Characterization of generic and specific effects within a host-circuit interface in E. coli

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Stefano Cardinale, Marcin Joachimiak

University of California - Berkeley, United States

As the number and complexity of genetic devices increase over time, they will also have to function in increasingly complex cellular systems, and control and interact with many more molecules and processes simultaneously. This cannot be achieved reliably if the number, type and properties of these interactions, as well as their impact on both synthetic and host systems, are not fully understood. Here we perform a detailed analysis of the interaction between constitutive expression from a test circuit and cell growth properties in a subset of genetic variants of the bacterium Escherichia coli. Differences in generic cellular parameters such as ribosome availability and growth rate are the main determinants (89%) of strain-specific differences of circuit performance in laboratory-adapted strains but are responsible for only 35% of expression variation across 88 mutants of E. coli BW25113. In the latter strains we identify specific cell functions, such as nitrogen metabolism, that cause a significant increase in fitness and circuit output. In contrast, deletion of genes involved in chemotaxis and quorum signaling, such as cheY or qseB as well as several other components of Signal Transduction Pathways, led to reduced cell growth and reporter expression. Finally, we expose aspects of carbon metabolism that act in strain- and sequence-specific manner. The study points to a broader program to discover and classify the mechanisms that govern the host-circuit interface and perhaps, ultimately, to design against them to increase the predictability of synthetic biological design. To this purpose we are expanding our analysis to include all the ~3800 single-gene knockout strains available for E. coli.