Modification of polysaccharides and plant cell wall by endo-1,4-beta-glucanase and cellulose-binding domains

The complex polyploid genome architecture of sugarcane

Sugarcane, the world's most harvested crop by tonnage, has shaped global history, trade and geopolitics, and is currently responsible for 80% of sugar production worldwide1. While traditional sugarcane breeding methods have effectively generated cultivars adapted to new environments and pathogens, sugar yield improvements have recently plateaued2. The cessation of yield gains may be due to limited genetic diversity within breeding populations, long breeding cycles and the complexity of its genome, the latter preventing breeders from taking advantage of the recent explosion of whole-genome sequencing that has benefited many other crops. Thus, modern sugarcane hybrids are the last remaining major crop without a reference-quality genome. Here we take a major step towards advancing sugarcane biotechnology by generating a polyploid reference genome for R570, a typical modern cultivar derived from interspecific hybridization between the domesticated species (Saccharum officinarum) and the wild species (Saccharum spontaneum). In contrast to the existing single haplotype ('monoploid') representation of R570, our 8.7 billion base assembly contains a complete representation of unique DNA sequences across the approximately 12 chromosome copies in this polyploid genome. Using this highly contiguous genome assembly, we filled a previously unsized gap within an R570 physical genetic map to describe the likely causal genes underlying the single-copy Bru1 brown rust resistance locus. This polyploid genome assembly with fine-grain descriptions of genome architecture and molecular targets for biotechnology will help accelerate molecular and transgenic breeding and adaptation of sugarcane to future environmental conditions.

Recent advances in polysaccharide biomodification by microbial fermentation: production, properties, bioactivities, and mechanisms

Polysaccharides are natural chemical compounds that are extensively employed in the food and pharmaceutical industries. They exhibit a wide range of physical and biological properties. These properties are commonly improved by using chemical and physical methods. However, with the advancement of biotechnology and increased demand for green, clean, and safe products, polysaccharide modification via microbial fermentation has gained importance in improving their physicochemical and biological activities. The physicochemical and structural characteristics, biological activity, and modification mechanisms of microbially fermented polysaccharides were reviewed and summarized in this study. Polysaccharide modifications were categorized and discussed in terms of strains and fermentation techniques. The effects of microbial fermentation on the physicochemical characteristics of polysaccharides were highlighted. The impact of modification of polysaccharides on their antioxidant, immune, hypoglycemic, and other activities, as well as probiotic digestive enhancement, were also discussed. Finally, we investigated a potential enzyme-based process for polysaccharide modification via microbial fermentation. Modification of polysaccharides via microbial fermentation has significant value and application potential.

Protein-protein interaction (PPI) network analysis reveals important hub proteins and sub-network modules for root development in rice (Oryza sativa)

BACKGROUND

The root system is vital to plant growth and survival. Therefore, genetic improvement of the root system is beneficial for developing stress-tolerant and improved plant varieties. This requires the identification of proteins that significantly contribute to root development. Analyzing protein-protein interaction (PPI) networks is vastly beneficial in studying developmental phenotypes, such as root development, because a phenotype is an outcome of several interacting proteins. PPI networks can be analyzed to identify modules and get a global understanding of important proteins governing the phenotypes. PPI network analysis for root development in rice has not been performed before and has the potential to yield new findings to improve stress tolerance.

RESULTS

Here, the network module for root development was extracted from the global Oryza sativa PPI network retrieved from the STRING database. Novel protein candidates were predicted, and hub proteins and sub-modules were identified from the extracted module. The validation of the predictions yielded 75 novel candidate proteins, 6 sub-modules, 20 intramodular hubs, and 2 intermodular hubs.

CONCLUSIONS

These results show how the PPI network module is organized for root development and can be used for future wet-lab studies for producing improved rice varieties.

Bacterial secondary metabolites: possible mechanism for weed suppression in wheat

Chemical weed control is an effective method, but has proved hazardous for humans, environment, and soil biodiversity. Use of allelopathic bacteria may be more efficient and sustainable weed control measure. The bacterial inoculants have never been studied in context of their interaction with weed root exudates and precursor-dependent production of the natural phytotoxins (cyanide, cytolytic enzymes and auxin) by these strains to understand their weed suppression and wheat growth promotion abilities. Therefore, root exudates of Avena fatua, Phalaris minor, Rumex dentatus, and wheat were quantified and their role in microbial root colonization and secondary metabolite production, i.e., cyanide, cytolytic enzymes, phenolics, and elevated auxin concentration, was studied. The results depicted l-tryptophan and glycine as major contributors of elevated cyanide and elevated levels in weed rhizosphere by the studied Pseudomonas strains, through their higher root colonization ability in weeds as compared with wheat. Furthermore, the higher root colonization also enhanced p-coumaric acid (photosynthesis inhibitor by impairing cytochrome c oxidase activity in plants) and cytolytic enzyme (root cell wall degradation) concentration in weed rhizosphere. In conclusion, the differential root colonization of wheat and weeds by these strains is responsible for enhancing weed suppression (enhancing phytotoxic effect) and wheat growth promotion (lowering phytotoxic effect).

Identification in silico and expression analysis of a β-1-4-endoglucanase and β-galactosidase genes related to ripening in guava fruit

BACKGROUND

Guava fruit softening is a crucial process during ripening and this process involves a number of enzymes that modifies the cell wall. Two of the enzymes that regulate this process are (a) the β-1, 4-endoglucanase 17 (BEG) which hydrolyze β-1, 4 bonds from cellulose and hemicellulose, and (b) β-galactosidase (BGA) that hydrolyzes pectin chains. Bioinformatics and expression analysis information on these genes is limited in guava fruit.

