Biosynthesis of pectin

EPIP-Evoked Modifications of Redox, Lipid, and Pectin Homeostasis in the Abscission Zone of Lupine Flowers

Yellow lupine is a great model for abscission-related research given that excessive flower abortion reduces its yield. It has been previously shown that the EPIP peptide, a fragment of LlIDL (INFLORESCENCE DEFICIENT IN ABSCISSION) amino-acid sequence, is a sufficient molecule to induce flower abortion, however, the question remains: What are the exact changes evoked by this peptide locally in abscission zone (AZ) cells? Therefore, we used EPIP peptide to monitor specific modifications accompanied by early steps of flower abscission directly in the AZ. EPIP stimulates the downstream elements of the pathway-HAESA and MITOGEN-ACTIVATED PROTEIN KINASE6 and induces cellular symptoms indicating AZ activation. The EPIP treatment disrupts redox homeostasis, involving the accumulation of H2O2 and upregulation of the enzymatic antioxidant system including superoxide dismutase, catalase, and ascorbate peroxidase. A weakening of the cell wall structure in response to EPIP is reflected by pectin demethylation, while a changing pattern of fatty acids and acyl lipids composition suggests a modification of lipid metabolism. Notably, the formation of a signaling molecule-phosphatidic acid is induced locally in EPIP-treated AZ. Collectively, all these changes indicate the switching of several metabolic and signaling pathways directly in the AZ in response to EPIP, which inevitably leads to flower abscission.

Plant Prebiotics and Their Role in the Amelioration of Diseases

Prebiotics are either natural or synthetic non-digestible (non-)carbohydrate substances that boost the proliferation of gut microbes. Undigested fructooligosaccharides in the large intestine are utilised by the beneficial microorganisms for the synthesis of short-chain fatty acids for their own growth. Although various food products are now recognized as having prebiotic properties, several others, such as almonds, artichoke, barley, chia seeds, chicory, dandelion greens, flaxseeds, garlic, and oats, are being explored and used as functional foods. Considering the benefits of these prebiotics in mineral absorption, metabolite production, gut microbiota modulation, and in various diseases such as diabetes, allergy, metabolic disorders, and necrotising enterocolitis, increasing attention has been focused on their applications in both food and pharmaceutical industries, although some of these food products are actually used as food supplements. This review aims to highlight the potential and need of these prebiotics in the diet and also discusses data related to the distinct types, sources, modes of action, and health benefits.

Cell wall β-1,4-galactan regulated by the BPC1/BPC2-GALS1 module aggravates salt sensitivity in Arabidopsis thaliana

Salinity severely reduces plant growth and limits agricultural productivity. Dynamic changes and rearrangement of the plant cell wall is an important response to salt stress, but relatively little is known about the biological importance of specific cell wall components in the response. Here, we demonstrate a specific function of β-1,4-galactan in salt hypersensitivity. We found that salt stress induces the accumulation of β-1,4-galactan in root cell walls by up regulating the expression of GALACTAN SYNTHASE 1 (GALS1), which encodes a β-1,4-galactan synthase. The accumulation of β-1,4-galactan negatively affects salt tolerance. Exogenous application of D-galactose (D-Gal) causes an increase in β-1,4-galactan levels in the wild type and GALS1 mutants, especially in GALS1 overexpressors, which correlated with the aggravated salt hypersensitivity. Furthermore, we discovered that the BARLEY B RECOMBINANT/BASIC PENTACYSTEINE transcription factors BPC1/BPC2 positively regulate plant salt tolerance by repressing GALS1 expression and β-1,4-galactan accumulation. Genetic analysis suggested that GALS1 is genetically epistatic to BPC1/BPC2 with respect to the control of salt sensitivity as well as accumulation of β-1,4-galactan. Taken together, our results reveal a new regulatory mechanism by which β-1,4-galactan regulated by the BPC1/BPC2-GALS1 module aggravates salt sensitivity in Arabidopsis thaliana.

Defining natural factors that stimulate and inhibit cellulose:xyloglucan hetero-transglucosylation

Certain transglucanases can covalently graft cellulose and mixed-linkage β-glucan (MLG) as donor substrates onto xyloglucan as acceptor substrate and thus exhibit cellulose:xyloglucan endotransglucosylase (CXE) and MLG:xyloglucan endotransglucosylase (MXE) activities in vivo and in vitro. However, missing information on factors that stimulate or inhibit these hetero-transglucosylation reactions limits our insight into their biological functions. To explore factors that influence hetero-transglucosylation, we studied Equisetum fluviatile hetero-trans-β-glucanase (EfHTG), which exhibits both CXE and MXE activity, exceeding its xyloglucan:xyloglucan homo-transglucosylation (XET) activity. Enzyme assays employed radiolabelled and fluorescently labelled oligomeric acceptor substrates, and were conducted in vitro and in cell walls (in situ). With whole denatured Equisetum cell walls as donor substrate, exogenous EfHTG (extracted from Equisetum or produced in Pichia) exhibited all three activities (CXE, MXE, XET) in competition with each other. Acting on pure cellulose as donor substrate, the CXE action of Pichia-produced EfHTG was up to approximately 300% increased by addition of methanol-boiled Equisetum extracts; there was no similar effect when the same enzyme acted on soluble donors (MLG or xyloglucan). The methanol-stable factor is proposed to be expansin-like, a suggestion supported by observations of pH dependence. Screening numerous low-molecular-weight compounds for hetero-transglucanase inhibition showed that cellobiose was highly effective, inhibiting the abundant endogenous CXE and MXE (but not XET) action in Equisetum internodes. Furthermore, cellobiose retarded Equisetum stem elongation, potentially owing to its effect on hetero-transglucosylation reactions. This work provides insight and tools to further study the role of cellulose hetero-transglucosylation in planta by identifying factors that govern this reaction.

Host Cell Wall Damage during Pathogen Infection: Mechanisms of Perception and Role in Plant-Pathogen Interactions

The plant cell wall (CW) is a complex structure that acts as a mechanical barrier, restricting the access to most microbes. Phytopathogenic microorganisms can deploy an arsenal of CW-degrading enzymes (CWDEs) that are required for virulence. In turn, plants have evolved proteins able to inhibit the activity of specific microbial CWDEs, reducing CW damage and favoring the accumulation of CW-derived fragments that act as damage-associated molecular patterns (DAMPs) and trigger an immune response in the host. CW-derived DAMPs might be a component of the complex system of surveillance of CW integrity (CWI), that plants have evolved to detect changes in CW properties. Microbial CWDEs can activate the plant CWI maintenance system and induce compensatory responses to reinforce CWs during infection. Recent evidence indicates that the CWI surveillance system interacts in a complex way with the innate immune system to fine-tune downstream responses and strike a balance between defense and growth.

