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Background Yaks are able to utilize the gastrointestinal microbiota to digest plant materials. Although the cellulolytic bacteria in the yak rumen have been reported, there is still limited information on the diversity of the major microorganisms and putative carbohydrate-metabolizing enzymes for the degradation of complex lignocellulosic biomass in its gut ecosystem. Results Here, this study aimed to decode biomass-degrading genes and genomes in the yak fecal microbiota using deep metagenome sequencing. A comprehensive catalog comprising 4.5 million microbial genes from the yak feces were established based on metagenomic assemblies from 92 Gb sequencing data. We identified a full spectrum of genes encoding carbohydrate-active enzymes, three-quarters of which were assigned to highly diversified enzyme families involved in the breakdown of complex dietary carbohydrates, including 120 families of glycoside hydrolases, 25 families of polysaccharide lyases, and 15 families of carbohydrate esterases. Inference of taxonomic assignments to the carbohydrate-degrading genes revealed the major microbial contributors were Bacteroidaceae , Ruminococcaceae , Rikenellaceae , Clostridiaceae , and Prevotellaceae . Furthermore, 68 prokaryotic genomes were reconstructed and the genes encoding glycoside hydrolases involved in plant-derived polysaccharide degradation were identified in these uncultured genomes, many of which were novel species with lignocellulolytic capability. Conclusions Our findings shed light on a great diversity of carbohydrate-degrading enzymes in the yak gut microbial community and uncultured species, which provides a useful genetic resource for future studies on the discovery of novel enzymes for industrial applications.

Two new alginate lyase genes, oalY1 and oalY2, have been cloned from the newly isolated marine bacterium Halomonas sp. QY114 and expressed in Escherichia coli. The deduced alginate lyases, OalY1 and OalY2, belonged to polysaccharide lyase (PL) family 17 and showed less than 45% amino acid identity with all of the characterized oligoalginate lyases. OalY1 and OalY2 exhibited the highest activities at 45°C and 50°C, respectively. Both of them showed more than 50% of the highest activity at 60°C, and 20% at 80°C. In addition, they were salt-dependent and salt-tolerant since both of them showed the highest activity in the presence of 0.5 M NaCl and preserved 63% and 68% of activity in the presence of 3 M NaCl. Significantly, OalY1 and OalY2 could degrade both polyM and polyG blocks into alginate monosaccharides in an exo-lytic type, indicating that they are bifunctional alginate lyases. In conclusion, our study indicated that OalY1 and OalY2 are good candidates for alginate saccharification application, and the salt-tolerance may present an exciting new concept for biofuel production from native brown seaweeds. Two new oligoalginate lyases, OalY1 and OalY2, have been cloned, expressed in Escherichia coli, purified and characterized.

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.

Root-knot nematodes (Meloidogyne spp.) cause major yield losses to many of the world’s crops, but efforts to understand how these pests recognize and interact with their hosts have been hampered by a lack of genetic resources. Starting with progeny of a cross between inbred strains (VW8 and VW9) of Meloidogyne hapla that differed in host range and behavioral traits, we exploited the novel, facultative meiotic parthenogenic reproductive mode of this species to produce a genetic linkage map. Molecular markers were derived from SNPs identified between the sequenced and annotated VW9 genome and de novo sequence of VW8. Genotypes were assessed in 183 F2 lines. The colinearity of the genetic and physical maps supported the veracity of both. Analysis of local crossover intervals revealed that the average recombination rate is exceptionally high compared with that in other metazoans. In addition, F2 lines are largely homozygous for markers flanking crossover points, and thus resemble recombinant inbred lines. We suggest that the unusually high recombination rate may be an adaptation to generate within-population genetic diversity in this organism. This work presents the most comprehensive linkage map of a parasitic nematode to date and, together with genomic and transcript sequence resources, empowers M. hapla as a tractable model. Alongside the molecular map, these progeny lines can be used for analyses of genome organization and the inheritance of phenotypic traits that have key functions in modulating parasitism, behavior, and survival and for the eventual identification of the responsible genes.

Antibodies have been raised against an alpha-1,4- glucan lyase purified from the red alga Gracilariopsis lemaneiformis (Bory) Dawson, Acleto et Foldvik. Localization of alpha-1,4-glucan lyase in ultra-thin sections of the red alga was performed using immunogold/transmission electron microscopy. The enzyme was found exclusively in the stroma of the chloroplasts of the algal cells, not in the cell wall, cytosol or around the cytosolic starch granules. Partial amino-acid sequences of the algal lyase, with a total length of 100 amino-acid residues, were obtained. No sequence homology was found with proteins and peptides of known sequences.

Interwoven networks of cellulose and pectin are the main components of plant cell walls, making them recalcitrant structures that can only be degraded by organisms producing a mix of synergistically acting enzymes. Animals were believed to be unable to synthesize these enzymes, depending instead on symbiotic microbes to render plants into a food source. Here we describe a metazoan pectinase gene that encodes a pectate lyase for breaking down the pectin component of plant cell walls. To our knowledge, this is the first example of non-symbiotic degradation of pectin in plant cell walls by an animal.

