scholarly journals Effects of Different Substrates on Lignocellulosic Enzyme Expression, Enzyme Activity, Substrate Utilization and Biological Efficiency of Pleurotus Eryngii

2016 ◽  
Vol 39 (4) ◽  
pp. 1479-1494 ◽  
Author(s):  
Chunliang Xie ◽  
Li Yan ◽  
Wenbing Gong ◽  
Zuohua Zhu ◽  
Senwei Tan ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Carbon Sources ◽  
Pleurotus Eryngii ◽  
Extracellular Proteins ◽  
Biological Efficiency ◽  
Biomass Degradation ◽  
Lignocellulosic Substrates ◽  
Proteomic Approach ◽  
Lignocellulosic Enzymes ◽  
Lignin Depolymerization

Background/Aims: Pleurotus eryngii is one of the most valued and delicious mushrooms which are commercially cultivated on various agro-wastes. How different substrates affect lignocellulosic biomass degradation, lignocellulosic enzyme production and biological efficiency in Pleurotus eryngii was unclear. Methods and Results: In this report, Pleurotus eryngii was cultivated in substrates including ramie stalks, kenaf stalks, cottonseed hulls and bulrush stalks. The results showed that ramie stalks and kenaf stalks were found to best suitable to cultivate Pleurotus eryngii with the biological efficiency achieved at 55% and 57%, respectively. In order to establish correlations between different substrates and lignocellulosic enzymes expression, the extracellular proteins from four substrates were profiled with high throughput TMT-based quantitative proteomic approach. 241 non-redundant proteins were identified and 74 high confidence lignocellulosic enzymes were quantified. Most of the cellulases, hemicellulases and lignin depolymerization enzymes were highly up-regulated when ramie stalks and kenaf stalks were used as carbon sources. The enzyme activities results suggested cellulases, hemicellulases and lignin depolymerization enzymes were significantly induced by ramie stalks and kenaf stalks. Conclusion: The lignocelluloses degradation, most of the lignocellulosic enzymes expressions and activities of Pleurotus eryngii had positive correlation with the biological efficiency, which depend on the nature of lignocellulosic substrates. In addition, the lignocellulosic enzymes expression profiles during Pleurotus eryngii growth in different substrates were obtained. The present study suggested that most of the lignocellulosic enzymes expressions and activities can be used as tools for selecting better performing substrates for commercial mushroom cultivation.

Protein expression profiles in pediatric multiple sclerosis: potential biomarkers

2009 ◽  
Vol 15 (4) ◽  
pp. 455-464 ◽  
Author(s):  
KN Rithidech ◽  
L Honikel ◽  
M Milazzo ◽  
D Madigan ◽  
R Troxell ◽  
...  
Keyword(s):  
Multiple Sclerosis ◽  
Mass Spectrometry ◽  
Protein Expression ◽  
Expression Profiles ◽  
Low Frequency ◽  
Complement Factor ◽  
Protein Biomarkers ◽  
Two Dimensional Gel Electrophoresis ◽  
Pediatric Multiple Sclerosis ◽  
Proteomic Approach

The diagnosis of pediatric multiple sclerosis (MS) is challenging due to its low frequency and the overlap with other acquired childhood demyelinating disorders of the central nervous system. To identify potential protein biomarkers which could facilitate the diagnosis, we used two-dimensional gel electrophoresis (2-DE) in combination with mass spectrometry to identify proteins associated with pediatric MS. Plasma samples from nine children with MS and nine healthy subjects, matched in aggregate by age and gender, were analyzed for differences in their patterns of protein expression. We found 12 proteins that were significantly up regulated in the pediatric MS group: alpha-1-acid-glycoprotein 1, alpha-1-B-glycoprotein, transthyretin, apoliprotein-C-III, serum amyloid P component, complement factor-I, clusterin, gelsolin, hemopexin, kininogen-1, hCG1993037-isoform, and vitamin D-binding protein. These results show that 2-DE in combination with mass spectrometry is a highly sensitive technique for the identification of blood-based biomarkers. This proteomic approach could lead to a new panel of diagnostic and prognostic markers in pediatric MS.

