Comparative Transcriptomic Analysis of Perfluoroalkyl Substances-Induced Responses of Exponential and Stationary Phase Escherichia coli

Per- and polyfluoroalkyl substances (PFAS) are highly stable chemical contaminants of emerging concern for human and environmental health due to their non-natural chemistry, widespread use, and environmental persistence. Despite conventional metrology, mitigation strategies, and removal technologies, the complexity of this growing problem necessitates the need for alternative approaches to tackle the immense challenges associated with complex environmental PFAS contamination. Recently, biology has emerged as an alternative approach to detect and mitigate PFAS and understand the molecular-level responses of living organisms, including microorganisms, to these compounds. However, further study is needed to understand how microorganisms in different environments and growth phases respond to PFAS. In this study, we performed RNA sequencing at mid-exponential, early stationary phase, and late stationary phase of bacterial growth to determine the global transcriptional response of a model chassis, Escherichia coli MG1655, induced by two PFAS, perfluorooctanoic acid (PFOA) and perfluorododecanoic acid (PFDoA), and equivalent non-fluorinated carboxylic acids (NFCA), octanoic acid and dodecanoic acid. Differential gene expression analysis revealed PFOA and PFDoA induced distinct changes in gene expression throughout cultivation. Specifically, we identified significant changes in expression of the formate regulon and sulfate assimilation at mid-exponential phase and ferrous iron transport, central metabolism, the molecular chaperone network, and motility processes during stationary phase. Importantly, many of these changes are not induced by NFCAs. In summary, we found PFAS induced a system-level change in gene expression, and our results expand the understanding of bacterial-PFAS interactions that could enable the development of future real-time environmental monitoring and mitigation technologies. Comparative gene expression analysis of RNA-Seq data for E. coli MG1655 treated with PFCAs or equivalent non-fluorinated carboxylic acids (NFCAs) to an untreated control group at three time points within the growth cycle was performed to investigate the transcriptional response of E. coli to PFAS.