Methods for Structural Characterization of the Products of Cellulose- and Xyloglucan-Hydrolyzing Enzymes

Sweet Secrets: Exploring Novel Glycans and Glycoconjugates in the Extracellular Polymeric Substances of "Candidatus Accumulibacter"

Biological wastewater treatment relies on microorganisms that grow as flocs, biofilms, or granules for efficient separation of biomass from cleaned water. This biofilm structure emerges from the interactions between microbes that produce, and are embedded in, extracellular polymeric substances (EPS). The true composition and structure of the EPS responsible for dense biofilm formation are still obscure. We conducted a bottom-up approach utilizing advanced glycomic techniques to explore the glycan diversity in the EPS from a highly enriched "Candidatus Accumulibacter" granular sludge. Rare novel sugar monomers such as N-Acetylquinovosamine (QuiNAc) and 2-O-Methylrhamnose (2-OMe-Rha) were identified to be present in the EPS of both enrichments. Further, a high diversity in the glycoprotein structures of said EPS was identified by means of lectin based microarrays. We explored the genetic potential of "Ca. Accumulibacter" high quality metagenome assembled genomes (MAGs) to showcase the shortcoming of top-down bioinformatics based approaches at predicting EPS composition and structure, especially when dealing with glycans and glycoconjugates. This work suggests that more bottom-up research is necessary to understand the composition and complex structure of EPS in biofilms since genome based inference cannot directly predict glycan structures and glycoconjugate diversity.

Structural characterization and biological activity of an α-glucan from the mollusk Marcia hiantina (Lamarck, 1818)

Marcia hiantina (Mollusca, Bivalvia) (Lamarck, 1818), is an edible clam mainly distributed along the tropical coastal regions. Recent researches have demonstrated that clams can possess compounds, including polysaccharides, with a wide range of biological actions including antioxidant, immunomodulatory and antitumor activities. Here an α-glucan was isolated from M. hiantina by hot water, purified by anion exchange chromatography, and its structure was characterized by a combination of multiple nuclear magnetic resonance (NMR) methods (1D 1H, 1H-1H COSY, 1H-1H TOCSY, 1H-1H NOESY, 1H-13C HSQC and 1H-13C HSQC-NOESY spectra), gas chromatography-mass spectrometry, and high performance size exclusion chromatography (HPSEC). The analysis from NMR, monosaccharide composition, methylation analyses and HPSEC combined with multi-angle light scattering (MALS) of M. hiantina-derived α-glycan confirmed a branched polysaccharide exclusively composed of glucose (Glc), mostly 4-linked in its backbone, branched occasionally at 6-positions, and having a molecular weight of ~ 570 kDa. The mollusk α-glucan was subjected to four cell-based assays: (i) viability of three cell lines (RAW264.7, HaCaT, and HT-29), (ii) activity on lipopolysaccharide (LPS)-induced prostaglandin production in RAW264.7 cells, (iii) inhibitory activities of in H2O2- and LPS-induced reactive oxygen species (ROS) production in HMC3 cells, and (iv) HaCaT cell proliferation. Results have indicated no cytotoxicity, potent inhibition of both H2O2- and LPS-induced ROS, and potent cell proliferative activity.

Algal Polysaccharides-Based Hydrogels: Extraction, Synthesis, Characterization, and Applications

Hydrogels are three-dimensional crosslinked hydrophilic polymer networks with great potential in drug delivery, tissue engineering, wound dressing, agrochemicals application, food packaging, and cosmetics. However, conventional synthetic polymer hydrogels may be hazardous and have poor biocompatibility and biodegradability. Algal polysaccharides are abundant natural products with biocompatible and biodegradable properties. Polysaccharides and their derivatives also possess unique features such as physicochemical properties, hydrophilicity, mechanical strength, and tunable functionality. As such, algal polysaccharides have been widely exploited as building blocks in the fabrication of polysaccharide-based hydrogels through physical and/or chemical crosslinking. In this review, we discuss the extraction and characterization of polysaccharides derived from algae. This review focuses on recent advances in synthesis and applications of algal polysaccharides-based hydrogels. Additionally, we discuss the techno-economic analyses of chitosan and acrylic acid-based hydrogels, drawing attention to the importance of such analyses for hydrogels. Finally, the future prospects of algal polysaccharides-based hydrogels are outlined.