Plant Glycan Metabolism by Bifidobacteria

Members of the genus Bifidobacterium, of which the majority have been isolated as gut commensals, are Gram-positive, non-motile, saccharolytic, non-sporulating, anaerobic bacteria. Many bifidobacterial strains are considered probiotic and therefore are thought to bestow health benefits upon their host. Bifidobacteria are highly abundant among the gut microbiota of healthy, full term, breast-fed infants, yet the relative average abundance of bifidobacteria tends to decrease as the human host ages. Because of the inverse correlation between bifidobacterial abundance/prevalence and health, there has been an increasing interest in maintaining, increasing or restoring bifidobacterial populations in the infant, adult and elderly gut. In order to colonize and persist in the gastrointestinal environment, bifidobacteria must be able to metabolise complex dietary and/or host-derived carbohydrates, and be resistant to various environmental challenges of the gut. This is not only important for the autochthonous bifidobacterial species colonising the gut, but also for allochthonous bifidobacteria provided as probiotic supplements in functional foods. For example, Bifidobacterium longum subsp. longum is a taxon associated with the metabolism of plant-derived poly/oligosaccharides in the adult diet, being capable of metabolising hemicellulose and various pectin-associated glycans. Many of these plant glycans are believed to stimulate the metabolism and growth of specific bifidobacterial species and are for this reason classified as prebiotics. In this review, bifidobacterial carbohydrate metabolism, with a focus on plant poly-/oligosaccharide degradation and uptake, as well as its associated regulation, will be discussed.

Breeding Targets to Improve Biomass Quality in Miscanthus

Lignocellulosic crops are attractive bioresources for energy and chemicals production within a sustainable, carbon circular society. Miscanthus is one of the perennial grasses that exhibits great potential as a dedicated feedstock for conversion to biobased products in integrated biorefineries. The current biorefinery strategies are primarily focused on polysaccharide valorization and require severe pretreatments to overcome the lignin barrier. The need for such pretreatments represents an economic burden and impacts the overall sustainability of the biorefinery. Hence, increasing its efficiency has been a topic of great interest. Inversely, though pretreatment will remain an essential step, there is room to reduce its severity by optimizing the biomass composition rendering it more exploitable. Extensive studies have examined the miscanthus cell wall structures in great detail, and pinpointed those components that affect biomass digestibility under various pretreatments. Although lignin content has been identified as the most important factor limiting cell wall deconstruction, the effect of polysaccharides and interaction between the different constituents play an important role as well. The natural variation that is available within different miscanthus species and increased understanding of biosynthetic cell wall pathways have specified the potential to create novel accessions with improved digestibility through breeding or genetic modification. This review discusses the contribution of the main cell wall components on biomass degradation in relation to hydrothermal, dilute acid and alkaline pretreatments. Furthermore, traits worth advancing through breeding will be discussed in light of past, present and future breeding efforts.

PHOTO-SENSITIVE LEAF ROLLING 1 encodes a polygalacturonase that modifies cell wall structure and drought tolerance in rice

The biosynthesis and modification of cell wall composition and structure are controlled by hundreds of enzymes and have a direct consequence on plant growth and development. However, the majority of these enzymes has not been functionally characterised. Rice mutants with leaf-rolling phenotypes were screened in a field. Phenotypic analysis under controlled conditions was performed for the selected mutant and the relevant gene was identified by map-based cloning. Cell wall composition was analysed by glycome profiling assay. We identified a photo-sensitive leaf rolling 1 (psl1) mutant with 'napping' (midday depression of photosynthesis) phenotype and reduced growth. The PSL1 gene encodes a cell wall-localised polygalacturonase (PG), a pectin-degrading enzyme. psl1 with a 260-bp deletion in its gene displayed leaf rolling in response to high light intensity and/or low humidity. Biochemical assays revealed PG activity of recombinant PSL1 protein. Significant modifications to cell wall composition in the psl1 mutant compared with the wild-type plants were identified. Such modifications enhanced drought tolerance of the mutant plants by reducing water loss under osmotic stress and drought conditions. Taken together, PSL1 functions as a PG that modifies cell wall biosynthesis, plant development and drought tolerance in rice.

Systematic Analysis and Functional Validation of Citrus Pectin Acetylesterases (CsPAEs) Reveals that CsPAE2 Negatively Regulates Citrus Bacterial Canker Development

The present study was designed to serve as a comprehensive analysis of Citrus sinensis (C. sinensis) pectin acetylesterases (CsPAEs), and to assess the roles of these PAEs involved in the development of citrus bacterial canker (CBC) caused by Xanthomonas citri subsp. citri (Xcc) infection. A total of six CsPAEs were identified in the genome of C. sinensis, with these genes being unevenly distributed across chromosomes 3, 6, and 9, and the unassembled scaffolds. A subset of CsPAEs were found to be involved in responses to Xcc infection. In particular, CsPAE2 was identified to be associated with such infections, as it was upregulated in CBC-susceptible variety Wanjincheng and inversely in CBC-resistant variety Calamondin. Transgenic citrus plants overexpressing CsPAE2 were found to be more susceptible to CBC, whereas the silencing of this gene was sufficient to confer CBC resistance. Together, these findings provide evolutionary insights into and functional information about the CsPAE family. This study also suggests that CsPAE2 is a potential candidate gene that negatively contributes to bacterial canker disease and can be used to breed CBC-resistant citrus plants.

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.

Molecular mechanisms of plant adaptive responses to heavy metals stress

Heavy metals (HMs) are among the main environmental pollutants that can enter the soil, water bodies, and the atmosphere as a result of natural processes (weathering of rocks, volcanic activity), and also as a result of human activities (mining, metallurgical and chemical industries, transport, application of mineral fertilizers). Plants counteract the HMs stresses through morphological and physiological adaptations, which are imparted through well-coordinated molecular mechanisms. New approaches, which include transcriptomics, genomics, proteomics, and metabolomics analyses, have opened the paths to understand such complex networks. This review sheds light on molecular mechanisms included in plant adaptive and defense responses during metal stress. It is focused on the entry of HMs into plants, its transport and accumulation, effects on the main physiological processes, gene expressions included in plant adaptive and defense responses during HM stress. Analysis of new data allowed the authors to conclude that the most important mechanism of HM tolerance is extracellular and intracellular HM sequestration. Organic anions (malate, oxalate, etc.) provide extracellular sequestration of HM ions. Intracellular HM sequestration depends not only on a direct binding mechanism with different polymers (pectin, lignin, cellulose, hemicellulose, etc.) or organic anions but also on the action of cellular receptors and transmembrane transporters. We focused on the functioning chloroplasts, mitochondria, and the Golgi complex under HM stress. The currently known molecular mechanisms of plant tolerance to the toxic effects of HMs are analyzed.

Biorefinery Approach for Aerogels

According to the International Energy Agency, biorefinery is "the sustainable processing of biomass into a spectrum of marketable bio-based products (chemicals, materials) and bioenergy (fuels, power, heat)". In this review, we survey how the biorefinery approach can be applied to highly porous and nanostructured materials, namely aerogels. Historically, aerogels were first developed using inorganic matter. Subsequently, synthetic polymers were also employed. At the beginning of the 21st century, new aerogels were created based on biomass. Which sources of biomass can be used to make aerogels and how? This review answers these questions, paying special attention to bio-aerogels' environmental and biomedical applications. The article is a result of fruitful exchanges in the frame of the European project COST Action "CA 18125 AERoGELS: Advanced Engineering and Research of aeroGels for Environment and Life Sciences".

Identifying candidate Aspergillus pathogenicity factors by annotation frequency

BACKGROUND

Members of the genus Aspergillus display a variety of lifestyles, ranging from saprobic to pathogenic on plants and/or animals. Increased genome sequencing of economically important members of the genus permits effective use of "-omics" comparisons between closely related species and strains to identify candidate genes that may contribute to phenotypes of interest, especially relating to pathogenicity. Protein-coding genes were predicted from 216 genomes of 12 Aspergillus species, and the frequencies of various structural aspects (exon count and length, intron count and length, GC content, and codon usage) and functional annotations (InterPro, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes terms) were compared.

