Establishing the core requirements and principles of cellular life is a fundamental challenge of biology and biological physics. This project addresses the Rules of Life question of the minimum biochemical functions that are necessary for a cell to grow and replicate. The project specifically involves the development of a simplified metabolic model for a minimal cell. The major contribution of this work is understanding interactions between the fundamental metabolic processes and large-scale economy of energy exchange among cellular processes in a given constrained environment. This model reveals the minimal chemical interacting processes between cellular events necessary for the growth of bacterial colonies over the time scale of cell cycles. While being derived for the simplest viable cell, this model encompasses processes essential to all forms of cellular life and hence yields insights applicable to cellular life as a whole. The simplicity of the developed model makes the principles of cellular life more accessible to a broad audience of researchers and non-scientists. Undergraduate students in the San Diego area are involved in the project through an arrangement with the J. Craig Venter Institute. According to this arrangement students perform essential lab work to use gene editing genetic tools to eliminate genes linking the metabolic networks in engineered bacterial cells.
The project involves use of the model system JCVI-syn3A, a minimal bacterial cell that was developed in conjunction with the Synthetic Biology group at the J. Craig Venter Institute. The approach used a bottom-up design method. This model displayed a highly reduced coupling between metabolic subsystems. Further simplification of JCVI-syn3A yields a cellular system where fundamental processes are not only well defined but also nearly isolated. These circumstances provide the foundation to study the basics of life and how specific cellular behaviors emerge from the output of individual processes. The plan is to construct a semi-analytical kinetic model of JCVI-syn3A coarse-grained at the level of representative metabolites and nutrients, metabolic enzymes, transporter proteins, genetic information processing proteins, DNA and RNA. Single-molecule experiments at single-cell resolution are performed to quantify the number of labeled transporter proteins in JCVI-syn3A to vary initial conditions for the models. The kinetic model is used to guide the minimization of the coupling between the metabolic subsystems which are validated through genetic modifications.
This project is co-funded by the Systems and Synthetic Biology cluster in the Division of Molecular and Cellular Biosciences and the Physics of Living Systems program in the Division of Physics.
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.
