RUI: Sugar-mediated remodeling of the E. coli transcriptome and its impact on biofilm growth and composition

抗生素耐药性降低了许多抗生素的功效，导致牲畜被扑杀，作物受损，死亡人数增加。当细菌细胞处于静止的生物膜状态时，对抗生素的耐药性会增强。该项目的总体目标是确定导致生物膜形成缺陷和/或生物膜相关细菌抗生素敏感性增加的环境条件。研究和教育将通过基于课程的本科研究经验（CURE）在一个高年级生物化学实验室进行整合，该实验室每年约有40名学生。该项目的中心假设是，不同的糖重塑细菌转录组，以调节生物膜生长和生物膜中细胞周围细胞外物质的组成。单糖对大肠杆菌生物膜形成和组成影响的综合分析尚未在表型或转录组水平上进行。为了了解糖如何影响生物膜的生长和组成，将采用两种研究方法。首先，环境单糖对生物膜生长和组成的影响将使用完善的紫外可见生长和生化分析以及共聚焦扫描激光显微镜进行测量。其次，这些单糖对浮游细菌和生物膜细菌转录组的影响将使用RNA-seq进行表征，并通过缺失研究证实假设的靶点。对生长和组成的独特关注将为该领域提供有关特定途径如何相互作用以改变细胞外基质的额外信息，这与生物膜的质量有关。了解各种糖对这些过程的影响将揭示不同的碳代谢途径如何与生物膜的形成和组成相互联系。此外，将在这些相关的代谢和信号通路中确定杠杆点，这些杠杆点可以协同工作以消除或促进生物膜的形成。这项工作将为更大的科学界提供一个途径和单个蛋白质的目标列表，这将增加药物化学家可以用来开发新抗生素的线索，并为材料化学家开发用于涂层的抗生素膜化合物提供一个起点。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。

Antibiotic resistance has reduced the efficacy of many antibiotics and led to livestock culling, compromised crops, and increased human deaths. Resistance to antibiotics is heightened when bacterial cells are in the sedentary, biofilm state. The overall goal of this project is to identify environmental conditions that lead to defects in biofilm formation and/or an increase in the antibiotic sensitivity of biofilm-associated bacteria. Research and education will be integrated through a course-based undergraduate research experience (CURE) in an upper-division biochemistry laboratory that has approximately 40 students annually. The central hypothesis of the project is that different sugars remodel the bacterial transcriptome to modulate biofilm growth and the composition of the extracellular substances surrounding cells in the biofilm. A comprehensive analysis of the influence of monosaccharides on E. coli biofilm formation and composition has not been conducted at either phenotypic or transcriptomic levels. To understand how sugars might be influencing biofilm growth and composition, two methods of inquiry will be pursued. First, the influence of environmental monosaccharides on biofilm growth and composition will be measured using well-established UV-visible growth and biochemical assays and confocal scanning laser microscopy. Second, the effect of these monosaccharides on the transcriptomes of planktonic and biofilm bacteria will be characterized using RNA-seq and putative targets will be confirmed with deletion studies. The unique focus on examining both growth and composition will provide the field with additional information about how specific pathways interact to change the extracellular matrix, which relates to the heartiness of biofilm. Understanding the influence of various sugars on these processes will reveal how different carbon metabolic pathways are interlinked with biofilm formation and composition. Moreover, leverage points will be identified in these linked metabolic and signaling pathways that could work synergistically to eradicate or promote biofilm formation. This work will provide the greater scientific community with a list of pathways and individual proteins to target, which will augment the leads medicinal chemists can use to develop new antibiotics and provide materials chemists with a starting point for developing antibiofilm compounds for coatings.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.