Yeast Cell Factory: Large-scale in silico strain design for enhanced production of +100 chemicals in S. cerevisiae

• Brief Model Description:

This repository contains the data and scripts necessary for in silico strain design for enhanced production of +103 chemicals using an enzyme-constrained model of S. cerevisiae's metabolism.

• KeyWords:

Category: Constraint-based methods; Utilisation: predictive simulation, in silico strain design; Field: cell factory in silico design; Metabolic engineering Model Source: yeast-GEM,ecYeastGEM; Taxonomy: Saccharomyces cerevisiae; Metabolic System: General Metabolism; enzyme constraints.

• Last update: 2025-02-12

Product list:

• Note: The predicted gene targets for the following bioproducts can be found in https://github.com/SysBioChalmers/CellFactory-ecYeastGEM/tree/dev/results/production_targets. For each bioproduct, the gene targets could be divided into three levels- L1, L2, and L3 based on the filtration steps in ecFactory (https://github.com/SysBioChalmers/ecFactory).”

Name	Formula	KEGG ID	CHEBI ID	Group	class	Gene target
(R,R)-2,3-butanediol	C4H10O2	C03044	16982	native	alcohol	Link
2-phenylethanol	C8H10O	C05853	49000	native	alcohol	Link
glycerol	C3H8O3	C00116	17754	native	alcohol	Link
isoamylol	C5H12O	C07328	15837	native	alcohol	Link
isobutanol	C4H10O	C14710	46645	native	alcohol	Link
choline	C5H14NO	C00114	15354	native	alkaloid	Link
hypoxanthine	C5H4N4O	C00262	17368	native	alkaloid	Link
xanthine	C5H4N4O2	C00385	17712	native	alkaloid	Link
glutathione	C10H17N3O6S	C00051	16856	native	amino acid	Link
L-alanine	C3H7NO2	C00041	16977	native	amino acid	Link
L-arginine	C6H14N4O2	C00062	16467	native	amino acid	Link
L-asparagine	C4H8N2O3	C00152	17196	native	amino acid	Link
L-aspartate	C4H7NO4	C00049	17053	native	amino acid	Link
L-citrulline	C6H13N3O3	C00327	16349	native	amino acid	Link
L-cysteine	C3H7NO2S	C00097	17561	native	amino acid	Link
L-glutamate	C5H8NO4	C00025	29985	native	amino acid	Link
L-glutamine	C5H10N2O3	C00064	18050	native	amino acid	Link
L-glycine	C2H5NO2	C00037	15428	native	amino acid	Link
L-histidine	C6H9N3O2	C00135	15971	native	amino acid	Link
L-homoserine	C4H9NO3	C00263	15699	native	amino acid	Link
L-isoleucine	C6H13NO2	C00407	17191	native	amino acid	Link
L-leucine	C6H13NO2	C00123	15603	native	amino acid	Link
L-lysine	C6H15N2O2	C00047	32551	native	amino acid	Link
L-methionine	C5H11NO2S	C00073	16643	native	amino acid	Link
L-phenylalanine	C9H11NO2	C00079	17295	native	amino acid	Link
L-proline	C5H9NO2	C00148	17203	native	amino acid	Link
L-serine	C3H7NO3	C00065	17115	native	amino acid	Link
L-threonine	C4H9NO3	C00188	16857	native	amino acid	Link
L-tryptophan	C11H12N2O2	C00078	16828	native	amino acid	Link
L-tyrosine	C9H11NO3	C00082	17895	native	amino acid	Link
L-valine	C5H11NO2	C00183	16414	native	amino acid	Link
ornithine	C5H13N2O2	C01602	46912	native	amino acid	Link
putrescine	C4H14N2	C00134	326268	native	bioamine	Link
spermine	C10H30N4	C00750	45725	native	bioamine	Link
Free fatty acids	nan	nan	nan	native	fatty acids and lipids	Link
laurate	C12H23O2	C02679	18262	native	fatty acids and lipids	Link
oleate	C18H34O2	C00712	16196	native	fatty acids and lipids	Link
palmitoleate	C16H29O2	C08362	32372	native	fatty acids and lipids	Link
succinate	C4H4O4	C00042	30031	native	fatty acids and lipids	Link
triacylglycerol	C6H5O6R3	C00422	17855	native	fatty acids and lipids	Link
guanine	C5H5N5O	C00242	16235	native	nucleic acid	Link
thymidine	C10H14N2O5	C00214	17748	native	nucleic acid	Link
(S)-lactate	C3H6O3	C00186	16651	native	organic acid	Link
(S)-malate	C4H6O5	C00149	15589	native	organic acid	Link
2-oxoglutarate	C5H6O5	C00026	16810	native	organic acid	Link
acetate	C2H4O2	C00033	15366	native	organic acid	Link
citrate	C6H8O7	C00158	16947	native	organic acid	Link
fumarate	C4H4O4	C00122	18012	native	organic acid	Link
glycolate	C2H4O3	C00160	17497	native	organic acid	Link
hexanoate	C6H12O2	C01585	17120	native	organic acid	Link
pyruvate	C3H3O3	C00022	15361	native	organic acid	Link
acetaldehyde	C2H4O	C00084	15343	native	other	Link
