Enhanced production of heterologous proteins by a synthetic microbial community: Conditions and trade-offs

Abstract

Synthetic microbial consortia have been increasingly utilized in biotechnology and experimental evidence shows that suitably engineered consortia can outperform individual species in the synthesis of valuable products. Despite significant achievements, though, a quantitative understanding of the conditions that make this possible, and of the trade-offs due to the concurrent growth of multiple species, is still limited. In this work, we contribute to filling this gap by the investigation of a known prototypical synthetic consortium. A first E. coli strain, producing a heterologous protein, is sided by a second E. coli strain engineered to scavenge toxic byproducts, thus favoring the growth of the producer at the expense of diverting part of the resources to the growth of the cleaner. The simplicity of the consortium is ideal to perform an in depth-analysis and draw conclusions of more general interest. We develop a coarse-grained mathematical model that quantitatively accounts for literature data from different key growth phenotypes. Based on this, assuming growth in chemostat, we first investigate the conditions enabling stable coexistence of both strains and the effect of the metabolic load due to heterologous protein production. In these conditions, we establish when and to what extent the consortium outperforms the producer alone in terms of productivity. Finally, we show in chemostat as well as in a fed-batch scenario that gain in productivity comes at the price of a reduced yield, reflecting at the level of the consortium resource allocation trade-offs that are well-known for individual species.

Global dynamics of the chemostat with overflow metabolism

“…Thus, the by-product R has an inhibitory effect on the substrate uptake rate. An example for r S is given by (see [22]):…”

“…Assumption ( 4) is satisfied by the parameters given in [22]. We also assume that r S (S in , 0) > r S0 (i.e.…”

“…productivity defined as P * = Dx * , with x * the steady state concentration of bacteria at the dilution rate D. P * quantifies the biomass that is produced per unit of time at steady state. To determine P * numerically, let us assume that r S is given by (2), and consider the parameters estimated by Mauri and collaborators in [22] (see Table 1). Figure 3B shows that the steady state productivity is maximal at a value of the dilution rate higher than Y S r S0 (continuous line).…”

“…The model is mainly inspired by the recently proposed model in [22] that describes the growth of an E. coli culture producing a recombinant protein. In contrast to our model, the authors in [22] consider growth on the by-product (acetate) and an additional variable describing the dynamics of a recombinant protein concentration. E. coli consume acetate only after the glucose (substrate) is totally consumed, phenomenon known as carbon catabolite repression [31].…”

Feedback ratiometric control of two microbial populations in a single chemostat

“…However, the complexity and hence the capabilities of these engineered genetic circuits are limited by inherent factors in their host cells, such as excessive metabolic burden, competition of limited resources and incompatible chemical reactions. To overcome these limitations a promising strategy is to distribute the required functionalities among several cell populations forming a microbial consortium, so that each cell strain embeds a smaller subset of engineered genes [1]- [3]. In this way each cell carries out a specialized role and, by dividing the labor, contributes more efficiently to the achievement of the final goal.…”