Development of a Genome-Scale Metabolic Model and Phenome Analysis of the Probiotic Escherichia coli Strain Nissle 1917
Abstract
:1. Introduction
2. Results
2.1. Reconstruction of the Draft Metabolic Model
2.2. Phenome Analysis
2.3. Gene Clusters Responsible for the Phenotypic Differences
2.4. Revision and Validation of the Metabolic Model
2.5. Gene Essentiality Analysis
2.6. Simulation of Utilization of Carbon Sources under Anaerobic Intestinal Environments
3. Discussion
4. Materials and Methods
4.1. Identification of Metabolic Genes and Reactions
4.2. PM Test
4.3. FBA
4.4. DNA Sequencing
4.5. Availability of Data and Materials (Nucleotide Sequence Accession Numbers)
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
AKG | α-ketoglutarate |
EcN | Escherichia coli Nissle 1917 |
ED | Entner–Doudoroff |
EMP | Embden–Meyerhof–Parnas |
FBA | Flux balance analysis |
L-LDH | L-lactate dehydrogenase |
LPS | Lipopolysaccharide |
MSP | Methionine salvage pathway |
PM | Phenotype microarray |
PTS | Phosphotransferase system |
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Substrates | PM a | Prediction b (Draft/iDK1463) | Associated Reactions c | Modification |
---|---|---|---|---|
Carbon Sources | ||||
acetoacetic acid | - | +/− | ACACtex | Deletion |
γ-amino-N-butyric acid | - | +/− | ABUTtex | Deletion |
butyric acid | - | +/− | BUTt2rpp | Deletion |
D-cellobiose | - | +/− | CELLBpts | Deactivated |
1,2-propanediol | - | +/− | LCARS | Deactivated |
L-ornithine | - | +/− | PTRCORNt7pp | Deactivated |
L-sorbose | + | −/+ | EX_srb__L_e, SRBtex, SRBptspp, SRB1PR | Addition |
PTS sugars d | + | −/+ | ACGAptspp, ACMANAptspp, FRUptspp, SBTptspp, MNLptspp, MANptspp, GAMptspp | Addition |
D-tartaric acid | - | +/− | DTARTD, SUCTARTtpp | Deactivated |
L-tartaric acid | - | +/− | TARTD, TARTRt7pp | Deactivated |
Nitrogen Sources | ||||
ethanolamine | - | +/− | ETHAtex | Deletion |
inosine | - | +/− | URIC | Deletion |
uric acid | - | +/− | URIC | Deletion |
xanthine | - | +/− | XANtex | Deletion |
Metabolic Model | iDK1463 |
---|---|
Genes | 1463 |
Metabolic reactions | 2984 |
Enzymatic reactions | 1633 |
Transport reactions | 903 |
Exchange reactions | 441 |
Demand reactions | 7 |
Gene-reaction association | 2986 |
Gene-associated reactions | 2368 |
Not gene-associated reactions | 578 |
Spontaneous reactions | 40 |
Metabolites | 2112 |
Cytoplasmic | 1160 |
Periplasmic | 509 |
Extracellular | 443 |
Unique metabolites | 1313 |
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Kim, D.; Kim, Y.; Yoon, S.H. Development of a Genome-Scale Metabolic Model and Phenome Analysis of the Probiotic Escherichia coli Strain Nissle 1917. Int. J. Mol. Sci. 2021, 22, 2122. https://doi.org/10.3390/ijms22042122
Kim D, Kim Y, Yoon SH. Development of a Genome-Scale Metabolic Model and Phenome Analysis of the Probiotic Escherichia coli Strain Nissle 1917. International Journal of Molecular Sciences. 2021; 22(4):2122. https://doi.org/10.3390/ijms22042122
Chicago/Turabian StyleKim, Dohyeon, Youngshin Kim, and Sung Ho Yoon. 2021. "Development of a Genome-Scale Metabolic Model and Phenome Analysis of the Probiotic Escherichia coli Strain Nissle 1917" International Journal of Molecular Sciences 22, no. 4: 2122. https://doi.org/10.3390/ijms22042122