RESULTS

A fragment of a β-1, 4-endoglucanase 17 (PgE17), and another of a β-galactosidase (PgGa1) were identified. These sequences have a similarity of more than 85% with those reported in the NCBI database. In the guava genome, one homologous sequence was found for PgE17 in Chr 4 and two homologous to PgGa1: one in Chr 3 and the other one in Chr 6. Putative protein PgE17 contains part of the glyco_hydro_9 domain. Putative protein PgGa1 has a part of the glyco_hydro_35 domain. Phylogenetic analysis of PgE17 and PgGa1 revealed that both are highly conserved inside the Myrtaceae family. In silico expression analysis showed that both PgE17 and PgGa1 work in a coordinated way with other cell wall modifier enzymes. Expression of these genes was found in all the guava samples analyzed. However, the highest expression was found in the fruit in the breaking and ripe states.

CONCLUSIONS

A β-1, 4-endoglucanase 17, and β-galactosidase 1 sequences were identified. PgE17 and PgGa1 are expressed in all the plant tissues, and fruit ripening states. Although, the highest expression was on breaker and ripe states.

Genes Associated with the Flax Plant Type (Oil or Fiber) Identified Based on Genome and Transcriptome Sequencing Data

As a result of the breeding process, there are two main types of flax (Linum usitatissimum L.) plants. Linseed is used for obtaining seeds, while fiber flax is used for fiber production. We aimed to identify the genes associated with the flax plant type, which could be important for the formation of agronomically valuable traits. A search for polymorphisms was performed in genes involved in the biosynthesis of cell wall components, lignans, fatty acids, and ion transport based on genome sequencing data for 191 flax varieties. For 143 of the 424 studied genes (4CL, C3'H, C4H, CAD, CCR, CCoAOMT, COMT, F5H, HCT, PAL, CTL, BGAL, ABC, HMA, DIR, PLR, UGT, TUB, CESA, RGL, FAD, SAD, and ACT families), one or more polymorphisms had a strong correlation with the flax type. Based on the transcriptome sequencing data, we evaluated the expression levels for each flax type-associated gene in a wide range of tissues and suggested genes that are important for the formation of linseed or fiber flax traits. Such genes were probably subjected to the selection press and can determine not only the traits of seeds and stems but also the characteristics of the root system or resistance to stresses at a particular stage of development, which indirectly affects the ability of flax plants to produce seeds or fiber.

Cell Wall Polysaccharide-Mediated Cadmium Tolerance Between Two Arabidopsis thaliana Ecotypes

Cadmium (Cd) is a toxic metal element and the mechanism(s) underlying Cd tolerance in plants are still unclear. Increasingly more studies have been conducted on Cd binding to plant cell walls (CW) but most of them have focused on Cd fixation by CW pectin, and few studies have examined Cd binding to cellulose and hemicellulose. Here we found that Cd binding to CW pectin, cellulose, and hemicellulose was significantly higher in Tor-1, a Cd tolerant A. thaliana ecotype, than in Ph2-23, a sensitive ecotype, as were the concentrations of pectin, cellulose, and hemicellulose. Transcriptome analysis revealed that the genes regulating CW pectin, cellulose, and hemicellulose polysaccharide concentrations in Tor-1 differed significantly from those in Ph2-23. The expressions of most genes such as pectin methyl esterase inhibitors (PMEIs), pectin lyases, xyloglucan endotransglucosylase/hydrolase, expansins (EXPAs), and cellulose hydrolase were higher in Ph2-23, while the expressions of cellulose synthase-like glycosyltransferase 3 (CSLG3) and pectin ethyl esterase 4 (PAE4) were higher in Tor-1. The candidate genes identified here seem to regulate CW Cd fixation by polysaccharides. In conclusion, an increase in pectin demethylation activity, the higher concentration of cellulose and hemicellulose, regulated by related genes, in Tor-1 than in Ph2-23 are likely involved in enhanced Cd CW retention and reduce Cd toxicity.

Improving photosynthesis, plant productivity and abiotic stress tolerance - current trends and future perspectives

With unfavourable climate changes and an increasing global population, there is a great need for more productive and stress-tolerant crops. As traditional methods of crop improvement have probably reached their limits, a further increase in the productivity of crops is expected to be possible using genetic engineering. The number of potential genes and metabolic pathways, which when genetically modified could result in improved photosynthesis and biomass production, is multiple. Photosynthesis, as the only source of carbon required for the growth and development of plants, attracts much attention is this respect, especially the question concerning how to improve CO₂ fixation and limit photorespiration. The most promising direction for increasing CO₂ assimilation is implementating carbon concentrating mechanisms found in cyanobacteria and algae into crop plants, while hitherto performed experiments on improving the CO₂ fixation versus oxygenation reaction catalyzed by Rubisco are less encouraging. On the other hand, introducing the C₄ pathway into C₃ plants is a very difficult challenge. Among other points of interest for increased biomass production is engineering of metabolic regulation, certain proteins, nucleic acids or phytohormones. In this respect, enhanced sucrose synthesis, assimilate translocation to sink organs and starch synthesis is crucial, as is genetic engineering of the phytohormone metabolism. As abiotic stress tolerance is one of the key factors determining crop productivity, extensive studies are being undertaken to develop transgenic plants characterized by elevated stress resistance. This can be accomplished due to elevated synthesis of antioxidants, osmoprotectants and protective proteins. Among other promising targets for the genetic engineering of plants with elevated stress resistance are transcription factors that play a key role in abiotic stress responses of plants. In this review, most of the approaches to improving the productivity of plants that are potentially promising and have already been undertaken are described. In addition to this, the limitations faced, potential challenges and possibilities regarding future research are discussed.

