11 results on '"Zhang, Ruifu"'
Search Results
2. Specialized metabolic functions of keystone taxa sustain soil microbiome stability
- Author
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Xun, Weibing, Liu, Yunpeng, Li, Wei, Ren, Yi, Xiong, Wu, Xu, Zhihui, Zhang, Nan, Miao, Youzhi, Shen, Qirong, and Zhang, Ruifu
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- 2021
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3. Robotic versus laparoscopic gastrectomy for gastric cancer: a systematic review and meta-analysis
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Ma, Jianglei, Li, Xiaoyao, Zhao, Shifu, Zhang, Ruifu, and Yang, Dejun
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- 2020
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4. A predatory myxobacterium controls cucumber Fusarium wilt by regulating the soil microbial community
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Ye, Xianfeng, Li, Zhoukun, Luo, Xue, Wang, Wenhui, Li, Yongkai, Li, Rui, Zhang, Bo, Qiao, Yan, Zhou, Jie, Fan, Jiaqin, Wang, Hui, Huang, Yan, Cao, Hui, Cui, Zhongli, and Zhang, Ruifu
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- 2020
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5. Grazing-induced microbiome alterations drive soil organic carbon turnover and productivity in meadow steppe
- Author
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Xun, Weibing, Yan, Ruirui, Ren, Yi, Jin, Dongyan, Xiong, Wu, Zhang, Guishan, Cui, Zhongli, Xin, Xiaoping, and Zhang, Ruifu
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- 2018
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6. Whole transcriptomic analysis of the plant-beneficial rhizobacterium Bacillus amyloliquefaciens SQR9 during enhanced biofilm formation regulated by maize root exudates.
- Author
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Zhang N, Yang D, Wang D, Miao Y, Shao J, Zhou X, Xu Z, Li Q, Feng H, Li S, Shen Q, and Zhang R
- Subjects
- Adaptation, Biological genetics, Bacillus growth & development, Bacterial Proteins genetics, Bacterial Proteins metabolism, Chemotaxis genetics, Cluster Analysis, Extracellular Matrix metabolism, Gene Expression Profiling, Genome, Bacterial, Genomics methods, Host-Pathogen Interactions, Metabolic Networks and Pathways genetics, Multigene Family, Bacillus genetics, Biofilms, Plant Roots microbiology, Rhizosphere, Symbiosis, Transcriptome, Zea mays microbiology
- Abstract
Background: Bacillus amyloliquefaciens SQR9 is a plant growth-promoting rhizobacteria (PGPR) with outstanding abilities to enhance plant growth and to control soil-borne diseases. Root exudates is known to play important roles in plant-microbe interactions. To explore the rhizosphere interactions and plant-beneficial characteristics of SQR9, the complete genome sequence as well as the transcriptome in response to maize root exudates under biofilm-forming conditions were elucidated., Results: Maize root exudates stimulated SQR9 biofilm formation in liquid culture, which is known to be positively correlated with enhanced root colonization. Transcriptional profiling via RNA-sequencing of SQR9 under static conditions indicated that, at 24 h post-inoculation, root exudates stimulated the expression of metabolism-relevant genes, while at 48 h post-inoculation, genes related to extracellular matrix production (tapA-sipW-tasA operon) were activated by root exudates. The individual components in maize root exudates that stimulated biofilm formation included glucose, citric acid, and fumaric acid, which either promoted the growth of SQR9 cells or activated extracellular matrix production. In addition, numerous groups of genes involved in rhizosphere adaptation and in plant-beneficial traits, including plant polysaccharide utilization, cell motility and chemotaxis, secondary antibiotics synthesis clusters, and plant growth promotion-relevant, were identified in the SQR9 genome. These genes also appeared to be induced by the maize root exudates., Conclusions: Enhanced biofilm formation of B. amyloliquefaciens SQR9 by maize root exudates could mainly be attributed to promoting cell growth and to inducing extracellular matrix production. The genomic analysis also highlighted the elements involved in the strain's potential as a PGPR. This study provides useful information for understanding plant-rhizobacteria interactions and hence for promoting the agricultural applications of this strain.
