Engineering and screening of novel β-1,3-xylanases with desired hydrolysate type by optimized ancestor sequence reconstruction and data mining.

Engineering of hydrolases to shift their hydrolysate types has not been attempted so far, though computer-assisted enzyme design has been successful. A novel integrative strategy for engineering and screening the β-1,3-xylanase with desired hydrolysate types was proposed, with the purpose to solve problems that the separation and preparation of β-1,3--oligosaccharides was in high cost yet in low yield as monosaccharides existed in the hydrolysates. By classifying the hydrolysate types and coding them into numerical values, two robust mathematical models with five selected attributes from molecular docking were established based on LogitBoost and partial least squares regression with overall accuracy of 83.

The first characterization of a Ca-dependent carbohydrate-binding module of β-1,3-xylanase from Flammeovirga pacifica.

A novel carbohydrate binding module (CBM) was identified in a β-1,3-xylanase from Flammeovirga pacifica, which showed only 25.0% sequence identity with the reported CBMs with the coverage of 36.4%.

Aphidicolin Chemistry of the Deep-Sea-Derived Fungus MCCC 3A00494.

Aphidicolin, a potent DNA polymerase α inhibitor, has been explored in clinical trials for the treatment of cancer. So far, about 300 modified aphidicolins have been discovered. However, none have shown a stronger effect.

π-π stacking interaction is a key factor for the stability of GH11 xylanases at low pH.

Acidic xylanases possess the unique features necessary for the tolerance of acidic environments, which may have great potentials for industrial purposes. However, factors controlling the pH-dependent stability of xylanases are only partially known. Here we proposed a residue interaction networks based method to analyze the differences of residue interactions between 6 pairs of experimentally verified acidic and neutral xylanases.

Biosynthetic Functional Gene Analysis of Bis-Indole Metabolites from 25D7, a Clone Derived from a Deep-Sea Sediment Metagenomic Library.

This work investigated the metabolites and their biosynthetic functional hydroxylase genes of the deep-sea sediment metagenomic clone 25D7. 5-Bromoindole was added to the 25D7 clone derived Escherichia coli fermentation broth. The new-generated metabolites and their biosynthetic byproducts were located through LC-MS, in which the isotope peaks of brominated products emerged.

A new macrolactin antibiotic from deep sea-derived bacteria Bacillus subtilis B5.

A new macrolactin derivate, 7-O-2'E-butenoyl macrolactin A (1), together with three known macrolactin compounds, macrolactin A (2), 7-O-malonyl macrolactin A (3) and 7-O-succinyl macrolactin A (4), was isolated from the bacterial strain Bacillus subtilis B5, which was isolated from the 3000 m deep sea sediment of the Southwest Pacific Ocean. The structures of the new compounds were assigned by spectroscopic methods including 1-D/2-D NMR and MS analysis techniques. Compounds 1 and 2 demonstrated antifungal activities against tea pathogenic fungi Pestalotiopsis theae and Colletotrichum gloeosporioides.

Shewanella mangrovi sp. nov., an acetaldehyde-degrading bacterium isolated from mangrove sediment.

A taxonomic study was carried out on strain YQH10T, which was isolated from mangrove sediment collected from Zhangzhou, China during the screening of acetaldehyde-degrading bacteria. Cells of strain YQH10T were Gram-stain-negative rods and pale brown-pigmented. Growth was observed at salinities from 0 to 11% and at temperatures from 4 to 42 °C.

Two new cytotoxic indole alkaloids from a deep-sea sediment derived metagenomic clone.

Two new indole alkaloids, metagenetriindole A (1) and metagenebiindole A (2), were identified from deep-sea sediment metagenomic clone derived Escherichia coli fermentation broth. The structures of new compounds were elucidated by spectroscopic methods. The two new indole alkaloids demonstrated moderately cytotoxic activity against CNE2, Bel7402 and HT1080 cancer cell lines in vitro.

Two new compounds from marine-derived fungus Penicillium sp. F11.

Two new compounds, penicillone A (1) and penicillactam (2), were isolated together with 17 known compounds from a marine-derived fungus Penicillium sp. F11. The structures of the new compounds as well as a firstly literatural reported known compound (3) were assigned by spectroscopic methods including 1D/2D NMR and MS analysis techniques.

A novel indole alkaloid from deep-sea sediment metagenomic clone-derived Escherichia coli fermentation broth.

To explore secondary metabolites in deep-sea sediment metagenomic clone-derived Escherichia coli fermentation broth, different kinds of chromatography methods were used in the isolation procedures, while the structures of the isolated compounds were assigned based on the MS analysis and their (1)H and (13)C NMR spectra including 2D NMR techniques such as COSY, HMQC, and HMBC experiments. As a result, a novel compound was isolated and characterized as N-{1-[4-(acetylamino)phenyl]-3-hydroxy-1-(1H-indol-3-yl)propan-2-yl}-2,2-dichloroacetamide (1). In addition, eight known compounds were also obtained.

Three-dimensional architecture of phycobilisomes from Nostoc flagelliforme revealed by single particle electron microscopy.

Phycobilisomes are protein complexes that harvest light and transfer energy to the photo system. Here, the three dimensional structure of intact phycobilisomes from Nostoc flagelliforme is studied by a combination of negative stain electron microscopy and cryo-electron microscopy. Results show that the intact phycobilisomes are composed of a tricylindrical core and six rods.