Reconstruction and analysis of a genome-scale metabolic model for Eriocheir sinensis eyestalks

2016 ◽  
Vol 12 (1) ◽  
pp. 246-252 ◽  
Author(s):  
Bin Wang ◽  
Qianji Ning ◽  
Tong Hao ◽  
Ailing Yu ◽  
Jinsheng Sun
Keyword(s):  
Metabolic Network ◽  
Network Model ◽  
Transcriptome Sequencing ◽  
Metabolic Model ◽  
Eriocheir Sinensis ◽  
Metabolic Network Model ◽  
A Genome ◽  
Genome Scale

We reconstructed a metabolic network model for E. sinensis eyestalks based on transcriptome sequencing which contains 1304 reactions, 1381 unigenes and 1243 metabolites distributing in 98 pathways.

scholarly journals Generation and Evaluation of a Genome-Scale Metabolic Network Model of Synechococcus elongatus PCC7942

Metabolites ◽  
2014 ◽  
Vol 4 (3) ◽  
pp. 680-698 ◽  
Author(s):  
Julián Triana ◽  
Arnau Montagud ◽  
Maria Siurana ◽  
David Fuente ◽  
Arantxa Urchueguía ◽  
...  
Keyword(s):  
Metabolic Network ◽  
Network Model ◽  
Synechococcus Elongatus ◽  
Metabolic Network Model ◽  
Synechococcus Elongatus Pcc7942 ◽  
A Genome ◽  
Genome Scale

scholarly journals Integrating quantitative proteomics and metabolomics with a genome-scale metabolic network model

2010 ◽  
Vol 26 (12) ◽  
pp. i255-i260 ◽  
Author(s):  
K. Yizhak ◽  
T. Benyamini ◽  
W. Liebermeister ◽  
E. Ruppin ◽  
T. Shlomi
Keyword(s):  
Metabolic Network ◽  
Network Model ◽  
Quantitative Proteomics ◽  
Metabolic Network Model ◽  
A Genome ◽  
Genome Scale

scholarly journals Manually curated genome-scale reconstruction of the metabolic network of Bacillus megaterium DSM319

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Javad Aminian-Dehkordi ◽  
Seyyed Mohammad Mousavi ◽  
Arezou Jafari ◽  
Ivan Mijakovic ◽  
Sayed-Amir Marashi
Keyword(s):  
Experimental Data ◽  
Metabolic Network ◽  
Bacillus Megaterium ◽  
In Silico ◽  
Metabolic Model ◽  
Growth Behavior ◽  
Industrial Biotechnology ◽  
Flux Analysis ◽  
A Genome ◽  
Genome Scale

AbstractBacillus megaterium is a microorganism widely used in industrial biotechnology for production of enzymes and recombinant proteins, as well as in bioleaching processes. Precise understanding of its metabolism is essential for designing engineering strategies to further optimize B. megaterium for biotechnology applications. Here, we present a genome-scale metabolic model for B. megaterium DSM319, iJA1121, which is a result of a metabolic network reconciliation process. The model includes 1709 reactions, 1349 metabolites, and 1121 genes. Based on multiple-genome alignments and available genome-scale metabolic models for other Bacillus species, we constructed a draft network using an automated approach followed by manual curation. The refinements were performed using a gap-filling process. Constraint-based modeling was used to scrutinize network features. Phenotyping assays were performed in order to validate the growth behavior of the model using different substrates. To verify the model accuracy, experimental data reported in the literature (growth behavior patterns, metabolite production capabilities, metabolic flux analysis using 13C glucose and formaldehyde inhibitory effect) were confronted with model predictions. This indicated a very good agreement between in silico results and experimental data. For example, our in silico study of fatty acid biosynthesis and lipid accumulation in B. megaterium highlighted the importance of adopting appropriate carbon sources for fermentation purposes. We conclude that the genome-scale metabolic model iJA1121 represents a useful tool for systems analysis and furthers our understanding of the metabolism of B. megaterium.

scholarly journals Improvement of l-arginine production by in silico genome-scale metabolic network model guided genetic engineering

3 Biotech ◽  
2020 ◽  
Vol 10 (3) ◽  
Author(s):  
Mingzhu Huang ◽  
Yue Zhao ◽  
Rong Li ◽  
Weihua Huang ◽  
Xuelan Chen
Keyword(s):  
Genetic Engineering ◽  
Metabolic Network ◽  
Network Model ◽  
In Silico ◽  
Metabolic Network Model ◽  
Genome Scale

IN SILICO GENOME-SCALE RECONSTRUCTION AND ANALYSIS OF THE SHEWANELLA LOIHICA PV-4 METABOLIC NETWORK

2018 ◽  
Vol 26 (03) ◽  
pp. 373-397
Author(s):  
ZIXIANG XU ◽  
JING GUO ◽  
YUNXIA YUE ◽  
JING MENG ◽  
XIAO SUN
Keyword(s):  
Metabolic Network ◽  
Network Model ◽  
Microbial Fuel Cells ◽  
Metabolic Networks ◽  
Acid Metabolism ◽  
Electricity Production ◽  
Nucleic Acid Metabolism ◽  
Exchange Reactions ◽  
A Genome ◽  
Genome Scale

Microbial Fuel Cells (MFCs) are devices that generate electricity directly from organic compounds with microbes (electricigens) serving as anodic catalysts. As a novel environment-friendly energy source, MFCs have extensive practical value. Since the biological features and metabolic mechanism of electricigens have a great effect on the electricity production of MFCs, it is a big deal to screen strains with high electricity productivity for improving the power output of MFC. Reconstructions and simulations of metabolic networks are of significant help in studying the metabolism of microorganisms so as to guide gene engineering and metabolic engineering to improve their power-generating efficiency. Herein, we reconstructed a genome-scale constraint-based metabolic network model of Shewanella loihica PV-4, an important electricigen, based on its genomic functional annotations, reaction databases and published metabolic network models of seven microorganisms. The resulting network model iGX790 consists of 902 reactions (including 71 exchange reactions), 798 metabolites and 790 genes, covering the main pathways such as carbon metabolism, energy metabolism, amino acid metabolism, nucleic acid metabolism and lipid metabolism. Using the model, we simulated the growth rate, the maximal synthetic rate of ATP, the flux variability analysis of metabolic network, gene deletion and so on to examine the metabolism of S. loihica PV-4.

scholarly journals Reconstruction and Analysis of a Genome-Scale Metabolic Network for Eriocheir Sinensis Hepatopancreas

IEEE Access ◽  
2018 ◽  
Vol 6 ◽  
pp. 79235-79244 ◽  
Author(s):  
Tong Hao ◽  
Bin Wang ◽  
Lingxuan Zhao ◽  
Xin Feng ◽  
Jinsheng Sun
Keyword(s):  
Metabolic Network ◽  
Eriocheir Sinensis ◽  
A Genome ◽  
Genome Scale
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