RESULTS

Using principal component analyses, the three sets of functional annotations for each strain were clustered by species. The species clusters appeared to separate by pathogenicity on plants along the first dimensions, which accounted for over 20% of the variance. More annotations for genes encoding pectinases and secondary metabolite biosynthetic enzymes were assigned to phytopathogenic strains from species such as Aspergillus flavus. In contrast, Aspergillus fumigatus strains, which are pathogenic to animals but not plants, were assigned relatively more terms related to phosphate transferases, and carbohydrate and amino-sugar metabolism. Analyses of publicly available RNA-Seq data indicated that one A. fumigatus protein among 17 amino-sugar processing candidates, a hexokinase, was up-regulated during co-culturing with human immune system cells.

CONCLUSION

Genes encoding hexokinases and other proteins of interest may be subject to future manipulations to further refine understanding of Aspergillus pathogenicity factors.

The role of arabinogalactan proteins (AGPs) in fruit ripening-a review

Arabinogalactan proteins (AGPs) are proteoglycans challenging researchers for decades. However, despite the extremely interesting polydispersity of their structure and essential application potential, studies of AGPs in fruit are limited, and only a few groups deal with this scientific subject. Here, we summarise the results of pioneering studies on AGPs in fruit tissue with their structure, specific localization pattern, stress factors influencing their presence, and a focus on recent advances. We discuss the properties of AGPs, i.e., binding calcium ions, ability to aggregate, adhesive nature, and crosslinking with other cell wall components that may also be implicated in fruit metabolism. The aim of this review is an attempt to associate well-known features and properties of AGPs with their putative roles in fruit ripening. The putative physiological significance of AGPs might provide additional targets of regulation for fruit developmental programme. A comprehensive understanding of the AGP expression, structure, and untypical features may give new information for agronomic, horticulture, and renewable biomaterial applications.

Close arrangement of CARK3 and PMEIL affects ABA-mediated pollen sterility in Arabidopsis thaliana

Abscisic acid (ABA) signaling is a vital plant signaling pathway for plant responses to stress conditions. ABA treatment can alter global gene expression patterns and cause significant phenotypic changes. We investigated the responses to ABA treatment during flowering in Arabidopsis thaliana. Dipping the flowers of CARK3 T-DNA mutants in ABA solution, led to less reduction of pollen fertility than in the wild type plants (Col-0). We demonstrated that PMEIL, a gene located downstream of CARK3, directly affects pollen fertility. Due to the close arrangement of CARK3 and PMEIL, CARK3 expression represses transcription of PMEIL in an ABA-dependent manner through transcriptional interference. Our study uncovers a molecular mechanism underlying ABA-mediated pollen sterility and provides an example of how transcriptional interference caused by close arrangement of genes may mediate stress responses during plant reproduction.

Hydrogen sulfide promotes hypocotyl elongation via increasing cellulose content and changing the arrangement of cellulose fibrils in alfalfa

Hydrogen sulfide (H2S) is known to have positive physiological functions in plant growth, but limited data are available on its influence on cell walls. Here, we demonstrate a novel mechanism by which H2S regulates the biosynthesis and deposition of cell wall cellulose in alfalfa (Medicago sativa). Treatment with NaHS was found to increase the length of epidermal cells in the hypocotyl, and transcriptome analysis indicated that it caused the differential expression of numerous of cell wall-related genes. These differentially expressed genes were directly associated with the biosynthesis of cellulose and hemicellulose, and with the degradation of pectin. Analysis of cell wall composition showed that NaHS treatment increased the contents of cellulose and hemicellulose, but decreased the pectin content. Atomic force microscopy revealed that treatment with NaHS decreased the diameter of cellulose fibrils, altered the arrangement of the fibrillar bundles, and increased the spacing between the bundles. The dynamics of cellulose synthase complexes (CSCs) were closely related to cellulose synthesis, and NaHS increased the rate of mobility of the particles. Overall, our results suggest that the H2S signal enhances the plasticity of the cell wall by regulating the deposition of cellulose fibrils and by decreasing the pectin content. The resulting increases in cellulose and hemicellulose contents lead to cell wall expansion and cell elongation.

Catabolism of L-rhamnose in A. nidulans proceeds via the non-phosphorylated pathway and is glucose repressed by a CreA-independent mechanism

l-rhamnose (6-deoxy-mannose) occurs in nature mainly as a component of certain plant structural polysaccharides and bioactive metabolites but has also been found in some microorganisms and animals. The release of l-rhamnose from these substrates is catalysed by extracellular enzymes including α-l-rhamnosidases, the production of which is induced in its presence. The free sugar enters cells via specific uptake systems where it can be metabolized. Of two l-rhamnose catabolic pathways currently known in microorganisms a non-phosphorylated pathway has been identified in fungi and some bacteria but little is known of the regulatory mechanisms governing it in fungi. In this study two genes (lraA and lraB) are predicted to be involved in the catabolism of l-rhamnose, along with lraC, in the filamentous fungus Aspergillus nidulans. Transcription of all three is co-regulated with that of the genes encoding α-l-rhamnosidases, i.e. induction mediated by the l-rhamnose-responsive transcription factor RhaR and repression of induction in the presence of glucose via a CreA-independent mechanism. The participation of lraA/AN4186 (encoding l-rhamnose dehydrogenase) in l-rhamnose catabolism was revealed by the phenotypes of knock-out mutants and their complemented strains. lraA deletion negatively affects both growth on l-rhamnose and the synthesis of α-l-rhamnosidases, indicating not only the indispensability of this pathway for l-rhamnose utilization but also that a metabolite derived from this sugar is the true physiological inducer.

BEL1-LIKE HOMEODOMAIN4 regulates chlorophyll accumulation, chloroplast development, and cell wall metabolism in tomato fruit

Tomato (Solanum lycopersicum) is a model plant for studying fruit development and ripening. In this study, we found that down-regulation of a tomato bell-like homeodomain 4 (SlBL4) resulted in a slightly darker-green fruit phenotype and increased accumulation of starch, fructose, and glucose. Analysis of chlorophyll content and TEM observations was consistent with these phenotypes, indicating that SlBL4 was involved in chlorophyll accumulation and chloroplast formation. Ripened fruit of SlBL4-RNAi plants had noticeably decreased firmness, larger intercellular spaces, and thinner cell walls than the wild-type. RNA-seq identified differentially expressed genes involved in chlorophyll metabolism, chloroplast development, cell wall metabolism, and carotenoid metabolism. ChIP-seq identified (G/A) GCCCA (A/T/C) and (C/A/T) (C/A/T) AAAAA (G/A/T) (G/A) motifs. SlBL4 directly inhibited the expression of protoporphyrinogen oxidase (SlPPO), magnesium chelatase H subunit (SlCHLD), pectinesterase (SlPE), protochlorophyllide reductase (SlPOR), chlorophyll a/b binding protein 3B (SlCAB-3B), and homeobox protein knotted 2 (TKN2). In contrast, it positively regulated the expression of squamosa promoter binding protein-like colorless non-ripening (LeSPL-CNR). Our results indicate that SlBL4 is involved in chlorophyll accumulation, chloroplast development, cell wall metabolism, and the accumulation of carotenoids during tomato fruit ripening, and provide new insights for the transcriptional regulation mechanism of BELL-mediated fruit growth and ripening.

