species-selective gene

Robust and predictably performing synthetic circuits rely on the use of well-characterized regulatory parts across different genetic backgrounds and environmental contexts. Here, we report the large-scale metagenomic mining of thousands of natural 5 ′ -regulatory sequences from diverse bacteria and their multiplexed gene expression characterization in industrially-relevant microbes. We identified regulatory sequences with broad and host-specific expression properties that are robust in various growth conditions. We further observed significant differences between species’ capacity to utilize exogenous regulatory sequences. Finally, we demonstrated programmable species-selective gene expression that produces distinct and diverse output patterns in different microbes by leveraging regulatory sequences with pre-defined host-specificities. Together, these findings provide a rich resource of characterized and annotated natural regulatory sequences and a framework to engineer synthetic gene circuits with unique and tunable cross-species functionality and properties. and ONR (N00014-15-1-2704). N.I.J. is supported by a NSF Graduate Research Fellowship (DGE-16-44869). S.S.Y. thanks support from Basic Science Research Program through the National Research Foundation of Korea funded by the Ministry of Education (NRF-2017R1A6A3A03003401). We also thank T. Seto for help with plasmid construction, A. Figueroa for assistance with cell sorting, H. Salis for helpful discussions regarding the RBS calculator, D.B. Goodman for discussions regarding FACS-seq, as well as D. Dubnau, S. Lory and A. Rasouly for providing the BD3182 and PAO1 Δ psy2 strains.

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