Cell Walls Of Higher Plants Research Articles

Engineered reduction of S-adenosylmethionine alters lignin in sorghum

BackgroundLignin is an aromatic polymer deposited in secondary cell walls of higher plants to provide strength, rigidity, and hydrophobicity to vascular tissues. Due to its interconnections with cell wall polysaccharides, lignin plays important roles during plant growth and defense, but also has a negative impact on industrial processes aimed at obtaining monosaccharides from plant biomass. Engineering lignin offers a solution to this issue. For example, previous work showed that heterologous expression of a coliphage S-adenosylmethionine hydrolase (AdoMetase) was an effective approach to reduce lignin in the model plant Arabidopsis. The efficacy of this engineering strategy remains to be evaluated in bioenergy crops.ResultsWe studied the impact of expressing AdoMetase on lignin synthesis in sorghum (Sorghum bicolor L. Moench). Lignin content, monomer composition, and size, as well as biomass saccharification efficiency were determined in transgenic sorghum lines. The transcriptome and metabolome were analyzed in stems at three developmental stages. Plant growth and biomass composition was further evaluated under field conditions. Results evidenced that lignin was reduced by 18% in the best transgenic line, presumably due to reduced activity of the S-adenosylmethionine-dependent O-methyltransferases involved in lignin synthesis. The modified sorghum features altered lignin monomer composition and increased lignin molecular weights. The degree of methylation of glucuronic acid on xylan was reduced. These changes enabled a ~20% increase in glucose yield after biomass pretreatment and saccharification compared to wild type. RNA-seq and untargeted metabolomic analyses evidenced some pleiotropic effects associated with AdoMetase expression. The transgenic sorghum showed developmental delay and reduced biomass yields at harvest, especially under field growing conditions.ConclusionsThe expression of AdoMetase represents an effective lignin engineering approach in sorghum. However, considering that this strategy potentially impacts multiple S-adenosylmethionine-dependent methyltransferases, adequate promoters for fine-tuning AdoMetase expression will be needed to mitigate yield penalty.

Extraction, Characterization, and Antioxidant Activity of Pectin from Lemon Peels.

Pectin is a natural polymer that is found in the cell walls of higher plants. This study presents a comprehensive analysis of pectin extracted from lemon in two different geographic regions (Peddie and Fort Beaufort) in two consecutive years (2023 and 2024) named PP 2023, PP 2024, FBP 2023, and FBP 2024. The dried lemon peels were ground into a powder, sifted to obtain particles of 500 μm, and then subjected to pectin extraction using a conventional method involving mixing lemon peel powder with distilled water, adjusting the pH level to 2.0 with HCl, heating the mixture at 70 °C for 45 min, filtering the acidic extract, and precipitating pectin with ethanol. The yield of these pectin samples was statistically significant, as FBP 2024 had a maximum yield of 12.2 ± 0.02%, PP 2024 had a maximum yield of 13.0 ± 0.02%, FBP 2023 had a maximum yield of 12.2 ± 0.03%, and PP 2023 had a maximum yield of 13.1 ± 0.03%, The variation in yield could be due to the differences in the growing conditions, such as the climate and soil, which could have affected the pectin content in the lemons. The physicochemical characterization of all samples proved that our pectin samples could be used in the pharmaceutical and food industries, with anhydrouronic acid content which was greater than 65%, as suggested by the FAO. The scanning electron microscope analysis of all extracted pectin was rough and jagged, while the commercial pectin displayed a smooth surface morphology with a consistent size. FTIR confirmed the functional groups which were present in our samples. Thermogravimetric analysis was employed to investigate the thermal behavior of the extracted pectin in comparison with commercial pectin. It was found that the extracted pectin had three-step degradation while the commercial pectin had four-step degradation. Additionally, pectin samples have been shown to have antioxidants, as the IC50 of PP 2024, PP 2023, FBP 2023, FBP 2024, and Commercial P was 1062.5 ± 20.0, 1201.3 ± 22.0, 1304.6 ± 19.0, 1382.6 ± 29.9, and 1019.4 ± 17.1 mg/L, respectively. These findings indicate that lemon pectin has promising characteristics as a biopolymer for use in biomedical applications.