Drought Disrupts Auxin Localization in Abscission Zone and Modifies Cell Wall Structure Leading to Flower Separation in Yellow Lupine

Drought causes the excessive abscission of flowers in yellow lupine, leading to yield loss and serious economic consequences in agriculture. The structure that determines the time of flower shedding is the abscission zone (AZ). Its functioning depends on the undisturbed auxin movement from the flower to the stem. However, little is known about the mechanism guiding cell-cell adhesion directly in an AZ under water deficit. Therefore, here, we seek a fuller understanding of drought-dependent reactions and check the hypothesis that water limitation in soil disturbs the natural auxin balance within the AZ and, in this way, modifies the cell wall structure, leading to flower separation. Our strategy combined microscopic, biochemical, and chromatography approaches. We show that drought affects indole-3-acetic acid (IAA) distribution and evokes cellular changes, indicating AZ activation and flower abortion. Drought action was manifested by the accumulation of proline in the AZ. Moreover, cell wall-related modifications in response to drought are associated with reorganization of methylated homogalacturonans (HG) in the AZ, and upregulation of pectin methylesterase (PME) and polygalacturonase (PG)-enzymes responsible for pectin remodeling. Another symptom of stress action is the accumulation of hemicelluloses. Our data provide new insights into cell wall remodeling events during drought-induced flower abscission, which is relevant to control plant production.

Enzymically attaching oligosaccharide-linked 'cargoes' to cellulose and other commercial polysaccharides via stable covalent bonds

The Equisetum enzyme hetero-trans-β-glucanase (HTG) covalently grafts native plant cellulose (donor-substrate) to xyloglucan (acceptor-substrate), potentially offering a novel 'green' method of cellulose functionalisation. However, the range of cellulosic and non-cellulosic donor substrates that can be utilised by HTG is unknown, limiting our insight into its biotechnological potential. Here we show that HTG binds all celluloses tested (papers, tissues, hydrogels, bacterial cellulose) to radioactively- or fluorescently-labelled xyloglucan-heptasaccharide (XXXGol; acceptor-substrate). Glycol-chitin, glycol-chitosan and chitosan also acted as donor substrates but less effectively than cellulose. Cellulose-XXXGol conjugates were formed throughout the volume of a block of hydrogel, demonstrating penetration. Plant-derived celluloses (cellulose Iβ) became more effective donor-substrates after 'mercerisation' in ≥3 M NaOH; the opposite was true for bacterial cellulose Iα. Cellulose-XXXGol bonds resisted boiling 6 M NaOH, demonstrating strong glycosidic bonding. In conclusion, HTG stably grafts native and processed celluloses to xyloglucan-oligosaccharides, which may carry valuable 'cargoes', exemplified by sulphorhodamine. We thus demonstrate HTG's biotechnological potential to modify various cellulose-based substrates such as textiles, pulps, papers, packaging, sanitary products and hydrogels.

Exploration of Two Pectate Lyases from Caldicellulosiruptor bescii Reveals that the CBM66 Module Has a Crucial Role in Pectic Biomass Degradation

Pectin deconstruction is the initial step in breaking the recalcitrance of plant biomass by using selected microorganisms that encode pectinolytic enzymes. Pectate lyases that cleave the α-1,4-galacturonosidic linkage of pectin are widely used in industries such as papermaking and fruit softening. However, there are few reports on pectate lyases with good thermostability. Here, two pectate lyases (CbPL3 and CbPL9) from a hyperthermophilic bacterium, Caldicellulosiruptor bescii, belonging to family 3 and family 9 polysaccharide lyases, respectively, were investigated. The biochemical properties of the two CbPLs were shown to be similar under optimized conditions of 80°C to 85°C and pH 8 to 9. However, the degradation products from pectin and polygalacturonic acids (pGAs) were different. A family 66 carbohydrate-binding module (CbCBM66) located in the N terminus of the two CbPLs shares 100% amino acid identity. A CbCBM66-truncated mutant of CbPL9 showed lower activities than the wild type, whereas CbPL3 with a CbCBM66 knockout portion was reported to have enhanced activities, thereby revealing the different effect of CbCBM66. Prediction by the I-TASSER server revealed that CbCBM66 is structurally close to BsCBM66 from Bacillus subtilis; however, the COFACTOR and COACH programs indicated that the substrate-binding sites between CbCBM66 and BsCBM66 are different. Furthermore, a substrate-binding assay indicated that the catalytic domains in the two CbPLs had strong affinities for pectate-related substrates, but CbCBM66 showed a weak interaction with a number of lignocellulosic carbohydrates. Finally, scanning electron microscopy (SEM) analysis and a total reducing sugar assay showed that the two enzymes could improve the saccharification of switchgrass. The two CbPLs are impressive sources for the degradation of plant biomass.IMPORTANCE Thermophilic proteins could be implemented in diverse industrial applications. We sought to characterize two pectate lyases, CbPL3 and CbPL9, from a thermophilic bacterium, Caldicellulosiruptor bescii The two enzymes share a high optimum temperature, a low optimum pH, and good thermostability at the evaluated temperature. A family 66 carbohydrate-binding module (CbCBM66) was identified in the two CbPLs, sharing 100% amino acid identity. The deletion of CbCBM66 dramatically decreased the activity of CbPL9 but increased the activity and thermostability of CbPL3, suggesting different roles of CbCBM66 in the two enzymes. Moreover, the degradation products of the two CbPLs were different. These results revealed that these enzymes could represent potential pectate lyases for applications in the paper and textile industries.

Pectin Drives Cell Wall Morphogenesis without Turgor Pressure

How the plant cell wall expands and forms shapes is a long-standing mystery. Traditional thought is that turgor pressure drives these processes. However, a recent study by Haas and colleagues shows for the first time that the expansion of pectin homogalacturonan nanofilaments drives morphogenesis without turgor pressure in plant epidermal cells.

Physiological Importance of Pectin Modifying Genes During Rice Pollen Development

Although cell wall dynamics, particularly modification of homogalacturonan (HGA, a major component of pectin) during pollen tube growth, have been extensively studied in dicot plants, little is known about how modification of the pollen tube cell wall regulates growth in monocot plants. In this study, we assessed the role of HGA modification during elongation of the rice pollen tube by adding a pectin methylesterase (PME) enzyme or a PME-inhibiting catechin extract (Polyphenon 60) to in vitro germination medium. Both treatments led to a severe decrease in the pollen germination rate and elongation. Furthermore, using monoclonal antibodies toward methyl-esterified and de-esterified HGA epitopes, it was found that exogenous treatment of PME and Polyphenon 60 resulted in the disruption of the distribution patterns of low- and high-methylesterified pectins upon pollen germination and during pollen tube elongation. Eleven PMEs and 13 PME inhibitors (PMEIs) were identified by publicly available transcriptome datasets and their specific expression was validated by qRT-PCR. Enzyme activity assays and subcellular localization using a heterologous expression system in tobacco leaves demonstrated that some of the pollen-specific PMEs and PMEIs possessed distinct enzymatic activities and targeted either the cell wall or other compartments. Taken together, our findings are the first line of evidence showing the essentiality of HGA methyl-esterification status during the germination and elongation of pollen tubes in rice, which is primarily governed by the fine-tuning of PME and PMEI activities.