Release, Recycle, Rebuild: Cell-Wall Remodeling, Autodegradation, and Sugar Salvage for New Wall Biosynthesis during Plant Development

Plant cell walls contain elaborate polysaccharide networks and regulate plant growth, development, mechanics, cell-cell communication and adhesion, and defense. Despite conferring rigidity to support plant structures, the cell wall is a dynamic extracellular matrix that is modified, reorganized, and degraded to tightly control its properties during growth and development. Far from being a terminal carbon sink, many wall polymers can be degraded and recycled by plant cells, either via direct re-incorporation by transglycosylation or via internalization and metabolic salvage of wall-derived sugars to produce new precursors for wall synthesis. However, the physiological and metabolic contributions of wall recycling to plant growth and development are largely undefined. In this review, we discuss long-standing and recent evidence supporting the occurrence of cell-wall recycling in plants, make predictions regarding the developmental processes to which wall recycling might contribute, and identify outstanding questions and emerging experimental tools that might be used to address these questions and enhance our understanding of this poorly characterized aspect of wall dynamics and metabolism.

Growth modulation effects of CBM2a under the control of AtEXP4 and CaMV35S promoters in Arabidopsis thaliana, Nicotiana tabacum and Eucalyptus camaldulensis

The expression of cell-wall-targeted Carbohydrate Binding Modules (CBMs) can alter cell wall properties and modulate growth and development in plants such as tobacco and potato. CBM2a identified in xylanase 10A from Cellulomonas fimi is of particular interest for its ability to bind crystalline cellulose. However, its potential for promoting plant growth has not been explored. In this work, we tested the ability of CBM2a to promote growth when expressed using both CaMV35S and a vascular tissue-specific promoter derived from Arabidopsis expansin4 (AtEXP4) in three plant species: Arabidopsis, Nicotiana tabacum and Eucalyptus camaldulensis. In Arabidopsis, the expression of AtEXP4pro:CBM2a showed trends for growth promoting effects including the increase of root and hypocotyl lengths and the enlargements of the vascular xylem area, fiber cells and vessel cells. However, in N. tabacum, the expression of CBM2a under the control of either CaMV35S or AtEXP4 promoter resulted in subtle changes in the plant growth, and the thickness of secondary xylem and vessel and fiber cell sizes were generally reduced in the transgenic lines with AtEXP4pro:CBM2a. In Eucalyptus, while transgenics expressing CaMV35S:CBM2a showed very subtle changes compared to wild type, those transgenics with AtEXP4pro:CBM2a showed increases in plant height, enlargement of xylem areas and xylem fiber and vessel cells. These data provide comparative effects of expressing CBM2a protein in different plant species, and this finding can be applied for plant biomass improvement.

The targeting of starch binding domains from starch synthase III to the cell wall alters cell wall composition and properties

Starch binding domains of starch synthase III from Arabidopsis thaliana (SBD123) binds preferentially to cell wall polysaccharides rather than to starch in vitro. Transgenic plants overexpressing SBD123 in the cell wall are larger than wild type. Cell wall components are altered in transgenic plants. Transgenic plants are more susceptible to digestion than wild type and present higher released glucose content. Our results suggest that the transgenic plants have an advantage for the production of bioethanol in terms of saccharification of essential substrates. The plant cell wall, which represents a major source of biomass for biofuel production, is composed of cellulose, hemicelluloses, pectins and lignin. A potential biotechnological target for improving the production of biofuels is the modification of plant cell walls. This modification is achieved via several strategies, including, among others, altering biosynthetic pathways and modifying the associations and structures of various cell wall components. In this study, we modified the cell wall of A. thaliana by targeting the starch-binding domains of A. thaliana starch synthase III to this structure. The resulting transgenic plants (E8-SDB123) showed an increased biomass, higher levels of both fermentable sugars and hydrolyzed cellulose and altered cell wall properties such as higher laxity and degradability, which are valuable characteristics for the second-generation biofuels industry. The increased biomass and degradability phenotype of E8-SBD123 plants could be explained by the putative cell-wall loosening effect of the in tandem starch binding domains. Based on these results, our approach represents a promising biotechnological tool for reducing of biomass recalcitrance and therefore, the need for pretreatments.

Copy number variation of a gene cluster encoding endopolygalacturonase mediates flesh texture and stone adhesion in peach

Texture is an important attribute affecting consumer perception of fruit quality. Peach melting flesh and flesh adhesion to stone (endocarp) are simply inherited and controlled by the F-M locus on linkage group (LG) 4. Here, we report that two genes encoding endopolygalacturonase (endoPG) in the F-M locus, designated PpendoPGF and PpendoPGM, are associated with the melting flesh and stone adhesion traits. PpendoPGM controls melting flesh while PpendoPGF has pleiotropic effects on both melting flesh and stone adhesion. The F-M locus has three allelic copy number variants of endoPG, H1 (PpendoPGF and PpendoPGM), H2 (PpendoPGM), and H3 (null). The H2 haplotype represents the ancestral one while the H1 and H3 haplotypes are two variants due to duplication and deletion of PpendoPGM, respectively. Accessions with H1H1, H1H2, or H1H3 genotypes show the freestone or semi-freestone and melting flesh phenotype, while both H2H2 and H2H3 accessions have the clingstone and melting flesh phenotype. The H3H3 accessions have the clingstone and non-melting flesh phenotype. Our study not only demonstrates a driving role of gene copy number variations in flesh texture diversification in fruit trees, but also provides a useful diagnostic tool for early seedling selection in peach breeding programmes.

Overexpression of the carbohydrate binding module of strawberry expansin2 in Arabidopsis thaliana modifies plant growth and cell wall metabolism

Several cell wall enzymes are carbohydrate active enzymes that contain a putative Carbohydrate Binding Module (CBM) in their structures. The main function of these non-catalitic modules is to facilitate the interaction between the enzyme and its substrate. Expansins are non-hydrolytic proteins present in the cell wall, and their structure includes a CBM in the C-terminal that bind to cell wall polymers such as cellulose, hemicelluloses and pectins. We studied the ability of the Expansin2 CBM (CBMFaEXP2) from strawberry (Fragaria x ananassa, Duch) to modify the cell wall of Arabidopsis thaliana. Plants overexpressing CBMFaEXP2 were characterized phenotypically and biochemically. Transgenic plants were taller than wild type, possibly owing to a faster growth of the main stem. Cell walls of CBMFaEXP2-expressing plants were thicker and contained higher amount of pectins. Lower activity of a set of enzymes involved in cell wall degradation (PG, β-Gal, β-Xyl) was found, and the expression of the corresponding genes (AtPG, Atβ-Gal, Atβ-Xyl5) was reduced also. In addition, a decrease in the expression of two A. thaliana Expansin genes (AtEXP5 and AtEXP8) was observed. Transgenic plants were more resistant to Botrytis cinerea infection than wild type, possibly as a consequence of higher cell wall integrity. Our results support the hypothesis that the overexpression of a putative CBM is able to modify plant cell wall structure leading to modulation of wall loosening and plant growth. These findings might offer a tool to controlling physiological processes where cell wall disassembly is relevant, such as fruit softening.