Therapeutic Potential of Pectin and Its Derivatives in Chronic Diseases.

Non-communicable diseases (NCDs) are described as a collection of chronic diseases that do not typically develop from an acute infection, have long-term health effects, and frequently require ongoing care and therapy. These diseases include heart disease, stroke, cancer, chronic lung disease, neurological diseases, osteoporosis, mental health disorders, etc. Known synthetic drugs for the treatment or prevention of NCDs become increasingly dangerous over time and pose high risks due to side effects such as hallucination, heart attack, liver failure, etc. As a result, scientists have had to look for other alternatives that are natural products and that are known to be less detrimental and contain useful bioactive compounds. The increasing understanding of the biological and pharmacological significance of carbohydrates has helped to raise awareness of their importance in living systems and medicine, given they play numerous biological roles. For example, pectin has been identified as a class of secondary metabolites found in medicinal plants that may play a significant role in the treatment and management of a variety of NCDs. Pectin is mainly made of homogalacturonan, which is a linear polymer composed primarily of D-galacturonic acid units (at least 65%) linked in a chain by α-(1,4)-glycosidic linkages. There are also modified pectins or derivatives that improve pectin's bioavailability. Pectin is found in the cell walls of higher plants (pteridophytes, angiosperms, and gymnosperms), particularly in the middle lamella of the plant material. Citrus pectin is used in various industries. This article compiles information that has been available for years about the therapeutic importance of pectin in chronic diseases, different modes of pectin extraction, the chemistry of pectin, and the potency of pectin and its derivatives.

Lead phytochemicals and marine compounds against ceruloplasmin in cancer targeting

In silico docking studies serve as a swift and efficient means to sift through a vast array of natural and synthetic small molecules, aiding in the identification of potential inhibitors for cancer biomarkers. One such biomarker, ceruloplasmin (CP), has been implicated in various tumor types due to its overexpression, earning it recognition as a marker of aggressive tumors. This study focused on pinpointing inhibitors for the CP –Myeloperoxidase (MPO) interaction site, a complex formation known to impede HOCl production, a crucial process for inducing apoptotic cell death in tumor cells. The initial phase of our investigation involved in silico docking studies, which screened a diverse library of phytochemicals and marine compounds. Through this process, we identified several promising drug candidates based on their binding affinities. Subsequently, these candidates underwent rigorous filtration based on Absorption, Distribution, Metabolism, Excretion, and Toxicity (ADMET) properties. Finally, we subjected the selected compounds to molecular dynamics (MDs) simulation to further assess their viability. Lycoperoside F, a steroidal alkaloid glycoside derived from tomatoes (Lycopersicon esculentum), stood out with notable interactions at the binding site. Another noteworthy compound was Xyloglucan (XG) oligosaccharides, predominantly found in the primary cell walls of higher plants. During the subsequent MDs simulations, these interactions were accompanied by highly stable root mean square deviation (RMSD) plots, signifying the consistency and robustness of the observed MDs behavior. XG oligosaccharides demonstrated the highest binding affinity with CP, reaffirming their potential as strong candidates. Additionally, Ardimerin digallate, known as a retroviral ribonuclease H inhibitor for HIV-1 and HIV-2, displayed favorable interactions at the MPO interaction site. Given that promising drug candidates must meet stringent criteria, including non-toxicity, effectiveness, specificity, stability and potency, these phytochemicals have the potential to progress to in vitro studies as CP inhibitors. Ultimately, this could contribute to the suppression of tumor growth, marking a significant step in cancer treatment research. Communicated by Ramaswamy H. Sarma

Chitosan derivatives as promising green corrosion inhibitors for carbon steel in acidic environment: Inhibition performance and interfacial adsorption mechanism

