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。细菌病原体之间经常分享有益的遗传物质，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)，这是细菌迅速适应不同环境的最常见方式。虽然人们把很多注意力放在鉴定已经通过HGT获得有益特征的病原体上，但相对较少的人知道细胞必须经历什么直接适应才能成功获得这些特征。该项目调查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(因此更流行)。所产生的结果和见解适用于广泛的生物学领域和开放问题，并促进整个微生物学研究界正在进行的和未来的合作努力。除了其科学目标外，该项目还为本科生，特别是女性和STEM学科中代表性不足的背景的学生提供了重要的教育机会。具体地说，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，以及对尖端研究技术的理解和欣赏。该项目支持四名学生全年从事实践研究，受益于首席研究人员的密切指导。水平基因转移(HGT)，特别是通过细胞间直接接触(称为“接合”)转移质粒，是细菌病原体通过获得分解代谢、毒力或抗生素耐药基因来适应环境应激源的最常见方式。以前的研究主要集中在将质粒适合度成本作为决定质粒菌株成功与否的一个因素：携带高成本质粒的菌株要么处于竞争优势，要么进化出补偿突变，从而改善了质粒的代谢负担。除了适合度成本外，获得一个质粒会立即但短暂地扰乱新陈代谢，这也会影响种群增长动力。这些短期效应的影响仍然是共轭动力学研究不足的特征。该项目协同利用纵向转录学、计算建模和全基因组测序来研究这一收购成本的机制基础。在这样做的过程中，该项目直接将由于获得质粒而产生的基因表达模式与其种群水平的影响联系起来。第一个目标是结合转录学、遗传/生化验证和代谢网络建模，阐明导致代表性质粒Rp4获得成本的机制决定因素。第二个目标是通过接合实验、基因组学和数学模型来确定获得的质粒如何影响从废水中分离的大肠杆菌的种群动态和克隆优势。通过结合多个尺度的数据，该项目阐明了获得质粒的遗传决定因素，并利用这一知识来预测正在进行接合的种群的短期、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智力优势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.