Redesigning metabolism based on orthogonality principles

Abstract

Modifications made during metabolic engineering for overproduction of chemicals have network-wide effects on cellular function due to ubiquitous metabolic interactions. These interactions, that make metabolic network structures robust and optimized for cell growth, act to constrain the capability of the cell factory. To overcome these challenges, we explore the idea of an orthogonal network structure that is designed to operate with minimal interaction between chemical production pathways and the components of the network that produce biomass. We show that this orthogonal pathway design approach has significant advantages over contemporary growth-coupled approaches using a case study on succinate production. We find that natural pathways, fundamentally linked to biomass synthesis, are less orthogonal in comparison to synthetic pathways. We suggest that the use of such orthogonal pathways can be highly amenable for dynamic control of metabolism and have other implications for metabolic engineering.

When Do Two‐Stage Processes Outperform One‐Stage Processes?

“…However, to reach the product yield of a corresponding OSF process, a higher growth‐coupled product yield and thus a lower biomass yield compared to the OSF would then be required in the production phase of the TSF process to counterbalance the low (or even zero) product yield during the TSF growth phase. Recently, an approach to design such TSF processes using the principle of orthogonality between the biomass and the production pathways was outlined . The use of such orthogonal pathway design might be valuable to minimize potential interactions with the native biomass synthesis pathways and allow for more efficient implementation of TSF processes especially for cases where the OSF is sub‐optimal.…”

“…Recently, an approach to design such TSF processes using the principle of orthogonality between the biomass and the production pathways was outlined. [40] The use of such orthogonal pathway design might be valuable to minimize potential interactions with the native biomass synthesis pathways and allow for more efficient implementation of TSF processes especially for cases where the OSF is sub-optimal. Further development of computational methods for the systematic design of TSF processes might also elucidate the relative merits of TSF and OSF for different biochemical products.…”

Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non‐traditional microorganisms

“…Metabolic orthogonality is a major objective (as well as a significant challenge) in the field of metabolic engineering. The design of authentic orthogonal metabolic pathways, a concept referring to the minimization (and, ideally, suppression) of potential interactions between the synthetic metabolic pathway to be implanted and the extant metabolism of the bacterial chassis, has become a holy grail to optimize bioproduction (Pandit et al, 2017). A much needed further step into this direction would be to rationally combine the different tools so far developed for genome engineering and experimentally curated computational prediction [e.g.…”

Expanding Metabolic Capabilities Using Novel Pathway Designs: Computational Tools and Case Studies

“…EFMs span the full space of feasible steady-state flux distributions using a set of nondecomposable pathways, and thus, they can be used to predict and rank bioproduction pathways based on their length, [48] yield, [49] thermodynamic realizability, [50] and more recently, on orthogonality principles. [51] Due to the combinatorial explosion in the number of modes, enumeration of all mass-balanced pathways is unfortunately restricted to small-to-medium size networks. Although the calculation of all EFMs from a large network is computationally intractable, calculation of subset, e.g., a random sample [52] or K-shortest EFMs, [53] can be readily achieved.…”