A New, Quick, and Simple Protocol to Evaluate Microalgae Polysaccharide Composition

In this work, a new methodological approach, relying on the high specificity of enzymes in a complex mixture, was developed to estimate the composition of bioactive polysaccharides produced by microalgae, directly in algal cultures. The objective was to set up a protocol to target oligomers commonly known to be associated with exopolysaccharides' (EPS) nutraceutical and pharmaceutical activities (i.e., rhamnose, fucose, acidic sugars, etc.) without the constraints classically associated with chromatographic methods, while maintaining a resolution sufficiently high to enable their monitoring in the culture system. Determination of the monosaccharide content required the application of acid hydrolysis (2 M trifluoroacetic acid) followed by NaOH (2 M) neutralization. Quantification was then carried out directly on the fresh hydrolysate using enzyme kits corresponding to the main monosaccharides in a pre-determined composition of the polysaccharides under analysis. Initial results showed that the enzymes were not sensitive to the presence of TFA and NaOH, so the methodology could be carried out on fresh hydrolysate. The limits of quantification of the method were estimated as being in the order of the log of nanograms of monosaccharides per well, thus positioning it among the chromatographic methods in terms of analytical performance. A comparative analysis of the results obtained by the enzymatic method with a reference method (high-performance anion-exchange chromatography) confirmed good recovery rates, thus validating the closeness of the protocol. Finally, analyses of raw culture media were carried out and compared to the results obtained in miliQ water; no differences were observed. The new approach is a quick, functional analysis method allowing routine monitoring of the quality of bioactive polysaccharides in algal cultures grown in photobioreactors.

Chronic exposure to low doses of ionizing radiation impacts the processing of glycoprotein N-linked glycans in Medaka (Oryzias latipes)

PURPOSE

Ionizing radiation is found naturally in the environment. Low doses of IR may have beneficial applications, yet there is also potential for detrimental long-term health effects. Impacts following exposure to low levels of IR have been refractory to identification and quantification. Glycoprotein glycosylation is vital to cell-cell communication and organismal function, and sensitive to changes in an organism's macro- and cellular environment. We investigated whether accumulated low doses of IR (LoDIR) affect the N-linked glycoprotein glycans using Medaka fish (Oryzias latipes).

MATERIALS AND METHODS

State-of-the-art methods in radiation exposure and glycan analysis were applied to study N-glycan changes after 190 day exposure at three different rates of gamma irradiation (2.25, 21.01, and 204.3 mGy/day) in wild-type adult Medaka. Tissue N-glycans were analyzed following enzymatic release from extracted proteins.

RESULTS

N-linked glycan profiles are dominated by complex type N-glycans modified with terminal sialic acid and core fucose. Fucosylation and sialylation of N-linked glycoprotein glycans are affected by LoDIR and a subset of N-glycans are involved in the organismal radio-response.

CONCLUSION

This is the first indication that the glycome can be interrogated for biomarkers that report the impact of chronic exposure to environmental stressors, such as low-level IR.

The unusual cell wall of the Lyme disease spirochaete Borrelia burgdorferi is shaped by a tick sugar

Peptidoglycan-a mesh sac of glycans that are linked by peptides-is the main component of bacterial cell walls. Peptidoglycan provides structural strength, protects cells from osmotic pressure and contributes to shape. All bacterial glycans are repeating disaccharides of N-acetylglucosamine (GlcNAc) β-(1-4)-linked to N-acetylmuramic acid (MurNAc). Borrelia burgdorferi, the tick-borne Lyme disease pathogen, produces glycan chains in which MurNAc is occasionally replaced with an unknown sugar. Nuclear magnetic resonance, liquid chromatography-mass spectroscopy and genetic analyses show that B. burgdorferi produces glycans that contain GlcNAc-GlcNAc. This unusual disaccharide is chitobiose, a component of its chitinous tick vector. Mutant bacteria that are auxotrophic for chitobiose have altered morphology, reduced motility and cell envelope defects that probably result from producing peptidoglycan that is stiffer than that in wild-type bacteria. We propose that the peptidoglycan of B. burgdorferi probably evolved by adaptation to obligate parasitization of a tick vector, resulting in a biophysical cell-wall alteration to withstand the atypical torque associated with twisting motility.

