Multiscale Models for Synthetic Biological Antibiotic Technologies

1412283

Kaznessis, Yiannis N.

It is proposed to build tools that facilitate development of new antibiotic technologies. For eighty years the life expectancy and the standards of living of humans greatly improved largely thanks to antibiotics. But the era of antibiotics may be coming to an end, as bacteria are developing resistance to all available antibiotics and rendering important therapies obsolete. The specific challenge addressed is related to foodborne bacterial gastrointestinal infections that jeopardize food safety and sustainable agriculture practices. These infections are significant causes of morbidity and mortality worldwide. It is proposed to explore the therapeutic potential of probiotic lactic acid bacteria (LAB) that express and release antimicrobial peptides (AMPs) by developing a toolbox for testing LAB as 'smart' AMP-delivery vehicles against foodborne bacteria. The proposed work will have significant broader societal impact, as it constitutes a new strategy to reduce over-consumption of antibiotics. In addition, high school students will be trained in elements of microbiology, antibiotic technologies and bioinformatics. These students will be recruited from inner city schools with large percentages of students from ethnic or racial minorities. These students will also benefit from rich interdisciplinary interactions in this project.

Tools will be developed to detect and inhibit three Gram-positive bacterial species: Clostridia spp., Listeria spp. and Enterococcus spp. (in short CLE). In particular, experimental tools will be developed that facilitate modification of LAB to detect CLE and then produce a molecular arsenal that targets CLE pathogens. Detection will be based on pheromone-responding genetic promoters, moved from CLE into LAB. The molecular arsenal will consist of AMPs and phage endolysins. In parallel, multiscale modeling tools will be developed that provide mechanistic understanding and aid in experimental design of both the promoters and the antimicrobial molecules. There are two major objectives: (1) Develop a toolbox of protein expression and secretion systems in LAB. Libraries of promoters will be constructed to express AMPs and endolysins in LAB. Aided by multiscale modeling techniques, three libraries of promoters will be constructed in LAB: (i) promoters that respond to CLE pheromones; (ii) environment-sensitive promoters; (iii) constitutive promoters. (2) Develop a toolbox of methods for high-throughput discovery of peptide antibiotics by discovering and characterizing effective AMPs combining high-throughput AMP screening experiments with multiscale mathematical models, and by testing phage endolysins, a distinct class of potent antimicrobial enzymes.