A major challenge in synthetic genetic circuit development is the inter-dependency between heterologous gene expressions by circuits and host's growth rate. Increasing heterologous gene expression increases burden to the host, resulting in host growth reduction; which reduces overall heterologous protein abundance. Hence, it is difficult to design predictable genetic circuits. Here, we develop two biophysical models; one for promoter, another for RBS; to correlate heterologous gene expression and growth reduction. We model cellular resource allocation in E. coli to describe the burden, as growth reduction, caused by genetic circuits. To facilitate their uses in genetic circuit design, inputs to the model are common characteristics of biological parts [e.g. relative promoter strength (RPU) and relative ribosome binding sites strength (RRU)]. The models suggest that E. coli's growth rate reduces linearly with increasing RPU / RRU of the genetic circuits; thus, providing 2 handy models taking parts characteristics as input to estimate growth rate reduction for fine tuning genetic circuit design in silico prior to construction. Our promoter model correlates well with experiments using various genetic circuits, both single and double expression cassettes, up to a relative promoter unit of 3.7 with a 60% growth rate reduction (average R2 ~ 0.9).

翻译：合成基因回路开发中的一个主要挑战是异源基因表达与宿主生长速率之间的相互依赖性。增加异源基因表达会加重宿主负担，导致宿主生长减缓，进而降低总异源蛋白丰度。因此，设计可预测的基因回路具有较大难度。本研究开发了两个生物物理模型——一个针对启动子，另一个针对核糖体结合位点（RBS），用于关联异源基因表达与生长减缓。我们通过建模大肠杆菌中的细胞资源分配，描述基因回路所引起的负担（即生长减缓）。为便于在基因回路设计中使用，模型的输入为生物元件的常见特性（如相对启动子强度RPU和相对核糖体结合位点强度RRU）。模型表明，大肠杆菌的生长速率随基因回路的RPU/RRU增加呈线性下降；由此提供了两个便捷模型，以元件特性为输入，在构建前通过计算机模拟估算生长速率降低幅度，从而精细调整基因回路设计。我们的启动子模型与多种基因回路（包括单表达盒和双表达盒）的实验结果高度吻合，在相对启动子单位达3.7、生长速率降低60%时，平均R²约为0.9。