Over-expression of AtEXLA2 alters etiolated arabidopsis hypocotyl growth

BACKGROUND AND AIMS

Plant stature and shape are largely determined by cell elongation, a process that is strongly controlled at the level of the cell wall. This is associated with the presence of many cell wall proteins implicated in the elongation process. Several proteins and enzyme families have been suggested to be involved in the controlled weakening of the cell wall, and these include xyloglucan endotransglucosylases/hydrolases (XTHs), yieldins, lipid transfer proteins and expansins. Although expansins have been the subject of much research, the role and involvement of expansin-like genes/proteins remain mostly unclear. This study investigates the expression and function of AtEXLA2 (At4g38400), a member of the expansin-like A (EXLA) family in arabidposis, and considers its possible role in cell wall metabolism and growth.

METHODS

Transgenic plants of Arabidopsis thaliana were grown, and lines over-expressing AtEXLA2 were identified. Plants were grown in the dark, on media containing growth hormones or precursors, or were gravistimulated. Hypocotyls were studied using transmission electron microscopy and extensiometry. Histochemical GUS (β-glucuronidase) stainings were performed.

KEY RESULTS

AtEXLA2 is one of the three EXLA members in arabidopsis. The protein lacks the typical domain responsible for expansin activity, but contains a presumed cellulose-interacting domain. Using promoter::GUS lines, the expression of AtEXLA2 was seen in germinating seedlings, hypocotyls, lateral root cap cells, columella cells and the central cylinder basally to the elongation zone of the root, and during different stages of lateral root development. Furthermore, promoter activity was detected in petioles, veins of leaves and filaments, and also in the peduncle of the flowers and in a zone just beneath the papillae. Over-expression of AtEXLA2 resulted in an increase of >10 % in the length of dark-grown hypocotyls and in slightly thicker walls in non-rapidly elongating etiolated hypocotyl cells. Biomechanical analysis by creep tests showed that AtEXLA2 over-expression may decrease the wall strength in arabidopsis hypocotyls.

CONCLUSIONS

It is concluded that AtEXLA2 may function as a positive regulator of cell elongation in the dark-grown hypocotyl of arabidopsis by possible interference with cellulose metabolism, deposition or its organization.

Cellulose synthesis and its regulation

Cellulose, the most abundant biopolymer synthesized on land, is made of linear chains of ß (1-4) linked D-glucose. As a major structural component of the cell wall, cellulose is important not only for industrial use but also for plant growth and development. Cellulose microfibrils are tethered by other cell wall polysaccharides such as hemicellulose, pectin, and lignin. In higher plants, cellulose is synthesized by plasma membrane-localized rosette cellulose synthase complexes. Despite the recent advances using a combination of molecular genetics, live cell imaging, and spectroscopic tools, many aspects of the cellulose synthesis remain a mystery. In this chapter, we highlight recent research progress towards understanding the mechanism of cellulose synthesis in Arabidopsis.

PtrCel9A6, an endo-1,4-β-glucanase, is required for cell wall formation during xylem differentiation in populus

Endo-1,4-β-glucanases (EGases) are involved in many aspects of plant growth. Our previous study found that an EGase, PtrCel9A6, is specifically expressed in differentiating xylem cells during Populus secondary growth. In this study, the xylem-specific PtrCel9A6 was characterized for its role in xylem differentiation. The EGase is localized on the plasma membrane with catalytic domain toward the outside cell wall, hydrolyzing amorphous cellulose. Suppression of PtrCel9A6 expression caused secondary cell wall defects in xylem cells and significant cellulose reduction in Populus. Heterologous expression of PtrCel9A6 in Arabidopsis enhanced plant growth as well as increased fiber cell length. In addition, introduction of PtrCel9A6 into Arabidopsis resulted in male sterility due to defects in anther dehiscence. Together, these results demonstrate that PtrCel9A6 plays a critical role in remodeling the 1,4-β-glucan chains in the wall matrix and is required for cell wall thickening during Populus xylem differentiation.

A mutation in the expansin-like A2 gene enhances resistance to necrotrophic fungi and hypersensitivity to abiotic stress in Arabidopsis thaliana

Expansins are cell wall loosening agents, known for their endogenous function in cell wall extensibility. The Arabidopsis expansin-like A2 (EXLA2) gene was identified by its down-regulation in response to infection by the necrotrophic pathogen Botrytis cinerea, and by the reduced susceptibility of an exla2 mutant to the same pathogen. The exla2 mutant was equally susceptible to Pseudomonas syringae pv. tomato, but was more resistant to the necrotrophic fungus Alternaria brassicicola, when compared with the wild-type or with transgenic, ectopic EXLA2-overexpressing lines. The exla2 mutants also enhanced tolerance to the phytoprostane-A1 . This suggests that the absence or down-regulation of EXLA2 leads to increased resistance to B. cinerea in a CORONATINE INSENSITIVE 1 (COI1)-dependent manner, and this down-regulation can be achieved by phytoprostane-A1 treatment. EXLA2 is induced significantly by salinity and cold, and by the exogenous application of abscisic acid. The exla2 mutant also showed hypersensitivity towards increased salt and cold, and this hypersensitivity required a functional abscisic acid pathway. The differential temporal expression of EXLA2 and the phenotypes in transgenic plants with altered expression of EXLA2 indicate that plant cell wall structure is an important player during Arabidopsis developmental stages. Our results indicate that EXLA2 appears to be important in response to various biotic and abiotic stresses, particularly in the pathogenesis of necrotrophic pathogens and in the tolerance to abiotic stress.