Polysaccharide length affects mycobacterial cell shape and antibiotic susceptibility

Bacteria control the length of their polysaccharides, which can control cell viability, physiology, virulence, and immune evasion. Polysaccharide chain length affects immunomodulation, but its impact on bacterial physiology and antibiotic susceptibility was unclear. We probed the consequences of truncating the mycobacterial galactan, an essential linear polysaccharide of about 30 residues. Galactan covalently bridges cell envelope layers, with the outermost cell wall linkage point occurring at residue 12. Reducing galactan chain length by approximately half compromises fitness, alters cell morphology, and increases the potency of hydrophobic antibiotics. Systematic variation of the galactan chain length revealed that it determines periplasm size. Thus, glycan chain length can directly affect cellular physiology and antibiotic activity, and mycobacterial glycans, not proteins, regulate periplasm size.

Oligosaccharides and Complex Carbohydrates: A New Paradigm for Cranberry Bioactivity

Cranberry is a well-known functional food, but the compounds directly responsible for many of its reported health benefits remain unidentified. Complex carbohydrates, specifically xyloglucan and pectic oligosaccharides, are the newest recognized class of biologically active compounds identified in cranberry materials. Cranberry oligosaccharides have shown similar biological properties as other dietary oligosaccharides, including effects on bacterial adhesion, biofilm formation, and microbial growth. Immunomodulatory and anti-inflammatory activity has also been observed. Oligosaccharides may therefore be significant contributors to many of the health benefits associated with cranberry products. Soluble oligosaccharides are present at relatively high concentrations (~20% w/w or greater) in many cranberry materials, and yet their possible contributions to biological activity have remained unrecognized. This is partly due to the inherent difficulty of detecting these compounds without intentionally seeking them. Inconsistencies in product descriptions and terminology have led to additional confusion regarding cranberry product composition and the possible presence of oligosaccharides. This review will present our current understanding of cranberry oligosaccharides and will discuss their occurrence, structures, ADME, biological properties, and possible prebiotic effects for both gut and urinary tract microbiota. Our hope is that future investigators will consider these compounds as possible significant contributors to the observed biological effects of cranberry.

Structural features and rheological behavior of a water-soluble polysaccharide extracted from the seeds of Plantago ciliata Desf

A water-soluble polysaccharide (PSPC) was extracted from the seeds of Plantago ciliata Desf., a spontaneous Algerian Saharan plant by a hot aqueous extraction then purified by successive ethanolic precipitations. The final extraction yield for PSPC was close to 18.6% (w/v). PSPC was then investigated regarding its global composition, structural features and rheological properties. PSPC is a neutral arabinoxylan, composed of a β-(1,3)/β-(1,4)-d-xylan backbone with side chains of Xylp, and Araf residues attached in O-2 and O-3 positions. The macromolecular characteristics of PSPC in water was determined by SEC/MALLS, with a high molecular weight (Mw) of 700 kDa, a low polydispersity index (PDI) of 1.47 and an intrinsic viscosity [η] close to 157 mL/g. PSPC showed a pseudoplastic behavior in semi-dilute media and the critical overlay concentration (C*) was estimated around 0.32-0.37% (w/v). This current research has supplied original structural information on a new arabinoxylan which could be particularly useful as a novel source of soluble fiber belonging to psyllium.

Comprehensive Monosaccharide Composition Analysis of Insoluble Polysaccharides by Permethylation To Produce Methyl Alditol Derivatives for Gas Chromatography/Mass Spectrometry

Knowledge of the monosaccharide composition of plant and microbial cell wall polysaccharides is critical for the understanding of polysaccharide structure and function. Differences in the hydrolytic stability of the glycosidic bonds and in the susceptibility of monosaccharides to acid-catalyzed degradation cause inconsistency of signal response in the common glycosyl composition methods. In addition, many polysaccharides are insoluble, partially soluble, or form highly viscous gels in water, and this also hinders or even prevents detection by traditional methods. As a result, currently available methods for monosaccharide composition analysis lack accuracy and are limited to the soluble portions of biological samples or expose the polysaccharides to very harsh conditions, resulting in loss of less stable residues. Here we present a new approach to accomplish the monosaccharide composition analysis of polysaccharides, including those that are not or sparingly soluble, based on permethylation in DMSO as the initial derivatization step. Our key finding is that the permethylation solubilizes the polysaccharide before the hydrolysis step, so that differences in solubility are no longer a factor in the efficiency of the acid-catalyzed depolymerization. After the hydrolysis, the partially methylated monosaccharides are reduced to alditols and remethylated for GC/MS analysis. In addition to enabling composition analysis of insoluble polysaccharides, this method also has the advantages that it is comprehensive, allowing quantification of all types of sugars, including uronic acids, on the same column and gives consistent response factors for different monosaccharide classes.

