Godavarti, D. R. | Search bioRxiv

bioRxiv2025

Harnessing Plasmid Crosstalk in Transcription Factor Mediated Cell-Free Biosensors

Plasmid crosstalk--unexpected changes to protein expression levels due to interactions between genetic cassettes in cell-free systems--complicates the creation of multi-plasmid cell-free tools. While the potential underlying mechanisms for crosstalk have been previously investigated, the practical impact of crosstalk on the implementation of cell-free genetic circuits has not been thoroughly examined. Here, we contextualize plasmid crosstalk in genetic circuits by examining its impact on the design and performance of multiple, diverse transcription factor biosensors. Guided by a deeper understanding, we harness crosstalk to enhance cell-free biosensor performance. Together, these findings demonstrate that plasmid crosstalk can serve as a tunable property in the development of cell-free genetic circuits.

synthetic biology↗

bioRxiv2024

High-resolution profiling reveals coupled transcriptional and translational regulation of transgenes

Concentrations of RNAs and proteins provide important determinants of cell fate. Robust gene circuit design requires an understanding of how the combined actions of individual genetic components influence both mRNA and protein levels. Here, we simultaneously measure mRNA and protein levels in single cells using HCR Flow-FISH for a set of commonly used synthetic promoters. We find that promoters generate differences in both the mRNA abundance and the effective translation rate of these transcripts. Stronger promoters not only transcribe more RNA but also show higher effective translation rates. While the strength of the promoter is largely preserved upon genome integration with identical elements, the choice of polyadenylation signal and coding sequence can generate large differences in the profiles of the mRNAs and proteins. We used long-read direct RNA sequencing to characterize full-length mRNA isoforms and observe remarkable uniformity of mRNA isoforms from the transgenic units. Together, our high-resolution profiling of transgenic mRNAs and proteins offers insight into the impact of common synthetic genetic components on transcriptional and translational mechanisms. By developing a novel framework for quantifying expression profiles of transgenes, we have established a system for comparing native and synthetic gene regulation and for building more robust transgenic systems.

synthetic biology↗