Among the biodegradable polysaccharide, chitosan is widely present in the cell membranes of bacteria and algae and in the cell walls of higher plants. As a promising biopolymer, chitosan has great potential as eco-friendly corrosion inhibitor. Herein, two synthetic chitosan derivatives (N-phenylthiourea chitosan (CS-PT), N-phenyl-O-benzylthiourea chitosan (CS-PT-Bn)) were investigated as high-efficient acidic corrosion inhibitors to deal with the corrosion issue of carbon steel. The anti-corrosion property of the chitosan derivatives was explored by electrochemical tests, surface characterization and theoretical calculations. The experimental results indicate that both CS-PT and CS-PT-Bn present high-efficient inhibition performance with the inhibition efficiency of 98.4% and 98.5% at the concentration of 100 mg/L, respectively. Their adsorption mechanism at steel/solution interface is revealed by quantum chemical calculations, molecular dynamics (MD) and GFN-xTB calculations. It is found that CS-PT and CS-PT-Bn adsorb at the steel/solution interface by forming Fe-N and Fe-S bonds. Compared to CS-PT molecule, the introduction of benzyl group endows CS-PT-Bn molecule with stronger electrostatic effect and hydrophobicity, which favors the interfacial adsorption of CS-PT-Bn molecule on carbon steel surface.

Production of pectinases towards the extraction of natural pectin from orange peels using fungal sources

Pectin is a polysaccharide, which is present in middle lamella of cell wall of higher plants. Almost all fruits have a part of pectin in their cell walls. Pectinases are used in the degradation of the plant material and promptly extract juices from different fruits. For this purpose, identified fungi were screened qualitatively and quantitatively for the production of pectinase at 30 ºC for 92 hours of incubation time. In liquid state fermentation, identified strains of Trichoderma asperellum, Aspergillus niger and Thermomyces were treated in which Trichoderma asperellum produced maximum pectinase activities (9.2 U/ml) after 24 hours of incubation by using orange peels as a sole carbon source. Furthermore, pectinases produced from fungal strains were used to produce natural pectin from fruit waste like orange peels. During fermentation process, pectinase produced from fungal strains were inoculated to dried orange peels for 24 hours of incubation time at 30 ºC. The filtered extract was treated with 3 volumes of 80% ethanol for washing to extract pectin. Trichoderma asperellum gave maximum pectin yield [(11.7%)], Aspergillus niger and Thermomyces gave minimum pectin yield [(9.7%, 7.5%)] from orange peels respectively and the amount of pectin yield extracted from orange peels control was [(3.5%)]. Pectinases and pectin has found huge industrial applications in soft drinks, dairy products, pharmaceuticals and food industries, therefore, the present work has focused on the cost effective production of pectinase enzyme and extraction of natural pectin by using potential indigenous fungal strains.

Progress on Materials Reinforcement using Mechanically Defibrillated Cellulose Nanofibers

Cellulose nanofibers (CNFs) are highly crystalline, fibrous materials with a high aspect ratio of long cellulose molecules linked together with strong hydrogen bonds. These long cellulose molecules are incorporated into hemicellulose and lignin, the cell walls of higher plants. The modulus of elasticity of CNF remains constant between −200 °C and +200 °C. However, the linear coefficient of thermal expansion of cellulose fibers was 0.17 ppm/K, which is comparable to that of quartz glass. Further, CNFs have a thermal conductivity in the same order of magnitude as glass. Therefore, they are promising next-generation fiber owing to the excellent mechanical and thermal properties, sustainability, and biodegradability of CNF. Most studies on using CNFs to increase strength have focused on polymer matrix composites, particularly biodegradable polymers. However, it is difficult to increase the strength of materials using CNFs due to the agglomeration of CNFs. Compared to other composite materials, the uniform dispersion of nanosized CNFs is crucial. This article reports that CNFs may behave not as reinforcing fibers but as cross-linking agents to strengthen the polymer when the amount of CNFs is very small in polymer matrix composites, and the addition of CNFs is also effective in strengthening silk yarn and Ti. The mechanical properties of the ceramic green bodies can be increased using CNFs as an auxiliary agent in ceramic slurry. Moreover, the fabrication of composite materials using CNFs is essential for expanding the CNFs applications.