Bioethanol production from rice straw residues

A rice straw - cellulose utilizing mold was isolated from rotted rice straw residues. The efficient rice straw degrading microorganism was identified as Trichoderma reesei. The results showed that different carbon sources in liquid culture such as rice straw, carboxymethyl cellulose, filter paper, sugar cane bagasse, cotton stalk and banana stalk induced T. reesei cellulase production whereas glucose or Potato Dextrose repressed the synthesis of cellulase. T. reesei cellulase was produced by the solid state culture on rice straw medium. The optimal pH and temperature for T. reesei cellulase production were 6 and 25 °C, respectively. Rice straw exhibited different susceptibilities towards cellulase to their conversion to reducing sugars. The present study showed also that, the general trend of rice straw bioconversion with cellulase was more than the general trend by T. reesei. This enzyme effectively led to enzymatic conversion of acid, alkali and ultrasonic pretreated cellulose from rice straw into glucose, followed by fermentation into ethanol. The combined method of acid pretreatment with ultrasound and subsequent enzyme treatment resulted the highest conversion of lignocellulose in rice straw to sugar and consequently, highest ethanol concentration after 7 days fermentation with S. cerevisae yeast. The ethanol yield in this study was about 10 and 11 g.L(-1).

The carbohydrate-binding module of Fragaria × ananassa expansin 2 (CBM-FaExp2) binds to cell wall polysaccharides and decreases cell wall enzyme activities "in vitro"

A putative carbohydrate binding module (CBM) from strawberry (Fragaria × ananassa Duch.) expansin 2 (CBM-FaExp2) was cloned and the encoding protein was over-expressed in Escherichia coli and purified in order to evaluate its capacity to bind different cell wall polysaccharides "in vitro". The protein CBM-FaExp2 bound to microcrystalline cellulose, xylan and pectin with different affinities (K(ad) = 33.6 ± 0.44 mL g(-1), K(ad) = 11.37 ± 0.87 mL g(-1), K(ad) = 10.4 ± 0.19 mL g(-1), respectively). According to "in vitro" enzyme assays, this CBM is able to decrease the activity of cell wall degrading enzymes such as polygalacturonase, endo-glucanase, pectinase and xylanase, probably because the binding of CBM-FaExp2 to the different substrates interferes with enzyme activity. The results suggest that expansins would bind not only cellulose but also a wide range of cell wall polymers.

Overexpression of two cambium-abundant Chinese fir (Cunninghamia lanceolata) α-expansin genes ClEXPA1 and ClEXPA2 affect growth and development in transgenic tobacco and increase the amount of cellulose in stem cell walls

Expansins are unique plant cell wall proteins that possess the ability to induce immediately cell wall extension in vitro and cell expansion in vivo. To investigate the biological functions of expansins that are abundant in wood-forming tissues, we cloned two expansin genes from the differentiating xylem of Chinese fir (Cunninghamia lanceolata (Lamb.) Hook). Phylogenetic reconstruction indicated that they belong to α-expansin (EXPA), named ClEXPA1 and ClEXPA2. Expression pattern analysis demonstrated that they are preferentially expressed in the cambium region. Overexpression of ClEXPA1 and ClEXPA2 in tobacco plants yielded pleiotropic phenotypes of plant height, stem diameter, leaf number and seed pod. The height and diameter growth of the 35S(pro) :ClEXPA1 and 35S(pro) :ClEXPA2 transgenic plants were increased drastically, exhibiting an enlargement of pith parenchyma cell size. Isolated cell walls of ClEXPA1 and ClEXPA2 overexpressors contained 30%-50% higher cellulose contents than the wild type, accompanied by a thickening of the cell walls in the xylem region. Both ClEXPA1 and ClEXPA2 are involved in plant growth and development, with a partially functional overlap. Expansins are not only able to induce cell expansion in different tissues/organs in vivo, but they also can act as a potential activator during secondary wall formation by directly or indirectly affecting cellulose metabolism, probably in a cell type-dependent manner.

Synthesis, regulation and utilization of lignocellulosic biomass

Increasing the range of fuels and bioproducts that are derived from lignocellulosic biomass and the efficiency at which they are produced hinges on a detailed understanding of the cell wall biosynthetic process. Herein, we review the structure and biosynthesis of lignocellulosic biomass and also highlight recent breakthroughs that demonstrate a complex regulatory system of transcription factors, small interfering RNAs and phosphorylation that ultimately dictate the development of the polyalaminate cell wall. Finally, we provide an update on cases where plant biotechnology has been used to improve lignocellulosic biomass utilization as a second-generation biofuel source.

Bacterial thermostable beta-glucanases as a tool for plant functional genomics

A new strategy for creating experimental models for functional genomics has been proposed. It is based on the expression in transgenic plants of genes from thermophilic bacteria encoding functional analogues of plant proteins with high specific activity and thermal stability. We have validated this strategy by comparing physiological, biochemical and molecular properties of control tobacco plants and transgenic plants expressing genes of beta-glucanases with different substrate specificity. We demonstrate that the expression of bacterial beta-1,3-1,4-glucanase gene exerts no significant influence on tobacco plant metabolism, while the expression of bacterial beta-1,3-glucanase affects plant metabolism only at early stages of growth and development. By contrast, the expression of bacterial beta-1,4-glucanase has a significant effect on transgenic tobacco plant metabolism, namely, it affects plant morphology, the thickness of the primary cell wall, phytohormonal status, and the relative sugar content. We propose a hypothesis of beta-glucanase action as an important factor of genetic regulation of metabolic processes in plants.