Sr-90 soil to plant transfer factor reduction using calcium and polymer soil amendments

Introducing calcium into soils can inhibit Sr-90 uptake by plants. To test the efficacy of calcium amendments on the inhibition of Sr-90 uptake by edible plants, a number of different calcium applications, including calcium nitrate, calcium thiosulfate and a mixture of both liquid solutions, were used in this study. Pea plants (Pisum sativum 'Sabre') grown in Sr-90 contaminated soil from seeds to maturity were watered with these calcium solutions. Two different polymers, one inert and one nutrient enriched, were incorporated into the contaminated soil where pea seeds were sowed to ascertain a continuous supply of calcium and essential nutrients. Results show that the heterogeneity of Sr-90 distribution in soil translated to disparate Sr-90 contents in plant tissues. However, on average, irrigation with calcium solutions in conjunction with the usage of polymers consistently yielded a reduction in Sr-90 uptake by the plants. The lowest soil-to-plant transfer factor (TF) values were measured in the edible pea part of the plant, followed by the flowers, roots, stems, pea shells and then leaves. TF values for pea shells were between 4.9 and 20.9, and between 0.3 and 2.8 for the peas. Results do not allow the identification of one particular chemical solution that would systematically be the best choice to minimize Sr-90 uptake.

Optimization of nucleotide sugar supply for polysaccharide formation via thermodynamic buffering

Plant polysaccharides (cellulose, hemicellulose, pectin, starch) are either direct (i.e. leaf starch) or indirect products of photosynthesis, and they belong to the most abundant organic compounds in nature. Although each of these polymers is made by a specific enzymatic machinery, frequently in different cell locations, details of their synthesis share certain common features. Thus, the production of these polysaccharides is preceded by the formation of nucleotide sugars catalyzed by fully reversible reactions of various enzymes, mostly pyrophosphorylases. These 'buffering' enzymes are, generally, quite active and operate close to equilibrium. The nucleotide sugars are then used as substrates for irreversible reactions of various polysaccharide-synthesizing glycosyltransferases ('engine' enzymes), e.g. plastidial starch synthases, or plasma membrane-bound cellulose synthase and callose synthase, or ER/Golgi-located variety of glycosyltransferases forming hemicellulose and pectin backbones. Alternatively, the irreversible step might also be provided by a carrier transporting a given immediate precursor across a membrane. Here, we argue that local equilibria, established within metabolic pathways and cycles resulting in polysaccharide production, bring stability to the system via the arrangement of a flexible supply of nucleotide sugars. This metabolic system is itself under control of adenylate kinase and nucleoside-diphosphate kinase, which determine the availability of nucleotides (adenylates, uridylates, guanylates and cytidylates) and Mg2+, the latter serving as a feedback signal from the nucleotide metabolome. Under these conditions, the supply of nucleotide sugars to engine enzymes is stable and constant, and the metabolic process becomes optimized in its load and consumption, making the system steady and self-regulated.

Transcriptomic changes associated with husk scald incidence on pomegranate fruit peel during cold storage

Pomegranate fruit is valued for its social, economic, aesthetic and health benefits. The fruit rapidly loses quality after harvest due to continued metabolic responses and physiological disorders under sub-optimal conditions. The incidence of physiological disorder such as husk scald manifests during storage and commercial shipping, which affects the appearance and limits marketability. Despite the importance of pomegranate husk scald, little information is available about the origin and molecular mechanisms. Therefore, the aim of this study was to investigate the scald incidence of pomegranate fruit at molecular level using RNA-Seq (Ion Proton™ Next Generation Sequencing) by analyzing peel transcriptomic changes. The RNA-seq analysis generated 98,441,278 raw reads. 652 Differentially Expressed Genes (DEGs) with a fold change of > |2|, a p value ≤ 0.05 and a false discovery rate (FDR) of <0.05 were identified between healthy and scald fruit peels. An analysis of the gene ontologies of these DEGs revealed the 432 genes were assigned with molecular functions, 272 as cellular components and 205 as part of biological processes. In this analysis, genes (Pgr023188 and Pgr025081) that encode uncharacterized protein and gene (Pgr007593) that encodes glycosyltransferase showed significantly highest fold changes. Genes (Pgr003448, Pgr006024 and Pgr023696) involved in various iron binding and oxidoreductase activities were significantly suppressed. This is the first transcriptome analysis of pomegranate fruit peel related to husk scald development. Results obtained from this study will add valuable information on husk scald related changes on pomegranate fruit at genomic level and provide insight on other related physiological disorders.

Structural characteristics of oxalate-soluble polysaccharides from Norway spruce (Picea abies) foliage

Structurally different polymers were derived from Picea abies foliage by successive extraction with water (PA_W), HCl solution (PA_A) and (NH₄)₂C₂O₄ solution (PA_O). The P. abies foliage was found to contain basically low-methoxyl pectin extractable with an (NH₄)₂C₂O₄ solution. PA_W was shown to comprise primarily arabinogalactan-proteins (AGPs); PA_A was composed of mixed AGPs and pectic polysaccharides, with the latter prevailing; and polysaccharide PA_O isolated in the highest yield included chiefly pectic polysaccharides. The major constituents of PA_O were low-methoxyl and low-acetylated 1,4-α-d-galacturonan and partially acetylated RG-I. The sugar side chains of RG-I contained chiefly highly branched 1,5-α-l-arabinan and arabinogalactan type I as a minor constituent. RG-I whose side chains had 1,5-α-l-arabinan represented short regions alternating with non-acetylated and unmethylesterified galacturonan regions. In addition to pectins, polysaccharide PA_O contained AGPs, xylanes and glucomannans, indicating that these polysaccharides are in an intimate interaction.

Golgi-localized exo-β1,3-galactosidases involved in cell expansion and root growth in Arabidopsis

Plant arabinogalactan proteins (AGPs) are a diverse group of cell surface- and wall-associated glycoproteins. Functionally important AGP glycans are synthesized in the Golgi apparatus, but the relationships among their glycosylation levels, processing, and functionalities are poorly understood. Here, we report the identification and functional characterization of two Golgi-localized exo-β-1,3-galactosidases from the glycosyl hydrolase 43 (GH43) family in Arabidopsis thaliana GH43 loss-of-function mutants exhibited root cell expansion defects in sugar-containing growth media. This root phenotype was associated with an increase in the extent of AGP cell wall association, as demonstrated by Yariv phenylglycoside dye quantification and comprehensive microarray polymer profiling of sequentially extracted cell walls. Characterization of recombinant GH43 variants revealed that the exo-β-1,3-galactosidase activity of GH43 enzymes is hindered by β-1,6 branches on β-1,3-galactans. In line with this steric hindrance, the recombinant GH43 variants did not release galactose from cell wall-extracted glycoproteins or AGP-rich gum arabic. These results indicate that the lack of exo-β-1,3-galactosidase activity alters cell wall extensibility in roots, a phenotype that could be explained by the involvement of galactosidases in AGP glycan biosynthesis.