Construction of thorough cross-linked networks in soybean meal adhesive system by biomimetic boronic acid-anchored cellulose nanofibril for multifunctionality of high-performance, mildew resistance, anti-bacterial, and flame resistance

The soybean meal (SM) adhesive has become the most promising bio-adhesive in wood industry. However, the insufficient mechanical properties and poor water resistance limits their practical applications. Current researches mostly focus on the cross-linking modification of soy protein isolate (SPI) components in SM, whereas ignoring the adverse effects of soy polysaccharide (SPS) components on the SM adhesive system. Herein, inspired of the borate chemistry in the higher plant cell walls, the thorough and strong cross-linked networks were constructed in SM adhesive system by the boronic acid-anchored cellulose nanofibril (BCNF) and tannic acid (TA). The combination of entanglement and interpenetration of polymer backbone molecular chains, dynamic covalent interactions and hydrogen bonds can promote the formation of tough and stable cross-linked network structure in SM adhesive system, and endowed the SM adhesive with excellent wet adhesion strength and water-resistant property. The wet shear strength of resultant SM adhesive increased to 0.92 MPa, which was 3 times of the pristine SM adhesive. Additionally, the resultant SM adhesive exhibited excellent mildew resistance, antibacterial activity, and flame retardance. This biomimetic strategy can achieve the construction of the thorough and strong cross-linked networks in SM adhesive, which provides a novel and versatile route to high-performance and multifunitional bio-adhesive.

Pectins and Olive Pectins: From Biotechnology to Human Health.

Simple SummaryPectins comprise complex polysaccharides rich in galacturonic acid, that exert many functions in higher plants as components of the cell walls, together with cellulose or lignin. The food industry has traditionally used pectins as an additive due to their gelling or thickening properties. Pharmaceutical research is also taking advantage of pectin bioactivity, providing evidence of the role of these polysaccharides as health promoters. Fruits and vegetables are natural sources of pectins that can be obtained as by-products during food or beverage production. In line with this, the aim of our study is gathering data on the current methods to extract pectins from fruit or vegetable wastes, optimizing yield and environmentally friendly protocols. Updated information about pectin applications in food or non-food industries are provided. We also point to olives as novel source of pectins that strengthen the evidence that this fruit is as remarkably healthy part of the Mediterranean diet. This work exhibits the need to explore natural bioactive components of our daily intake to improve our health, or prevent or treat chronical diseases present in our society.Pectins are a component of the complex heteropolysaccharide mixture present in the cell wall of higher plants. Structurally, the pectin backbone includes galacturonic acid to which neutral sugars are attached, resulting in functional regions in which the esterification of residues is crucial. Pectins influence many physiological processes in plants and are used industrially for both food and non-food applications. Pectin-based compounds are also a promising natural source of health-beneficial bioactive molecules. The properties of pectins have generated interest in the extraction of these polysaccharides from natural sources using environmentally friendly protocols that maintain the native pectin structure. Many fruit by-products are sources of pectins; however, owing to the wide range of applications in various fields, novel plants are now being explored as potential sources. Olives, the fruit of the olive tree, are consumed as part of the healthy Mediterranean diet or processed into olive oil. Pectins from olives have recently emerged as promising compounds with health-beneficial effects. This review details the current knowledge on the structure of pectins and describes the conventional and novel techniques of pectin extraction. The versatile properties of pectins, which make them promising bioactive compounds for industry and health promotion, are also considered.

Orthogonal Active-Site Labels for Mixed-Linkage endo-β-Glucanases.