Gene expression profiles based flux balance model to predict the carbon source for Bacillus subtilis

2019 ◽  
Author(s):  
Kulwadee Thanamit ◽  
Franziska Hoerhold ◽  
Marcus Oswald ◽  
Rainer Koenig
Keyword(s):  
Gene Expression ◽  
Carbon Source ◽  
Drug Targets ◽  
Expression Profiles ◽  
Carbon Sources ◽  
Gene Expression Profiles ◽  
Fast Method ◽  
Flux Balance ◽  
Metabolic Fluxes

ABSTRACTFinding drug targets for antimicrobial treatment is a central focus in biomedical research. To discover new drug targets, we developed a method to identify which nutrients are essential for microorganisms. Using 13C labeled metabolites to infer metabolic fluxes is the most informative way to infer metabolic fluxes to date. However, the data can get difficult to acquire in complicated environments, for example, if the pathogen homes in host cells. Although data from gene expression profiling is less informative compared to metabolic tracer derived data, its generation is less laborious, and may still provide the relevant information. Besides this, metabolic fluxes have been successfully predicted by flux balance analysis (FBA). We developed an FBA based approach using the stoichiometric knowledge of the metabolic reactions of a cell combining them with expression profiles of the coding genes. We aimed to identify essential drug targets for specific nutritional uptakes of microorganisms. As a case study, we predicted each single carbon source out of a pool of eight different carbon sources for B. subtilis based on gene expression profiles. The models were in good agreement to models basing on 13C metabolic flux data of the same conditions. We could well predict every carbon source. Later, we applied successfully the model to unseen data from a study in which the carbon source was shifted from glucose to malate and vice versa. Technically, we present a new and fast method to reduce thermodynamically infeasible loops, which is a necessary preprocessing step for such model-building algorithms.SIGNIFICANCEIdentifying metabolic fluxes using 13C labeled tracers is the most informative way to gain insight into metabolic fluxes. However, obtaining the data can be laborious and challenging in a complex environment. Though transcriptional data is an indirect mean to estimate the fluxes, it can help to identify this. Here, we developed a new method employing constraint-based modeling to predict metabolic fluxes embedding gene expression profiles in a linear regression model. As a case study, we used the data from Bacillus subtilis grown under different carbon sources. We could well predict the correct carbon source. Additionally, we established a novel and fast method to remove thermodynamically infeasible loops.

scholarly journals Evaluation of Using Spent Mushroom Sawdust Wastes for Cultivation of Auricularia polytricha

Agronomy ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 1892
Author(s):  
Chiu-Yeh Wu ◽  
Chih-Hung Liang ◽  
Zeng-Chin Liang
Keyword(s):  
Fruiting Body ◽  
Pleurotus Ostreatus ◽  
Pleurotus Eryngii ◽  
Biological Efficiency ◽  
Main Ingredient ◽  
Auricularia Polytricha ◽  
Pleurotus Cystidiosus

The purpose of this study was to investigate the suitability of different spent mushroom sawdust wastes (SMSWs) and different proportions of SMSWs as potential substrates for the cultivation of Auricularia polytricha by evaluating yield and biological efficiency of the fruiting body. Nine SMSWs were respectively utilized as the main ingredient in the cultivation of A. polytricha. Then, spent Pleurotus eryngii, Pleurotus cystidiosus, and Pleurotus ostreatus sawdust wastes were screened among these nine SMSWs to be utilized as substrate and to determine the suitable proportion of SMSW in the cultivation of A. polytricha based on their yields and biological efficiencies. The highest yield and biological efficiency (total of two flushes) of A. polytricha cultivation on a single SMSW substrate was obtained with spent P. eryngii sawdust waste, followed by spent P. cystidiosus and P. ostreatus sawdust wastes. These three SMSWs were then applied in nine combination substrates, which were screened based on yield and biological efficiency for cultivation of A. polytricha. The combination substrate with the highest yield and biological efficiency of A. polytricha cultivation was P. eryngii (PES) + P. cystidiosus spent sawdust (PCYS) (235.4 g/bag yield and 58.85% biological efficiency); its yield was 1.62 folds higher than that of the control. From the results, we found that it was feasible to use spent sawdust wastes of P. eryngii and P. cystidiosus to replace sawdust for cultivation of A. polytricha.

scholarly journals Comparative Proteomic Analysis of Extracellular Proteins of Enterohemorrhagic and Enteropathogenic Escherichia coli Strains and Their ihf and ler Mutants

2004 ◽  
Vol 70 (9) ◽  
pp. 5274-5282 ◽  
Author(s):  
M. Li ◽  
I. Rosenshine ◽  
S. L. Tung ◽  
X. H. Wang ◽  
D. Friedberg ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Polyacrylamide Gel Electrophoresis ◽  
Integration Host Factor ◽  
Extracellular Proteins ◽  
Major Protein ◽  
Human Pathogens ◽  
Protein Database ◽  
Flight Mass Spectrometry ◽  
Proteomic Approach ◽  
In The Wild