ObjectivesBifunctional alginate lyase can efficiently saccharify alginate biomass and prepare functional oligosaccharides of alginate.ResultsA new BP-2 strain that produces alginate lyase was screened and identified from rotted Sargassum. A new alginate lyase, Alg17B, belonging to the polysaccharide lyase family 17, was isolated and purified from BP-2 fermentation broth by freeze-drying, dialysis, and ion exchange chromatography. The enzymatic properties of the purified lyase were investigated. The molecular weight of Alg17B was approximately 77 kDa, its optimum reaction temperature was 40–45 °C, and its optimum reaction pH was 7.5–8.0. The enzyme was relatively stable at pH 7.0–8.0, with a temperature range of 25–35 °C, and the specific activity of the purified enzyme reached 4036 U/mg. A low Na+ concentration stimulated Alg17B enzyme activity, but Ca2+, Zn2+, and other metal ions inhibited it. Substrate specificity analysis, thin-layer chromatography, and mass spectrometry showed that Alg17B is an alginate lyase that catalyses the hydrolysis of sodium alginate, polymannuronic acid (polyM) and polyguluronic acid to produce monosaccharides and low molecular weight oligosaccharides. Alg17B is also bifunctional, exhibiting both endolytic and exolytic activities toward alginate, and has a wide substrate utilization range with a preference for polyM.ConclusionsAlg17B can be used to saccharify the main carbohydrate, alginate, in the ethanolic production of brown algae fuel as well as in preparing and researching oligosaccharides.

Macroalgae are considered to be promising biomass for fuels and chemicals production. To utilize brown macroalgae as biomass, the degradation of alginate, which is the main carbohydrate of brown macroalgae, into monomeric units is a critical prerequisite step. Saccharophagus degradans 2-40 is capable of degrading more than ten different polysaccharides including alginate, and its genome sequence demonstrated that this bacterium contains several putative alginate lyase genes including alg17C. The gene for Alg17C, which is classified into the PL-17 family, was cloned and overexpressed in Escherichia coli. The recombinant Alg17C was found to preferentially act on oligoalginates with degrees of polymerization higher than 2 to produce the alginate monomer, 4-deoxy-l-erythro-5-hexoseulose uronic acid. The optimal pH and temperature for Alg17C were found to be 6 and 40 °C, respectively. The K ^sub M^ and V ^sub max^ of Alg17C were 35.2 mg/ml and 41.7 U/mg, respectively. Based on the results of this study, Alg17C could be used as the key enzyme to produce alginate monomers in the process of utilizing alginate for biofuels and chemicals production.[PUBLICATION ABSTRACT]

Key Points The human genome encodes only a small number of digestive glycoside hydrolases for the breakdown of sucrose, lactose and starch. Instead, the large diversity of complex polysaccharides in our diet is mainly digested by specialized enzymes encoded by the gut microbiome. A model human microbiome was constructed from 177 microbial genomes in proportions that approximate their representation in the healthy adult gut, and this mini-microbiome was used to evaluate the diversity of carbohydrate-active enzymes (CAZymes) in the gut microbiota. Gut bacteria from the phylum Bacteroidetes encode more CAZymes, and encode CAZymes from more families, than the other phyla represented in the model mini-microbiome. The large substrate range of these CAZymes is compatible with the diversity of the dietary plant cell wall polysaccharides that are presented to members of the microbiota. The human genome encodes very few enzymes involved in the digestion of complex polysaccharides, and this deficit is compensated for by the myriad of carbohydrate-active enzymes (CAZymes) encoded by members of the gut microbiome. In this Analysis article, Henrissat and colleagues characterize the CAZymes present in a representative human mini-microbiome. Descriptions of the microbial communities that live on and in the human body have progressed at a spectacular rate over the past 5 years, fuelled primarily by highly parallel DNA-sequencing technologies and associated advances in bioinformatics, and by the expectation that understanding how to manipulate the structure and functions of our microbiota will allow us to affect health and prevent or treat diseases. Among the myriad of genes that have been identified in the human gut microbiome, those that encode carbohydrate-active enzymes (CAZymes) are of particular interest, as these enzymes are required to digest most of our complex repertoire of dietary polysaccharides. In this Analysis article, we examine the carbohydrate-digestive capacity of a simplified but representative mini-microbiome in order to highlight the abundance and variety of bacterial CAZymes that are represented in the human gut microbiota.

Pectin is abundant in modern day diets, as it comprises the middle lamellae and one-third of the dry carbohydrate weight of fruit and vegetable cell walls. Currently there is no specialized model organism for studying pectin fermentation in the human colon, as our collective understanding is informed by versatile glycan-degrading bacteria rather than by specialist pectin degraders. Here we show that the genome of Monoglobus pectinilyticus possesses a highly specialized glycobiome for pectin degradation, unique amongst Firmicutes known to be in the human gut. Its genome encodes a simple set of metabolic pathways relevant to pectin sugar utilization, and its predicted glycobiome comprises an unusual distribution of carbohydrate-active enzymes (CAZymes) with numerous extracellular methyl/acetyl esterases and pectate lyases. We predict the M. pectinilyticus degradative process is facilitated by cell-surface S-layer homology (SLH) domain-containing proteins, which proteomics analysis shows are differentially expressed in response to pectin. Some of these abundant cell surface proteins of M. pectinilyticus share unique modular organizations rarely observed in human gut bacteria, featuring pectin-specific CAZyme domains and the cell wall-anchoring SLH motifs. We observed M. pectinilyticus degrades various pectins, RG-I, and galactan to produce polysaccharide degradation products (PDPs) which are presumably shared with other inhabitants of the human gut microbiome (HGM). This strain occupies a new ecological niche for a primary degrader specialized in foraging a habitually consumed plant glycan, thereby enriching our understanding of the diverse community profile of the HGM.