Polysaccharide lyases: recent developments as biotechnological tools

Polysaccharide lyases, which are polysaccharide cleavage enzymes, act mainly on anionic polysaccharides. Produced by prokaryote and eukaryote organisms, these enzymes degrade (1,4) glycosidic bond by a beta elimination mechanism and have unsaturated oligosaccharides as major products. New polysaccharides are cleaved only by their specific polysaccharide lyases. From anionic polysaccharides controlled degradations, various biotechnological applications were investigated. This review catalogues the degradation of bacterial, plant and animal polysaccharides (neutral and anionic) by this family of carbohydrate acting enzymes.     

Carbohydrate microarrays for the recognition of cross-reactive molecular markers of microbes and host cells

We describe here the development of a carbohydrate-based microarray to extend the scope of biomedical research on carbohydrate-mediated molecular recognition and anti-infection responses. We have demonstrated that microbial polysaccharides can be immobilized on a surface-modified glass slide without chemical conjugation. With this procedure, a large repertoire of microbial antigens (approximately 20,000 spots) can be patterned on a single micro-glass slide, reaching the capacity to include most common pathogens. Glycoconjugates of different structural characteristics are shown here to be applicable for microarray fabrication, extending the repertoires of diversity and complexity of carbohydrate microarrays. The printed microarrays can be air-dried and stably stored at room temperature for long periods of time. In addition, the system is highly sensitive, allowing simultaneous detection of a broad spectrum of antibody specificities with as little as a few microliters of serum specimen. Finally, the potential of carbohydrate microarrays is demonstrated by the discovery of previously undescribed cellular markers, Dex-Ids.     

家蚕半乳糖凝集素BmGalectin-4的表达、纯化及性质分析

【目的】鉴定一种新的家蚕Bombyx mori半乳糖凝集素(galectin)基因,分析其序列和结构特征,测定其在微生物感染后的表达变化,分析其重组表达蛋白与微生物及微生物表面多糖分子的结合特性。【方法】利用TBlastN从家蚕基因组数据库中搜索得到一种新的半乳糖凝集素基因,命名为BmGalectin-4。利用生物信息学分析其序列和结构特征,用半定量RT-PCR检测家蚕分别感染病原菌绿脓杆菌Pseudomonas aeruginosa、金黄色葡萄球菌Staphylococcus aureus和白色念珠菌Candidiasis albicans后BmGalectin-4在不同组织中的表达变化,采用原核表达技术对该基因进行重组表达,并利用亲和层析得到纯化的蛋白。通过ELISA检测BmGalectin-4与细菌和真菌的结合;通过Western blot检测它与多糖的结合。【结果】序列分析显示,BmGalectin-4是一种串联重复型半乳糖凝集素,含有2个糖识别结构域,其结构非常保守。RT-PCR检测表明,BmGalectin-4在家蚕脂肪体、血细胞和中肠中都有表达,且感染细菌和真菌后其表达有显著变化。纯化的重组BmGalectin-4与革兰氏阳性菌、阴性菌和真菌有较强的结合,与微生物表面多糖的结合试验表明其识别有较高的特异性。【结论】BmGalectin-4 是一个典型的串联重复型半乳糖凝集素,可能参与家蚕对病原微生物的免疫防御反应。本研究为进一步研究昆虫中半乳糖凝集素的功能奠定了基础。     

Capturing single cell genomes of active polysaccharide degraders: an unexpected contribution of Verrucomicrobia

Microbial hydrolysis of polysaccharides is critical to ecosystem functioning and is of great interest in diverse biotechnological applications, such as biofuel production and bioremediation. Here we demonstrate the use of a new, efficient approach to recover genomes of active polysaccharide degraders from natural, complex microbial assemblages, using a combination of fluorescently labeled substrates, fluorescence-activated cell sorting, and single cell genomics. We employed this approach to analyze freshwater and coastal bacterioplankton for degraders of laminarin and xylan, two of the most abundant storage and structural polysaccharides in nature. Our results suggest that a few phylotypes of Verrucomicrobia make a considerable contribution to polysaccharide degradation, although they constituted only a minor fraction of the total microbial community. Genomic sequencing of five cells, representing the most predominant, polysaccharide-active Verrucomicrobia phylotype, revealed significant enrichment in genes encoding a wide spectrum of glycoside hydrolases, sulfatases, peptidases, carbohydrate lyases and esterases, confirming that these organisms were well equipped for the hydrolysis of diverse polysaccharides. Remarkably, this enrichment was on average higher than in the sequenced representatives of Bacteroidetes, which are frequently regarded as highly efficient biopolymer degraders. These findings shed light on the ecological roles of uncultured Verrucomicrobia and suggest specific taxa as promising bioprospecting targets. The employed method offers a powerful tool to rapidly identify and recover discrete genomes of active players in polysaccharide degradation, without the need for cultivation.     