A Comprehensive Gene Expression Profile of Pectin Degradation Enzymes Reveals the Molecular Events during Cell Wall Degradation and Pathogenesis of Rice Sheath Blight Pathogen Rhizoctonia solani AG1-IA

Sheath blight disease of rice caused by Rhizoctonia solani Kühn (teleomorph: Thanatephorus cucumeris) remains a global challenge due to the absence of reliable resistance genes and poor understanding of pathogen biology. Pectin, one of the most vital constituents of the plant cell wall, is targeted by pectin methylesterases, polygalacturonases, and few other enzymes of fungal pathogens. In this study, we catalogued the expressed genes of the fungal genome from RNAseq of R. solani infected four rice genotypes. Analysis of RNAseq revealed 3325 pathogen genes commonly expressed in all rice genotypes, in which 49, 490, and 83 genes were specific to BPT5204, Tetep, and Pankaj genotypes, respectively. To identify the early and late responding genes of R. solani during plant cell wall degradation, a real-time PCR analysis of 30 pectinolytic enzymes was done at six different time points after inoculation. The majority of these genes showed maximum induction at the 72 h time point, suggesting that it is the most crucial stage of infection. Pankaj showed lesser induction of these genes as compared to other genotypes. Leaf-blade tissue and 45 days old-growth stage are more favorable for the expression of pectin degradation genes of R. solani. Additionally, the expression analysis of these genes from four different strains of R. solani suggested differential regulation of genes but no distinct expression pattern between highly virulent and mild strains. The implications of the differential regulation of these genes in disease development have been discussed. This study provides the first such comprehensive analysis of R. solani genes encoding pectin degrading enzymes, which would help to decipher the pathogen biology and sheath blight disease development.

Cell wall O-acetyl and methyl esterification patterns of leaves reflected in atmospheric emission signatures of acetic acid and methanol

Plants emit high rates of methanol (meOH), generally assumed to derive from pectin demethylation, and this increases during abiotic stress. In contrast, less is known about the emission and source of acetic acid (AA). In this study, Populus trichocarpa (California poplar) leaves in different developmental stages were desiccated and quantified for total meOH and AA emissions together with bulk cell wall acetylation and methylation content. While young leaves showed high emissions of meOH (140 μmol m^-2) and AA (42 μmol m^-2), emissions were reduced in mature (meOH: 69%, AA: 60%) and old (meOH: 83%, AA: 76%) leaves. In contrast, the ratio of AA/meOH emissions increased with leaf development (young: 35%, mature: 43%, old: 82%), mimicking the pattern of O-acetyl/methyl ester ratios of leaf bulk cell walls (young: 35%, mature: 38%, old: 51%), which is driven by an increase in O-acetyl and decrease in methyl ester content with age. The results are consistent with meOH and AA emission sources from cell wall de-esterification, with young expanding tissues producing highly methylated pectin that is progressively demethyl-esterified. We highlight the quantification of AA/meOH emission ratios as a potential tool for rapid phenotype screening of structural carbohydrate esterification patterns.

Pectin polymers for colon-targeted antitumor drug delivery

The use of chemotherapeutic drugs in the treatment of malignant tumors is always associated with the severe side effects negatively affecting all organs and systems in human body. One of the approaches for reduction of the toxic influence and enhancement of the antitumor drug administration efficiency is supposed to be the use of the biopolymer delivery systems. Pectins are considered the most promising components for colon targeted drug dosage forms as they are stable in the changing gastrointestinal media and easily degraded by pectinases produced by colonic microflora. A various range of the pectin-containing delivery systems were developed contributing higher concentration of the active drug molecules in particular site inside intestine and their lower blood level resulting in lowered risk of the severe side effects. This review discusses the various forms of the pectin-based materials such as hydrogels, tablets and pellets, films, microspheres, microsponges, nanoparticles, etc. as drug delivery device and attempted to report the vast literature available on pectin biopolymers in drug delivery applications.

Transcription Factors BLH2 and BLH4 Regulate Demethylesterification of Homogalacturonan in Seed Mucilage

The polysaccharide pectin is a major component of the plant cell wall. The pectic glycan homogalacturonan (HG) is a proportionally small but important component of a specialized seed cell wall called mucilage. HG is synthesized in a highly methylesterified form, and, following secretion, is de-methylesterified by pectin methylesterases (PMEs). The degree of methylesterification of HG determines the structural and functional properties of pectin, but how methylesterification is regulated remains largely unknown. Here, we identified two BEL1-Like homeodomain (BLH) transcription factors, BLH2 and BLH4, as positive regulators of HG de-methylesterification in Arabidopsis (Arabidopsis thaliana) seed coat mucilage. BLH2 and BLH4 were significantly expressed in mucilage secretory cells during seed mucilage production. BLH2 and BLH4 single mutants exhibited no obvious mucilage phenotype, but the blh2 blh4 double mutant displayed significantly reduced mucilage adherence to the seed. Reduced mucilage adherence in blh2 blh4 was caused by decreased PME activity in the seed coat, which increased the degree of methylesterification of HG in mucilage. The expression of several PME metabolism-related genes, including PME58, PECTIN METHYLESTERASE INHIBITOR6, SEEDSTICK, and MYB52 was significantly altered in blh2 blh4 seeds. BLH2 and BLH4 directly activated PME58 expression by binding to its TGACAGGT cis-element. Moreover, pme58 mutants exhibited reduced mucilage adherence similar to that of blh2 blh4, and the blh2 blh4 pme58 triple mutant exhibited no additional mucilage adherence defects. Furthermore, overexpression of PME58 in blh2 blh4 rescued the mucilage adherence defect. Together, these results demonstrate that BLH2 and BLH4 redundantly regulate de-methylesterification of HG in seed mucilage by directly activating PME58.

Comparative evaluation of Aspergillus niger strains for endogenous pectin-depolymerization capacity and suitability for D-galacturonic acid production

Pectinaceous agricultural residues rich in D-galacturonic acid (D-GalA), such as sugar beet pulp, are considered as promising feedstocks for waste-to-value conversions. Aspergillus niger is known for its strong pectinolytic activity. However, while specialized strains for production of citric acid or proteins are well characterized, this is not the case for the production of pectinases. We, therefore, systematically compared the pectinolytic capabilities of six A. niger strains (ATCC 1015, ATCC 11414, NRRL 3122, CBS 513.88, NRRL 3, and N402) using controlled batch cultivations in stirred-tank bioreactors. A. niger ATCC 11414 showed the highest polygalacturonase activity, specific protein secretion, and a suitable morphology. Furthermore, D-GalA release from sugar beet pulp was 75% higher compared to the standard lab strain A. niger N402. Our study, therefore, presents a robust initial strain selection to guide future process improvement of D-GalA production from agricultural residues and identifies a high-performance base strain for further genetic optimizations.

Overexpression and Biochemical Characterization of an Endo-α-1,4-polygalacturonase from Aspergillus nidulans in Pichia pastoris

Pectinases have many applications in the industry of food, paper, and textiles, therefore finding novel polygalacturonases is required. Multiple sequence alignment and phylogenetic analysis of AnEPG (an endo-α-1,4-polygalacturonase from Aspergillus nidulans) and other GH 28 endo-polygalacturonases suggested that AnEPG is different from others. AnEPG overexpressed in Pichia pastoris was characterized. AnEPG showed the highest activity at pH 4.0, and exhibited moderate activity over a narrow pH range (pH 2.0-5.0) and superior stability in a wide pH range (pH 2.0-12.0). It displayed the highest activity at 60 °C, and retained >42.2% of maximum activity between 20 and 80 °C. It was stable below 40 °C and lost activity very quickly above 50 °C. Its apparent kinetic parameters against PGA (polygalacturonic acid) were determined, with the K_m and k_cat values of 8.3 mg/mL and 5640 μmol/min/mg, respectively. Ba²⁺ and Ni²⁺ enhanced activity by 12.2% and 9.4%, respectively, while Ca²⁺, Cu²⁺, and Mn²⁺ inhibited activity by 14.8%, 12.8%, and 10.2% separately. Analysis of hydrolysis products by AnEPG proved that AnEPG belongs to an endo-polygalacturonase. Modelled structure of AnEPG by I-TASSER showed structural characteristics of endo-polygalacturonases. This pectinase has great potential to be used in food industry and as feed additives.