Comparative Structural and Antigenic Characterization of Genetically Distinct Flavobacterium psychrophilum O-Polysaccharides

Little is known about the underlying basis of serotype specificity among strains of Flavobacterium psychrophilum, the agent of rainbow trout fry syndrome and bacterial cold-water disease. The identification of different heat-stable O-serotypes among strains of this gram-negative pathogen does, however, suggest structural variations in the O-polysaccharide (O-PS) moiety of cell surface lipopolysaccharide (LPS). A trisaccharide composed of L-rhamnose (L-Rha), 2-acetamido-2-deoxy-L-fucose (L-FucNAc) and 2-acetamido-4-R-2,4-dideoxy-D-quinovose (D-Qui2NAc4NR), where R represents a dihydroxyhexanamido derivative, was previously identified as the repeating unit of Fp CSF259-93 O-PS. Interestingly, the O-PS gene cluster of this strain and that of Fp 950106-1/1, which belongs to a different O-serotype, are identical except for wzy, which encodes the putative polymerase that links trisaccharide repeats into O-PS chains. We have now found from results of glycosyl composition analysis and high-resolution nuclear magnetic resonance, that the linkage of D-Qui2NAc4NR to L-Rha, which is α1-2 for Fp CSF259-93 versus β1-3 for Fp 950106-1/1, is the only structural difference between O-PS from these strains. The corresponding difference in O-serotype specificity was established from the reactions of rabbit and trout anti-F. psychrophilum antibody with purified O-PS and LPS. Moreover, LPS-based differences in antigenicity were noted between strains with O-PS loci identical to those of Fp CSF259-93 or Fp 950106-1/1, except for the genes predicted to direct synthesis of different R-groups in Qui2NAc4NR. The findings provide a framework for defining the genetic basis of O-PS structure and antigenicity and suggest that the repertoire of F. psychrophilum O-serotypes extends beyond what is presently recognized from serological studies of this important fish pathogen.

Structural characterization and antioxidant activity of water-soluble polysaccharides from the Tunisian brown seaweed Cystoseira compressa

A fucoidan (CCF) and a sodium alginate (CCSA) were extracted and purified from the Tunisian brown seaweed Cystoseira compressa. CCF was a highly sulfated heterogalactofucan composed of α-(1→3), α-(1→4)-linked l-Fucp as main backbone which could be highly branched (31.84%) at O-3 and O-4 positions of α-(1→4)-l-Fucp and α-(1→3)-l-Fucp by terminal monosaccharides and side chains such as terminal α-l-Fucp, terminal β-d-Galp, β-d-Galp-(1→3)-α-l-Fucp and β-d-Galp-(1→4)-α-l-Fucp. The ratio of α-(1→3)/α-(1→4) linkages was estimated at 3.86:1. CCSA was characterized by HPAEC-PAD, GC/MS-EI, ATR-FTIR, and 1H-NMR. The M/G ratio was M/G = 0.77, indicating that CCSA respectively contained 44% and 56% of mannuronic and guluronic acids. The values of FGG, FMM, FGM (or FMG) blocks as well as the parameter η were estimated. The two polysaccharides exhibited effective antioxidant activities by ferrous ion chelation, ferric ion reduction and DPPH radical-scavenging, outlining their potentials as natural additives.

“Pillaring Effects” in Cross-Linked Cellulose Biopolymers: A Study of Structure and Properties