Spatial distribution of transcript changes in the maize primary root elongation zone at low water potential

BACKGROUND

Previous work showed that the maize primary root adapts to low Psiw (-1.6 MPa) by maintaining longitudinal expansion in the apical 3 mm (region 1), whereas in the adjacent 4 mm (region 2) longitudinal expansion reaches a maximum in well-watered roots but is progressively inhibited at low Psiw. To identify mechanisms that determine these responses to low Psiw, transcript expression was profiled in these regions of water-stressed and well-watered roots. In addition, comparison between region 2 of water-stressed roots and the zone of growth deceleration in well-watered roots (region 3) distinguished stress-responsive genes in region 2 from those involved in cell maturation.

RESULTS

Responses of gene expression to water stress in regions 1 and 2 were largely distinct. The largest functional categories of differentially expressed transcripts were reactive oxygen species and carbon metabolism in region 1, and membrane transport in region 2. Transcripts controlling sucrose hydrolysis distinguished well-watered and water-stressed states (invertase vs. sucrose synthase), and changes in expression of transcripts for starch synthesis indicated further alteration in carbon metabolism under water deficit. A role for inositols in the stress response was suggested, as was control of proline metabolism. Increased expression of transcripts for wall-loosening proteins in region 1, and for elements of ABA and ethylene signaling were also indicated in the response to water deficit.

CONCLUSION

The analysis indicates that fundamentally different signaling and metabolic response mechanisms are involved in the response to water stress in different regions of the maize primary root elongation zone.

Cellulose-binding domains: cellulose associated-defensive sensing partners?

The cellulose-binding domains (CBDs) in the Phytophthora cellulose-binding elicitor lectin (CBEL) are potent elicitors of plant defence responses. Induction of defence has also been reported in various cellulose-deficient mutants of Arabidopsis thaliana. Based on these observations, we propose a model linking cellulose alteration to defence induction. This integrates the fast increase in cytosolic calcium recorded in response to CBEL, mechano-stimulated calcium uptake mechanisms, and proteins that interact functionally with the cellulose synthase complex. In this context, CBDs emerge as new tools to decipher the signalling cascades that result from cell wall-cellulose perturbations.

Quantification of the CBD-FITC conjugates surface coating on cellulose fibres

Background

Cellulose Binding Domains (CBD) were conjugated with fluorescein isothiocyanate (FITC). The surface concentration of the Binding Domains adsorbed on cellulose fibres was determined by fluorescence image analysis.

Results

For a CBD-FITC concentration of 60 mg/L, a coating fraction of 78% and 110% was estimated for Portucel and Whatman fibres, respectively. For a saturating CBD concentration, using Whatman CF11 fibres, a surface concentration of 25.2 × 10^-13 mol/mm² was estimated, the equivalent to 4 protein monolayers. This result does not imply the existence of several adsorbed protein layers.

Conclusion

It was verified that CBDs were able to penetrate the fibres, according to confocal microscopy and TEM-immunolabelling analysis. The surface concentration of adsorbed CBDs was greater on amorphous fibres (phosphoric acid swollen) than on more crystalline ones (Whatman CF11 and Sigmacell 20).

Promiscuous, non-catalytic, tandem carbohydrate-binding modules modulate the cell-wall structure and development of transgenic tobacco (Nicotiana tabacum) plants

We have compared heterologous expression of two types of carbohydrate binding module (CBM) in tobacco cell walls. These are the promiscuous CBM29 modules (a tandem CBM29-1-2 and its single derivative CBM29-2), derived from a non-catalytic protein1, NCP1, of the Piromyces equi cellulase/hemicellulase complex, and the less promiscuous tandem CBM2b-1-2 from the Cellulomonas fimi xylanase 11A. CBM-labelling studies revealed that CBM29-1-2 binds indiscriminately to every tissue of the wild-type tobacco stem whereas binding of CBM2b-1-2 was restricted to vascular tissue. The promiscuous CBM29-1-2 had much more pronounced effects on transgenic tobacco plants than the less promiscuous CBM2b-1-2. Reduced stem elongation and prolonged juvenility, resulting in delayed flower development, were observed in transformants expressing CBM29-1-2 whereas such growth phenotypes were not observed for CBM2b-1-2 plants. Histological examination and electron microscopy revealed layers of collapsed cortical cells in the stems of CBM29-1-2 plants whereas cellular deformation in the stem cortical cells of CBM2b-1-2 transformants was less severe. Altered cell expansion was also observed in most parts of the CBM29-1-2 stem whereas for the CBM2b-1-2 stem this was observed in the xylem cells only. The cellulose content of the transgenic plants was not altered. These results support the hypothesis that CBMs can modify cell wall structure leading to modulation of wall loosening and plant growth.

The tobacco Cel7 gene promoter is auxin-responsive and locally induced in nematode feeding sites of heterologous plants

Emerging evidence suggests that plant cell-wall-modifying enzymes induced by root-parasitic nematodes play important roles in feeding cell formation. We previously identified a tobacco endo-beta-1,4-glucanase (cellulase) gene, NtCel7, that was strongly induced in both root-knot and cyst nematode feeding cells. To characterize further the developmental and nematode-responsive regulation of NtCel7, we isolated the NtCel7 promoter and analysed its expression over a time course of nematode infection and in response to auxin, gibberellin, ethylene and sucrose in soybean and tomato hairy roots and in Arabidopsis containing the NtCel7 promoter fused to the beta-glucuronidase (GUS) reporter gene. Histochemical analyses of transgenic plant materials revealed that the NtCel7 promoter exhibited a unique organ-specific expression pattern during plant development suggestive of important roles for NtCel7 in both vegetative and reproductive growth. In all plant species tested, strong GUS expression was observed in root tips and lateral root primordia of uninfected roots with weaker expression in the root vasculature. Further analyses of transgenic Arabidopsis plants revealed expression in shoot and root meristems and the vasculature of most organs during plant development. We also determined that the NtCel7 promoter was induced by auxin, but not gibberellin, ethylene or sucrose. Moreover, strong GUS activity was observed in both cyst and root-knot nematode-induced feeding sites in transgenic roots of soybean, tomato and Arabidopsis. The conserved developmental and nematode-responsive expression of the NtCel7 promoter in heterologous plants indicates that motifs of this regulatory element play a fundamental role in regulating NtCel7 gene expression within nematode feeding sites and that this regulation may be mediated by auxin.