Small molecule irreversible inhibitors are valuable tools for determining catalytically important active-site residues and revealing key details of the specificity, structure, and function of glycoside hydrolases (GHs). β-glucans that contain backbone β(1,3) linkages are widespread in nature, e.g., mixed-linkage β(1,3)/β(1,4)-glucans in the cell walls of higher plants and β(1,3)glucans in yeasts and algae. Commensurate with this ubiquity, a large diversity of mixed-linkage endoglucanases (MLGases, EC 3.2.1.73) and endo-β(1,3)-glucanases (laminarinases, EC 3.2.1.39 and EC 3.2.1.6) have evolved to specifically hydrolyze these polysaccharides, respectively, in environmental niches including the human gut. To facilitate biochemical and structural analysis of these GHs, with a focus on MLGases, we present here the facile chemo-enzymatic synthesis of a library of active-site-directed enzyme inhibitors based on mixed-linkage oligosaccharide scaffolds and N-bromoacetylglycosylamine or 2-fluoro-2-deoxyglycoside warheads. The effectiveness and irreversibility of these inhibitors were tested with exemplar MLGases and an endo-β(1,3)-glucanase. Notably, determination of inhibitor-bound crystal structures of a human-gut microbial MLGase from Glycoside Hydrolase Family 16 revealed the orthogonal labeling of the nucleophile and catalytic acid/base residues with homologous 2-fluoro-2-deoxyglycoside and N-bromoacetylglycosylamine inhibitors, respectively. We anticipate that the selectivity of these inhibitors will continue to enable the structural and mechanistic analyses of β-glucanases from diverse sources and protein families.

Extraction and characterization of pectin from fruit peels of Irvingia gabonensis and pulp of Cola milleni and Theobroma cacao as precursor for industrial applications

Pectin is a complex polysaccharide that makes up about one third of the cell wall of higher plants. It was extracted from fruit peels of Irvingia gabonensis and pulp of Cola milleni and Theobroma cacao using acid extraction and alcohol precipitation methods. The effects of temperature and time on the yield and physicochemical properties of the extracted pectin were evaluated. Optimum yields of pectin from C. milleni, I. gabonensis, and T. Cacao were 10.73%, 19.83%, and 11.73% respectively at extracting period of 150 min and temperature of 100 °C. Although there was significant difference in moisture content, degree of esterification, equivalent weight, and methoxyl content of the extracted pectins, there was no significant difference in yield, protein, and ash content at 95% confidence interval. The monosaccharide composition of the three pectins shows that the extracted pectin composed of galacturonic acid and minor neutral sugars. Major functional groups in the extracted pectin show peaks in the region between 1000 and 2000 cm−1. The bands observed between 1627–1651 cm−1 and 1739–1793 cm−1 indicated the presence of the carbonyl group stretching. The surface morphologies of the extracted pectins show irregular shapes, non-smooth surfaces, and unequal sizes which also reveals more silica nodes in cocoa pulp pectin than in other pectins. Thermogravimetric analysis of the pectin samples shows multi-step stages of thermal decomposition, indicating wide range of thermal stability. The overall results specified that the pectins extracted from these plants are suitable for industrial applications.

The Living Fossil Psilotum nudum Has Cortical Fibers With Mannan-Based Cell Wall Matrix.

Cell wall thickening and development of secondary cell walls was a major step in plant terrestrialization that provided the mechanical support, effective functioning of water-conducting elements and fortification of the surface tissues. Despite its importance, the diversity, emergence and evolution of secondary cell walls in early land plants have been characterized quite poorly. Secondary cell walls can be present in different cell types with fibers being among the major ones. The necessity for mechanical support upon increasing plant height is widely recognized; however, identification of fibers in land plants of early taxa is quite limited. In an effort to partially fill this gap, we studied the fibers and the composition of cell walls in stems of the sporophyte of the living fossil Psilotum nudum. Various types of light microscopy, combined with partial tissue maceration demonstrated that this perennial, rootless, fern-like vascular plant, has abundant fibers located in the middle cortex. Extensive immunodetection of cell wall polymers together with various staining and monosaccharide analysis of cell wall constituents revealed that in P. nudum, the secondary cell wall of its cortical fibers is distinct from that of its tracheids. Primary cell walls of all tissues in P. nudum shoots are based on mannan, which is also common in other extant early land plants. Besides, the primary cell wall contains epitope for LM15 specific for xyloglucan and JIM7 that binds methylesterified homogalacturonans, two polymers common in the primary cell walls of higher plants. Xylan and lignin were detected as the major polymers in the secondary cell walls of P. nudum tracheids. However, the secondary cell wall in its cortical fibers is quite similar to their primary cell walls, i.e., enriched in mannan. The innermost secondary cell wall layer of its fibers but not its tracheids has epitope to bind the LM15, LM6, and LM5 antibodies recognizing, respectively, xyloglucan, arabinan and galactan. Together, our data provide the first description of a mannan-based cell wall in sclerenchyma fibers, and demonstrate in detail that the composition and structure of secondary cell wall in early land plants are not uniform in different tissues.

