Development of synthetic, methylation based, epigenetic gene circuits

在我们最近发表的文章中，我们描述了大肠杆菌的合成表观遗传回路，它可以感知瞬时触发信号，并在几代细胞中以DNA甲基化模式的形式存储这些信息。这种合成表观遗传系统的潜在应用是多方面的，包括开发细菌，这些细菌可以用作监测冷却链的活传感器，检测生产场所或原子能发电厂附近的环境污染，或通过人体收集有关疾病标志物和代谢状态的输入。生物技术应用包括用于诱导工业蛋白表达或生物控制系统的记忆开关。本项目旨在进一步开发这些新系统的基本特性，并更好地了解它们的信号特征。我们将改进现有的热检测，采用新的输入信号，可以检测抗生素、代谢物、毒素、细菌细胞密度和放射性。为了改进信号处理，我们计划开发以与现有系统相反的方式工作的其他系统，这将允许开发与细菌细胞周期振荡的系统，以识别代谢活跃的细菌并将其与死亡或休眠细胞区分开来。这里开发的基于DNA甲基化的记忆系统的一个特殊优势是它们易于复用，允许收集许多不同的输入信号，并将信息存储在一个细胞中的不同DNA甲基化代码中。为了实现这一目标，我们计划整合其他兼容的DNA甲基转移酶和新的甲基化位点。不同的输入设备将被组合以产生逻辑门，显示与或或行为，用于初始数据处理。我们的目标是利用定量动态建模作为主要工具来获得表观遗传回路的调控原理，信息处理和存储的机制理解。这些模型和它们的分析对于整个设计和实现周期也将是高度支持的。总之，我们的工作将为含有合成表观遗传电路的设计细菌的应用铺平道路，这些设计细菌可以作为活的生物传感器检测生物信号，将信息存储在DNA甲基化模式中作为细菌存储设备，并作为细菌微处理器执行初始数据处理。

In our recent publication, we described synthetic epigenetic circuits in E. coli that can sense transient trigger signals and store this information in form of DNA methylation patterns over several cell generations. Potential applications of such synthetic epigenetic systems are manifold and include the development of bacteria that could be used as live sensors to monitor cooling chains, detect environmental pollution next to production sites or atomic power plants, or passage through the human body and collect input about disease markers and metabolic states. Biotechnological applications include memory switches for induction of industrial protein expression or in biocontainment systems. This project aims to further develop fundamental properties of these novel systems and better understand their signaling characteristics. We will improve the existing heat detection and adopt new input signals allowing the detection of antibiotics, metabolites, toxins, bacterial cell density and radioactivity. To improve signal processing, we plan to develop additional systems working in an inverted manner than the existing ones, which will allow to develop systems that oscillate with the bacterial cell cycle to identify metabolically active bacteria and distinguish them from dead or dormant cells. One particular strength of the DNA methylation based memory systems developed here is their amenability to multiplexing allowing to collect many different input signals and deposit the information in different DNA methylation codes in one cell. Heading towards this goal, we plan to integrate additional compatible DNA methyltransferases and novel methylation sites. The different input devices will be combined to generate logic gates exhibiting AND or OR behavior for initial data processing. We aim to use quantitative dynamic modeling as a major tool to obtain a mechanistic understanding of the regulation principles, information processing and storage by epigenetic circuits. These models and their analysis will also be highly supportive for the entire design and implementation cycle. In summary, our work will pave the way towards the application of designer bacteria containing synthetic, epigenetic circuits in the detection of biological signals as live biosensors, storing the information in DNA methylation patters as bacterial storage devices and performing initial data processing as bacterial microprocessors.