Estimate of the degradation potentials of cellulose, xylan, and chitin across global prokaryotic communities.

Complex polysaccharides (e.g. cellulose, xylan, and chitin), the most abundant renewable biomass resources available on Earth, are mainly degraded by microorganisms in nature. However, little is known about the global distribution of the enzymes and microorganisms responsible for the degradation of cellulose, xylan, and chitin in natural environments. Through large-scale alignments between the sequences released by the Earth Microbiome Project and sequenced prokaryotic genomes, we determined that almost all prokaryotic communities have the functional potentials to degrade cellulose, xylan, and chitin. The median abundances of genes encoding putative cellulases, xylanases, and chitinases in global prokaryotic communities are 0.51 (0.17-1.01), 0.24 (0.05-0.57), and 0.33 (0.11-0.71) genes/cell, respectively, and the composition and abundance of these enzyme systems are environmentally varied. The taxonomic sources of the three enzymes are highly diverse within prokaryotic communities, and the main factor influencing the diversity is the community's alpha diversity index rather than gene abundance. Moreover, there are obvious differences in taxonomic sources among different communities, and most genera with degradation potentials are narrowly distributed. In conclusion, our analysis preliminarily depicts a panorama of cellulose-, xylan-, and chitin-degrading enzymatic systems across global prokaryotic communities.

The Gut Bacterial Community Composition of Wild Cervus albirostris (White-Lipped Deer) Detected by the 16S Ribosomal RNA Gene Sequencing.

Cervus albirostris (white-lipped deer) is an endemic species in China. As the name implies, C. albirostris has a characteristic pure white marking around their mouth and on the underside of the throat. The animal is a typical alpine species normally living at the height of 3500-4300 m. In this study, by pyrosequencing the 16S rRNA gene sequences, we for the first time analyzed the gut bacterial community composition in eight feces samples of wild C. albirostris. From a total of 243,634 high-quality sequences, we identified 186 genera, included in 17 prokaryotic phyla in the feces. The relative proportions of Firmicutes and Bacteroidetes were highly consistent in each individual sample. The most frequently detected genus was Ruminococcaceae UCG-005, ranging from 6.70 to 21.00%, displaying positively connections with the Rikenellaceae RC9 gut group. The bacterial communities associated with C. albirostris provide the basic knowledge for further microbiological studies and facilitates the conservation efforts of this vulnerable deer species.

Docking-guided rational engineering of a macrolide glycosyltransferase glycodiversifies epothilone B.

Glycosyltransferases typically display acceptor substrate flexibility but more stringent donor specificity. BsGT-1 is a highly effective glycosyltransferase to glycosylate macrolides, including epothilones, promising antitumor compounds. Here, we show that BsGT-1 has three major regions significantly influencing the glycodiversification of epothilone B based on structural molecular docking, "hot spots" alanine scanning, and site saturation mutagenesis. Mutations in the PSPG-like motif region and the C2 loop region are more likely to expand donor preference; mutations of the flexible N3 loop region located at the mouth of the substrate-binding cavity produce novel epothilone oligosaccharides. These "hot spots" also functioned in homologues of BsGT-1. The glycosides showed significantly enhanced water solubility and decreased cytotoxicity, although the glycosyl appendages of epothilone B also reduced drug permeability and attenuated antitumor efficacy. This study laid a foundation for the rational engineering of other GTs to synthesize valuable small molecules.

Catalytic performance of lignin peroxidase in a novel reverse micelle.

To enhance the catalytic activity of lignin peroxidase (LiP) in a reverse micelle, a synthesized two-tail nonionic surfactant N-gluconyl glutamic acid didecyl ester (GGDE) was used to formulate a novel reverse micelle. Based on the LiP catalyzed oxidation of veratryl alcohol (VA) in this novel GGDE/TritonX-100-cyclohexane-H(2)O reverse micelle, the effects of the size of the reverse micelle, the buffer pH, and the concentration of H(2)O(2) on the catalytic activity of LiP were investigated. Under the optimized conditions, the catalytic efficiency of LiP in the GGDE/TritonX-100 reverse micelle was 40 times higher than that in the AOT reverse micelle. The full expression of catalytic activity of LiP in this medium was mainly due to the lack of electrostatic interaction between LiP and the head group of GGDE and TritonX-100 and to the size fit between LiP and the inner water cavity of the reverse micelle.

Evaluation of fusion between liposomes and erythrocytes for intracellular derivatization of amino acids in cells.

Erythrocytes were fused with liposome for intracellular derivatization of amino acids in cells. The fusion efficiency was evaluated with capillary electrophoresis (CE) and laser-induced fluorescence (LIF) detection. Reagent fluorescein isothiocyanate (FITC) was enveloped in liposomes and introduced into erythrocytes by fusion between liposomes and erythrocytes. The amino acids in the fused cells were derivated by the introduced FITC and the derivated amino acids were extracted for detection by capillary electrophoresis equipped with laser-induced fluorescence detector. The fusion conditions were investigated. It was found that incubation of liposome and erythrocytes in the presence of 13% polyethylene glycol 6000 (PEG 6000) for 15min produced the highest fusion efficiency and kept the erythrocytes stability.

Analysis of purified tubulin in high concentration of glutamate for application in high throughput screening for microtubule-stabilizing agents.

High-throughput screening (HTS) is a powerful approach for the discovery of potential and effective drugs from a number of candidates. The dynamics of tubulin assembly and disassembly in vitro are an important target for the screening of anti-tumor agents. However, previously described methods are not amenable for HTS. In this paper, we compared preparation methods of tubulin and suggest a combination method, i.e., one cycle of assembly and disassembly following ion-exchange chromatography using high concentrations of glutamate to increase the recovery of tubulin with high purity. The resultant highly purified microtubule-associated proteins-free tubulin in high glutamate solution was directly employed in tubulin polymerization assays. Our results indicate that the system is feasible and practicable as a model for HTS for microtubule-stabilizing agents.

Morphologies and phylogenetic classification of cellulolytic myxobacteria.

The evolutionary distances of the 16S rDNA sequences in cellulolytic myxobacteria are less than 3%, which units all the strains into a single genus, Sorangium. The size of myxospores and the shape of sporangioles, rather than fruiting body colors or swarm morphologies are consistent with the changes of the 16S rDNA sequences. It is suggested that there are at least two species in the genus Sorangium: one includes strains with small myxospores and spherical sporangioles, and the color of the fruiting bodies is normally orange or brown, though sometimes yellow or black. The second species has large myxospores, polyhedral sporangioles with many inter-cystic substrates, and normally deep brown to black color.