Sugar contents and oligosaccharide mass profiling of selected red seaweeds to assess the possible utilization of biomasses for third-generation biofuel production

In the present study, we report the sugar contents and oligosaccharide mass profiles of Kappaphycus alvarezii (Doty) Doty ex Silva, Solieria robusta (Greville) Kylin, Gracilariacorticata (J. Agardh), and Gracilariacorticata v. cylindrica Børgesen. Sugar contents in the biomasses of the studied seaweeds indicated that they represent potential sources of raw material for biofuel conversion. Fractionation improved the sugar yield by loosening cell wall components. A Fourier-transform infrared spectroscopy (FTIR) analysis of different cell wall fractions revealed differences in their structural components. Fractionation exposed and released some of the functional groups, depending on the harshness of treatments. However, variable carbohydrate moieties were observed in each fraction. A MALDI TOF-TOF MS analysis of cell wall revealed a complex and dynamic network of polymers in cell walls. K. alvarezii produced the greatest number of oligosaccharide units, followed by S. robusta, G. corticata v. cylindrica and G. corticata. The cell wall of seaweeds was similar to the polymers in the cell wall of higher plants, which indicated the potential to utilize seaweed biomasses for biofuel production. To the best of our knowledge, the present study is the first to report the oligosaccharide mass profiling (OLIMPs) of red seaweeds. A further detailed analysis of the sugar composition of the cell wall and a linkage analysis of OLIMPs would provide detailed structural information. Present results confirmed the potential utilization of red seaweed biomass as an alternative for biofuel production and potential of red seaweed species to be developed as new industrial crops under blue revolution program.

Quantitative mRNA Expression Profiles of Germin-Like and Extensin-Like Proteins under Drought Stress in Triticum aestivum

Drought stress can severaly damage plant growth and the most important factor in the reduction of wheat yield in cultivated areas. Development of new methodologies to improve wheat productivity and quality under drought conditions has a primary importance Extensin-like and Germin-like Protein transcripts were selected from our RNAseq data for their relation with defense mechanism. We aim to show the expression patterns of these genes in drought tolerant and non-tolerant T. aestivum cultivars under drought stress conditions using qRT-PCR technique. Extensin is the most abundant proteins present in the cell wall of higher plants and has an important role in plant defense through strengthening the cell wall and preventing tissue damage. GLPs are involve in different biological processes; e.g., disease resistance and superoxide scavenging metabolism. We established different mRNA expression regulation of Extensin like and Germin-like mRNAs in root and leaf tissues of tolerant and non-tolerant T. aestivum cultivars under drought stress. We observed GLP transcript was significantly up-regulated (5 fold) in 4h drought- stressed root tissues of tolerant cultivar Gerek and then decreased in 8h. On the other hand there was no dramatic difference in leaf tissue of each cultivar. Extensin-like gene up-regulation was approximately 6 and 3.5 fold in 4h stressed root tissues of tolerant cultivars. In leaf tissues, different expression pattern was observed in tolerant and non-tolerant cultivars. Drought stress caused to up-regulation (4 fold) in 4h stressed leaf tissues of tolerant cultivar. On the contrary, down-regulation (4 fold) was identified in non-tolerant stressed leaf tissues. These results suggest that overexpression of Extensin-like gene under drought stress conditions may offer drought tolerance. The qRTPCR results from root and leaf tissues from 3 different cultivars were in agreement with our RNAseq data. This is the first report shows the expression profiles of these defense proteins under drought stress conditions in T. aestivum.

