Toward a modeling, optimization, and predictive control framework for fed‐batch metabolic cybergenetics

• Published in: Biotechnology and bioengineering 2024-01, Vol.121 (1), p.366-379
• Main Authors: Espinel‐Ríos, Sebastián, Morabito, Bruno, Pohlodek, Johannes, Bettenbrock, Katja, Klamt, Steffen, Findeisen, Rolf
• Format: Article
• Language: English
• Subjects: Batch processes; Batch processing; Bioreactors; Biotechnology; Constraint modelling; constraint‐based modeling; Disturbances; dynamic metabolic control; Feedback; Feedback control; Feeding rates; Gene expression; Genetic engineering; Genetics; Information processing; Light intensity; Luminous intensity; metabolic cybergenetics; Metabolic engineering; Metabolism; model predictive control; Modulation; Optics; Optimal control; Optimization; optogenetics; Predictive control; Resource allocation; state estimation; Substrates; Sustainable production
• ISSN: 0006-3592; 1097-0290
• DOI: 10.1002/bit.28575

Biotechnology offers many opportunities for the sustainable manufacturing of valuable products. The toolbox to optimize bioprocesses includes extracellular process elements such as the bioreactor design and mode of operation, medium formulation, culture conditions, feeding rates, and so on. However, these elements are frequently insufficient for achieving optimal process performance or precise product composition. One can use metabolic and genetic engineering methods for optimization at the intracellular level. Nevertheless, those are often of static nature, failing when applied to dynamic processes or if disturbances occur. Furthermore, many bioprocesses are optimized empirically and implemented with little‐to‐no feedback control to counteract disturbances. The concept of cybergenetics has opened new possibilities to optimize bioprocesses by enabling online modulation of the gene expression of metabolism‐relevant proteins via external inputs (e.g., light intensity in optogenetics). Here, we fuse cybergenetics with model‐based optimization and predictive control for optimizing dynamic bioprocesses. To do so, we propose to use dynamic constraint‐based models that integrate the dynamics of metabolic reactions, resource allocation, and inducible gene expression. We formulate a model‐based optimal control problem to find the optimal process inputs. Furthermore, we propose using model predictive control to address uncertainties via online feedback. We focus on fed‐batch processes, where the substrate feeding rate is an additional optimization variable. As a simulation example, we show the optogenetic control of the ATPase enzyme complex for dynamic modulation of enforced ATP wasting to adjust product yield and productivity. Metabolic cybergenetic feedback in fed‐batch bioreactors exploiting dynamic optimization and model predictive control: Key proteins, like enzyme preg ${p}_{reg}$, adjust using inducible gene systems to achieve various metabolic modes, influenced by factors such as light intensity. Through model‐based optimization, the best conditions are pinpointed. Outcomes are monitored using biosensors, and state estimators capture any unmeasured data. Continual optimization ensures precise feedback control within the framework of model predictive control.