M13 Phage: A Model System for Complex Control of Multicomponent Processes in Biology

University Of Colorado At Denver-Downtown Campus, Denver CO

Investigators

Abstract

Naturally evolved systems often contain complex nested control mechanisms involving coordinated and competing biomolecular interactions that translate into a myriad of phenotypes and behaviors. One of the grand challenges in biology is the development of a molecular level understanding of how genetically-encoded instructions are converted into the behaviors observed in living systems. However, tractable model systems for quantitatively investigating the complex control of biological processes are generally lacking but would advance the understanding of control in biology and translate, as other model systems have, into tools for engineering complex control architectures in designed biological systems. The focus of this project is on improving the quantitative molecular level understanding of a simple biological system, bacteriophage M13. Bacteriophages, viruses that infect bacteria, have been central to the development of molecular biology. As model systems for understanding molecular phenomena, phage systems remain at the forefront of research in nanomaterials and nanomedicine and act as important component-generating technologies for drug and material discovery through phage display. The PI will develop a detailed model of the molecular interactions that govern the behavior of phage systems, which will provide quantitative insight to enable applications in synthetic biology, nanotechnology, bio-manufacturing and medicine. The PI will use interactive platforms to engage K-12 students in computational systems biology projects, integrate undergraduates in research, and train students thus contributing to the preparation of the next generation of interdisciplinary scientists and engineers. Building on previous work involving a simulation of M13 growth that integrates 50 years of experimental observations, the goals of this project are to evaluate the nested feedback control loops in the M13 life cycle and fill in gaps in the quantitative understanding of M13 biology. The first objective of the current project involves quantification of the poorly-understood M13 protein-protein and protein-DNA interactions that govern phage DNA replication and the system level response to modifications of the DNA replication program. The second objective involves the identification and quantification of the protein-RNA interactions that regulate the timing and extent of phage protein production. Within this aim the system level effects of modifying the protein-RNA control mechanisms will be investigated. The final objective of the project is to integrate the results of the experiments into the simulation model. This aim will focus on augmenting the model with new quantitative data from Aims 1 and 2, and evaluating the present state of understanding by comparing the results of the system level experiments to predictions. Repeated cycles of theoretical refinement and experimental testing are required to build an engineering design cycle for M13 phage. This proposal will result in a greatly improved quantitative understanding of M13 biology and an infrastructure for the design and production of highly modified particles. 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.