Pectin acetylesterase PAE5 is associated with the virulence of plant pathogenic oomycete Peronophythora litchii

Pectin is a major component of the primary cell wall of higher plants. Some galacturonyl residues in pectin are often O-acetylated. Pectin acetylesterases (PAEs) involved in enzymatic deacetylation of pectin are widespread in the plant pathogenic oomycetes and show sequence and transcriptional polymorphism. Peronophythora litchii is the most destructive pathogens known on lychee (Litchi chinensis Sonn). Out of the 38 PAEs predicted from sequence analysis of P. litchii, Phytophthora species and Pythium species, five P. litchii PAE genes were selected for further study. Of these, P. litchii PAE4 and PAE5, named PlPAE4 and PlPAE5, were knocked out using CRISPR/Cas9 technique. The plpae5 mutants were less capable of host invasion than the wild-type P. litchii strain SHS3, as tested by lychee plant inoculation. Heterologous expression of PlPAE5 in Nicotiana benthamiana could promote the infection by Phytophthora capsici. These results demonstrate that PlPAE5 plays an important role in oomycete pathogenicity.

Functional assignment of multiple catabolic pathways for D-apiose.

Colocation of the genes encoding ABC, TRAP, and TCT transport systems and catabolic pathways for the transported ligand provides a strategy for discovering novel microbial enzymes and pathways. We screened solute-binding proteins (SBPs) for ABC transport systems and identified three that bind D-apiose, a branched pentose in the cell walls of higher plants. Guided by sequence similarity networks (SSNs) and genome neighborhood networks (GNNs), the identities of the SBPs enabled the discovery of four catabolic pathways for D-apiose with eleven previously unknown reactions. The new enzymes include D-apionate oxidoisomerase, which catalyzes hydroxymethyl group migration, as well as 3-oxo-isoapionate-4-phosphate decarboxylase and 3-oxo-isoapionate-4-phosphate transcarboxylase/hydrolase, which are RuBisCO-like proteins (RLPs). The web tools for generating SSNs and GNNs are publicly accessible ( http://efi.igb.illinois.edu/efi-est/ ), so similar 'genomic enzymology' strategies for discovering novel pathways can be used by the community.

Xylan epitope profiling: an enhanced approach to study organ development-dependent changes in xylan structure, biosynthesis, and deposition in plant cell walls

BackgroundXylan is a major hemicellulosic component in the cell walls of higher plants especially in the secondary walls of vascular cells which are playing important roles in physiological processes and overall mechanical strength. Being the second most abundant cell wall polymer after cellulose, xylan is an abundant non-cellulosic carbohydrate constituent of plant biomass. Xylan structures have been demonstrated to contribute to plant biomass recalcitrance during bioenergy applications. A critical understanding of xylan composition, structure, and biosynthesis in developing plant stems will allow an increased understanding of how cell walls are put together in this organ in a basic research, and, in applied research, will improve strategies in xylan engineering to reduce biomass recalcitrance for economically feasible biofuel production. MethodsWe describe an approach to enable the monitoring of xylan epitope structures in cell walls during the stem maturation process in Arabidopsis. The technique integrates glycome profiling, an in vitro immunoanalytical platform, and in situ immunolocalisation to provide comprehensive details on the presence, relative abundances, and dynamics with which diverse xylan epitope structures are integrated to the cell walls throughout the stem maturation process.ResultsOur experimental results and the supporting in silico analysis demonstrated that xylan deposition in stems occurs early on in stem development; however, xylan epitope types (representing substituted and unsubstituted regions on xylan backbone made of β-(1,4)-linked xylose residues) and the strength of their integration into the final wall structure vary during stem maturation.ConclusionsOur novel approach thus provides a method to comprehensively survey the differences in xylan epitope patterning and deposition occurring in stem development and thereby providing a robust tool for characterising altered xylan integration patterns in cell walls during the stem maturation process in diverse plant cell wall biosynthetic mutants. Our findings also suggest that this approach could rapidly and reliably delineate xylan deposition patterns in the cell walls of plants belonging to diverse phylogenetic classes providing novel insights into the functional roles of xylans in overall growth and development.