Biomimetic engineering of cellulose-based materials

Biomimetics is a field of science that investigates biological structures and processes for their use as models for the development of artificial systems. Biomimetic approaches have considerable potential in the development of new high-performance materials with low environmental impact. The cell walls of different plant species represent complex and highly sophisticated composite materials that can provide inspiration on how to design and fabricate lightweight materials with unique properties. Such materials can provide environmentally compatible solutions in advanced packaging, electronic devices, vehicles and sports equipment. This review gives an overview of the structures and interactions in natural plant cell walls and describes the first attempts towards mimicking them to develop novel biomaterials.

Construction of the bifunctional enzyme cellulase-beta-glucosidase from the hyperthermophilic bacterium Thermotoga maritima

An artificial bifunctional enzyme, cellulase-beta-glucosidase, was prepared by gene fusion from the hyperthermophilic bacterium Thermotoga maritima MSB8. The fusion protein exhibited both cellulase (Cel5C) and beta-glucosidase (BglB) activity when the bglB gene was fused to downstream of cel5C, but not when cel5C was fused to downstream of bglB. The specific activity of the bifunctional enzyme was 70% lower than that of cellulase or beta-glucosidase. The fusion enzyme was purified, and the MW was estimated as 114 kDa. The fusion enzyme displayed optimum cellulase activity at pH 8.0 and 70 degrees C over 30 min, and optimal beta-glucosidase activity at pH 7.0 and 80 degrees C over 30 min.

Cellulose binding domains of a Phytophthora cell wall protein are novel pathogen-associated molecular patterns

The cellulose binding elicitor lectin (CBEL) from Phytophthora parasitica nicotianae contains two cellulose binding domains (CBDs) belonging to the Carbohydrate Binding Module1 family, which is found almost exclusively in fungi. The mechanism by which CBEL is perceived by the host plant remains unknown. The role of CBDs in eliciting activity was investigated using modified versions of the protein produced in Escherichia coli or synthesized in planta through the potato virus X expression system. Recombinant CBEL produced by E. coli elicited necrotic lesions and defense gene expression when injected into tobacco (Nicotiana tabacum) leaves. CBEL production in planta induced necrosis. Site-directed mutagenesis on aromatic amino acid residues located within the CBDs as well as leaf infiltration assays using mutated and truncated recombinant proteins confirmed the importance of intact CBDs to induce defense responses. Tobacco and Arabidopsis thaliana leaf infiltration assays using synthetic peptides showed that the CBDs of CBEL are essential and sufficient to stimulate defense responses. Moreover, CBEL elicits a transient variation of cytosolic calcium levels in tobacco cells but not in protoplasts. These results define CBDs as a novel class of molecular patterns in oomycetes that are targeted by the innate immune system of plants and might act through interaction with the cell wall.

Carbohydrate binding modules: biochemical properties and novel applications

Polysaccharide-degrading microorganisms express a repertoire of hydrolytic enzymes that act in synergy on plant cell wall and other natural polysaccharides to elicit the degradation of often-recalcitrant substrates. These enzymes, particularly those that hydrolyze cellulose and hemicellulose, have a complex molecular architecture comprising discrete modules which are normally joined by relatively unstructured linker sequences. This structure is typically comprised of a catalytic module and one or more carbohydrate binding modules (CBMs) that bind to the polysaccharide. CBMs, by bringing the biocatalyst into intimate and prolonged association with its substrate, allow and promote catalysis. Based on their properties, CBMs are grouped into 43 families that display substantial variation in substrate specificity, along with other properties that make them a gold mine for biotechnologists who seek natural molecular "Velcro" for diverse and unusual applications. In this article, we review recent progress in the field of CBMs and provide an up-to-date summary of the latest developments in CBM applications.

A model plant pathogen from the kingdom Animalia: Heterodera glycines, the soybean cyst nematode

The soybean cyst nematode, Heterodera glycines, adversely affects the production of soybean, Glycine max, in many areas of the world, particularly in the United States, where it is the most economically important soybean pathogen. Despite the availability of hundreds of H. glycines-resistant soybean cultivars, the nematode continues to be a major limiting factor in soybean production. The use of nonhost rotation and resistance are the primary means of reducing losses caused by the nematode, but each of these options has disadvantages. As a subject for study of nematode parasitism and virulence, H. glycines provides a useful model despite its obligately parasitic nature. Its obligately sexual reproduction and ready adaptation to resistant cultivars, formerly referred to as "race shift," presents an excellent opportunity for the study of virulence in nematodes. Recent advances in H. glycines genomics have helped identify putative nematode parasitism genes, which, in turn, will aid in the understanding of nematode pathogenicity and virulence and may provide new targets for engineering nematode resistance.

Expressed sequence tags from the oomycete fish pathogen Saprolegnia parasitica reveal putative virulence factors

Background

The oomycete Saprolegnia parasitica is one of the most economically important fish pathogens. There is a dramatic recrudescence of Saprolegnia infections in aquaculture since the use of the toxic organic dye malachite green was banned in 2002. Little is known about the molecular mechanisms underlying pathogenicity in S. parasitica and other animal pathogenic oomycetes. In this study we used a genomics approach to gain a first insight into the transcriptome of S. parasitica.