Modified cellulose materials (CLE-4, CLE-1, and CLE-0.5) were prepared by cross-linking with epichlorohydrin (EP), where the products display variable structure, morphology, and thermal stability. Adsorptive probes such as nitrogen gas and phenolic dyes in aqueous solution reveal that cross-linked cellulose has greater accessible surface area (SA) than native cellulose. The results also reveal that the SA of cross-linked cellulose increased with greater EP content, except for CLE-0.5. The attenuation of SA for CLE-0.5 may relate to surface grafting onto cellulose beyond the stoichiometric cellulose and EP ratio since ca. 30% of the hydroxyl groups of cellulose are accessible for cross-linking reaction due to its tertiary fibril nature. Scanning electron microscopy (SEM) results reveal the variable surface roughness and fibre domains of cellulose due to cross-linking. X-ray diffraction (XRD) and 13C NMR spectroscopy indicate that cellulose adopts a one-chain triclinic unit cell structure (P1 space group) with gauche-trans (gt) and trans-gauche (tg) conformations of the glucosyl linkages and hydroxymethyl groups. The structural characterization results reveal that cross-linking of cellulose occurs at the amorphous domains. By contrast, the crystalline domains are preserved according to similar features in the XRD, FTIR, and 13C NMR spectra of cellulose and its cross-linked forms. This study contributes to an improved understanding of the role of cross-linking of native cellulose in its structure and functional properties. Cross-linked cellulose has variable surface functionality, structure, and textural properties that contribute significantly to their unique physicochemical properties over its native form.

Two-Dimensional High-Throughput Endo-Enzyme Screening Assays Based on Chromogenic Polysaccharide Hydrogel and Complex Biomass Substrates

In this chapter, we present a two-dimensional approach for high-throughput screening of endo-cellulases as well as other endo-acting enzymes. The method is based on chromogenic substrates, produced either from purified or complex material, providing valuable information about enzyme activity toward its target as well as that same target in a context of complex natural material normally encountered in bioindustrial settings. The enzymes that can be tested using this assay can be from virtually any source: in purified form, directly from microbial cultures or even from raw materials, enabling study of the interplay between enzyme mixtures such as synergistic or inhibitory effects. By using the method of analysis described in this chapter, enzymes can be screened and evaluated quickly and information pertinent to both the inherent properties of the enzyme itself as well as predictions about its performance on complex biomass samples can be obtained.

RElative QUantitation Inferred by Evaluating Mixtures (REQUIEM)

Motivated by the lack of easily implementable and generally applicable strategies to increase and assess data accuracy, we devised a novel label-free approach, termed REQUIEM, to address challenges in relative quantitation. For comparing the relative amounts of analytes in two samples, a mixture is prepared from aliquots of the samples, and the samples and the mixture are analyzed in parallel according to the intended workflow. Processing of the resulting data using the REQUIEM algorithm yields unbiased analyte fold-changes and associated statistics, allowing several types of errors to be diagnosed or eliminated. Extensive simulations and analysis of carefully prepared standard samples demonstrated the rigorous foundations of REQUIEM. We applied REQUIEM to several real-world analytical techniques and workflows, notably to tandem mass spectrometry analysis by using isomeric oligosaccharides as test analytes. We conclude that REQUIEM can reveal inaccuracies in the data that are difficult to identify by using traditional approaches.

Structural characterization and rheological behavior of a heteroxylan extracted from Plantago notata Lagasca (Plantaginaceae) seeds

Plantago notata (Plantaginaceae) is a spontaneous plant from Septentrional Algerian Sahara currently used by traditional healers to treat stomach disorders, inflammations or wound healing. A water-soluble polysaccharide, called PSPN (PolySaccharide fraction from Plantago Notata), was extracted and purified from the seeds of this semi-arid plant. The structural features of this mucilage were evaluated by colorimetric assays, Fourier transformed infrared spectroscopy (FT-IR), gas chromatography coupled to mass spectrometry (GC/MS) and ¹H/¹³C Nuclear Magnetic Resonance (NMR) spectroscopy. PSPN is a heteroxylan with a backbone composed of β-(1,3)-d-Xylp and β-(1,4)-d-Xylp highly branched, through (O)-2 and (O)-3 positions of β-(1,4)-d-Xylp by various side chains and terminal monosaccharides such as α-l-Araf-(1,3)-β-d-Xylp, β-d-Xylp-(1,2)-β-d-Xylp, terminal Xylp or terminal Araf. The physico-chemical and rheological analysis of this polysaccharide in dilute and semi diluted regimes showed that PSPN exhibites a molecular weight of 2.3×10⁶g/mol and a pseudoplastic behavior.

