CAREER: Form and Function of Bacterial Amyloid Fibers

Stanford University, Stanford CA

Investigators

Abstract

The propensity for bacteria to associate with surfaces in nearly all ecosystems far exceeds the tendency to persist in suspension, living freely in a planktonic state. Bacteria secrete proteins, polysaccharides, and other components to assemble a spider-web like matrix that surrounds cells to promote the formation of protective communities termed biofilms. The protective physical matrix enables bacteria to colonize and even thrive in an astonishing range of environments, in niches ranging from the harsh acidic microbial mats in Yellowstone to ship hulls and industrial oil pipelines. Improved biofilm models are crucial to understanding how they function. Across biology, chemistry, and materials research, measuring parameters of chemical, physical, and mechanical properties is key to understanding how complex assemblies function. In this project, experiments are designed to achieve breakthrough discoveries needed to transform biofilm descriptors from vague terms like "glue" and "slime" to scientific and quantitative descriptions based on chemical composition and molecular architecture by using high resolution techniques. The self-assembly of these macromolecular architectures by bacteria also inspire us to use or build such mechanically robust molecular frameworks for new functions. In this project, the PI will engage in broad dissemination of scientific research and educational outreach activities. She will mentor undergraduate and graduate students, including many from groups under-represented in STEM; design coursework changes to introduce more quantitative concepts into biochemistry courses; and lead comprehensive outreach activities, engaging students, teachers, and the general public. Major specific activities include: (i) developing a biochemical biofilm laboratory module for the high-school science curriculum with assistance from a high-school teacher who joins the PI's laboratory each summer, (ii) integrating exploratory-based lab modules in undergraduate laboratory courses to encourage true engagement and the hands-on "a-ha" moments that enhance learning; (iii) assisting in the mentoring of incoming first-generation and under-represented undergraduate students in preparation for university coursework in STEM; and (iv) sharing engineering protocols for a custom-built active-control feedback system to stabilize NMR pulse power levels over long acquisition times, enhancing the stability of NMR experiments and also of general value in spectrometer monitoring. Overall, the commitment to educational and scientific outreach in this project integrates research with teaching, mentoring, and K-12 outreach activities to inspire and empower others to impact and improve the society. In this project, amyloid fibers produced by E. coli, known as curli, will be studied. Curli mediate bacterial adhesion and contribute to biofilm formation. This project will provide unprecedented detail into the atomic structure and function of native curli fibers and will map their interactions with amyloid dyes and their cognate biofilm polysaccharide partners by integrating unique solid-state nuclear magnetic resonance (NMR) strategies to measure atomic-level distances together with super-resolution microscopy to examine the larger-scale spatial arrangement of curli and other components in the biofilm. This project is jointly funded by Molecular Biophysics and Cellular Dynamics and Function Clusters in the Division of Molecular and Cellular Biosciences.