Beta-1,3-Glucanase Activities in Wheat and Relative Species

Abstract The (1,3)-β-D-glucan also referred to as callose is a main component of cell walls of higher plants. Many physiological processes are associated with the changes in callose deposition. Callose is synthesised by the callose synthase complex while its degradation is regulated by the hydrolytic enzymes β-1,3-glucanases. The latter one specifically degrade (1,3)-β-D-glucans. This work is aimed to study β-1,3-glucanase activities in the leaves of plants at two leaf stage in two diploids (Agilops tauschii, Triticum monococcum L.), four tetraploids (Ae. cylindrica, Ae. triuncialis, T. araraticum, T. dicoccum) and two hexaploids (T. aestivum L, T. spelta L.). The leaves were subjected to qualitative and quantitative β-1,3-glucanase activity assays. Our results showed that the total β-1,3-glucanase activities were variable and genotype dependent. No significant correlation between β-1,3-glucanase activities and ploidy level was observed. The gel activity assays revealed a single fraction of ~52 kDa Glu1 that was found in all genotypes. The Glu1 fraction corresponds to a single or two acidic Glu isoforms in dependence on genotype. However, none of the acidic Glu fractions can be assigned as a specific for di-, tetra- or hexaploid genotypes. A single basic GluF isoform was detected and found as present in all genotypes.

Cellulosic Microfibril and Its EmbeddingMatrix within Plant Cell Wall

Cellulose is the homopolymer of (1→4)-β-D-glucopyranose. Glucan chains are aggregated to form microfibrils with cross dimensions ranged from 2 to 20 nm. The variation in each of microfibrilluar dimension, hydrogen-bonding network and molecular orientation depends on their parent nature. Cellulosic microfibrils isolated from bacteria and certain algae (10–25 nm in diameter) were found to be thicker than those extracted from the primary cell walls in higher plants ( 3–10 nm in diameter).Three biopolymers, namely hemicellulose, lignin and/or pectin contribute to the embedding matrix enveloping the cellulosic microfibrils.The secondary cell wall was found to be differentiated into three consecutive layers (S1, S2, S3). Within each layer, cellulose microfibrils are found parallel and of high order with a different microfibrilluar angle. The bundling process of cellulose microfibrils in both primary and secondary cell walls may involve the aggregation of the closely arranged cellulosic microfibrils. Some models for the microfibril construction have been proposed. Along the longitudinal microfibril’s axe, crystalline regions are alternated with amorphous ones. The most important methods of estimating the crystallinity of cellulose microfibrils such as Xray diffraction (XRD), 13C solid-state NMR spectroscopy (13C-NMR), small-angle neutron scattering (SANS) and sum frequency generation (SFG) spectroscopy were concluded.

A Genome-Wide Association Study for Culm Cellulose Content in Barley Reveals Candidate Genes Co-Expressed with Members of the CELLULOSE SYNTHASE A Gene Family.

Cellulose is a fundamentally important component of cell walls of higher plants. It provides a scaffold that allows the development and growth of the plant to occur in an ordered fashion. Cellulose also provides mechanical strength, which is crucial for both normal development and to enable the plant to withstand both abiotic and biotic stresses. We quantified the cellulose concentration in the culm of 288 two – rowed and 288 six – rowed spring type barley accessions that were part of the USDA funded barley Coordinated Agricultural Project (CAP) program in the USA. When the population structure of these accessions was analysed we identified six distinct populations, four of which we considered to be comprised of a sufficient number of accessions to be suitable for genome-wide association studies (GWAS). These lines had been genotyped with 3072 SNPs so we combined the trait and genetic data to carry out GWAS. The analysis allowed us to identify regions of the genome containing significant associations between molecular markers and cellulose concentration data, including one region cross-validated in multiple populations. To identify candidate genes we assembled the gene content of these regions and used these to query a comprehensive RNA-seq based gene expression atlas. This provided us with gene annotations and associated expression data across multiple tissues, which allowed us to formulate a supported list of candidate genes that regulate cellulose biosynthesis. Several regions identified by our analysis contain genes that are co-expressed with CELLULOSE SYNTHASE A (HvCesA) across a range of tissues and developmental stages. These genes are involved in both primary and secondary cell wall development. In addition, genes that have been previously linked with cellulose synthesis by biochemical methods, such as HvCOBRA, a gene of unknown function, were also associated with cellulose levels in the association panel. Our analyses provide new insights into the genes that contribute to cellulose content in cereal culms and to a greater understanding of the interactions between them.