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- 2015
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7. Analysis and cloning of the synthetic pathway of the phytohormone indole-3-acetic acid in the plant-beneficial Bacillus amyloliquefaciens SQR9.
- Author
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Shao J, Li S, Zhang N, Cui X, Zhou X, Zhang G, Shen Q, and Zhang R
- Subjects
- Bacillus metabolism, Cloning, Molecular, Genetic Engineering methods, Plant Growth Regulators metabolism, Bacillus genetics, Genes, Bacterial, Indoleacetic Acids metabolism, Metabolic Networks and Pathways, Plant Growth Regulators genetics
- Abstract
Background: The plant growth-promoting rhizobacteria (PGPR) strain Bacillus amyloliquefaciens SQR9, isolated from the cucumber rhizosphere, protects the host plant from pathogen invasion and promotes plant growth through efficient root colonization. The phytohormone indole-3-acetic acid (IAA) has been suggested to contribute to the plant-growth-promoting effect of Bacillus strains. The possible IAA synthetic pathways in B. amyloliquefaciens SQR9 were investigated in this study, using a combination of chemical and genetic analysis., Results: Gene candidates involved in tryptophan-dependent IAA synthesis were identified through tryptophan response transcriptional analysis, and inactivation of genes ysnE, dhaS, yclC, and yhcX in SQR9 led to 86, 77, 55, and 24 % reductions of the IAA production, respectively. The genes patB (encoding a conserved hypothetical protein predicted to be an aminotransferase), yclC (encoding a UbiD family decarboxylase), and dhaS (encoding indole 3-acetaldehyde dehydrogenase), which were proposed to constitute the indole-3-pyruvic acid (IPyA) pathway for IAA biosynthesis, were separately expressed in SQR9 or co-expressed as an entire IAA synthesis pathway cluster in SQR9 and B. subtilis 168, all these recombinants showed increased IAA production. These results suggested that gene products of dhaS, patB, yclB, yclC, yhcX and ysnE were involved in IAA biosynthesis. Genes patB, yclC and dhaS constitute a potential complete IPyA pathway of IAA biosynthesis in SQR9., Conclusions: In conclusion, biosynthesis of IAA in B. amyloliquefaciens SQR9 occurs through multiple pathways.
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- 2015
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8. Characterization and identification of the xylanolytic enzymes from Aspergillus fumigatus Z5.
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Miao Y, Li J, Xiao Z, Shen Q, and Zhang R
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- Aspergillus fumigatus genetics, Electrophoresis, Gel, Two-Dimensional, Enzyme Stability, Fungal Proteins chemistry, Fungal Proteins genetics, Genome, Fungal, Hydrogen-Ion Concentration, Temperature, Aspergillus fumigatus enzymology, Fungal Proteins isolation & purification, Fungal Proteins metabolism, Xylans metabolism
- Abstract
Background: Plant biomass, the most abundant natural material on earth, represents a vast source of food and energy in nature. As the main component of plant biomass, xylan is a complex polysaccharide comprising a linear β(1,4)-linked backbone of xylosyl residues substituted by acetyl, arabinosyl, glucuronysyl and 4-O-methylglucuronycyl residues., Results: Aspergillus fumigatus Z5 is an efficient plant biomass depolymerization fungus. In this study, its crude xylanolytic enzymes were characterized and identified by two-dimensional gel electrophoresis (2-DE). The optimal temperature for the crude xylanases was close to 60 °C, the highest xylanase activity was achieved at pH ranged from 3 to 6, and the crude xylanases also showed a very broad region of pH (3-11) stability. The maximal xylanase activity of 21.45 U · ml(-1) was observed in the fourth day of cultivation at 50 °C and 150 rpm with 2 % xylan as the sole carbon source. Zymogram analysis indicated that there were more than seven secreted proteins with xylanase activity. In the crude enzyme, two major endoxylanases, five cellulases and several associated enzymes were identified to be involved in the hydrolysis of polysaccharides. Of the total 13 xylanase genes in the Z5 genome, 11 were observed using q-PCR to be induced by xylan, one of which, An endo-1,4-β-xylanase with a low secretion level, was also expressed and characterized. The final hydrolysis products of xylan by crude enzyme mainly consisted of xylobiose., Conclusions: This study provides a comprehensive understanding of the depolymerization of xylan by Z5 and will help to design enzymatic strategies for plant biomass utilization.
