(217a) Genome-Scale Modeling of the Core Proteome of Metabolism and Expression, and Its Transcriptional Regulation

The cell ‘chassis’ is of fundamental importance for synthetic biology applications. To predictively engineer this chassis, a systems biology understanding of it is critical. In this work, we broaden our understanding of the chassis using integrated genome-scale models of metabolism and expression. We first define a core proteome consisting of 356 gene products, accounting for 44% of the Escherichia coli proteome by mass based on proteomics data. This core proteome includes 212 genes not found in previous comparative genomics-based core proteome definitions, accounts for 65% of known essential genes in E. coli, and has functional overlap with minimal genomes (Buchnera aphidicola and Mycoplasma genitalium) (AUC = 0.78). Based on transcriptomics data across growth conditions and genetic backgrounds, the systems biology core proteome is significantly enriched in non-differentially expressed genes, and depleted in differentially expressed genes. Compared to the non-core, core gene expression levels are also similar across genetic backgrounds. Furthermore, core genes exhibit significantly more complex transcriptional and post-transcriptional regulatory features (40% more transcription start sites per gene, >20% longer 5’UTR). Thus, genome-scale systems biology approaches rigorously identify a functional core proteome needed to support growth. This framework, discerned and validated using high-throughput datasets, facilitates a mechanistic understanding of systems-level core proteome function through in silico models. We then investigate how the core proteome is regulated using a genome-scale, transcriptional regulatory network of E. coli. Taken together, the tightly regulated core proteome of E. coli comprises a fundamental repertoire of genes and biological functions that are of importance to a broad range of microbial synthetic biology applications.