Protein coating composition targets nanoparticles to leaf stomata and trichomes

Plant nanobiotechnology has the potential to revolutionize agriculture. However, the lack of effective methods to deliver nanoparticles (NPs) to the precise locations in plants where they are needed impedes these technological innovations. Here, model gold nanoparticles (AuNP) were coated with citrate, bovine serum albumin (BSA) as a protein control, or LM6-M, an antibody with an affinity for functional groups unique to stomata on leaf surfaces to deliver the AuNPs to stomata. One-month-old Vicia faba leaves were exposed via drop deposition to aqueous suspensions of LM6-M-coated AuNPs and allowed to air dry. After rinsing, Au distribution on the leaf surface was investigated by enhanced dark-field microscopy and X-ray fluorescence mapping. While citrate-coated AuNPs randomly covered the plant leaves, LM6M-AuNPs strongly adhered to the stomata and remained on the leaf surface after rinsing, and BSA-AuNPs specifically targeted trichome hairs. To the authors' knowledge, this is the first report of active targeting of live leaf structures using NPs coated with molecular recognition molecules. This proof-of-concept study provides a strategy for future targeted nanopesticide delivery research.

Arabidopsis FLYING SAUCER 2 Functions Redundantly with FLY1 to Establish Normal Seed Coat Mucilage

Following exposure to water, mature Arabidopsis seeds are surrounded by a gelatinous capsule, termed mucilage. The mucilage consists of pectin-rich polysaccharides, which are produced in epidermal cells of the seed coat. Although pectin is a major component of plant cell walls, its biosynthesis and biological functions are not fully understood. Previously, we reported that a transmembrane RING E3 ubiquitin ligase, FLYING SAUCER 1 (FLY1) regulates the degree of pectin methyl esterification for mucilage capsule formation. The Arabidopsis thaliana genome has a single FLY1 homolog, FLY2. In this study, we show that the FLY2 protein functions in mucilage modification together with FLY1. FLY2 was expressed in seed coat epidermal cells during mucilage synthesis, but its expression level was much lower than that of FLY1. While fly2 showed no obvious difference in mucilage capsule formation from wild type, the fly1 fly2 double mutants showed more severe defects in mucilage than fly1 alone. FLY2-EYFP that was expressed under the control of the FLY1 promoter rescued fly1 mucilage, showing that FLY2 has the same molecular function as FLY1. FLY2-EYFP colocalized with marker proteins of Golgi apparatus (sialyltransferase-mRFP) and late endosome (mRFP-ARA7), indicating that as FLY1, FLY2 controls pectin modification by functioning in these endomembrane organelles. Furthermore, phylogenetic analysis suggests that FLY1 and FLY2 originated from a common ancestral gene by gene duplication prior to the emergence of Brassicaceae. Taken together, our findings suggest that FLY2 functions in the Golgi apparatus and/or the late endosome of seed coat epidermal cells in a manner similar to FLY1.

The Dynamic Responses of Cell Walls in Resurrection Plants During Dehydration and Rehydration

Plant cell walls define the shape of the cells and provide mechanical support. They function as osmoregulators by controlling the transport of molecules between cells and provide transport pathways within the plant. These diverse functions require a well-defined and flexible organization of cell wall components, i.e., water, polysaccharides, proteins, and other diverse substances. Cell walls of desiccation tolerant resurrection plants withstand extreme mechanical stress during complete dehydration and rehydration. Adaptation to the changing water status of the plant plays a crucial role during this process. This review summarizes the compositional and structural variations, signal transduction and changes of gene expression which occur in cell walls of resurrection plants during dehydration and rehydration.

Imaging and Analysis of the Content of Callose, Pectin, and Cellulose in the Cell Wall of Arabidopsis Pollen Tubes Grown In Vitro

To achieve fertilization, pollen tubes have to protect and properly deliver sperm cells through the pistil to the ovules. Pollen tube growth is a representative example of polarized growth where new components of the cell wall and plasma membrane are continuously deposited at the tip of the growing cell. The integrity of the cell wall is of fundamental importance to maintain apical growth. For this reason, pollen tube growth has become an excellent model to study the role of polysaccharides and structural cell wall proteins involved in polar cell expansion. However, quantification of structural polysaccharides at the pollen tube cell wall has been challenging due to technical complexity and the difficulty of finding specific dyes. Here, we propose simple methods for imaging and quantification of callose, pectin , and cellulose using specific dyes such as Aniline Blue, Propidium Iodide, and Pontamine Fast Scarlet 4B.

Illumina-based transcriptomic analysis on recalcitrant seeds of Panax notoginseng for the dormancy release during the after-ripening process

Panax notoginseng (Burk) F.H. Chen is an economically and medicinally important plant of the family Araliacease, with seed dormancy being a key factor limiting the extended cultivation of P. notoginseng. The seeds belong to the morphophysiological dormancy (MPD) group, and it has also been described as the recalcitrant seed. To date, the molecular mechanism of dormancy release in the recalcitrant seed of P. notoginseng is unknown. In the present study, the transcript profiles of seeds from different after-ripening stages (0, 20, 40 and 60 days) were investigated using Illumina Hiseq 2500 technology. 91 979 946 clean reads were generated, and 81 575 unigenes were annotated in at least one database. In addition, the differentially expressed genes (DEGs) were identified by the pairwise comparisons. We screened out 2483 DEGs by the three key groups of 20 days vs 0 d, 40 d vs 0 d and 60 d vs 0 d. The DEGs were analyzed by gene ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway annotation. Meanwhile, we obtained 78 DEGs related to seeds dormancy release at different after-ripening stages of P. notoginseng, of which 15 DEGs were associated with abscisic acid and gibberellin. 26 DEGs that encode late embryogenesis abundant protein and antioxidant enzyme were correlated with desiccation tolerance in seeds. In summary, the results obtained here showed that PECTINESTERASE-2-LIKE, GA-INSENSITIVE, ENT-KAURENE SYNTHASE, PROTEIN PHOSPHATASE 2C, GIBBERELLIN 2-BETA-DIOXYGENASE, SUPEROXIDE DISMUTASE, L-ASCORBATE PEROXIDASE, CATALASE, LATE EMBRYOGENESIS ABUNDANT PROTEIN DC3 and DEHYDRIN 9 were potentially involved in dormancy release and desiccation sensitivity of P. notoginseng seeds. The data might provide a basis for researches on MPD.