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- 2015
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9. Genome-wide transcriptomic analysis of a superior biomass-degrading strain of A. fumigatus revealed active lignocellulose-degrading genes.
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Miao Y, Liu D, Li G, Li P, Xu Y, Shen Q, and Zhang R
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- Biomass, Cellulases genetics, Cellulose genetics, Fungi genetics, Gene Expression Profiling methods, Genome, Fungal genetics, Genomics methods, Glycoside Hydrolases genetics, Transcription, Genetic genetics, Aspergillus fumigatus genetics, Fungal Proteins genetics, Lignin genetics, Transcriptome genetics
- Abstract
Background: Various saprotrophic microorganisms, especially filamentous fungi, can efficiently degrade lignocellulose that is one of the most abundant natural materials on earth. It consists of complex carbohydrates and aromatic polymers found in the plant cell wall and thus in plant debris. Aspergillus fumigatus Z5 was isolated from compost heaps and showed highly efficient plant biomass-degradation capability., Results: The 29-million base-pair genome of Z5 was sequenced and 9540 protein-coding genes were predicted and annotated. Genome analysis revealed an impressive array of genes encoding cellulases, hemicellulases and pectinases involved in lignocellulosic biomass degradation. Transcriptional responses of A. fumigatus Z5 induced by sucrose, oat spelt xylan, Avicel PH-101 and rice straw were compared. There were 444, 1711 and 1386 significantly differently expressed genes in xylan, cellulose and rice straw, respectively, when compared to sucrose as a control condition., Conclusions: Combined analysis of the genomic and transcriptomic data provides a comprehensive understanding of the responding mechanisms to the most abundant natural polysaccharides in A. fumigatus. This study provides a basis for further analysis of genes shown to be highly induced in the presence of polysaccharide substrates and also the information which could prove useful for biomass degradation and heterologous protein expression.
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- 2015
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10. Secretome diversity and quantitative analysis of cellulolytic Aspergillus fumigatus Z5 in the presence of different carbon sources.
- Author
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Liu D, Li J, Zhao S, Zhang R, Wang M, Miao Y, Shen Y, and Shen Q
- Abstract
Background: Aspergillus fumigatus Z5 has a strong ability to decompose lignocellulose biomass, and its extracellular protein secretion has been reported in earlier studies employing traditional techniques. However, a comprehensive analysis of its secretion in the presence of different carbon sources is still lacking. The goal of this work was to identify, quantify and compare the secretome of A. fumigatus Z5 in the presence of different carbon sources to understand in more details the mechanisms of lignocellulose decomposition by Aspergillus fumigatus Z5., Results: Cellulolytic A. fumigatus Z5 was grown in the presence of glucose (Gl), Avicel (Av) and rice straw (RS), and the activities of several lignocellulosic enzymes were determined with chromatometry method. The maximum activities of endoglucanase, exoglucanase, β-glucosidase, laminarinase, lichenase, xylanase and pectin lyase were 12.52, 0.59, 2.30, 2.37, 1.68, 15.02 and 11.40 U·ml-1, respectively. A total of 152, 125 and 61 different proteins were identified in the presence of RS, Av and Gl, respectively, and the proteins were functionally divided into glycoside hydrolases, lipases, peptidases, peroxidases, esterases, protein translocating transporters and hypothetical proteins. A total of 49 proteins were iTRAQ-quantified in all the treatments, and the quantification results indicated that most of the cellulases, hemicellulases and glycoside hydrolases were highly upregulated when rice straw and Avicel were used as carbon sources (compared with glucose)., Conclusions: The proteins secreted from A. fumigatus Z5 in the present of different carbon source conditions were identified by LC-MS/MS and quantified by iTRAQ-based quantitative proteomics. The results indicated that A. fumigatus Z5 could produce considerable cellulose-, hemicellulose-, pectin- and lignin-degrading enzymes that are valuable for the lignocellulosic bioenergy industry.
