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

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.合成微生物群落（synthetic microbial consortia）已在生物技术领域得到愈发广泛的应用。实验证据表明，经过适当工程化改造的群落，在高价值产物合成方面的表现可优于单一菌株。尽管相关研究已取得诸多重要进展，但对于实现这一优势的必要条件，以及多菌株同步生长所带来的权衡关系，目前仍缺乏充分的定量认知。本研究针对某一经典原型合成微生物群落展开探究，以期填补这一研究空白。该群落包含两株大肠杆菌（E. coli）：一株用于表达异源蛋白，另一株经工程改造以清除有毒代谢副产物——通过将部分资源转向用于“清道夫”菌株的生长，助力目标蛋白生产菌株的增殖。该群落结构简洁，便于开展深入分析并推导具有更广普适性的结论。本研究构建了粗粒度数学模型，可定量吻合不同关键生长表型的已有文献数据。基于该模型，本研究首先以恒化器（chemostat）培养为前提，探究了两菌株稳定共存的必要条件，以及异源蛋白表达带来的代谢负荷所产生的影响。在此前提下，本研究明确了该群落相较于单一生产菌株在生产力层面具备优势的时机与程度。最终，本研究在恒化器与补料分批（fed-batch）培养场景中均证实：生产力提升往往以产物得率降低为代价，这一现象反映了群落层面的资源分配权衡关系，而该权衡关系在单一菌株中已是广为人知的结论。