Structural insights into the innate immune recognition specificities of L- and H-ficolins

Innate immunity relies critically upon the ability of a few pattern recognition molecules to sense molecular markers on pathogens, but little is known about these interactions at the atomic level. Human L- and H-ficolins are soluble oligomeric defence proteins with lectin-like activity, assembled from collagen fibers prolonged by fibrinogen-like recognition domains. The X-ray structures of their trimeric recognition domains, alone and in complex with various ligands, have been solved to resolutions up to 1.95 and 1.7 A, respectively. Both domains have three-lobed structures with clefts separating the distal parts of the protomers. Ca(2+) ions are found at sites homologous to those described for tachylectin 5A (TL5A), an invertebrate lectin. Outer binding sites (S1) homologous to the GlcNAc-binding pocket of TL5A are present in the ficolins but show different structures and specificities. In L-ficolin, three additional binding sites (S2-S4) surround the cleft. Together, they define an unpredicted continuous recognition surface able to sense various acetylated and neutral carbohydrate markers in the context of extended polysaccharides such as 1,3-beta-D-glucan, as found on microbial or apoptotic surfaces.     

Cellular and Extracellular Polysaccharides of the Blue green Alga Nostoc

The carbohydrate content of various cellular fractions of theblue-green alga Nostoc was studied as a function of age of theculture. The production of extracellular and intracellular polysaccharideswas higher in actively growing cultures. Mannose and glucosewere the main components of cell wall polysaccharides. Glucosamineand diaminopimelic acid were also detected in the cell walls.The kinetics of incorporation of radioactivity from sodium [¹⁴C]bicarbonate showed that the extracellular polysaccharides werelabelled within 10 min of incubation suggesting the active exudationof polysaccharides by this alga. The selective excretion ofpolysaccharides by the alga Nostoc is also suggested.     

Microbial polysaccharides with actual potential industrial applications

The microbial polysaccharides reviewed include xanthan gum, scleroglucan, PS-10, PS-21 and PS-53 gums, polysaccharides from Alcaligenes sp., PS-7 gum, gellan gum, curdlan, bacterial alginate, dextran, pullulan, Baker's Yeast Glycan, 6-deoxy-hexose-containing polysaccharides and bacterial cellulose. Factors limiting the commercial potential of certain microbial polysaccharides such as availability, rheological properties, and polyvalency are outlined. The polysaccharides are classified according to their uses as viscosity-increasing agents and as gelling agents. A third category includes polysaccharides with specific applications such as tailor-made dextran and pullulan and polysaccharides used as substrates for the preparation of rare sugars. The difficulties encountered in development of a polysaccharide at the industrial level are pointed out.     

Growth of loblolly pine callus on a variety of carbohydrate sources

Callus derived from stem segments of loblolly pine (Pinus taeda L.) was subcultured to media containing 0.5% of various mono-, di-, tri- or polysaccharides. None of the carbohydrate sources tested were superior to sucrose. Growth on twelve of the 20 carbohydrates tested was more than 75% of that obtained for sucrose; growth on two other carbohydrates became >75% of the value for sucrose by the second interval on the new carbon source. Ribose and galactose-containing sugars are among those which support pine callus growth. Dramatic differences in ribose utilization are noted on media supplemented with glutamine vs. NH₄/NO₃ nitrogen sources.Abbreviations NAA -naphthaleneacetic acid - BAP benzylaminopurine - BL Brown and Lawrence's medium Paper No. 10377 of the Journal Series of the North Carolina Agricultural Research Service, Raleigh, NC 27695-7601, USA     

Effect of molecular structure on thermodynamic properties of carbohydrates. A calorimetric study of aqueous di- and oligosaccharides at subzero temperatures

For aqueous solutions of di- and oligosaccharides thermodynamic properties have been investigated at subzero temperatures using differential scanning calorimetry. The amount of unfrozen water observed is found to increase linearly with the glass transition temperatures of anhydrous carbohydrates. Furthermore, the amount of unfrozen water shows a linear relationship with known solution properties of aqueous carbohydrates, such as partial molar compressibility and heat of solution. The different effectiveness among various di- and oligosaccharides to avoid ice formation is associated with the combination of constitutive monosaccharides and attendant molecular structure features including the position and type of the glycosidic linkage between the constituent units. More unfrozen water is induced in the presence of a carbohydrate having a poorer compatibility with the three-dimensional hydrogen-bond network of water. A series of these results obtained imply that there is a common key of carbohydrate stereochemistry governing several different thermodynamic amounts of a given system involving carbohydrates. In this context, a modified stereospecific-hydration model can be used to interpret the present results in terms of stereochemical effects of carbohydrates.     