urea	CH4N2O	C00086	16199	native	other	Link
ergosterol	C28H44O	C01694	16933	native	other	Link
L-phenylacetylcarbinol	C9H10O2	nan	nan	heterologous	alcohol	Link
n-butanol	C4H10O	C06142	28885	heterologous	alcohol	Link
(S)-Reticuline	C19H23NO4	C02105	16718	heterologous	alkaloid	Link
psilocybin	C12H17N2O4P	C07576	8614	heterologous	alkaloid	Link
Nicotianamine	C12H21N3O6	C05324	17721	heterologous	amino acid	Link
4-hydroxymandelic	C8H8O4	C11527	16388	heterologous	aromatic	Link
cinnamate	C9H8O2	C00423	15669	heterologous	aromatic	Link
mandelic	C8H8O3	C01984	17756	heterologous	aromatic	Link
p-coumaric acid	C9H8O3	C00811	32374	heterologous	aromatic	Link
rosmarinate	C18H16O8	C01850	50371	heterologous	aromatic	Link
Salidroside	C14H20O7	C06046	9009	heterologous	aromatic	Link
Tyrosol	C8H10O2	C06044	1879	heterologous	aromatic	Link
vanillinbetaglucoside	nan	nan	nan	heterologous	aromatic	Link
ARA	C20H32O2	C00219	15843	heterologous	fatty acids and lipids	Link
DHA	C22H32O2	C06429	28125	heterologous	fatty acids and lipids	Link
EPA	C20H30O2	C06428	28364	heterologous	fatty acids and lipids	Link
docosanol	C22H46O	D03884	31000	heterologous	alcohol	Link
catechin	C15H14O6	C06562	15600	heterologous	flavonoid	Link
genistein	C15H10O5	C06563	28088	heterologous	flavonoid	Link
kaempferol	C15H10O6	C05903	28499	heterologous	flavonoid	Link
naringenin	C15H12O5	C00509	17846	heterologous	flavonoid	Link
quercetin	C15H10O7	C00389	16243	heterologous	flavonoid	Link
astaxanthin	C40H52O4	C08580	40968	heterologous	terpene	Link
betaxanthin	C18H18N2O7	C08565	8341	heterologous	terpene	Link
_-carotene	C40H56	C02094	17579	heterologous	terpene	Link
artemisinic acid	C15H22O2	C20309	63749	heterologous	terpene	Link
3-hydroxypropanoate	C3H6O3	C01013	16510	heterologous	organic acid	Link
3-hydroxypropanoate	C3H6O3	C01013	16510	heterologous	organic acid	Link
Adipic acid	C6H10O4	D08839	30832	heterologous	organic acid	Link
cis,cis-muconate	C6H6O4	C02480	16508	heterologous	organic acid	Link
Itaconic acid	C5H6O4	C00490	17240	heterologous	organic acid	Link
Ethylene	C2H4	C06547	18153	heterologous	other	Link
1,3,5-trihydroxyxanthone	C13H8O5	C10094	514	heterologous	other	Link
glucagon	C153H225N43O49S	C01501	5391	heterologous	protein	Link
Human Serum Albumin	nan	nan	nan	heterologous	protein	Link
hemoglobin	nan	C01708	5656	heterologous	protein	Link
lactase	nan	EC 3.2.1.23	nan	heterologous	protein	Link
_-Amylase	-	EC 3.2.1.1	-	heterologous	protein	Link
resveratrol	C14H12O3	C03582	27881	heterologous	other	Link
alpha-Farnesene	C15H24	C09665	10280	heterologous	terpene	Link
amorphadiene	C15H24	C16028	52026	heterologous	terpene	Link
Geraniol	C10H18O	C01500	17447	heterologous	terpene	Link
Limonene	C10H16	C06078	15384	heterologous	terpene	Link
linalool	C10H18O	C03985	17580	heterologous	terpene	Link
lupeol	C30H50O	C08628	6570	heterologous	terpene	Link
Oleanolic acid	C30H48O3	C17148	37659	heterologous	terpene	Link
patchoulol	C15H26O	C19755	7940	heterologous	terpene	Link
protopanaxadiol	C30H52O3	C20715	75950	heterologous	terpene	Link
Santalene	C15H24	C19736	nan	heterologous	terpene	Link
_-Amyrin	C30H50O	C08616	10352	heterologous	terpene	Link
_-ionone	C13H20O	C12287	32325	heterologous	terpene	Link

Installation

Required Software:

• A functional Matlab installation (MATLAB 7.3 or higher).
• The RAVEN toolbox
• A git wrapper added to the search path.

Dependencies - Recommended Software:

• For Matlab, the libSBML MATLAB API (version 5.17.0 is recommended).
• Gurobi Optimizer for any simulations.

Installation Instructions

• For users: Clone it from master in the Github repo, or just download the latest release.
• For contributors: Fork it to your Github account, and create a new branch from devel.

Contributing

Contributions are always welcome! Please read the contributions guideline to get started.

Contributors

• Hongzhong Lu (@hongzhonglu), Chalmers University of Technology, Gothenburg Sweden
• Ivan Domenzain (@IVANDOMENZAIN), Chalmers University of Technology, Gothenburg Sweden
• Yao Lu, Chalmers University of Technology, Gothenburg Sweden