ABSTRACT Enterohemorrhagic and enteropathogenic Escherichia coli (EHEC and EPEC, respectively) strains are closely related human pathogens that are responsible for food-borne epidemics in many countries. Integration host factor (IHF) and the locus of enterocyte effacement-encoded regulator (Ler) are needed for the expression of virulence genes in EHEC and EPEC, including the elicitation of actin rearrangements for attaching and effacing lesions. We applied a proteomic approach, using two-dimensional polyacrylamide gel electrophoresis in combination with matrix-assisted laser desorption ionization-time of flight mass spectrometry and a protein database search, to analyze the extracellular protein profiles of EHEC EDL933, EPEC E2348/69, and their ihf and ler mutants. Fifty-nine major protein spots from the extracellular proteomes were identified, including six proteins of unknown function. Twenty-six of them were conserved between EHEC EDL933 and EPEC E2348/69, while some of them were strain-specific proteins. Four common extracellular proteins (EspA, EspB, EspD, and Tir) were regulated by both IHF and Ler in EHEC EDL933 and EPEC E2348/69. TagA in EHEC EDL933 and EspC and EspF in EPEC E2348/69 were present in the wild-type strains but absent from their respective ler and ihf mutants, while FliC was overexpressed in the ihf mutant of EPEC E2348/69. Two dominant forms of EspB were found in EHEC EDL933 and EPEC E2348/69, but the significance of this is unknown. These results show that proteomics is a powerful platform technology for accelerating the understanding of EPEC and EHEC pathogenesis and identifying markers for laboratory diagnoses of these pathogens.

Transcriptional profiling of biomass degradation-related genes during Trichoderma reesei growth on different carbon sources

2014 ◽  
Vol 173 ◽  
pp. 59-64 ◽  
Author(s):  
Xiuzhen Chen ◽  
Yingfeng Luo ◽  
Hongtao Yu ◽  
Yuhui Sun ◽  
Hong Wu ◽  
...  
Keyword(s):  
Trichoderma Reesei ◽  
Transcriptional Profiling ◽  
Carbon Sources ◽  
Biomass Degradation

scholarly journals Inferring Carbon Sources from Gene Expression Profiles Using Metabolic Flux Models

PLoS ONE ◽  
2012 ◽  
Vol 7 (5) ◽  
pp. e36947 ◽  
Author(s):  
Aaron Brandes ◽  
Desmond S. Lun ◽  
Kuhn Ip ◽  
Jeremy Zucker ◽  
Caroline Colijn ◽  
...  
Keyword(s):  
Gene Expression ◽  
Metabolic Flux ◽  
Expression Profiles ◽  
Carbon Sources ◽  
Gene Expression Profiles

scholarly journals Protein Expression Profiles in an Endosymbiotic Cyanobacterium Revealed by a Proteomic Approach

2006 ◽  
Vol 19 (11) ◽  
pp. 1251-1261 ◽  
Author(s):  
Martin Ekman ◽  
Petter Tollbäck ◽  
Johan Klint ◽  
Birgitta Bergman
Keyword(s):  
Mass Spectrometry ◽  
Protein Expression ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Calvin Cycle ◽  
Pentose Phosphate ◽  
Free Living ◽  
Two Dimensional Gel Electrophoresis ◽  
Proteomic Approach ◽  
Nostoc Strain

Molecular mechanisms behind adaptations in the cyano-bacterium (Nostoc sp.) to a life in endosymbiosis with plants are still not clarified, nor are the interactions between the partners. To get further insights, the proteome of a Nostoc strain, freshly isolated from the symbiotic gland tissue of the angiosperm Gunnera manicata Linden, was analyzed and compared with the proteome of the same strain when free-living. Extracted proteins were separated by two-dimensional gel electrophoresis and were identified by matrix-assisted laser desorption/ionization-time of flight mass spectrometry combined with tandem mass spectrometry. Even when the higher percentage of differentiated cells (heterocysts) in symbiosis was compensated for, the majority of the proteins detected in the symbiotic cyanobacteria were present in the free-living counterpart, indicating that most cellular processes were common for both stages. However, differential expression profiling revealed a significant number of proteins to be down-regulated or missing in the symbiotic stage, while others were more abundant or only expressed in symbiosis. The differential protein expression was primarily connected to i) cell envelope-associated processes, including proteins involved in exopolysaccharide synthesis and surface and membrane associated proteins, ii) to changes in growth and metabolic activities (C and N), including upregulation of nitrogenase and proteins involved in the oxidative pentose phosphate pathway and downregu-lation of Calvin cycle enzymes, and iii) to the dark, micro-aerobic conditions offered inside the Gunnera gland cells, including changes in relative phycobiliprotein concentrations. This is the first comprehensive analysis of proteins in the symbiotic state.

