The production of recombinant proteins in a host using synthetic constructs such as plasmids comes at the cost of detrimental effects such as reduced growth, energetic inefficiencies, and other stress responses, collectively known as metabolic burden. Increasing the number of copies of the foreign gene increases the metabolic load but increases the expression of the foreign protein. Thus, there is a trade-off between biomass and product yield in response to changes in heterologous gene copy number. This work proposes a computational method, rETFL (recombinant Expression and Thermodynamic Flux), for analyzing and predicting the responses of recombinant organisms to the introduction of synthetic constructs. rETFL is an extension to the ETFL formulations designed to reconstruct models of metabolism and expression (ME-models). We have illustrated the capabilities of the method in four studies to (i) capture the growth reduction in plasmid-containing and recombinant protein production; (ii) explore the trade-off between biomass and product yield as plasmid copy number is varied; (iii) predict the emergence of overflow metabolism in recombinant in agreement with experimental data; and (iv) investigate the individual pathways and enzymes affected by the presence of the plasmid. We anticipate that rETFL will serve as a comprehensive platform for integrating available omics data for recombinant organisms and making context-specific predictions that can help optimize recombinant expression systems for biopharmaceutical production and gene therapy.

中文翻译：

---

代谢和表达的基因组规模模型预测重组蛋白表达的代谢负担


使用合成构建体（例如质粒）在宿主中生产重组蛋白会产生有害影响，例如生长减少、能量效率低下和其他应激反应，统称为代谢负担。增加外源基因的拷贝数会增加代谢负荷，但会增加外源蛋白的表达。因此，响应异源基因拷贝数的变化，在生物量和产物产量之间存在权衡。这项工作提出了一种计算方法 rETFL（重组表达和热力学通量），用于分析和预测重组生物体对引入合成构建体的反应。 rETFL 是 ETFL 配方的扩展，旨在重建代谢和表达模型（ME 模型）。我们在四项研究中说明了该方法的能力：(i) 捕获含质粒和重组蛋白生产中的生长减少； (ii) 探索当质粒拷贝数变化时生物量和产物产量之间的权衡； (iii) 预测重组体中溢出代谢的出现，与实验数据一致； (iv) 研究受质粒存在影响的各个途径和酶。我们预计 rETFL 将作为一个综合平台，用于整合重组生物体的可用组学数据并进行特定背景的预测，从而帮助优化生物制药生产和基因治疗的重组表达系统。