PMR5, an acetylation protein at the intersection of pectin biosynthesis and defense against fungal pathogens

Powdery mildew (Golovinomyces cichoracearum), one of the most prolific obligate biotrophic fungal pathogens worldwide, infects its host by penetrating the plant cell wall without activating the plant's innate immune system. The Arabidopsis mutant powdery mildew resistant 5 (pmr5) carries a mutation in a putative pectin acetyltransferase gene that confers enhanced resistance to powdery mildew. Here, we show that heterologously expressed PMR5 protein transfers acetyl groups from [¹⁴ C]-acetyl-CoA to oligogalacturonides. Through site-directed mutagenesis, we show that three amino acids within a highly conserved esterase domain in putative PMR5 orthologs are necessary for PMR5 function. A suppressor screen of mutagenized pmr5 seed selecting for increased powdery mildew susceptibility identified two previously characterized genes affecting the acetylation of plant cell wall polysaccharides, RWA2 and TBR. The rwa2 and tbr mutants also suppress powdery mildew disease resistance in pmr6, a mutant defective in a putative pectate lyase gene. Cell wall analysis of pmr5 and pmr6, and their rwa2 and tbr suppressor mutants, demonstrates minor shifts in cellulose and pectin composition. In direct contrast to their increased powdery mildew resistance, both pmr5 and pmr6 plants are highly susceptibile to multiple strains of the generalist necrotroph Botrytis cinerea, and have decreased camalexin production upon infection with B. cinerea. These results illustrate that cell wall composition is intimately connected to fungal disease resistance and outline a potential route for engineering powdery mildew resistance into susceptible crop species.

MUR1-mediated cell-wall fucosylation is required for freezing tolerance in Arabidopsis thaliana

Forward genetic screens play a key role in the identification of genes contributing to plant stress tolerance. Using a screen for freezing sensitivity, we have identified a novel freezing tolerance gene, SENSITIVE-TO-FREEZING8, in Arabidopsis thaliana. We identified SFR8 using recombination-based mapping and whole-genome sequencing. As SFR8 was predicted to have an effect on cell wall composition, we used GC-MS and polyacrylamide gel electrophoresis to measure cell-wall fucose and boron (B)-dependent dimerization of the cell-wall pectic domain rhamnogalacturonan II (RGII) in planta. After treatments to promote borate-bridging of RGII, we assessed freeze-induced damage in wild-type and sfr8 plants by measuring electrolyte leakage from freeze-thawed leaf discs. We mapped the sfr8 mutation to MUR1, a gene encoding the fucose biosynthetic enzyme GDP-d-mannose-4,6-dehydratase. sfr8 cell walls exhibited low cell-wall fucose levels and reduced RGII bridging. Freezing sensitivity of sfr8 mutants was ameliorated by B supplementation, which can restore RGII dimerization. B transport mutants with reduced RGII dimerization were also freezing-sensitive. Our research identifies a role for the structure and composition of the plant primary cell wall in determining basal plant freezing tolerance and highlights the specific importance of fucosylation, most likely through its effect on the ability of RGII pectin to dimerize.

Cotton CSLD3 restores cell elongation and cell wall integrity mainly by enhancing primary cellulose production in the Arabidopsis cesa6 mutant

Overexpression of cotton cellulose synthase like D3 (GhCSLD3) gene partially rescued growth defect of atcesa6 mutant with restored cell elongation and cell wall integrity mainly by enhancing primary cellulose production. Among cellulose synthase like (CSL) family proteins, CSLDs share the highest sequence similarity to cellulose synthase (CESA) proteins. Although CSLD proteins have been implicated to participate in the synthesis of carbohydrate-based polymers (cellulose, pectins and hemicelluloses), and therefore plant cell wall formation, the exact biochemical function of CSLD proteins remains controversial and the function of the remaining CSLD genes in other species have not been determined. In this study, we attempted to illustrate the function of CSLD proteins by overexpressing Arabidopsis AtCSLD2, -3, -5 and cotton GhCSLD3 genes in the atcesa6 mutant, which has a background that is defective for primary cell wall cellulose synthesis in Arabidopsis. We found that GhCSLD3 overexpression partially rescued the growth defect of the atcesa6 mutant during early vegetative growth. Despite the atceas6 mutant having significantly reduced cellulose contents, the defected cell walls and lower dry mass, GhCSLD3 overexpression largely restored cell wall integrity (CWI) and improved the biomass yield. Our result suggests that overexpression of the GhCSLD protein enhances primary cell wall synthesis and compensates for the loss of CESAs, which is required for cellulose production, therefore rescuing defects in cell elongation and CWI.

Genome-Wide Identification and Characterization of Glycosyltransferase Family 47 in Cotton

The glycosyltransferase (GT) 47 family is involved in the biosynthesis of xylose, pectin and xyloglucan and plays a significant role in maintaining the normal morphology of the plant cell wall. However, the functions of GT47s are less well known in cotton. In the present study, a total of 53, 53, 105 and 109 GT47 genes were detected by genome-wide identification in Gossypium arboreum, G. raimondii, G. hirsutum and G. barbadense, respectively. All the GT47s were classified into six major groups via phylogenetic analysis. The exon/intron structure and protein motifs indicated that each branch of the GT47 genes was highly conserved. Collinearity analysis showed that GT47 gene family expansion occurred in Gossypium spp. mainly through whole-genome duplication and that segmental duplication mainly promoted GT47 gene expansion within the A and D subgenomes. The Ka/Ks values suggested that the GT47 gene family has undergone purifying selection during the long-term evolutionary process. Transcriptomic data and qRT-PCR showed that GhGT47 genes exhibited different expression patterns in each tissue and during fiber development. Our results suggest that some genes in the GhGT47 family might be associated with fiber development and the abiotic stress response, which could promote further research involving functional analysis of GT47 genes in cotton.

Cloning of a COBL gene determining brittleness in diploid wheat using a MapRseq approach

Plant tissue brittleness is related to cellular structure and lodging. MED0031 is a mutant identified previously from ethyl methane sulfonate treatment of diploid wheat accession TA2726, showing brittleness in both stem and leaf. In microscopic and histological observations, the mutant was found to have less large vascular bundles per unit area, a thinner sclerenchyma cell wall, and a broader parenchyma, compared with the wild type. The mutated gene, TmBr1, was mapped to a 0.056 cM interval on chromosome 5A^m. This gene was cloned using a MapRseq approach that searched the candidate gene through combination of the prior target gene mapping information with SNP calling and discovery of differentially expressed genes from RNA_seq data of the wild type and a BC₃F₂ bulk showing the mutant phenotype. TmBr1 encodes a COBL protein and a nonsense mutation within the region coding for the conserved COBRA domain caused premature translation termination. Introduction of TmBr1 to Arabidopsis AtCOBL4 mutant rescued the phenotype, demonstrating their functional conservation. Apart from the effect on cellulose content, the TmBr1 mutation might modulate synthesis of noncellulosic polysaccharide pectin as well. Application of the MapRseq approach to isolation of genes present in recombination cold spots and complicated genomes was discussed.

Bacteria with natural chemotaxis towards methanol revealed by chemotaxis fishing technique

Motile bacteria often exhibit chemotaxis toward favorable compounds. However, the diversity of bacteria that are attracted to a given substance is largely unknown. This study aimed to reveal the diversity of bacteria with natural chemotaxis towards methanol. We tried to enrich environmental chemotactic bacteria using a glass capillary that is half-filled with methanol solidified with agarose as a trap ("chemotaxis fishing"). The pilot experiment using methanol-chemotactic Methylobacterium aquaticum strain 22A enriched the cells by 46-fold. The method was then applied to bacterial suspensions from paddy water and plants. Depending on the isolation sources and the methods of motility induction, methylotrophic bacteria were enriched 1.2-330-fold. The fished isolates belong to 32 species in 18 genera, mainly containing Acinetobacter, Methylobacterium and Pseudomonas species. Our chemotaxis fishing unveiled a part of diversity of the bacteria with natural chemotaxis towards methanol.