Glycomic and glycoproteomic analysis of glycoproteins-a tutorial

The structural analysis of glycoproteins is a challenging endeavor and is under steadily increasing demand, but only a very limited number of labs have the expertise required to accomplish this task. This tutorial is aimed at researchers from the fields of molecular biology and biochemistry that have discovered that glycoproteins are important in their biological research and are looking for the tools to elucidate their structure. It provides brief descriptions of the major and most common analytical techniques used in glycomics and glycoproteomics analysis, including explanations of the rationales for individual steps and references to published literature containing the experimental details necessary to carry out the analyses. Glycomics includes the comprehensive study of the structure and function of the glycans expressed in a given cell or organism along with identification of all the genes that encode glycoproteins and glycosyltransferases. Glycoproteomics which is subset of both glycomics and proteomics is the identification and characterization of proteins bearing carbohydrates as posttranslational modification. This tutorial is designed to ease entry into the glycomics and glycoproteomics field for those without prior carbohydrate analysis experience.

Glycomic and glycoproteomic analysis of glycoproteins-a tutorial

The structural analysis of glycoproteins is a challenging endeavor and is under steadily increasing demand, but only a very limited number of labs have the expertise required to accomplish this task. This tutorial is aimed at researchers from the fields of molecular biology and biochemistry that have discovered that glycoproteins are important in their biological research and are looking for the tools to elucidate their structure. It provides brief descriptions of the major and most common analytical techniques used in glycomics and glycoproteomics analysis, including explanations of the rationales for individual steps and references to published literature containing the experimental details necessary to carry out the analyses. Glycomics includes the comprehensive study of the structure and function of the glycans expressed in a given cell or organism along with identification of all the genes that encode glycoproteins and glycosyltransferases. Glycoproteomics which is subset of both glycomics and proteomics is the identification and characterization of proteins bearing carbohydrates as posttranslational modification. This tutorial is designed to ease entry into the glycomics and glycoproteomics field for those without prior carbohydrate analysis experience.

Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2011-2012

This review is the seventh update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2012. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, and fragmentation are covered in the first part of the review and applications to various structural types constitute the remainder. The main groups of compound are oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:255-422, 2017.

Nondestructive, real-time determination and visualization of cellulose, hemicellulose and lignin by luminescent oligothiophenes

Enabling technologies for efficient use of the bio-based feedstock are crucial to the replacement of oil-based products. We investigated the feasibility of luminescent conjugated oligothiophenes (LCOs) for non-destructive, rapid detection and quality assessment of lignocellulosic components in complex biomass matrices. A cationic pentameric oligothiophene denoted p-HTEA (pentamer hydrogen thiophene ethyl amine) showed unique binding affinities to cellulose, lignin, hemicelluloses, and cellulose nanofibrils in crystal, liquid and paper form. We exploited this finding using spectrofluorometric methods and fluorescence confocal laser scanning microscopy, for sensitive, simultaneous determination of the structural and compositional complexities of native lignocellulosic biomass. With exceptional photostability, p-HTEA is also demonstrated as a dynamic sensor for real-time monitoring of enzymatic cellulose degradation in cellulolysis. These results demonstrate the use of p-HTEA as a non-destructive tool for the determination of cellulose, hemicellulose and lignin in complex biomass matrices, thereby aiding in the optimization of biomass-converting technologies.

Function of Succinoglycan Polysaccharide in Sinorhizobium meliloti Host Plant Invasion Depends on Succinylation, Not Molecular Weight

The acidic polysaccharide succinoglycan produced by the rhizobial symbiont Sinorhizobium meliloti 1021 is required for this bacterium to invade the host plant Medicago truncatula and establish a nitrogen-fixing symbiosis. S. meliloti mutants that cannot make succinoglycan cannot initiate invasion structures called infection threads in plant root hairs. S. meliloti exoH mutants that cannot succinylate succinoglycan are also unable to form infection threads, despite the fact that they make large quantities of succinoglycan. Succinoglycan produced by exoH mutants is refractory to cleavage by the glycanases encoded by exoK and exsH, and thus succinoglycan produced by exoH mutants is made only in the high-molecular-weight (HMW) form. One interpretation of the symbiotic defect of exoH mutants is that the low-molecular-weight (LMW) form of succinoglycan is required for infection thread formation. However, our data demonstrate that production of the HMW form of succinoglycan by S. meliloti 1021 is sufficient for invasion of the host M. truncatula and that the LMW form is not required. Here, we show that S. meliloti strains deficient in the exoK- and exsH-encoded glycanases invade M. truncatula and form a productive symbiosis, although they do this with somewhat less efficiency than the wild type. We have also characterized the polysaccharides produced by these double glycanase mutants and determined that they consist of only HMW succinoglycan and no detectable LMW succinoglycan. This demonstrates that LMW succinoglycan is not required for host invasion. These results suggest succinoglycan function is not dependent upon the presence of a small, readily diffusible form.

