System-level analysis of essential bioprocesses for stand-alone operation of Chlamydomonas reinhardtii chloroplasts
Mentor: Dr. Ali Navid, Biochemical and Biophysical Systems Group, Lawrence Livermore National Laboratory
Date/Time: August 22nd, 2023 at 1pm.
Abstract: Phototrophic organisms play an important role in many biological processes, including food production, carbon sequestration, biofuel production, and other methods of climate change mitigation. The chloroplast is the primary power source for these organisms, making the generation of an artificial chloroplast platform essential for cell-free bioengineering research. In order to move towards a functional chloroplast platform outside of the cell, a computational systems-level analysis of different modes of metabolism (including autotrophic) in diatoms growing in different environmental niches was conducted. The goal of this project was to identify the essential compounds, reactions and genes that would be needed for the successful operation of a standalone chloroplast. This was primarily accomplished by using Flux Balance Analysis (FBA), a modeling method to predict biochemical flux patterns for optimum achievement of a desired biological process (e.g., cellular growth or ATP generation). In total, system-level analyses were performed on two separate genome-scale models of metabolism of Chlamydomonas reinhardtii and 3 chloroplast sub-models of metabolism (from C. reinhardtii and two marine diatoms). Through FBA, C. reinhardtii’s chloroplast was determined to be the least robust (highest percentage of essential reactions) to genetic mutations (i.e., loss of function) when compared to the chloroplasts of the two marine diatoms. Further analysis of C. reinhardtii’s essential reactions revealed that it has a more complex plasma membrane structure and hence greater nutritional needs than the other two diatoms. In the near future, the results of our computational analyses will be used to create an appropriate growth medium containing the necessary nutrients and proteins to enable the survival of a synthetic chloroplast platform.
- Summer 2023