Retrieving new Biomass composition data following genetic knockouts

[Eve Murray]

Hello,

I have simulated several knockouts but they rarely impact the biomass composition coefficients. I am trying to simulate a higher protein mutant and the Biomass Objective function coefficients directly align with the wild type experimental data for biomass composition. The metabolite production/consumption is altered as a result of the knockout but the protein biomass composition remains constant. 

Does anyone have any ideas for being able to calculate biomass composition changes as a result of genetic knockouts?

Thanks,

Eve Murray

[Bruno Batista]

Hello Eve,

I’m not sure if I fully understand your approach, so let me share how I see it and you can tell me if it makes sense.

In most GEMs, the biomass coefficients are predefined by the modeler. For example, the biomass reaction typically contains fixed fractions such as 0.3 protein, 0.02 DNA, and so on. These coefficients usually remain constant unless the biomass equation itself is reformulated.

One possible strategy would be to separate protein synthesis from the biomass equation and treat it as an independent reaction. For example:

• Protein_reaction: precursors → protein

• Biomass_reaction: 0.3 protein + 0.02 DNA + ... → biomass

In this framework, we could constrain the biomass reaction with a fixed lower bound (to maintain a defined growth rate) and set the objective to maximize the protein reaction. This would allow us to directly compare changes in protein production capacity without altering the global biomass structure with your Knockouts.

Let me know if this aligns with your reasoning, or if I misunderstood your proposal.

Best regards,
Bruno