scholarly journals OPTIMIZATION OF KING OYSTER MUSHROOM (PLEUROTUS ERYNGII) PRODUCTION AGAINST COTTON WASTE AND FENUGREEK STRAW

2018 ◽  
Vol 30 (2) ◽  
pp. 149
Author(s):  
Waseem Iqbal ◽  
Muhammad M. Jahangir ◽  
Chaudhary M. Ayyub ◽  
Nasir A. Khan ◽  
Ghufrana Samin ◽  
...  
Keyword(s):  
Pleurotus Eryngii ◽  
Growth And Yield ◽  
Yield Potential ◽  
Biological Efficiency ◽  
Nutritional Components ◽  
Body Development ◽  
Cotton Waste ◽  
Fruiting Body Development ◽  
King Oyster Mushroom ◽  
Set Up

King oyster (Pleurotus eryngii) mushroom is a palatable mushroom with high commercial potential due to relative ease of its growing technology, less cost of production and better yield potential, making it popular throughout the world. Therefore, an experiment was set up to assess the efficacy of different agro-wastes [cotton waste (CW) and fenugreek straw (FS)] on the morphology, yield and nutritional components of two strains (Pleurotus eryngii P9 strain and Pleurotus eryngii P10 strain) of Pleurotus eryngii. Studied indicators regarding time for pinhead formation, fruiting body development, biological efficiency and yield of both strains were significantly affected by different formulations of substrates. Substrates with 100 % CW exhibited maximum number of pinheads, yield and biological efficiency for both strains of king oyster as compared to other substrates alone or in mixture. This experiment indicates the possibility of Pleurotus eryngii cultivation on cotton waste and fenugreek straw in controlled conditions for enhanced growth and yield.

scholarly journals Genomic and transcriptomic analysis of the thermophilic lignocellulose-degrading fungus Thielavia terrestris LPH172

2020 ◽  
Author(s):  
Monika Tõlgo ◽  
Silvia Hüttner ◽  
Nguyen Than Thuy ◽  
Vu Nguyen Than ◽  
Johan Larsbrink ◽  
...  
Keyword(s):  
Gc Content ◽  
Low Ph ◽  
Biomass Degradation ◽  
Carbohydrate Active Enzymes ◽  
Thielavia Terrestris ◽  
Biomass Saccharification ◽  
Lignocellulosic Substrates ◽  
Lytic Polysaccharide Monooxygenases ◽  
Beechwood Xylan ◽  
Polysaccharide Monooxygenases

Abstract Background: Biomass-degrading enzymes with improved activity and stability can ameliorate substrate saccharification and make biorefineries economically feasible. Filamentous fungi are a rich source of carbohydrate-active enzymes (CAZymes) for biomass degradation. The newly isolated LPH172 strain of the thermophilic Ascomycete Thielavia terrestris has been shown to possess high xylanase and cellulase activities and tolerate well low pH and high temperatures. Here, we aimed to illuminate the lignocellulose degrading machinery and novel carbohydrate-active enzymes in LPH172 in detail.Results: We sequenced and analysed the 36.6-Mb genome and transcriptome of LPH172 during growth on glucose, cellulose, rice straw, and beechwood xylan. In total, 411 CAZy domains were found among 10,128 predicted genes. Compared to other fungi, auxiliary activity (AA) enzymes were particularly enriched. GC content was higher in coding sequences than in the overall genome. A high GC3 content was hypothesised to contribute to thermophilicity. T. terrestris employed mainly lytic polysaccharide monooxygenases (LPMOs) and glycoside hydrolase (GH) family 7 glucanases to attack cellulosic substrates, and conventional hemicellulases (GH10 and GH11) to degrade xylan. The observed co-expression and co-upregulation of AA9 LPMOs, other AA CAZymes, and (hemi)cellulases points to a complex and nuanced degradation strategy. Growth on more complex and heterogeneous substrates resulted in a more varied but generally lower gene expression. Conclusions: Our analysis of the genome and transcriptome of T. terrestris LPH172 elucidates the enzyme arsenal the fungus uses to degrade lignocellulosic substrates. The study provides the basis for future characterisation of potential new enzymes for industrial biomass saccharification.

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