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- 2013
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11. Characterization of a thermostable β-glucosidase from Aspergillus fumigatus Z5, and its functional expression in Pichia pastoris X33.
- Author
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Liu D, Zhang R, Yang X, Zhang Z, Song S, Miao Y, and Shen Q
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- Amino Acid Sequence, Cloning, Molecular, Fungal Proteins chemistry, Fungal Proteins genetics, Gene Expression, Hydrogen-Ion Concentration, Kinetics, Molecular Sequence Data, Protein Stability, Recombinant Proteins chemistry, Recombinant Proteins genetics, Sequence Alignment, Substrate Specificity, Temperature, beta-Glucosidase chemistry, beta-Glucosidase genetics, Aspergillus fumigatus enzymology, Fungal Proteins biosynthesis, Pichia metabolism, Recombinant Proteins biosynthesis, beta-Glucosidase biosynthesis
- Abstract
Background: Recently, the increased demand of energy has strongly stimulated the research on the conversion of lignocellulosic biomass into reducing sugars for the subsequent production, and β-glucosidases have been the focus because of their important roles in a variety fundamental biological processes and the synthesis of useful β-glucosides. Although the β-glucosidases of different sources have been investigated, the amount of β-glucosidases are insufficient for effective conversion of cellulose. The goal of this work was to search for new resources of β-glucosidases, which was thermostable and with high catalytic efficiency., Results: In this study, a thermostable native β-glucosidase (nBgl3), which is secreted by the lignocellulose-decomposing fungus Aspergillus fumigatus Z5, was purified to electrophoretic homogeneity. Internal sequences of nBgl3 were obtained by LC-MS/MS, and its encoding gene, bgl3, was cloned based on the peptide sequences obtained from the LC-MS/MS results. bgl3 contains an open reading frame (ORF) of 2622 bp and encodes a protein with a predicted molecular weight of 91.47 kDa; amino acid sequence analysis of the deduced protein indicated that nBgl3 is a member of the glycoside hydrolase family 3. A recombinant β-glucosidase (rBgl3) was obtained by the functional expression of bgl3 in Pichia pastoris X33. Several biochemical properties of purified nBgl3 and rBgl3 were determined - both enzymes showed optimal activity at pH 6.0 and 60°C, and they were stable for a pH range of 4-7 and a temperature range of 50 to 70°C. Of the substrates tested, nBgl3 and rBgl3 displayed the highest activity toward 4-Nitrophenyl-β-D-glucopyranoside (pNPG), with specific activities of 103.5 ± 7.1 and 101.7 ± 5.2 U mg-1, respectively. However, these enzymes were inactive toward carboxymethyl cellulose, lactose and xylan., Conclusions: An native β-glucosidase nBgl3 was purified to electrophoretic homogeneity from the crude extract of A. fumigatus Z5. The gene bgl3 was cloned based on the internal sequences of nBgl3 obtained from the LC-MS/MS results, and the gene bgl3 was expressed in Pichia pastoris X33. The results of various biochemical properties of two enzymes including specific activity, pH stability, thermostability, and kinetic properties (Km and Vmax) indicated that they had no significant differences.
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- 2012
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