RUI: Biology-Physics Collaboration to Investigate the Genetic and Structural Basis of Competence in Bacteria

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Intellectual Merit: Bacteria have a covering membrane, analogous to human skin, designed to keep their internal components in and foreign bodies out. Some bacteria have developed the ability to import foreign DNA across this membrane and incorporate it into their own genomes. This ability is called natural transformation or competence. Because competent bacteria can import everything from their own native DNA to animal DNA, they can adapt rapidly in stressful environments, such as in the presence of antibiotics. This research project is to better understand how bacteria are able to find DNA and move it across their membranes. What is currently known is that some bacteria can make structures, called Type IV Pili, which consist of pores through their membranes and through which associated long appendages can project outward. Type IV Pili are used by bacteria to pull themselves across a surface, essentially using the appendages as retractable grappling hooks. The machinery responsible for competence is believed to be similar in structure to Type IV Pili. This similarity suggests two hypotheses: first, the set of genes that build the competence machine must be similar to the set of genes that build Type IV Pili, and second, the competence machine performs similar actions to Type IV Pili, albeit for a different purpose. This research will use Type IV Pili genes to identify potential competence genes and then evaluate whether those genes really do participate in building a competence machine. In addition, Atomic Force Microscopy will be used to take very high resolution pictures of competent bacteria to see both the competence machines and appendages. Looking at the competence machines themselves yields an understanding of how a population of cells becomes more competent. Perhaps populations become more competent when each cell makes more machines or when more cells makes machines or when each machine makes more appendages. The pictures will also indicate whether competent bacteria might use their appendages to "fish" for DNA by throwing them out and retracting them to move the DNA toward themselves. The overall goal of this research is to generate a much deeper understanding of both the genetic basis and the physical mechanisms of competence in bacteria.Broader Impacts: All the proposed research will take place in collaboration with undergraduate students. The PIs have a strong track record of involving undergraduates in research, having collectively worked with 108 students in ten years each at Colorado College. Many of these students were women and minorities, and the PIs actively recruit such students. The PIs are a physicist and a biologist in collaboration, and the dozen students expected to conduct research in their labs on this project will reflect this same combination of majors. In addition, the PIs developed a biophysics course for first-year students based on the research, which culminates with a project in which the students prepare a bacterial sample, image it with atomic force microscopy, and then write a journal-style paper to present their research, thus giving them an experiential taste of scientific research. This experience will be offered to 48 first-year students during the term of the award.