Sinorhizobium meliloti is a bacterium that forms a beneficial symbiosis with legume host plants. S. meliloti and other rhizobia convert atmospheric nitrogen to ammonia, a nutrient source for the host plant. To establish the symbiosis, rhizobia must invade plant roots, supplying the proper signals to prevent a plant immune response during invasion. A polysaccharide, succinoglycan, produced by S. meliloti is required for successful invasion. Here, we show that the critical feature of succinoglycan that allows infection to proceed is the attachment of a “succinyl” chemical group and that the chain length of succinoglycan is much less important for its function. We also show that none of the short-chain versions of succinoglycan is produced in the absence of two chain-cleaving enzymes.

Use of Nanostructure-Initiator Mass Spectrometry to Deduce Selectivity of Reaction in Glycoside Hydrolases

Chemically synthesized nanostructure-initiator mass spectrometry (NIMS) probes derivatized with tetrasaccharides were used to study the reactivity of representative Clostridium thermocellum β-glucosidase, endoglucanases, and cellobiohydrolase. Diagnostic patterns for reactions of these different classes of enzymes were observed. Results show sequential removal of glucose by the β-glucosidase and a progressive increase in specificity of reaction from endoglucanases to cellobiohydrolase. Time-dependent reactions of these polysaccharide-selective enzymes were modeled by numerical integration, which provides a quantitative basis to make functional distinctions among a continuum of naturally evolved catalytic properties. Consequently, our method, which combines automated protein translation with high-sensitivity and time-dependent detection of multiple products, provides a new approach to annotate glycoside hydrolase phylogenetic trees with functional measurements.

A new versatile microarray-based method for high throughput screening of carbohydrate-active enzymes

Carbohydrate-active enzymes have multiple biological roles and industrial applications. Advances in genome and transcriptome sequencing together with associated bioinformatics tools have identified vast numbers of putative carbohydrate-degrading and -modifying enzymes including glycoside hydrolases and lytic polysaccharide monooxygenases. However, there is a paucity of methods for rapidly screening the activities of these enzymes. By combining the multiplexing capacity of carbohydrate microarrays with the specificity of molecular probes, we have developed a sensitive, high throughput, and versatile semiquantitative enzyme screening technique that requires low amounts of enzyme and substrate. The method can be used to assess the activities of single enzymes, enzyme mixtures, and crude culture broths against single substrates, substrate mixtures, and biomass samples. Moreover, we show that the technique can be used to analyze both endo-acting and exo-acting glycoside hydrolases, polysaccharide lyases, carbohydrate esterases, and lytic polysaccharide monooxygenases. We demonstrate the potential of the technique by identifying the substrate specificities of purified uncharacterized enzymes and by screening enzyme activities from fungal culture broths.

A new generation of versatile chromogenic substrates for high-throughput analysis of biomass-degrading enzymes

BACKGROUND

Enzymes that degrade or modify polysaccharides are widespread in pro- and eukaryotes and have multiple biological roles and biotechnological applications. Recent advances in genome and secretome sequencing, together with associated bioinformatic tools, have enabled large numbers of carbohydrate-acting enzymes to be putatively identified. However, there is a paucity of methods for rapidly screening the biochemical activities of these enzymes, and this is a serious bottleneck in the development of enzyme-reliant bio-refining processes.

RESULTS

We have developed a new generation of multi-coloured chromogenic polysaccharide and protein substrates that can be used in cheap, convenient and high-throughput multiplexed assays. In addition, we have produced substrates of biomass materials in which the complexity of plant cell walls is partially maintained.

CONCLUSIONS

We show that these substrates can be used to screen the activities of glycosyl hydrolases, lytic polysaccharide monooxygenases and proteases and provide insight into substrate availability within biomass. We envisage that the assays we have developed will be used primarily for first-level screening of large numbers of putative carbohydrate-acting enzymes, and the assays have the potential to be incorporated into fully or semi-automated robotic enzyme screening systems.