Hemagglutinating activity of vibrio cholerae enterotoxin

Abstract The hemagglutinating activity and carbohydrate specificity of cholera toxin (cholera enterotoxin) was studied using hemagglutination and hemagglutination inhibition. Hemagglutination was obtained with cholera toxin at >108 μg/ml for human types A, B, and O erythrocytes, >216 μg/ml for chicken erythrocytes, and >865 μg/ml for sheep erythrocytes. When the erythrocytes were treated with either neuraminidase or pronase, the hemagglutinating activity of cholera toxin was enhanced about 8- to 32-fold. Hemagglutination of pronase-treated human type B erythrocytes induced by cholera toxin was inhibited by lactose, galactose, melibiose and l -arabinose. Lactose was the most effective of the mono-, di-, and polysaccharides used as inhibitors, being a slightly better inhibitor than galactose, and much more potent than melibiose. These results suggest that cholera toxin is a bacterial lectin specific for galactose and/or lactose.     

The structure and function of glycoproteins synthesized during slime-polysaccharide production by membranes of the root-cap cells of maize (Zea mays).

The synthesis of the maize root slime polysaccharides was investigated by using [1-3H]-fucose as a marker for slime production. Three fractions were separated by centrifugation in a CsCl density gradient. Two of these were glycoproteins and occurred within the membranes of the cells of the root tip; the third was the slime polysaccharides. Radioactive pulse-chase experiments showed that the glycoproteins were precursors of the slime polysaccharides, and the carbohydrate portion of the glycoproteins had a similar composition to that of the free slime. The linkage between the protein and the carbohydrate of one of the glycoproteins was shown to be a xylose-threonine bond. It is postulated that the slime polysaccharides are synthesized and transported on proteins within the membrane system of the root tip.     

Investigation of stretching vibrations of glycosidic linkages in disaccharides and polysaccharides with use of IR spectra deconvolution

The results are presented for the deconvolution of IR spectra of disaccharides and polysaccharides with alpha and beta configurations of the 1 --> 4 glycosidic linkage (maltose, cellobiose, amylose, and cellulose), as well as of their corresponding monosaccharides (alpha- and beta-D-glucose) in the 1200-920 cm(-1) frequency range. It is established that a characteristic of di- and polysaccharides with 1 --> 4 glycosidic linkage is the appearance of new absorption bands in the 1175-1140 cm(-1) spectral range, as opposed to the IR spectra of monosaccharides. This can be a spectroscopic manifestation of the glycosidic linkage formation. In the 1000-970 cm(-1) frequency range, absorption bands, which are not observed in the monomer spectrum, are separated as a result of the deconvolution of the IR spectra of cellobiose and cellulose. The number of bands in this range remains unchanged for maltose and amylose, as compared to the monomer spectra. It is shown that the application of the method of deconvolution leads to a considerable enhancement in the resolution of the absorption bands in the IR spectra of mono-, di-, and polysaccharides.     

Cartilage degradation by hyaluronate lyase and chondroitin ABC lyase: a MALDI-TOF mass spectrometric study

Matrix-assisted laser desorption ionization and time-of-flight mass spectrometry (MALDI-TOF MS) has been used to investigate degradation products of two selected polysaccharides of cartilage (chondroitin sulfate and hyaluronic acid). Testicular hyaluronate lyase and chondroitin ABC lyase were used for enzymic digestion of both polysaccharides as well as of cartilage specimens. Polysaccharide solutions and cartilage supernatants were assayed by positive and negative MALDI-TOF MS. Especially chondroitin ABC lyase produced high amounts of digestion products (unsaturated di- and tetrasaccharides) from polysaccharides as well as from cartilage, clearly monitored by MALDI-TOF MS. It is concluded that MALDI-TOF MS provides a precise and fast tool for the determination of oligosaccharides since no previous derivatization is required.     

Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis

The microbiota of the mammalian intestine depend largely on dietary polysaccharides as energy sources. Most of these polymers are not degradable by the host, but herbivores can derive 70% of their energy intake from microbial breakdown--a classic example of mutualism. Moreover, dietary polysaccharides that reach the human large intestine have a major impact on gut microbial ecology and health. Insight into the molecular mechanisms by which different gut bacteria use polysaccharides is, therefore, of fundamental importance. Genomic analyses of the gut microbiota could revolutionize our understanding of these mechanisms and provide new biotechnological tools for the conversion of polysaccharides, including lignocellulosic biomass, into monosaccharides.     

Use of inducible disaccharidases to assess the importance of different carbohydrate sources for Bacteroides ovatus growing in the intestinal tracts of germfree mice.

