Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, Tromsø, Norway.
The Arctic Centre for Sustainable Energy, UiT - The Arctic University of Norway, Tromsø, Norway.
mSystems. 2024 Sep 17;9(9):e0084924. doi: 10.1128/msystems.00849-24. Epub 2024 Aug 21.
Engineering identical genetic circuits into different species typically results in large differences in performance due to the unique cellular environmental context of each host, a phenomenon known as the "chassis-effect" or "context-dependency". A better understanding of how genomic and physiological contexts underpin the chassis-effect will improve biodesign strategies across diverse microorganisms. Here, we combined a pangenomic-based gene expression analysis with quantitative measurements of performance from an engineered genetic inverter device to uncover how genome structure and function relate to the observed chassis-effect across six closely related hosts. Our results reveal that genome architecture underpins divergent responses between our chosen non-model bacterial hosts to the engineered device. Specifically, differential expression of the core genome, gene clusters shared between all hosts, was found to be the main source of significant concordance to the observed differential genetic device performance, whereas specialty genes from respective accessory genomes were not significant. A data-driven investigation revealed that genes involved in denitrification and components of trans-membrane transporter proteins were among the most differentially expressed gene clusters between hosts in response to the genetic device. Our results show that the chassis-effect can be traced along differences among the most conserved genome-encoded functions and that these differences create a unique biodesign space among closely related species.IMPORTANCEContemporary synthetic biology endeavors often default to a handful of model organisms to host their engineered systems. Model organisms such as serve as attractive hosts due to their tractability but do not necessarily provide the ideal environment to optimize performance. As more novel microbes are domesticated for use as biotechnology platforms, synthetic biologists are urged to explore the chassis-design space to optimize their systems and deliver on the promises of synthetic biology. The consequences of the chassis-effect will therefore only become more relevant as the field of biodesign grows. In our work, we demonstrate that the performance of a genetic device is highly dependent on the host environment it operates within, promoting the notion that the chassis can be considered a design variable to tune circuit function. Importantly, our results unveil that the chassis-effect can be traced along similarities in genome architecture, specifically the shared core genome. Our study advocates for the exploration of the chassis-design space and is a step forward to empowering synthetic biologists with knowledge for more efficient exploration of the chassis-design space to enable the next generation of broad-host-range synthetic biology.
将相同的基因电路工程设计到不同的物种中通常会导致性能的巨大差异，这是由于每个宿主的独特细胞环境背景造成的，这种现象被称为“底盘效应”或“上下文相关性”。更好地理解基因组和生理环境如何支撑底盘效应将改善跨多种微生物的生物设计策略。在这里，我们结合基于泛基因组的基因表达分析和工程遗传逆变器设备性能的定量测量，揭示了在六个密切相关的宿主中，基因组结构和功能如何与观察到的底盘效应相关。我们的结果表明，基因组结构支撑着我们选择的非模型细菌宿主对工程设备的不同反应。具体来说，核心基因组的差异表达，即所有宿主共有的基因簇，是观察到的遗传设备性能差异的主要来源，而来自各自附属基因组的特殊基因则没有显著差异。数据驱动的研究表明，参与反硝化作用的基因和跨膜转运蛋白的组成部分是基因设备对宿主响应中差异表达最多的基因簇之一。我们的研究结果表明，底盘效应可以追溯到最保守的基因组编码功能之间的差异，这些差异在密切相关的物种之间创造了独特的生物设计空间。
当代合成生物学的努力通常默认使用少数几种模式生物来承载其工程系统。 等模式生物因其易于处理而成为有吸引力的宿主，但不一定提供优化性能的理想环境。 随着更多新型微生物被驯化用于生物技术平台，合成生物学家被敦促探索底盘设计空间，以优化他们的系统，并实现合成生物学的承诺。 随着生物设计领域的发展，底盘效应的后果只会变得更加相关。 在我们的工作中，我们证明了遗传设备的性能高度依赖于它在其中运行的宿主环境，这促进了底盘可以被视为调节电路功能的设计变量的观点。 重要的是，我们的结果表明，底盘效应可以沿着基因组结构的相似性（特别是共享的核心基因组）来追踪。 我们的研究提倡探索底盘设计空间，是朝着赋予合成生物学家更多知识以更有效地探索底盘设计空间迈进的一步，从而实现下一代广泛宿主范围的合成生物学。
