F. Bezold, J. Scheffer, P. Wendering, Z. Razaghi-Moghadam, J. Trauth, B. Pook, H. Nußhär, S. Hasenjäger, Z. Nikoloski, L.-O. Essen, C. Taxis, Optogenetic control of Cdc48 for dynamic metabolic engineering in yeast. Metab. Eng. 79, 97–107 (2023). doi: 10.1016/j.ymben.2023.06.013
- Matlab (tested with 2020a and b)
- COBRA Toolbox 3.0 (Heirendt et al. (2019), doi: 10.1038/s41596-018-0098-2
- GECKO Toolbox 2.0 (Sanchéz et al. (2017), doi: 10.15252/msb.20167411, Domenzain et al. (2021), doi: 10.1101/2021.03.05.433259)
- Gurobi solver (tested with version 9.1.1)
- clone repository, change into Code subdirectory
- add gurobi solver to Matlab path
- FVA_CDC48, FVA_Clb2: flux variability analysis in dark and blue light conditions
- enrichment_analysis: find enriched pathways in reactions with non-overlapping flux ranges
Run RENZO:
results = RENZO(model_mt, model_wt, msrd_protein_ids, Ptot_mt, Ptot_wt,...
protein_abundance_ratio, biomass_ratio, GAM, NCPU, bio_name, f, ratio_tol)
| Input parameter | Class | Description |
|---|---|---|
| model_mt | struct | mutant-specific ecModel |
| model_wt | struct | wild-type-specifc ecModel |
| msrd_protein_ids | cellstr | Swissprot IDs of measured proteins |
| Ptot_mt | double | total protein content (mutant) |
| Ptot_wt | double | total protein content (wild type) |
| protein_abundance_ratio | double | ratios of protein abundances (mutant/wild type) (number of rows must correspond to the number of Swissprot IDs) |
| biomass_ratio | double | ratio between mutant and wild type biomass |
| GAM | struct | fields: mut, wt, contain growth-associated maintenance for mutant and wild type |
| NCPU | double | number of workers for parallel pool (optional, default: 1) |
| bio_name | char | name of biomass reaction in model (optional, default: biomass) |
| f | double | fraction of protein mass that is accounted for in the ecModel (optional, default: 0.5) |
| ratio_tol | double | tolerance for the ratio between predicted and measured protein ratios (optional, default: 1e-5) |
results is a struct with fields
| Field | Content |
|---|---|
| FVA_min | reaction flux minima |
| FVA_max | reaction flux maxima |
| infeasible_min | number of infeasible minimization programs |
| infeasible_max | number of infeasible maximization programs |
| distinct_rxns | reactions with non-overlapping flux ranges |
| genes_in_distrinct_rxns | genes associated with distinct_rxns |