Vanillin production ------------------- In 2010, Brochado *et al* used heuristic optimization together with flux simulations to design a vanillin producing yeast strain. Brochado, A. R., Andrejev, S., Maranas, C. D., & Patil, K. R. (2012). Impact of stoichiometry representation on simulation of genotype-phenotype relationships in metabolic networks. PLoS Computational Biology, 8(11), e1002758. doi:10.1371/journal.pcbi.1002758 Genome-scale metabolic model ---------------------------- In their work, the authors used *iFF708* model, but recent insights in Yeast yielded newer and more complete versions. Becuase this algorithms should be agnostic to the model, we implement the same strategy with a newer model. .. code:: python from cameo import models .. code:: python model = models.bigg.iMM904 Constraints can be set in the model according to data found in the literature. The defined conditions allow the simulation of phenotypes very close to the experimental results. **Model validation by comparing in silico prediction of the specific growth rate with experimental data**. Growth phenotypes were collected from literature and compared to simulated values for chemostat cultivations at four different conditions, nitrogen limited aerobic (green) and anaerobic (red), carbon limited aerobic (blue) and anaerobic (white). Österlund, T., Nookaew, I., Bordel, S., & Nielsen, J. (2013). Mapping condition-dependent regulation of metabolism in yeast through genome-scale modeling. BMC Systems Biology, 7, 36. doi:10.1186/1752-0509-7-36 .. code:: python model.reactions.EX_glc__D_e.lower_bound = -13 #glucose exchange model.reactions.EX_o2_e.lower_bound = -3 #oxygen exchange .. code:: python model.medium .. raw:: html
reaction_id | reaction_name | lower_bound | upper_bound | |
---|---|---|---|---|
0 | EX_fe2_e | Fe2+ exchange | -999999.0 | 999999.0 |
1 | EX_glc__D_e | D-Glucose exchange | -13.0 | 999999.0 |
2 | EX_h2o_e | H2O exchange | -999999.0 | 999999.0 |
3 | EX_h_e | H+ exchange | -999999.0 | 999999.0 |
4 | EX_k_e | K+ exchange | -999999.0 | 999999.0 |
5 | EX_na1_e | Sodium exchange | -999999.0 | 999999.0 |
6 | EX_nh4_e | Ammonia exchange | -999999.0 | 999999.0 |
7 | EX_o2_e | O2 exchange | -3.0 | 999999.0 |
8 | EX_pi_e | Phosphate exchange | -999999.0 | 999999.0 |
9 | EX_so4_e | Sulfate exchange | -999999.0 | 999999.0 |
equation | lower_bound | upper_bound | |
---|---|---|---|
3DSD | 3-dehydroshikimate --> H2O + protocathechuic acid | 0.0 | 1000.0 |
ACAR_PPTase | ATP + protocathechuic acid + NADPH --> ADP + p... | 0.0 | 1000.0 |
hsOMT | S-adenosyl-L-methionine + protocatechuic aldeh... | 0.0 | 1000.0 |
UGT | Vanillin + UDP-glucose --> vanillin-B-glucoside | 0.0 | 1000.0 |
reactions | genes | size | fva_min | fva_max | target_flux | biomass_flux | yield | fitness | |
---|---|---|---|---|---|---|---|---|---|
0 | (OHPBAT, G6PI, PSERT, GLCGSD, OMCDCm, PGI, VAL... | ((YBR196C, YBL011W, YOR184W, YHR208W, YJL121C,... | 8.0 | 0.0 | 0.009158 | 0.023639 | 0.176487 | 0.001896 | 0.000335 |
1 | (OHPBAT, GLCGSD, G6PI, PSERT, OMCDCm, PGI, VAL... | ((YAR035W, YBR196C, YOR184W, YHR208W, YJL121C,... | 8.0 | 0.0 | 0.009158 | 0.023639 | 0.176487 | 0.001896 | 0.000335 |
2 | (OHPBAT, G6PI, PSERT, GLCGSD, PGI, G6PI3, RPE,... | ((YBR196C, YBL011W, YOR184W, YLR432W, YJL121C,... | 8.0 | 0.0 | 0.009158 | 0.023565 | 0.177159 | 0.001890 | 0.000335 |
3 | (OHPBAT, PMI12346PH, GLCGSD, G6PI, PSERT, PGI,... | ((YBR196C, YOR184W, YJL121C, YOR163W, YPR184W,... | 8.0 | 0.0 | 0.009158 | 0.023565 | 0.177159 | 0.001890 | 0.000335 |
4 | (OHPBAT, G6PI, PSERT, ALATA_L, PGI, G6PI3, RPE... | ((YDR111C, YBR196C, YOR184W, YOR377W, YJL121C,... | 8.0 | 0.0 | 0.009063 | 0.023205 | 0.180413 | 0.001862 | 0.000336 |
5 | (OHPBAT, GLCGSD, G6PI, PSERT, PGI, AMETt2, G6P... | ((YBR196C, YOR184W, YOR071C, YJL121C, YPR184W,... | 8.0 | 0.0 | 0.009158 | 0.023565 | 0.177159 | 0.001890 | 0.000335 |
6 | (OHPBAT, FAS120ACPm, PSERT, PGI, FAS80ACPm_L, ... | ((YAR035W, YBR196C, YER061C, YOR184W, YJL121C,... | 8.0 | 0.0 | 0.009158 | 0.023565 | 0.177159 | 0.001890 | 0.000335 |
... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
30 | (OHPBAT, ALLTTti, GLCGSD, G6PI, PSERT, PGI, G6... | ((YAR035W, YBR196C, YOR184W, YJL121C, YPR184W,... | 9.0 | 0.0 | 0.009158 | 0.023565 | 0.177159 | 0.001890 | 0.000335 |
31 | (OHPBAT, ALLTTti, GLCGSD, G6PI, PSERT, PGI, G6... | ((YBR196C, YOR184W, YBR166C, YJL121C, YPR184W,... | 9.0 | 0.0 | 0.009158 | 0.023494 | 0.177800 | 0.001891 | 0.000336 |
32 | (GALKr, OHPBAT, G6PI, PSERT, AGTi, PGI, G6PI3,... | ((YBR196C, YOR184W, YJL121C, YDL052C, YOL064C,... | 9.0 | 0.0 | 0.008878 | 0.023364 | 0.178975 | 0.001876 | 0.000336 |
33 | (GALKr, OHPBAT, DKMPPD2, G6PI, PSERT, AGTi, PG... | ((YLR354C, YBR196C, YOR184W, YMR009W, YER099C,... | 9.0 | 0.0 | 0.008878 | 0.023388 | 0.178755 | 0.001878 | 0.000336 |
34 | (FAO141p_odd, OHPBAT, FAO141p_even, PSERT, FAO... | ((YAR035W, YBR196C, YOR184W, YJL121C, YPR184W,... | 9.0 | 0.0 | 0.009158 | 0.023565 | 0.177159 | 0.001890 | 0.000335 |
35 | (OHPBAT, GLCGSD, G6PI, PSERT, ALLTTti, PGI, G6... | ((YBR196C, YOR184W, YJL121C, YPR184W, YMR118C,... | 9.0 | 0.0 | 0.009158 | 0.023565 | 0.177159 | 0.001890 | 0.000335 |
36 | (OHPBAT, PSERT, AGTi, PGI, RPE, POLYAO3, ORNDC... | ((YLR354C, YBR196C, YOR180C, YOR184W, YJL121C,... | 9.0 | 0.0 | 0.008878 | 0.023388 | 0.178755 | 0.001878 | 0.000336 |
37 rows × 9 columns