Results

We generated 1510 expressed sequence tags (ESTs) from a mycelial cDNA library of S. parasitica. A total of 1279 consensus sequences corresponding to 525944 base pairs were assembled. About half of the unigenes showed similarities to known protein sequences or motifs. The S. parasitica sequences tended to be relatively divergent from Phytophthora sequences. Based on the sequence alignments of 18 conserved proteins, the average amino acid identity between S. parasitica and three Phytophthora species was 77% compared to 93% within Phytophthora. Several S. parasitica cDNAs, such as those with similarity to fungal type I cellulose binding domain proteins, PAN/Apple module proteins, glycosyl hydrolases, proteases, as well as serine and cysteine protease inhibitors, were predicted to encode secreted proteins that could function in virulence. Some of these cDNAs were more similar to fungal proteins than to other eukaryotic proteins confirming that oomycetes and fungi share some virulence components despite their evolutionary distance

Conclusion

We provide a first glimpse into the gene content of S. parasitica, a reemerging oomycete fish pathogen. These resources will greatly accelerate research on this important pathogen. The data is available online through the Oomycete Genomics Database [1].

Origin, distribution and 3D-modeling of Gr-EXPB1, an expansin from the potato cyst nematode Globodera rostochiensis

Southern analysis showed that Gr-EXPB1, a functional expansin from the potato cyst nematode Globodera rostochiensis, is member of a multigene family, and EST data suggest expansins to be present in other plant parasitic nematodes as well. Homology modeling predicted that Gr-EXPB1 domain 1 (D1) has a flat beta-barrel structure with surface-exposed aromatic rings, whereas the 3D structure of Gr-EXPB1-D2 was remarkably similar to plant expansins. Gr-EXPB1 shows highest sequence similarity to two extracellular proteins from saprophytic soil-inhabiting Actinobacteria, and includes a bacterial type II carbohydrate-binding module. These results support the hypothesis that a number of pathogenicity factors of cyst nematodes is of procaryotic origin and were acquired by horizontal gene transfer.

Engineering a bifunctional starch–cellulose cross-bridge protein

Biodegradable starch- and cellulose-based polymers have a range of properties which make them suitable for use in a wide array of biomedical applications ranging from bone replacement to engineering of tissue scaffolds and drug delivery systems. A novel polysaccharide cross-bridging protein was designed which was comprised of a cellulose-binding domain from Clostridium cellulovorans (CBD(clos)) and a starch-binding domain from Aspergillus niger B1 (SBD(Asp)). The two genes were fused in-frame via a synthetic elastin gene to construct a Cellulose/Starch Cross bridging Protein (CSCP). Recombinant CSCP was expressed in Escherichia coli, and successfully refolded from inclusion bodies. CSCP demonstrated cross-bridging ability in different model systems composed of insoluble or soluble starch and cellulose. The aspect that different carbohydrate-binding module maintain their binding capacity over a wide range of conditions, without the need for chemical reactions, makes them attractive domains for designing new classes of chimeric polysaccharide-binding domains which demonstrate potential for use in a wide range of biomaterials.

Cell wall reactive proteins in the coat and wall of maize pollen: potential role in pollen tube growth on the stigma and through the style

The surface of a pollen grain consists of an outermost coat and an underlying wall. In maize (Zea mays L.), the pollen coat contains two major proteins derived from the adjacent tapetum cells in the anthers. One of the proteins is a 35-kDa endoxylanase (Wu, S. S. H., Suen, D. F., Chang, H. C., and Huang, A. H. C. (2002) J. Biol. Chem. 277, 49055-49064). The other protein of 70 kDa was purified to homogeneity and shown to be a beta-glucanase. Its gene sequence and the developmental pattern of its mRNA differ from those of the known beta-glucanases that hydrolyze the callose wall of the microspore tetrad. Mature pollen placed in a liquid medium released about nine major proteins. These proteins were partially sequenced and identified via GenBank trade mark data bases, and some had not been previously reported to be in pollen. They appear to have wall-loosening, structural, and enzymatic functions. A novel pollen wall-bound protein of 17 kDa has a unique pattern of cysteine distribution in its sequence (six tandem repeats of CX3CX10-15) that could chelate cations and form signal-receiving finger motifs. These pollen-released proteins were synthesized in the pollen interior, and their mRNA increased during pollen maturation and germination. They were localized mainly in the pollen tube wall. The pollen shell was isolated and found to contain no detectable proteins. We suggest that the pollen-coat beta-glucanase and xylanase hydrolyze the stigma wall for pollen tube entry and that the pollen secrete proteins to loosen or become new wall constituents of the tube and to break the wall of the transmitting track for tube advance.

A comparative study between an endoglucanase IV and its fused protein complex Cel5-CBM6

The recombinant endoglucanase IV (Cel5; encoded by egIV) of Ruminococcus albus was compared with protein Cel5-CBM6 comprised of Cel5 fused at the C-terminus with the single-cellulose binding domain II (CBM6) of Clostridium stercorarium xylanase A, in order to improve its binding ability. Previous analyses using ball-milled cellulose had suggested that a cellulose binding domain of xylanase A could enhance cellulase activity, especially with insoluble substrates. Comparison of the catalytic activities of Cel5 and Cel5-CBM6 were determined using carboxymethylcellulose, Avicel, and filter paper as substrates. This study confirmed previous findings, and provided further evidence suggesting that Cel5-CBM6 exhibits enhanced activity with insoluble cellulose compared to native Cel5. However, its hydrolytic activity with soluble substrates such as carboxymethylcellulose was comparable to Cel5. For both cellulases, central linkages of cellulooligosaccharides (up to six glucose residues) were found to be the preferred points of cleavage. The rates of hydrolysis with both cellulases increased with cellulooligosaccharide chain length, and at least three consecutive glycosyl residues seemed to be necessary for hydrolysis to occur. Cel5-CBM6 showed a higher affinity for cellulose substrates than did Cel5, as demonstrated by transmission electron microscopy. Taken together, these results suggest that CBM6 increases the affinity of Cel5 for insoluble substrates, and this increased binding capacity seems to result in increased catalytic activity.