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Yan R.,Fuzhou University | Yan R.,Fujian Key Laboratory of Marine Enzyme Engineering | Wang X.,Shanxi Normal University | Xu W.,Fuzhou University | And 6 more authors.
RSC Advances | Year: 2016

Residue depth is a solvent exposure measure that quantitatively describes the depth of a residue from the protein surface. It is an important parameter in protein structural biology. Residue depth can be used in protein ab initio folding, protein function annotation, and protein evolution simulation. Accordingly, accurate prediction of residue depth is an essential step towards the characterization of the protein function and development of novel protein structure prediction methods with optimized sensitivity and specificity. In this work, we propose an effective method termed as NNdepth for improved residue depth prediction. It uses sequence-derived features, including four types of sequence profiles, solvent accessibility, secondary structure and sequence length. Two sequence-to-depth neural networks were first constructed by incorporating various sources of information. Subsequently, a simple depth-to-depth equation was used to combine the two NN models and was shown to achieve an improved performance. We have designed and performed several experiments to systematically examine the performance of NNdepth. Our results demonstrate that NNdepth provides a more competitive performance when compared with our previous method evaluated using the Student t-test with a p-value < 0.001. Furthermore, we performed an in-depth analysis of the effect and importance of various features used by the models and also presented a case study to illustrate the utility and predictive power of NNdepth. To facilitate the wider research community, the NNdepth web server has been implemented and seamlessly incorporated as one of the components of our previously developed outer membrane prediction systems (available at http://genomics.fzu.edu.cn/OMP). In addition, a stand-alone software program is also publicly accessible and downloadable at the website. We envision that NNdepth should be a powerful tool for high-throughput structural genomics and protein functional annotations. © 2016 The Royal Society of Chemistry.


Ng T.B.,Chinese University of Hong Kong | Cheung R.C.F.,Chinese University of Hong Kong | Wong J.H.,Chinese University of Hong Kong | Chan Y.S.,Shenzhen University | And 10 more authors.
Applied Microbiology and Biotechnology | Year: 2016

Fungi comprise organisms like molds, yeasts and mushrooms. They have been used as food or medicine for a long time. A large number of fungal proteins or peptides with diverse biological activities are considered as antibacterial, antifungal, antiviral and anticancer agents. They encompass proteases, ribosome inactivating proteins, defensins, hemolysins, lectins, laccases, ribonucleases, immunomodulatory proteins, and polysaccharopeptides. The target of the present review is to update the status of the various bioactivities of these fungal proteins and peptides and discuss their therapeutic potential. © 2016, Springer-Verlag Berlin Heidelberg.


Yang J.,Fuzhou University | Yang J.,Fujian Key Laboratory of Marine Enzyme Engineering | Yang X.,Fuzhou University | Yang X.,Fujian Key Laboratory of Marine Enzyme Engineering | And 6 more authors.
PLoS ONE | Year: 2015

Malachite green (MG) was decolorized by laccase (LacA) of white-rot fungus Cerrena sp. with strong decolorizing ability. Decolorization conditions were optimized with response surface methodology. A highly significant quadratic model was developed to investigate MG decolorization with LacA, and the maximum MG decolorization ratio of 91.6% was predicted under the conditions of 2.8 U mL-1 LacA, 109.9 mg L-1 MG and decolorization for 172.4 min. Kinetic studies revealed the Km and kcat values of LacA toward MG were 781.9 mM and 9.5 s-1, respectively. UV-visible spectra confirmed degradation of MG, and the degradation mechanism was explored with liquid chromatography-mass spectrometry (LC-MS) analysis. Based on the LC-MS spectra of degradation products, LacA catalyzed MG degradation via two simultaneous pathways. In addition, the phytotoxicity of MG, in terms of inhibition on seed germination and seedling root elongation of Nicotiana tabacum and Lactuca sativa, was reduced after laccase treatment. These results suggest that laccase of Cerrena was effective in decolorizing MG and promising in bioremediation of wastewater in food and aquaculture industries. © 2015 Yang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


Yang J.,Fuzhou University | Yang J.,Fujian Key Laboratory of Marine Enzyme Engineering | Yang X.,Fuzhou University | Ye X.,Fuzhou University | And 3 more authors.
Analytical Biochemistry | Year: 2016

An enzyme-based method for destaining polyacrylamide gels stained with Coomassie Brilliant Blue R-250 is described. Distilled water supplemented with diluted fermentation broth of a laccase-producing white-rot fungus, Cerrena sp., was used for gel destaining, and a clear gel background was obtained in 2 h at 37 °C. Sensitivity of protein detection was 10 ng. The method did not require organic solvents or changing the destaining solution. Due to simultaneous gel destaining and dye decolorization, the colorless destaining solution can be disposed of directly. Laccase destaining of polyacrylamide gels was simple, efficient, and environmentally friendly. © 2015 Elsevier Inc. All rights reserved.


