotechnologies. The xyloglucan (XyG), β(1→3)/β(1→4) mixed-linkage glucan (MLG) and β(1→3) glucan components of lignocellulose represent significant carbohydrate energy sources for saprophytic microorganisms. The bacterium Cellvibrio japonicus has a robust capacity for plant polysaccharide degradation, due to a genome encoding a large contingent of Carbohydrate-Active enZymes (CAZymes), many of whose specific functions remain unknown. Using a comprehensive genetic and biochemical approach, we have delineated the physiological roles of the four C. japonicus glycoside hydrolase family 3 (GH3) members on diverse β-glucans. Despite high protein sequence similarity and partially overlapping activity profiles on disaccharides, these β-glucosidases are not functionally equivalent. Bgl3A has a major role in MLG and sophorose utilization, and supports β(1→3) glucan utilization, while Bgl3B underpins cellulose utilization and supports MLG utilization. Bgl3C drives β(1→3) glucan utilization. Finally, Bgl3D is the crucial β-glucosidase for XyG utilization. This study not only sheds the light on the metabolic machinery of C. japonicus, but also expands the repertoire of characterized CAZymes for future deployment in biotechnological applications. In particular, the precise functional analysis provided here serves as a reference for informed bioinformatics on the genomes of other Cellvibrio and related species.

A xylanase-aided enzymatic pretreatment facilitates cellulose nanofibrillation

Although biological pretreatment of cellulosic fiber based on endoglucanases has shown some promise to facilitate cellulose nanofibrillation, its efficacy is still limited. In this study, a xylanase-aided endoglucanase pretreatment was assessed on the bleached hardwood and softwood Kraft pulps to facilitate the downstream cellulose nanofibrillation. Four commercial xylanase preparations were compared and the changes of major fiber physicochemical characteristics such as cellulose/hemicellulose content, gross fiber properties, fiber morphologies, cellulose accessibility/degree of polymerization (DP)/crystallinity were systematically evaluated before and after enzymatic pretreatment. It showed that the synergistic cooperation between endoglucanase and certain xylanase (Biobrite) could efficiently "open up" the hardwood Kraft pulp with limited carbohydrates degradation (<7%), which greatly facilitated the downstream cellulose nanofibrillation during mild sonication process (90Wh) with more uniform disintegrated nanofibril products (50-150nm, as assessed by scanning electron microscopy and UV-vis spectroscopy).

Analysis of Xyloglucan Composition in Arabidopsis Leaves

Xyloglucan is one of the main components of the primary cell wall in most species of plants. This protocol describes a method to analyze the composition of the enzyme-accessible and enzyme-inaccessible fractions of xyloglucan in the model species Arabidopsis thaliana. It is based on digestion with an endoglucanase that attacks unsubstituted glucose residues in the backbone. The identities and relative amounts of released xyloglucan fragments are then determined using MALDI-TOF mass spectrometry.