Collaborative Research: RUI: A multiscale quantification of plasmid acquisition in Escherichia coli pathogens

这个项目的总体目标是更好地理解是什么使一些细菌比其他细菌更成功地适应环境。细菌病原体之间经常共享有益的遗传物质，使它们能够迅速适应周围环境。共享遗传物质的过程被称为水平基因转移（HGT），是细菌快速适应不同环境的最常见方式。虽然很多人都把重点放在描述已经通过HGT获得有益性状的病原体上，但对细胞成功获得这些性状必须经历的直接适应却知之甚少。该项目调查了HGT后的适应过程，以深入了解为什么某些病原体比其他病原体更成功（因此更普遍）。所产生的结果和见解适用于广泛的生物领域和开放问题，并促进微生物研究界正在进行和未来的合作努力。除了科学目标之外，该项目还为本科生提供了重要的教育机会，特别是女性和那些来自STEM学科中代表性不足的背景的学生。具体而言，该项目将研究方法和结果紧密结合到新开发的计算生物学专业和相关的高级课程中。学生被赋予了重要的计算技能，以及对前沿研究技术的理解和欣赏。该项目支持四名学生全年进行实践研究，受益于首席研究员的密切指导。水平基因转移（HGT），特别是通过直接细胞-细胞接触（称为“偶联”）的质粒转移，是细菌病原体通过获取分解代谢、毒力或抗生素抗性基因来适应环境应激源的最常见方式。先前的研究主要集中在质粒适应性成本作为质粒菌株成功的决定因素上：携带高成本质粒的菌株要么处于竞争劣势，要么进化出代偿性突变，以改善质粒的代谢负担。除了适应性成本之外，获得质粒还会对代谢造成直接但短暂的破坏，这也会影响种群的生长动态。这些短期效应的影响仍然是共轭动力学的一个未充分研究的特征。该项目协同利用纵向转录组学、计算建模和全基因组测序来研究这种获取成本的机制基础。通过这样做，该项目直接将质粒获得的基因表达模式与其种群水平的影响联系起来。第一个目标是通过结合转录组学、遗传/生化验证和代谢网络建模，阐明导致代表性质粒RP4质粒获取成本的机制决定因素。第二个目标是通过偶联实验、基因组学和数学模型确定质粒获取如何影响从废水中分离的大肠杆菌病原体的种群动态和克隆优势。通过结合多个尺度的数据，该项目阐明了质粒获取背后的遗传决定因素，并利用这些知识来预测正在进行结合的种群的短期、长期和竞争动态。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

The overall goal of this project is to better understand what enables some bacteria to adapt more successfully than others. Bacterial pathogens often share beneficial genetic material amongst themselves, enabling them to quickly adapt to their surroundings. The process of sharing genetic material, known as horizontal gene transfer (HGT), is the most common way that bacteria rapidly adapt to diverse environments. While much focus has been placed on characterizing pathogens that have already acquired beneficial traits via HGT, relatively little is known about the immediate adaptation that cells must undergo to successfully acquire such traits. This project investigates the adaptation process following HGT to provide insights into why certain pathogens are more successful (and therefore, prevalent) than others. The results and insights generated are applicable to a wide variety of biological areas and open questions and promotes ongoing and future collaborative efforts across the microbiology research community. In addition to its scientific objectives, this project facilitates significant educational opportunities for undergraduate students, particularly women and those from backgrounds underrepresented in STEM disciplines. Specifically, this project closely integrates research methods and results into a newly developed Computational Biology major and associated upper-level courses. Students are empowered with vital computational skills as well as an understanding and appreciation of cutting-edge research techniques. This project supports four students to pursue hands-on research year-round, benefiting from close guidance from the principal investigator.Horizontal gene transfer, (HGT), particularly through the transfer of plasmids via direct cell-cell contact (termed "conjugation"), is the most common way that bacterial pathogens adapt to environmental stressors by acquiring catabolic, virulence, or antibiotic resistance genes. Previous studies have primarily focused on the plasmid fitness cost as a determinant of plasmid-strain success: strains bearing high-cost plasmids are either out-competed or evolve compensatory mutations that ameliorate the plasmid's metabolic burden. In addition to the fitness cost, acquiring a plasmid introduces an immediate, but transient, disruption to metabolism which also impacts population growth dynamics. The impacts of these short-term effects remain an understudied feature of conjugation dynamics. This project synergistically leverages longitudinal transcriptomics, computational modeling, and whole-genome sequencing to investigate the mechanistic underpinnings of this acquisition cost. In so doing, the project directly connects gene expression patterns, arising as a consequence of plasmid acquisition, to their population-level effects. The first objective elucidates the mechanistic determinants that lead to plasmid acquisition cost for the representative plasmid RP4, using a combination of transcriptomics, genetic/biochemical validation, and metabolic network modeling. The second objective determines how plasmid acquisition impacts population dynamics and clonal dominance of Escherichia coli pathogens isolated from wastewater using conjugation experiments, genomics, and mathematical modeling. By combining multiple scales of data, this project elucidates the genetic determinants underlying plasmid acquisition, and leverages this knowledge to predict the short-term, long-term, and competitive dynamics of populations undergoing conjugation.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.