Systems and methods for determining genotypes for performing physiological functions
Systems and methods for determining genetic variations of an organism for performing a physiological function. The systems include a number of modules that can be integrated into existing metabolic engineering algorithms. The methods include use of the modules. The physiological function may include growth, compound production, and/or metabolic reaction flux, among others.
1. A method for identifying one or more modifications to a cell for performing a physiological function, the method comprising:
predicting, as an inner problem of a metabolic engineering algorithm configured to identify modifications for eliciting at least a first criterion of the physiological function, the one or more modifications as capable of eliciting the first criterion of the physiological function in addition to at least one additional criterion of the physiological function, wherein each of the one or more modifications is selected from the group consisting of a gene deletion and a gene addition, wherein the cell is a cell having a characterized network map, and wherein the at least one additional criterion comprises at least one of additional criteria (1), (4), (5), and (6):
(1) a first non-zero rate of flux through a second reaction in the network map implying a non-zero rate of flux through a first reaction in the network map if the first non-zero rate of flux through the second reaction is greater than a first user-defined second-reaction flux value, in combination with a second non-zero rate of flux through the second reaction implying a zero rate of flux through the first reaction if the second non-zero rate of flux through the second reaction equals a second user-defined second-reaction flux value that is greater than zero and less than the first user-defined second-reaction flux value, wherein the first reaction and the second reaction are different reactions;
(4) a ratio of a change of rate of flux through a seventh reaction in the network map per a change of rate of flux through an eighth reaction in the network map being greater than a user-defined ratio of a change of rate of flux through the seventh reaction per a change of rate of flux through the eighth reaction at rates of flux through the eighth reaction greater than a user-defined eighth-reaction flux value, wherein the seventh reaction and the eighth reaction are different reactions;
(5) a ratio of a change of rate of flux through a ninth reaction in the network map per a change of rate of flux through a tenth reaction in the network map being less than a user-defined ratio of a change of rate of flux through the ninth reaction per a change of rate of flux through the tenth reaction at rates of flux through the tenth reaction greater than a user-defined tenth-reaction flux value, wherein the ninth reaction and the tenth reaction are different reactions; and
(6) a ratio of a change of rate of flux through an eleventh reaction in the network map per a change of rate of maximal flux through a twelfth reaction in the network map being between user-specified values or being maximized or minimized, wherein the eleventh reaction and the twelfth reaction are different reactions; and
modifying the cell to have the one or more modifications.
2. The method of claim 1 , wherein a reaction selected from the group consisting of the first reaction, the seventh reaction, and the eleventh reaction comprises extracellular production of a desired compound and/or a desired enzyme activity.
3. The method of claim 1 , wherein the ninth reaction comprises extracellular production of an undesired compound and/or an undesired enzyme activity.
4. The method of claim 1 , wherein a reaction selected from the group consisting of the second reaction, the eighth reaction, the tenth reaction, and the twelfth reaction comprises biomass production.
5. The method of claim 1 , wherein the at least one additional criterion comprises at least two of additional criteria (1), (4), and (6), and wherein two or more reactions selected from the group consisting of the first reaction, the seventh reaction, and the eleventh reaction comprises extracellular production of a same compound.
6. The method of claim 1 , wherein the physiological function comprises increased or decreased production of a compound.
7. The method of claim 6 , wherein a reaction selected from the group consisting of the first reaction, the seventh reaction, and the eleventh reaction comprises production of the compound.
8. The method of claim 1 , wherein the physiological function comprises an increase or decrease in activity of one or more enzymes.
9. The method of claim 1 , wherein the cell is a microorganism.
10. The method of claim 1 , wherein the first criterion is producing a chemical at a specified level at a specified cell growth rate.
11. The method of claim 1 , wherein the first criterion is maximizing chemical production at a maximal cell growth rate.
12. The method of claim 1 , wherein the at least one additional criterion comprises at least additional criterion (1).
13. The method of claim 1 , wherein the at least one additional criterion further comprises additional criterion (2):
(2) each rate of flux through a third reaction in the network map being greater than a user-defined third-reaction flux value when the rate of flux through a fourth reaction in the network map is greater than a user-defined fourth-reaction flux value, wherein the third reaction and the fourth reaction are different reactions.
14. The method of claim 1 , wherein the at least one additional criterion further comprises additional criterion (3):
(3) each rate of flux through a fifth reaction in the network map being less than a user-defined fifth-reaction flux value when the rate of flux through a sixth reaction in the network map is greater than a user-defined sixth-reaction flux value, wherein the fifth reaction and the sixth reaction are different reactions.
15. The method of claim 1 , wherein the at least one additional criterion comprises at least additional criterion (4).
16. The method of claim 1 , wherein the at least one additional criterion comprises at least additional criterion (5).
17. The method of claim 1 , wherein the at least one additional criterion comprises at least additional criterion (6).
18. The method of claim 1 , wherein the at least one additional criterion comprises at least one of additional criteria (4), (5), and (6).