Yang J.,Fuzhou University | Yang J.,Fujian Key Laboratory of Marine Enzyme Engineering | Ng T.B.,Chinese University of Hong Kong | Lin J.,Fuzhou University | And 3 more authors.
International Journal of Biological Macromolecules | Year: 2015

A novel laccase gene Lac1 and its cDNA were cloned from a white-rot fungus Cerrena sp. and characterized. The 1554-bp cDNA of Lac1 encoded a mature protein with 497 amino acids, preceded by a signal peptide of 20 amino acids. An unconventional intron splice site and incomplete splicing variants of Lac1 were observed. Lac1 was heterologously expressed in the yeast host Pichia pastoris, and a maximal laccase activity of 6.3UmL-1 in the fermentation broth was achieved after fermentation for 9 days. The recombinant protein rLac1 was purified, and its enzymatic properties and functional characteristics were investigated. When ABTS was used as the substrate, the enzyme was most active at pH 3.5 and 55°C, and stable at pH 4-10 and 20-60°C. The Km and kcat values of rLac1 toward ABTS were 28.9 μM and 332.4s-1, respectively. Furthermore, rLac1 was tolerant to common metal ions up to 100mM concentration and capable of decolorizing structurally different dyes in the absence of a redox mediator. Hence, Lac1 may be useful for industrial applications, such as dye decolorization and bioremediation. © 2015 Elsevier B.V.


Huang X.,Fuzhou University | Lin J.,Fuzhou University | Lin J.,Fujian Key Laboratory of Marine Enzyme Engineering | Ye X.,Fuzhou University | And 3 more authors.
Journal of Microbiology and Biotechnology | Year: 2015

To enrich the genetic resource of microbial xylanases with high activity and stability under alkaline conditions, a xylanase gene (xynSL4) was cloned from Planococcus sp. SL4, an alkaline xylanase-producing strain isolated from the sediment of soda lake Dabusu. Deduced XynSL4 consists of a putative signal peptide of 29 residues and a catalytic domain (30-380 residues) of glycosyl hydrolase family 10, and shares the highest identity of 77% with a hypothetical protein from Planomicrobium glaciei CHR 43. Phylogenetic analysis indicated that deduced XynSL4 is closely related with thermophilic and alkaline xylanases from Geobacillus and Bacillus species. The gene xynSL4 was expressed heterologously in Escherichia coli and the recombinant enzyme showed some superior properties. Purified recombinant XynSL4 (rXynSL4) was highly active and stable over the neutral and alkaline pH range from 6 to 11, with maximum activity at pH 7 and more than 60% activity at pH 11. It had an apparent temperature optimum of 70oC and retained stable at this temperature in the presence of substrate. rXynSL4 was highly halotolerant, retaining more than 55% activity with 0.25–3.0 M NaCl and was stable at the concentration of NaCl up to 4M. The enzyme activity was significantly enhanced by β-mercaptoethanol and Ca2+ but strongly inhibited by heavy-metal ions and SDS. This thermophilic and alkaline- and salt-tolerant enzyme has great potential for basic research and industrial applications. © 2015 by The Korean Society for Microbiology and Biotechnology.


Lin J.,Fujian Key Laboratory of Marine Enzyme Engineering | Ye X.,Fujian Key Laboratory of Marine Enzyme Engineering | Cao Z.,Fujian Key Laboratory of Marine Enzyme Engineering | Xie F.,Fujian Key Laboratory of Marine Enzyme Engineering | Xu M.,Fujian Key Laboratory of Marine Enzyme Engineering
Journal of Chinese Institute of Food Science and Technology | Year: 2015

Objective: Different microbes were isolated from Kombucha samples collected in Fujian, and different microbial combinations were fermented to produce Kombucha. Method: The isolated microbes were identified by morpholog-icalobservation and molecularbiology methods. The ingredients and sense of Kombucha fermented with different microbial combinations and traditional brewing were compared. Results: Three types of yeasts including Saccharomyces cerevisiae, Zygosaccharomycesbailiiand Candida parapsilosis, and three types of acetic acid bacteria including Gluconacetobacter sp., Acetobacter sp. and Gluconacetobacterhansenii were isolated from Kombucha samples. Candida parapsilosis and Glu-conacetobacterhansenii were isolated from Kombucha for the first time. The Kombucha fermented with Saccharomyces cerevisiae, Gluconacetobacter sp. and Lactobacillus plantarumnot only had the sweet and sour suitable, mellow and refreshing flavor, but also had various functional components. And the fermentation period was shortened from 10 d to 56 h. Conclusion: The content of functional components of Kombucha fermented with different combinations of strains is different. This may be due to the bacteria at different growth state during fermentation, thus affecting the synthesis of metabolites. ©, 2015, Chinese Institute of Food Science and Technology. All right reserved.

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