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Chen J.,Jiangnan University | Ding Y.,Jiangnan University | Ding Y.,Key Laboratory of Industrial Biotechnology | Xu W.,Jiangnan University
Journal of Biological Systems | Year: 2013

Metabolic networks are useful representations of the metabolic capabilities of cells. A comparison of metabolic networks across species is essential to better understand how evolutionary pressures shape these networks. By comparing the set of reactions that are expected to occur in an organism with the set of reactions in reference metabolic pathways, it is possible to infer the main metabolic functions of an organism. In this paper, the metabolic networks of the mesophilic archaeon Methanosarcina acetivorans and the thermophilic archaeon Methanopyrus kandleri have been reconstructed based on the KEGG LIGAND database, followed by four topological statistical analyses of the nodes in the two networks to compare their metabolic networks. The values of average degree and characteristic path length are very small but clustering coefficient is relatively large. The results show that the complete metabolic networks of M. acetivorans and M. kandleri possessed small-world network properties. Then we used Girvan-Newman modular algorithm to identify hub modules and compared hub modules with non-hub modules, respectively. The results show that M. kandleri metabolic network has a better modular organization than the M. acetivorans network. M. acetivorans includes 39 modules, 25 modules of them are independent, and 15 modules are functionally pure. On the other hand, M. kandleri includes 30 modules. Among them, there are 20 independent modules, and 14 of them are functionally pure. These results further indicated that the present approach for identifying modules yields modules that have biologically significant functions. We also identified hub modules of the metabolic networks and found that these hub modules are carbohydrate metabolism and amino acid metabolism. The conclusions obtained from such studies provide a broad overview of the similarities and differences between organism's metabolic networks. These will be very helpful for further research on thermostability of methanogens. © 2013 World Scientific Publishing Company.

Liu J.,University of Georgia | Liu J.,Key Laboratory of Industrial Biotechnology | Zeng L.,University of Georgia | Zeng L.,Qingdao Agricultural University | And 3 more authors.
Soil Research | Year: 2013

Soil water repellency (SWR) caused by organic coatings on soil particles can lead to serious loss in crop production and turfgrass quality. In laboratory experiments, we tested the novel concept of direct application of enzymes to alleviate SWR. In a biofuel research project on fungal pre-treatment of switchgrass (Panicum virgatum L.) for improved saccharification, enzymatic co-products (mainly laccase mixed with other trace enzymes) were produced based on fermentation periods of 18, 36, 54, and 72 days. We characterised enzyme activities of the 18-72-day crude enzyme extracts (CEE) and applied undiluted or diluted solutions (dilutions of 5-, 10-, and 100-fold) to eight air-dried, SWR soils from several golf courses. These soils exhibited water drop penetration times (WDPT) of 345-7439s (i.e. moderately to very strongly hydrophobic) and all showed a large decrease in SWR to WDPT <60s after application of undiluted CEE and various dilutions of CEE for 3 days with a 1:1 soil:solution ratio (10g air-dried soil and 10mL CEE solution). The observed decrease in WDPT was positively related to increased enzyme activity level for each soil in an exponential or logarithmic relationship. Most of the improvement in SWR was observed within 1 day. Enzyme activity was maintained to varying degrees in the soil solution for up to 5 days. These preliminary results suggest that it may be feasible to use direct enzyme application from CEE, as a biomass fermentation byproduct, for remediation of hydrophobic soils, which could also offer a cost benefit for biomass fermentation. © CSIRO 2013.

Tang C.-D.,Key Laboratory of Industrial Biotechnology | Wang J.-Q.,Key Laboratory of Industrial Biotechnology | Wu M.-C.,Jiangnan University
Journal of Agricultural and Food Chemistry | Year: 2012

A cDNA fragment of the Anman5A, a gene that encodes an acidophilic β-mannanase of Aspergillus niger LW-1 (abbreviated as AnMan5A), was cloned and functionally expressed in Pichia pastoris. Homology alignment of amino acid sequences verified that the AnMan5A belongs to the glycoside hydrolase (GH) family 5. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) assay demonstrated that the recombinant AnMan5A (reAnMan5A), a N-glycosylated protein with an apparent molecular weight of 52.0 kDa, was secreted into the medium. The highest reAnMan5A activity expressed by one P. pastoris transformant, labeled as GSAnMan4-12, reached 29.0 units/mL. The purified reAnMan5A displayed the highest activity at pH 3.5 and 70 °C. It was stable at a pH range of 3.0-7.0 and at a temperature of 60 °C or below. Its activity was not significantly affected by an array of metal ions and ethylenediaminetetraacetic acid (EDTA). The Km and Vmax of the reAnMan5A, toward locust bean gum, were 1.10 mg/mL and 266.7 units/mg, respectively. © 2011 American Chemical Society.

Tang B.,Key Laboratory of Industrial Biotechnology | Liao X.,Key Laboratory of Industrial Biotechnology | Zhang D.,Key Laboratory of Industrial Biotechnology | Li M.,Key Laboratory of Industrial Biotechnology | And 5 more authors.
Polymer Degradation and Stability | Year: 2010

Nowadays, poly(vinyl alcohol) (PVA) has caused serious pollution in the natural environment. To eliminate PVA pollution, PVA-degrading enzymes (PVADE) were studied. Previously our group has detected PVADE in a mixed microbial culture. In this study, it was found that 1,4-butanediol could enhance PVADE production. High PVADE activity (3.43 U ml-1), which was 4.6 folds of the control (0.75 U ml-1), was achieved with 1,4-butanediol as carbon source. Concomitantly, the average PVA-degrading rate improved 2.0 folds compared to the control. Specifically, diauxic growth coupled with increased PVA-degrading rate was observed. Based on this phenomenon, two-stage fermentation by adding another carbon source at a proper time was designed. By applying this strategy, high PVADE productivity (60.8 U l-1 h-1) was achieved. Further, the two-stage fermentation was extended to three-stage fermentation by adding PVA to improve PVADE production. The PVADE activity per unit biomass (YPVADE/x) was significantly enhanced over two-stage fermentation and the maximum increment was 418 U g-1. © 2010 Elsevier Ltd. All rights reserved.

Ding Y.,Jiangnan University | Ding Y.,Key Laboratory of Industrial Biotechnology | Cai Y.,Key Laboratory of Industrial Biotechnology | Cai Y.,Jiangnan University
Biopolymers | Year: 2013

The conformational dynamics of xylanase A from Streptomyces lividans (Sl-XlnA) were studied using Molecular Dynamics (MD) simulation to identify the thermally sensitive regions. Sl-XlnA begins to unfold at loop4 and this unfolding expands to the loops near the N-terminus. The high flexibility of loop6 during the 300 K simulation is related to its function. The intense movements of the 310-helices also affect the structural stability. The interaction between the α4β5-loop and the neighboring α5β6-loop plays a crucial role in stabilizing the region from the α4β5-loop to α6. The most thermally sensitive region is from β3 to loop4. The high mobility of the long loop4 easily transfers to the adjacent β4 and α4 and causes β4 and α4 to fluctuate. And, salt bridges ASP124-ARG79, ASP200-ARG159, and ASP231-LYS166 formed a "clamp" to stabilize the region including α4, β4, β5, β6, and β7. © 2013 Wiley Periodicals, Inc.

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