stu-RNAseq
Engineering identical genetic circuits into different species typically results in large differences in performance due to the unique cellular environmental context of each host, a phenomenon known as the “chassis-effect”. A better understanding of how genomic and physiological contexts underpin the chassis-effect will greatly improve biodesign strategies across diverse microorganisms. Here, we combined a pangenomics-based gene expression analysis with quantitative measurements of performance from an engineered genetic inverter device to uncover how genome structure and function relates to the observed chassis-effect across six closely related Stutzerimonas hosts. Our results reveal that genome architecture underpins divergent responses between our chosen non-model bacterial hosts to engineered genetic circuits. Specifically, differential expression of the core genome, gene clusters shared between all hosts, were found to be the main source of significant concordance to the observed genetic device performance, whereas specialty genes from respective accessory genomes were not significant. A data-driven investigation revealed that genes involved in denitrification and components of trans-membrane transporter proteins were among the most differentially expressed gene clusters in response to the genetic device. Our results show the chassis-effect can be traced along differences among genome-encoded functions that are mostly conserved and that these differences create a unique biodesign space among closely related species.