CAREER: A Systems Approach to Study Horizontal Acquisition of Regulatory DNA

水平基因转移是指基因在自然界中不同微生物之间传播的过程。这一过程对微生物快速进化新特性的能力至关重要，并与人类、牲畜和农业中的耐药性传播和发病机制有关。然而，控制基因如何在自然环境中传播的基本决定因素尚未得到很好的表征。这项工作利用系统和合成生物学方法来实验探索决定不同细菌物种之间基因水平传播的潜在规则。一个基本的观点是基因调控是基因转移的重要驱动因素。这项工作的结果将揭示微生物进化的基本特性，并解决理解遗传物质在自然和人为环境中传播的关键知识空白。这一努力还将导致基因部分的特征化，这将有助于在生物技术、生物材料和生物燃料领域设计各种微生物。这些新的见解可导致改进策略，以遏制可能导致人类、牲畜和作物疾病以及以不良方式改变自然生态系统的问题遗传物质的传播。这项研究还将为来自不同学生群体的高中和地区本科院校的学生提供创造性的教育和培训机会。技术描述最近的测序工作强调了水平基因转移（HGT）在塑造微生物进化中的重要性。然而，控制外来DNA向新宿主转移和同化的系统级原理在很大程度上仍未被探索。一个重要的推论是，决定下游蛋白质编码序列转录和翻译水平的外源调控元件可能在HGT中发挥关键作用。表达不良或翻译不良的外源基因对接受微生物没有好处，会丢失，而表达水平异常高的不受调控的基因也会被选择，因为它们会给宿主带来不必要的资源负担。因此，供体和受体微生物之间调节兼容性的“金发姑娘”窗口可能是HGT中一个重要的、迄今未被充分认识的决定因素。这个NSF CAREER项目旨在开发一个系统和合成生物学研究项目来回答这个领域的关键问题。该提案旨在确定供体DNA和受体调控机制中顺式调控元件的兼容性是否是HGT和新DNA基因组获取的关键决定因素。该提案旨在开发高通量方法，利用DNA文库合成和测序来测量数万个水平获得的调控元件的转录和翻译活性。本研究还旨在了解不同细菌系统中HGT的调控障碍，并确定混杂的移动DNA（如共轭质粒和转座子）能够克服这些障碍在不同物种中发挥作用的策略。

Non-technical DescriptionHorizontal gene transfer is the process by which genes are disseminated between different microbes in nature. This process is central to the ability of microbes to rapidly evolve new traits and has been linked to the spread of drug resistance and pathogenesis in humans, livestock, and agriculture. However, basic determinants that govern how genes spread in natural environments are not well characterized. This work utilizes a systems and synthetic biology approach to experimentally probe the underlying rules that determine the horizontal dissemination of genes between diverse bacteria species. A foundational idea is that gene regulation is an important driver in gene transfer. Results from this work will shed new light on a fundamental property of microbial evolution and address critical knowledge gaps for understanding the propagation of genetic material in natural and man-made environments. This endeavor will also lead to the characterization of genetic parts that will be useful for engineering a variety of microbes relevant in areas of biotechnology, biomaterials, and biofuels. These new insights can lead to improved strategies to contain the spread of problematic genetic materials that may lead to diseases in humans, livestock and crops, as well as those that alter the natural ecosystem in undesirable ways. This research will also provide creative educational and training opportunities for students from high school and regional undergraduate institutions with a diverse student population.Technical DescriptionRecent sequencing efforts have highlighted the significance of horizontal gene transfer (HGT) in shaping microbial evolution. However, systems-level principles that govern the transfer and assimilation of foreign DNA into new hosts remain largely unexplored. An important corollary is that foreign regulatory elements that determine the level of transcription and translation for downstream protein-coding sequences may play a key role in HGT. Poorly expressed or translated foreign genes will not be beneficial to the receiving microbe and will be lost, while deregulated genes with abnormally high levels of expression are also selected against as they cause unnecessary resource burdens on the host. Therefore, the "Goldilocks" window of regulatory compatibility between donor and recipient microbes may be a significant and thus far underappreciated determinant in HGT. This NSF CAREER project aims to develop a systems and synthetic biology research program to answer key questions in this area. The proposal aims to determine whether compatibility of cis-regulatory elements in the donor DNA and the recipient's regulatory machinery is a key determinant of HGT and genomic acquisition of new DNA. This proposal aims to develop high-throughput methods using DNA library synthesis and sequencing to measure transcriptional and translational activity of tens of thousands of horizontally acquired regulatory elements. This proposal also aims to understand the regulatory barriers of HGT in diverse bacterial systems and identify strategies by which promiscuous mobile DNA such as conjugative plasmids and transposons are able to overcome such barriers to function in different species.