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

该项目的总体目标是更好地了解是什么使某些细菌比其他细菌更成功地适应环境。细菌病原体通常在它们之间共享有益的遗传物质，使它们能够快速适应周围环境。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。虽然已经将很多重点放在表征已经通过HGT获得有益性状的病原体上，但对于细胞必须经历以成功获得这些性状的立即适应，相对知之甚少。该项目调查了HGT之后的适应过程，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）。产生的结果和见解适用于各种生物领域和开放性问题，并促进整个微生物学研究界正在进行和未来的合作努力。除了其科学目标外，该项目还为本科生提供了重要的教育机会，特别是女性和来自STEM学科背景的学生。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。学生被赋予重要的计算技能以及对尖端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“接合”）转移质粒，是细菌病原体通过获得分解代谢，毒力或抗生素抗性基因来适应环境压力的最常见方式。以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：携带高成本质粒的菌株要么被淘汰，要么进化出补偿突变，改善质粒的代谢负担。除了适应性成本，获得质粒会对新陈代谢产生直接但短暂的破坏，这也会影响种群的增长动力学。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收购成本的机械基础。在这样做的时候，该项目直接连接基因表达模式，产生质粒收购的结果，他们的人口水平的影响。第一个目标阐明了机制的决定因素，导致质粒收购成本的代表性质粒RP 4，使用转录组学，遗传/生化验证和代谢网络建模的组合。第二个目标是确定质粒收购如何影响人口动态和克隆优势的大肠杆菌病原体从废水中分离使用接合实验，基因组学和数学建模。通过结合多个尺度的数据，该项目阐明了质粒获得背后的遗传决定因素，并利用这些知识来预测进行接合的群体的短期、长期和竞争动态。该奖项反映了NSF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.