Patterns of disaccharidase expression were used to determine which polysaccharides were the major sources of carbohydrate for Bacteroides ovatus growing in the intestinal tracts of monocolonized germfree mice. Results indicate that B. ovatus grows on a variety of different carbohydrates, which are present in low concentrations, rather than relying on one type of carbohydrate as the major carbohydrate source.     

Use of inducible disaccharidases to assess the importance of different carbohydrate sources for Bacteroides ovatus growing in the intestinal tracts of germfree mice.

Patterns of disaccharidase expression were used to determine which polysaccharides were the major sources of carbohydrate for Bacteroides ovatus growing in the intestinal tracts of monocolonized germfree mice. Results indicate that B. ovatus grows on a variety of different carbohydrates, which are present in low concentrations, rather than relying on one type of carbohydrate as the major carbohydrate source.     

Production of extracellular polysaccharides by Lactobacillus delbrueckii ssp. bulgaricus NCFB 2772 grown in a chemically defined medium

Lactobacillus delbrueckii ssp. bulgaricus NCFB 2772 produced an extracellular polysaccharide when grown in a chemically defined medium with glucose or lactose as the substrate carbohydrate. The isolated extracellular polysaccharide had a sugar composition of glucose, galactose and rhamnose in a ratio of 1:6.8:0.7. The production of extracellular polysaccharides increased at higher temperatures, but the bacterium rapidly lost its polysaccharide producing ability at 47°C. Production of polysaccharides was growth-related: no polysaccharide production was found after growth had ceased. An excess carbohydrate did not result in increased polysaccharide production.     

The complete genome sequence of Fibrobacter succinogenes S85 reveals a cellulolytic and metabolic specialist

Fibrobacter succinogenes is an important member of the rumen microbial community that converts plant biomass into nutrients usable by its host. This bacterium, which is also one of only two cultivated species in its phylum, is an efficient and prolific degrader of cellulose. Specifically, it has a particularly high activity against crystalline cellulose that requires close physical contact with this substrate. However, unlike other known cellulolytic microbes, it does not degrade cellulose using a cellulosome or by producing high extracellular titers of cellulase enzymes. To better understand the biology of F. succinogenes, we sequenced the genome of the type strain S85 to completion. A total of 3,085 open reading frames were predicted from its 3.84 Mbp genome. Analysis of sequences predicted to encode for carbohydrate-degrading enzymes revealed an unusually high number of genes that were classified into 49 different families of glycoside hydrolases, carbohydrate binding modules (CBMs), carbohydrate esterases, and polysaccharide lyases. Of the 31 identified cellulases, none contain CBMs in families 1, 2, and 3, typically associated with crystalline cellulose degradation. Polysaccharide hydrolysis and utilization assays showed that F. succinogenes was able to hydrolyze a number of polysaccharides, but could only utilize the hydrolytic products of cellulose. This suggests that F. succinogenes uses its array of hemicellulose-degrading enzymes to remove hemicelluloses to gain access to cellulose. This is reflected in its genome, as F. succinogenes lacks many of the genes necessary to transport and metabolize the hydrolytic products of non-cellulose polysaccharides. The F. succinogenes genome reveals a bacterium that specializes in cellulose as its sole energy source, and provides insight into a novel strategy for cellulose degradation.     

Classification ofVibrio vulnificusStrains by the Carbohydrate Composition of Their Capsular Polysaccharides

Pathogenic bacteria are often classified on the basis of the complex polysaccharides found on the surface, usually capsular polysaccharides or lipopolysaccharides. It is common in clinical practice to use reactivity with antisera specific to the various cell surface carbohydrates for this purpose. In this work, we describe a chemotyping method for bacterial capsular polysaccharides which is based on a carbohydrate analysis of an acid hydrolysate of the capsule. High-performance anion-exchange chromatography at high pH (HPAE) with electrochemical detection, which is used for analysis of the hydrolysate, shows preferential sensitivity for sugars. A single acid hydrolysis condition is chosen for screening a large collection of bacterial isolates and a computerized autosampler is used to make possible a large number of rapid analyses. This procedure does not yield a quantitative carbohydrate analysis for the sample but produces a fingerprint which can be used to discriminate among isolates which have different capsular polysaccharide structures. The procedure has been applied to a collection of 120 isolates ofVibrio vulnificus,a water-born species common in shellfish which causes septicemia in immunocompromised individuals, most often from eating of raw oysters. The collection of bacterial isolates includes strains from both clinical cases of septicemia and from such environmental sources such as sea water, sediments, and shellfish. Our results show that a number of unusual sugars including many amino sugars are found in these polysaccharides and that a wide variety of capsular carbotypes inV. vulnificusmay be readily distinguished by the HPAE fingerprint.